| 1. |
- Ji, Yanzhu, et al.
(författare)
-
Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds
- 2022
-
Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:35
-
Tidskriftsartikel (refereegranskat)abstract
- The rate of mutation accumulation in germline cells can be affected by cell replication and/or DNA damage, which are further related to life history traits such as generation time and body mass. Leveraging the existing datasets of 233 neoavian bird species, here, we investigated whether generation time and body mass contribute to the interspecific variation of orthologous microsatellite length, transposable element (TE) length, and deletion length and how these genomic attributes affect genome sizes. In nonpasserines, we found that generation time is correlated to both orthologous microsatellite length and TE length, and body mass is negatively correlated to DNA deletions. These patterns are less pronounced in passerines. In all species, we found that DNA deletions relate to genome size similarly as TE length, suggesting a role of body mass dynamics in genome evolution. Our results indicate that generation time and body mass shape the evolution of genomic attributes in neoavian birds.
|
|
| 2. |
- 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.
|
|
| 3. |
|
|
| 4. |
- Cai, Tianlong, et al.
(författare)
-
The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds
- 2020
-
Ingår i: Journal of Biogeography. - : Wiley. - 0305-0270 .- 1365-2699. ; 47:7, s. 1612-1625
-
Tidskriftsartikel (refereegranskat)abstract
- Aim: Variation in species diversity among different geographical areas may result from differences in speciation and extinction rates, immigration and time for diversification. An area with high species diversity may be the result of a high net diversification rate, multiple immigration events from adjacent regions, and a long time available for the accumulation of species (known as the 'time-for-speciation effect'). Here, we examine the relative importance of the three aforementioned processes in shaping the geographical diversity patterns of a large radiation of passerine birds. Location: Global. Taxon: Babblers (Aves: Passeriformes). Methods: Using a comprehensive phylogeny of extant species (similar to 90% sampled) and distributions of the world's babblers, we reconstructed their biogeographical history and analysed the diversification dynamics. We examined how species richness correlates with the timing of regional colonization, the number of immigration events and the rate of speciation within all 13 geographical distribution regions. Results: We found that babblers likely originated in the Sino-Himalayan Mountains (SHM) in the early Miocene, suggesting a long time for diversification and species accumulation within the SHM. Regression analyses showed the regional diversity of babblers can be well explained by the timing of the first colonization within of these areas, while differences in rates of speciation or immigration have far weaker effects. Nonetheless, the rapid speciation of Zosterops during the Pleistocene has accounted for the increased diversification and accumulation of species in the oceanic islands. Main Conclusions: Our results suggest that the global diversity patterns of babblers have predominantly been shaped by the time-for-speciation effect. Our findings also support an origin centred in tropical and subtropical parts of the SHM, with a cradle of recent diversification in the oceanic islands of the Indo-Pacific and Indian Ocean regions, which provides new insights into the generation of global biodiversity hotspots.
|
|
| 5. |
|
|
| 6. |
- Chen, Yilin, et al.
(författare)
-
The combination of genomic offset and niche modelling provides insights into climate change-driven vulnerability
- 2022
-
Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
-
Tidskriftsartikel (refereegranskat)abstract
- Global warming is increasingly exacerbating biodiversity loss. Populations locally adapted to spatially heterogeneous environments may respond differentially to climate change, but this intraspecific variation has only recently been considered when modelling vulnerability under climate change. Here, we incorporate intraspecific variation in genomic offset and ecological niche modelling to estimate climate change-driven vulnerability in two bird species in the Sino-Himalayan Mountains. We found that the cold-tolerant populations show higher genomic offset but risk less challenge for niche suitability decline under future climate than the warm-tolerant populations. Based on a genome-niche index estimated by combining genomic offset and niche suitability change, we identified the populations with the least genome-niche interruption as potential donors for evolutionary rescue, i.e., the populations tolerant to climate change. We evaluated potential rescue routes via a landscape genetic analysis. Overall, we demonstrate that the integration of genomic offset, niche suitability modelling, and landscape connectivity can improve climate change-driven vulnerability assessments and facilitate effective conservation management.
|
|
| 7. |
- Feng, Shaohong, et al.
(författare)
-
Dense sampling of bird diversity increases power of comparative genomics
- 2020
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 587:7833
-
Tidskriftsartikel (refereegranskat)abstract
- Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.
|
|
| 8. |
- 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.
|
|
| 9. |
- Jiang, Zhiyong, et al.
(författare)
-
Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae)
- 2024
-
Ingår i: BMC Biology. - : BioMed Central (BMC). - 1741-7007. ; 22:1
-
Tidskriftsartikel (refereegranskat)abstract
- BackgroundResolving the phylogeny of rapidly radiating lineages presents a challenge when building the Tree of Life. An Old World avian family Prunellidae (Accentors) comprises twelve species that rapidly diversified at the Pliocene-Pleistocene boundary.ResultsHere we investigate the phylogenetic relationships of all species of Prunellidae using a chromosome-level de novo assembly of Prunella strophiata and 36 high-coverage resequenced genomes. We use homologous alignments of thousands of exonic and intronic loci to build the coalescent and concatenated phylogenies and recover four different species trees. Topology tests show a large degree of gene tree-species tree discordance but only 40-54% of intronic gene trees and 36-75% of exonic genic trees can be explained by incomplete lineage sorting and gene tree estimation errors. Estimated branch lengths for three successive internal branches in the inferred species trees suggest the existence of an empirical anomaly zone. The most common topology recovered for species in this anomaly zone was not similar to any coalescent or concatenated inference phylogenies, suggesting presence of anomalous gene trees. However, this interpretation is complicated by the presence of gene flow because extensive introgression was detected among these species. When exploring tree topology distributions, introgression, and regional variation in recombination rate, we find that many autosomal regions contain signatures of introgression and thus may mislead phylogenetic inference. Conversely, the phylogenetic signal is concentrated to regions with low-recombination rate, such as the Z chromosome, which are also more resistant to interspecific introgression.ConclusionsCollectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.
|
|
| 10. |
- 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.
|
|
| 11. |
- Rancilhac, Loïs, et al.
(författare)
-
Introgression Underlies Phylogenetic Uncertainty But Not Parallel Plumage Evolution in a Recent Songbird Radiation
- 2023
-
Ingår i: Systematic Biology. - : Oxford University Press. - 1063-5157 .- 1076-836X.
-
Tidskriftsartikel (refereegranskat)abstract
- Instances of parallel phenotypic evolution offer great opportunities to understand the evolutionary processes underlying phenotypic changes. However, confirming parallel phenotypic evolution and studying its causes requires a robust phylogenetic framework. One such example is the “black-and-white wagtails,” a group of 5 species in the songbird genus Motacilla: 1 species, Motacilla alba, shows wide intra-specific plumage variation, while the 4r others form 2 pairs of very similar-looking species (M. aguimp + M. samveasnae and M. grandis + M. maderaspatensis, respectively). However, the 2 species in each of these pairs were not recovered as sisters in previous phylogenetic inferences. Their relationships varied depending on the markers used, suggesting that gene tree heterogeneity might have hampered accurate phylogenetic inference. Here, we use whole genome resequencing data to explore the phylogenetic relationships within this group, with a special emphasis on characterizing the extent of gene tree heterogeneity and its underlying causes. We first used multispecies coalescent methods to generate a “complete evidence” phylogenetic hypothesis based on genome-wide variants, while accounting for incomplete lineage sorting (ILS) and introgression. We then investigated the variation in phylogenetic signal across the genome to quantify the extent of discordance across genomic regions and test its underlying causes. We found that wagtail genomes are mosaics of regions supporting variable genealogies, because of ILS and inter-specific introgression. The most common topology across the genome, supporting M. alba and M. aguimp as sister species, appears to be influenced by ancient introgression. Additionally, we inferred another ancient introgression event, between M. alba and M. grandis. By combining results from multiple analyses, we propose a phylogenetic network for the black-and-white wagtails that confirms that similar phenotypes evolved in non-sister lineages, supporting parallel plumage evolution. Furthermore, the inferred reticulations do not connect species with similar plumage coloration, suggesting that introgression does not underlie parallel plumage evolution in this group. Our results demonstrate the importance of investing genome-wide patterns of gene tree heterogeneity to help understand the mechanisms underlying phenotypic evolution. [Gene tree heterogeneity; incomplete lineage sorting; introgression; parallel evolution; phylogenomics; plumage evolution; wagtails.]
|
|
| 12. |
- She, Huishang, et al.
(författare)
-
Quantifying adaptive divergence of the snowfinches in a common landscape
- 2022
-
Ingår i: Diversity & distributions. - : Wiley. - 1366-9516 .- 1472-4642. ; 28, s. 2579-2592
-
Tidskriftsartikel (refereegranskat)abstract
- AimSpecies living in a shared environment face similar selective pressures and often evolve adaptive divergence to avoid competition. Quantifying phenotypic divergence and its genetic parallelism among sympatric species is important for understanding of ecologically moderated biodiversity. Here, we integrate ecologic, phenotypic and genomic datasets to study to what extent three sympatrically snowfinches (Montifringilla adamsi, Pyrgilauda ruficollis and Onychostruthus taczanowskii) differ in their adaptations in order to co-exist in a shared environment.LocationQinghai–Tibetan Plateau.MethodsWe used principal component analysis to summarize and compare environmental and phenotypic divergence. We compared phenotypes relevant to body and beak sizes (n = 68) because they are indicators of niche and food segregation, thus critical for establishing co-existence of sympatric birds. We used comparative genomics (n = 33) to identify genetic loci that are highly divergent between species as well as loci unique for each of species. Using vector analyses, we integrated correlation and permutation to quantify parallelism between phenotypic and genetic divergences.ResultsWe found that body and beak sizes are significantly different among three snowfinches. The phenotypic differentiations are greater in species that share similar ecological conditions than in those that do not. We showed that genes related to developmental process are over-represented within highly divergent genomic regions and unique genetic loci of each species. We found that the extent of phenotypic divergence between snowfinch pairs is more strongly correlated with the magnitude of divergence in developmental genes than in the whole genome.Main conclusionsAdaptive divergence of sympatric snowfinches is highly constrained on developmental genes. As this genetic divergence is strongly correlated with divergence of the traits related to segregation in niche and food resources, this correlation reflects either causal effects or indirect consequences of ecological mediated changes. Our study provides novel insights into the mechanisms underlying evolutionary versatility and ecological success among sympatric species.
|
|
| 13. |
- Song, Gang, et al.
(författare)
-
Great journey of Great Tits (Parus major group) : Origin, diversification and historical demographics of a broadly distributed bird lineage
- 2020
-
Ingår i: Journal of Biogeography. - : WILEY. - 0305-0270 .- 1365-2699. ; 47:7, s. 1585-1598
-
Tidskriftsartikel (refereegranskat)abstract
- Aim The Pleistocene glacial cycles play a prominent role in shaping phylogeographical patterns of organisms, while few studies have focused on the regional difference of glacial effects. By acquiring comprehensive knowledge of the origin, diversification and historical demography of an intensively studied passerine species complex, Great Tit, we aim to test the regional variation of the Late Pleistocene glaciation impacts on this widely distributed bird lineage. Location Eurasia and associated peninsulas and archipelagos. Taxa Parus major species complex. Methods Phylogeny, divergence times and demographic dynamics were estimated with Bayesian methods. Population structure, genetic diversity and correlation between genetic and physical distances were estimated based on mtDNA variation. Glacial-to-present distributional changes were assessed via ecological niche modelling (ENM). Results Five major clades (Central Asia, Eastern Asia, Eastern Himalaya, Northern and Western Eurasia and Southern Asia) were detected, with divergence times ranging 1.57-0.50 million years ago. Genetic diversity values and Bayesian skyline plots suggest that the three eastern clades had a deeper population history. A more complex geographic structure was observed in East Asia. Demographic expansion during the last glacial cycle was indicated for all five clades. ENM results showed broad conservatism of traits related to climate tolerances, and generally broader and more continuous distributional patterns under glacial conditions. Main Conclusions The Great Tit complex probably originated in Southeast Asia. Geographic barriers, such as the deserts of Central Asia and the Qinghai-Tibet Plateau appear to be related to the lineage divergence. Late Pleistocene climate cycles influenced both demographic dynamics and divergence, especially in terms of east-west differences in relation to geographic complexity.
|
|
| 14. |
|
|
| 15. |
- 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.
|
|
| 16. |
- 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.
|
|
