1
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Pezzi PH, Wheeler LC, Freitas LB, Smith SD. Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae). Mol Phylogenet Evol 2024; 198:108136. [PMID: 38909873 DOI: 10.1016/j.ympev.2024.108136] [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: 03/27/2024] [Revised: 06/06/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.
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Affiliation(s)
- Pedro H Pezzi
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.
| | - Lucas C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
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2
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Wang Y, Wu X, Chen Y, Xu C, Wang Y, Wang Q. Phylogenomic analyses revealed widely occurring hybridization events across Elsholtzieae (Lamiaceae). Mol Phylogenet Evol 2024; 198:108112. [PMID: 38806075 DOI: 10.1016/j.ympev.2024.108112] [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: 02/06/2024] [Revised: 05/14/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
Abstract
Obtaining a robust phylogeny proves challenging due to the intricate evolutionary history of species, where processes such as hybridization and incomplete lineage sorting can introduce conflicting signals, thereby complicating phylogenetic inference. In this study, we conducted comprehensive sampling of Elsholtzieae, with a particular focus on its largest genus, Elsholtzia. We utilized 503 nuclear loci and complete plastome sequences obtained from 99 whole-genome sequencing datasets to elucidate the interspecific relationships within the Elsholtzieae. Additionally, we explored various sources of conflicts between gene trees and species trees. Fully supported backbone phylogenies were recovered, and the monophyly of Elsholtzia and Keiskea was not supported. Significant gene tree heterogeneity was observed at numerous nodes, particularly regarding the placement of Vuhuangia and the E. densa clade. Further investigations into potential causes of this discordance revealed that incomplete lineage sorting (ILS), coupled with hybridization events, has given rise to substantial gene tree discordance. Several species, represented by multiple samples, exhibited a closer association with geographical distribution rather than following a strictly monophyletic pattern in plastid trees, suggesting chloroplast capture within Elsholtzieae and providing evidence of hybridization. In conclusion, this study provides phylogenomic insights to untangle taxonomic problems in the tribe Elsholtzieae, especially the genus Elsholtzia.
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Affiliation(s)
- Yan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; National Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuexue Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; National Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyi Chen
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; National Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Xu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; National Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yinghui Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; National Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; National Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Leal JL, Milesi P, Hodková E, Zhou Q, James J, Eklund DM, Pyhäjärvi T, Salojärvi J, Lascoux M. Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles. Syst Biol 2024; 73:392-418. [PMID: 38613229 PMCID: PMC11282369 DOI: 10.1093/sysbio/syae012] [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: 08/17/2023] [Revised: 12/18/2023] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Introgression allows polyploid species to acquire new genomic content from diploid progenitors or from other unrelated diploid or polyploid lineages, contributing to genetic diversity and facilitating adaptive allele discovery. In some cases, high levels of introgression elicit the replacement of large numbers of alleles inherited from the polyploid's ancestral species, profoundly reshaping the polyploid's genomic composition. In such complex polyploids, it is often difficult to determine which taxa were the progenitor species and which taxa provided additional introgressive blocks through subsequent hybridization. Here, we use population-level genomic data to reconstruct the phylogenetic history of Betula pubescens (downy birch), a tetraploid species often assumed to be of allopolyploid origin and which is known to hybridize with at least four other birch species. This was achieved by modeling polyploidization and introgression events under the multispecies coalescent and then using an approximate Bayesian computation rejection algorithm to evaluate and compare competing polyploidization models. We provide evidence that B. pubescens is the outcome of an autoploid genome doubling event in the common ancestor of B. pendula and its extant sister species, B. platyphylla, that took place approximately 178,000-188,000 generations ago. Extensive hybridization with B. pendula, B. nana, and B. humilis followed in the aftermath of autopolyploidization, with the relative contribution of each of these species to the B. pubescens genome varying markedly across the species' range. Functional analysis of B. pubescens loci containing alleles introgressed from B. nana identified multiple genes involved in climate adaptation, while loci containing alleles derived from B. humilis revealed several genes involved in the regulation of meiotic stability and pollen viability in plant species.
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Affiliation(s)
- J Luis Leal
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
| | - Eva Hodková
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 16521 Prague, Czech Republic
| | - Qiujie Zhou
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Jennifer James
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - D Magnus Eklund
- Physiology and Environmental Toxicology, Department of Organismal Biology, Uppsala University, Norbyvägen 18A, 75236 Uppsala, Sweden
| | - Tanja Pyhäjärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Jarkko Salojärvi
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
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4
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Bernardini G, Iersel L, Julien E, Stougie L. Inferring Phylogenetic Networks from Multifurcating Trees via Cherry Picking and Machine Learning. Mol Phylogenet Evol 2024:108137. [PMID: 39029549 DOI: 10.1016/j.ympev.2024.108137] [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: 11/18/2023] [Revised: 02/19/2024] [Accepted: 06/29/2024] [Indexed: 07/21/2024]
Abstract
The Hybridization problem asks to reconcile a set of conflicting phylogenetic trees into a single phylogenetic network with the smallest possible number of reticulation nodes. This problem is computationally hard and previous solutions are restricted to small and/or severely restricted data sets, for example, a set of binary trees with the same taxon set or only two non-binary trees with non-equal taxon sets. Building on our previous work on binary trees, we present FHyNCH, the first algorithmic framework to heuristically solve the Hybridization problem for large sets of multifurcating trees whose sets of taxa may differ. Our heuristics combine the cherry-picking technique, recently proposed to solve the same problem for binary trees, with two carefully designed machine-learning models. We demonstrate that our methods are practical and produce qualitatively good solutions through experiments on both synthetic and real data sets.
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Affiliation(s)
| | - Leo Iersel
- Delft Institute of Applied Mathematics, Delft, The Netherlands
| | - Esther Julien
- Delft Institute of Applied Mathematics, Delft, The Netherlands
| | - Leen Stougie
- CWI, Amsterdam, The Netherlands; Vrije Universiteit, Amsterdam, The Netherlands; INRIA-Erable, France
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5
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Probst RS, Longino JT, Branstetter MG. Evolutionary déjà vu? A case of convergent evolution in an ant-plant association. Proc Biol Sci 2024; 291:20241214. [PMID: 38981524 DOI: 10.1098/rspb.2024.1214] [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: 10/01/2023] [Accepted: 06/10/2024] [Indexed: 07/11/2024] Open
Abstract
Obligatory ant-plant symbioses often appear to be single evolutionary shifts within particular ant lineages; however, convergence can be revealed once natural history observations are complemented with molecular phylogenetics. Here, we describe a remarkable example of convergent evolution in an ant-plant symbiotic system. Exclusively arboreal, Myrmelachista species can be generalized opportunists nesting in several plant species or obligately symbiotic, live-stem nesters of a narrow set of plant species. Instances of specialization within Myrmelachista are known from northern South America and throughout Middle America. In Middle America, a diverse radiation of specialists occupies understory treelets of lowland rainforests. The morphological and behavioural uniformity of specialists suggests that they form a monophyletic assemblage, diversifying after a single origin of specialization. Using ultraconserved element phylogenomics and ancestral state reconstructions, we show that shifts from opportunistic to obligately symbiotic evolved independently in South and Middle America. Furthermore, our analyses support a remarkable case of convergence within the Middle American radiation, with two independently evolved specialist clades, arising nearly simultaneously from putative opportunistic ancestors during the late Pliocene. This repeated evolution of a complex phenotype suggests similar mechanisms behind trait shifts from opportunists to specialists, generating further questions about the selective forces driving specialization.
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Affiliation(s)
- Rodolfo S Probst
- Science Research Initiative (SRI), College of Science, University of Utah , Salt Lake City, UT 84112, USA
- School of Biological Sciences, University of Utah , Salt Lake City, UT 84112, USA
| | - John T Longino
- School of Biological Sciences, University of Utah , Salt Lake City, UT 84112, USA
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University , Logan, UT 84322, USA
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6
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Caetano-Anollés G. Are Viruses Taxonomic Units? A Protein Domain and Loop-Centric Phylogenomic Assessment. Viruses 2024; 16:1061. [PMID: 39066224 PMCID: PMC11281659 DOI: 10.3390/v16071061] [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: 06/05/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/28/2024] Open
Abstract
Virus taxonomy uses a Linnaean-like subsumption hierarchy to classify viruses into taxonomic units at species and higher rank levels. Virus species are considered monophyletic groups of mobile genetic elements (MGEs) often delimited by the phylogenetic analysis of aligned genomic or metagenomic sequences. Taxonomic units are assumed to be independent organizational, functional and evolutionary units that follow a 'natural history' rationale. Here, I use phylogenomic and other arguments to show that viruses are not self-standing genetically-driven systems acting as evolutionary units. Instead, they are crucial components of holobionts, which are units of biological organization that dynamically integrate the genetics, epigenetic, physiological and functional properties of their co-evolving members. Remarkably, phylogenomic analyses show that viruses share protein domains and loops with cells throughout history via massive processes of reticulate evolution, helping spread evolutionary innovations across a wider taxonomic spectrum. Thus, viruses are not merely MGEs or microbes. Instead, their genomes and proteomes conduct cellularly integrated processes akin to those cataloged by the GO Consortium. This prompts the generation of compositional hierarchies that replace the 'is-a-kind-of' by a 'is-a-part-of' logic to better describe the mereology of integrated cellular and viral makeup. My analysis demands a new paradigm that integrates virus taxonomy into a modern evolutionarily centered taxonomy of organisms.
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Affiliation(s)
- Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, C. R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA
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7
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Fouqueau L, Polechová J. Eco-evolutionary dynamics in changing environments: integrating theory with data. J Evol Biol 2024; 37:579-587. [PMID: 38941551 DOI: 10.1093/jeb/voae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/30/2024]
Affiliation(s)
- Louise Fouqueau
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Jitka Polechová
- Department of Mathematics, University of Vienna, Vienna, Austria
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8
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Murphy WJ, Harris AJ. Toward telomere-to-telomere cat genomes for precision medicine and conservation biology. Genome Res 2024; 34:655-664. [PMID: 38849156 PMCID: PMC11216403 DOI: 10.1101/gr.278546.123] [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] [Indexed: 06/09/2024]
Abstract
Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation.
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Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA;
- Department of Biology, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
| | - Andrew J Harris
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
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9
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Salgado-Roa FC, Pardo-Diaz C, Rueda-M N, Cisneros-Heredia DF, Lasso E, Salazar C. The Andes as a semi-permeable geographical barrier: Genetic connectivity between structured populations in a widespread spider. Mol Ecol 2024; 33:e17361. [PMID: 38634856 DOI: 10.1111/mec.17361] [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: 01/16/2024] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
Geographical barriers like mountain ranges impede genetic exchange among populations, promoting diversification. The effectiveness of these barriers in limiting gene flow varies between lineages due to each species' dispersal modes and capacities. Our understanding of how the Andes orogeny contributes to species diversification comes from well-studied vertebrates and a few arthropods and plants, neglecting organisms unable to fly or walk long distances. Some arachnids, such as Gasteracantha cancriformis, have been hypothesized to disperse long distances via ballooning (i.e. using their silk to interact with the wind). Yet, we do not know how the environment and geography shape its genetic diversity. Therefore, we tested whether the Andes contributed to the diversification of G. cancriformis acting as an absolute or semi-permeable barrier to genetic connectivity between populations of this spider at opposite sides of the mountain range. We sampled thousands of loci across the distribution of the species and implemented population genetics, phylogenetic, and landscape genetic analyses. We identified two genetically distinct groups structured by the Central Andes, and a third less structured group in the Northern Andes that shares ancestry with the previous two. This structure is largely explained by the altitude along the Andes, which decreases in some regions, possibly facilitating cross-Andean dispersal and gene flow. Our findings support that altitude in the Andes plays a major role in structuring populations in South America, but the strength of this barrier can be overcome by organisms with long-distance dispersal modes together with altitudinal depressions.
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Affiliation(s)
- Fabian C Salgado-Roa
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Carolina Pardo-Diaz
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Nicol Rueda-M
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Diego F Cisneros-Heredia
- Colegio de Ciencias Biológicas y Ambientales, Instituto de Biodiversidad Tropical IBIOTROP, Laboratorio de Zoología Terrestre, Museo de Zoología & Extensión USFQ Galápagos GAIAS, Galapagos Science Center, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Eloisa Lasso
- Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
- Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Estación Científica Coiba AIP, Panama, Republic of Panama
| | - Camilo Salazar
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
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10
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Pang XX, Zhang DY. Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information. Syst Biol 2024; 73:207-222. [PMID: 38224495 PMCID: PMC11129598 DOI: 10.1093/sysbio/syad077] [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: 05/01/2023] [Revised: 12/17/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024] Open
Abstract
In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression-the transfer of genetic material from extinct or unsampled lineages to extant species-emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving 3 species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP uses multilocus sequence alignments directly-hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.
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Affiliation(s)
- Xiao-Xu Pang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Da-Yong Zhang
- 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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11
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Musher LJ, Del-Rio G, Marcondes RS, Brumfield RT, Bravo GA, Thom G. Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops). Syst Biol 2024; 73:36-52. [PMID: 37804132 DOI: 10.1093/sysbio/syad061] [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: 12/20/2022] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/08/2023] Open
Abstract
Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, and gene flow interact to produce a genomic landscape of divergence wherein patterns of differentiation and genealogy vary nonrandomly across the genomes of diverging populations. For instance, genealogical patterns that arise due to gene flow should be more likely to occur on smaller chromosomes, which experience high recombination, whereas those tracking histories of geographic isolation (reduced gene flow caused by a barrier) and divergence should be more likely to occur on larger and sex chromosomes. In Amazonia, populations of many bird species diverge and introgress across rivers, resulting in reticulated genomic signals. Herein, we used reduced representation genomic data to disentangle the evolutionary history of 4 populations of an Amazonian antbird, Thamnophilus aethiops, whose biogeographic history was associated with the dynamic evolution of the Madeira River Basin. Specifically, we evaluate whether a large river capture event ca. 200 Ka, gave rise to reticulated genealogies in the genome by making spatially explicit predictions about isolation and gene flow based on knowledge about genomic processes. We first estimated chromosome-level phylogenies and recovered 2 primary topologies across the genome. The first topology (T1) was most consistent with predictions about population divergence and was recovered for the Z-chromosome. The second (T2), was consistent with predictions about gene flow upon secondary contact. To evaluate support for these topologies, we trained a convolutional neural network to classify our data into alternative diversification models and estimate demographic parameters. The best-fit model was concordant with T1 and included gene flow between non-sister taxa. Finally, we modeled levels of divergence and introgression as functions of chromosome length and found that smaller chromosomes experienced higher gene flow. Given that (1) genetrees supporting T2 were more likely to occur on smaller chromosomes and (2) we found lower levels of introgression on larger chromosomes (and especially the Z-chromosome), we argue that T1 represents the history of population divergence across rivers and T2 the history of secondary contact due to barrier loss. Our results suggest that a significant portion of genomic heterogeneity arises due to extrinsic biogeographic processes such as river capture interacting with intrinsic processes associated with genome architecture. Future phylogeographic studies would benefit from accounting for genomic processes, as different parts of the genome reveal contrasting, albeit complementary histories, all of which are relevant for disentangling the intricate geogenomic mechanisms of biotic diversification. [Amazonia; biogeography; demographic modeling; gene flow; gene tree; genome architecture; geogenomics; introgression; linked selection; neural network; phylogenomic; phylogeography; reproductive isolation; speciation; species tree.].
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Affiliation(s)
- Lukas J Musher
- Department of Ornithology, The Academy of Natural Sciences of Drexel University, Philadelphia, PA 19103, USA
- Department of Ornithology, American Museum of Natural History, New York, NY 10024, USA
| | - Glaucia Del-Rio
- Cornell Laboratory of Ornithology and Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Rafael S Marcondes
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
- Department of BioSciences, Rice University, Houston, TX 77005, USA
| | - Robb T Brumfield
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Gustavo A Bravo
- Sección de Ornitología, Colecciones Biológicas, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Claustro de San Agustín, Villa de Leyva, Boyacá 111311, Colombia
- Museum of Comparative Zoology and Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Gregory Thom
- Department of Biology and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA
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12
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Morales-Saldaña S, Hipp AL, Valencia-Ávalos S, Hahn M, González-Elizondo MS, Gernandt DS, Pham KK, Oyama K, González-Rodríguez A. Divergence and reticulation in the Mexican white oaks: ecological and phylogenomic evidence on species limits and phylogenetic networks in the Quercus laeta complex (Fagaceae). ANNALS OF BOTANY 2024; 133:1007-1024. [PMID: 38428030 PMCID: PMC11089265 DOI: 10.1093/aob/mcae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/28/2024] [Indexed: 03/03/2024]
Abstract
BACKGROUND AND AIMS Introgressive hybridization poses a challenge to taxonomic and phylogenetic understanding of taxa, particularly when there are high numbers of co-occurring, intercrossable species. The genus Quercus exemplifies this situation. Oaks are highly diverse in sympatry and cross freely, creating syngameons of interfertile species. Although a well-resolved, dated phylogeny is available for the American oak clade, evolutionary relationships within many of the more recently derived clades remain to be defined, particularly for the young and exceptionally diverse Mexican white oak clade. Here, we adopted an approach bridging micro- and macroevolutionary scales to resolve evolutionary relationships in a rapidly diversifying clade endemic to Mexico. METHODS Ecological data and sequences of 155 low-copy nuclear genes were used to identify distinct lineages within the Quercus laeta complex. Concatenated and coalescent approaches were used to assess the phylogenetic placement of these lineages relative to the Mexican white oak clade. Phylogenetic network methods were applied to evaluate the timing and genomic significance of recent or historical introgression among lineages. KEY RESULTS The Q. laeta complex comprises six well-supported lineages, each restricted geographically and with mostly divergent climatic niches. Species trees corroborated that the different lineages are more closely related to other species of Mexican white oaks than to each other, suggesting that this complex is polyphyletic. Phylogenetic networks estimated events of ancient introgression that involved the ancestors of three present-day Q. laeta lineages. CONCLUSIONS The Q. laeta complex is a morphologically and ecologically related group of species rather than a clade. Currently, oak phylogenetics is at a turning point, at which it is necessary to integrate phylogenetics and ecology in broad regional samples to figure out species boundaries. Our study illuminates one of the more complicated of the Mexican white oak groups and lays groundwork for further taxonomic study.
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Affiliation(s)
- Saddan Morales-Saldaña
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Andrew L Hipp
- The Morton Arboretum, Lisle, IL 60532-1293, USA
- The Field Museum, Chicago, IL 60605, USA
| | - Susana Valencia-Ávalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | | | | | - David S Gernandt
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), 04510, Ciudad de México, México
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex‐Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Antigua Carretera a Pátzcuaro No. 8701, Col. Ex-Hacienda de San José de la Huerta, Morelia, 58190, Michoacán, México
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13
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Rurik I, Melichárková A, Gbúrová Štubová E, Kučera J, Kochjarová J, Paun O, Vďačný P, Slovák M. Homoplastic versus xenoplastic evolution: exploring the emergence of key intrinsic and extrinsic traits in the montane genus Soldanella (Primulaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:753-765. [PMID: 38217489 DOI: 10.1111/tpj.16630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/02/2023] [Accepted: 12/27/2023] [Indexed: 01/15/2024]
Abstract
Specific ecological conditions in the high mountain environment exert a selective pressure that often leads to convergent trait evolution. Reticulations induced by incomplete lineage sorting and introgression can lead to discordant trait patterns among gene and species trees (hemiplasy/xenoplasy), providing a false illusion that the traits under study are homoplastic. Using phylogenetic species networks, we explored the effect of gene exchange on trait evolution in Soldanella, a genus profoundly influenced by historical introgression. At least three features evolved independently multiple times: the single-flowered dwarf phenotype, dysploid cytotype, and ecological generalism. The present analyses also indicated that the recurring occurrence of stoloniferous growth might have been prompted by an introgression event between an ancestral lineage and a still extant species, although its emergence via convergent evolution cannot be completely ruled out. Phylogenetic regression suggested that the independent evolution of larger genomes in snowbells is most likely a result of the interplay between hybridization events of dysploid and euploid taxa and hostile environments at the range margins of the genus. The emergence of key intrinsic and extrinsic traits in snowbells has been significantly impacted not only by convergent evolution but also by historical and recent introgression events.
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Affiliation(s)
- Ivan Rurik
- Department of Zoology, Comenius University Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Andrea Melichárková
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
| | - Eliška Gbúrová Štubová
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
- Slovak National Museum, Natural History Museum, Vajanského nábrežie 2, 810 06, Bratislava, Slovak Republic
| | - Jaromír Kučera
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
| | - Judita Kochjarová
- Department of Phytology, Faculty of Forestry, Technical University Zvolen, Masarykova 24, 960 53, Zvolen, Slovak Republic
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Vienna, Austria
| | - Peter Vďačný
- Department of Zoology, Comenius University Bratislava, Ilkovičova 6, 842 15, Bratislava, Slovak Republic
| | - Marek Slovák
- Institute of Botany, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 845 23, Bratislava, Slovak Republic
- Department of Botany, Charles University, Benátská 2, 128 01, Prague, Czech Republic
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14
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van der Gulik PTS, Hoff WD, Speijer D. The contours of evolution: In defence of Darwin's tree of life paradigm. Bioessays 2024; 46:e2400012. [PMID: 38436469 DOI: 10.1002/bies.202400012] [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: 01/15/2024] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.
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Affiliation(s)
| | - Wouter D Hoff
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Dave Speijer
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
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15
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Hu XZ, Guo C, Qin SY, Li DZ, Guo ZH. Deep genome skimming reveals the hybrid origin of Pseudosasa gracilis (Poaceae: Bambusoideae). PLANT DIVERSITY 2024; 46:344-352. [PMID: 38798728 PMCID: PMC11119509 DOI: 10.1016/j.pld.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/24/2023] [Accepted: 06/02/2023] [Indexed: 05/29/2024]
Abstract
Pseudosasa gracilis (Poaceae: Bambusoideae) is a temperate woody bamboo species endemic to South-central China with a narrow distribution. Previous phylogenetic studies revealed an unexpected, isolated phylogenetic position of Ps. gracilis. Here we conducted phylogenomic analysis by sampling populations of Ps. gracilis and its sympatric species Ps. nanunica and Sinosasa polytricha reflecting different genomic signals, by deep genome skimming. Integrating molecular evidence from chloroplast genes and genome-wide SNPs, we deciphered the phylogenetic relationships of Ps. gracilis. Both plastid and nuclear data indicate that Ps. gracilis is more closely related to Sinosasa, which is discordant with the taxonomic treatment. To further explore this molecular-morphological conflict, we screened 411 "perfect-copy" syntenic genes to reconstruct phylogenies using both the concatenation and coalescent methods. We observed extensive discordance between gene trees and the putative species tree. A significant hybridization event was detected based on 411 genes from the D subgenome, showing Ps. gracilis was a hybrid descendant between Sinosasa longiligulata and Ps. nanunica, with 63.56% and 36.44% inheritance probabilities of each parent. Moreover, introgression events were detected in the C subgenome between Ps. gracilis and S. polytricha in the same distribution region. Our findings suggest that sympatric hybridization and introgression play a crucial role in the origin of Ps. gracilis. By providing an empirical example of bamboo of hybrid origin using comprehensive analyses based on genomic data from different inheritance systems and morphological characters, our study represents a step forward in understanding of reticulate evolution of bamboos.
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Affiliation(s)
- Xiang-Zhou Hu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Sheng-Yuan Qin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Wróbel A, Klichowska E, Nobis M. Hybrids as mirrors of the past: genomic footprints reveal spatio-temporal dynamics and extinction risk of alpine extremophytes in the mountains of Central Asia. FRONTIERS IN PLANT SCIENCE 2024; 15:1369732. [PMID: 38693932 PMCID: PMC11061500 DOI: 10.3389/fpls.2024.1369732] [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: 01/12/2024] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
Hybridization is one of the key processes shaping lineage diversification, particularly in regions that experienced strong climate oscillations. The alpine biome with its rich history of glacial-interglacial cycles and complex patterns of species distribution shifts offers an excellent system to investigate the impact of gene flow on population dynamics and speciation, important issues for evolutionary biology and biodiversity conservation. In this study, we combined genomic data (DArTseq), chloroplast markers, and morphology to examine phylogenetic relationships and the permeability of species boundaries and their evolutionary outcomes among the alpine extremophilic species of Puccinellia (Poaceae) in the Pamir Mountains, a part of the Mountains of Central Asia biodiversity hotspot. We determined the occurrence of interspecific hybrids between P. himalaica and P. pamirica, which demonstrated almost symmetric ancestry from their parental species and did not show signals of introgression. According to our integrative revision, the natural hybrids between P. himalaica and P. pamirica should be classified as Puccinellia ×vachanica (pro species). Using approximate Bayesian computation for population history inference, we uncovered that P. himalaica hybridized with P. pamirica independently in multiple localities over the Holocene. Hybrids inherited the fine-scale genetic structure from their parental species, which developed these patterns earlier, during the Late Pleistocene. Hybridization had different consequences for the involved parental lineages, likely playing an important role in a continuing decline of P. himalaica in the Pamir Mountains over the Holocene. Our results show that P. himalaica should be considered a critically endangered species in the Pamir Mountains and could also be retreating across its entire range of distribution in High Mountain Asia. Using a comparative phylogeographic framework, we revealed the risk of extinction of a cold-adapted alpine species in a global biodiversity hotspot. This study highlights that genomics could unravel diversity trends under climate change and provides valuable evidence for conservation management.
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Affiliation(s)
- Anna Wróbel
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
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17
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Bertola LD, Quinn L, Hanghøj K, Garcia-Erill G, Rasmussen MS, Balboa RF, Meisner J, Bøggild T, Wang X, Lin L, Nursyifa C, Liu X, Li Z, Chege M, Moodley Y, Brüniche-Olsen A, Kuja J, Schubert M, Agaba M, Santander CG, Sinding MHS, Muwanika V, Masembe C, Siegismund HR, Moltke I, Albrechtsen A, Heller R. Giraffe lineages are shaped by major ancient admixture events. Curr Biol 2024; 34:1576-1586.e5. [PMID: 38479386 DOI: 10.1016/j.cub.2024.02.051] [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: 06/11/2023] [Revised: 09/29/2023] [Accepted: 02/21/2024] [Indexed: 04/11/2024]
Abstract
Strong genetic structure has prompted discussion regarding giraffe taxonomy,1,2,3 including a suggestion to split the giraffe into four species: Northern (Giraffa c. camelopardalis), Reticulated (G. c. reticulata), Masai (G. c. tippelskirchi), and Southern giraffes (G. c. giraffa).4,5,6 However, their evolutionary history is not yet fully resolved, as previous studies used a simple bifurcating model and did not explore the presence or extent of gene flow between lineages. We therefore inferred a model that incorporates various evolutionary processes to assess the drivers of contemporary giraffe diversity. We analyzed whole-genome sequencing data from 90 wild giraffes from 29 localities across their current distribution. The most basal divergence was dated to 280 kya. Genetic differentiation, FST, among major lineages ranged between 0.28 and 0.62, and we found significant levels of ancient gene flow between them. In particular, several analyses suggested that the Reticulated lineage evolved through admixture, with almost equal contribution from the Northern lineage and an ancestral lineage related to Masai and Southern giraffes. These new results highlight a scenario of strong differentiation despite gene flow, providing further context for the interpretation of giraffe diversity and the process of speciation in general. They also illustrate that conservation measures need to target various lineages and sublineages and that separate management strategies are needed to conserve giraffe diversity effectively. Given local extinctions and recent dramatic declines in many giraffe populations, this improved understanding of giraffe evolutionary history is relevant for conservation interventions, including reintroductions and reinforcements of existing populations.
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Affiliation(s)
- Laura D Bertola
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Liam Quinn
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Renzo F Balboa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jonas Meisner
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bøggild
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xi Wang
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Long Lin
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Casia Nursyifa
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xiaodong Liu
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Zilong Li
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mumbi Chege
- Institute of Environmental Sciences (CML), Leiden University, Leiden, The Netherlands; Wildlife Research and Training Institute, Naivasha, Kenya
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
| | | | - Josiah Kuja
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Morris Agaba
- School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Nelson Mandela Road, Arusha, Tanzania
| | - Cindy G Santander
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Vincent Muwanika
- College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Charles Masembe
- College of Natural Sciences, Makerere University, P O. Box 7062, Kampala, Uganda
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | | | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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18
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Roycroft E, Ford F, Ramm T, Schembri R, Breed WG, Burns PA, Rowe KC, Moritz C. Speciation across biomes: Rapid diversification with reproductive isolation in the Australian delicate mice. Mol Ecol 2024; 33:e17301. [PMID: 38385302 DOI: 10.1111/mec.17301] [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: 10/17/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
Phylogeographic studies of continental clades, especially when combined with palaeoclimate modelling, provide powerful insight into how environment drives speciation across climatic contexts. Australia, a continent characterized by disparate modern biomes and dynamic climate change, provides diverse opportunity to reconstruct the impact of past and present environments on diversification. Here, we use genomic-scale data (1310 exons and whole mitogenomes from 111 samples) to investigate Pleistocene diversification, cryptic diversity, and secondary contact in the Australian delicate mice (Hydromyini: Pseudomys), a recent radiation spanning almost all Australian environments. Across northern Australia, we find no evidence for introgression between cryptic lineages within Pseudomys delicatulus sensu lato, with palaeoclimate models supporting contraction and expansion of suitable habitat since the last glacial maximum. Despite multiple contact zones, we also find little evidence of introgression at a continental scale, with the exception of a potential hybrid zone in the mesic biome. In the arid zone, combined insights from genetic data and palaeomodels support a recent expansion in the arid specialist P. hermannsburgensis and contraction in the semi-arid P. bolami. In the face of repeated secondary contact, differences in sperm morphology and chromosomal rearrangements are potential mechanisms that maintain species boundaries in these recently diverged species. Additionally, we describe the western delicate mouse as a new species and recommend taxonomic reinstatement of the eastern delicate mouse. Overall, we show that speciation in an evolutionarily young and widespread clade has been driven by environmental change, and potentially maintained by divergence in reproductive morphology and chromosome rearrangements.
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Affiliation(s)
- Emily Roycroft
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
| | - Fred Ford
- Biodiversity Conservation and Science, New South Wales Department of Planning and Environment, Queanbeyan, New South Wales, Australia
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Till Ramm
- Zoo Leipzig, Leipzig, Germany
- Museum für Naturkunde Berlin, Berlin, Germany
| | - Rhiannon Schembri
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
- School of Natural Sciences, Macquarie University, Macquarie Park, New South Wales, Australia
| | - William G Breed
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Phoebe A Burns
- Wildlife Conservation and Science, Zoos Victoria, Parkville, Victoria, Australia
| | - Kevin C Rowe
- Sciences Department, Museums Victoria, Melbourne, Victoria, Australia
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Craig Moritz
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australian Capital Territory, Australia
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19
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Bohutínská M, Peichel CL. Divergence time shapes gene reuse during repeated adaptation. Trends Ecol Evol 2024; 39:396-407. [PMID: 38155043 DOI: 10.1016/j.tree.2023.11.007] [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: 08/10/2023] [Revised: 11/15/2023] [Accepted: 11/20/2023] [Indexed: 12/30/2023]
Abstract
When diverse lineages repeatedly adapt to similar environmental challenges, the extent to which the same genes are involved (gene reuse) varies across systems. We propose that divergence time among lineages is a key factor driving this variability: as lineages diverge, the extent of gene reuse should decrease due to reductions in allele sharing, functional differentiation among genes, and restructuring of genome architecture. Indeed, we show that many genomic studies of repeated adaptation find that more recently diverged lineages exhibit higher gene reuse during repeated adaptation, but the relationship becomes less clear at older divergence time scales. Thus, future research should explore the factors shaping gene reuse and their interplay across broad divergence time scales for a deeper understanding of evolutionary repeatability.
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Affiliation(s)
- Magdalena Bohutínská
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland; Department of Botany, Faculty of Science, Charles University, Prague, 12800, Czech Republic.
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, 3012, Switzerland
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20
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Jay P, Aubier TG, Joron M. The interplay of local adaptation and gene flow may lead to the formation of supergenes. Mol Ecol 2024:e17297. [PMID: 38415327 DOI: 10.1111/mec.17297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 12/28/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024]
Abstract
Supergenes are genetic architectures resulting in the segregation of alternative combinations of alleles underlying complex phenotypes. The co-segregation of alleles at linked loci is often facilitated by polymorphic chromosomal rearrangements suppressing recombination locally. Supergenes are involved in many complex polymorphisms, including sexual, colour or behavioural polymorphisms in numerous plants, fungi, mammals, fish, and insects. Despite a long history of empirical and theoretical research, the formation of supergenes remains poorly understood. Here, using a two-island population genetic model, we explore how gene flow and the evolution of overdominant chromosomal inversions may jointly lead to the formation of supergenes. We show that the evolution of inversions in differentiated populations, both under disruptive selection, leads to an increase in frequency of poorly adapted, immigrant haplotypes. Indeed, rare allelic combinations, such as immigrant haplotypes, are more frequently reshuffled by recombination than common allelic combinations, and therefore benefit from the recombination suppression generated by inversions. When an inversion capturing a locally adapted haplotype spreads but is associated with a fitness cost hampering its fixation (e.g. a recessive mutation load), the maintenance of a non-inverted haplotype in the population is enhanced; under certain conditions, the immigrant haplotype persists alongside the inverted local haplotype, while the standard local haplotype disappears. This establishes a stable, local polymorphism with two non-recombining haplotypes encoding alternative adaptive strategies, that is, a supergene. These results bring new light to the importance of local adaptation, overdominance, and gene flow in the formation of supergenes and inversion polymorphisms in general.
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Affiliation(s)
- Paul Jay
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
- Center for GeoGenetics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas G Aubier
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), Université de Toulouse, CNRS, IRD, Toulouse INP, Université Toulouse 3 - Paul Sabatier (UT3), Toulouse, France
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
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21
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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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22
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Wang X, Xiao Y, Lv YW, He ZH, Yeh FC, Hu XS. A Community-Based Framework Integrates Interspecific Interactions into Forest Genetic Conservation. PLANTS (BASEL, SWITZERLAND) 2024; 13:435. [PMID: 38337968 PMCID: PMC10856838 DOI: 10.3390/plants13030435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Forest genetic conservation is typically species-specific and does not integrate interspecific interaction and community structure. It mainly focuses on the theories of population and quantitative genetics. This approach depicts the intraspecific patterns of population genetic structure derived from genetic markers and the genetic differentiation of adaptive quantitative traits in provenance trials. However, it neglects possible interspecific interaction in natural forests and overlooks natural hybridization or subspeciation. We propose that the genetic diversity of a given species in a forest community is shaped by both intraspecific population and interspecific community evolutionary processes, and expand the traditional forest genetic conservation concept under the community ecology framework. We show that a community-specific phylogeny derived from molecular markers would allow us to explore the genetic mechanisms of a tree species interacting with other resident species. It would also facilitate the exploration of a species' ecological role in forest community assembly and the taxonomic relationship of the species with other species specific to its resident forest community. Phylogenetic β-diversity would assess the similarities and differences of a tree species across communities regarding ecological function, the strength of selection pressure, and the nature and extent of its interaction with other species. Our forest genetic conservation proposal that integrates intraspecific population and interspecific community genetic variations is suitable for conserving a taxonomic species complex and maintaining its evolutionary potential in natural forests. This provides complementary information to conventional population and quantitative genetics-based conservation strategies.
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Affiliation(s)
- Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Francis C. Yeh
- Department of Renewable Resources, University of Alberta, 751 General Service Building, Edmonton, AB T6G 2H1, Canada;
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
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23
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Ray DD, Flagel L, Schrider DR. IntroUNET: Identifying introgressed alleles via semantic segmentation. PLoS Genet 2024; 20:e1010657. [PMID: 38377104 PMCID: PMC10906877 DOI: 10.1371/journal.pgen.1010657] [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: 02/06/2023] [Revised: 03/01/2024] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
A growing body of evidence suggests that gene flow between closely related species is a widespread phenomenon. Alleles that introgress from one species into a close relative are typically neutral or deleterious, but sometimes confer a significant fitness advantage. Given the potential relevance to speciation and adaptation, numerous methods have therefore been devised to identify regions of the genome that have experienced introgression. Recently, supervised machine learning approaches have been shown to be highly effective for detecting introgression. One especially promising approach is to treat population genetic inference as an image classification problem, and feed an image representation of a population genetic alignment as input to a deep neural network that distinguishes among evolutionary models (i.e. introgression or no introgression). However, if we wish to investigate the full extent and fitness effects of introgression, merely identifying genomic regions in a population genetic alignment that harbor introgressed loci is insufficient-ideally we would be able to infer precisely which individuals have introgressed material and at which positions in the genome. Here we adapt a deep learning algorithm for semantic segmentation, the task of correctly identifying the type of object to which each individual pixel in an image belongs, to the task of identifying introgressed alleles. Our trained neural network is thus able to infer, for each individual in a two-population alignment, which of those individual's alleles were introgressed from the other population. We use simulated data to show that this approach is highly accurate, and that it can be readily extended to identify alleles that are introgressed from an unsampled "ghost" population, performing comparably to a supervised learning method tailored specifically to that task. Finally, we apply this method to data from Drosophila, showing that it is able to accurately recover introgressed haplotypes from real data. This analysis reveals that introgressed alleles are typically confined to lower frequencies within genic regions, suggestive of purifying selection, but are found at much higher frequencies in a region previously shown to be affected by adaptive introgression. Our method's success in recovering introgressed haplotypes in challenging real-world scenarios underscores the utility of deep learning approaches for making richer evolutionary inferences from genomic data.
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Affiliation(s)
- Dylan D. Ray
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lex Flagel
- Division of Data Science, Gencove Inc., New York, New York, United States of America
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota, United States of America
| | - Daniel R. Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
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24
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Ray DD, Flagel L, Schrider DR. IntroUNET: identifying introgressed alleles via semantic segmentation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.02.07.527435. [PMID: 36865105 PMCID: PMC9979274 DOI: 10.1101/2023.02.07.527435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
A growing body of evidence suggests that gene flow between closely related species is a widespread phenomenon. Alleles that introgress from one species into a close relative are typically neutral or deleterious, but sometimes confer a significant fitness advantage. Given the potential relevance to speciation and adaptation, numerous methods have therefore been devised to identify regions of the genome that have experienced introgression. Recently, supervised machine learning approaches have been shown to be highly effective for detecting introgression. One especially promising approach is to treat population genetic inference as an image classification problem, and feed an image representation of a population genetic alignment as input to a deep neural network that distinguishes among evolutionary models (i.e. introgression or no introgression). However, if we wish to investigate the full extent and fitness effects of introgression, merely identifying genomic regions in a population genetic alignment that harbor introgressed loci is insufficient-ideally we would be able to infer precisely which individuals have introgressed material and at which positions in the genome. Here we adapt a deep learning algorithm for semantic segmentation, the task of correctly identifying the type of object to which each individual pixel in an image belongs, to the task of identifying introgressed alleles. Our trained neural network is thus able to infer, for each individual in a two-population alignment, which of those individual's alleles were introgressed from the other population. We use simulated data to show that this approach is highly accurate, and that it can be readily extended to identify alleles that are introgressed from an unsampled "ghost" population, performing comparably to a supervised learning method tailored specifically to that task. Finally, we apply this method to data from Drosophila, showing that it is able to accurately recover introgressed haplotypes from real data. This analysis reveals that introgressed alleles are typically confined to lower frequencies within genic regions, suggestive of purifying selection, but are found at much higher frequencies in a region previously shown to be affected by adaptive introgression. Our method's success in recovering introgressed haplotypes in challenging real-world scenarios underscores the utility of deep learning approaches for making richer evolutionary inferences from genomic data.
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Affiliation(s)
- Dylan D. Ray
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lex Flagel
- Division of Data Science, Gencove Inc., New York, NY 11101, USA
- Department of Plant and Microbial Biology, University of Minnesota, St Paul MN, 55108, USA
| | - Daniel R. Schrider
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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25
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Caetano DS, Quental TB. How Important Is Budding Speciation for Comparative Studies? Syst Biol 2023; 72:1443-1453. [PMID: 37586404 DOI: 10.1093/sysbio/syad050] [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: 05/30/2022] [Revised: 07/26/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023] Open
Abstract
The acknowledgment of evolutionary dependence among species has fundamentally changed how we ask biological questions. Phylogenetic models became the standard approach for studies with 3 or more lineages, in particular those using extant species. Most phylogenetic comparative methods (PCMs) translate relatedness into covariance, meaning that evolutionary changes before lineages split should be interpreted together whereas after the split lineages are expected to change independently. This clever realization has shaped decades of research. Here, we discuss one element of the comparative method often ignored or assumed as unimportant: if nodes of a phylogeny represent the dissolution of the ancestral lineage into two new ones or if the ancestral lineage can survive speciation events (i.e., budding). Budding speciation is often reported in paleontological studies, due to the nature of the evidence for budding in the fossil record, but it is surprisingly absent in comparative methods. Here, we show that many PCMs assume that divergence happens as a symmetric split, even if these methods do not explicitly mention this assumption. We discuss the properties of trait evolution models for continuous and discrete traits and their adequacy under a scenario of budding speciation. We discuss the effects of budding speciation under a series of plausible evolutionary scenarios and show when and how these can influence our estimates. We also propose that long-lived lineages that have survived through a series of budding speciation events and given birth to multiple new lineages can produce evolutionary patterns that challenge our intuition about the most parsimonious history of trait changes in a clade. We hope our discussion can help bridge comparative approaches in paleontology and neontology as well as foster awareness about the assumptions we make when we use phylogenetic trees.
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Affiliation(s)
- Daniel S Caetano
- Department of Biological Sciences, Towson University, 8000 York Road, Towson, MD 21252, USA
- Department of Ecology, University of São Paulo, Rua do Matão, 321 - Trav. 14, São Paulo, SP, 05508-090, Brazil
| | - Tiago B Quental
- Department of Ecology, University of São Paulo, Rua do Matão, 321 - Trav. 14, São Paulo, SP, 05508-090, Brazil
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26
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Hensen N, Bonometti L, Westerberg I, Brännström IO, Guillou S, Cros-Aarteil S, Calhoun S, Haridas S, Kuo A, Mondo S, Pangilinan J, Riley R, LaButti K, Andreopoulos B, Lipzen A, Chen C, Yan M, Daum C, Ng V, Clum A, Steindorff A, Ohm RA, Martin F, Silar P, Natvig DO, Lalanne C, Gautier V, Ament-Velásquez SL, Kruys Å, Hutchinson MI, Powell AJ, Barry K, Miller AN, Grigoriev IV, Debuchy R, Gladieux P, Hiltunen Thorén M, Johannesson H. Genome-scale phylogeny and comparative genomics of the fungal order Sordariales. Mol Phylogenet Evol 2023; 189:107938. [PMID: 37820761 DOI: 10.1016/j.ympev.2023.107938] [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: 06/26/2023] [Revised: 09/28/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
The order Sordariales is taxonomically diverse, and harbours many species with different lifestyles and large economic importance. Despite its importance, a robust genome-scale phylogeny, and associated comparative genomic analysis of the order is lacking. In this study, we examined whole-genome data from 99 Sordariales, including 52 newly sequenced genomes, and seven outgroup taxa. We inferred a comprehensive phylogeny that resolved several contentious relationships amongst families in the order, and cleared-up intrafamily relationships within the Podosporaceae. Extensive comparative genomics showed that genomes from the three largest families in the dataset (Chaetomiaceae, Podosporaceae and Sordariaceae) differ greatly in GC content, genome size, gene number, repeat percentage, evolutionary rate, and genome content affected by repeat-induced point mutations (RIP). All genomic traits showed phylogenetic signal, and ancestral state reconstruction revealed that the variation of the properties stems primarily from within-family evolution. Together, the results provide a thorough framework for understanding genome evolution in this important group of fungi.
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Affiliation(s)
- Noah Hensen
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden
| | - Lucas Bonometti
- University of Montpellier, PHIM Plant Health Institute, Montpellier, France
| | - Ivar Westerberg
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden
| | - Ioana Onut Brännström
- Oslo University, Natural History Museum, Oslo, Norway; Uppsala University, Department of Ecology and Genetics, Uppsala, Sweden
| | - Sonia Guillou
- University of Montpellier, PHIM Plant Health Institute, Montpellier, France
| | | | - Sara Calhoun
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Sajeet Haridas
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Alan Kuo
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Stephen Mondo
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Jasmyn Pangilinan
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Robert Riley
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Kurt LaButti
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Bill Andreopoulos
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Cindy Chen
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Mi Yan
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Chris Daum
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Alicia Clum
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Andrei Steindorff
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Robin A Ohm
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | | | - Philippe Silar
- Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France
| | - Donald O Natvig
- University of New Mexico, Department of Biology, Albuquerque, USA
| | - Christophe Lalanne
- Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France
| | - Valérie Gautier
- Université de Paris Cité, Laboratoire Interdisciplinaire des Energies de Demain, Paris, France
| | | | - Åsa Kruys
- Uppsala University, Museum of Evolution, Uppsala, Sweden
| | | | - Amy Jo Powell
- Sandia National Laboratories, Dept. of Systems Design and Architecture, Albuquerque, USA
| | - Kerrie Barry
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA
| | - Andrew N Miller
- University of Illinois Urbana-Champaign, Illinois Natural History Survey, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute, Berkeley, CA, USA; University of California Berkeley, Department of Plant and Microbial Biology, Berkeley, CA, USA
| | - Robert Debuchy
- Université Paris-Saclay, Institute for Integrative Biology of the Cell, Gif-sur-Yvette, France
| | - Pierre Gladieux
- University of Montpellier, PHIM Plant Health Institute, Montpellier, France
| | - Markus Hiltunen Thorén
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden; The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Hanna Johannesson
- Stockholm University, Department of Ecology, Environment and Plants Sciences, Stockholm, Sweden; The Royal Swedish Academy of Sciences, Stockholm, Sweden.
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27
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Porretta D, Canestrelli D. The ecological importance of hybridization. Trends Ecol Evol 2023; 38:1097-1108. [PMID: 37620217 DOI: 10.1016/j.tree.2023.07.003] [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: 03/12/2023] [Revised: 07/16/2023] [Accepted: 07/20/2023] [Indexed: 08/26/2023]
Abstract
Hybridization as an evolutionary process has been studied in depth over the past few decades. Research has focused on its role in shaping reproductive barriers, its adaptive value, and its genomic consequences. In contrast, our knowledge of ecological dimensions of hybridization is still in its infancy, despite hybridization being an inherently ecological interaction. Using examples from various organisms, we show that hybridization can affect and be affected by non-reproductive interactions, including predation, competition, parasitism, mutualism, commensalism, and organism-environment interactions, with significant implications for community structure and ecosystem functioning. However, since these dimensions of hybridization have mostly been revealed from studies designed to decipher other evolutionary processes, we argue that much of the eco-evolutionary importance of hybridization is yet to be discovered.
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Affiliation(s)
- Daniele Porretta
- Department of Environmental Biology, Sapienza University of Rome, Italy.
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28
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Fogg J, Allman ES, Ané C. PhyloCoalSimulations: A Simulator for Network Multispecies Coalescent Models, Including a New Extension for the Inheritance of Gene Flow. Syst Biol 2023; 72:1171-1179. [PMID: 37254872 DOI: 10.1093/sysbio/syad030] [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: 01/11/2023] [Revised: 05/03/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2023] Open
Abstract
We consider the evolution of phylogenetic gene trees along phylogenetic species networks, according to the network multispecies coalescent process, and introduce a new network coalescent model with correlated inheritance of gene flow. This model generalizes two traditional versions of the network coalescent: with independent or common inheritance. At each reticulation, multiple lineages of a given locus are inherited from parental populations chosen at random, either independently across lineages or with positive correlation according to a Dirichlet process. This process may account for locus-specific probabilities of inheritance, for example. We implemented the simulation of gene trees under these network coalescent models in the Julia package PhyloCoalSimulations, which depends on PhyloNetworks and its powerful network manipulation tools. Input species phylogenies can be read in extended Newick format, either in numbers of generations or in coalescent units. Simulated gene trees can be written in Newick format, and in a way that preserves information about their embedding within the species network. This embedding can be used for downstream purposes, such as to simulate species-specific processes like rate variation across species, or for other scenarios as illustrated in this note. This package should be useful for simulation studies and simulation-based inference methods. The software is available open source with documentation and a tutorial at https://github.com/cecileane/PhyloCoalSimulations.jl.
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Affiliation(s)
- John Fogg
- Department of Statistics, University of Wisconsin - Madison, WI, 53706, USA
| | - Elizabeth S Allman
- Department of Mathematics and Statistics, University of Alaska - Fairbanks, AK, 99775, USA
| | - Cécile Ané
- Department of Statistics, University of Wisconsin - Madison, WI, 53706, USA
- Department of Botany, University of Wisconsin - Madison, WI, 53706, USA
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29
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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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30
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Roberts WR, Ruck EC, Downey KM, Pinseel E, Alverson AJ. Resolving Marine-Freshwater Transitions by Diatoms Through a Fog of Gene Tree Discordance. Syst Biol 2023; 72:984-997. [PMID: 37335140 DOI: 10.1093/sysbio/syad038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 06/02/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023] Open
Abstract
Despite the obstacles facing marine colonists, most lineages of aquatic organisms have colonized and diversified in freshwaters repeatedly. These transitions can trigger rapid morphological or physiological change and, on longer timescales, lead to increased rates of speciation and extinction. Diatoms are a lineage of ancestrally marine microalgae that have diversified throughout freshwater habitats worldwide. We generated a phylogenomic data set of genomes and transcriptomes for 59 diatom taxa to resolve freshwater transitions in one lineage, the Thalassiosirales. Although most parts of the species tree were consistently resolved with strong support, we had difficulties resolving a Paleocene radiation, which affected the placement of one freshwater lineage. This and other parts of the tree were characterized by high levels of gene tree discordance caused by incomplete lineage sorting and low phylogenetic signal. Despite differences in species trees inferred from concatenation versus summary methods and codons versus amino acids, traditional methods of ancestral state reconstruction supported six transitions into freshwaters, two of which led to subsequent species diversification. Evidence from gene trees, protein alignments, and diatom life history together suggest that habitat transitions were largely the product of homoplasy rather than hemiplasy, a condition where transitions occur on branches in gene trees not shared with the species tree. Nevertheless, we identified a set of putatively hemiplasious genes, many of which have been associated with shifts to low salinity, indicating that hemiplasy played a small but potentially important role in freshwater adaptation. Accounting for differences in evolutionary outcomes, in which some taxa became locked into freshwaters while others were able to return to the ocean or become salinity generalists, might help further distinguish different sources of adaptive mutation in freshwater diatoms.
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Affiliation(s)
- Wade R Roberts
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Elizabeth C Ruck
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Kala M Downey
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Eveline Pinseel
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
| | - Andrew J Alverson
- Department of Biological Sciences, University of Arkansas, 1 University of Arkansas, Fayetteville, AR, 72701, USA
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Flouri T, Jiao X, Huang J, Rannala B, Yang Z. Efficient Bayesian inference under the multispecies coalescent with migration. Proc Natl Acad Sci U S A 2023; 120:e2310708120. [PMID: 37871206 PMCID: PMC10622872 DOI: 10.1073/pnas.2310708120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/15/2023] [Indexed: 10/25/2023] Open
Abstract
Analyses of genome sequence data have revealed pervasive interspecific gene flow and enriched our understanding of the role of gene flow in speciation and adaptation. Inference of gene flow using genomic data requires powerful statistical methods. Yet current likelihood-based methods involve heavy computation and are feasible for small datasets only. Here, we implement the multispecies-coalescent-with-migration model in the Bayesian program bpp, which can be used to test for gene flow and estimate migration rates, as well as species divergence times and population sizes. We develop Markov chain Monte Carlo algorithms for efficient sampling from the posterior, enabling the analysis of genome-scale datasets with thousands of loci. Implementation of both introgression and migration models in the same program allows us to test whether gene flow occurred continuously over time or in pulses. Analyses of genomic data from Anopheles mosquitoes demonstrate rich information in typical genomic datasets about the mode and rate of gene flow.
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Affiliation(s)
- Tomáš Flouri
- Department of Genetics, Evolution, and Environment, University College London, LondonWC1E 6BT, United Kingdom
| | - Xiyun Jiao
- Department of Statistics and Data Science, China Southern University of Science and Technology, Shenzhen518055, China
| | - Jun Huang
- Department of Intelligent Medical Engineering, School of Biomedical Engineering, Capital Medical University, Beijing100069, China
| | - Bruce Rannala
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Ziheng Yang
- Department of Genetics, Evolution, and Environment, University College London, LondonWC1E 6BT, United Kingdom
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32
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Coimbra RTF, Winter S, Muneza A, Fennessy S, Otiende M, Mijele D, Masiaine S, Stacy-Dawes J, Fennessy J, Janke A. Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biol 2023; 21:215. [PMID: 37833744 PMCID: PMC10576358 DOI: 10.1186/s12915-023-01722-y] [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: 02/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. RESULTS We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. CONCLUSIONS Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
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Affiliation(s)
- Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | | | | | | | | | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek, Namibia
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
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Yang F, Ge J, Guo Y, Olmstead R, Sun W. Deciphering complex reticulate evolution of Asian Buddleja (Scrophulariaceae): insights into the taxonomy and speciation of polyploid taxa in the Sino-Himalayan region. ANNALS OF BOTANY 2023; 132:15-28. [PMID: 36722368 PMCID: PMC10550280 DOI: 10.1093/aob/mcad022] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND AIMS Species of the genus Buddleja in Asia are mainly distributed in the Sino-Himalayan region and form a challenging taxonomic group, with extensive hybridization and polyploidization. A phylogenetic approach to unravelling the history of reticulation in this lineage will deepen our understanding of the speciation in biodiversity hotspots. METHODS For this study, we obtained 80 accessions representing all the species in the Asian Buddleja clade, and the ploidy level of each taxon was determined by flow cytometry analyses. Whole plastid genomes, nuclear ribosomal DNA, single nucleotide polymorphisms and a large number of low-copy nuclear genes assembled from genome skimming data were used to investigate the reticulate evolutionary history of Asian Buddleja. Complex cytonuclear conflicts were detected through a comparison of plastid and species trees. Gene tree incongruence was also analysed to detect any reticulate events in the history of this lineage. KEY RESULTS Six hybridization events were detected, which are able to explain the cytonuclear conflict in Asian Buddleja. Furthermore, PhyloNet analysis combining species ploidy data indicated several allopolyploid speciation events. A strongly supported species tree inferred from a large number of low-copy nuclear genes not only corrected some earlier misinterpretations, but also indicated that there are many Asian Buddleja species that have been lumped mistakenly. Divergent time estimation shows two periods of rapid diversification (8-10 and 0-3 Mya) in the Asian Buddleja clade, which might coincide with the final uplift of the Hengduan Mountains and Quaternary climate fluctuations, respectively. CONCLUSIONS This study presents a well-supported phylogenetic backbone for the Asian Buddleja species, elucidates their complex and reticulate evolutionary history and suggests that tectonic activity, climate fluctuations, polyploidization and hybridization together promoted the diversification of this lineage.
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Affiliation(s)
- Fengmao Yang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming 650201, Yunnan, China
| | - Jia Ge
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming 650201, Yunnan, China
| | - Yongjie Guo
- Germplasm Bank of Wild Species of China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Richard Olmstead
- Department of Biology and Burke Museum, University of Washington, Seattle, WA 98195, USA
| | - Weibang Sun
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming 650201, Yunnan, China
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Carscadden KA, Batstone RT, Hauser FE. Origins and evolution of biological novelty. Biol Rev Camb Philos Soc 2023; 98:1472-1491. [PMID: 37056155 DOI: 10.1111/brv.12963] [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: 01/28/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.
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Affiliation(s)
- Kelly A Carscadden
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St, Boulder, CO, 80309, USA
| | - Rebecca T Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
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Kamimura Y, Nishikawa M, Yamasako J. DNA barcoding of Japanese earwig species (Insecta, Dermaptera), with sequence diversity analyses of three species of Anisolabididae. Biodivers Data J 2023; 11:e107001. [PMID: 38318508 PMCID: PMC10840520 DOI: 10.3897/bdj.11.e107001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 09/19/2023] [Indexed: 02/07/2024] Open
Abstract
Dermaptera is a polyneopteran insect order that includes more than 2,000 described species, commonly known as earwigs, that mainly inhabit tropical, subtropical and warm temperate regions. Although 40 species have been found in Japan, their distribution and habitat preferences have remained ambiguous due to sample misidentification, particularly amongst immature specimens. To overcome this problem, we sequenced and analysed the DNA barcoding region of the mitochondrial cytochrome oxidase I gene (cox1) of dermapteran species recorded from Japan. Including publicly available data, 72.5% of known Japanese dermapteran species were subjected to molecular identification. We extensively sampled three wingless species of subfamily Anisolabidinae (Anisolabididae): Anisolabismaritima, Anisolabellamarginalis and Euborelliapallipes. Although these species exhibit similar habitat preferences as semi-synanthropes, A.maritima, a cosmopolitan species with the highest affinity to seashore, had significantly higher sequence diversity than the latter two species, which are considered endemic to East Asia. A similar trend was observed for (at least partly) winged cosmopolitan species of other families. Introgression with the congener Anisolabisseirokui is also suggested for A.maritima. Possible causes of the varying levels of sequence diversity are discussed.
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Affiliation(s)
| | - Masaru Nishikawa
- Ehime University, Matsuyama, JapanEhime UniversityMatsuyamaJapan
| | - Junsuke Yamasako
- National Agriculture and Food Research Organization, Tsukuba, JapanNational Agriculture and Food Research OrganizationTsukubaJapan
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36
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Kim J, Harris KD, Kim IK, Shemesh S, Messer PW, Greenbaum G. Incorporating ecology into gene drive modelling. Ecol Lett 2023; 26 Suppl 1:S62-S80. [PMID: 37840022 DOI: 10.1111/ele.14194] [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: 10/19/2022] [Revised: 02/13/2023] [Accepted: 02/15/2023] [Indexed: 10/17/2023]
Abstract
Gene drive technology, in which fast-spreading engineered drive alleles are introduced into wild populations, represents a promising new tool in the fight against vector-borne diseases, agricultural pests and invasive species. Due to the risks involved, gene drives have so far only been tested in laboratory settings while their population-level behaviour is mainly studied using mathematical and computational models. The spread of a gene drive is a rapid evolutionary process that occurs over timescales similar to many ecological processes. This can potentially generate strong eco-evolutionary feedback that could profoundly affect the dynamics and outcome of a gene drive release. We, therefore, argue for the importance of incorporating ecological features into gene drive models. We describe the key ecological features that could affect gene drive behaviour, such as population structure, life-history, environmental variation and mode of selection. We review previous gene drive modelling efforts and identify areas where further research is needed. As gene drive technology approaches the level of field experimentation, it is crucial to evaluate gene drive dynamics, potential outcomes, and risks realistically by including ecological processes.
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Affiliation(s)
- Jaehee Kim
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Keith D Harris
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isabel K Kim
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Shahar Shemesh
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, New York, USA
| | - Gili Greenbaum
- Department of Ecology, Evolution and Behavior, The Hebrew University of Jerusalem, Jerusalem, Israel
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37
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Burbrink FT, Harrington SM, Bobo D, Myers EA. Considering admixture when producing draft genomes: an example in North American ratsnakes (Pantherophis alleghaniensis/Pantherophis obsoletus). G3 (BETHESDA, MD.) 2023; 13:jkad113. [PMID: 37228097 PMCID: PMC10411579 DOI: 10.1093/g3journal/jkad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/27/2023]
Abstract
The number of reference genomes of snakes lags behind several other vertebrate groups (e.g. birds and mammals). However, in the last two years, a concerted effort by researchers from around the world has produced new genomes of snakes representing members from several new families. Here, we present a high-quality, annotated genome of the central ratsnake (Pantherophis alleghaniensis), a member of the most diverse snake lineage, Colubroidea. Pantherophis alleghaniensis is found in the central part of the Nearctic, east of the Mississippi River. This genome was sequenced using 10X Chromium synthetic long reads and polished using Illumina short reads. The final genome assembly had an N50 of 21.82 Mb and an L50 of 22 scaffolds with a maximum scaffold length of 82.078 Mb. The genome is composed of 49.24% repeat elements dominated by long interspersed elements. We annotated this genome using transcriptome assemblies from 14 tissue types and recovered 28,368 predicted proteins. Finally, we estimated admixture proportions between two species of ratsnakes and discovered that this specimen is an admixed individual containing genomes from the western (Pantherophis obsoletus) and central ratsnakes (P. alleghaniensis). We discuss the importance of considering interspecific admixture in downstream approaches for inferring demography and phylogeny.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
| | - Sean M Harrington
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
- INBRE Data Science Core, University of Wyoming, Laramie, WY 82071, USA
| | - Dean Bobo
- Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024, USA
| | - Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY 10024, USA
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA
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Folk RA, Gaynor ML, Engle-Wrye NJ, O’Meara BC, Soltis PS, Soltis DE, Guralnick RP, Smith SA, Grady CJ, Okuyama Y. Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method. Syst Biol 2023; 72:856-873. [PMID: 37073863 PMCID: PMC10405357 DOI: 10.1093/sysbio/syad018] [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: 08/26/2022] [Revised: 03/23/2023] [Accepted: 04/17/2023] [Indexed: 04/20/2023] Open
Abstract
Applications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.].
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Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Michelle L Gaynor
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Nicholas J Engle-Wrye
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Brian C O’Meara
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Robert P Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Charles J Grady
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA
| | - Yudai Okuyama
- Tsukuba Botanical Garden, National Museum of Nature and Science, Tsukuba, Japan
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Kinneberg VB, Lü DS, Peris D, Ravinet M, Skrede I. Introgression between highly divergent fungal sister species. J Evol Biol 2023; 36:1133-1149. [PMID: 37363874 DOI: 10.1111/jeb.14190] [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: 11/24/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
To understand how species evolve and adapt to changing environments, it is important to study gene flow and introgression due to their influence on speciation and radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The system is based on two fungal sister species with morphological and ecological similarities occurring in overlapping habitats. We examined introgression between these species by conducting whole genome sequencing of individuals from populations in North America and Europe. We assessed genome-wide nucleotide divergence and performed crossing experiments to study reproductive barriers. We further used ABBA-BABA statistics together with a network analysis to investigate introgression, and conducted demographic modelling to gain insight into divergence times and introgression events. The results revealed that the species are highly divergent and incompatible in vitro. Despite this, small regions of introgression were scattered throughout the genomes and one introgression event likely involves a ghost population (extant or extinct). This study demonstrates that introgression can be found among divergent species and that population histories can be studied without collections of all the populations involved. Moreover, the experimental system is shown to be a useful tool for research on reproductive isolation in natural populations.
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Affiliation(s)
- Vilde Bruhn Kinneberg
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Evolution and Paleobiology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Dabao Sun Lü
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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Langschied F, Leisegang MS, Brandes RP, Ebersberger I. ncOrtho: efficient and reliable identification of miRNA orthologs. Nucleic Acids Res 2023; 51:e71. [PMID: 37260093 PMCID: PMC10359484 DOI: 10.1093/nar/gkad467] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/04/2023] [Accepted: 05/30/2023] [Indexed: 06/02/2023] Open
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that finetune gene expression via translational repression or degradation of their target mRNAs. Despite their functional relevance, frameworks for the scalable and accurate detection of miRNA orthologs are missing. Consequently, there is still no comprehensive picture of how miRNAs and their associated regulatory networks have evolved. Here we present ncOrtho, a synteny informed pipeline for the targeted search of miRNA orthologs in unannotated genome sequences. ncOrtho matches miRNA annotations from multi-tissue transcriptomes in precision, while scaling to the analysis of hundreds of custom-selected species. The presence-absence pattern of orthologs to 266 human miRNA families across 402 vertebrate species reveals four bursts of miRNA acquisition, of which the most recent event occurred in the last common ancestor of higher primates. miRNA families are rarely modified or lost, but notable exceptions for both events exist. miRNA co-ortholog numbers faithfully indicate lineage-specific whole genome duplications, and miRNAs are powerful markers for phylogenomic analyses. Their exceptionally low genetic diversity makes them suitable to resolve clades where the phylogenetic signal is blurred by incomplete lineage sorting of ancestral alleles. In summary, ncOrtho allows to routinely consider miRNAs in evolutionary analyses that were thus far reserved to protein-coding genes.
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Affiliation(s)
- Felix Langschied
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt, Germany
- German Center of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University, Frankfurt, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
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Tukhbatullin A, Ermakov O, Kapustina S, Starikov V, Tambovtseva V, Titov S, Brandler O. Surrounded by Kindred: Spermophilus major Hybridization with Other Spermophilus Species in Space and Time. BIOLOGY 2023; 12:880. [PMID: 37372163 DOI: 10.3390/biology12060880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Among the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrel Spermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into the S. major range, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR, cytb) and nuclear (SmcY, BGN, PRKCI, c-myc, i6p53) markers, we determined the contribution of neighboring species to the S. major genome. We showed that 36% of S. major individuals had extraneous alleles. All peripheral species that were in contact with S. major contributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of the S. major genome implications of introgression highlights the importance of implementing conservation measures to protect this species.
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Affiliation(s)
- Andrey Tukhbatullin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Oleg Ermakov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Svetlana Kapustina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Vladimir Starikov
- Department of Biology and Biotechnology, Institute of Natural and Technical Sciences, Surgut State University, Lenin Avenue 1, Surgut 628412, Russia
| | - Valentina Tambovtseva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Sergey Titov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Oleg Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
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Slovák M, Melichárková A, Štubňová EG, Kučera J, Mandáková T, Smyčka J, Lavergne S, Passalacqua NG, Vďačný P, Paun O. Pervasive Introgression During Rapid Diversification of the European Mountain Genus Soldanella (L.) (Primulaceae). Syst Biol 2023; 72:491-504. [PMID: 36331548 PMCID: PMC10276626 DOI: 10.1093/sysbio/syac071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 03/19/2024] Open
Abstract
Hybridization is a key mechanism involved in lineage diversification and speciation, especially in ecosystems that experienced repeated environmental oscillations. Recently radiated plant groups, which have evolved in mountain ecosystems impacted by historical climate change provide an excellent model system for studying the impact of gene flow on speciation. We combined organellar (whole-plastome) and nuclear genomic data (RAD-seq) with a cytogenetic approach (rDNA FISH) to investigate the effects of hybridization and introgression on evolution and speciation in the genus Soldanella (snowbells, Primulaceae). Pervasive introgression has already occurred among ancestral lineages of snowbells and has persisted throughout the entire evolutionary history of the genus, regardless of the ecology, cytotype, or distribution range size of the affected species. The highest extent of introgression has been detected in the Carpathian species, which is also reflected in their extensive karyotype variation. Introgression occurred even between species with dysploid and euploid cytotypes, which were considered to be reproductively isolated. The magnitude of introgression detected in snowbells is unprecedented in other mountain genera of the European Alpine System investigated hitherto. Our study stresses the prominent evolutionary role of hybridization in facilitating speciation and diversification on the one hand, but also enriching previously isolated genetic pools. [chloroplast capture; diversification; dysploidy; European Alpine system; introgression; nuclear-cytoplasmic discordance; ribosomal DNA.].
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Affiliation(s)
- Marek Slovák
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Department of Botany, Charles University, Prague, Czech Republic
| | - Andrea Melichárková
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Eliška Gbúrová Štubňová
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
- Slovak National Museum, Natural History Museum, Bratislava, Slovakia
| | - Jaromír Kučera
- Department of Evolution and Systematics, Plant Science and Biodiversity Centre, Slovak Academy of Sciences, Institute of Botany, Bratislava, Slovakia
| | - Terezie Mandáková
- Central European Institute of Technology, Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-625 00 Brno, Czech Republic
| | - Jan Smyčka
- Department of Botany, Charles University, Prague, Czech Republic
- Center for Theoretical Study, Charles University and the Academy of Sciences of the Czech Republic, Jilská 1, 110 00 Praha, Czech Republic
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | - Sébastien Lavergne
- Université Grenoble Alpes, University of Savoie Mont Blanc, CNRS, Grenoble, France
| | | | - Peter Vďačný
- Department of Zoology, Comenius University in Bratislava, Bratislava, Slovakia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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Ji J, Jackson DJ, Leaché AD, Yang Z. Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks. Syst Biol 2023; 72:446-465. [PMID: 36504374 PMCID: PMC10275556 DOI: 10.1093/sysbio/syac077] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 11/15/2022] [Accepted: 12/01/2022] [Indexed: 10/25/2023] Open
Abstract
In the past two decades, genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HYDE to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program BPP to re-analyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HYDE and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid-speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data. [Bayesian test; BPP; chipmunks; introgression; MSci; multispecies coalescent; Savage-Dickey density ratio.].
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Affiliation(s)
- Jiayi Ji
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Donavan J Jackson
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Box 351800, Seattle, WA 98195-1800, USA
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
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Leal JL, Milesi P, Salojärvi J, Lascoux M. Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences. Syst Biol 2023; 72:372-390. [PMID: 36932679 PMCID: PMC10275558 DOI: 10.1093/sysbio/syad009] [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: 01/05/2022] [Revised: 10/14/2022] [Accepted: 03/10/2023] [Indexed: 03/19/2023] Open
Abstract
Phylogenetic analysis of polyploid hybrid species has long posed a formidable challenge as it requires the ability to distinguish between alleles of different ancestral origins in order to disentangle their individual evolutionary history. This problem has been previously addressed by conceiving phylogenies as reticulate networks, using a two-step phasing strategy that first identifies and segregates homoeologous loci and then, during a second phasing step, assigns each gene copy to one of the subgenomes of an allopolyploid species. Here, we propose an alternative approach, one that preserves the core idea behind phasing-to produce separate nucleotide sequences that capture the reticulate evolutionary history of a polyploid-while vastly simplifying its implementation by reducing a complex multistage procedure to a single phasing step. While most current methods used for phylogenetic reconstruction of polyploid species require sequencing reads to be pre-phased using experimental or computational methods-usually an expensive, complex, and/or time-consuming endeavor-phasing executed using our algorithm is performed directly on the multiple-sequence alignment (MSA), a key change that allows for the simultaneous segregation and sorting of gene copies. We introduce the concept of genomic polarization that, when applied to an allopolyploid species, produces nucleotide sequences that capture the fraction of a polyploid genome that deviates from that of a reference sequence, usually one of the other species present in the MSA. We show that if the reference sequence is one of the parental species, the polarized polyploid sequence has a close resemblance (high pairwise sequence identity) to the second parental species. This knowledge is harnessed to build a new heuristic algorithm where, by replacing the allopolyploid genomic sequence in the MSA by its polarized version, it is possible to identify the phylogenetic position of the polyploid's ancestral parents in an iterative process. The proposed methodology can be used with long-read and short-read high-throughput sequencing data and requires only one representative individual for each species to be included in the phylogenetic analysis. In its current form, it can be used in the analysis of phylogenies containing tetraploid and diploid species. We test the newly developed method extensively using simulated data in order to evaluate its accuracy. We show empirically that the use of polarized genomic sequences allows for the correct identification of both parental species of an allotetraploid with up to 97% certainty in phylogenies with moderate levels of incomplete lineage sorting (ILS) and 87% in phylogenies containing high levels of ILS. We then apply the polarization protocol to reconstruct the reticulate histories of Arabidopsis kamchatica and Arabidopsis suecica, two allopolyploids whose ancestry has been well documented. [Allopolyploidy; Arabidopsis; genomic polarization; homoeologs; incomplete lineage sorting; phasing; polyploid phylogenetics; reticulate evolution.].
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Affiliation(s)
- J Luis Leal
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Pascal Milesi
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, P.O. Box 65 (Viikinkaari 1), 00014 Helsinki, Finland
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Martin Lascoux
- Plant Ecology and Evolution, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
- Science for Life Laboratory (SciLifeLab), Uppsala University, 75237 Uppsala, Sweden
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45
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Hibbins MS, Breithaupt LC, Hahn MW. Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance. Proc Natl Acad Sci U S A 2023; 120:e2220389120. [PMID: 37216509 PMCID: PMC10235958 DOI: 10.1073/pnas.2220389120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for the study of trait evolution across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating phylogenetic tree describing the shared history among species. However, modern phylogenomic analyses have shown that genomes are often composed of mosaic histories that can disagree both with the species tree and with each other-so-called discordant gene trees. These gene trees describe shared histories that are not captured by the species tree, and therefore that are unaccounted for in classic comparative approaches. The application of standard comparative methods to species histories containing discordance leads to incorrect inferences about the timing, direction, and rate of evolution. Here, we develop two approaches for incorporating gene tree histories into comparative methods: one that constructs an updated phylogenetic variance-covariance matrix from gene trees, and another that applies Felsenstein's pruning algorithm over a set of gene trees to calculate trait histories and likelihoods. Using simulation, we demonstrate that our approaches generate much more accurate estimates of tree-wide rates of trait evolution than standard methods. We apply our methods to two clades of the wild tomato genus Solanum with varying rates of discordance, demonstrating the contribution of gene tree discordance to variation in a set of floral traits. Our approaches have the potential to be applied to a broad range of classic inference problems in phylogenetics, including ancestral state reconstruction and the inference of lineage-specific rate shifts.
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Affiliation(s)
- Mark S. Hibbins
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ONM5S 3B2, Canada
- Department of Biology, Indiana University, Bloomington, IN47405
| | - Lara C. Breithaupt
- Department of Biology, Indiana University, Bloomington, IN47405
- Department of Computer Science, Duke University, Durham, NC27710
| | - Matthew W. Hahn
- Department of Biology, Indiana University, Bloomington, IN47405
- Department of Computer Science, Indiana University, Bloomington, IN47405
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46
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Amorim JA, de Oliveira TMP, de Sá ILR, da Silva TP, Sallum MAM. DNA Barcodes of Mansonia ( Mansonia) Blanchard, 1901 (Diptera, Culicidae). Genes (Basel) 2023; 14:1127. [PMID: 37372310 DOI: 10.3390/genes14061127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
Females of the genus Mansonia feed on the blood of humans, livestock, and other vertebrates to develop their eggs. The females' biting behavior may cause severe disturbance to blood hosts, with a negative impact on public health and economics. Certain species have been identified as potential or effective disease vectors. The accurate species identification of field-collected specimens is of paramount importance for the success of monitoring and control strategies. Mansonia (Mansonia) morphological species boundaries are blurred by patterns of intraspecific heteromorphism and interspecific isomorphism. DNA barcodes can help to solve taxonomic controversies, especially if combined with other molecular tools. We used cytochrome c oxidase subunit I (COI) gene 5' end (DNA barcode) sequences to identify 327 field-collected specimens of Mansonia (Mansonia) spp. The sampling encompassed males and females collected from three Brazilian regions and previously assigned to species based on their morphological characteristics. Eleven GenBank and BOLD sequences were added to the DNA barcode analyses. Initial morphospecies assignments were mostly corroborated by the results of five clustering methods based on Kimura two-parameter distance and maximum likelihood phylogeny. Five to eight molecular operational taxonomic units may represent taxonomically unknown species. The first DNA barcode records for Mansonia fonsecai, Mansonia iguassuensis, and Mansonia pseudotitillans are presented.
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Affiliation(s)
- Jandui Almeida Amorim
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, SP, Brazil
- Departamento de Ciências e Matemática, Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, São Paulo 01109-010, SP, Brazil
| | | | - Ivy Luizi Rodrigues de Sá
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, SP, Brazil
| | - Taires Peniche da Silva
- Laboratório de Entomologia Médica, Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá, Macapá 68903-419, AP, Brazil
| | - Maria Anice Mureb Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo 01246-904, SP, Brazil
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47
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Everson KM, Donohue ME, Weisrock DW. A Pervasive History of Gene Flow in Madagascar's True Lemurs (Genus Eulemur). Genes (Basel) 2023; 14:1130. [PMID: 37372308 DOI: 10.3390/genes14061130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
In recent years, it has become widely accepted that interspecific gene flow is common across the Tree of Life. Questions remain about how species boundaries can be maintained in the face of high levels of gene flow and how phylogeneticists should account for reticulation in their analyses. The true lemurs of Madagascar (genus Eulemur, 12 species) provide a unique opportunity to explore these questions, as they form a recent radiation with at least five active hybrid zones. Here, we present new analyses of a mitochondrial dataset with hundreds of individuals in the genus Eulemur, as well as a nuclear dataset containing hundreds of genetic loci for a small number of individuals. Traditional coalescent-based phylogenetic analyses of both datasets reveal that not all recognized species are monophyletic. Using network-based approaches, we also find that a species tree containing between one and three ancient reticulations is supported by strong evidence. Together, these results suggest that hybridization has been a prominent feature of the genus Eulemur in both the past and present. We also recommend that greater taxonomic attention should be paid to this group so that geographic boundaries and conservation priorities can be better established.
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Affiliation(s)
- Kathryn M Everson
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
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48
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Sun QH, Morales-Briones DF, Wang HX, Landis JB, Wen J, Wang HF. Target sequence capture data shed light on the deeper evolutionary relationships of subgenus Chamaecerasus in Lonicera (Caprifoliaceae). Mol Phylogenet Evol 2023; 184:107808. [PMID: 37156329 DOI: 10.1016/j.ympev.2023.107808] [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: 08/11/2022] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023]
Abstract
The genus Lonicera L. is widely distributed in the north temperate zone and is well-known for its high species richness and morphological diversity. Previous studies have suggested that many sections of Lonicera are not monophyletic and phylogenetic relationships within the genus are still poorly resolved. In this study, we sampled 37 accessions of Lonicera, covering four sections of subgenus Chamaecerasus plus six outgroup taxa, to recover the main clades of Lonicera based on sequences of nuclear loci generated by target enrichment and cpDNA from genome skimming. We found extensive cytonuclear discordance across the subgenus. Both nuclear and plastid phylogenetic analyses supported subgenus Chamaecerasus sister to subgenus Lonicera. Within subgenus Chamaecerasus, sections Isika and Nintooa were each polyphyletic. Based on the nuclear and chloroplast phylogenies, we propose to merge Lonicera korolkowii into section Coeloxylosteum and Lonicera caerulea into section Nintooa. In addition, Lonicera is estimated to have originated in the mid Oligocene (26.45 Ma). The stem age of section Nintooa was estimated to be 17.09 Ma (95% HPD: 13.30-24.45). The stem age of subgenus Lonicera was estimated to be 16.35 Ma (95% HPD: 14.12-23.66). Ancestral area reconstruction analyses indicate that subgenus Chamaecerasus originated in East Asia and Central Asia. In addition, sections Coeloxylosteum and Nintooa originated in East Asia, with subsequent dispersals into other areas. The aridification of the Asian interior likely promoted the rapid radiation of sections Coeloxylosteum and Nintooa within this region. Moreover, our biogeographic analysis fully supports the Bering and the North Atlantic Land Bridge hypotheses for the intercontinental migrations in the Northern Hemisphere. Overall, this study provides new insights into the taxonomically complex lineages of subgenus Chamaecerasus and the process of speciation.
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Affiliation(s)
- Qing-Hui Sun
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; School of Tropical Medicine, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Diego F Morales-Briones
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, 140 Gortner Laboratory, 1479 Gortner Avenue, Saint Paul, MN 55108, USA; Systematics, Biodiversity and Evolution of Plants, Department of Biology I, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638, Munich, Germany
| | - Hong-Xin Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Zhai Mingguo Academician Work Station, Sanya University, Sanya 572022, China
| | - Jacob B Landis
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14850, USA; BTI Computational Biology Center, Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC-166, Smithsonian Institution, PO Box 37012, Washington, DC 20013-7012, USA
| | - Hua-Feng Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Tropical Crops, Hainan University, Haikou 570228, China.
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49
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Walsh J, Billerman SM, Butcher BG, Rohwer VG, Toews DPL, Vila-Coury V, Lovette IJ. A complex genomic architecture underlies reproductive isolation in a North American oriole hybrid zone. Commun Biol 2023; 6:154. [PMID: 36747071 PMCID: PMC9902562 DOI: 10.1038/s42003-023-04532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Natural hybrid zones provide powerful opportunities for identifying the mechanisms that facilitate and inhibit speciation. Documenting the extent of genomic admixture allows us to discern the architecture of reproductive isolation through the identification of isolating barriers. This approach is particularly powerful for characterizing the accumulation of isolating barriers in systems exhibiting varying levels of genomic divergence. Here, we use a hybrid zone between two species-the Baltimore (Icterus galbula) and Bullock's (I. bullockii) orioles-to investigate this architecture of reproductive isolation. We combine whole genome re-sequencing with data from an additional 313 individuals amplityped at ancestry-informative markers to characterize fine-scale patterns of admixture, and to quantify links between genes and the plumage traits. On a genome-wide scale, we document several putative barriers to reproduction, including elevated peaks of divergence above a generally high genomic baseline, a large putative inversion on the Z chromosome, and complex interactions between melanogenesis-pathway candidate genes. Concordant and coincident clines for these different genomic regions further suggest the coupling of pre- and post-mating barriers. Our findings of complex and coupled interactions between pre- and post-mating barriers suggest a relatively rapid accumulation of barriers between these species, and they demonstrate the complexities of the speciation process.
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Affiliation(s)
- Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.
| | - Shawn M. Billerman
- grid.5386.8000000041936877XFuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY USA
| | - Bronwyn G. Butcher
- grid.5386.8000000041936877XFuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY USA
| | - Vanya G. Rohwer
- grid.5386.8000000041936877XFuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY USA
| | - David P. L. Toews
- grid.29857.310000 0001 2097 4281Department of Biology, Penn State University, University Park, Pennsylvania, USA
| | - Vicens Vila-Coury
- grid.5386.8000000041936877XFuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY USA
| | - Irby J. Lovette
- grid.5386.8000000041936877XFuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY USA ,grid.5386.8000000041936877XDepartment of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY USA
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50
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Genome structure-based Juglandaceae phylogenies contradict alignment-based phylogenies and substitution rates vary with DNA repair genes. Nat Commun 2023; 14:617. [PMID: 36739280 PMCID: PMC9899254 DOI: 10.1038/s41467-023-36247-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 01/20/2023] [Indexed: 02/06/2023] Open
Abstract
In lineages of allopolyploid origin, sets of homoeologous chromosomes may coexist that differ in gene content and syntenic structure. Presence or absence of genes and microsynteny along chromosomal blocks can serve to differentiate subgenomes and to infer phylogenies. We here apply genome-structural data to infer relationships in an ancient allopolyploid lineage, the walnut family (Juglandaceae), by using seven chromosome-level genomes, two of them newly assembled. Microsynteny and gene-content analyses yield identical topologies that place Platycarya with Engelhardia as did a 1980s morphological-cladistic study. DNA-alignment-based topologies here and in numerous earlier studies instead group Platycarya with Carya and Juglans, perhaps misled by past hybridization. All available data support a hybrid origin of Juglandaceae from extinct or unsampled progenitors nested within, or sister to, Myricaceae. Rhoiptelea chiliantha, sister to all other Juglandaceae, contains proportionally more DNA repair genes and appears to evolve at a rate 2.6- to 3.5-times slower than the remaining species.
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