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1.
  • Ericson, Per G P, 1956-, et al. (författare)
  • Dating the diversification of the major lineages of Passeriformes (Aves)
  • 2014
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 14:8, s. 1-15
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The avian Order Passeriformes is an enormously species-rich group, which comprises almost 60% ofall living bird species. This diverse order is believed to have originated before the break-up of Gondwana in the lateCretaceous. However, previous molecular dating studies have relied heavily on the geological split between NewZealand and Antarctica, assumed to have occurred 85–82 Mya, for calibrating the molecular clock and might thusbe circular in their argument.Results: This study provides a time-scale for the evolution of the major clades of passerines using seven nuclearmarkers, five taxonomically well-determined passerine fossils, and an updated interpretation of the New Zealandsplit from Antarctica 85–52 Mya in a Bayesian relaxed-clock approach. We also assess how different interpretationsof the New Zealand–Antarctica vicariance event influence our age estimates. Our results suggest that thediversification of Passeriformes began in the late Cretaceous or early Cenozoic. Removing the root calibration forthe New Zealand–Antarctica vicariance event (85–52 Mya) dramatically increases the 95% credibility intervals andleads to unrealistically old age estimates. We assess the individual characteristics of the seven nuclear genesanalyzed in our study. Our analyses provide estimates of divergence times for the major groups of passerines,which can be used as secondary calibration points in future molecular studies.Conclusions: Our analysis takes recent paleontological and geological findings into account and provides the bestestimate of the passerine evolutionary time-scale currently available. This time-scale provides a temporalframework for further biogeographical, ecological, and co-evolutionary studies of the largest bird radiation, andadds to the growing support for a Cretaceous origin of Passeriformes.
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2.
  • Guy, Lionel, et al. (författare)
  • A genome-wide study of recombination rate variation in Bartonella henselae
  • 2012
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 12, s. 65-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Rates of recombination vary by three orders of magnitude in bacteria but the reasons for this variation is unclear. We performed a genome-wide study of recombination rate variation among genes in the intracellular bacterium Bartonella henselae, which has among the lowest estimated ratio of recombination relative to mutation in prokaryotes. Results: The 1.9 Mb genomes of B. henselae strains IC11, UGA10 and Houston-1 genomes showed only minor gene content variation. Nucleotide sequence divergence levels were less than 1% and the relative rate of recombination to mutation was estimated to 1.1 for the genome overall. Four to eight segments per genome presented significantly enhanced divergences, the most pronounced of which were the virB and trw gene clusters for type IV secretion systems that play essential roles in the infection process. Consistently, multiple recombination events were identified inside these gene clusters. High recombination frequencies were also observed for a gene putatively involved in iron metabolism. A phylogenetic study of this gene in 80 strains of Bartonella quintana, B. henselae and B. grahamii indicated different population structures for each species and revealed horizontal gene transfers across Bartonella species with different host preferences. Conclusions: Our analysis has shown little novel gene acquisition in B. henselae, indicative of a closed pan-genome, but higher recombination frequencies within the population than previously estimated. We propose that the dramatically increased fixation rate for recombination events at gene clusters for type IV secretion systems is driven by selection for sequence variability.
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3.
  • Kautsky, Lena, et al. (författare)
  • Rapid speciation in a newly opened postglacial marine environment, the Baltic Sea
  • 2009
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 9:70
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Theory predicts that speciation can be quite rapid. Previous examples comprise a wide range of organisms such as sockeye salmon, polyploid hybrid plants, fruit flies and cichlid fishes. However, few studies have shown natural examples of rapid evolution giving rise to new species in marine environments. Results: Using microsatellite markers, we show the evolution of a new species of brown macroalga (Fucus radicans) in the Baltic Sea in the last 400 years, well after the formation of this brackish water body ~8–10 thousand years ago. Sympatric individuals of F. radicans and F. vesiculosus (bladder wrack) show significant reproductive isolation. Fucus radicans, which is endemic to the Baltic, is most closely related to Baltic Sea F. vesiculosus among north Atlantic populations, supporting the hypothesis of a recent divergence. Fucus radicans exhibits considerable clonal reproduction, probably induced by the extreme conditions of the Baltic. This reproductive mode is likely to have facilitated the rapid foundation of the new taxon. Conclusion: This study represents an unparalleled example of rapid speciation in a species-poor open marine ecosystem and highlights the importance of increasing our understanding on the role of these habitats in species formation. This observation also challenges presumptions that rapid speciation takes place only in hybrid plants or in relatively confined geographical places such as postglacial or crater lakes, oceanic islands or rivers.
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4.
  • Lundin, Daniel, 1965-, et al. (författare)
  • Ribonucleotide reduction : horizontal transfer of a required function spans all three domains
  • 2010
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 10:383
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • Background Ribonucleotide reduction is the only de novo pathway for synthesis ofdeoxyribonucleotides, the building blocks of DNA. The reaction is catalysed byribonucleotide reductases (RNRs), an ancient enzyme family comprised of threeclasses. Each class has distinct operational constraints, and are broadly distributedacross organisms from all three domains, though few class I RNRs have beenidentified in archaeal genomes, and classes II and III likewise appear rare acrosseukaryotes. In this study, we examine whether this distribution is best explained bypresence of all three classes in the Last Universal Common Ancestor (LUCA), or byhorizontal gene transfer (HGT) of RNR genes. We also examine to what extentenvironmental factors may have impacted the distribution of RNR classes. Results Our phylogenies show that the Last Eukaryotic Common Ancestor (LECA) possesseda class I RNR, but that the eukaryotic class I enzymes are not directly descended fromclass I RNRs in archaea. Instead, our results indicate that archaeal class I RNR geneshave been independently transferred from bacteria on two occasions. While LECApossessed a class I RNR, our trees indicate that this is ultimately bacterial in origin.We also find convincing evidence that eukaryotic class I RNR has been transferred tothe bacteroidetes, providing a stunning example of HGT from eukaryotes back tobacteria. Based on our phylogenies and available genetic and genomic evidence, classII and III RNRs in eukaryotes also appear to have been transferred from bacteria, with subsequent within-domain transfer between distantly-related eukaryotes. Under the three-domains hypothesis the RNR present in the last common ancestor of archaeaand eukaryotes appears, through a process of elimination, to have been a dimeric classII RNR, though limited sampling of eukaryotes precludes a firm conclusion as the data may be equally well accounted for by HGT. Conclusions Horizontal gene transfer has clearly played an important role in the evolution of theRNR repertoire of organisms from all three domains of life. Our results clearly showthat class I RNRs have spread to archaea and eukaryotes via transfers from thebacterial domain, indicating that class I likely evolved in the bacteria. We find noclear evolutionary trace placing either class II or III RNRs in the LUCA, despite thefact that ribonucleotide reduction is an essential cellular reaction and was pivotal tothe transition from RNA to DNA genomes. Instead, a general pattern emerges whereenvironmental and enzyme operational constraints, especially the presence or absenceof oxygen, coupled with horizontal transmission are major determinants of the RNR repertoire of genomes.
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5.
  • Pauliny, Angela, 1972, et al. (författare)
  • Telomere dynamics in a long-lived bird, the barnacle goose
  • 2012
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 12:257
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Theories of ageing predict a trade-off between metabolism, reproduction, and maintenance. Species with low investment in early reproduction are thus expected to be able to evolve more efficient maintenance and repair mechanisms, allowing for a longer potential life span (intrinsic longevity). The erosion of telomeres, the protective caps at the ends of linear chromosomes, plays an important role in cellular and organismal senescence, signalling the onset of age-related disease due to accumulation of unrepaired somatic damage. Using extensive longitudinal data from a long-term study of a natural population of barnacle geese Branta leucopsis, we investigated individual rates of telomere length changes over two years in 34 birds between 0 and 22 years of age, covering almost 80% of the species’ lifespan. RESULTS: We show that telomeres in this long-lived bird are very well maintained, as theoretically expected, with an average loss rate of only 5 base pairs per year among adults. We thus found no significant relationship between change in telomere length and age. However, telomeres tended to shorten at a faster pace in juveniles compared to adults. For the first time, we demonstrate a faster telomere attrition rate in females compared to males. We found no correlation between telomere loss rate and adult survival or change in body mass. CONCLUSIONS: Our results add further support for a link between longevity and telomere maintenance, and highlight the complexities of telomere dynamics in natural populations.
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6.
  • Rautenberg, Anja, 1976-, et al. (författare)
  • Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene
  • 2008
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8:1, s. 299-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Increasing evidence from DNA sequence data has revealed that phylogenies based on different genes may drastically differ from each other. This may be due to either inter- or intralineage processes, or to methodological or stochastic errors. Here we investigate a spectacular case where two parts of the same gene (SlX1/Y1) show conflicting phylogenies within Silene (Caryophyllaceae). SlX1 and SlY1 are sex-linked genes on the sex chromosomes of dioecious members of Silene sect. Elisanthe. Results: We sequenced the homologues of the SlX1/Y1 genes in several Sileneae species. We demonstrate that different parts of the SlX1/Y1 region give different phylogenetic signals. The major discrepancy is that Silene vulgaris and S. sect. Conoimorpha (S. conica and relatives) exchange positions. To determine whether gene duplication followed by recombination (an intralineage process) may explain the phylogenetic conflict in the Silene SlX1/Y1 gene, we use a novel probabilistic, multiple primer-pair PCR approach. We did not find any evidence supporting gene duplication/loss as explanation to the phylogenetic conflict. Conclusion: The phylogenetic conflict in the Silene SlX1/Y1 gene cannot be explained by paralogy or artefacts, such as in vitro recombination during PCR. The support for the conflict is strong enough to exclude methodological or stochastic errors as likely sources. Instead, the phylogenetic incongruence may have been caused by recombination of two divergent alleles following ancient interspecific hybridization or incomplete lineage sorting. These events probably took place several million years ago. This example clearly demonstrates that different parts of the genome may have different evolutionary histories and stresses the importance of using multiple genes in reconstruction of taxonomic relationships.
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7.
  • Gonzalez-Voyer, Alejandro, et al. (författare)
  • Brain structure evolution in a basal vertebrate clade: evidence from phylogenetic comparative analysis of cichlid fishes
  • 2009
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 9, s. 238-
  • Tidskriftsartikel (refereegranskat)abstract
    •  Background: The vertebrate brain is composed of several interconnected, functionally distinct structures and much debate has surrounded the basic question of how these structures evolve. On the one hand, according to the 'mosaic evolution hypothesis', because of the elevated metabolic cost of brain tissue, selection is expected to target specific structures mediating the cognitive abilities which are being favored. On the other hand, the 'concerted evolution hypothesis' argues that developmental constraints limit such mosaic evolution and instead the size of the entire brain varies in response to selection on any of its constituent parts. To date, analyses of these hypotheses of brain evolution have been limited to mammals and birds; excluding Actinopterygii, the basal and most diverse class of vertebrates. Using a combination of recently developed phylogenetic multivariate allometry analyses and comparative methods that can identify distinct rates of evolution, even in highly correlated traits, we studied brain structure evolution in a highly variable clade of ray-finned fishes; the Tanganyikan cichlids.Results: Total brain size explained 86% of the variance in brain structure volume in cichlids, a lower proportion than what has previously been reported for mammals. Brain structures showed variation in pair-wise allometry suggesting some degree of independence in evolutionary changes in size. This result is supported by variation among structures on the strength of their loadings on the principal size axis of the allometric analysis. The rate of evolution analyses generally supported the results of the multivariate allometry analyses, showing variation among several structures in their evolutionary patterns. The olfactory bulbs and hypothalamus were found to evolve faster than other structures while the dorsal medulla presented the slowest evolutionary rate.Conclusion: Our results favor a mosaic model of brain evolution, as certain structures are evolving in a modular fashion, with a small but non-negligible influence of concerted evolution in cichlid fishes. Interestingly, one of the structures presenting distinct evolutionary patterns within cichlids, the olfactory bulbs, has also been shown to evolve differently from other structures in mammals. Hence, our results for a basal vertebrate clade also point towards a conserved developmental plan for all vertebrates.
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8.
  • Anderberg, Hanna, et al. (författare)
  • Algal MIPs, high diversity and conserved motifs
  • 2011
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Major intrinsic proteins (MIPs) also named aquaporins form channels facilitating the passive transport of water and other small polar molecules across membranes. MIPs are particularly abundant and diverse in terrestrial plants but little is known about their evolutionary history. In an attempt to investigate the origin of the plant MIP subfamilies, genomes of chlorophyte algae, the sister group of charophyte algae and land plants, were searched for MIP encoding genes. Results: A total of 22 MIPs were identified in the nine analysed genomes and phylogenetic analyses classified them into seven subfamilies. Two of these, Plasma membrane Intrinsic Proteins (PIPs) and GlpF-like Intrinsic Proteins (GIPs), are also present in land plants and divergence dating support a common origin of these algal and land plant MIPs, predating the evolution of terrestrial plants. The subfamilies unique to algae were named MIPA to MIPE to facilitate the use of a common nomenclature for plant MIPs reflecting phylogenetically stable groups. All of the investigated genomes contained at least one MIP gene but only a few species encoded MIPs belonging to more than one subfamily. Conclusions: Our results suggest that at least two of the seven subfamilies found in land plants were present already in an algal ancestor. The total variation of MIPs and the number of different subfamilies in chlorophyte algae is likely to be even higher than that found in land plants. Our analyses indicate that genetic exchanges between several of the algal subfamilies have occurred. The PIP1 and PIP2 groups and the Ca2+ gating appear to be specific to land plants whereas the pH gating is a more ancient characteristic shared by all PIPs. Further studies are needed to discern the function of the algal specific subfamilies MIPA-E and to fully understand the evolutionary relationship of algal and terrestrial plant MIPs.
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9.
  • Atkinson, Gemma C., et al. (författare)
  • An evolutionary ratchet leading to loss of elongation factors in eukaryotes
  • 2014
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 14, s. 1-9
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The GTPase eEF1A is the eukaryotic factor responsible for the essential, universal function of aminoacyl-tRNA delivery to the ribosome. Surprisingly, eEF1A is not universally present in eukaryotes, being replaced by the paralog EFL independently in multiple lineages. The driving force behind this unusually frequent replacement is poorly understood. Results: Through sequence searching of genomic and EST databases, we find a striking association of eEF1A replacement by EFL and loss of eEF1A's guanine exchange factor, eEF1Bα, suggesting that EFL is able to spontaneously recharge with GTP. Sequence conservation and homology modeling analyses indicate several sequence regions that may be responsible for EFL's lack of requirement for eEF1Bα. Conclusions: We propose that the unusual pattern of eEF1A, eEF1Bα and EFL presence and absence can be explained by a ratchet-like process: if either eEF1A or eEF1Bα diverges beyond functionality in the presence of EFL, the system is unable to return to the ancestral, eEF1A:eEFBα-driven state.
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10.
  • Hallström, Björn, et al. (författare)
  • Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations
  • 2008
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: A number of the deeper divergences in the placental mammal tree are still inconclusively resolved despite extensive phylogenomic analyses. A recent analysis of 200 kbp of protein coding sequences yielded only limited support for the relationships among Laurasiatheria (cow, dog, bat and shrew), probably because the divergences occurred only within a few million years from each other. It is generally expected that increasing the amount of data and improving the taxon sampling enhance the resolution of narrow divergences. Therefore these and other difficult splits were examined by phylogenomic analysis of the hitherto largest sequence alignment. The increasingly complete genome data of placental mammals also allowed developing a novel and stringent data search method. Results: The rigorous data handling, recursive BLAST, successfully removed the sequences from gene families, including those from well-known families hemoglobin, olfactory, myosin and HOX genes, thus avoiding alignment of possibly paralogous sequences. The current phylogenomic analysis of 3,012 genes (2,844,615 nucleotides) from a total of 22 species yielded statistically significant support for most relationships. While some major clades were confirmed using genomic sequence data, the placement of the treeshrew, bat and the relationship between Boreoeutheria, Xenarthra and Afrotheria remained problematic to resolve despite the size of the alignment. Phylogenomic analysis of divergence times dated the basal placental mammal splits at 95-100 million years ago. Many of the following divergences occurred only a few (2-4) million years later. Relationships with narrow divergence time intervals received unexpectedly limited support even from the phylogenomic analyses. Conclusion: The narrow temporal window within which some placental divergences took place suggests that inconsistencies and limited resolution of the mammalian tree may have their natural explanation in speciation processes such as lineage sorting, introgression from species hybridization or hybrid speciation. These processes obscure phylogenetic analysis, making some parts of the tree difficult to resolve even with genome data.
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11.
  • Henze, Miriam, et al. (författare)
  • Opsin evolution and expression in Arthropod compound Eyes and Ocelli: Insights from the cricket Gryllus bimaculatus
  • 2012
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 12
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Opsins are key proteins in animal photoreception. Together with a light-sensitive group, the chromophore, they form visual pigments which initiate the visual transduction cascade when photoactivated. The spectral absorption properties of visual pigments are mainly determined by their opsins, and thus opsins are crucial for understanding the adaptations of animal eyes. Studies on the phylogeny and expression pattern of opsins have received considerable attention, but our knowledge about insect visual opsins is still limited. Up to now, researchers have focused on holometabolous insects, while general conclusions require sampling from a broader range of taxa. We have therefore investigated visual opsins in the ocelli and compound eyes of the two-spotted cricket Gryllus bimaculatus, a hemimetabolous insect. Results: Phylogenetic analyses place all identified cricket sequences within the three main visual opsin clades of insects. We assign three of these opsins to visual pigments found in the compound eyes with peak absorbances in the green (515 nm), blue (445 nm) and UV (332 nm) spectral range. Their expression pattern divides the retina into distinct regions: (1) the polarization-sensitive dorsal rim area with blue- and UV-opsin, (2) a newly-discovered ventral band of ommatidia with blue-and green-opsin and (3) the remainder of the compound eye with UV-and green-opsin. In addition, we provide evidence for two ocellar photopigments with peak absorbances in the green (511 nm) and UV (350 nm) spectral range, and with opsins that differ from those expressed in the compound eyes. Conclusions: Our data show that cricket eyes are spectrally more specialized than has previously been assumed, suggesting that similar adaptations in other insect species might have been overlooked. The arrangement of spectral receptor types within some ommatidia of the cricket compound eyes differs from the generally accepted pattern found in holometabolous insect taxa and awaits a functional explanation. From the opsin phylogeny, we conclude that gene duplications, which permitted differential opsin expression in insect ocelli and compound eyes, occurred independently in several insect lineages and are recent compared to the origin of the eyes themselves.
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12.
  • Jansen van Rensburg, Alexandra, et al. (författare)
  • Ancestral polymorphism at the major histocompatibility complex (MHCII ss) in the Nesospiza bunting species complex and its sister species (Rowettia goughensis)
  • 2012
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 12
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The major histocompatibility complex (MHC) is an important component of the vertebrate immune system and is frequently used to characterise adaptive variation in wild populations due to its co-evolution with pathogens. Passerine birds have an exceptionally diverse MHC with multiple gene copies and large numbers of alleles compared to other avian taxa. The Nesospiza bunting species complex (two species on Nightingale Island; one species with three sub-species on Inaccessible Island) represents a rapid adaptive radiation at a small, isolated archipelago, and is thus an excellent model for the study of adaptation and speciation. In this first study of MHC in Nesospiza buntings, we aim to characterize MHCII ss variation, determine the strength of selection acting at this gene region and assess the level of shared polymorphism between the Nesospiza species complex and its putative sister taxon, Rowettia goughensis, from Gough Island. Results: In total, 23 unique alleles were found in 14 Nesospiza and 2 R. goughensis individuals encoding at least four presumably functional loci and two pseudogenes. There was no evidence of ongoing selection on the peptide binding region (PBR). Of the 23 alleles, 15 were found on both the islands inhabited by Nesospiza species, and seven in both Nesospiza and Rowettia; indications of shared, ancestral polymorphism. A gene tree of Nesospiza MHCII ss alleles with several other passerine birds shows three highly supported Nesospiza-specific groups. All R. goughensis alleles were shared with Nesospiza, and these alleles were found in all three Nesospiza sequence groups in the gene tree, suggesting that most of the observed variation predates their phylogenetic split. Conclusions: Lack of evidence of selection on the PBR, together with shared polymorphism across the gene tree, suggests that population variation of MHCII ss among Nesospiza and Rowettia is due to ancestral polymorphism rather than local selective forces. Weak or no selection pressure could be attributed to low parasite load at these isolated Atlantic islands. The deep divergence between the highly supported Nesospiza-specific sequence Groups 2 and 3, and the clustering of Group 3 close to the distantly related passerines, provide strong support for preserved ancestral polymorphism, and present evidence of one of the rare cases of extensive ancestral polymorphism in birds.
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13.
  • Liénard, Marjorie, et al. (författare)
  • Key biosynthetic gene subfamily recruited for pheromone production prior to the extensive radiation of Lepidoptera
  • 2008
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8:270
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Moths have evolved highly successful mating systems, relying on species-specific mixtures of sex pheromone components for long-distance mate communication. Acyl-CoA desaturases are key enzymes in the biosynthesis of these compounds and to a large extent they account for the great diversity of pheromone structures in Lepidoptera. A novel desaturase gene subfamily that displays Δ11 catalytic activities has been highlighted to account for most of the unique pheromone signatures of the taxonomically advanced ditrysian species. To assess the mechanisms driving pheromone evolution, information is needed about the signalling machinery of primitive moths. The currant shoot borer, Lampronia capitella, is the sole reported primitive non-ditrysian moth known to use unsaturated fatty-acid derivatives as sex-pheromone. By combining biochemical and molecular approaches we elucidated the biosynthesis paths of its main pheromone component, the (Z,Z)-9,11-tetradecadien-1-ol and bring new insights into the time point of the recruitment of the key Δ11-desaturase gene subfamily in moth pheromone biosynthesis. Results The reconstructed evolutionary tree of desaturases evidenced two ditrysian-specific lineages (the Δ11 and Δ9 (18C>16C)) to have orthologs in the primitive moth L. capitella despite being absent in Diptera and other insect genomes. Four acyl-CoA desaturase cDNAs were isolated from the pheromone gland, three of which are related to Δ9-desaturases whereas the fourth cDNA clusters with Δ11-desaturases. We demonstrated that this transcript (Lca-KPVQ) exclusively accounts for both steps of desaturation involved in pheromone biosynthesis. This enzyme possesses a Z11-desaturase activity that allows transforming the palmitate precursor (C16:0) into (Z)-11-hexadecenoic acid and the (Z)-9-tetradecenoic acid into the conjugated intermediate (Z,Z)-9,11-tetradecadienoic acid. Conclusion The involvement of a single Z11-desaturase in pheromone biosynthesis of a non-ditrysian moth species, supports that the duplication event leading to the origin of the Lepidoptera-specific Δ11-desaturase gene subfamily took place before radiation of ditrysian moths and their divergence from other heteroneuran lineages. Our findings uncover that this novel class of enzymes affords complex combinations of unique unsaturated fatty acyl-moieties of variable chain-lengths, regio- and stereo-specificities since early in moth history and contributes a notable innovation in the early evolution of moth-pheromones.
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14.
  • Maslov, S, et al. (författare)
  • Upstream plasticity and downstream robustness in evolution of molecular networks
  • 2004
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 4
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Gene duplication followed by the functional divergence of the resulting pair of paralogous proteins is a major force shaping molecular networks in living organisms. Recent species-wide data for protein-protein interactions and transcriptional regulations allow us to assess the effect of gene duplication on robustness and plasticity of these molecular networks. Results: We demonstrate that the transcriptional regulation of duplicated genes in baker's yeast Saccharomyces cerevisiae diverges fast so that on average they lose 3% of common transcription factors for every 1% divergence of their amino acid sequences. The set of protein-protein interaction partners of their protein products changes at a slower rate exhibiting a broad plateau for amino acid sequence similarity above 70%. The stability of functional roles of duplicated genes at such relatively low sequence similarity is further corroborated by their ability to substitute for each other in single gene knockout experiments in yeast and RNAi experiments in a nematode worm Caenorhabditis elegans. We also quantified the divergence rate of physical interaction neighborhoods of paralogous proteins in a bacterium Helicobacter pylori and a fly Drosophila melanogaster. However, in the absence of system-wide data on transcription factors' binding in these organisms we could not compare this rate to that of transcriptional regulation of duplicated genes. Conclusions: For all molecular networks studied in this work we found that even the most distantly related paralogous proteins with amino acid sequence identities around 20% on average have more similar positions within a network than a randomly selected pair of proteins. For yeast we also found that the upstream regulation of genes evolves more rapidly than downstream functions of their protein products. This is in accordance with a view which puts regulatory changes as one of the main driving forces of the evolution. In this context a very important open question is to what extent our results obtained for homologous genes within a single species (paralogs) carries over to homologous proteins in different species (orthologs).
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15.
  • Morgan-Richards, Mary, et al. (författare)
  • Bird evolution: testing the Metaves clade with six new mitochondrial genomes
  • 2008
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8:20
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Evolutionary biologists are often misled by convergence of morphology and this has been common in the study of bird evolution. However, the use of molecular data sets have their own problems and phylogenies based on short DNA sequences have the potential to mislead us too. The relationships among clades and timing of the evolution of modern birds (Neoaves) has not yet been well resolved. Evidence of convergence of morphology remain controversial. With six new bird mitochondrial genomes (hummingbird, swift, kagu, rail, flamingo and grebe) we test the proposed Metaves/Coronaves division within Neoaves and the parallel radiations in this primary avian clade. Results: Our mitochondrial trees did not return the Metaves clade that had been proposed based on one nuclear intron sequence. We suggest that the high number of indels within the seventh intron of the beta-fibrinogen gene at this phylogenetic level, which left a dataset with not a single site across the alignment shared by all taxa, resulted in artifacts during analysis. With respect to the overall avian tree, we find the flamingo and grebe are sister taxa and basal to the shorebirds (Charadriiformes). Using a novel site-stripping technique for noise-reduction we found this relationship to be stable. The hummingbird/swift clade is outside the large and very diverse group of raptors, shore and sea birds. Unexpectedly the kagu is not closely related to the rail in our analysis, but because neither the kagu nor the rail have close affinity to any taxa within this dataset of 41 birds, their placement is not yet resolved. Conclusion: Our phylogenetic hypothesis based on 41 avian mitochondrial genomes ( 13,229 bp) rejects monophyly of seven Metaves species and we therefore conclude that the members of Metaves do not share a common evolutionary history within the Neoaves.
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16.
  • Nilsson, Dan-E, et al. (författare)
  • The giant eyes of giant squid are indeed unexpectedly large, but not if used for spotting sperm whales
  • 2013
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 13
  • Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
    • Background: We recently reported (Curr Biol 22:683-688, 2012) that the eyes of giant and colossal squid can grow to three times the diameter of the eyes of any other animal, including large fishes and whales. As an explanation to this extreme absolute eye size, we developed a theory for visual performance in aquatic habitats, leading to the conclusion that the huge eyes of giant and colossal squid are uniquely suited for detection of sperm whales, which are important squid-predators in the depths where these squid live. A paper in this journal by Schmitz et al. (BMC Evol Biol 13:45, 2013) refutes our conclusions on the basis of two claims: (1) using allometric data they argue that the eyes of giant and colossal squid are not unexpectedly large for the size of the squid, and (2) a revision of the values used for modelling indicates that large eyes are not better for detection of approaching sperm whales than they are for any other task. Results and conclusions: We agree with Schmitz et al. that their revised values for intensity and abundance of planktonic bioluminescence may be more realistic, or at least more appropriately conservative, but argue that their conclusions are incorrect because they have not considered some of the main arguments put forward in our paper. We also present new modelling to demonstrate that our conclusions remain robust, even with the revised input values suggested by Schmitz et al.
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17.
  • Paun, Ovidiu, et al. (författare)
  • Altered gene expression and ecological divergence in sibling allopolyploids of Dactylorhiza (Orchidaceae)
  • 2011
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Hybridization and polyploidy are potent forces that have regularly stimulated plant evolution and adaptation. Dactylorhiza majalis s.s., D. traunsteineri s.l. and D. ebudensis are three allopolyploid species of a polyploid complex formed through unidirectional (and, in the first two cases, recurrent) hybridization between the widespread diploids D. fuchsii and D. incarnata. Differing considerably in geographical extent and ecological tolerance, the three allopolyploids together provide a useful system to explore genomic responses to allopolyploidization and reveal their role in adaptation to contrasting environments. Results: Analyses of cDNA-AFLPs show a significant increase in the range of gene expression of these allopolyploid lineages, demonstrating higher potential for phenotypic plasticity than is shown by either parent. Moreover, allopolyploid individuals express significantly more gene variants (including novel alleles) than their parents, providing clear evidence of increased biological complexity following allopolyploidization. More genetic mutations seem to have accumulated in the older D. majalis compared with the younger D. traunsteineri since their respective formation. Conclusions: Multiple origins of the polyploids contribute to differential patterns of gene expression with a distinct geographic structure. However, several transcripts conserved within each allopolyploid taxon differ between taxa, indicating that habitat preferences shape similar expression patterns in these independently formed tetraploids. Statistical signals separate several transcripts - some of them novel in allopolyploids - that appear correlated with adaptive traits and seem to play a role favouring the persistence of individuals in their native environments. In addition to stabilizing the allopolyploid genome, genetic and epigenetic alterations are key determinants of adaptive success of the new polyploid species after recurrent allopolyploidization events, potentially triggering reproductive isolation between the resulting lineages.
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18.
  • Runemark, Anna, et al. (författare)
  • Island biology and morphological divergence of the Skyros wall lizard Podarcis gaigeae: a combined role for local selection and genetic drift on color morph frequency divergence?
  • 2010
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Patterns of spatial variation in discrete phenotypic traits can be used to draw inferences about the adaptive significance of traits and evolutionary processes, especially when compared to patterns of neutral genetic variation. Population divergence in adaptive traits such as color morphs can be influenced by both local ecology and stochastic factors such as genetic drift or founder events. Here, we use quantitative color measurements of males and females of Skyros wall lizard, Podarcis gaigeae, to demonstrate that this species is polymorphic with respect to throat color, and the morphs form discrete phenotypic clusters with limited overlap between categories. We use divergence in throat color morph frequencies and compare that to neutral genetic variation to infer the evolutionary processes acting on islet- and mainland populations. RESULTS: Geographically close islet- and mainland populations of the Skyros wall lizard exhibit strong divergence in throat color morph frequencies. Population variation in throat color morph frequencies between islets was higher than that between mainland populations, and the effective population sizes on the islets were small (Ne:s < 100). Population divergence (FST) for throat color morph frequencies fell within the neutral FST-distribution estimated from microsatellite markers, and genetic drift could thus not be rejected as an explanation for the pattern. Moreover, for both comparisons among mainland-mainland population pairs and between mainland-islet population pairs, morph frequency divergence was significantly correlated with neutral divergence, further pointing to some role for genetic drift in divergence also at the phenotypic level of throat color morphs. CONCLUSIONS: Genetic drift could not be rejected as an explanation for the pattern of population divergence in morph frequencies. In spite of an expected stabilising selection, throat color frequencies diverged in the islet populations. These results suggest that there is an interaction between selection and genetic drift causing divergence even at a phenotypic level in these small, subdivided populations.
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19.
  • Sanchez Guillen, Rosa, et al. (författare)
  • Introgression and rapid species turnover in sympatric damselflies
  • 2011
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11:article no 210
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Studying contemporary hybridization increases our understanding of introgression, adaptation and, ultimately, speciation. The sister species Ischnura elegans and I. graellsii (Odonata: Coenagrionidae) are ecologically, morphologically and genetically similar and hybridize. Recently, I. elegans has colonized northern Spain, creating a broad sympatric region with I. graellsii. Here, we review the distribution of both species in Iberia and evaluate the degree of introgression of I. graellsii into I. elegans using six microsatellite markers (442 individuals from 26 populations) and five mitochondrial genes in sympatric and allopatric localities. Furthermore, we quantify the effect of hybridization on the frequencies of the genetically controlled colour polymorphism in females of both species. Results: In a principal component analysis of the microsatellite data, the first two principal components summarised almost half (41%) of the total genetic variation. The first axis revealed a clear separation of I. graellsii and I. elegans populations, while the second axis separated I. elegans populations. Admixture analyses showed extensive hybridization and introgression in I. elegans populations, consistent with I. elegans backcrosses and occasional F-1-hybrids, suggesting hybridization is on-going. More specifically, approximately 58% of the 166 Spanish I. elegans individuals were assigned to the I. elegans backcross category, whereas not a single of those individuals was assigned to the backcross with I. graellsii. The mitochondrial genes held little genetic variation, and the most common haplotype was shared by the two species. Conclusions: The results suggest rapid species turnover in sympatric regions in favour of I. elegans, corroborating previous findings that I. graellsii suffers a mating disadvantage in sympatry with I. elegans. Examination of morph frequency dynamics indicates that hybridization is likely to have important implications for the maintenance of multiple female morphs, in particular during the initial period of hybridization.
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20.
  • Sanchez Guillen, Rosa, et al. (författare)
  • Ontogenetic shifts in male mating preference and morph-specific polyandry in a female colour polymorphic insect
  • 2013
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Sexual conflict over mating rates may favour the origin and maintenance of phenotypes with contrasting reproductive strategies. The damselfly Ischnura elegans is characterised by a female colour polymorphism that consists of one androchrome and two gynochrome female morphs. Previous studies have shown that the polymorphism is genetic and to a high extent maintained by negative frequency-dependent mating success that varies temporally and spatially. However, the role of learning in male mating preferences has received little attention. We used molecular markers to investigate differences in polyandry between female morphs. In addition, we experimentally investigated innate male mating preferences and experience-dependent shifts in male mating preferences for female morphs. Results: Field and molecular data show that androchrome females were less polyandrous than gynochrome females. Interestingly, we found that naive males showed significantly higher sexual preferences to androchrome than to gynochrome females in experimental trials. In contrast, experienced males showed no preference for androchrome females. Conclusions: The ontogenetic change in male mate preferences occurs most likely because of learned mate recognition after experience with females, which in this case does not result in a preference for one of the morphs, but rather in the loss of an innate preference for androchrome females.
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21.
  • Weisbecker, Vera, et al. (författare)
  • Integration, heterochrony, and adaptation in pedal digits of syndactylous marsupials
  • 2008
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8:160
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Marsupial syndactyly is a curious morphology of the foot found in all species of diprotodontian and peramelemorph marsupials. It is traditionally defined as a condition in which digits II and III of the foot are bound by skin and are reduced. Past treatments of marsupial syndactyly have not considered the implications of this unique morphology for broader issues of digit development and evolution, and the ongoing debate regarding its phylogenetic meaning lacks a broad empirical basis. This study undertakes the first interdisciplinary characterisation of syndactyly, using variance/covariance matrix comparisons of morphometric measurements, locomotor indices, ossification sequences, and re-assessment of the largely anecdotal data on the phylogenetic distribution of tarsal/metatarsal articulations and "incipient syndactyly". Results: Syndactylous digits have virtually identical variance/covariance matrices and display heterochronic ossification timing with respect to digits IV/V. However, this does not impact on overall locomotor adaptation patterns in the syndactylous foot as determined by analysis of locomotor predictor ratios. Reports of incipient syndactyly in some marsupial clades could not be confirmed; contrary to previous claims, syndactyly does not appear to impact on tarsal bone arrangement. Conclusion: The results suggest that marsupial syndactyly originates from a constraint that is rooted in early digit ontogeny and results in evolution of the syndactylous digits as a highly integrated unit. Although convergent evolution appears likely, syndactyly in Diprotodontia and Peramelemorpha may occur through homologous developmental processes. We argue that the term "syndactyly" is a misnomer because the marsupial condition only superficially resembles its name-giving human soft-tissue syndactyly.
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22.
  • Ödeens, Anders, et al. (författare)
  • The phylogenetic distribution of ultraviolet sensitivity in birds
  • 2013
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • Conclusions: By mapping our results together with data from previous studies on a molecular phylogeny we show that avian colour vision shifted between VS and UVS at least 14 times. Single nucleotide substitutions can explain all these shifts. The common ancestor of birds most likely had a VS phenotype. However, the ancestral state of the avian SWS1 opsin's spectral tuning sites cannot be resolved, since the Palaeognathae are F86, C90 while the Neognathae are ancestrally S86, S90. The phylogenetic distribution of UVS and VS colour vision in birds is so complex that inferences of spectral sensitivities from closely related taxa should be used with caution.
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23.
  • Sloan, Daniel B., et al. (författare)
  • Phylogenetic analysis of mitochondrial mutation rate variation in the angiosperm tribe Sileneae
  • 2009
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 9, s. 260-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Recent phylogenetic studies have revealed that the   mitochondrial genome of the angiosperm Silene noctiflora   (Caryophyllaceae) has experienced a massive mutation-driven   acceleration in substitution rate, placing it among the fastest   evolving eukaryotic genomes ever identified. To date, it appears that   other species within Silene have maintained more typical substitution   rates, suggesting that the acceleration in S. noctiflora is a recent   and isolated evolutionary event. This assessment, however, is based on   a very limited sampling of taxa within this diverse genus.   Results: We analyzed the substitution rates in 4 mitochondrial genes   (atp1, atp9, cox3 and nad9) across a broad sample of 74 species within   Silene and related genera in the tribe Sileneae. We found that S.   noctiflora shares its history of elevated mitochondrial substitution   rate with the closely related species S. turkestanica. Another section   of the genus (Conoimorpha) has experienced an acceleration of   comparable magnitude. The phylogenetic data remain ambiguous as to   whether the accelerations in these two clades represent independent   evolutionary events or a single ancestral change. Rate variation among   genes was equally dramatic. Most of the genus exhibited elevated rates   for atp9 such that the average tree-wide substitution rate for this   gene approached the values for the fastest evolving branches in the   other three genes. In addition, some species exhibited major   accelerations in atp1 and/or cox3 with no correlated change in other   genes. Rates of nonsynonymous substitution did not increase   proportionally with synonymous rates but instead remained low and   relatively invariant.   Conclusion: The patterns of phylogenetic divergence within Sileneae   suggest enormous variability in plant mitochondrial mutation rates and   reveal a complex interaction of gene and species effects. The variation   in rates across genomic and phylogenetic scales raises questions about   the mechanisms responsible for the evolution of mutation rates in plant   mitochondrial genomes.
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24.
  • Malmström, Helena, et al. (författare)
  • High frequency of lactose intolerance in a prehistoric hunter-gatherer population in northern Europe
  • 2010
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 10, s. 89-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Genes and culture are believed to interact, but it has been difficult to find direct evidence for the process. One candidate example that has been put forward is lactase persistence in adulthood, i.e. the ability to continue digesting the milk sugar lactose after childhood, facilitating the consumption of raw milk. This genetic trait is believed to have evolved within a short time period and to be related with the emergence of sedentary agriculture. Results: Here we investigate the frequency of an allele (-13910*T) associated with lactase persistence in a Neolithic Scandinavian population. From the 14 individuals originally examined, 10 yielded reliable results. We find that the T allele frequency was very low (5%) in this Middle Neolithic hunter-gatherer population, and that the frequency is dramatically different from the extant Swedish population (74%). Conclusions: We conclude that this difference in frequency could not have arisen by genetic drift and is either due to selection or, more likely, replacement of hunter-gatherer populations by sedentary agriculturalists.
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25.
  • Ajawatanawong, Pravech, et al. (författare)
  • Evolution of protein indels in plants, animals and fungi
  • 2013
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 13, s. 140-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Insertions/deletions (indels) in protein sequences are useful as drug targets, protein structure predictors, species diagnostics and evolutionary markers. However there is limited understanding of indel evolutionary patterns. We sought to characterize indel patterns focusing first on the major groups of multicellular eukaryotes. Results: Comparisons of complete proteomes from a taxonically broad set of primarily Metazoa, Fungi and Viridiplantae yielded 299 substantial (>250aa) universal, single-copy (in-paralog only) proteins, from which 901 simple (present/absent) and 3,806 complex (multistate) indels were extracted. Simple indels are mostly small (1-7aa) with a most frequent size class of 1aa. However, even these simple looking indels show a surprisingly high level of hidden homoplasy (multiple independent origins). Among the apparently homoplasy-free simple indels, we identify 69 potential clade-defining indels (CDIs) that may warrant closer examination. CDIs show a very uneven taxonomic distribution among Viridiplante (13 CDIs), Fungi (40 CDIs), and Metazoa (0 CDIs). An examination of singleton indels shows an excess of insertions over deletions in nearly all examined taxa. This excess averages 2.31 overall, with a maximum observed value of 7.5 fold. Conclusions: We find considerable potential for identifying taxon-marker indels using an automated pipeline. However, it appears that simple indels in universal proteins are too rare and homoplasy-rich to be used for pure indel-based phylogeny. The excess of insertions over deletions seen in nearly every genome and major group examined maybe useful in defining more realistic gap penalties for sequence alignment. This bias also suggests that insertions in highly conserved proteins experience less purifying selection than do deletions.
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26.
  • Alho, Jussi S., et al. (författare)
  • Increasing melanism along a latitudinal gradient in a widespread amphibian : local adaptation, ontogenic or environmental plasticity?
  • 2010
  • Ingår i: BMC Evolutionary Biology. - 1471-2148 .- 1471-2148. ; 10, s. 317-
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundThe thermal benefits of melanism in ectothermic animals are widely recognized, but relatively little is known about population differentiation in the degree of melanism along thermal gradients, and the relative contributions of genetic vs. environmental components into the level of melanism expressed. We investigated variation in the degree of melanism in the common frog (Rana temporaria; an active heliotherm thermoregulator) by comparing the degree of melanism (i) among twelve populations spanning over 1500 km long latitudinal gradient across the Scandinavian Peninsula and (ii) between two populations from latitudinal extremes subjected to larval temperature treatments in a common garden experiment.ResultsWe found that the degree of melanism increased steeply in the wild as a function of latitude. Comparison of the degree of population differentiation in melanism (PST) and neutral marker loci (FST) revealed that the PST > FST, indicating that the differences cannot be explained by random genetic drift alone. However, the latitudinal trend observed in the wild was not present in the common garden data, suggesting that the cline in nature is not attributable to direct genetic differences.ConclusionsAs straightforward local adaptation can be ruled out, the observed trend is likely to result from environment-driven phenotypic plasticity or ontogenetic plasticity coupled with population differences in age structure. In general, our results provide an example how phenotypic plasticity or even plain ontogeny can drive latitudinal clines and result in patterns perfectly matching the genetic differences expected under adaptive hypotheses. 
  •  
27.
  • Alho, Jussi S., et al. (författare)
  • Increasing melanism along a latitudinal gradient in a widespread amphibian : local adaptation, ontogenic or environmental plasticity?
  • 2010
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 10:1, s. 317-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The thermal benefits of melanism in ectothermic animals are widely recognized, but relatively little is known about population differentiation in the degree of melanism along thermal gradients, and the relative contributions of genetic vs. environmental components into the level of melanism expressed. We investigated variation in the degree of melanism in the common frog (Rana temporaria; an active heliotherm thermoregulator) by comparing the degree of melanism (i) among twelve populations spanning over 1500 km long latitudinal gradient across the Scandinavian Peninsula and (ii) between two populations from latitudinal extremes subjected to larval temperature treatments in a common garden experiment. Results: We found that the degree of melanism increased steeply in the wild as a function of latitude. Comparison of the degree of population differentiation in melanism (P-ST) and neutral marker loci (F-ST) revealed that the P-ST >F-ST, indicating that the differences cannot be explained by random genetic drift alone. However, the latitudinal trend observed in the wild was not present in the common garden data, suggesting that the cline in nature is not attributable to direct genetic differences. Conclusions: As straightforward local adaptation can be ruled out, the observed trend is likely to result from environment-driven phenotypic plasticity or ontogenetic plasticity coupled with population differences in age structure. In general, our results provide an example how phenotypic plasticity or even plain ontogeny can drive latitudinal clines and result in patterns perfectly matching the genetic differences expected under adaptive hypotheses.
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28.
  • Alström, Per, et al. (författare)
  • New insights into family relationships within the avian superfamily Sylvioidea (Passeriformes) based on seven molecular markers
  • 2012
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 12, s. 1-12
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The circumscription of the avian superfamily Sylvioidea is a matter of long ongoing debate. While the overall inclusiveness has now been mostly agreed on and 20 families recognised, the phylogenetic relationships among the families are largely unknown. We here present a phylogenetic hypothesis for Sylvioidea based on one mitochondrial and six nuclear markers, in total ~6.3 kbp, for 79 ingroup species representing all currently recognised families and some species with uncertain affinities, making this the most comprehensive analysis of this taxon.  Results: The resolution, especially of the deeper nodes, is much improved compared to previous studies. However, many relationships among families remain uncertain and are in need of verification. Most families themselves are very well supported based on the total data set and also by indels. Our data do not support the inclusion of Hylia in Cettiidae, but do not strongly reject a close relationship with Cettiidae either. The genera Scotocerca and Erythrocercus are closely related to Cettiidae, but separated by relatively long internodes. The families Paridae, Remizidae and Stenostiridae clustered among the outgroup taxa and not within Sylvioidea.  Conclusions: Although the phylogenetic position of Hylia is uncertain, we tentatively support the recognition of the family Hyliidae Bannerman, 1923 for this genus and Pholidornis. We propose new family names for the genera Scotocerca and Erythrocercus, Scotocercidae and Erythrocercidae, respectively, rather than including these in Cettiidae, and we formally propose the name Macrosphenidae, which has been in informal use for some time. We recommend that Paridae, Remizidae and Stenostiridae are not included in Sylvioidea. We also briefly discuss the problems of providing a morphological diagnosis when proposing a new family-group name (or genus-group name) based on a clade.
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29.
  • Alström, Per, et al. (författare)
  • Non-monophyly and intricate morphological evolution within the avian family Cettiidae revealed by multilocus analysis of a taxonomically densely sampled dataset.
  • 2011
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 352-
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: The avian family Cettiidae, including the genera Cettia, Urosphena, Tesia, Abroscopus and Tickellia and Orthotomus cucullatus, has recently been proposed based on analysis of a small number of loci and species. The close relationship of most of these taxa was unexpected, and called for a comprehensive study based on multiple loci and dense taxon sampling. In the present study, we infer the relationships of all except one of the species in this family using one mitochondrial and three nuclear loci. We use traditional gene tree methods (Bayesian inference, maximum likelihood bootstrapping, parsimony bootstrapping), as well as a recently developed Bayesian species tree approach (*BEAST) that accounts for lineage sorting processes that might produce discordance between gene trees. We also analyse mitochondrial DNA for a larger sample, comprising multiple individuals and a large number of subspecies of polytypic species.RESULTS: There are many topological incongruences among the single-locus trees, although none of these is strongly supported. The multi-locus tree inferred using concatenated sequences and the species tree agree well with each other, and are overall well resolved and well supported by the data. The main discrepancy between these trees concerns the most basal split. Both methods infer the genus Cettia to be highly non-monophyletic, as it is scattered across the entire family tree. Deep intraspecific divergences are revealed, and one or two species and one subspecies are inferred to be non-monophyletic (differences between methods).CONCLUSIONS: The molecular phylogeny presented here is strongly inconsistent with the traditional, morphology-based classification. The remarkably high degree of non-monophyly in the genus Cettia is likely to be one of the most extraordinary examples of misconceived relationships in an avian genus. The phylogeny suggests instances of parallel evolution, as well as highly unequal rates of morphological divergence in different lineages. This complex morphological evolution apparently misled earlier taxonomists. These results underscore the well-known but still often neglected problem of basing classifications on overall morphological similarity. Based on the molecular data, a revised taxonomy is proposed. Although the traditional and species tree methods inferred much the same tree in the present study, the assumption by species tree methods that all species are monophyletic is a limitation in these methods, as some currently recognized species might have more complex histories.
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30.
  • Anderson, Jennifer L, et al. (författare)
  • Does thermoregulatory behavior maximize reproductive fitness of natural isolates of Caenorhabditis elegans?
  • 2011
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: A central premise of physiological ecology is that an animal's preferred body temperature should correspond closely with the temperature maximizing performance and Darwinian fitness. Testing this co-adaptational hypothesis has been problematic for several reasons. First, reproductive fitness is the appropriate measure, but is difficult to measure in most animals. Second, no single fitness measure applies to all demographic situations, complicating interpretations. Here we test the co-adaptation hypothesis by studying an organism (Caenorhabditis elegans) in which both fitness and thermal preference can be reliably measured.RESULTS: We find that natural isolates of C. elegans display a range of mean thermal preferences and also vary in their thermal sensitivities for fitness. Hot-seeking isolates CB4854 and CB4857 prefer temperatures that favor population growth rate (r), whereas the cold-seeking isolate CB4856 prefers temperatures that favor Lifetime Reproductive Success (LRS).CONCLUSIONS: Correlations between fitness and thermal preference in natural isolates of C. elegans are driven primarily by isolate-specific differences in thermal preference. If these differences are the result of natural selection, then this suggests that the appropriate measure of fitness for use in evolutionary ecology studies might differ even within species, depending on the unique ecological and evolutionary history of each population.
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31.
  • Aspeborg, Henrik, 1970-, et al. (författare)
  • Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)
  • 2012
  • Ingår i: BMC Evolutionary Biology. - : Springer Nature. - 1471-2148. ; 12:1, s. 186-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on beta-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5. Results: About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data. Examination of subfamilies with catalytically-active members revealed that one third are monospecific (containing a single enzyme activity), although new functions may be discovered with biochemical characterization in the future. Furthermore, twenty subfamilies presently have no characterization whatsoever and many others have only limited structural and biochemical data. Mapping of functional knowledge onto the GH5 phylogenetic tree revealed that the sequence space of this historical and industrially important family is far from well dispersed, highlighting targets in need of further study. The analysis also uncovered a number of GH5 proteins which have lost their catalytic machinery, indicating evolution towards novel functions. Conclusion: Overall, the subfamily division of GH5 provides an actively curated resource for large-scale protein sequence annotation for glycogenomics; the subfamily assignments are openly accessible via the Carbohydrate-Active Enzyme database at http://www.cazy.org/GH5.html.
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32.
  • Atkinson, Gemma C., et al. (författare)
  • Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components
  • 2008
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8, s. 290-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Members of the eukaryote/archaea specific eRF1 and eRF3 protein families have central roles in translation termination. They are also central to various mRNA surveillance mechanisms, together with the eRF1 paralogue Dom34p and the eRF3 paralogues Hbs1p and Ski7p. We have examined the evolution of eRF1 and eRF3 families using sequence similarity searching, multiple sequence alignment and phylogenetic analysis. Results: Extensive BLAST searches confirm that Hbs1p and eRF3 are limited to eukaryotes, while Dom34p and eRF1 (a/eRF1) are universal in eukaryotes and archaea. Ski7p appears to be restricted to a subset of Saccharomyces species. Alignments show that Dom34p does not possess the characteristic class-1 RF minidomains GGQ, NIKS and YXCXXXF, in line with recent crystallographic analysis of Dom34p. Phylogenetic trees of the protein families allow us to reconstruct the evolution of mRNA surveillance mechanisms mediated by these proteins in eukaryotes and archaea. Conclusion: We propose that the last common ancestor of eukaryotes and archaea possessed Dom34p-mediated no-go decay (NGD). This ancestral Dom34p may or may not have required a trGTPase, mostly like a/eEF1A, for its delivery to the ribosome. At an early stage in eukaryotic evolution, eEF1A was duplicated, giving rise to eRF3, which was recruited for translation termination, interacting with eRF1. eRF3 evolved nonsense-mediated decay (NMD) activity either before or after it was again duplicated, giving rise to Hbs1p, which we propose was recruited to assist eDom34p in eukaryotic NGD. Finally, a third duplication within ascomycete yeast gave rise to Ski7p, which may have become specialised for a subset of existing Hbs1p functions in non-stop decay (NSD). We suggest Ski7p-mediated NSD may be a specialised mechanism for counteracting the effects of increased stop codon read-through caused by prion-domain [ PSI+] mediated eRF3 precipitation.
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33.
  • Backström, Niclas, et al. (författare)
  • Inferring the demographic history of European Ficedula flycatcher populations
  • 2013
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 13, s. 2-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Inference of population and species histories and population stratification using genetic data is important for discriminating between different speciation scenarios and for correct interpretation of genome scans for signs of adaptive evolution and trait association. Here we use data from 24 intronic loci re-sequenced in population samples of two closely related species, the pied flycatcher and the collared flycatcher. Results: We applied Isolation-Migration models, assignment analyses and estimated the genetic differentiation and diversity between species and between populations within species. The data indicate a divergence time between the species of <1 million years, significantly shorter than previous estimates using mtDNA, point to a scenario with unidirectional gene-flow from the pied flycatcher into the collared flycatcher and imply that barriers to hybridisation are still permeable in a recently established hybrid zone. Furthermore, we detect significant population stratification, predominantly between the Spanish population and other pied flycatcher populations. Conclusions: Our results provide further evidence for a divergence process where different genomic regions may be at different stages of speciation. We also conclude that forthcoming analyses of genotype-phenotype relations in these ecological model species should be designed to take population stratification into account.
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34.
  • Backström, Niclas, et al. (författare)
  • Sex- and species-biased gene flow in a spotted eagle hybrid zone.
  • 2011
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Recent theoretical and empirical work points toward a significant role for sex-chromosome linked genes in the evolution of traits that induce reproductive isolation and for traits that evolve under influence of sexual selection. Empirical studies including recently diverged (Pleistocene), short-lived avian species pairs with short generation times have found that introgression occurs on the autosomes but not on the Z-chromosome. Here we study genetic differentiation and gene flow in the long-lived greater spotted eagle (Aquila clanga) and lesser spotted eagle (A. pomarina), two species with comparatively long generation times.RESULTS: Our data suggest that there is a directional bias in migration rates between hybridizing spotted eagles in eastern Europe. We find that a model including post divergence gene flow fits our data best for both autosomal and Z-chromosome linked loci but, for the Z-chromosome, the rate is reduced in the direction from A. pomarina to A. clanga.CONCLUSIONS: The fact that some introgression still occurs on the Z-chromosome between these species suggests that the differentiation process is in a more premature phase in our study system than in previously studied avian species pairs and that could be explained by a shorter divergence time and/or a longer average generation time in the spotted eagles. The results are in agreement with field observations and provide further insight into the role of sex-linked loci for the build-up of barriers to gene flow among diverging populations and species.
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35.
  • Bernhardsson, Sebastian, et al. (författare)
  • Structural correlations in bacterial metabolic networks
  • 2011
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11:20
  • Tidskriftsartikel (refereegranskat)abstract
    • Background Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution. Results We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD), a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart. Conclusions The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery of the network. This suggests that natural selection and biochemical correlations can act both to diversify and to narrow down metabolic evolution.
  •  
36.
  • Bilde, Trine, et al. (författare)
  • Sex differences in the genetic architecture of lifespan in a seed beetle : extreme inbreeding extends male lifespan
  • 2009
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 9, s. 33-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Sex differences in lifespan are ubiquitous throughout the animal kingdom but the causes underlying this phenomenon remain poorly understood. Several explanations based on asymmetrical inheritance patterns (sex chromosomes or mitochondrial DNA) have been proposed, but these ideas have rarely been tested experimentally. Alternatively, sexual dimorphism in lifespan could result from sex-specific selection, caused by fundamental differences in how males and females optimize their fitness by allocating resources into current and future reproduction. Results: Here we used sex-specific responses to inbreeding to study the genetic architecture of lifespan and mortality rates in Callosobruchus maculatus, a seed beetle that shows sexual dimorphism in lifespan. Two independent assays revealed opposing sex-specific responses to inbreeding. The combined data set showed that inbred males live longer than outbred males, while females show the opposite pattern. Both sexes suffered reduced fitness measured as lifetime reproductive success as a result of inbreeding. Conclusion: No model based on asymmetrical inheritance can explain increased male lifespan in response to inbreeding. Our results are however compatible with models based on sex-specific selection on reproductive strategies. We therefore suggest that sex-specific differences in lifespan in this species primarily result from sexually divergent selection.
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37.
  • Bilde, T., et al. (författare)
  • The genetic architecture of fitness in a seed beetle : assessing the potential for indirect genetic benefits of female choice
  • 2008
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8, s. 295-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Quantifying the amount of standing genetic variation in fitness represents an empirical challenge. Unfortunately, the shortage of detailed studies of the genetic architecture of fitness has hampered progress in several domains of evolutionary biology. One such area is the study of sexual selection. In particular, the evolution of adaptive female choice by indirect genetic benefits relies on the presence of genetic variation for fitness. Female choice by genetic benefits fall broadly into good genes (additive) models and compatibility (non-additive) models where the strength of selection is dictated by the genetic architecture of fitness. To characterize the genetic architecture of fitness, we employed a quantitative genetic design (the diallel cross) in a population of the seed beetle Callosobruchus maculatus, which is known to exhibit post-copulatory female choice. From reciprocal crosses of inbred lines, we assayed egg production, egg-to-adult survival, and lifetime offspring production of the outbred F1 daughters (F1 productivity). Results: We used the bio model to estimate six components of genetic and environmental variance in fitness. We found sizeable additive and non-additive genetic variance in F-1 productivity, but lower genetic variance in egg-to-adult survival, which was strongly influenced by maternal and paternal effects. Conclusion: Our results show that, in order to gain a relevant understanding of the genetic architecture of fitness, measures of offspring fitness should be inclusive and should include quantifications of offspring reproductive success. We note that our estimate of additive genetic variance in F-1 productivity (CVA = 14%) is sufficient to generate indirect selection on female choice. However, our results also show that the major determinant of offspring fitness is the genetic interaction between parental genomes, as indicated by large amounts of non-additive genetic variance (dominance and/or epistasis) for F-1 productivity. We discuss the processes that may maintain additive and non-additive genetic variance for fitness and how these relate to indirect selection for female choice.
  •  
38.
  • Björnerfeldt, S, et al. (författare)
  • Assortative mating and fragmentation within dog breeds
  • 2008
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 8, s. 28-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results: Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion: The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure.
  •  
39.
  • Blomqvist, Donald, 1954, et al. (författare)
  • Trapped in the extinction vortex? Strong genetic effects in a declining vertebrate population
  • 2010
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 10:33
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Inbreeding and loss of genetic diversity are expected to increase the extinction risk of small populations, but detailed tests in natural populations are scarce. We combine long-term population and fitness data with those from two types of molecular markers to examine the role of genetic effects in a declining metapopulation of southern dunlins Calidris alpina schinzii, an endangered shorebird. RESULTS: The decline is associated with increased pairings between related individuals, including close inbreeding (as revealed by both field observations of parentage and molecular markers). Furthermore, reduced genetic diversity seems to affect individual fitness at several life stages. Higher genetic similarity between mates correlates negatively with the pair's hatching success. Moreover, offspring produced by related parents are more homozygous and suffer from increased mortality during embryonic development and possibly also after hatching. CONCLUSIONS: Our results demonstrate strong genetic effects in a rapidly declining population, emphasizing the importance of genetic factors for the persistence of small populations.
  •  
40.
  • Bolund, Elisabeth, et al. (författare)
  • Correlates of male fitness in captive zebra finches : a comparison of methods to disentangle genetic and environmental effects
  • 2011
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 327-
  • Tidskriftsartikel (refereegranskat)abstract
    • Backgound: It is a common observation in evolutionary studies that larger, more ornamented or earlier breeding individuals have higher fitness, but that body size, ornamentation or breeding time does not change despite of sometimes substantial heritability for these traits. A possible explanation for this is that these traits do not causally affect fitness, but rather happen to be indirectly correlated with fitness via unmeasured non-heritable aspects of condition (e. g. undernourished offspring grow small and have low fitness as adults due to poor health). Whether this explanation applies to a specific case can be examined by decomposing the covariance between trait and fitness into its genetic and environmental components using pedigree-based animal models. We here examine different methods of doing this for a captive zebra finch population where male fitness was measured in communal aviaries in relation to three phenotypic traits (tarsus length, beak colour and song rate). Results: Our case study illustrates how methods that regress fitness over breeding values for phenotypic traits yield biased estimates as well as anti-conservative standard errors. Hence, it is necessary to estimate the genetic and environmental covariances between trait and fitness directly from a bivariate model. This method, however, is very demanding in terms of sample sizes. In our study parameter estimates of selection gradients for tarsus were consistent with the hypothesis of environmentally induced bias (beta(A) = 0.035 +/- 0.25 (SE), beta(E) = 0.57 +/- 0.28 (SE)), yet this differences between genetic and environmental selection gradients falls short of statistical significance. Conclusions: To examine the generality of the idea that phenotypic selection gradients for certain traits (like size) are consistently upwardly biased by environmental covariance a meta-analysis across study systems will be needed.
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41.
  •  
42.
  • Bukontaite, Rasa, et al. (författare)
  • The utility of CAD in recovering Gondwanan vicariance events and the evolutionary history of Aciliini (Coleoptera: Dytiscidae)
  • 2014
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 14, s. 5-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Aciliini presently includes 69 species of medium-sized water beetles distributed on all continents except Antarctica. The pattern of distribution with several genera confined to different continents of the Southern Hemisphere raises the yet untested hypothesis of a Gondwana vicariance origin. The monophyly of Aciliini has been questioned with regard to Eretini, and there are competing hypotheses about the intergeneric relationship in the tribe. This study is the first comprehensive phylogenetic analysis focused on the tribe Aciliini and it is based on eight gene fragments. The aims of the present study are: 1) to test the monophyly of Aciliini and clarify the position of the tribe Eretini and to resolve the relationship among genera within Aciliini, 2) to calibrate the divergence times within Aciliini and test different biogeographical scenarios, and 3) to evaluate the utility of the gene CAD for phylogenetic analysis in Dytiscidae. Results: Our analyses confirm monophyly of Aciliini with Eretini as its sister group. Each of six genera which have multiple species are also supported as monophyletic. The origin of the tribe is firmly based in the Southern Hemisphere with the arrangement of Neotropical and Afrotropical taxa as the most basal clades suggesting a Gondwana vicariance origin. However, the uncertainty as to whether a fossil can be used as a stem-or crowngroup calibration point for Acilius influenced the result: as crowngroup calibration, the 95% HPD interval for the basal nodes included the geological age estimate for the Gondwana break-up, but as a stem group calibration the basal nodes were too young. Our study suggests CAD to be the most informative marker between 15 and 50 Ma. Notably, the 2000 bp CAD fragment analyzed alone fully resolved the tree with high support. Conclusions: 1) Molecular data confirmed Aciliini as a monophyletic group. 2) Bayesian optimizations of the biogeographical history are consistent with an influence of Gondwana break-up history, but were dependent on the calibration method. 3) The evaluation using a method of phylogenetic signal per base pair indicated Wnt and CAD as the most informative of our sampled genes.
  •  
43.
  • Castroviejo-Fisher, Santiago, et al. (författare)
  • Vanishing Native American dog lineages
  • 2011
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 73-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Dogs were an important element in many native American cultures at the time Europeans arrived. Although previous ancient DNA studies revealed the existence of unique native American mitochondrial sequences, these have not been found in modern dogs, mainly purebred, studied so far. Results: We identified many previously undescribed mitochondrial control region sequences in 400 dogs from rural and isolated areas as well as street dogs from across the Americas. However, sequences of native American origin proved to be exceedingly rare, and we estimate that the native population contributed only a minor fraction of the gene pool that constitutes the modern population. Conclusions: The high number of previously unidentified haplotypes in our sample suggests that a lot of unsampled genetic variation exists in non-breed dogs. Our results also suggest that the arrival of European colonists to the Americas may have led to an extensive replacement of the native American dog population by the dogs of the invaders.
  •  
44.
  • Davis, Robert B, et al. (författare)
  • The origins of species richness in the Hymenoptera : insights from a family-level supertree
  • 2010
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 10
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: The order Hymenoptera (bees, ants, wasps, sawflies) contains about eight percent of all described species, but no analytical studies have addressed the origins of this richness at family-level or above. To investigate which major subtaxa experienced significant shifts in diversification, we assembled a family-level phylogeny of the Hymenoptera using supertree methods. We used sister-group species-richness comparisons to infer the phylogenetic position of shifts in diversification.RESULTS: The supertrees most supported by the underlying input trees are produced using matrix representation with compatibility (MRC) (from an all-in and a compartmentalised analysis). Whilst relationships at the tips of the tree tend to be well supported, those along the backbone of the tree (e.g. between Parasitica superfamilies) are generally not. Ten significant shifts in diversification (six positive and four negative) are found common to both MRC supertrees. The Apocrita (wasps, ants, bees) experienced a positive shift at their origin accounting for approximately 4,000 species. Within Apocrita other positive shifts include the Vespoidea (vespoid wasps/ants containing 24,000 spp.), Anthophila + Sphecidae (bees/thread-waisted wasps; 22,000 spp.), Bethylidae + Chrysididae (bethylid/cuckoo wasps; 5,200 spp.), Dryinidae (dryinid wasps; 1,100 spp.), and Proctotrupidae (proctotrupid wasps; 310 spp.). Four relatively species-poor families (Stenotritidae, Anaxyelidae, Blasticotomidae, Xyelidae) have undergone negative shifts. There are some two-way shifts in diversification where sister taxa have undergone shifts in opposite directions.CONCLUSIONS: Our results suggest that numerous phylogenetically distinctive radiations contribute to the richness of large clades. They also suggest that evolutionary events restricting the subsequent richness of large clades are common. Problematic phylogenetic issues in the Hymenoptera are identified, relating especially to superfamily validity (e.g. "Proctotrupoidea", "Mymarommatoidea"), and deeper apocritan relationships. Our results should stimulate new functional studies on the causes of the diversification shifts we have identified. Possible drivers highlighted for specific adaptive radiations include key anatomical innovations, the exploitation of rich host groups, and associations with angiosperms. Low richness may have evolved as a result of geographical isolation, specialised ecological niches, and habitat loss or competition.
  •  
45.
  • de Boer, Hugo J., 1978-, et al. (författare)
  • Evolution and loss of long-fringed petals : A case study using a dated phylogeny of the snake gourds, Trichosanthes (Cucurbitaceae)
  • 2012
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 12, s. 108-
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundThe Cucurbitaceae genus Trichosanthes comprises 90–100 species that occur from India to Japan and southeast to Australia and Fiji. Most species have large white or pale yellow petals with conspicuously fringed margins, the fringes sometimes several cm long. Pollination is usually by hawkmoths. Previous molecular data for a small number of species suggested that a monophyletic Trichosanthes might include the Asian genera Gymnopetalum (four species, lacking long petal fringes) and Hodgsonia (two species with petals fringed). Here we test these groups’ relationships using a species sampling of c. 60% and 4759 nucleotides of nuclear and plastid DNA. To infer the time and direction of the geographic expansion of the Trichosanthes clade we employ molecular clock dating and statistical biogeographic reconstruction, and we also address the gain or loss of petal fringes.ResultsTrichosanthes is monophyletic as long as it includes Gymnopetalum, which itself is polyphyletic. The closest relative of Trichosanthes appears to be the sponge gourds, Luffa, while Hodgsonia is more distantly related. Of six morphology-based sections in Trichosanthes with more than one species, three are supported by the molecular results; two new sections appear warranted. Molecular dating and biogeographic analyses suggest an Oligocene origin of Trichosanthes in Eurasia or East Asia, followed by diversification and spread throughout the Malesian biogeographic region and into the Australian continent.ConclusionsLong-fringed corollas evolved independently in Hodgsonia and Trichosanthes, followed by two losses in the latter coincident with shifts to other pollinators but not with long-distance dispersal events. Together with the Caribbean Linnaeosicyos, the Madagascan Ampelosicyos and the tropical African Telfairia, these cucurbit lineages represent an ideal system for more detailed studies of the evolution and function of petal fringes in plant-pollinator mutualisms.
  •  
46.
  • Dekker, Teun, et al. (författare)
  • Ostrinia revisited: Evidence for sex linkage in European Corn Borer Ostrinia nubilalis (Hubner) pheromone reception
  • 2010
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 10, s. 1-12
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The European Corn Borer, Ostrinia nubilalis (Hubner), is a keystone model for studies on the evolution of sex pheromone diversity and its role in establishing reproductive isolation. This species consists of two sympatric races, each utilizing opposite isomers of the same compound as their major pheromone component. Female production and male response are congruent in each race, and males from each strain exhibit phenotypic differences in peripheral physiology. Both strains possess co-localized pheromone-sensitive olfactory sensory neurons characterized by a larger amplitude action potential (spike) responding to the major pheromone component, and a smaller spike amplitude cell responding to the minor component, i.e. the opposite isomer. These differences in amplitude correspond to differences in dendritic diameter between the two neurons. Previous studies showed that behavioral response to the pheromone blend was sex-linked, but spike amplitude response to pheromone components matched autosomal, not sex-linked inheritance. Results: As part of a larger study to finely map the loci responsible for pheromone communication in this species, we have reanalyzed peripheral physiology among parental, and first and second generation hybrids between the two pheromone strains using tungsten electrode electrophysiology. Our results reveal that differences in spike amplitude ratio between male pheromone-sensitive sensory neurons in O. nubilalis races are controlled, at least partially, by sex-linked genes that exhibit E-strain dominance. Conclusions: We propose that peripheral olfactory response in O. nubilalis may be affected both by autosomal and sex-linked genes exhibiting a cross-locus dominance effect, and suggest that the genetic basis for pheromone reception and response in the species is more closely linked than previously thought
  •  
47.
  • Dwivedi, Bhakti, et al. (författare)
  • A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes
  • 2013
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 13:1, s. 1-17
  • Tidskriftsartikel (refereegranskat)abstract
    • BackgroundRibonucleotide reductase (RNR), the enzyme responsible for the formation of deoxyribonucleotides from ribonucleotides, is found in all domains of life and many viral genomes. RNRs are also amongst the most abundant genes identified in environmental metagenomes. This study focused on understanding the distribution, diversity, and evolution of RNRs in phages (viruses that infect bacteria). Hidden Markov Model profiles were used to analyze the proteins encoded by 685 completely sequenced double-stranded DNA phages and 22 environmental viral metagenomes to identify RNR homologs in cultured phages and uncultured viral communities, respectively.ResultsRNRs were identified in 128 phage genomes, nearly tripling the number of phages known to encode RNRs. Class I RNR was the most common RNR class observed in phages (70%), followed by class II (29%) and class III (28%). Twenty-eight percent of the phages contained genes belonging to multiple RNR classes. RNR class distribution varied according to phage type, isolation environment, and the host’s ability to utilize oxygen. The majority of the phages containing RNRs are Myoviridae (65%), followed by Siphoviridae (30%) and Podoviridae (3%). The phylogeny and genomic organization of phage and host RNRs reveal several distinct evolutionary scenarios involving horizontal gene transfer, co-evolution, and differential selection pressure. Several putative split RNR genes interrupted by self-splicing introns or inteins were identified, providing further evidence for the role of frequent genetic exchange. Finally, viral metagenomic data indicate that RNRs are prevalent and highly dynamic in uncultured viral communities, necessitating future research to determine the environmental conditions under which RNRs provide a selective advantage.ConclusionsThis comprehensive study describes the distribution, diversity, and evolution of RNRs in phage genomes and environmental viral metagenomes. The distinct distributions of specific RNR classes amongst phages, combined with the various evolutionary scenarios predicted from RNR phylogenies suggest multiple inheritance sources and different selective forces for RNRs in phages. This study significantly improves our understanding of phage RNRs, providing insight into the diversity and evolution of this important auxiliary metabolic gene as well as the evolution of phages in response to their bacterial hosts and environments.
  •  
48.
  • Ericson, Per G P, 1956-, et al. (författare)
  • Inter-familial relationships of the shorebirds (Aves : Charadriiformes) based on nuclear DNA sequence data.
  • 2003
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 3, s. 16-
  • Tidskriftsartikel (refereegranskat)abstract
    • BACKGROUND: Phylogenetic hypotheses of higher-level relationships in the order Charadriiformes based on morphological data, partly disagree with those based on DNA-DNA hybridisation data. So far, these relationships have not been tested by analysis of DNA sequence data. Herein we utilize 1692 bp of aligned, nuclear DNA sequences obtained from 23 charadriiform species, representing 15 families. We also test earlier suggestions that bustards and sandgrouses may be nested with the charadriiforms. The data is analysed with methods based on the parsimony and maximum-likelihood criteria.RESULTS: Several novel phylogenetic relationships were recovered and strongly supported by the data, regardless of which method of analysis was employed. These include placing the gulls and allied groups as a sistergroup to the sandpiper-like birds, and not to the plover-like birds. The auks clearly belong to the clade with the gulls and allies, and are not basal to most other charadriiform birds as suggested in analyses of morphological data. Pluvialis, which has been supposed to belong to the plover family (Charadriidae), represents a basal branch that constitutes the sister taxon to a clade with plovers, oystercatchers and avocets. The thick-knees and sheathbills unexpectedly cluster together.CONCLUSION: The DNA sequence data contains a strong phylogenetic signal that results in a well-resolved phylogenetic tree with many strongly supported internodes. Taxonomically it is the most inclusive study of shorebird families that relies on nucleotide sequences. The presented phylogenetic hypothesis provides a solid framework for analyses of macroevolution of ecological, morphological and behavioural adaptations observed within the order Charadriiformes.
  •  
49.
  • Fiz-Palacios, Omar, et al. (författare)
  • Diversification of land plants : insights from a family-level phylogenetic analysis
  • 2011
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 341-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Some of the evolutionary history of land plants has been documented based on the fossil record and a few broad-scale phylogenetic analyses, especially focusing on angiosperms and ferns. Here, we reconstructed phylogenetic relationships among all 706 families of land plants using molecular data. We dated the phylogeny using multiple fossils and a molecular clock technique. Applying various tests of diversification that take into account topology, branch length, numbers of extant species as well as extinction, we evaluated diversification rates through time. We also compared these diversification profiles against the distribution of the climate modes of the Phanerozoic. Results: We found evidence for the radiations of ferns and mosses in the shadow of angiosperms coinciding with the rather warm Cretaceous global climate. In contrast, gymnosperms and liverworts show a signature of declining diversification rates during geological time periods of cool global climate. Conclusions: This broad-scale phylogenetic analysis helps to reveal the successive waves of diversification that made up the diversity of land plants we see today. Both warm temperatures and wet climate may have been necessary for the rise of the diversity under a successive lineage replacement scenario.
  •  
50.
  • Gos, Gesseca, et al. (författare)
  • Signatures of balancing selection are maintained at disease resistance loci following mating system evolution and a population bottleneck in the genus Capsella
  • 2012
  • Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 12, s. 152-
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: Population bottlenecks can lead to a loss of variation at disease resistance loci, which could have important consequences for the ability of populations to adapt to pathogen pressure. Alternatively, current or past balancing selection could maintain high diversity, creating a strong heterogeneity in the retention of polymorphism across the genome of bottlenecked populations. We sequenced part of the LRR region of 9 NBS-LRR disease resistance genes in the outcrossing Capsella grandiflora and the recently derived, bottlenecked selfing species Capsella rubella, and compared levels and patterns of nucleotide diversity and divergence with genome-wide reference loci. Results: In strong contrast with reference loci, average diversity at resistance loci was comparable between C. rubella and C. grandiflora, primarily due to two loci with highly elevated diversity indicative of past or present balancing selection. Average between-species differentiation was also reduced at the set of R-genes compared with reference loci, which is consistent with the maintenance of ancestral polymorphism. Conclusions: Historical or ongoing balancing selection on plant disease resistance genes is a likely contributor to the retention of ancestral polymorphism in some regions of the bottlenecked Capella rubella genome.
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