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- Jarvis, Erich D., et al.
(author)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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In: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Journal article (peer-reviewed)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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- Chattopadhyay, Balaji, et al.
(author)
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Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change
- 2021
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In: Genomics. - : Elsevier BV. - 0888-7543 .- 1089-8646.
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Journal article (peer-reviewed)abstract
- We produced a high-quality de novo genome assembly of the red-legged partridge A. rufa, the first reference genome of its genus, by utilising novel 10× Chromium technology. The estimated genome size was 1.19 Gb with an overall genome heterozygosity of 0.0022; no runs of homozygosity were observed. In total, 21,589 protein coding genes were identified and assigned to 16,772 orthologs. Of these, 201 emerged as unique to Alectoris and were enriched for positive regulation of epithelial cell migration, viral genome integration and maturation. Using PSMC analysis, we inferred a major demographic decline commencing ~140,000 years ago, consistent with forest expansion and reduction of open habitats during the Eemian interglacial. Present-day populations exhibit the historically lowest genetic diversity. Besides implications for management and conservation, this genome also promises key insights into the physiology of these birds with a view to improving poultry husbandry practices.
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| 4. |
- Cros, Emilie, et al.
(author)
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Fine‐scale barriers to connectivity across a fragmented South‐East Asian landscape in six songbird species
- 2020
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In: Evolutionary Applications. - 1752-4571. ; 13:5, s. 1026-1036
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Journal article (peer-reviewed)abstract
- Habitat fragmentation is a major extinction driver. Despite dramatically increas-ing fragmentation across the globe, its specific impacts on population connectivityacross species with differing life histories remain difficult to characterize, let alonequantify. Here, we investigate patterns of population connectivity in six songbirdspecies from Singapore, a highly fragmented tropical rainforest island. Using massivepanels of genome-wide single nucleotide polymorphisms across dozens of samplesper species, we examined population genetic diversity, inbreeding, gene flow andconnectivity among species along a spectrum of ecological specificities. We found ahigher resilience to habitat fragmentation in edge-tolerant and forest-canopy speciesas compared to forest-dependent understorey insectivores. The latter exhibited lev-els of genetic diversity up to three times lower in Singapore than in populations fromcontiguous forest elsewhere. Using dense genomic and geographic sampling, weidentified individual barriers such as reservoirs that effectively minimize gene flowin sensitive understorey birds, revealing that terrestrial forest species may exhibitlevels of sensitivity to fragmentation far greater than previously expected. This studyprovides a blueprint for conservation genomics at small scales with a view to iden-tifying preferred locations for habitat corridors, flagging candidate populations forrestocking with translocated individuals and improving the design of future reserves.
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- Garg, Kritika M., et al.
(author)
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When colors mislead : Genomics and bioacoustics prompt re-classification of Asian flycatcher radiation (Aves: Niltavinae)
- 2024
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In: Molecular Phylogenetics and Evolution. - : Elsevier. - 1055-7903 .- 1095-9513. ; 193
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Journal article (peer-reviewed)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.
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| 8. |
- Gwee, Chyi Yin, et al.
(author)
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Cryptic diversity in Cyornis (Ayes : Muscicapidae) jungle-flycatchers flagged by simple bioacoustic approaches
- 2019
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In: Zoological Journal of the Linnean Society. - : OXFORD UNIV PRESS. - 0024-4082 .- 1096-3642. ; 186:3, s. 725-741
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Journal article (peer-reviewed)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.
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| 10. |
- Suh, Alexander, et al.
(author)
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Ancient horizontal transfers of retrotransposons between birds and ancestors of human pathogenic nematodes
- 2016
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 7
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Journal article (peer-reviewed)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.
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