| 1. |
- Wintersparv Stervander, Martin, et al.
(author)
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Multiple instances of paraphyletic species and cryptic taxa revealed by mitochondrial and nuclear RAD data for Calandrella larks (Aves: Alaudidae)
- 2016
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In: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 102, s. 233-245
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Journal article (peer-reviewed)abstract
- The avian genus Calandrella (larks) was recently suggested to be non-monophyletic, and was divided into two genera, of which Calandrella sensu stricto comprises 4-5 species in Eurasia and Africa. We analysed mitochondrial cytochrome b (cytb) and nuclear Restriction-site Associated DNA (RAD) sequences from all species, and for cytb we studied 21 of the 22 recognised subspecies, with the aim to clarify the phylogenetic relationships within the genus and to compare large-scale nuclear sequence patterns with a widely used mitochondrial marker. Cytb indicated deep splits among the currently recognised species, although it failed to support the interrelationships among most of these. It also revealed unexpected deep divergences within C. brachydactyla, C. blanfordi/C erlangeri, C. cinerea, and C. acutirostris. It also suggested that both C. brachydactyla and C. blanfordi, as presently circumscribed, are paraphyletic. In contrast, most of the many subspecies of C brachydactyla and C. cinerea were unsupported by cytb, although two populations of C. cinerea were found to be genetically distinct. The RAD data corroborated the cytb tree (for the smaller number of taxa analysed) and recovered strongly supported interspecific relationships. However, coalescence analyses of the RAD data, analysed in SNAPP both with and without an outgroup, received equally strong support for two conflicting topologies. We suggest that the tree rooted with an outgroup - which is not recommended for SNAPP - is more trustworthy, and suggest that the reliability of analyses performed without any outgroup species should be thoroughly evaluated. We also demonstrate that degraded museum samples can be phylogenetically informative in RAD analyses following careful bioinformatic treatment. We note that the genus Calandrella is in need of taxonomic revision. (C) 2016 Elsevier Inc. All rights reserved.
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| 2. |
- Strandh, Maria, et al.
(author)
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Natural selection acts on floral traits associated with selfing rate among populations of Mixed-Mating collinsia heterophylla (Plantaginaceae)
- 2017
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In: International Journal of Plant Sciences. - : University of Chicago Press. - 1058-5893 .- 1537-5315. ; 178:8, s. 594-606
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Journal article (peer-reviewed)abstract
- Premise of research. A major aim in plant research is to understand the micro-and macroevolutionary processes generating the great diversity of mating systems and floral traits found in flowering plants. Using Collinsia heterophylla, a mixed-mating species in a genus with described variation in selfing rate and associated floral traits among species, we investigated (i) intraspecific selfing rate variation in relation to variation in environmental factors and floral traits and (ii) whether selection or genetic drift determine floral trait variation. Methodology. We estimated selfing rate in 21 Californian populations by means of microsatellite markers and investigated its relationship with sampling region, altitude, population ground cover, stage of stigma receptivity, stage of anther-stigma contact (indicating stage of self-pollination), flower size, and start of flowering. Phenotypic floral trait differentiation (PST) for the floral traits was contrasted with neutral genetic differentiation (FST). Pivotal results. The population selfing rate ranged between 0.16 and 0.71 and differed between regions, but it did not correlate with environmental factors. The best predictor of high selfing rate was early stigma receptivity. Stage of anther-stigma contact showed a nonlinear quadratic relation with selfing rate. PST was substantially higher than FST in the four traits, suggesting that variation in mating-related floral traits is shaped by natural selection. Conclusions. The importance of stage of stigma receptivity for predicting selfing rate in C. heterophylla is in line with the pattern found among Collinsia species, potentially indicating that microevolutionary processes in mixed mating influence macroevolutionary processes. The detected effect of natural selection acting on stage of stigma receptivity, in combination with previously detected genetic influence on this trait, gives support to the hypothesis that variability in mating system is adaptive.
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| 3. |
- Dussex, Nicolas, et al.
(author)
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Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass
- 2020
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In: Communications biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Ancient remains found in permafrost represent a rare opportunity to study past ecosystems. Here, we present an exceptionally well-preserved ancient bird carcass found in the Siberian permafrost, along with a radiocarbon date and a reconstruction of its complete mitochondrial genome. The carcass was radiocarbon dated to approximately 44-49 ka BP, and was genetically identified as a female horned lark. This is a species that usually inhabits open habitat, such as the steppe environment that existed in Siberia at the time. This near-intact carcass highlights the potential of permafrost remains for evolutionary studies that combine both morphology and ancient nucleic acids. Nicolas Dussex et al. identify a 44,000-49,000 year old bird found in Siberian permafrost as a female horned lark using ancient DNA. This exceptionally well-preserved specimen illustrates the potential contribution to science of permafrost deposits, such as the study of ecology and evolution of ancient ecosystems, calibration of molecular clocks, and furthering our understanding of processes such as biological regulation and gene expression in relation to climate change.
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| 4. |
- Hansson, Bengt, et al.
(author)
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Avian genome evolution : insights from a linkage map of the blue tit (Cyanistes caeruleus)
- 2010
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In: Heredity. - : Springer Science and Business Media LLC. - 0018-067X .- 1365-2540. ; 104:1, s. 67-78
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Journal article (peer-reviewed)abstract
- We provide a first-generation linkage map of the blue tit (Cyanistes caeruleus), a passerine within the previously genetically uncharacterized family Paridae, which includes 91 orthologous loci with a single anchored position in the chicken (Gallus gallus) sequence assembly. The map consists of 18 linkage groups and covers 935 cM. There was highly conserved synteny between blue tit and chicken with the exception of a split on chromosome 1, potential splits on chromosome 4 and the translocation of two markers from chromosome 2 and 3, respectively, to chromosome 5. Gene order was very well conserved for the majority of chromosomes, an exception being chromosome 1 where multiple rearrangements were detected. Similar results were obtained in a comparison to the zebra finch (Taeniopygia guttata) genome assembly. The recombination rate in females was slightly higher than in males, implying a moderate degree of heterochiasmy in the blue tit. The map distance of the blue tit was similar to 78% of that of the Wageningen chicken broiler population, and very similar to the Uppsala chicken mapping population, over homologous genome regions. Apart from providing insights into avian recombination and genome evolution, our blue tit linkage map forms a valuable genetic resource for ecological and evolutionary research in Paridae. Heredity (2010) 104, 67-78; doi:10.1038/hdy.2009.107; published online 26 August 2009
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| 5. |
- Knief, Ulrich, et al.
(author)
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Epistatic mutations under divergent selection govern phenotypic variation in the crow hybrid zone
- 2019
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In: Nature Ecology & Evolution. - : Springer Science and Business Media LLC. - 2397-334X. ; 3:4, s. 570-576
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Journal article (peer-reviewed)abstract
- The evolution of genetic barriers opposing interspecific gene flow is key to the origin of new species. Drawing from information on over 400 admixed genomes sourced from replicate transects across the European hybrid zone between all-black carrion crows and grey-coated hooded crows, we decipher the interplay between phenotypic divergence and selection at the molecular level. Over 68% of plumage variation was explained by epistasis between the gene NDP and a similar to 2.8-megabase region on chromosome 18 with suppressed recombination. Both pigmentation loci showed evidence for divergent selection resisting introgression. This study reveals how few, large-effect loci can govern prezygotic isolation and shield phenotypic divergence from gene flow.
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| 6. |
- Lemke, Hilger, et al.
(author)
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Annual cycle and migration strategies of a trans-saharan migratory songbird: a geolocator study in the great reed warbler.
- 2013
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:10
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Journal article (peer-reviewed)abstract
- Recent technological advancements now allow us to obtain geographical position data for a wide range of animal movements. Here we used light-level geolocators to study the annual migration cycle in great reed warblers (Acrocephalus arundinaceus), a passerine bird breeding in Eurasia and wintering in sub-Saharan Africa. We were specifically interested in seasonal strategies in routes and schedules of migration. We found that the great reed warblers (all males, no females were included) migrated from the Swedish breeding site in early August. After spending up to three weeks at scattered stopover sites in central to south-eastern Europe, they resumed migration and crossed the Mediterranean Sea and Sahara Desert without lengthy stopovers. They then spread out over a large overwintering area and each bird utilised two (or even three) main wintering sites that were spatially separated by a distinct mid-winter movement. Spring migration initiation date differed widely between individuals (1-27 April). Several males took a more westerly route over the Sahara in spring than in autumn, and in general there were fewer long-distance travels and more frequent shorter stopovers, including one in northern Africa, in spring. The shorter stopovers made spring migration on average faster than autumn migration. There was a strong correlation between the spring departure dates from wintering sites and the arrival dates at the breeding ground. All males had a high migration speed in spring despite large variation in departure dates, indicating a time-minimization strategy to achieve an early arrival at the breeding site; the latter being decisive for high reproductive success in great reed warblers. Our results have important implications for the understanding of long-distance migrants' ability to predict conditions at distant breeding sites and adapt to rapid environmental change.
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| 7. |
- Roved, Jacob, et al.
(author)
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MHCtools - an R package for MHC high-throughput sequencing data : Genotyping, haplotype and supertype inference, and downstream genetic analyses in non-model organisms
- 2022
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In: Molecular Ecology Resources. - : John Wiley & Sons. - 1755-098X .- 1755-0998. ; 22:7, s. 2775-2792
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Journal article (peer-reviewed)abstract
- The major histocompatibility complex (MHC) plays a central role in the vertebrate adaptive immune system and has been of long-term interest in evolutionary biology. While several protocols have been developed for MHC genotyping, there is a lack of transparent and standardized tools for downstream analysis of MHC data. Here, we present the r package mhctools and demonstrate the use of its functions to (i) assist accurate MHC genotyping from high-throughput amplicon-sequencing data, (ii) infer functional MHC supertypes using bootstrapped clustering analysis, (iii) identify segregating MHC haplotypes from family data, and (iv) analyse functional and genetic distances between MHC sequences. We employed mhctools to analyse MHC class I (MHC-I) amplicon data of 559 great reed warblers (Acrocephalus arundinaceus). We identified 390 MHC-I alleles which clustered into 14 functional supertypes. A phylogenetic analysis and analyses of positive selection suggested that the MHC-I alleles belong to several distinct functional groups. We furthermore identified 107 segregating haplotypes among 116 families, and found substantial variation in diversity with 4-21 MHC-I alleles and 3-13 MHC-I supertypes per haplotype. Finally, we show that the great reed warbler haplotypes harboured combinations of MHC-I supertypes with greater functional divergence than observed in simulated populations of possible haplotypes, a result that is in accordance with the divergent allele advantage hypothesis. Our study demonstrates the power of mhctools to support genotyping and analysis of MHC in non-model species, which we hope will encourage broad implementation among researchers in MHC genetics and evolution.
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| 8. |
- Sigeman, Hanna, et al.
(author)
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Avian Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and W Degeneration
- 2021
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In: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 38:12, s. 5275-5291
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Journal article (peer-reviewed)abstract
- How the avian sex chromosomes first evolved from autosomes remains elusive as 100 million years (My) of divergence and degeneration obscure their evolutionary history. The Sylvioidea group of songbirds is interesting for understanding avian sex chromosome evolution because a chromosome fusion event similar to 24 Ma formed "neo-sex chromosomes" consisting of an added (new) and an ancestral (old) part. Here, we report the complete female genome (ZW) of one Sylvioidea species, the great reed warbler (Acrocephalus arundinaceus). Our long-read assembly shows that the added region has been translocated to both Z and W, and whereas the added-Z has retained its gene order the added-W part has been heavily rearranged. Phylogenetic analyses show that recombination between the homologous added-Z and -W regions continued after the fusion event, and that recombination suppression across this region took several million years to be completed. Moreover, recombination suppression was initiated across multiple positions over the added-Z, which is not consistent with a simple linear progression starting from the fusion point. As expected following recombination suppression, the added-W show signs of degeneration including repeat accumulation and gene loss. Finally, we present evidence for nonrandom maintenance of slowly evolving and dosage-sensitive genes on both ancestral- and added-W, a process causing correlated evolution among orthologous genes across broad taxonomic groups, regardless of sex linkage.
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| 9. |
- Tarka, Maja, et al.
(author)
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Intralocus sexual conflict over wing length in a wild migratory bird
- 2014
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In: American Naturalist. - : University of Chicago Press. - 0003-0147 .- 1537-5323. ; 183:1, s. 62-73
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Journal article (peer-reviewed)abstract
- Intralocus sexual conflict (ISC) occurs when males and females have different adaptive peaks but are constrained fromevolving sexual dimorphism because of shared genes. Implications of this conflict on evolutionary dynamics in wild populations have not been investigated in detail. In comprehensive analyses of selection, heritability, and genetic correlations, we found evidence for an ISC over wing length, a key trait for flight performance and migration, in a long-term study of wild great reed warblers (Acrocephalus arundinaceus). We found moderate sexual dimorphism, high heritability, moderate sexually antagonistic selection, and strong positive crosssex genetic correlation in wing length, together supporting the presence of ISC. A negative genetic correlation between male wing length and female fitness indicated that females inheriting alleles for longer wings from their male relatives also inherited lower fitness.Moreover, cross-sex genetic correlations imposed constraint on the predicted microevolutionary trajectory of wing length (based on selection gradients), especially in females where the predicted response was reversed. The degree of sexual dimorphism in wing length did not change over time, suggesting no sign of conflict resolution. Our study provides novel insight into how an ISC over a fitness trait can affect microevolution in a wild population under natural selection.
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| 10. |
- Tende, Talatu, et al.
(author)
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Individual Identification and Genetic Variation of Lions (Panthera leo) from Two Protected Areas in Nigeria.
- 2014
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:1
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Journal article (peer-reviewed)abstract
- This survey was conducted in two protected areas in Nigeria to genetically identify individual lions and to determine the genetic variation within and between the populations. We used faecal sample DNA, a non-invasive alternative to the risky and laborious task of taking samples directly from the animals, often preceded by catching and immobilization. Data collection in Yankari Game Reserve (YGR) spanned through a period of five years (2008 -2012), whereas data in Kainji Lake National Park (KLNP) was gathered for a period of three years (2009, 2010 and 2012). We identified a minimum of eight individuals (2 males, 3 females, 3 unknown) from YGR and a minimum of ten individuals (7 males, 3 females) from KLNP. The two populations were found to be genetically distinct as shown by the relatively high fixation index (FST = 0.17) with each population exhibiting signs of inbreeding (YGR FIS = 0.49, KLNP FIS = 0.38). The genetic differentiation between the Yankari and Kainji lions is assumed to result from large spatial geographic distance and physical barriers reducing gene flow between these two remaining wild lion populations in Nigeria. To mitigate the probable inbreeding depression in the lion populations within Nigeria it might be important to transfer lions between parks or reserves or to reintroduce lions from the zoos back to the wild.
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