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Zhang M, Kang C, Xing K, Zhao F. Complete mitochondrial genome of Rhopalosiphum maidis (Hemiptera: Aphididae) and its phylogenetic implications. Mitochondrial DNA B Resour 2024; 9:1227-1231. [PMID: 39291129 PMCID: PMC11407400 DOI: 10.1080/23802359.2024.2404210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Rhopalosiphum maidis Fitch, 1856 is widespread in tropical and temperate regions. R. maidis can spread viral diseases in maize and harm various important crops. In the present study, we report the first complete mitochondrial genome of R. maidis. The circular genome is found to be 17,021 bp in length, includes a standard set of 22 transfer RNAs, two ribosomal RNAs, 13 protein-coding genes, and two non-coding control regions. The base composition is 84.32% AT and 15.79% GC. The phylogenetic tree of the 17 Aphidini families constructed based on the nucleotide sequences of complete mitochondrial genomes strongly supports the conclusion that R. maidis is closely related to R. rufiabdominalis.
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Affiliation(s)
- Miao Zhang
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
| | - Chen Kang
- Shennong Technology Company Limited, Taigu, China
| | - Kun Xing
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
| | - Fei Zhao
- Shanxi Key Laboratory of Integrated Pest Management in Agriculture, College of Plant Protection, Shanxi Agricultural University, Taiyuan, China
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2
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Wang S, Wu L, Zhu Q, Wu J, Tang S, Zhao Y, Cheng Y, Zhang D, Qiao G, Zhang R, Lei F. Trait Variation and Spatiotemporal Dynamics across Avian Secondary Contact Zones. BIOLOGY 2024; 13:643. [PMID: 39194581 DOI: 10.3390/biology13080643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024]
Abstract
A secondary contact zone (SCZ) is an area where incipient species or divergent populations may meet, mate, and hybridize. Due to the diverse patterns of interspecific hybridization, SCZs function as field labs for illuminating the on-going evolutionary processes of speciation and the establishment of reproductive isolation. Interspecific hybridization is widely present in avian populations, making them an ideal system for SCZ studies. This review exhaustively summarizes the variations in unique traits within avian SCZs (vocalization, plumage, beak, and migratory traits) and the various movement patterns of SCZs observed in previous publications. It also highlights several potential future research directions in the genomic era, such as the relationship between phenotypic and genomic differentiation in SCZs, the genomic basis of trait differentiation, SCZs shared by multiple species, and accurate predictive models for forecasting future movements under climate change and human disturbances. This review aims to provide a more comprehensive understanding of speciation processes and offers a theoretical foundation for species conservation.
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Affiliation(s)
- Shangyu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qianghui Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahao Wu
- University of Chinese Academy of Sciences, Beijing 100049, China
- Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou 510260, China
| | - Shiyu Tang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yifang Zhao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalin Cheng
- College of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Runzhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Ma XG, Ren YB, Sun H. Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China. Cladistics 2024; 40:357-373. [PMID: 38197450 DOI: 10.1111/cla.12570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 11/27/2023] [Accepted: 12/09/2023] [Indexed: 01/11/2024] Open
Abstract
Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.
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Affiliation(s)
- Xiang-Guang Ma
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yue-Bo Ren
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
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4
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Zhang D, She H, Wang S, Wang H, Li S, Cheng Y, Song G, Jia C, Qu Y, Rheindt FE, Olsson U, Alström P, Lei F. Phylogenetic Conflict Between Species Tree and Maternally Inherited Gene Trees in a Clade of Emberiza Buntings (Aves: Emberizidae). Syst Biol 2024; 73:279-289. [PMID: 38157277 DOI: 10.1093/sysbio/syad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 12/06/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024] Open
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 ~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.
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Affiliation(s)
- Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Shangyu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Haitao Wang
- School of Life Sciences, Jilin Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130024, China
| | - Shi Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Republic of Singapore
| | - Urban Olsson
- Department of Biology and Environmental Science, University of Gothenburg, Box 463, SE-405 30 Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Box 461, SE-405 30 Gothenburg, Sweden
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, SE-752 36 Uppsala, Sweden
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, China
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5
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Zhang Z, Liu G, Li M. Incomplete lineage sorting and gene flow within Allium (Amayllidaceae). Mol Phylogenet Evol 2024; 195:108054. [PMID: 38471599 DOI: 10.1016/j.ympev.2024.108054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/01/2024] [Accepted: 03/07/2024] [Indexed: 03/14/2024]
Abstract
The phylogeny and systematics of the genus Allium have been studied with a variety of diverse data types, including an increasing amount of molecular data. However, strong phylogenetic discordance and high levels of uncertainty have prevented the identification of a consistent phylogeny. The difficulty in establishing phylogenetic consensus and evidence for genealogical discordance make Allium a compelling test case to assess the relative contribution of incomplete lineage sorting (ILS), gene flow and gene tree estimation error on phylogenetic reconstruction. In this study, we obtained 75 transcriptomes of 38 Allium species across 10 subgenera. Whole plastid genome, single copy genes and consensus CDS were generated to estimate phylogenetic trees both using coalescence and concatenation methods. Multiple approaches including coalescence simulation, quartet sampling, reticulate network inference, sequence simulation, theta of ILS and reticulation index were carried out across the CDS gene trees to investigate the degrees of ILS, gene flow and gene tree estimation error. Afterward, a regression analysis was used to test the relative contributions of each of these forms of uncertainty to the final phylogeny. Despite extensive topological discordance among gene trees, we found a fully supported species tree that agrees with the most of well-accepted relationships and establishes monophyly of the genus Allium. We presented clear evidence for substantial ILS across the phylogeny of Allium. Further, we identified two ancient hybridization events for the formation of the second evolutionary line and subg. Butomissa as well as several introgression events between recently diverged species. Our regression analysis revealed that gene tree inference error and gene flow were the two most dominant factors explaining for the overall gene tree variation, with the difficulty in disentangling the effects of ILS and gene tree estimation error due to a positive correlation between them. Based on our efforts to mitigate the methodological errors in reconstructing trees, we believed ILS and gene flow are two principal reasons for the oft-reported phylogenetic heterogeneity of Allium. This study presents a strongly-supported and well-resolved phylogenetic backbone for the sampled Allium species, and exemplifies how to untangle heterogeneity in phylogenetic signal and reconstruct the true evolutionary history of the target taxa.
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Affiliation(s)
- ZengZhu Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Gang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Minjie Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, People's Republic of China.
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Rancilhac L, Enbody ED, Harris R, Saitoh T, Irestedt M, Liu Y, Lei F, Andersson L, Alström P. Introgression Underlies Phylogenetic Uncertainty But Not Parallel Plumage Evolution in a Recent Songbird Radiation. Syst Biol 2024; 73:12-25. [PMID: 37801684 PMCID: PMC11129591 DOI: 10.1093/sysbio/syad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/11/2023] [Accepted: 10/05/2023] [Indexed: 10/08/2023] Open
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.].
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Affiliation(s)
- Loïs Rancilhac
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36 Uppsala, Sweden
| | - Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Biomolecular Engineering, University of California, 95064 Santa Cruz, CA, USA
| | - Rebecca Harris
- Department of Biology, University of Washington, Seattle, WA 98105, USA
| | - Takema Saitoh
- Yamashina Institute for Ornithology, 115 Konoyama, Abiko, Chiba 270-1145, Japan
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, P.O. Box 50007, 104 05 Stockholm, Sweden
| | - Yang Liu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA
| | - Per Alström
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36 Uppsala, Sweden
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, 100101 Beijing, China
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7
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Jiang Z, Zang W, Ericson PGP, Song G, Wu S, Feng S, Drovetski SV, Liu G, Zhang D, Saitoh T, Alström P, Edwards SV, Lei F, Qu Y. Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae). BMC Biol 2024; 22:49. [PMID: 38413944 PMCID: PMC10900574 DOI: 10.1186/s12915-024-01848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Resolving 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. RESULTS Here 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. CONCLUSIONS Collectively, our results suggest that phylogenomic inference should consider the underlying genomic architecture to maximize the consistency of phylogenomic signal.
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Affiliation(s)
- Zhiyong Jiang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenqing Zang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm, SE-104 05, Sweden
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Shaoyuan Wu
- Jiangsu International Joint Center of Genomics, Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, Jiangsu, China
| | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, 310058, China
- Liangzhu Laboratory, Zhejiang University, 1369 West Wenyi Road, Hangzhou, 311121, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, 314102, China
| | - Sergei V Drovetski
- National Museum of Natural History, Smithsonian Institution, Washington, DC, 20004, USA
- Present address: U.S. Geological Survey, Eastern Ecological Science Center at Patuxent Research Refuge, Laurel, MD, 20708, USA
| | - Gang Liu
- Chinese Academy of Forestry, Institute of Ecological Conservation and Restoration, Beijing, 100091, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Takema Saitoh
- Yamashina Institute for Ornithology, Abiko, Chiba, Japan
| | - Per Alström
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18 D, 752 36, Uppsala, Sweden
| | - Scott V Edwards
- Museum of Comparative Zoology and Department of Organismic & Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, PO Box 50007, Stockholm, SE-104 05, Sweden.
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Gao K, He Z, Xiong J, Chen Q, Lai B, Liu F, Chen P, Chen M, Luo W, Huang J, Ding W, Wang H, Pu Y, Zheng L, Jiao Y, Zhang M, Tang Z, Yue Q, Yang D, Yan T. Population structure and adaptability analysis of Schizothorax o'connori based on whole-genome resequencing. BMC Genomics 2024; 25:145. [PMID: 38321406 PMCID: PMC10845765 DOI: 10.1186/s12864-024-09975-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Schizothorax o'connori is an endemic fish distributed in the upper and lower reaches of the Yarlung Zangbo River in China. It has experienced a fourth round of whole gene replication events and is a good model for exploring the genetic differentiation and environmental adaptability of fish in the Qinghai-Tibet Plateau. The uplift of the Qinghai-Tibet Plateau has led to changes in the river system, thereby affecting gene exchange and population differentiation between fish populations. With the release of fish whole genome data, whole genome resequencing has been widely used in genetic evolutionary analysis and screening of selected genes in fish, which can better elucidate the genetic basis and molecular environmental adaptation mechanisms of fish. Therefore, our purpose of this study was to understand the population structure and adaptive characteristics of S. o'connori using the whole-genome resequencing method. RESULTS The results showed that 23,602,746 SNPs were identified from seven populations, mostly distributed on chromosomes 2 and 23. There was no significant genetic differentiation between the populations, and the genetic diversity was relatively low. However, the Zangga population could be separated from the Bomi, Linzhi, and Milin populations in the cluster analysis. Based on historical dynamics analysis of the population, the size of the ancestral population of S. o'connori was affected by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Glacial Age. The selected sites were mostly enriched in pathways related to DNA repair and energy metabolism. CONCLUSION Overall, the whole-genome resequencing analysis provides valuable insights into the population structure and adaptive characteristics of S. o'connori. There was no obvious genetic differentiation at the genome level between the S. o'connori populations upstream and downstream of the Yarlung Zangbo River. The current distribution pattern and genetic diversity are influenced by the late accelerated uplift of the Qinghai Tibet Plateau and the Fourth Ice Age. The selected sites of S. o'connori are enriched in the energy metabolism and DNA repair pathways to adapt to the low temperature and strong ultraviolet radiation environment at high altitude.
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Affiliation(s)
- Kuo Gao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jinxin Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qiqi Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Bolin Lai
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Fei Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ping Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingqiang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenjie Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junjie Huang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenxiang Ding
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Haochen Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yong Pu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Li Zheng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yuanyuan Jiao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mingwang Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ziting Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingsong Yue
- Huadian Tibet Hydropower Development Co.,Ltd, Dagu Hydropower Station, Sangri, 856200, Shannan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.
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9
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Steenwyk JL, Li Y, Zhou X, Shen XX, Rokas A. Incongruence in the phylogenomics era. Nat Rev Genet 2023; 24:834-850. [PMID: 37369847 DOI: 10.1038/s41576-023-00620-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 06/29/2023]
Abstract
Genome-scale data and the development of novel statistical phylogenetic approaches have greatly aided the reconstruction of a broad sketch of the tree of life and resolved many of its branches. However, incongruence - the inference of conflicting evolutionary histories - remains pervasive in phylogenomic data, hampering our ability to reconstruct and interpret the tree of life. Biological factors, such as incomplete lineage sorting, horizontal gene transfer, hybridization, introgression, recombination and convergent molecular evolution, can lead to gene phylogenies that differ from the species tree. In addition, analytical factors, including stochastic, systematic and treatment errors, can drive incongruence. Here, we review these factors, discuss methodological advances to identify and handle incongruence, and highlight avenues for future research.
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Affiliation(s)
- Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Xing-Xing Shen
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
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10
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Overson RP, Johnson MG, Bechen LL, Kinosian SP, Douglas NA, Fant JB, Hoch PC, Levin RA, Moore MJ, Raguso RA, Wagner WL, Skogen KA, Wickett NJ. A phylogeny of the evening primrose family (Onagraceae) using a target enrichment approach with 303 nuclear loci. BMC Ecol Evol 2023; 23:66. [PMID: 37974080 PMCID: PMC10655384 DOI: 10.1186/s12862-023-02151-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/16/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND The evening primrose family (Onagraceae) includes 664 species (803 taxa) with a center of diversity in the Americas, especially western North America. Ongoing research in Onagraceae includes exploring striking variation in floral morphology, scent composition, and breeding system, as well as the role of these traits in driving diversity among plants and their interacting pollinators and herbivores. However, these efforts are limited by the lack of a comprehensive, well-resolved phylogeny. Previous phylogenetic studies based on a few loci strongly support the monophyly of the family and the sister relationship of the two largest tribes but fail to resolve several key relationships. RESULTS We used a target enrichment approach to reconstruct the phylogeny of Onagraceae using 303 highly conserved, low-copy nuclear loci. We present a phylogeny for Onagraceae with 169 individuals representing 152 taxa sampled across the family, including extensive sampling within the largest tribe, Onagreae. Deep splits within the family are strongly supported, whereas relationships among closely related genera and species are characterized by extensive conflict among individual gene trees. CONCLUSIONS This phylogenetic resource will augment current research projects focused throughout the family in genomics, ecology, coevolutionary dynamics, biogeography, and the evolution of characters driving diversification in the family.
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Affiliation(s)
- Rick P Overson
- Arizona State University, PO Box 875502, Tempe, AZ, 85287, USA
| | | | - Lindsey L Bechen
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Whitehead Institute for Biomedical Research, 455 Main St, Cambridge, MA, 02142, USA
| | - Sylvia P Kinosian
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Department of Ecology and Evolutionary Biology, University of Arizona, PO Box 210088, Tucson, AZ, 85721, USA
| | - Norman A Douglas
- University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Jeremie B Fant
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Northwestern University, 2205 Tech Dr, Evanston, IL, 60208, USA
| | - Peter C Hoch
- Missouri Botanical Garden, 4344 Shaw Blvd, St. Louis, MO, 63110, USA
| | | | | | | | - Warren L Wagner
- Smithsonian Institution, MRC-166, PO Box 37012, Washington, DC, 20013, USA
| | - Krissa A Skogen
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA
- Northwestern University, 2205 Tech Dr, Evanston, IL, 60208, USA
- Clemson University, 132 Long Hall, Clemson, SC, 29634, USA
| | - Norman J Wickett
- Negaunee Institute for Plant Conservation Science and Action, Chicago Botanic Garden, 1000 Lake Cook Rd, Glencoe, IL, 60022, USA.
- Northwestern University, 2205 Tech Dr, Evanston, IL, 60208, USA.
- Clemson University, 132 Long Hall, Clemson, SC, 29634, USA.
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11
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San Jose M, Doorenweerd C, Geib S, Barr N, Dupuis JR, Leblanc L, Kauwe A, Morris KY, Rubinoff D. Interspecific gene flow obscures phylogenetic relationships in an important insect pest species complex. Mol Phylogenet Evol 2023; 188:107892. [PMID: 37524217 DOI: 10.1016/j.ympev.2023.107892] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/07/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023]
Abstract
As genomic data proliferates, the prevalence of post-speciation gene flow is making species boundaries and relationships increasingly ambiguous. Although current approaches inferring fully bifurcating phylogenies based on concatenated datasets provide simple and robust answers to many species relationships, they may be inaccurate because the models ignore inter-specific gene flow and incomplete lineage sorting. To examine the potential error resulting from ignoring gene flow, we generated both a RAD-seq and a 500 protein-coding loci highly multiplexed amplicon (HiMAP) dataset for a monophyletic group of 12 species defined as the Bactrocera dorsalis sensu lato clade. With some of the world's worst agricultural pests, the taxonomy of the B. dorsalis s.l. clade is important for trade and quarantines. However, taxonomic confusion confounds resolution due to intra- and interspecific phenotypic variation and convergence, mitochondrial introgression across half of the species, and viable hybrids. We compared the topological convergence of our datasets using concatenated phylogenetic and various multispecies coalescent approaches, some of which account for gene flow. All analyses agreed on species delimitation, but there was incongruence between species relationships. Under concatenation, both datasets suggest identical species relationships with mostly high statistical support. However, multispecies coalescent and multispecies network approaches suggest markedly different hypotheses and detected significant gene flow. We suggest that the network approaches are likely more accurate because gene flow violates the assumptions of the concatenated phylogenetic analyses, but the data-reductive requirements of network approaches resulted in reduced statistical support and could not unambiguously resolve gene flow directions. Our study highlights the importance of testing for gene flow, particularly with phylogenomic datasets, even when concatenated approaches receive high statistical support.
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Affiliation(s)
- Michael San Jose
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA.
| | - Camiel Doorenweerd
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
| | - Scott Geib
- Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Norman Barr
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Plant Protection and Quarantine, Science & Technology, Insect Management and Molecular Diagnostics Laboratory, 22675 N. Moorefield Road, Edinburg, TX 78541, USA
| | - Julian R Dupuis
- University of Kentucky, Department of Entomology, S225 Ag Science Center North, 1100 South Limestone, Lexington, KY, 40546-0091, USA
| | - Luc Leblanc
- University of Idaho, Department of Entomology, Plant Pathology and Nematology, 875 Perimeter Drive, MS2329, Moscow, ID, 83844-2329, USA
| | - Angela Kauwe
- Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Kimberley Y Morris
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA; Tropical Crop and Commodity Protection Research Unit, Daniel K Inouye U.S. Pacific Basin Agricultural Center, USDA Agricultural Research Services, Hilo, HI, USA
| | - Daniel Rubinoff
- University of Hawaii, College of Tropical Agriculture and Human Resources, Department of Plant and Environmental Protection Sciences, Entomology Section, 3050 Maile Way, Honolulu, HI, 96822-2231, USA
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12
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Yang C, Dong X, Wang Q, Hou X, Yuan H, Li X. Mitochondrial genome characteristics of six Phylloscopus species and their phylogenetic implication. PeerJ 2023; 11:e16233. [PMID: 37842035 PMCID: PMC10576491 DOI: 10.7717/peerj.16233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
The mitochondrial genomes of six Phylloscopus species-small insectivores belonging to the Phylloscopidae family-were obtained using the Illumina sequencing platform. The mitogenomes were closed circular molecules 16,922-17,007 bp in size, containing 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two control regions (CR1 and remnant CR2). The gene orders were conserved in 35 sampled Phylloscopus mitogenomes in the GenBank database, with a gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. The average base compositions of the six Phylloscopus mitogenomes were 29.43% A, 32.75% C, 14.68% G, and 23.10% T, with the A+T content slightly higher than that of G+C. ATG and TAA were the most frequent initiating and terminating codons, respectively. Several conserved boxes were identified in CR1, including C-string in domain I; F, E, D, and C boxes, as well as bird similarity and B boxes, in domain II; and CSB1 in domain III. Tandem repeats were observed in remnant CR2 of the Phylloscopus fuscatus and Phylloscopus proregulus mitogenomes. A phylogenetic analysis with maximum likelihood (ML) and Bayesian inference (BI) methods, based on 13 protein-coding genes and two rRNA genes, indicated that the Phylloscopus species was divided into two larger clades, with a splitting time approximately 11.06 million years ago (mya). The taxa of Phylloscopus coronatus/Phylloscopus burkii and Phylloscopus inornatus/P. proregulus were located at the basal position of the different clades. The phylogenetic result of the cox1 gene showed that Seicercus was nested within Phylloscopus. The complete set of mitogenomes of the Phylloscopus species provides potentially useful resources for the further exploration of the taxonomic status and phylogenetic history of Phylloscopidae.
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Affiliation(s)
- Chao Yang
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi’an, China
| | - Xiaomei Dong
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Qingxiong Wang
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi’an, China
| | - Xiang Hou
- Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Institute of Zoology, Xi’an, China
| | - Hao Yuan
- School of Basic Medical Sciences, Xi’an Medical University, Xi’an, China
| | - Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
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13
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Zhang BL, Chen W, Wang Z, Pang W, Luo MT, Wang S, Shao Y, He WQ, Deng Y, Zhou L, Chen J, Yang MM, Wu Y, Wang L, Fernández-Bellon H, Molloy S, Meunier H, Wanert F, Kuderna L, Marques-Bonet T, Roos C, Qi XG, Li M, Liu Z, Schierup MH, Cooper DN, Liu J, Zheng YT, Zhang G, Wu DD. Comparative genomics reveals the hybrid origin of a macaque group. SCIENCE ADVANCES 2023; 9:eadd3580. [PMID: 37262187 PMCID: PMC10413639 DOI: 10.1126/sciadv.add3580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/25/2023] [Indexed: 06/03/2023]
Abstract
Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that the fascicularis group originated from an ancient hybridization between the sinica and silenus groups ~3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions exhibited equal contributions from each parental lineage, suggesting that they were less affected by subsequent backcrossing and hence could have played an important role in maintaining hybrid integrity. We identified many reproduction-associated genes that could have contributed to the development of the mixed sexual phenotypes characteristic of the fascicularis group. The phylogeny within the silenus group was also resolved, and functional experimentation confirmed that all extant Western silenus species are susceptible to HIV-1 infection. Our study provides novel insights into macaque evolution and reveals a hybrid speciation event that has occurred only very rarely in primates.
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Affiliation(s)
- Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wu Chen
- Guangzhou Zoo and Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Zefu Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Meng-Ting Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen-Qiang He
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yuan Deng
- BGI-Shenzhen, Shenzhen 518083, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Long Zhou
- Center for Evolutionary and Organismal Biology and Women’s Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | | | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yajiang Wu
- Guangzhou Zoo and Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Lu Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, China
| | | | | | - Hélène Meunier
- Centre de Primatologie, de l'Université de Strasbourg, Niederhausbergen, France
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR 7364, Université de Strasbourg, Strasbourg, France
| | - Fanélie Wanert
- Plateforme SILABE, Université de Strasbourg, Niederhausbergen, France
| | - Lukas Kuderna
- Genome Interpretation Department, Illumina Inc., Foster City, CA, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, Barcelona 08003, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona 08010, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Göttingen, Germany
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | | | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Jianquan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Evolutionary and Organismal Biology and Women’s Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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14
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Zhou W, Furey NM, Soisook P, Thong VD, Lim BK, Rossiter SJ, Mao X. Diversification and introgression in four chromosomal taxa of the Pearson's horseshoe bat (Rhinolophus pearsoni) group. Mol Phylogenet Evol 2023; 183:107784. [PMID: 37040825 DOI: 10.1016/j.ympev.2023.107784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/11/2023] [Accepted: 04/07/2023] [Indexed: 04/13/2023]
Abstract
Chromosomal variation among closely related taxa is common in both plants and animals, and can reduce rates of introgression as well as promote reproductive isolation and speciation. In mammals, studies relating introgression to chromosomal variation have tended to focus on a few model systems and typically characterized levels of introgression using small numbers of loci. Here we took a genome-wide approach to examine how introgression rates vary among four closely related horseshoe bats (Rhinolophus pearsoni group) that possess different diploid chromosome numbers (2n = 42, 44, 46, and 60) resulting from Robertsonian (Rb) changes (fissions/fusions). Using a sequence capture we obtained orthologous loci for thousands of nuclear loci, as well as mitogenomes, and performed phylogenetic and population genetic analyses. We found that the taxon with 2n = 60 was the first to diverge in this group, and that the relationships among the three other taxa (2n = 42, 44 and 46) showed discordance across our different analyses. Our results revealed signatures of multiple ancient introgression events between the four taxa, with evidence of mitonuclar discordance in phylogenetic trees and reticulation events in their evolutionary history. Despite this, we found no evidence of recent and/or ongoing introgression between taxa. Overall, our results indicate that the effects of Rb changes on the reduction of introgression are complicated and that these may contribute to reproductive isolation and speciation in concert with other factors (e.g. phenotypic and genic divergence).
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Affiliation(s)
- Weiwei Zhou
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China
| | - Neil M Furey
- Fauna & Flora International (Cambodia), PO Box 1380, No. 19, Street 360, Boeng Keng Kong 1, Phnom Penh 12000, Cambodia
| | - Pipat Soisook
- Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Vu D Thong
- Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet Road, Cau Giay District, Hanoi, Viet Nam; Graduate University of Science and Technology, VAST, Viet Nam
| | - Burton K Lim
- Department of Natural History, Royal Ontario Museum, Toronto, Ontario M5S 2C6, Canada
| | - Stephen J Rossiter
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China.
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15
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Feng C, Wang K, Xu W, Yang L, Wanghe K, Sun N, Wu B, Wu F, Yang L, Qiu Q, Gan X, Chen Y, He S. Monsoon boosted radiation of the endemic East Asian carps. SCIENCE CHINA. LIFE SCIENCES 2023; 66:563-578. [PMID: 36166180 DOI: 10.1007/s11427-022-2141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 10/14/2022]
Abstract
Major historical events often trigger the rapid flourishing of a few lineages, which in turn shape established biodiversity patterns. How did this process occur and develop? This study provides a window into this issue. The endemic East Asian carps (EEAC) dominated the ichthyofauna of East Asia and exhibited a high degree of adaptation to monsoonal river-lake ecosystems. A series of evidence, including ecogeography, phylogenetics, and macroevolution, suggests that the EEAC is a lineage that arose with the East Asian monsoon and thrived intimately with subsequent monsoon activities. We further deduce the evolution of the EEAC and find that a range of historical events in the monsoon setting (e.g., marine transgression and regression and glacial-interglacial cycle) have further reshaped the distribution patterns of EEAC's members. Comparative genomics analyses reveal that introgressions during the initial period of EEAC radiation and innovations in the regulation of the brain and nervous system may have aided their adaptation to river-lake ecosystems in a monsoon setting, which boosted radiation. Overall, this study strengthens knowledge of the evolutionary patterns of freshwater fishes in East Asia and provides a model case for understanding the impact of major historical events on the evolution of biota.
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Affiliation(s)
- Chenguang Feng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Kun Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Wenjie Xu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Liandong Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Kunyuan Wanghe
- Key Laboratory of Adaptation and Evolution of Plateau Biota of Chinese Academy of Sciences, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, China
| | - Ning Sun
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Baosheng Wu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Feixiang Wu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, 100044, China
| | - Lei Yang
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China
| | - Xiaoni Gan
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yiyu Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
- National Natural Science Foundation of China, Beijing, 100085, China
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
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16
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Ottenburghs J, Honka J, Heikkinen ME, Madsen J, Müskens GJDM, Ellegren H. Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex. BMC Ecol Evol 2023; 23:2. [PMID: 36658479 PMCID: PMC9854053 DOI: 10.1186/s12862-023-02103-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Reconstructing phylogenetic relationships with genomic data remains a challenging endeavor. Numerous phylogenomic studies have reported incongruent gene trees when analyzing different genomic regions, complicating the search for a 'true' species tree. Some authors have argued that genomic regions of increased divergence (i.e. differentiation islands) reflect the species tree, although other studies have shown that these regions might produce misleading topologies due to species-specific selective sweeps or ancient introgression events. In this study, we tested the extent to which highly differentiated loci can resolve phylogenetic relationships in the Bean Goose complex, a group of goose taxa that includes the Taiga Bean Goose (Anser fabalis), the Tundra Bean Goose (Anser serrirostris) and the Pink-footed Goose (Anser brachyrhynchus). RESULTS First, we show that a random selection of genomic loci-which mainly samples the undifferentiated regions of the genome-results in an unresolved species complex with a monophyletic A. brachyrhynchus embedded within a paraphyletic cluster of A. fabalis and A. serrirostris. Next, phylogenetic analyses of differentiation islands converged upon a topology of three monophyletic clades in which A. brachyrhynchus is sister to A. fabalis, and A. serrirostris is sister to the clade uniting these two species. Close inspection of the locus trees within the differentiated regions revealed that this topology was consistently supported over other phylogenetic arrangements. As it seems unlikely that selection or introgression events have impacted all differentiation islands in the same way, we are convinced that this topology reflects the 'true' species tree. Additional analyses, based on D-statistics, revealed extensive introgression between A. fabalis and A. serrirostris, which partly explains the failure to resolve the species complex with a random selection of genomic loci. Recent introgression between these taxa has probably erased the phylogenetic branching pattern across a large section of the genome, whereas differentiation islands were unaffected by the homogenizing gene flow and maintained the phylogenetic patterns that reflect the species tree. CONCLUSIONS The evolution of the Bean Goose complex can be depicted as a simple bifurcating tree, but this would ignore the impact of introgressive hybridization. Hence, we advocate that the evolutionary relationships between these taxa are best represented as a phylogenetic network.
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Affiliation(s)
- Jente Ottenburghs
- Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden.
| | - Johanna Honka
- grid.10858.340000 0001 0941 4873Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Marja E. Heikkinen
- grid.10858.340000 0001 0941 4873Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Jesper Madsen
- grid.7048.b0000 0001 1956 2722Department of Ecoscience, Aarhus University, C. F. Møllers Allé 8, 8000 Aarhus C, Denmark
| | - Gerhard J. D. M. Müskens
- grid.4818.50000 0001 0791 5666Team Animal Ecology, Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3-3A, 6708 PB Wageningen, The Netherlands
| | - Hans Ellegren
- grid.8993.b0000 0004 1936 9457Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden
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17
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Stubbs RL, Theodoridis S, Mora‐Carrera E, Keller B, Yousefi N, Potente G, Léveillé‐Bourret É, Celep F, Kochjarová J, Tedoradze G, Eaton DAR, Conti E. Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot. THE NEW PHYTOLOGIST 2023; 237:656-671. [PMID: 36210520 PMCID: PMC10099377 DOI: 10.1111/nph.18525] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Biodiversity hotspots, such as the Caucasus mountains, provide unprecedented opportunities for understanding the evolutionary processes that shape species diversity and richness. Therefore, we investigated the evolution of Primula sect. Primula, a clade with a high degree of endemism in the Caucasus. We performed phylogenetic and network analyses of whole-genome resequencing data from the entire nuclear genome, the entire chloroplast genome, and the entire heterostyly supergene. The different characteristics of the genomic partitions and the resulting phylogenetic incongruences enabled us to disentangle evolutionary histories resulting from tokogenetic vs cladogenetic processes. We provide the first phylogeny inferred from the heterostyly supergene that includes all species of Primula sect. Primula. Our results identified recurrent admixture at deep nodes between lineages in the Caucasus as the cause of non-monophyly in Primula. Biogeographic analyses support the 'out-of-the-Caucasus' hypothesis, emphasizing the importance of this hotspot as a cradle for biodiversity. Our findings provide novel insights into causal processes of phylogenetic discordance, demonstrating that genome-wide analyses from partitions with contrasting genetic characteristics and broad geographic sampling are crucial for disentangling the diversification of species-rich clades in biodiversity hotspots.
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Affiliation(s)
- Rebecca L. Stubbs
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Spyros Theodoridis
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F)Frankfurt am Main60325Germany
| | - Emiliano Mora‐Carrera
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Barbara Keller
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Narjes Yousefi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Giacomo Potente
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
| | - Étienne Léveillé‐Bourret
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale (IRBV)Université de MontréalQuébecH1X 2B2Canada
| | - Ferhat Celep
- Department of Biology, Faculty of Arts and SciencesKırıkkale UniversityKırıkkale71450Turkey
| | - Judita Kochjarová
- Department of Phytology, Faculty of ForestryTechnical University in ZvolenZvolen96001Slovak Republic
| | - Giorgi Tedoradze
- Department of Plant Systematics and Geography, Institute of BotanyIlia State UniversityTbilisi0105Georgia
| | - Deren A. R. Eaton
- Department of Ecology, Evolution and Environmental BiologyColumbia UniversityNew YorkNY10027USA
| | - Elena Conti
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107Zurich8008Switzerland
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18
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Wang T, Li TZ, Chen SS, Yang T, Shu JP, Mu YN, Wang KL, Chen JB, Xiang JY, Yan YH. Untying the Gordian knot of plastid phylogenomic conflict: A case from ferns. FRONTIERS IN PLANT SCIENCE 2022; 13:918155. [PMID: 36507421 PMCID: PMC9730426 DOI: 10.3389/fpls.2022.918155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 10/11/2022] [Indexed: 06/17/2023]
Abstract
Phylogenomic studies based on plastid genome have resolved recalcitrant relationships among various plants, yet the phylogeny of Dennstaedtiaceae at the level of family and genera remains unresolved due to conflicting plastid genes, limited molecular data and incomplete taxon sampling of previous studies. The present study generated 30 new plastid genomes of Dennstaedtiaceae (9 genera, 29 species), which were combined with 42 publicly available plastid genomes (including 24 families, 27 genera, 42 species) to explore the evolution of Dennstaedtiaceae. In order to minimize the impact of systematic errors on the resolution of phylogenetic inference, we applied six strategies to generate 30 datasets based on CDS, intergenic spacers, and whole plastome, and two tree inference methods (maximum-likelihood, ML; and multispecies coalescent, MSC) to comprehensively analyze the plastome-scale data. Besides, the phylogenetic signal among all loci was quantified for controversial nodes using ML framework, and different topologies hypotheses among all datasets were tested. The species trees based on different datasets and methods revealed obvious conflicts at the base of the polypody ferns. The topology of the "CDS-codon-align-rm3" (CDS with the removal of the third codon) matrix was selected as the primary reference or summary tree. The final phylogenetic tree supported Dennstaedtiaceae as the sister group to eupolypods, and Dennstaedtioideae was divided into four clades with full support. This robust reconstructed phylogenetic backbone establishes a framework for future studies on Dennstaedtiaceae classification, evolution and diversification. The present study suggests considering plastid phylogenomic conflict when using plastid genomes. From our results, reducing saturated genes or sites can effectively mitigate tree conflicts for distantly related taxa. Moreover, phylogenetic trees based on amino acid sequences can be used as a comparison to verify the confidence of nucleotide-based trees.
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Affiliation(s)
- Ting Wang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Ting-Zhang Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Si-Si Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Tuo Yang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jiang-Ping Shu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Yu-Nong Mu
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
| | - Kang-Lin Wang
- Green Development Institute, Southwest Forestry University, Kunming, China
| | - Jian-Bing Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
| | - Jian-Ying Xiang
- Yunnan Academy of Biodiversity, Southwest Forestry University, Kunming, China
| | - Yue-Hong Yan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, The Orchid Conservation and Research Center of Shenzhen, Shenzhen, China
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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19
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Pang XX, Zhang DY. Impact of Ghost Introgression on Coalescent-based Species Tree Inference and Estimation of Divergence Time. Syst Biol 2022; 72:35-49. [PMID: 35799362 DOI: 10.1093/sysbio/syac047] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/25/2022] [Accepted: 07/05/2022] [Indexed: 11/15/2022] Open
Abstract
The species studied in any evolutionary investigation generally constitute a small proportion of all the species currently existing or that have gone extinct. It is therefore likely that introgression, which is widespread across the tree of life, involves "ghosts," i.e., unsampled, unknown, or extinct lineages. However, the impact of ghost introgression on estimations of species trees has rarely been studied and is poorly understood. Here, we use mathematical analysis and simulations to examine the robustness of species tree methods based on the multispecies coalescent model to introgression from a ghost or extant lineage. We found that many results originally obtained for introgression between extant species can easily be extended to ghost introgression, such as the strongly interactive effects of incomplete lineage sorting (ILS) and introgression on the occurrence of anomalous gene trees (AGTs). The relative performance of the summary species tree method (ASTRAL) and the full-likelihood method (*BEAST) varies under different introgression scenarios, with the former being more robust to gene flow between non-sister species whereas the latter performing better under certain conditions of ghost introgression. When an outgroup ghost (defined as a lineage that diverged before the most basal species under investigation) acts as the donor of the introgressed genes, the time of root divergence among the investigated species generally was overestimated, whereas ingroup introgression, as commonly perceived, can only lead to underestimation. In many cases of ingroup introgression that may or may not involve ghost lineages, the stronger the ILS, the higher the accuracy achieved in estimating the time of root divergence, although the topology of the species tree is more prone to be biased by the effect of introgression.
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Affiliation(s)
- Xiao-Xu Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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20
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Interpreting phylogenetic conflict: Hybridization in the most speciose genus of lichen-forming fungi. Mol Phylogenet Evol 2022; 174:107543. [PMID: 35690378 DOI: 10.1016/j.ympev.2022.107543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 02/06/2022] [Accepted: 05/13/2022] [Indexed: 11/24/2022]
Abstract
While advances in sequencing technologies have been invaluable for understanding evolutionary relationships, increasingly large genomic data sets may result in conflicting evolutionary signals that are often caused by biological processes, including hybridization. Hybridization has been detected in a variety of organisms, influencing evolutionary processes such as generating reproductive barriers and mixing standing genetic variation. Here, we investigate the potential role of hybridization in the diversification of the most speciose genus of lichen-forming fungi, Xanthoparmelia. As Xanthoparmelia is projected to have gone through recent, rapid diversification, this genus is particularly suitable for investigating and interpreting the origins of phylogenomic conflict. Focusing on a clade of Xanthoparmelia largely restricted to the Holarctic region, we used a genome skimming approach to generate 962 single-copy gene regions representing over 2 Mbp of the mycobiont genome. From this genome-scale dataset, we inferred evolutionary relationships using both concatenation and coalescent-based species tree approaches. We also used three independent tests for hybridization. Although different species tree reconstruction methods recovered largely consistent and well-supported trees, there was widespread incongruence among individual gene trees. Despite challenges in differentiating hybridization from ILS in situations of recent rapid radiations, our genome-wide analyses detected multiple potential hybridization events in the Holarctic clade, suggesting one possible source of trait variability in this hyperdiverse genus. This study highlights the value in using a pluralistic approach for characterizing genome-scale conflict, even in groups with well-resolved phylogenies, while highlighting current challenges in detecting the specific impacts of hybridization.
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21
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Piller KR, Parker E, Lemmon AR, Moriarty Lemmon E. Investigating the utility of Anchored Hybrid Enrichment data to investigate the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes. Mol Phylogenet Evol 2022; 173:107482. [PMID: 35452841 DOI: 10.1016/j.ympev.2022.107482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 04/06/2022] [Accepted: 04/06/2022] [Indexed: 10/18/2022]
Abstract
The Killifishes (Cyprinodontiformes) are a diverse and well-known group of fishes that contains sixteen families inclusive of Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae, Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae, Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae, and Valenciidae and more than 1,200 species that are globally distributed in tropical and temperate, freshwater and estuarine habitats. The evolutionary relationships among the families within the group, based on different molecular and morphological data sets, have remained uncertain. Therefore, the objective of this study was to use a targeted approach, anchored hybrid enrichment, to investigate the phylogenetic relationships among the families within the Cyprindontiformes. This study included more than 100 individuals, representing all sixteen families within the Cyprinodontiformes, including many recently diagnosed families. We recovered an average of 244 loci per individual. These data were submitted to phylogenetic analyses (RaxML and ASTRAL) and although we recovered many of the same relationships as in previous studies of the group, several novel sets of relationships for other families also were recovered. In addition, two well-established clades (Suborders Cyprinodontoidei and Aplocheilodei) were recovered as monophyletic and are in agreement with most previous studies. We also assessed the degree of gene tree discordance in our dataset to evaluate support for alternative topological hypotheses for interfamilial relationships within the Cyprinodontiformes using a variety of different analyses. The results from this study will provide a robust, historical framework needed to investigate a plethora of biogeographic, taxonomic, ecological, and physiological questions for this group of fishes.
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Affiliation(s)
- Kyle R Piller
- Department of Biological Science, Southeastern Louisiana University, Hammond, LA 70402, USA.
| | - Elyse Parker
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Dirac Science Library, Tallahassee, FL, 32306-4120, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, Biomedical Research Facility, Tallahassee, FL, 32306-4295, USA
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22
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Ottenburghs J. Avian introgression patterns are consistent with Haldane's Rule. J Hered 2022; 113:363-370. [PMID: 35134952 PMCID: PMC9308041 DOI: 10.1093/jhered/esac005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
According to Haldane’s Rule, the heterogametic sex will show the greatest fitness reduction in a hybrid cross. In birds, where sex is determined by a ZW system, female hybrids are expected to experience lower fitness compared to male hybrids. This pattern has indeed been observed in several bird groups, but it is unknown whether the generality of Haldane’s Rule also extends to the molecular level. First, given the lower fitness of female hybrids, we can expect maternally inherited loci (i.e., mitochondrial and W-linked loci) to show lower introgression rates than biparentally inherited loci (i.e., autosomal loci) in females. Second, the faster evolution of Z-linked loci compared to autosomal loci and the hemizygosity of the Z-chromosome in females might speed up the accumulation of incompatible alleles on this sex chromosome, resulting in lower introgression rates for Z-linked loci than for autosomal loci. I tested these expectations by conducting a literature review which focused on studies that directly quantified introgression rates for autosomal, sex-linked, and mitochondrial loci. Although most studies reported introgression rates in line with Haldane’s Rule, it remains important to validate these genetic patterns with estimates of hybrid fitness and supporting field observations to rule out alternative explanations. Genomic data provide exciting opportunities to obtain a more fine-grained picture of introgression rates across the genome, which can consequently be linked to ecological and behavioral observations, potentially leading to novel insights into the genetic mechanisms underpinning Haldane’s Rule.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and Conservation, Wageningen University & Research, Wageningen, The Netherlands.,Forest Ecology and Forest Management, Wageningen University & Research, Wageningen, The Netherlands
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23
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Sunde J, Yıldırım Y, Tibblin P, Bekkevold D, Skov C, Nordahl O, Larsson P, Forsman A. Drivers of neutral and adaptive differentiation in pike (Esox lucius) populations from contrasting environments. Mol Ecol 2021; 31:1093-1110. [PMID: 34874594 DOI: 10.1111/mec.16315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 01/28/2023]
Abstract
Understanding how eco-evolutionary processes and environmental factors drive population differentiation and adaptation are key challenges in evolutionary biology of relevance for biodiversity protection. Differentiation requires at least partial reproductive separation, which may result from different modes of isolation such as geographic isolation (allopatry) or isolation by distance (IBD), resistance (IBR), and environment (IBE). Despite that multiple modes might jointly influence differentiation, studies that compare the relative contributions are scarce. Using RADseq, we analyse neutral and adaptive genetic diversity and structure in 11 pike (Esox lucius) populations from contrasting environments along a latitudinal gradient (54.9-63.6°N), to investigate the relative effects of IBD, IBE and IBR, and to assess whether the effects differ between neutral and adaptive variation, or across structural levels. Patterns of neutral and adaptive variation differed, probably reflecting that they have been differently affected by stochastic and deterministic processes. The importance of the different modes of isolation differed between neutral and adaptive diversity, yet were consistent across structural levels. Neutral variation was influenced by interactions among all three modes of isolation, with IBR (seascape features) playing a central role, wheares adaptive variation was mainly influenced by IBE (environmental conditions). Taken together, this and previous studies suggest that it is common that multiple modes of isolation interactively shape patterns of genetic variation, and that their relative contributions differ among systems. To enable identification of general patterns and understand how various factors influence the relative contributions, it is important that several modes are simultaneously investigated in additional populations, species and environmental settings.
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Affiliation(s)
- Johanna Sunde
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Petter Tibblin
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Dorte Bekkevold
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Christian Skov
- National Institute of Aquatic Resources, Technical University of Denmark, Silkeborg, Denmark
| | - Oscar Nordahl
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Per Larsson
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Ecology and Evolution in Microbial Model Systems, EEMiS, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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24
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Hamilton CA, Winiger N, Rubin JJ, Breinholt J, Rougerie R, Kitching IJ, Barber JR, Kawahara AY. Hidden phylogenomic signal helps elucidate arsenurine silkmoth phylogeny and the evolution of body size and wing shape trade-offs. Syst Biol 2021; 71:859-874. [PMID: 34791485 DOI: 10.1093/sysbio/syab090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
One of the key objectives in biological research is understanding how evolutionary processes have produced Earth's diversity. A critical step towards revealing these processes is an investigation of evolutionary tradeoffs - that is, the opposing pressures of multiple selective forces. For millennia, nocturnal moths have had to balance successful flight, as they search for mates or host plants, with evading bat predators. However, the potential for evolutionary trade-offs between wing shape and body size are poorly understood. In this study, we used phylogenomics and geometric morphometrics to examine the evolution of wing shape in the wild silkmoth subfamily Arsenurinae (Saturniidae) and evaluate potential evolutionary relationships between body size and wing shape. The phylogeny was inferred based on 782 loci from target capture data of 42 arsenurine species representing all 10 recognized genera. After detecting in our data one of the most vexing problems in phylogenetic inference - a region of a tree that possesses short branches and no "support" for relationships (i.e., a polytomy), we looked for hidden phylogenomic signal (i.e., inspecting differing phylogenetic inferences, alternative support values, quartets, and phylogenetic networks) to better illuminate the most probable generic relationships within the subfamily. We found there are putative evolutionary trade-offs between wing shape, body size, and the interaction of fore- and hindwing shape. Namely, body size tends to decrease with increasing hindwing length but increases as forewing shape becomes more complex. Additionally, the type of hindwing (i.e., tail or no tail) a lineage possesses has a significant effect on the complexity of forewing shape. We outline possible selective forces driving the complex hindwing shapes that make Arsenurinae, and silkmoths as a whole, so charismatic.
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Affiliation(s)
- Chris A Hamilton
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA.,Department of Entomology, Plant Pathology & Nematology, University of Idaho, Moscow, ID, 83844 USA
| | - Nathalie Winiger
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA.,Wildlife Ecology and Management, Albert-Ludwigs-Universität Freiburg, 79106 Freiburg, Germany
| | - Juliette J Rubin
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA
| | - Jesse Breinholt
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA.,Division of Bioinformatics, Intermountain Healthcare, Precision Genomics, St. George, UT 84790 USA
| | - Rodolphe Rougerie
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Ian J Kitching
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Jesse R Barber
- Department of Biological Sciences, Boise State University, Boise, ID, 83725 USA
| | - Akito Y Kawahara
- Florida Museum of Natural History, McGuire Center for Lepidoptera and Biodiversity, University of Florida, Gainesville, FL 32611 USA
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25
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Sun Q, Yang Y, Hao X, Xiao J, Liu J, Yuan X. Comparative Mitogenomic Analysis of Five Awl Skippers (Lepidoptera: Hesperiidae: Coeliadinae) and Their Phylogenetic Implications. INSECTS 2021; 12:insects12080757. [PMID: 34442323 PMCID: PMC8397065 DOI: 10.3390/insects12080757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/11/2021] [Accepted: 08/21/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The subfamily Coeliadinae (Lepidoptera: Hesperiidae) is a unique group of over 70 species in the butterfly family, and its mitochondrial genome data still needs to be supplemented. This study sequenced and analyzed five additional complete mitochondrial genomes of the Coeliadinae species (Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis) and compared them in detail with those of the other known skipper mitogenomes. All five of these mitogenomes have the typical lepidopteran mitogenome characteristics of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a non-coding region. Our results indicate that their structure, nucleotide composition, codon usage, secondary structure of tRNAs, and so on, are highly conserved. Expanded sampling and gene data from the GenBank, phylogenetic analyses using maximum likelihood, and Bayesian inference methods indicate that Coeliadinae is monophyletic. These results contribute toward refining the phylogeny. Abstract To determine the significance of mitochondrial genome characteristics in revealing phylogenetic relationships and to shed light on the molecular evolution of the Coeliadinae species, the complete mitochondrial genomes (mitogenomes) of five Coeliadinae species were newly sequenced and analyzed, including Hasora schoenherr, Burara miracula, B. oedipodea, B. harisa, and Badamia exclamationis. The results show that all five mitogenomes are double-strand circular DNA molecules, with lengths of 15,340 bp, 15,295 bp, 15,304 bp, 15,295 bp, and 15,289 bp, respectively, and contain the typical 37 genes and a control region. Most protein-coding genes (PCGs) begin with ATN, with 3 types of stop codons including TAA, TAG, and an incomplete codon T-; most of the genes terminate with TAA. All of the transfer RNA genes (tRNAs) present the typical cloverleaf secondary structure except for the trnS1. Several conserved structural elements are found in the AT-rich region. Phylogenetic analyses based on three datasets (PCGs, PRT, and 12PRT) and using maximum likelihood (ML) and Bayesian inference (BI) methods show strong support for the monophyly of Coeliadinae, and the relationships of the five species are (B. exclamationis + ((B. harisa + (B. oedipodea + B. miracula)) + H. schoenherr)).
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Affiliation(s)
- Qi Sun
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (Q.S.); (X.H.)
| | - Yumeng Yang
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China;
| | - Xiangyu Hao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; (Q.S.); (X.H.)
| | - Jintian Xiao
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (J.X.); (J.L.)
| | - Jiaqi Liu
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (J.X.); (J.L.)
| | - Xiangqun Yuan
- Key Laboratory of Plant Protection Resources and Pest Management, Ministry of Education, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (J.X.); (J.L.)
- Correspondence: ; Tel.: +86-137-5998-5152
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26
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Suvorov A, Scornavacca C, Fujimoto MS, Bodily P, Clement M, Crandall KA, Whiting MF, Schrider DR, Bybee SM. Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies. Syst Biol 2021; 71:526-546. [PMID: 34324671 PMCID: PMC9017697 DOI: 10.1093/sysbio/syab063] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Introgression is an important biological process affecting at least 10% of the extant species in the animal kingdom. Introgression significantly impacts inference of phylogenetic species relationships where a strictly binary tree model cannot adequately explain reticulate net-like species relationships. Here we use phylogenomic approaches to understand patterns of introgression along the evolutionary history of a unique, non-model insect system: dragonflies and damselflies (Odonata). We demonstrate that introgression is a pervasive evolutionary force across various taxonomic levels within Odonata. In particular, we show that the morphologically "intermediate" species of Anisozygoptera (one of the three primary suborders within Odonata besides Zygoptera and Anisoptera), which retain phenotypic characteristics of the other two suborders, experienced high levels of introgression likely coming from zygopteran genomes. Additionally, we find evidence for multiple cases of deep inter-superfamilial ancestral introgression.
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Affiliation(s)
- Anton Suvorov
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Celine Scornavacca
- Institut des Sciences de l'Evolution Université de Montpellier, CNRS, IRD, EPHE CC 064, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - M Stanley Fujimoto
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Paul Bodily
- Department of Computer Science, Idaho State University, Pocatello, ID, United States
| | - Mark Clement
- Department of Computer Science, Brigham Young University, Provo, UT, United States
| | - Keith A Crandall
- Computational Biology Institute, Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States
| | - Michael F Whiting
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
| | - Daniel R Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Seth M Bybee
- Department of Biology, Brigham Young University, Provo, UT, United States.,M.L. Bean Museum, Brigham Young University, Provo, UT, United States
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Jennings WB. Evolutionary relationships among the snakelike pygopodid lizards: a review of phylogenetic studies of an enigmatic Australian adaptive radiation. PeerJ 2021; 9:e11502. [PMID: 34249485 PMCID: PMC8253114 DOI: 10.7717/peerj.11502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 05/03/2021] [Indexed: 12/03/2022] Open
Abstract
Here, I review phylogenetic studies of the lizard family Pygopodidae, a group of 47 extant species that diversified in Australia and New Guinea. The goal of this study was to examine published phylogenetic and phylogenomic hypotheses on pygopodids to identify the strengths and weaknesses in our understanding of their phylogeny. Many parts of the pygopodid family tree are well established by multiple independent tree inferences including: (1) all multispecies genera (i.e., Aprasia, Delma, Lialis, Pletholax, and Pygopus) are monophyletic groups; (2) the root of the pygopodid tree is located along the branch leading to the Delma clade, thus showing that Delma is the sister group to all other pygopodid genera; (3) the Aprasia repens group, Delma tincta group, and several other groups of closely related species are demonstrated to be monophyletic entities; and (4) the monotypic Paradelma orientalis is the sister lineage to the Pygopus clade. Based on accumulated phylogenetic evidence, two taxonomic recommendations are given: Paradelma merits generic status rather than being subsumed into Pygopus as some earlier studies had suggested, and the monotypic Aclys concinna should be recognized as a member of Delma (following current practice) until future studies clarify its placement inside or outside the Delma clade. One chronic problem with phylogenetic studies of pygopodids, which has limited the explanatory power of many tree hypotheses, concerns the undersampling of known species. Although the continual addition of newly described species, especially over the past two decades, has been a major reason for these taxon sampling gaps, deficits in species sampling for ingroups and/or outgroups in several studies of pygopodid species complexes has confounded the testing of some ingroup monophyly hypotheses. Ancient hybridization between non-sister lineages may also be confounding attempts to recover the relationships among pygopodids using molecular data. Indeed, such a phenomenon can explain at least five cases of mito-nuclear discordance and conflicts among trees based on nuclear DNA datasets. Another problem has been the lack of consensus on the relationships among most pygopodid genera, an issue that may stem from rapid diversification of these lineages early in the group's history. Despite current weaknesses in our understanding of pygopodid phylogeny, enough evidence exists to clarify many major and minor structural parts of their family tree. Accordingly, a composite tree for the Pygopodidae was able to be synthesized. This novel tree hypothesis contains all recognized pygopodid species and reveals that about half of the clades are corroborated by multiple independent tree hypotheses, while the remaining clades have less empirical support.
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Affiliation(s)
- W. Bryan Jennings
- Department of Evolution, Ecology, & Organismal Biology, University of California, Riverside, Riverside, California, United States of America
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
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28
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Hao X, Liu J, Chiba H, Xiao J, Yuan X. Complete mitochondrial genomes of three skippers in the tribe Aeromachini (Lepidoptera: Hesperiidae: Hesperiinae) and their phylogenetic implications. Ecol Evol 2021; 11:8381-8393. [PMID: 34188893 PMCID: PMC8216930 DOI: 10.1002/ece3.7666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
The mitochondrial genome is now widely used in the study of phylogenetics and molecular evolution due to its maternal inheritance, fast evolutionary rate, and highly conserved gene content. To explore the phylogenetic relationships of the tribe Aeromachini within the subfamily Hesperiinae at the mitochondrial genomic level, we sequenced and annotated the complete mitogenomes of 3 skippers: Ampittia virgata, Halpe nephele, and Onryza maga (new mitogenomes for 2 genera) with a total length of 15,333 bp, 15,291 bp, and 15,381 bp, respectively. The mitogenomes all contain 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a noncoding A + T-rich region and are consistent with other lepidopterans in gene order and type. In addition, we reconstructed the phylogenetic trees of Hesperiinae using maximum likelihood (ML) and Bayesian inference (BI) methods based on mitogenomic data. Results show that the tribe Aeromachini in this study robustly constitute a monophyletic group in the subfamily Hesperiinae, with the relationships Coeliadinae + (Euschemoninae + (Pyrginae + ((Eudaminae + Tagiadinae) + (Heteropterinae + ((Trapezitinae + Barcinae) + Hesperiinae))))). Moreover, our study supports the view that Apostictopterus fuliginosus and Barca bicolor should be placed out of the subfamily Hesperiinae.
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Affiliation(s)
- Xiangyu Hao
- College of Life SciencesNorthwest A&F UniversityYanglingChina
| | - Jiaqi Liu
- Key Laboratory of Plant Protection Resources and Pest ManagementMinistry of EducationEntomological MuseumCollege of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | | | - Jintian Xiao
- Key Laboratory of Plant Protection Resources and Pest ManagementMinistry of EducationEntomological MuseumCollege of Plant ProtectionNorthwest A&F UniversityYanglingChina
| | - Xiangqun Yuan
- Key Laboratory of Plant Protection Resources and Pest ManagementMinistry of EducationEntomological MuseumCollege of Plant ProtectionNorthwest A&F UniversityYanglingChina
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