| 1. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 2. |
- Ng, E. Y. X., et al.
(författare)
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Genome-wide SNPs confirm plumage polymorphism and hybridisation within a Cyornis flycatcher species complex
- 2022
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Ingår i: Zoologica Scripta. - : Wiley. - 0300-3256 .- 1463-6409. ; 52:1, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- Morphology has been a leading taxonomic guiding light to systematists for the last couple of hundred years. However, the genetic and - more recently - genomic revolution have produced numerous demonstrations of erroneous classifications that were based on labile morphological traits. We used thousands of genome-wide markers to shed light on evolutionary dynamics in a confusing and taxonomically obscure group of Asian Cyornis flycatchers. Using genomic data, we corroborated recent findings based on three mitochrondrial and five nuclear genes that the two taxa hainanus and klossi which were previously treated as separate species (Cyornis hainanus and Cyornis rubeculoides klossi, respectively) are genomically homogeneous and form a single species, C. hainanus. We also uncovered a novel case of interbreeding between C. hainanus and a non-sister species, C. glaucicomans, illustrating these flycatchers' ability to hybridise in marginal situations even after substantial times of divergence. Our study illustrates how genome-wide loci can shed light on complicated taxonomic problems, resulting in a better integration of phenotypic and genotypic data.
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| 3. |
- Alström, Per, et al.
(författare)
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Complete species-level phylogeny of the leaf warbler (Aves: Phylloscopidae) radiation
- 2018
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Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier BV. - 1055-7903 .- 1095-9513. ; 126, s. 141-152
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Tidskriftsartikel (refereegranskat)abstract
- The leaf warbler radiation (Aves: Phylloscopidae) has undergone a c. 50% increase in the number of recognised species over the last three decades, mainly as a result of analyses of vocalisations and DNA. Using a multilocus dataset for all of the species in this family, and multispecies coalescent-based as well as concatenation methods, we provide the first complete species-level phylogeny for this important group, as well as an estimate of the timing of diversification. The most recent common ancestor for the family was dated at 11.7 million years ago (mya) (95% highest posterior density 9.8-13.7 mya), and divergence times between sister species ranged from 0.5 mya (0.3-0.8 mya) to 6.1 mya (4.8-7.5 mya). Based on our results, we support synonymising Seicercus with Phylloscopus, which results in a monogeneric Phylloscopidae. We discuss the pros and cons of this treatment, and we argue against proliferation of taxonomic names, and conclude that a large monogeneric Phylloscopidae leads to the fewest taxonomic changes compared to traditional classifications. We briefly discuss morphological evolution in the light of the phylogeny. The time calibrated phylogeny is a major improvement compared to previous studies based on a smaller number of species and loci and can provide a basis for future studies of other aspects of phylloscopid evolution.
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| 4. |
- Zhang, D. Z., et al.
(författare)
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Genomic and phenotypic changes associated with alterations of migratory behaviour in a songbird
- 2022
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 32:2, s. 381-92
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Tidskriftsartikel (refereegranskat)abstract
- The seasonal migration of birds is a fascinating natural wonder. Avian migratory behaviour changes are common and are probably a polygenic process as avian migration is governed by multiple correlated components with a variable genetic basis. However, the genetic and phenotypic changes involving migration changes are poorly studied. Using one annotated near-chromosomal level de novo genome assembly, 50 resequenced genomes, hundreds of morphometric data and species distribution information, we investigated population structure and genomic and phenotypic differences associated with differences in migratory behaviour in a songbird species, Yellow-throated Bunting Emberiza elegans (Aves: Emberizidae). Population genomic analyses reveal extensive gene flow between the southern resident and the northern migratory populations of this species. The hand-wing index is significantly lower in the resident populations than in the migratory populations, indicating reduced flight efficiency of the resident populations. Here, we discuss the possibility that nonmigratory populations may have originated from migratory populations though migration loss. We further infer that the alterations of genes related to energy metabolism, nervous system and circadian rhythm may have played major roles in regulating migration change. Our study sheds light on phenotypic and polygenic changes involving migration change.
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| 5. |
- Sadanandan, K. R., et al.
(författare)
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Genetic and biometric variation across the fragmented range of Jerdon's Babbler, Chrysomma altirostre, a threatened Oriental grassland specialist
- 2018
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Ingår i: Journal of Ornithology. - : Springer Science and Business Media LLC. - 0021-8375 .- 2193-7192 .- 2193-7206. ; 159:2, s. 575-579
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Tidskriftsartikel (refereegranskat)abstract
- Jerdon's Babbler Chrysomma altirostre is a threatened Oriental grassland specialist passerine heavily affected by habitat loss. Its now-relictual range spans from Pakistan to Myanmar covering three poorly-studied subspecies. Our study of subspecific differentiation revealed limited range-wide mitochondrial divergences, suggesting that mountain ranges and other geographic barriers may not have been insurmountable obstacles to inter-subspecific Pleistocene connectivity of this highly specialized grassland bird. For the westernmost subspecies scindicum, we report on phenotypic differentiation consistent with Gloger's Rule, and ecomorphological adaptations to arid environments requiring increased mobility.
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