| 1. |
- Jarvis, Erich D., et al.
(författare)
-
Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
-
Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
-
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.
|
|
| 2. |
- Garg, Kritika M., et al.
(författare)
-
When colors mislead : Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae)
- 2024
-
Ingår i: Molecular Phylogenetics and Evolution. - : Elsevier. - 1055-7903 .- 1095-9513. ; 193
-
Tidskriftsartikel (refereegranskat)abstract
- Traditional classification of many animals, including birds, has been highly dependent on external morphological characters like plumage coloration. However, both bioacoustics and genetic or genomic data have revolutionized our understanding of the relationships of certain lineages and led to sweeping taxonomic re-organizations. In this study, we present a case of erroneous delimitation of genus boundaries in the species-rich flycatcher subfamily Niltavinae. Genera within this subfamily have historically been delineated based on blue versus brown male body plumage until recent studies based on a few mitochondrial and nuclear loci unearthed several cases of generic misclassification. Here we use extensive bioacoustic data from 43 species and genomic data from 28 species for a fundamental reclassification of species in the Niltavinae. Our study reveals that song is an important trait to classify these birds even at the genus level, whereas plumage traits exhibit ample convergence and have led to numerous historic misattributions. Our taxonomic re-organization leads to new biogeographic limits of major genera, such that the genus Cyornis now only extends as far east as the islands of Sulawesi, Sula, and Banggai, whereas Eumyias is redefined to extend far beyond Wallace's Line to the islands of Seram and Timor. Our conclusions advise against an over-reliance on morphological traits and underscore the importance of integrative datasets.
|
|
| 3. |
- Gwee, Chyi Yin, et al.
(författare)
-
Cryptic diversity in Cyornis (Ayes : Muscicapidae) jungle-flycatchers flagged by simple bioacoustic approaches
- 2019
-
Ingår i: Zoological Journal of the Linnean Society. - : OXFORD UNIV PRESS. - 0024-4082 .- 1096-3642. ; 186:3, s. 725-741
-
Tidskriftsartikel (refereegranskat)abstract
- Despite the ongoing taxonomic revolution incorporating multiple species delimitation methods, knowledge gaps persist in the taxonomy of comparatively well-studied animal groups such as birds. Morphologically cryptic species risk slipping under the conservation radar, as they get mistakenly united with other species. Here, we employed six to 11 vocal parameters of each population to examine the species delimitation of nine Cyornis jungle-flycatcher species complexes distributed across Asia. We found moderate to strong vocal evidence for the taxonomic elevation of ten cryptic Cyornis species. Additionally, we conducted mitochondrial and genome-wide SNP analyses for two of the Cyornis complexes to examine the effectiveness of bioacoustics as a tool for avian species delineation and found congruent results between vocal and molecular data. Therefore, we propose a taxonomic reclassification of the complicated Cyornis species complexes and recommend routine application of bioacoustics in avian taxonomic classification.
|
|
| 4. |
- Suh, Alexander, et al.
(författare)
-
Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes
- 2016
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
-
Tidskriftsartikel (refereegranskat)abstract
- Parasite host switches may trigger disease emergence, but prehistoric host ranges are often unknowable. Lymphatic filariasis and loiasis are major human diseases caused by the insect-borne filarial nematodes Brugia, Wuchereria and Loa. Here we show that the genomes of these nematodes and seven tropical bird lineages exclusively share a novel retrotransposon, AviRTE, resulting from horizontal transfer (HT). AviRTE subfamilies exhibit 83-99% nucleotide identity between genomes, and their phylogenetic distribution, paleobiogeography and invasion times suggest that HTs involved filarial nematodes. The HTs between bird and nematode genomes took place in two pantropical waves, >25-22 million years ago (Myr ago) involving the Brugia/Wuchereria lineage and >20-17 Myr ago involving the Loa lineage. Contrary to the expectation from the mammal-dominated host range of filarial nematodes, we hypothesize that these major human pathogens may have independently evolved from bird endoparasites that formerly infected the global breadth of avian biodiversity.
|
|
| 5. |
- Zhang, Dezhi, et al.
(författare)
-
"Ghost Introgression" As a Cause of Deep Mitochondrial Divergence in a Bird Species Complex
- 2019
-
Ingår i: Molecular biology and evolution. - : OXFORD UNIV PRESS. - 0737-4038 .- 1537-1719. ; 36:11, s. 2375-2386
-
Tidskriftsartikel (refereegranskat)abstract
- In the absence of nuclear-genomic differentiation between two populations, deep mitochondrial divergence (DMD) is a form of mito-nuclear discordance. Such instances of DMD are rare and might variably be explained by unusual cases of female-linked selection, by male-biased dispersal, by "speciation reversal" or by mitochondrial capture through genetic introgression. Here, we analyze DMD in an Asian Phylloscopus leaf warbler (Aves: Phylloscopidae) complex. Bioacoustic, morphological, and genomic data demonstrate close similarity between the taxa affinis and occisinensis, even though DMD previously led to their classification as two distinct species. Using population genomic and comparative genomic methods on 45 whole genomes, including historical reconstructions of effective population size, genomic peaks of differentiation and genomic linkage, we infer that the form affinis is likely the product of a westward expansion in which it replaced a now-extinct congener that was the donor of its mtDNA and small portions of its nuclear genome. This study provides strong evidence of "ghost introgression" as the cause of DMD, and we suggest that "ghost introgression" may be a widely overlooked phenomenon in nature.
|
|
| 6. |
- Zhang, Dezhi, et al.
(författare)
-
Most Genomic Loci Misrepresent the Phylogeny of an Avian Radiation Because of Ancient Gene Flow
- 2021
-
Ingår i: Systematic Biology. - : Oxford University Press. - 1063-5157 .- 1076-836X. ; 70:5, s. 961-975
-
Tidskriftsartikel (refereegranskat)abstract
- Phylogenetic trees based on genome-wide sequence data may not always represent the true evolutionary history for a variety of reasons. One process that can lead to incorrect reconstruction of species phylogenies is gene flow, especially if interspecific gene flow has affected large parts of the genome. We investigated phylogenetic relationships within a clade comprising eight species of passerine birds (Phylloscopidae, Phylloscopus, leafwarblers) using one de novo genome assembly and 78 resequenced genomes. Onthe basis of hypothesis-exclusion trials based on D-statistics, phylogenetic network analysis, and demographic inference analysis, we identified ancient gene flow affecting large parts of the genome between one species and the ancestral lineage of a sister species pair. This ancient gene flow consistently caused erroneous reconstruction of the phylogeny when using large amounts of genome-wide sequence data. In contrast, the true relationships were captured when smaller parts of the genome were analyzed, showing that the "winner-takes-all democratic majority tree" is not necessarily the true species tree. Under this condition, smaller amounts of data may sometimes avoid the effects of gene flow due to stochastic sampling, as hidden reticulation histories are more likely to emerge from the use of larger data sets, especially whole-genome data sets. In addition, we also found that genomic regions affected by ancient gene flow generally exhibited higher genomic differentiation but a lower recombination rate and nucleotide diversity. Our study highlights the importance of considering reticulation in phylogenetic reconstructions in the genomic era.
|
|
