| 1. |
- Irestedt, Martin, 1968-, et al.
(författare)
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No Signs of Genetic Erosion in a 19th Century Genome of the Extinct Paradise Parrot (Psephotellus pulcherrimus)
- 2019
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Ingår i: DIVERSITY-BASEL. - : MDPI. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- The Paradise Parrot, Psephotellus pulcherrimus, was a charismatic Australian bird that became extinct around 1928. While many extrinsic factors have been proposed to explain its disappearance, it remains unclear as to what extent genetic erosion might have contributed to the species’ demise. In this study, we use whole-genome resequencing to reconstruct a 15x coverage genome based on a historical museum specimen and shed further light on the evolutionary history that preceded the extinction of the Paradise Parrot. By comparing the genetic diversity of this genome with genomes from extant endangered birds, we show that during the species’ dramatic decline in the second half of the 19th century, the Paradise Parrot was genetically more diverse than individuals from species that are currently classified as endangered. Furthermore, demographic analyses suggest that the population size of the Paradise Parrot changed with temperature fluctuations during the last glacial cycle. We also confirm that the Golden-shouldered Parrot, Psephotellus chrysopterygius, is the closest living relative of this extinct parrot. Overall, our study highlights the importance of museum collections as repositories of biodiversity across time and demonstrates how historical specimens can provide a broader context on the circumstances that lead to species extinctions.
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| 2. |
- Jonsson, Knud Andreas, et al.
(författare)
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Unrecognised (species) diversity in New Guinean passerine birds
- 2019
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Ingår i: Emu (Print). - : TAYLOR & FRANCIS AUSTRALASIA. - 0158-4197 .- 1448-5540. ; 119:3, SI, s. 233-241
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Tidskriftsartikel (refereegranskat)abstract
- Species represent an important unit for the study of diversity, but may not always be delimited consistently across regions and clades. Many of these taxonomic inconsistencies are due to the variable views of taxonomists. In recent years, however, new methodologies have attempted to circumvent this problem by assigning more objective criteria for the delimitation of species, drawing on a wide range of data such as DNA, morphology, vocalisation and ecology. Here, we apply a genetic screening approach in which we sequence the mitochondrial gene ND2 for all recognised subspecies of 16 species in eight genera (a mix of lowland and montane species) from the geologically complex tropical island of New Guinea. We show that populations within some species are genetically highly divergent despite little morphological differentiation, but we also find an example in which populations from five morphologically distinct species are genetically very similar. Overall, our data show higher levels of genetic differentiation than expected, but also highlight the difficulty of predicting which groups contain unrecognised diversity. These results are interesting in their own right, but also have implications for further analyses that focus on increasing our understanding of how diversity builds up over time.
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| 3. |
- Le Pepke, Michael, et al.
(författare)
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Reconciling supertramps, great speciators and relict species with the taxon cycle stages of a large island radiation (Aves: Campephagidae)
- 2019
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Ingår i: Journal of Biogeography. - : WILEY. - 0305-0270 .- 1365-2699. ; 46:6, s. 1214-1225
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Tidskriftsartikel (refereegranskat)abstract
- Aim The taxon cycle concept provides a geographically explicit and testable set of hypotheses for exploring the evolutionary processes underlying the distribution of species in space and time. Here, we test taxon cycle predictions within a large avian island radiation, the core Campephagidae and explicitly integrate the concepts of ‘supertramps’, ‘great speciators’ and relictualization. Location The Indo-Pacific, Australia, Asia and Africa. Taxon Corvoid passerine birds. Methods We constructed a new time-calibrated molecular phylogeny of the core Campephagidae (cuckooshrikes, cicadabirds and trillers) using Bayesian phylogenetic methods. Ancestral range estimation methods and diversification rate analyses were used to explore the dispersal and diversification history of the group. We used an extensive dataset on wing morphology and range distributions to test for correlations between evolutionary age of species and dispersal capacity, diversification and distribution, while accounting for phylogenetic non-independence. Results The core Campephagidae represents an ecologically homogeneous radiation distributed across the Indo-Pacific, Australia, Southeast Asia and Africa. Its members represent a continuum of dispersal abilities; some species are widespread and undifferentiated (’supertramps’) or show strong differentiation of local populations (’great speciators’), and a few are endemic to single islands (relicts). We show that older species relative to younger species inhabit fewer and larger islands at higher elevations. The level of intraspecific variation measured as the number of subspecies also decreases with species age, and is highest in ‘great speciators’ with intermediate levels of dispersal abilities (as per hand-wing index). Main conclusions Based on trait correlations with species age, we infer phases of range expansion and contraction over millions of years (taxon cycles), within a single monophyletic group of birds. These observations demonstrate reconciliation of the concepts of ‘supertramps’, ‘great speciators’ and relictual palaeoendemics within the temporal stages of the taxon cycle.
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| 4. |
- Prost, Stefan, et al.
(författare)
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Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise
- 2019
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Ingår i: GigaScience. - : OXFORD UNIV PRESS. - 2047-217X. ; 8:5
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Tidskriftsartikel (refereegranskat)abstract
- The diverse array of phenotypes and courtship displays exhibited by birds-of-paradise have long fascinated scientists and nonscientists alike. Remarkably, almost nothing is known about the genomics of this iconic radiation. There are 41 species in 16 genera currently recognized within the birds-of-paradise family (Paradisaeidae), most of which are endemic to the island of New Guinea. In this study, we sequenced genomes of representatives from all five major clades within this family to characterize genomic changes that may have played a role in the evolution of the group's extensive phenotypic diversity. We found genes important for coloration, morphology, and feather and eye development to be under positive selection. In birds-of-paradise with complex lekking systems and strong sexual dimorphism, the core birds-of-paradise, we found Gene Ontology categories for "startle response" and "olfactory receptor activity" to be enriched among the gene families expanding significantly faster compared to the other birds in our study. Furthermore, we found novel families of retrovirus-like retrotransposons active in all three de novo genomes since the early diversification of the birds-of-paradise group, which might have played a role in the evolution of this fascinating group of birds.
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| 5. |
- Song, Gang, et al.
(författare)
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Complete taxon sampling of the avian genus Pica (magpies) reveals ancient relictual populations and synchronous Late-Pleistocene demographic expansion across the Northern Hemisphere
- 2018
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Ingår i: Journal of Avian Biology. - : WILEY. - 0908-8857 .- 1600-048X. ; 49:2
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies have suggested that bird populations in east Asia were less affected by Pleistocene climatic fluctuations than those in Europe and North America. However, this is mainly based on comparisons among species. It would be more relevant to analyse geographical populations of widespread species or species complexes. We analyzed two mitochondrial genes and two nuclear introns for all taxa of Pica to investigate 1) which Earth history factors have shaped the lineage divergence, and 2) whether different geographical populations were differently affected by the Pleistocene climatic changes. Our mitochondrial tree recovered three widespread lineages, 1) in east Asia, 2) across north Eurasia, and 3) in North America, respectively, with three isolated lineages in northwest Africa, Arabia and the Qinghai‐Tibet Plateau, respectively. Divergences among lineages took place 1.4–3.1 million yr ago. The northwest African population was sister to the others, which formed two main clades. In one of these, Arabia was sister to Qinghai‐Tibet, and these formed the sister clade to the east Asia clade. The other main clade comprised the North American and north Eurasian clades. There was no or very slight structure within these six geographical clades, including a lack of differentiation between the two North American species black‐billed magpie P. hudsonia and yellow‐billed magpie P. nutalli. Demographic expansion was recorded in the three most widespread lineages after 0.06 Ma. Asymmetric gene flow was recorded in the north Eurasian clade from southwestern Europe eastward, whereas the east Asian clade was rooted in south central China. Our results indicate that the fragmentation of the six clades of Pica was related to climatic cooling and aridification during periods of the Pliocene–Pleistocene. Populations on both sides of the Eurasian continent were similarly influenced by the Pleistocene climate changes and expanded concomitantly with the expansion of steppes. Based on results we also propose a revised taxonomy recognising seven species of Pica.
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| 6. |
- Xu, Luohao, et al.
(författare)
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Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds
- 2019
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Ingår i: Nature Ecology & Evolution. - : NATURE PUBLISHING GROUP. - 2397-334X. ; 3:5, s. 834-844
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Tidskriftsartikel (refereegranskat)abstract
- Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed ‘evolutionary strata’. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.
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