| 1. |
- Jønsson, Knud A., et al.
(författare)
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Biogeographical history of cuckoo‐shrikes (Aves: Passeriformes) : transoceanic colonization of Africa from Australo-Papua
- 2010
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Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 37:9, s. 1767-1781
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Tidskriftsartikel (refereegranskat)abstract
- Aim Cuckoo-shrikes and allies (Campephagidae) form a radiation of birds widely distributed in the Indo-Pacific and Africa. Recent studies on the group have been hampered by poor taxon sampling, causing inferences about systematics and biogeography to be rather speculative. With improved taxon sampling and analyses within an explicit spatiotemporal framework, we elucidate biogeographical patterns of dispersal and diversification within this diverse clade of passerine birds. Location Africa, Asia, Australo-Papua, the Pacific, the Philippines and Wallacea. Methods We use model-based phylogenetic methods (MrBayes and garli) to construct a phylogenetic hypothesis of the core Campephagidae (Campephagidae with the exclusion of Pericrocotus). The phylogeny is used to assess the biogeographical history of the group with a newly developed Bayesian approach to dispersal-vicariance analysis (Bayes-diva). We also made use of a partitioned beast analysis, with several calibration points taken from island ages, passerine mitochondrial substitution rates and secondary calibration points for passerine birds, to assess the timing of diversification and dispersal. Results We present a robust molecular phylogeny that includes all genera and 84% of the species within the core Campephagidae. Furthermore, we estimate divergence dates and ancestral area relationships. We demonstrate that Campephagidae originated in Australo-Papua with a single lineage (Pericrocotus) dispersing to Asia early. Later, there was further extensive transoceanic dispersal from Australo-Papua to Africa involving lineages within the core Campephagidae radiation. Main conclusions The phylogenetic relationships, along with the results of the ancestral area analysis and the timing of dispersal events, support a transoceanic dispersal scenario from Australo-Papua to Africa by the core Campephagidae. The sister group to core Campephagidae, Pericrocotus, dispersed to mainland Asia in the late Oligocene. Asia remained uncolonized by the core Campephagidae until the Pliocene. Transoceanic dispersal is by no means an unknown phenomenon, but our results represent a convincing case of colonization over a significant water gap of thousands of kilometres from Australo-Papua to Africa.
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| 2. |
- Irestedt, Martin, 1968-, et al.
(författare)
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A crowd-sourced genomic project to assess hybrid content in a rare avian vagrant (Azure Tit Cyanistes cyanus (Pallas, 1770))
- 2023
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Ingår i: Avian Research. - : Elsevier. - 2053-7166. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to correlate plumage variation with the amount of genomic hybrid content in hybrids between Azure Tits Cyanistes cyanus (Pallas, 1770) and European Blue Tit Cyanistes caeruleus (Linnaeus, 1758), by re-sequencing the genomes of museum specimens of non-hybrids and presumed hybrids with varying plumages. The project was funded by crowdsourcing and initiated when two presumed Azure Tits, observed by hundreds of Swedish birdwatchers, were rejected as hybrids based on minor plumage deviations assumed to indicate hybrid contents from the European Blue Tit. The results confirm that hybrids with intermediate plumages, so called Pleske’s Tits, are first generation hybrids (F1 hybrids). Individuals, whose plumages are similar to Azure Tits, but assessed as hybrids based on minor plumage deviations, are all backcrosses but vary in their degree of hybrid content. However, some individuals morphologically recognized as pure Azure Tits expressed similar degrees of hybrid content. The results indicate that: (1) hybrid content may be widespread in Azure Tits in the western part of its habitat distribution; (2) plumage deviation in backcrosses is not linearly correlated with the genetic degree of hybrid origin; and (3) all Azure Tits observed in Europe outside its natural distribution may have some degree of hybrid origin. We therefore suggest that it is very difficult to phenotypically single out hybrids beyond first generation backcrosses. We argue that decreased sequencing costs and improved analytical tools open the doors for museomic crowd-sourced projects that may not address outstanding biological questions but have a major interest for lay citizens such as birdwatchers.
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| 3. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences
- 2012
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Ingår i: MycoKeys. - : Pensoft Publishers. - 1314-4057 .- 1314-4049. ; 4, s. 37-63
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Tidskriftsartikel (refereegranskat)abstract
- Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
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| 4. |
- Nylander, Johan A. A., 1969-
(författare)
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Bayesian Phylogenetics and the Evolution of Gall Wasps
- 2004
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis concerns the phylogenetic relationships and the evolution of the gall-inducing wasps belonging to the family Cynipidae. Several previous studies have used morphological data to reconstruct the evolution of the family. DNA sequences from several mitochondrial and nuclear genes where obtained and the first molecular, and combined molecular and morphological, analyses of higher-level relationships in the Cynipidae is presented. A Bayesian approach to data analysis is adopted, and models allowing combined analysis of heterogeneous data, such as multiple DNA data sets and morphology, are developed. The performance of these models is evaluated using methods that allow the estimation of posterior model probabilities, thus allowing selection of most probable models for the use in phylogenetics. The use of Bayesian model averaging in phylogenetics, as opposed to model selection, is also discussed. It is shown that Bayesian MCMC analysis deals efficiently with complex models and that morphology can influence combined-data analyses, despite being outnumbered by DNA data. This emphasizes the utility and potential importance of using morphological data in statistical analyses of phylogeny. The DNA-based and combined-data analyses of cynipid relationships differ from previous studies in two important respects. First, it was previously believed that there was a monophyletic clade of woody rosid gallers but the new results place the non-oak gallers in this assemblage (tribes Pediaspidini, Diplolepidini, and Eschatocerini) outside the rest of the Cynipidae. Second, earlier studies have lent strong support to the monophyly of the inquilines (tribe Synergini), gall wasps that develop inside the galls of other species. The new analyses suggest that the inquilines either originated several times independently, or that some inquilines secondarily regained the ability to induce galls. Possible reasons for the incongruence between morphological and DNA data is discussed in terms of heterogeneity in evolutionary rates among lineages, and convergent evolution of morphological characters.
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| 5. |
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| 6. |
- Ronquist, Fredrik, et al.
(författare)
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Phylogeny, evolution and classification of gall wasps : the plot thickens.
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- Gall wasps (Cynipidae) represent the most spectacular radiation of gall-inducing insects. In addition to true gall formers, gall wasps also include phytophagous inquilines, which live inside the galls induced by gall wasps or other insects. Here we present the first comprehensive molecular and total-evidence analyses of higher-level gall wasp relationships. We studied more than 100 taxa representing a rich selection of outgroups and the majority of described cynipid genera outside the diverse oak gall wasps (Cynipini), which were more sparsely sampled. About 5 kb of nucleotide data from one mitochondrial (COI) and four nuclear (28S, LWRh, EF1alpha F1, and EF1alpha F2) markers were analyzed separately and in combination with morphological and life-history data. According to previous morphology-based studies, gall wasps evolved in the Northern Hemisphere and were initially herb gallers. Inquilines originated once from gall inducers that lost the ability to initiate galls. Our results, albeit not conclusive, suggest a different scenario. The first gall wasps were more likely associated with woody host plants, and there must have been multiple origins of gall inducers, inquilines or both. One possibility is that gall inducers arose independently from inquilines in several lineages. Except for these surprising results, our analyses are largely consistent with previous studies. They confirm that gall wasps are conservative in their host-plant preferences, and that herb-galling lineages have radiated repeatedly onto the same set of unrelated host plants. We propose a revised classification of the family into twelve tribes, which are strongly supported as monophyletic across independent datasets. Four are new: Aulacideini, Phanacidini, Diastrophini and Ceroptresini. We present a key to the tribes and discuss their morphological and biological diversity. Until the relationships among the tribes are resolved, the origin and early evolution of gall wasps will remain elusive.
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| 7. |
- Antonelli, Alexandre, 1978, et al.
(författare)
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Tracing the impact of the Andean uplift on Neotropical plant evolution
- 2009
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424. ; 106:24, s. 9749-9754
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Tidskriftsartikel (refereegranskat)abstract
- Recent phylogenetic studies have revealed the major role played by the uplift of the Andes in the extraordinary diversification of the Neotropical flora. These studies, however, have typically considered the Andean uplift as a single, time-limited event fostering the evolution of highland elements. This contrasts with geological reconstructions indicating that the uplift occurred in discrete periods from west to east and that it affected different regions at different times. We introduce an approach for integrating Andean tectonics with biogeographic reconstructions of Neotropical plants, using the coffee family (Rubiaceae) as a model group. The distribution of this family spans highland and montane habitats as well as tropical lowlands of Central and South America, thus offering a unique opportunity to study the influence of the Andean uplift on the entire Neotropical flora. Our results suggest that the Rubiaceae originated in the Paleotropics and used the boreotropical connection to reach South America. The biogeographic patterns found corroborate the existence of a long-lasting dispersal barrier between the Northern and Central Andes, the "Western Andean Portal.'' The uplift of the Eastern Cordillera ended this barrier, allowing dispersal of boreotropical lineages to the South, but gave rise to a huge wetland system ("Lake Pebas'') in western Amazonia that prevented in situ speciation and floristic dispersal between the Andes and Amazonia for at least 6 million years. Here, we provide evidence of these events in plants.
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| 8. |
- Buckley, Thomas R., et al.
(författare)
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The phylogenetic placement and biogeographical origins of the New Zealand stick insects (Phasmatodea)
- 2010
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Ingår i: Systematic Entomology. - : Wiley. - 0307-6970 .- 1365-3113. ; 35:2, s. 207-225
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Forskningsöversikt (refereegranskat)abstract
- The Lanceocercata are a clade of stick insects (Phasmatodea) that have undergone an impressive evolutionary radiation in Australia, New Caledonia, the Mascarene Islands and areas of the Pacific. Previous research showed that this clade also contained at least two of the nine New Zealand stick insect genera. We have constructed a phylogeny of the Lanceocercata using 2277 bp of mitochondrial and nuclear DNA sequence data to determine whether all nine New Zealand genera are indeed Lanceocercata and whether the New Zealand fauna is monophyletic. DNA sequence data were obtained from mitochondrial cytochrome oxidase subunits I and II and the nuclear large subunit ribosomal RNA and histone subunit 3. These data were subjected to Bayesian phylogenetic inference under a partitioned model and maximum parsimony. The resulting trees show that all the New Zealand genera are nested within a large New Caledonian radiation. The New Zealand genera do not form a monophyletic group, with the genus Spinotectarchus Salmon forming an independent lineage from the remaining eight genera. We analysed Lanceocercata apomorphies to confirm the molecular placement of the New Zealand genera and to identify characters that confirm the polyphyly of the fauna. Molecular dating analyses under a relaxed clock coupled with a Bayesian extension to dispersal-vicariance analysis was used to reconstruct the biogeographical history for the Lanceocercata. These analyses show that Lanceocercata and their sister group, the Stephanacridini, probably diverged from their South American relatives, the Cladomorphinae, as a result of the separation of Australia, Antarctica and South America. The radiation of the New Caledonian and New Zealand clade began 41.06 million years ago (mya, 29.05-55.40 mya), which corresponds to a period of uplift in New Caledonia. The main New Zealand lineage and Spinotectarchus split from their New Caledonian sister groups 33.72 (23.9-45.62 mya) and 29.9 mya (19.79-41.16 mya) and began to radiate during the late Oligocene and early Miocene, probably in response to a reduction in land area and subsequent uplift in the late Oligocene and early Miocene. We discuss briefly shared host plant patterns between New Zealand and New Caledonia. Because Acrophylla sensu Brock & Hasenpusch is polyphyletic, we have removed Vetilia Stal from synonymy with Acrophylla Gray.
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| 9. |
- Buerki, Sven, et al.
(författare)
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An evaluation of new parsimony-based versus parametric inference methods in biogeography : a case study using the globally distributed plant family Sapindaceae
- 2011
-
Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 38:3, s. 531-550
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Tidskriftsartikel (refereegranskat)abstract
- Aim Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersal-extinction-cladogenesis (DEC), against a parsimony-based method, dispersal-vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study. Location World-wide. Methods Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes-DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years. Results Despite differences in the underlying biogeographical model, Bayes-DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events - which in Bayes-DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node. Main conclusions By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide-spanning spatial and temporal model proposed here could prove useful for testing large-scale biogeographical patterns in plants.
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| 10. |
- Caputo, Andrea, et al.
(författare)
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The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration
- 2019
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 0378-1097 .- 1574-6968. ; 366:2
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Tidskriftsartikel (refereegranskat)abstract
- Diatom diazotroph associations (DDAs) are a widespread marine planktonic symbiosis between several diatom genera and di-nitrogen (N2)-fixing bacteria. Combining single cell confocal microscopy observations and molecular genetic approaches on individual field collected cells, we determined the phylogenetic diversity, distribution and evolution of the DDAs. Confocal analyses coupled with 3-D imaging re-evaluated the cellular location of DDA symbionts. DDA diversity was resolved by paired gene sequencing (18S rRNA and rbcL genes, 16S rRNA and nifH genes). A survey using the newly acquired sequences against public databases found sequences with high similarity (99–100%) to either host (18S rRNA) or symbiont (16S rRNA) in atypical regions for DDAs (high latitudes, anoxic basin and copepod gut). Concatenated phylogenies were congruent for the host and cyanobacteria sequences and implied co-evolution. Time-calibrated trees dated the appearance of N2 fixing planktonic symbiosis from 100–50Mya and were consistent with the symbiont cellular location: symbioses with internal partners are more ancient. An ancestral state reconstruction traced the evolution of traits in DDAs and highlight that the adaptive radiation to the marine environment was likely facilitated by the symbiosis. Our results present the evolutionary nature of DDAs and provide new genetic and phenotypic information for these biogeochemically relevant populations.
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| 11. |
- Dalen, Love, et al.
(författare)
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Identifying Bird Remains Using Ancient DNA Barcoding
- 2017
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Ingår i: Genes. - : MDPI AG. - 2073-4425. ; 8:6
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Tidskriftsartikel (refereegranskat)abstract
- Bird remains that are difficult to identify taxonomically using morphological methods, are common in the palaeontological record. Other types of challenging avian material include artefacts and food items from endangered taxa, as well as remains from aircraft strikes. We here present a DNA-based method that enables taxonomic identification of bird remains, even from material where the DNA is heavily degraded. The method is based on the amplification and sequencing of two short variable parts of the 16S region in the mitochondrial genome. To demonstrate the applicability of this approach, we evaluated the method on a set of Holocene and Late Pleistocene postcranial bird bones from several palaeontological and archaeological sites in Europe with good success.
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| 12. |
- Díez, Beatriz, et al.
(författare)
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Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community : Structure, Potential Function and Evolution.
- 2016
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 11:5
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Tidskriftsartikel (refereegranskat)abstract
- Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.
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| 13. |
- Dupont, Chris L., et al.
(författare)
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Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:2, s. e89549-
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Tidskriftsartikel (refereegranskat)abstract
- Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
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| 14. |
- Ericson, Per G P, 1956-, et al.
(författare)
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Dating the diversification of the major lineages of Passeriformes (Aves)
- 2014
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 14:8, s. 1-15
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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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| 15. |
- Ericson, Per G P, et al.
(författare)
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Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics
- 2020
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Ingår i: Systematic Biology. - 1063-5157 .- 1076-836X. ; 69:5, s. 820-829
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Tidskriftsartikel (refereegranskat)abstract
- The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits.
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| 16. |
- Hart Reeve, Andrew, et al.
(författare)
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The formation of the Indo-Pacific montane avifauna
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- The processes generating the earth’s montane biodiversity remain a matter of debate. Two contrasting hypotheses have been advanced to explain how montane populations form: via direct colonization from other mountains, or, alternatively, via upslope range shifts from adjacent lowland areas. We seek to reconcile these apparently conflicting hypotheses by asking whether a species’ ancestral geographic origin determines its mode of mountain colonization. Island-dwelling passerine birds at the faunal crossroads between Eurasia and Australo-Papua provide an ideal study system. We recover the phylogenetic relationships of the region’s montane species and reconstruct their ancestral geographic ranges, elevational ranges, and migratory behavior. We also perform genomic population studies of three super-dispersive montane species/clades with broad island distributions. Eurasian-origin species populated archipelagos via direct colonization between mountains. This mode of colonization appears related to ancestral adaptations to cold and seasonal climates, specifically short-distance migration. Australo-Papuan-origin mountain populations, by contrast, evolved from lowland ancestors, and highland distribution mostly precludes their further colonization of island mountains. Our study explains much of the distributional variation within a complex biological system, and provides a synthesis of two seemingly discordant hypotheses for montane community formation.
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| 17. |
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| 18. |
- Irestedt, Martin, et al.
(författare)
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Phylogenetic relationships of typical antbirds (Thamnophilidae) and test of incongruence based on Bayes factors
- 2004
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Ingår i: BMC Evolutionary Biology. - : BioMed Central. - 1471-2148. ; 4:23
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Tidskriftsartikel (refereegranskat)abstract
- The typical antbirds (Thamnophilidae) form a monophyletic and diverse family of suboscine passerines that inhabit neotropical forests. However, the phylogenetic relationships within this assemblage are poorly understood. Herein, we present a hypothesis of the generic relationships of this group based on Bayesian inference analyses of two nuclear introns and the mitochondrial cytochrome b gene. The level of phylogenetic congruence between the individual genes has been investigated utilizing Bayes factors. We also explore how changes in the substitution models affected the observed incongruence between partitions of our data set.
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| 19. |
- Larsson, John, et al.
(författare)
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Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits
- 2011
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11, s. 187-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Cyanobacteria belong to an ancient group of photosynthetic prokaryotes with pronounced variations in their cellular differentiation strategies, physiological capacities and choice of habitat. Sequencing efforts have shown that genomes within this phylum are equally diverse in terms of size and protein-coding capacity. To increase our understanding of genomic changes in the lineage, the genomes of 58 contemporary cyanobacteria were analysed for shared and unique orthologs. Results: A total of 404 protein families, present in all cyanobacterial genomes, were identified. Two of these are unique to the phylum, corresponding to an AbrB family transcriptional regulator and a gene that escapes functional annotation although its genomic neighbourhood is conserved among the organisms examined. The evolution of cyanobacterial genome sizes involves a mix of gains and losses in the clade encompassing complex cyanobacteria, while a single event of reduction is evident in a clade dominated by unicellular cyanobacteria. Genome sizes and gene family copy numbers evolve at a higher rate in the former clade, and multi-copy genes were predominant in large genomes. Orthologs unique to cyanobacteria exhibiting specific characteristics, such as filament formation, heterocyst differentiation, diazotrophy and symbiotic competence, were also identified. An ancestral character reconstruction suggests that the most recent common ancestor of cyanobacteria had a genome size of approx. 4.5 Mbp and 1678 to 3291 protein-coding genes, 4%-6% of which are unique to cyanobacteria today. Conclusions: The different rates of genome-size evolution and multi-copy gene abundance suggest two routes of genome development in the history of cyanobacteria. The expansion strategy is driven by gene-family enlargment and generates a broad adaptive potential; while the genome streamlining strategy imposes adaptations to highly specific niches, also reflected in their different functional capacities. A few genomes display extreme proliferation of non-coding nucleotides which is likely to be the result of initial expansion of genomes/gene copy number to gain adaptive potential, followed by a shift to a life-style in a highly specific niche (e. g. symbiosis). This transition results in redundancy of genes and gene families, leading to an increase in junk DNA and eventually to gene loss. A few orthologs can be correlated with specific phenotypes in cyanobacteria, such as filament formation and symbiotic competence; these constitute exciting exploratory targets.
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| 20. |
- Lilja, Tobias, et al.
(författare)
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Species identification of Swedish mosquitoes through DNA metabarcoding
- 2017
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Ingår i: Journal of the European Mosquito Control Association. ; 35, s. 1-9
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Tidskriftsartikel (refereegranskat)abstract
- DNA-barcoding utilises a fragment of the mitochondrial cytochrome oxidase subunit 1 (COI) gene to identify most animal species. Using next generation sequencing (NGS), this method can be further developed into metabarcoding processes that allow the simultaneous identification of several species from a mixed sample. We created a database of COI sequences of 27 mosquito species collected in Sweden, and combined our data with 27 additional sequences from GenBank to cover the taxa recently documented in Sweden and to include possible invasive taxa. Comparisons show that COI metabarcoding reliably identifies 41 of 54 species and the remainder to species group. Using three independent primer pairs along the COI gene, we further developed this barcoding approach to simultaneously identify Swedish mosquitoes in communities using NGS and quantify relative abundance of each mosquito species in the sample, using bioinformatics methods. We tested the accuracy of the metabarcoding method using communities assembled from morphologically identified mosquitoes, revealing 80% positive identification rate and the estimates of population structure which reflects the input sample. We conclude that metabarcoding is useful as a high throughput identification technique and for the quantification of species.
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| 21. |
- Lähteenaro, Meri, et al.
(författare)
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Phylogenomic species delimitation of the twisted-winged parasite genus Stylops (Strepsiptera)
- 2024
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Ingår i: Systematic Entomology. - : John Wiley & Sons. - 0307-6970 .- 1365-3113. ; 49:2, s. 294-313
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Tidskriftsartikel (refereegranskat)abstract
- The twisted-winged parasite genus Stylops has a history of different species concepts with varying host specificity resulting in diverse species diversity estimates in different regions of the Holarctic. The adoption of a supergeneralist species concept in Europe, proposing synonymization of all Western Palaearctic Stylops species, did not facilitate taxonomic clarity and obscured the available life-history data in the region for decades. Lack of molecular data has allowed divergent opinions on species hypotheses and little opportunity for evaluating them in this morphologically challenging genus. To solve these discrepancies and gain novel information about host associations, we applied whole-genome sequencing to 163 specimens, representing a significant portion of putative European species. We evaluate the existing and conflicting species hypotheses with molecular species delimitation using Species bOundry Delimitation using Astral (SODA) and use a maximum likelihood phylogeny to investigate host associations of the species. Furthermore, we evaluate the effect of a number of loci used in SODA for the number of inferred species. We find justification for synonymization of multiple species and indications of undescribed species, as well as new host-parasite relationships. We show that the number of inferred species in SODA is exceedingly and positively correlated with the number of loci used, urging for cautious application. The results of our study bring clarity to the Western Palaearctic species diversity of Stylops. Furthermore, the comprehensive molecular dataset generated in this study will be a valuable resource for future studies on Stylops and the evolution of parasites in general.
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| 22. |
- Lähteenaro, Meri, et al.
(författare)
-
Phylogenomic species delimitation of the twisted-winged parasite genus Stylops (Strepsiptera)
- 2024
-
Ingår i: Systematic Entomology. - 0307-6970 .- 1365-3113. ; 49:2, s. 294-313
-
Tidskriftsartikel (refereegranskat)abstract
- The twisted-winged parasite genus Stylops has a history of different species concepts with varying host specificity resulting in diverse species diversity estimates in different regions of the Holarctic. The adoption of a supergeneralist species concept in Europe, proposing synonymization of all Western Palaearctic Stylops species, did not facilitate taxonomic clarity and obscured the available life-history data in the region for decades. Lack of molecular data has allowed divergent opinions on species hypotheses and little opportunity for evaluating them in this morphologically challenging genus. To solve these discrepancies and gain novel information about host associations, we applied whole-genome sequencing to 163 specimens, representing a significant portion of putative European species. We evaluate the existing and conflicting species hypotheses with molecular species delimitation using Species bOundry Delimitation using Astral (SODA) and use a maximum likelihood phylogeny to investigate host associations of the species. Furthermore, we evaluate the effect of a number of loci used in SODA for the number of inferred species. We find justification for synonymization of multiple species and indications of undescribed species, as well as new host–parasite relationships. We show that the number of inferred species in SODA is exceedingly and positively correlated with the number of loci used, urging for cautious application. The results of our study bring clarity to the Western Palaearctic species diversity of Stylops. Furthermore, the comprehensive molecular dataset generated in this study will be a valuable resource for future studies on Stylops and the evolution of parasites in general.
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| 23. |
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| 24. |
- Nylander, Johan A. A., et al.
(författare)
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Bayesian phylogenetic analysis of combined data
- 2004
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 53:1, s. 47-67
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Tidskriftsartikel (populärvet., debatt m.m.)abstract
- The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology. Based on this foundation, we developed a Bayesian MCMC approach to the analysis of combined data sets and explored its utility in inferring relationships among gall wasps based on data from morphology and four genes (nuclear and mitochondrial, ribosomal and protein coding). Examined models range in complexity from those recognizing only a morphological and a molecular partition to those having complex substitution models with independent parameters for each gene. Bayesian MCMC analysis deals efficiently with complex models: convergence occurs faster and more predictably for complex models, mixing is adequate for all parameters even under very complex models, and the parameter update cycle is virtually unaffected by model partitioning across sites. Morphology contributed only 5% of the characters in the data set but nevertheless influenced the combined-data tree, supporting the utility of morphological data in multigene analyses. We used Bayesian criteria (Bayes factors) to show that process heterogeneity across data partitions is a significant model component, although not as important as among-site rate variation. More complex evolutionary models are associated with more topological uncertainty and less conflict between morphology and molecules. Bayes factors sometimes favor simpler models over considerably more parameter-rich models, but the best model overall is also the most complex and Bayes factors do not support exclusion of apparently weak parameters from this model. Thus, Bayes factors appear to be useful for selecting among complex models, but it is still unclear whether their use strikes a reasonable balance between model complexity and error in parameter estimates.
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| 25. |
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