| 1. |
- Liu, Simin, et al.
(författare)
-
Taxonomic revision of the Long-tailed RosefinchCarpodacus sibiricuscomplex
- 2020
-
Ingår i: Journal of Ornithology. - : SPRINGER HEIDELBERG. - 2193-7192 .- 2193-7206. ; 161:4, s. 1061-1070
-
Tidskriftsartikel (refereegranskat)abstract
- The Long-tailed RosefinchCarpodacus sibiricusbreeds in two widely disjunct areas in East Asia. Five subspecies are usually recognized. The plumage differences between different subspecies groups withinC. sibiricusare notable, suggesting it may actually comprise more than one species. However, proper taxonomic assessment has not been carried out, probably in part due to the scarcity and lack of museum specimens of some of these subspecies. In the current study, we re-evaluated the taxonomy of theC. sibiricuscomplex using molecular, acoustic and morphological data. Using mitochondrial DNA, the samples formed two clades, a northern clade (C. s. sibiricus,C. s. ussuriensisandC. s. sanguinolentus) and a southern clade (C. s. henriciandC. s. lepidus). We also revealed thatC. s. ussuriensisandC. s. sanguinolentusare mostly indistinguishable based on mitochondrial markers. This north/south split pattern is congruent with the pattern of plumage differences among north and south taxa. However, no diagnosable differences were found in their songs. We propose synonymizingC. s. ussuriensiswithC. s. sanguinolentus. At the species level, we suggest splitting the complex into two species, with Siberian Long-tailed RosefinchC. sibiricuscomprisingC. s. sibiricusandC. s. sanguinolentus, and Chinese Long-tailed RosefinchC. lepiduscomprisingC. l. henriciandC. l. lepidus.
|
|
| 2. |
- Qu, Yanhua, 1974-, et al.
(författare)
-
The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau
- 2021
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 10.1073/pnas.2012398118:13, s. e2012398118-e2012398118
-
Tidskriftsartikel (refereegranskat)abstract
- Species in a shared environment tend to evolve similar adaptations under the influence of their phylogenetic context. Using snowfinches, a monophyletic group of passerine birds (Passeridae), we study the relative roles of ancestral and species-specific adaptations to an extreme high-elevation environment, the Qinghai–Tibet Plateau. Our ancestral trait reconstruction shows that the ancestral snowfinch occupied high elevations and had a larger body mass than most nonsnowfinches in Passeridae. Subsequently, this phenotypic adaptation diversified in the descendant species. By comparing high-quality genomes from representatives of the three phylogenetic lineages, we find that about 95% of genes under positive selection in the descendant species are different from those in the ancestor. Consistently, the biological functions enriched for these species differ from those of their ancestor to various degrees (semantic similarity values ranging from 0.27 to 0.5), suggesting that the three descendant species have evolved divergently from the initial adaptation in their common ancestor. Using a functional assay to a highly selective gene, DTL, we demonstrate that the nonsynonymous substitutions in the ancestor and descendant species have improved the repair capacity of ultraviolet-induced DNA damage. The repair kinetics of the DTL gene shows a twofold to fourfold variation across the ancestor and the descendants. Collectively, this study reveals an exceptional case of adaptive evolution to high-elevation environments, an evolutionary process with an initial adaptation in the common ancestor followed by adaptive diversification of the descendant species.
|
|
| 3. |
- Wu, Lei, et al.
(författare)
-
Limited Song Mixing Without Genomic Gene Flow in a Contact Zone Between Two Songbird Species
- 2023
-
Ingår i: Molecular biology and evolution. - : Oxford University Press. - 0737-4038 .- 1537-1719. ; 40:3
-
Tidskriftsartikel (refereegranskat)abstract
- Song is considered to play an important role in the maintenance of prezygotic reproductive isolation between closely related songbird species. Therefore, song mixing in a contact zone between closely related species is often considered as evidence of hybridization. The Sichuan Leaf Warbler Phylloscopus forresti and the Gansu Leaf Warbler Phylloscopus kansuensis, which diverged 2 million years ago, have formed a contact zone in the south of the Gansu Province of China, where mixed songs have been observed. In this study, we investigated the potential causes and consequences of song mixing by integrating bioacoustic, morphological, mitochondrial, and genomic data with field ecological observations. We found that the two species display no apparent morphological differences, whereas their songs differ dramatically. We demonstrated that ∼11% of the males in the contact zone sang mixed songs. Two males singing mixed song were genotyped, and both were found to be P. kansuensis. Despite the presence of mixed singers, population genomic analyses detected no signs of recent gene flow between the two species, although two possible cases of mitochondrial introgression were identified. We conclude that the rather limited song mixing does not lead to, or result from, hybridization, and hence does not result in the breakdown of reproductive barriers between these cryptic species.
|
|
| 4. |
- 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.
|
|
| 5. |
- 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.
|
|
| 6. |
- Zhang, Dezhi, et al.
(författare)
-
Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae)
- 2023
-
Ingår i: SYSTEMATIC BIOLOGY. - 1063-5157 .- 1076-836X.
-
Tidskriftsartikel (refereegranskat)abstract
- Different genomic regions may reflect conflicting phylogenetic topologies primarily due to incomplete lineage sorting and/or gene flow. Genomic data are necessary to reconstruct the true species tree and explore potential causes of phylogenetic conflict. Here, we investigate the phylogenetic relationships of 4 Emberiza species (Aves: Emberizidae) and discuss the potential causes of the observed mitochondrial non-monophyly of Emberiza godlewskii (Godlewski's bunting) using phylogenomic analyses based on whole genome resequencing data from 41 birds. Analyses based on both the whole mitochondrial genome and similar to 39 kilobases from the non-recombining W chromosome reveal sister relationships between each the northern and southern populations of E. godlewskii with E. cioides and E. cia, respectively. In contrast, the monophyly of E. godlewskii is reflected by the phylogenetic signal of autosomal and Z chromosomal sequence data as well as demographic inference analyses, which-in combination-support the following tree topology: ([{E. godlewskii, E. cia}, E. cioides], E. jankowskii). Using D-statistics, we detected multiple gene flow events among different lineages, indicating pervasive introgressive hybridization within this clade. Introgression from an unsampled lineage that is sister to E. cioides or introgression from an unsampled mitochondrial + W chromosomal lineage of E. cioides into northern E. godlewskii may explain the phylogenetic conflict between the species tree estimated from genome-wide data versus mtDNA/W tree topologies. These results underscore the importance of using genomic data for phylogenetic reconstruction and species delimitation.
|
|
