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Glover AN, Sousa VC, Ridenbaugh RD, Sim SB, Geib SM, Linnen CR. Recurrent selection shapes the genomic landscape of differentiation between a pair of host-specialized haplodiploids that diverged with gene flow. Mol Ecol 2024:e17509. [PMID: 39165007 DOI: 10.1111/mec.17509] [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: 05/03/2024] [Revised: 07/16/2024] [Accepted: 08/02/2024] [Indexed: 08/22/2024]
Abstract
Understanding the genetics of adaptation and speciation is critical for a complete picture of how biodiversity is generated and maintained. Heterogeneous genomic differentiation between diverging taxa is commonly documented, with genomic regions of high differentiation interpreted as resulting from differential gene flow, linked selection and reduced recombination rates. Disentangling the roles of each of these non-exclusive processes in shaping genome-wide patterns of divergence is challenging but will enhance our knowledge of the repeatability of genomic landscapes across taxa. Here, we combine whole-genome resequencing and genome feature data to investigate the processes shaping the genomic landscape of differentiation for a sister-species pair of haplodiploid pine sawflies, Neodiprion lecontei and Neodiprion pinetum. We find genome-wide correlations between genome features and summary statistics are consistent with pervasive linked selection, with patterns of diversity and divergence more consistently predicted by exon density and recombination rate than the neutral mutation rate (approximated by dS). We also find that both global and local patterns of FST, dXY and π provide strong support for recurrent selection as the primary selective process shaping variation across pine sawfly genomes, with some contribution from balancing selection and lineage-specific linked selection. Because inheritance patterns for haplodiploid genomes are analogous to those of sex chromosomes, we hypothesize that haplodiploids may be especially prone to recurrent selection, even if gene flow occurred throughout divergence. Overall, our study helps fill an important taxonomic gap in the genomic landscape literature and contributes to our understanding of the processes that shape genome-wide patterns of genetic variation.
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Affiliation(s)
- Ashleigh N Glover
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Vitor C Sousa
- Department of Animal Biology, CE3C - Center for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Lisbon, Lisboa, Portugal
| | - Ryan D Ridenbaugh
- Department of Biology, University of Kentucky, Lexington, Kentucky, USA
| | - Sheina B Sim
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, Hawaii, USA
| | - Scott M Geib
- USDA-ARS Daniel K. Inouye US Pacific Basin Agricultural Research Center Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, Hawaii, USA
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2
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Russo A, Alessandrini M, El Baidouri M, Frei D, Galise TR, Gaidusch L, Oertel HF, Garcia Morales SE, Potente G, Tian Q, Smetanin D, Bertrand JAM, Onstein RE, Panaud O, Frey JE, Cozzolino S, Wicker T, Xu S, Grossniklaus U, Schlüter PM. Genome of the early spider-orchid Ophrys sphegodes provides insights into sexual deception and pollinator adaptation. Nat Commun 2024; 15:6308. [PMID: 39060266 PMCID: PMC11282089 DOI: 10.1038/s41467-024-50622-4] [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: 11/06/2023] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Pollinator-driven evolution of floral traits is thought to be a major driver of angiosperm speciation and diversification. Ophrys orchids mimic female insects to lure male pollinators into pseudocopulation. This strategy, called sexual deception, is species-specific, thereby providing strong premating reproductive isolation. Identifying the genomic architecture underlying pollinator adaptation and speciation may shed light on the mechanisms of angiosperm diversification. Here, we report the 5.2 Gb chromosome-scale genome sequence of Ophrys sphegodes. We find evidence for transposable element expansion that preceded the radiation of the O. sphegodes group, and for gene duplication having contributed to the evolution of chemical mimicry. We report a highly differentiated genomic candidate region for pollinator-mediated evolution on chromosome 2. The Ophrys genome will prove useful for investigations into the repeated evolution of sexual deception, pollinator adaptation and the genomic architectures that facilitate evolutionary radiations.
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Affiliation(s)
- Alessia Russo
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
| | - Mattia Alessandrini
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Moaine El Baidouri
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Daniel Frei
- Department of Methods Development and Analytics, Agroscope, Wädenswil, Switzerland
| | | | - Lara Gaidusch
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Hannah F Oertel
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Sara E Garcia Morales
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Giacomo Potente
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Qin Tian
- Naturalis Biodiversity Centre, Leiden, The Netherlands
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Dmitry Smetanin
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Joris A M Bertrand
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Renske E Onstein
- Naturalis Biodiversity Centre, Leiden, The Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle - Jena - Leipzig, Leipzig, Germany
| | - Olivier Panaud
- Université Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- CNRS, Laboratoire Génome et Développement des Plantes, UMR5096, Perpignan, France
- EMR269 MANGO, Institut de Recherche pour le Développement, Perpignan, France
| | - Jürg E Frey
- Department of Methods Development and Analytics, Agroscope, Wädenswil, Switzerland
| | | | - Thomas Wicker
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Shuqing Xu
- Institute of Organismic and Molecular Evolution, University of Mainz, Mainz, Germany
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland
| | - Philipp M Schlüter
- Department of Plant Evolutionary Biology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
- Department of Systematic and Evolutionary Botany and Zürich-Basel Plant Science Centre, University of Zurich, Zürich, Switzerland.
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3
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Manthey JD, Spellman GM. Recombination rate variation shapes genomic variability of phylogeographic structure in a widespread North American songbird (Aves: Certhia americana). Mol Phylogenet Evol 2024; 196:108088. [PMID: 38697377 DOI: 10.1016/j.ympev.2024.108088] [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: 01/29/2024] [Revised: 04/11/2024] [Accepted: 04/24/2024] [Indexed: 05/05/2024]
Abstract
The nonrandom distribution of chromosomal characteristics and functional elements-genomic architecture-impacts the relative strengths and impacts of population genetic processes across the genome. Due to this relationship, genomic architecture has the potential to shape variation in population genetic structure across the genome. Population genetic structure has been shown to vary across the genome in a variety of taxa, but this body of work has largely focused on pairwise population genomic comparisons between closely related taxa. Here, we used whole genome sequencing of seven phylogeographically structured populations of a North American songbird, the Brown Creeper (Certhia americana), to determine the impacts of genomic architecture on phylogeographic structure variation across the genome. Using multiple methods to infer phylogeographic structure-ordination, clustering, and phylogenetic methods-we found that recombination rate variation explained a large proportion of phylogeographic structure variation. Genomic regions with low recombination showed phylogeographic structure consistent with the genome-wide pattern. In regions with high recombination, we found strong phylogeographic structure, but with discordant patterns relative to the genome-wide pattern. In regions with high recombination rate, we found that populations with small effective population sizes evolve relatively more rapidly than larger populations, leading to discordant signatures of phylogeographic structure. These results suggest that the interplay between recombination rate variation and effective population sizes shape the relative impacts of selection and genetic drift in different parts of the genome. Overall, the combined interactions of population genetic processes, genomic architecture, and effective population sizes shape patterns of variability in phylogeographic structure across the genome of the Brown Creeper.
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Affiliation(s)
- Joseph D Manthey
- Department of Biological Sciences, Texas Tech University. Lubbock, TX, USA.
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, CO, USA
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4
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Morales P, Gajardo F, Valdivieso C, Valladares MA, Di Genova A, Orellana A, Gutiérrez RA, González M, Montecino M, Maass A, Méndez MA, Allende ML. Genomes of the Orestias pupfish from the Andean Altiplano shed light on their evolutionary history and phylogenetic relationships within Cyprinodontiformes. BMC Genomics 2024; 25:614. [PMID: 38890559 PMCID: PMC11184842 DOI: 10.1186/s12864-024-10416-w] [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: 10/05/2023] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order. RESULTS We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group. CONCLUSIONS The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
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Affiliation(s)
- Pamela Morales
- Millennium Institute Center for Genome Regulation, Santiago, Chile.
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.
| | - Felipe Gajardo
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Valdivieso
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Moisés A Valladares
- Laboratorio de Biología Evolutiva, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Grupo de Biodiversidad y Cambio Global (GBCG), Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Alex Di Genova
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- DiGenoma-Lab, Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
- Centro de Modelamiento Matemático UMI-CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Ariel Orellana
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo A Gutiérrez
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- ANID Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Chile
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Mauricio González
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Bioinformatic and Gene Expression Laboratory, INTA-Universidad de Chile, Santiago, Chile
| | - Martin Montecino
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, 837001, Chile
| | - Alejandro Maass
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Centro de Modelamiento Matemático IRL 2807 CNRS, Universidad de Chile, Santiago, Chile
- Departamento de Ingeniería Matemática, Universidad de Chile, Santiago, Chile
| | - Marco A Méndez
- Institute of Ecology and Biodiversity (IEB), Las Palmeras 3425, Ñuñoa, Santiago, Chile
- Laboratorio de Genética y Evolución, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro de Ecología Aplicada y Sustentabilidad (CAPES), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Cape Horn International Center (CHIC), Parque Etnobotánico Omora, Universidad de Magallanes, Puerto Williams, Chile
| | - Miguel L Allende
- Millennium Institute Center for Genome Regulation, Santiago, Chile
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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5
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Jackson TK, Rhode C. Comparative genomics of dusky kob (Argyrosomus japonicus, Sciaenidae) conspecifics: Evidence for speciation and the genetic mechanisms underlying traits. JOURNAL OF FISH BIOLOGY 2024. [PMID: 38885946 DOI: 10.1111/jfb.15844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 04/17/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024]
Abstract
Dusky kob (Argyrosomus japonicus) is a commercially important finfish, indigenous to South Africa, Australia, and China. Previous studies highlighted differences in genetic composition, life history, and morphology of the species across geographic regions. A draft genome sequence of 0.742 Gb (N50 = 5.49 Mb; BUSCO completeness = 97.8%) and 22,438 predicted protein-coding genes was generated for the South African (SA) conspecific. A comparison with the Chinese (CN) conspecific revealed a core set of 32,068 orthologous protein clusters across both genomes. The SA genome exhibited 440 unique clusters compared to 1928 unique clusters in the CN genome. Transportation and immune response processes were overrepresented among the SA accessory genome, whereas the CN accessory genome was enriched for immune response, DNA transposition, and sensory detection (FDR-adjusted p < 0.01). These unique clusters may represent an adaptive component of the species' pangenome that could explain population divergence due to differential environmental specialisation. Furthermore, 700 single-copy orthologues (SCOs) displayed evidence of positive selection between the SA and CN genomes, and globally these genomes shared only 92% similarity, suggesting they might be distinct species. These genes primarily play roles in metabolism and digestion, illustrating the evolutionary pathways that differentiate the species. Understanding these genomic mechanisms underlying adaptation and evolution within and between species provides valuable insights into growth and maturation of kob, traits that are particularly relevant to commercial aquaculture.
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Affiliation(s)
- Tassin Kim Jackson
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa
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6
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Martin CA, Sheppard EC, Ali HAA, Illera JC, Suh A, Spurgin LG, Richardson DS. Genomic landscapes of divergence among island bird populations: Evidence of parallel adaptation but at different loci? Mol Ecol 2024; 33:e17365. [PMID: 38733214 DOI: 10.1111/mec.17365] [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: 02/26/2023] [Accepted: 03/01/2024] [Indexed: 05/13/2024]
Abstract
When populations colonise new environments, they may be exposed to novel selection pressures but also suffer from extensive genetic drift due to founder effects, small population sizes and limited interpopulation gene flow. Genomic approaches enable us to study how these factors drive divergence, and disentangle neutral effects from differentiation at specific loci due to selection. Here, we investigate patterns of genetic diversity and divergence using whole-genome resequencing (>22× coverage) in Berthelot's pipit (Anthus berthelotii), a passerine endemic to the islands of three north Atlantic archipelagos. Strong environmental gradients, including in pathogen pressure, across populations in the species range, make it an excellent system in which to explore traits important in adaptation and/or incipient speciation. First, we quantify how genomic divergence accumulates across the speciation continuum, that is, among Berthelot's pipit populations, between sub species across archipelagos, and between Berthelot's pipit and its mainland ancestor, the tawny pipit (Anthus campestris). Across these colonisation timeframes (2.1 million-ca. 8000 years ago), we identify highly differentiated loci within genomic islands of divergence and conclude that the observed distributions align with expectations for non-neutral divergence. Characteristic signatures of selection are identified in loci associated with craniofacial/bone and eye development, metabolism and immune response between population comparisons. Interestingly, we find limited evidence for repeated divergence of the same loci across the colonisation range but do identify different loci putatively associated with the same biological traits in different populations, likely due to parallel adaptation. Incipient speciation across these island populations, in which founder effects and selective pressures are strong, may therefore be repeatedly associated with morphology, metabolism and immune defence.
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Affiliation(s)
- Claudia A Martin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Terrestrial Ecology Unit, Biology Department, Ghent University, Ghent, Belgium
- School of Biological Sciences, The University of Edinburgh, Edinburgh, UK
| | | | - Hisham A A Ali
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Juan Carlos Illera
- Biodiversity Research Institute (CSIC-Oviedo University-Principality of Asturias), University of Oviedo, Mieres, Asturias, Spain
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norfolk, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre (EBC), Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lewis G Spurgin
- School of Biological Sciences, University of East Anglia, Norfolk, UK
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7
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Maier PA, Vandergast AG, Bohonak AJ. Yosemite toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression. Mol Ecol 2024; 33:e17317. [PMID: 38488670 DOI: 10.1111/mec.17317] [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: 05/11/2023] [Revised: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 04/09/2024]
Abstract
Genomes are heterogeneous during the early stages of speciation, with small 'islands' of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA ('rivers') to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad (Anaxyrus canorus) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.
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Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, San Diego, California, USA
- Family TreeDNA, Gene by Gene, Houston, Texas, USA
| | - Amy G Vandergast
- Western Ecological Research Center, San Diego Field Station, U.S. Geological Survey, San Diego, California, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, San Diego, California, USA
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8
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Johannesson K, Faria R, Le Moan A, Rafajlović M, Westram AM, Butlin RK, Stankowski S. Diverse pathways to speciation revealed by marine snails. Trends Genet 2024; 40:337-351. [PMID: 38395682 DOI: 10.1016/j.tig.2024.01.002] [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: 09/30/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 02/25/2024]
Abstract
Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems.
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Affiliation(s)
- Kerstin Johannesson
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Rui Faria
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Alan Le Moan
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; CNRS & Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Marina Rafajlović
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Department of Marine Sciences, University of Gothenburg, SE 41390 Gothenburg, Sweden; Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Anja Marie Westram
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Roger K Butlin
- Department of Marine Sciences, University of Gothenburg, Tjärnö Marine Laboratory, SE 45296 Strömstad, Sweden; The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Sean Stankowski
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden; Institute of Science and Technology Austria, Klosterneuburg, Austria; Department of Ecology and Evolution, University of Sussex, Brighton, UK
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9
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Stanojković A, Skoupý S, Johannesson H, Dvořák P. The global speciation continuum of the cyanobacterium Microcoleus. Nat Commun 2024; 15:2122. [PMID: 38459017 PMCID: PMC10923798 DOI: 10.1038/s41467-024-46459-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.
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Affiliation(s)
- Aleksandar Stanojković
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic
| | - Svatopluk Skoupý
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic
| | - Hanna Johannesson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- The Royal Swedish Academy of Sciences, Stockholm, Sweden
| | - Petr Dvořák
- Palacký University Olomouc, Faculty of Sciences, Department of Botany, Olomouc, Czech Republic.
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10
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Polic D, Yıldırım Y, Merilaita S, Franzén M, Forsman A. Genetic structure, UV-vision, wing coloration and size coincide with colour polymorphism in Fabriciana adippe butterflies. Mol Ecol 2024; 33:e17272. [PMID: 38240162 DOI: 10.1111/mec.17272] [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: 08/05/2022] [Revised: 12/18/2023] [Accepted: 01/08/2024] [Indexed: 02/22/2024]
Abstract
Colour polymorphisms have long served as model systems in evolutionary studies and continue to inform about processes involved in the origin and dynamics of biodiversity. Modern sequencing tools allow for evaluating whether phenotypic differences between morphs reflect genetic differentiation rather than developmental plasticity, and for investigating whether polymorphisms represent intermediate stages of diversification towards speciation. We investigated phenotypic and genetic differentiation between two colour morphs of the butterfly Fabriciana adippe using a combination of ddRAD-sequencing and comparisons of body size, colour patterns and optical properties of bright wing spots. The silvery-spotted adippe form had larger and darker wings and reflected UV light, while the yellow cleodoxa form displayed more green scales and reflected very little UV, showcasing that they constitute distinct and alternative integrated phenotypes. Genomic analyses revealed genetic structuring according to source population, and to colour morph, suggesting that the phenotypic differentiation reflects evolutionary modifications. We report 17 outlier loci associated with colour morph, including ultraviolet-sensitive visual pigment (UVRh1), which is associated with intraspecific communication and mate choice in butterflies. Together with the demonstration that the wings of the adippe (but essentially not the cleodoxa) morph reflect UV light, that UV reflectance is higher in females than males and that morphs differ in wing size, this suggests that these colour morphs might represent genetically integrated phenotypes, possibly adapted to different microhabitats. We propose that non-random mating might contribute to the differentiation and maintenance of the polymorphism.
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Affiliation(s)
- Daniela Polic
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Sami Merilaita
- Department of Biology, University of Turku, Turku, Finland
| | - Markus Franzén
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Anders Forsman
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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11
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Fuentes‐Pardo AP, Stanley R, Bourne C, Singh R, Emond K, Pinkham L, McDermid JL, Andersson L, Ruzzante DE. Adaptation to seasonal reproduction and environment-associated factors drive temporal and spatial differentiation in northwest Atlantic herring despite gene flow. Evol Appl 2024; 17:e13675. [PMID: 38495946 PMCID: PMC10940790 DOI: 10.1111/eva.13675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
Understanding how marine organisms adapt to local environments is crucial for predicting how populations will respond to global climate change. The genomic basis, environmental factors and evolutionary processes involved in local adaptation are however not well understood. Here we use Atlantic herring, an abundant, migratory and widely distributed marine fish with substantial genomic resources, as a model organism to evaluate local adaptation. We examined genomic variation and its correlation with environmental variables across a broad environmental gradient, for 15 spawning aggregations in Atlantic Canada and the United States. We then compared our results with available genomic data of northeast Atlantic populations. We confirmed that population structure lies in a fraction of the genome including likely adaptive genetic variants of functional importance. We discovered 10 highly differentiated genomic regions distributed across four chromosomes. Nine regions show strong association with seasonal reproduction. One region, corresponding to a known inversion on chromosome 12, underlies a latitudinal pattern discriminating populations north and south of a biogeographic transition zone on the Scotian Shelf. Genome-environment associations indicate that winter seawater temperature best correlates with the latitudinal pattern of this inversion. The variation at two so-called 'islands of divergence' related to seasonal reproduction appear to be private to the northwest Atlantic. Populations in the northwest and northeast Atlantic share variation at four of these divergent regions, simultaneously displaying significant diversity in haplotype composition at another four regions, which includes an undescribed structural variant approximately 7.7 Mb long on chromosome 8. Our results suggest that the timing and geographic location of spawning and early development may be under diverse selective pressures related to allelic fitness across environments. Our study highlights the role of genomic architecture, ancestral haplotypes and selection in maintaining adaptive divergence in species with large population sizes and presumably high gene flow.
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Affiliation(s)
- Angela P. Fuentes‐Pardo
- Department of BiologyDalhousie UniversityHalifaxNova ScotiaCanada
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
| | - Ryan Stanley
- Fisheries and Oceans CanadaMaritimes RegionDartmouthNova ScotiaCanada
| | - Christina Bourne
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreSt John'sNewfoundland and LabradorCanada
| | - Rabindra Singh
- Fisheries and Oceans CanadaSt. Andrews Biological StationSt. AndrewsNew BrunswickCanada
| | - Kim Emond
- Fisheries and Oceans CanadaMaurice Lamontagne InstituteMont‐JoliQuebecCanada
| | - Lisa Pinkham
- Department of Marine ResourcesWest Boothbay HarborMaineUSA
| | - Jenni L. McDermid
- Fisheries and Oceans CanadaGulf Fisheries CentreMonctonNew BrunswickCanada
| | - Leif Andersson
- Department of Medical Biochemistry and MicrobiologyUppsala UniversityUppsalaSweden
- Department of Veterinary Integrative BiosciencesTexas A&M UniversityCollege StationTexasUSA
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12
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Lukaszewicz M, Salia OI, Hohenlohe PA, Buzbas EO. Approximate Bayesian computational methods to estimate the strength of divergent selection in population genomics models. JOURNAL OF COMPUTATIONAL MATHEMATICS AND DATA SCIENCE 2024; 10:100091. [PMID: 38616846 PMCID: PMC11014422 DOI: 10.1016/j.jcmds.2024.100091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Statistical estimation of parameters in large models of evolutionary processes is often too computationally inefficient to pursue using exact model likelihoods, even with single-nucleotide polymorphism (SNP) data, which offers a way to reduce the size of genetic data while retaining relevant information. Approximate Bayesian Computation (ABC) to perform statistical inference about parameters of large models takes the advantage of simulations to bypass direct evaluation of model likelihoods. We develop a mechanistic model to simulate forward-in-time divergent selection with variable migration rates, modes of reproduction (sexual, asexual), length and number of migration-selection cycles. We investigate the computational feasibility of ABC to perform statistical inference and study the quality of estimates on the position of loci under selection and the strength of selection. To expand the parameter space of positions under selection, we enhance the model by implementing an outlier scan on summarized observed data. We evaluate the usefulness of summary statistics well-known to capture the strength of selection, and assess their informativeness under divergent selection. We also evaluate the effect of genetic drift with respect to an idealized deterministic model with single-locus selection. We discuss the role of the recombination rate as a confounding factor in estimating the strength of divergent selection, and emphasize its importance in break down of linkage disequilibrium (LD). We answer the question for which part of the parameter space of the model we recover strong signal for estimating the selection, and determine whether population differentiation-based summary statistics or LD-based summary statistics perform well in estimating selection.
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Affiliation(s)
- Martyna Lukaszewicz
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, ID, United States of America
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Ousseini Issaka Salia
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, ID, United States of America
- Institute for Modeling Collaboration and Innovation (IMCI), University of Idaho, Moscow, ID, United States of America
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
- Department of Horticulture, Washington State University, Pullman, WA, United States of America
| | - Paul A. Hohenlohe
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, ID, United States of America
- Institute for Modeling Collaboration and Innovation (IMCI), University of Idaho, Moscow, ID, United States of America
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, United States of America
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States of America
| | - Erkan O. Buzbas
- Institute for Interdisciplinary Data Sciences (IIDS), University of Idaho, Moscow, ID, United States of America
- Institute for Modeling Collaboration and Innovation (IMCI), University of Idaho, Moscow, ID, United States of America
- Department of Mathematics and Statistical Science, University of Idaho, Moscow, ID, United States of America
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13
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Valim HF, Grande FD, Wong ELY, Schmitt I. Circadian clock- and temperature-associated genes contribute to overall genomic differentiation along elevation in lichenized fungi. Mol Ecol 2024; 33:e17252. [PMID: 38146927 DOI: 10.1111/mec.17252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 11/24/2023] [Accepted: 12/11/2023] [Indexed: 12/27/2023]
Abstract
Circadian regulation is linked to local environmental adaptation, and many species with broad climatic niches display variation in circadian genes. Here, we hypothesize that lichenizing fungi occupying different climate zones tune their metabolism to local environmental conditions with the help of their circadian systems. We study two species of the genus Umbilicaria occupying similar climatic niches (Mediterranean and the cold temperate) in different continents. Using homology to Neurospora crassa genes, we identify gene sets associated with circadian rhythms (11 core, 39 peripheral genes) as well as temperature response (37 genes). Nucleotide diversity of these genes is significantly correlated with mean annual temperature, minimum temperature of the coldest month and mean temperature of the coldest quarter. Furthermore, we identify altitudinal clines in allele frequencies in several non-synonymous substitutions in core clock components, for example, white collar-like, frh-like and various ccg-like genes. A dN/dS approach revealed a few significant peripheral clock- and temperature-associated genes (e.g. ras-1-like, gna-1-like) that may play a role in fine-tuning the circadian clock and temperature-response machinery. An analysis of allele frequency changes demonstrated the strongest evidence for differentiation above the genomic background in the clock-associated genes in U. pustulata. These results highlight the likely relevance of the circadian clock in environmental adaptation, particularly frost tolerance, of lichens. Whether or not the fungal clock modulates the symbiotic interaction within the lichen consortium remains to be investigated. We corroborate the finding of genetic variation in clock components along altitude-not only latitude-as has been reported in other species.
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Affiliation(s)
- Henrique F Valim
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Department of Biology, University of Padova, Padua, Italy
| | - Edgar L Y Wong
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Frankfurt am Main, Germany
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14
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Delmore K, Justen H, Kay KM, Kitano J, Moyle LC, Stelkens R, Streisfeld MA, Yamasaki YY, Ross J. Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041438. [PMID: 37848243 PMCID: PMC10835617 DOI: 10.1101/cshperspect.a041438] [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] [Indexed: 10/19/2023]
Abstract
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
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Affiliation(s)
- Kira Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California 93740, USA
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15
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Ali HAA, Coulson T, Clegg SM, Quilodrán CS. The effect of divergent and parallel selection on the genomic landscape of divergence. Mol Ecol 2024; 33:e17225. [PMID: 38063473 DOI: 10.1111/mec.17225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/25/2023] [Accepted: 11/16/2023] [Indexed: 01/25/2024]
Abstract
While the role of selection in divergence along the speciation continuum is theoretically well understood, defining specific signatures of selection in the genomic landscape of divergence is empirically challenging. Modelling approaches can provide insight into the potential role of selection on the emergence of a heterogenous genomic landscape of divergence. Here, we extend and apply an individual-based approach that simulates the phenotypic and genotypic distributions of two populations under a variety of selection regimes, genotype-phenotype maps, modes of migration, and genotype-environment interactions. We show that genomic islands of high differentiation and genomic valleys of similarity may respectively form under divergent and parallel selection between populations. For both types of between-population selection, negative and positive frequency-dependent selection within populations generated genomic islands of higher magnitude and genomic valleys of similarity, respectively. Divergence rates decreased under strong dominance with divergent selection, as well as in models including genotype-environment interactions under parallel selection. For both divergent and parallel selection models, divergence rate was higher under an intermittent migration regime between populations, in contrast to a constant level of migration across generations, despite an equal number of total migrants. We highlight that interpreting a particular evolutionary history from an observed genomic pattern must be done cautiously, as similar patterns may be obtained from different combinations of evolutionary processes. Modelling approaches such as ours provide an opportunity to narrow the potential routes that generate the genomic patterns of specific evolutionary histories.
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Affiliation(s)
- Hisham A A Ali
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Tim Coulson
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Sonya M Clegg
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
| | - Claudio S Quilodrán
- Department of Biology, Edward Grey Institute of Field Ornithology, University of Oxford, Oxford, UK
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
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16
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De Luna-Bonilla OÁ, Valencia-Á S, Ibarra-Manríquez G, Morales-Saldaña S, Tovar-Sánchez E, González-Rodríguez A. Leaf morphometric analysis and potential distribution modelling contribute to taxonomic differentiation in the Quercus microphylla complex. JOURNAL OF PLANT RESEARCH 2024; 137:3-19. [PMID: 37740854 PMCID: PMC10764464 DOI: 10.1007/s10265-023-01495-z] [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: 06/06/2023] [Accepted: 08/31/2023] [Indexed: 09/25/2023]
Abstract
Mexico is a major center of evolutionary radiation for the genus Quercus, with oak species occurring across different habitat types and showing a wide variation in morphology and growth form. Despite representing about 20% of Mexican species, scrub oaks have received little attention and even basic aspects of their taxonomy and geographic distribution remain unresolved. In this study, we analyzed the morphological and climatic niche differentiation of scrub oak populations forming a complex constituted by six named species, Quercus cordifolia, Quercus frutex, Quercus intricata, Quercus microphylla, Quercus repanda, Quercus striatula and a distinct morphotype of Q. striatula identified during field and herbarium work (hereafter named Q. striatula II). Samples were obtained from 35 sites covering the geographic distribution of the complex in northern and central Mexico. Morphological differentiation was analyzed through geometric morphometrics of leaf shape and quantification of trichome traits. Our results indicated the presence of two main morphological groups with geographic concordance. The first was formed by Q. frutex, Q. microphylla, Q. repanda and Q. striatula, distributed in the Trans-Mexican Volcanic Belt, the Sierra Madre Occidental and a little portion of the south of the Mexican Altiplano (MA). The second group consists of Q. cordifola, Q. intricata and Q. striatula II, found in the Sierra Madre Oriental and the MA. Therefore, our evidence supports the distinctness of the Q. striatula II morphotype, indicating the need for a taxonomic revision. Within the two groups, morphological differentiation among taxa varied from very clear to low or inexistent (i.e. Q. microphylla-Q. striatula and Q. cordifolia-Q. striatula II) but niche comparisons revealed significant niche differentiation in all pairwise comparisons, highlighting the relevance of integrative approaches for the taxonomic resolution of complicated groups such as the one studied here.
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Affiliation(s)
- Oscar Ángel De Luna-Bonilla
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, 58190, Morelia, México
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1° Piso, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510, Ciudad de Mexico, México
| | - Susana Valencia-Á
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México, Circuito Exterior, s.n, Ciudad Universitaria, Coyoacán, 04510, México City, México
| | - Guillermo Ibarra-Manríquez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, 58190, Morelia, México
| | - Saddan Morales-Saldaña
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, 58190, Morelia, México
| | - Efraín Tovar-Sánchez
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, CP, 62209, Cuernavaca, Morelos, Mexico
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, 58190, Morelia, México.
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17
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Bredemeyer KR, Hillier L, Harris AJ, Hughes GM, Foley NM, Lawless C, Carroll RA, Storer JM, Batzer MA, Rice ES, Davis BW, Raudsepp T, O'Brien SJ, Lyons LA, Warren WC, Murphy WJ. Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution. Nat Genet 2023; 55:1953-1963. [PMID: 37919451 PMCID: PMC10845050 DOI: 10.1038/s41588-023-01548-y] [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: 06/23/2023] [Accepted: 09/20/2023] [Indexed: 11/04/2023]
Abstract
The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes were hotspots of structural variation, including enrichment with inversions in a large recombination desert with characteristics of a supergene. The X-linked macrosatellite DXZ4 evolves more rapidly than 99.5% of the genome clarifying its role in felid hybrid incompatibility. Resolved sensory gene repertoires revealed functional copy number changes associated with ecomorphological adaptations, sociality and domestication. This study highlights the value of gapless genomes to reveal structural mechanisms underpinning karyotypic evolution, reproductive isolation and ecological niche adaptation.
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Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Graham M Hughes
- School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Colleen Lawless
- School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Rachel A Carroll
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | | | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Edward S Rice
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Brian W Davis
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Stephen J O'Brien
- Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, MO, USA
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA.
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA.
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18
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Pratt EAL, Beheregaray LB, Fruet P, Tezanos-Pinto G, Bilgmann K, Zanardo N, Diaz-Aguirre F, Secchi ER, Freitas TRO, Möller LM. Genomic Divergence and the Evolution of Ecotypes in Bottlenose Dolphins (Genus Tursiops). Genome Biol Evol 2023; 15:evad199. [PMID: 37935115 PMCID: PMC10655200 DOI: 10.1093/gbe/evad199] [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: 10/27/2023] [Revised: 10/03/2023] [Accepted: 10/14/2023] [Indexed: 11/09/2023] Open
Abstract
Climatic changes have caused major environmental restructuring throughout the world's oceans. Marine organisms have responded to novel conditions through various biological systems, including genomic adaptation. Growing accessibility of next-generation DNA sequencing methods to study nonmodel species has recently allowed genomic changes underlying environmental adaptations to be investigated. This study used double-digest restriction-site associated DNA (ddRAD) sequence data to investigate the genomic basis of ecotype formation across currently recognized species and subspecies of bottlenose dolphins (genus Tursiops) in the Southern Hemisphere. Subspecies-level genomic divergence was confirmed between the offshore common bottlenose dolphin (T. truncatus truncatus) and the inshore Lahille's bottlenose dolphin (T. t. gephyreus) from the southwestern Atlantic Ocean (SWAO). Similarly, subspecies-level divergence is suggested between inshore (eastern Australia) Indo-Pacific bottlenose dolphin (T. aduncus) and the proposed Burrunan dolphin (T. australis) from southern Australia. Inshore bottlenose dolphin lineages generally had lower genomic diversity than offshore lineages, a pattern particularly evident for T. t. gephyreus, which showed exceptionally low diversity. Genomic regions associated with cardiovascular, musculoskeletal, and energy production systems appear to have undergone repeated adaptive evolution in inshore lineages across the Southern Hemisphere. We hypothesize that comparable selective pressures in the inshore environment drove similar adaptive responses in each lineage, supporting parallel evolution of inshore bottlenose dolphins. With climate change altering marine ecosystems worldwide, it is crucial to gain an understanding of the adaptive capacity of local species and populations. Our study provides insights into key adaptive pathways that may be important for the long-term survival of cetaceans and other organisms in a changing marine environment.
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Affiliation(s)
- Eleanor A L Pratt
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Pedro Fruet
- Laboratório de Ecologia e Conservação da Megafauna Marinha (ECOMEGA), Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Museu Oceanográfico Prof. Eliézer de C. Rios, Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Kaosa, Rio Grande, Brazil
| | | | - Kerstin Bilgmann
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Nikki Zanardo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Department of Environment and Water, Adelaide, South Australia, Australia
| | - Fernando Diaz-Aguirre
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
| | - Eduardo R Secchi
- Laboratório de Ecologia e Conservação da Megafauna Marinha (ECOMEGA), Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
- Museu Oceanográfico Prof. Eliézer de C. Rios, Universidade Federal do Rio Grande-FURG, Rio Grande, Brazil
| | - Thales R O Freitas
- Laboratório de Citogenética e Evolução, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciana M Möller
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
- Cetacean Ecology, Behaviour and Evolution Laboratory, College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia
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19
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Bock DG, Cai Z, Elphinstone C, González-Segovia E, Hirabayashi K, Huang K, Keais GL, Kim A, Owens GL, Rieseberg LH. Genomics of plant speciation. PLANT COMMUNICATIONS 2023; 4:100599. [PMID: 37050879 PMCID: PMC10504567 DOI: 10.1016/j.xplc.2023.100599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
Studies of plants have been instrumental for revealing how new species originate. For several decades, botanical research has complemented and, in some cases, challenged concepts on speciation developed via the study of other organisms while also revealing additional ways in which species can form. Now, the ability to sequence genomes at an unprecedented pace and scale has allowed biologists to settle decades-long debates and tackle other emerging challenges in speciation research. Here, we review these recent genome-enabled developments in plant speciation. We discuss complications related to identification of reproductive isolation (RI) loci using analyses of the landscape of genomic divergence and highlight the important role that structural variants have in speciation, as increasingly revealed by new sequencing technologies. Further, we review how genomics has advanced what we know of some routes to new species formation, like hybridization or whole-genome duplication, while casting doubt on others, like population bottlenecks and genetic drift. While genomics can fast-track identification of genes and mutations that confer RI, we emphasize that follow-up molecular and field experiments remain critical. Nonetheless, genomics has clarified the outsized role of ancient variants rather than new mutations, particularly early during speciation. We conclude by highlighting promising avenues of future study. These include expanding what we know so far about the role of epigenetic and structural changes during speciation, broadening the scope and taxonomic breadth of plant speciation genomics studies, and synthesizing information from extensive genomic data that have already been generated by the plant speciation community.
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Affiliation(s)
- Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Zhe Cai
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Cassandra Elphinstone
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Eric González-Segovia
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Graeme L Keais
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Amy Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gregory L Owens
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.
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20
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Crawford NG, McGreevy TJ, Mullen SP, Schneider CJ. The genetic basis of conspicuous coloration in the Guadeloupean anole: Evolution by sexual and ecological selection. Ecol Evol 2023; 13:e10266. [PMID: 37435022 PMCID: PMC10330958 DOI: 10.1002/ece3.10266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/13/2023] Open
Abstract
Understanding how natural selection acts on the genome and contributes to the process of speciation is a primary aim of the study of evolution. Here we used natural variation in two subspecies of the Guadeloupean anole (Anolis marmoratus ssp.), from the island of Guadeloupe in the Lesser Antilles, to explore the genomic basis of adaptation and speciation in Anolis lizards. These subspecies inhabit distinct ecological environments and display marked differences in adult male color and pattern. We sequenced the complete genomes of 20 anoles, 10 from each subspecies, at 1.4× coverage. We used genome-wide scans of population differentiation, allele frequency spectrum, and linkage disequilibrium to characterize the genomic architecture within and between the subspecies. While most of the genome was undifferentiated, we observed five large divergent regions. Within these regions we identified blocks, 5 kb pairs in length, enriched for fixed single nucleotide polymorphisms. These blocks encompass 97 genes, two of which are candidate pigmentation genes. One is melanophilin (mlph), which helps transport melanosomes within melanocytes. The other is a cluster of differentiation 36 (cd36), which regulates carotenoid pigment sequestration. We used high-pressure liquid chromatography to confirm that carotenoid pigments are significantly more abundant in the conspicuous orange-pigmented skin of male A. m. marmoratus suggesting that cd36 may be regulating pigment deposition in this tissue. We identified for the first time a carotenoid gene that is a potential target of divergent sexual selection and may be contributing to the early stages of speciation in Anolis lizards.
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Affiliation(s)
| | - Thomas J. McGreevy
- Department of BiologyBoston UniversityBostonMassachusettsUSA
- Department of Natural Resources ScienceUniversity of Rhode IslandKingstonRhode IslandUSA
| | - Sean P. Mullen
- Department of BiologyBoston UniversityBostonMassachusettsUSA
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21
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Caeiro-Dias G, Brelsford A, Meneses-Ribeiro M, Crochet PA, Pinho C. Hybridization in late stages of speciation: Strong but incomplete genome-wide reproductive isolation and 'large Z-effect' in a moving hybrid zone. Mol Ecol 2023. [PMID: 37316984 DOI: 10.1111/mec.17035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023]
Abstract
In organisms reproducing sexually, speciation occurs when increasing divergence results in pre- or post-zygotic reproductive isolation between lineages. Studies focusing on reproductive isolation origin in early stages of speciation are common and many rely on genomic scans to infer introgression providing limited information on the genomic architecture of reproductive isolation long-term maintenance. This study analyses a natural hybrid zone between two species in a late stage of speciation. We used ddRADseq genotyping in the contact between Podarcis bocagei and P. carbonelli to examine admixture extent, analyse hybrid zone stability and assess genome-wide variation in selection against introgression. We confirmed strong but incomplete reproductive isolation in a bimodal hybrid zone. New findings revealed population genetic structure within P. carbonelli in the contact zone; geographical and genomic clines analysis suggested strong selection against gene flow, but a relatively small proportion of the loci can introgress, mostly within the narrow contact zone. However, geographical clines revealed that a few introgressed loci show signs of potential positive selection, particularly into P. bocagei. Geographical clines also detected a signal of hybrid zone movement towards P. bocagei distribution. Genomic cline analysis revealed heterogeneous patterns of introgression among loci within the syntopy zone, but the majority maintain a strong association with the genomic background of origin. However, incongruences between both cline approaches were found, potentially driven by confounding effects on genomic clines. Last, an important role of the Z chromosome in reproductive isolation is suggested. Importantly, overall patterns of restricted introgression seem to result from numerous strong intrinsic barriers across the genome.
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Affiliation(s)
- Guilherme Caeiro-Dias
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Biology Department, University of California Riverside, Riverside, California, USA
| | - Mariana Meneses-Ribeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pierre-André Crochet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Catarina Pinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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22
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Lackey ACR, Murray AC, Mirza NA, Powell THQ. The role of sexual isolation during rapid ecological divergence: Evidence for a new dimension of isolation in Rhagoletis pomonella. J Evol Biol 2023. [PMID: 37173822 DOI: 10.1111/jeb.14179] [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: 05/03/2022] [Revised: 03/05/2023] [Accepted: 03/23/2023] [Indexed: 05/15/2023]
Abstract
The pace of divergence and likelihood of speciation often depends on how and when different types of reproductive barriers evolve. Questions remain about how reproductive isolation evolves after initial divergence. We tested for the presence of sexual isolation (reduced mating between populations due to divergent mating preferences and traits) in Rhagoletis pomonella flies, a model system for incipient ecological speciation. We measured the strength of sexual isolation between two very recently diverged (~170 generations) sympatric populations, adapted to different host fruits (hawthorn and apple). We found that flies from both populations were more likely to mate within than between populations. Thus, sexual isolation may play an important role in reducing gene flow allowed by early-acting ecological barriers. We also tested how warmer temperatures predicted under climate change could alter sexual isolation and found that sexual isolation was markedly asymmetric under warmer temperatures - apple males and hawthorn females mated randomly while apple females and hawthorn males mated more within populations than between. Our findings provide a window into the early speciation process and the role of sexual isolation after initial ecological divergence, in addition to examining how environmental conditions could shape the likelihood of further divergence.
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Affiliation(s)
- Alycia C R Lackey
- University of Louisville, Louisville, Kentucky, USA
- Binghamton University, Binghamton, New York, USA
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23
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Lu CW, Huang ST, Cheng SJ, Lin CT, Hsu YC, Yao CT, Dong F, Hung CM, Kuo HC. Genomic architecture underlying morphological and physiological adaptation to high elevation in a songbird. Mol Ecol 2023; 32:2234-2251. [PMID: 36748940 DOI: 10.1111/mec.16875] [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: 11/04/2022] [Revised: 01/17/2023] [Accepted: 02/03/2023] [Indexed: 02/08/2023]
Abstract
Organisms often acquire physiological and morphological modifications to conquer ecological challenges when colonizing new environments which lead to their adaptive evolution. However, deciphering the genomic mechanism of ecological adaptation is difficult because ecological environments are often too complex for straightforward interpretation. Thus, we examined the adaptation of a widespread songbird-the rufous-capped babbler (Cyanoderma ruficeps)-to a relatively simple system: distinct environments across elevational gradients on the mountainous island of Taiwan. We focused on the genomic sequences of 43 birds from five populations to show that the Taiwan group split from its sister group in mainland China around 1-2 million years ago (Ma) and colonized the montane habitats of Taiwan at least twice around 0.03-0.22 Ma. The montane and lowland Taiwan populations diverged with gene flow between them, suggesting strong selection associated with different elevations. We found that the montane babblers had smaller beaks than the lowland ones, consistent with Allen's rule, and identified candidate genes-COL9A1 and SOX11-underlying the beak size changes. We also found that altitudinally divergent mutations were mostly located in noncoding regions and tended to accumulate in chromosomal inversions and autosomes. The altitudinally divergent mutations might regulate genes related to haematopoietic, metabolic, immune, auditory and vision functions, as well as cerebrum morphology and plumage development. The results reveal the genomic bases of morphological and physiological adaptation in this species to the low temperature, hypoxia and high UV light environment at high elevation. These findings improve our understanding of how ecological adaptation drives population divergence from the perspective of genomic architecture.
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Affiliation(s)
- Chia-Wei Lu
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shih-Ting Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Shun-Jen Cheng
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Chen-Tau Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Cheng Hsu
- Department of Natural Resources and Environmental Studies, National Dong Hwa University, Hualien, Taiwan
| | - Cheng-Te Yao
- Division of Zoology, Endemic Species Research Institute, Nantou, Taiwan
| | - Feng Dong
- Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chih-Ming Hung
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Hao-Chih Kuo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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24
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Poikela N, Laetsch DR, Kankare M, Hoikkala A, Lohse K. Experimental introgression in Drosophila: Asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromosome. Mol Ecol 2023; 32:854-866. [PMID: 36461113 PMCID: PMC10107139 DOI: 10.1111/mec.16803] [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: 07/08/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 12/04/2022]
Abstract
Interspecific gene flow (introgression) is an important source of new genetic variation, but selection against it can reinforce reproductive barriers between interbreeding species. We used an experimental approach to trace the role of chromosomal inversions and incompatibility genes in preventing introgression between two partly sympatric Drosophila virilis group species, D. flavomontana and D. montana. We backcrossed F1 hybrid females from a cross between D. flavomontana female and D. montana male with the males of the parental species for two generations and sequenced pools of parental strains and their reciprocal second generation backcross (BC2 mon and BC2 fla) females. Contrasting the observed amount of introgression (mean hybrid index, HI) in BC2 female pools along the genome to simulations under different scenarios allowed us to identify chromosomal regions of restricted and increased introgression. We found no deviation from the HI expected under a neutral null model for any chromosome for the BC2 mon pool, suggesting no evidence for genetic incompatibilities in backcrosses towards D. montana. In contrast, the BC2 fla pool showed high variation in the observed HI between different chromosomes, and massive reduction of introgression on the X chromosome (large X-effect). This observation is compatible with reduced recombination combined with at least one dominant incompatibility locus residing within the X inversion(s). Overall, our study suggests that genetic incompatibilities arising within chromosomal inversions can play an important role in speciation.
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Affiliation(s)
- Noora Poikela
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
| | - Dominik R Laetsch
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Maaria Kankare
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
| | - Anneli Hoikkala
- Department of Biological and Environmental Science, University of Jyväskylä, Jyvaskyla, Finland
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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25
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Ferrer Obiol J, Herranz JM, Paris JR, Whiting JR, Rozas J, Riutort M, González-Solís J. Species delimitation using genomic data to resolve taxonomic uncertainties in a speciation continuum of pelagic seabirds. Mol Phylogenet Evol 2023; 179:107671. [PMID: 36442764 DOI: 10.1016/j.ympev.2022.107671] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/28/2022] [Accepted: 11/17/2022] [Indexed: 11/27/2022]
Abstract
Speciation is a continuous and complex process shaped by the interaction of numerous evolutionary forces. Despite the continuous nature of the speciation process, the implementation of conservation policies relies on the delimitation of species and evolutionary significant units (ESUs). Puffinus shearwaters are globally distributed and threatened pelagic seabirds. Due to remarkable morphological status the group has been under intense taxonomic debate for the past three decades. Here, we use double digest Restriction-Site Associated DNA sequencing (ddRAD-Seq) to genotype species and subspecies of North Atlantic and Mediterranean Puffinus shearwaters across their entire geographical range. We assess the phylogenetic relationships and population structure among and within the group, evaluate species boundaries, and characterise the genomic landscape of divergence. We find that current taxonomies are not supported by genomic data and propose a more accurate taxonomy by integrating genomic information with other sources of evidence. Our results show that several taxon pairs are at different stages of a speciation continuum. Our study emphasises the potential of genomic data to resolve taxonomic uncertainties, which can help to focus management actions on relevant taxa, even if they do not necessarily coincide with the taxonomic rank of species.
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Affiliation(s)
- Joan Ferrer Obiol
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain; Department of Environmental Science and Policy, University of Milan, Milan, Italy.
| | - Jose M Herranz
- National Institute for the Study of Liver and Gastrointestinal Diseases, CIBERehd, Carlos III Health Institute, Madrid, Spain; Program of Hepatology, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Josephine R Paris
- Department of Health, Life and Environmental Sciences, University of l'Aquila, Coppito, Italy; Department of Biosciences, University of Exeter, Exeter, UK
| | - James R Whiting
- Department of Biosciences, University of Exeter, Exeter, UK; Department of Biological Sciences, Faculty of Sciences, University of Calgary, Calgary, Canada
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Marta Riutort
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain; Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Barcelona, Catalonia, Spain; Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Facultat de Biologia, Universitat de Barcelona (UB), Barcelona, Catalonia, Spain
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26
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Li Y, Wang S, Zhang Z, Luo J, Lin GL, Deng WD, Guo Z, Han FM, Wang LL, Li J, Wu SF, Liu HQ, He S, Murphy RW, Zhang ZJ, Cooper DN, Wu DD, Zhang YP. Large-Scale Chromosomal Changes Lead to Genome-Level Expression Alterations, Environmental Adaptation, and Speciation in the Gayal (Bos frontalis). Mol Biol Evol 2023; 40:6980758. [PMID: 36625089 PMCID: PMC9874039 DOI: 10.1093/molbev/msad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Determining the functional consequences of karyotypic changes is invariably challenging because evolution tends to obscure many of its own footprints, such as accumulated mutations, recombination events, and demographic perturbations. Here, we describe the assembly of a chromosome-level reference genome of the gayal (Bos frontalis) thereby revealing the structure, at base-pair-level resolution, of a telo/acrocentric-to-telo/acrocentric Robertsonian translocation (2;28) (T/A-to-T/A rob[2;28]). The absence of any reduction in the recombination rate or genetic introgression within the fusion region of gayal served to challenge the long-standing view of a role for fusion-induced meiotic dysfunction in speciation. The disproportionate increase noted in the distant interactions across pro-chr2 and pro-chr28, and the change in open-chromatin accessibility following rob(2;28), may, however, have led to the various gene expression irregularities observed in the gayal. Indeed, we found that many muscle-related genes, located synthetically on pro-chr2 and pro-chr28, exhibited significant changes in expression. This, combined with genome-scale structural variants and expression alterations in genes involved in myofibril composition, may have driven the rapid sarcomere adaptation of gayal to its rugged mountain habitat. Our findings not only suggest that large-scale chromosomal changes can lead to alterations in genome-level expression, thereby promoting both adaptation and speciation, but also illuminate novel avenues for studying the relationship between karyotype evolution and speciation.
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Affiliation(s)
- Yan Li
- Corresponding authors: E-mails: ;
| | | | | | | | | | | | | | | | - Li-Li Wang
- Biomarker Technologies Corporation, Beijing, China
| | - Jie Li
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Shi-Fang Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Sheng He
- Nujiang Livestock Technology Promotion Station, Nujiang, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, ON, Canada
| | - Zi-Jie Zhang
- State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan and School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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27
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Peres PA, Bracken-Grissom H, Timm LE, Mantelatto FL. Genomic Analyses Implicate the Amazon-Orinoco Plume as the Driver of Cryptic Speciation in a Swimming Crab. Genes (Basel) 2022; 13:genes13122263. [PMID: 36553531 PMCID: PMC9777557 DOI: 10.3390/genes13122263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/04/2022] Open
Abstract
The Amazon-Orinoco plume (AOP) is the world's largest freshwater and sediment discharge into the ocean. Previous studies limited to mtDNA suggest that the swimming crab Callinectes ornatus Ordway, 1863 exists as two distinct genetic clusters separated by the AOP. However, questions concerning migration, diversification time, and species delimitation are unresolved. Densely sampling markers across the genome (SNPs) could elucidate the evolutionary processes within this species. Here, we combined mtDNA data and ddRAD-seq to explore the diversification patterns and processes within the swimming crab C. ornatus. We show great genetic differentiation between groups on the north and south sides of the plume but also signs of hybridization. Demographic modeling indicates the divergence between groups starting around 8 Mya following the AOP's formation. After a period of isolation, we detect two incidences of secondary contact with stronger migration in concordance with the North Brazil Current flow. Our results suggest speciation with gene flow explained by the interplay among the AOP, oceanographic currents, and long larval dispersal. This work represents the first investigation employing ddRAD-seq in a marine invertebrate species with distribution encompassing the north and south Atlantic and sheds light on the role of the AOP in the diversification of a marine species.
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Affiliation(s)
- Pedro A. Peres
- Department of Biology, Institute of Environment, Florida International University (FIU), Miami, FL 33199, USA
- Laboratory of Bioecology and Systematics of Crustaceans (LBSC), Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto 14040-901, Brazil
- Correspondence:
| | - Heather Bracken-Grissom
- Department of Biology, Institute of Environment, Florida International University (FIU), Miami, FL 33199, USA
- Department of Invertebrate Zoology, National Museum of Natural History-Smithsonian, Washington, WA 20013-7012, USA
| | - Laura E. Timm
- College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK 99775, USA
- Auke Bay Laboratories, Alaska Fisheries Science Center, NOAA National Marine Fisheries Service, Juneau, AK 99801, USA
| | - Fernando L. Mantelatto
- Laboratory of Bioecology and Systematics of Crustaceans (LBSC), Faculty of Philosophy, Sciences and Letters at Ribeirão Preto (FFCLRP), University of São Paulo (USP), Ribeirão Preto 14040-901, Brazil
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28
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Arnqvist G, Sayadi A. A possible genomic footprint of polygenic adaptation on population divergence in seed beetles? Ecol Evol 2022; 12:e9440. [PMID: 36311399 PMCID: PMC9608792 DOI: 10.1002/ece3.9440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 09/14/2022] [Accepted: 09/29/2022] [Indexed: 11/25/2022] Open
Abstract
Efforts to unravel the genomic basis of incipient speciation are hampered by a mismatch between our toolkit and our understanding of the ecology and genetics of adaptation. While the former is focused on detecting selective sweeps involving few independently acting or linked speciation genes, the latter states that divergence typically occurs in polygenic traits under stabilizing selection. Here, we ask whether a role of stabilizing selection on polygenic traits in population divergence may be unveiled by using a phenotypically informed integrative approach, based on genome‐wide variation segregating in divergent populations. We compare three divergent populations of seed beetles (Callosobruchus maculatus) where previous work has demonstrated a prominent role for stabilizing selection on, and population divergence in, key life history traits that reflect rate‐dependent metabolic processes. We derive and assess predictions regarding the expected pattern of covariation between genetic variation segregating within populations and genetic differentiation between populations. Population differentiation was considerable (mean FST = 0.23–0.26) and was primarily built by genes showing high selective constraints and an imbalance in inferred selection in different populations (positive Tajima's DNS in one and negative in one), and this set of genes was enriched with genes with a metabolic function. Repeatability of relative population differentiation was low at the level of individual genes but higher at the level of broad functional classes, again spotlighting metabolic genes. Absolute differentiation (dXY) showed a very different general pattern at this scale of divergence, more consistent with an important role for genetic drift. Although our exploration is consistent with stabilizing selection on polygenic metabolic phenotypes as an important engine of genome‐wide relative population divergence and incipient speciation in our study system, we note that it is exceedingly difficult to firmly exclude other scenarios.
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Affiliation(s)
- Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden
| | - Ahmed Sayadi
- Animal Ecology, Department of Ecology and Genetics, EBCUppsala UniversityUppsalaSweden,Rheumatology, Department of Medical SciencesUppsala UniversityUppsalaSweden
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29
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Cortés AJ, López-Hernández F, Blair MW. Genome–Environment Associations, an Innovative Tool for Studying Heritable Evolutionary Adaptation in Orphan Crops and Wild Relatives. Front Genet 2022; 13:910386. [PMID: 35991553 PMCID: PMC9389289 DOI: 10.3389/fgene.2022.910386] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/30/2022] [Indexed: 11/23/2022] Open
Abstract
Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources of adaptation from landraces, crop wild relatives, and orphan crops is a key prerequisite to accelerate genetic gain of abiotic stress tolerance in annual crops such as legumes and cereals, many of which are still orphan species despite advances in major row crops. Here, we review a novel, interdisciplinary approach to combine ecological climate data with evolutionary genomics under the paradigm of a new field of study: genome–environment associations (GEAs). We first exemplify how GEA utilizes in situ georeferencing from genotypically characterized, gene bank accessions to pinpoint genomic signatures of natural selection. We later discuss the necessity to update the current GEA models to predict both regional- and local- or micro-habitat–based adaptation with mechanistic ecophysiological climate indices and cutting-edge GWAS-type genetic association models. Furthermore, to account for polygenic evolutionary adaptation, we encourage the community to start gathering genomic estimated adaptive values (GEAVs) for genomic prediction (GP) and multi-dimensional machine learning (ML) models. The latter two should ideally be weighted by de novo GWAS-based GEA estimates and optimized for a scalable marker subset. We end the review by envisioning avenues to make adaptation inferences more robust through the merging of high-resolution data sources, such as environmental remote sensing and summary statistics of the genomic site frequency spectrum, with the epigenetic molecular functionality responsible for plastic inheritance in the wild. Ultimately, we believe that coupling evolutionary adaptive predictions with innovations in ecological genomics such as GEA will help capture hidden genetic adaptations to abiotic stresses based on crop germplasm resources to assist responses to climate change. “I shall endeavor to find out how nature’s forces act upon one another, and in what manner the geographic environment exerts its influence on animals and plants. In short, I must find out about the harmony in nature” Alexander von Humboldt—Letter to Karl Freiesleben, June 1799.
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Affiliation(s)
- Andrés J. Cortés
- Corporacion Colombiana de Investigacion Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
- *Correspondence: Andrés J. Cortés, ; Matthew W. Blair,
| | - Felipe López-Hernández
- Corporacion Colombiana de Investigacion Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Matthew W. Blair
- Department of Agricultural & Environmental Sciences, Tennessee State University, Nashville, TN, United States
- *Correspondence: Andrés J. Cortés, ; Matthew W. Blair,
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Brachmann MK, Parsons K, Skúlason S, Gaggiotti O, Ferguson M. Variation in the genomic basis of parallel phenotypic and ecological divergence in benthic and pelagic morphs of Icelandic Arctic charr (Salvelinus alpinus). Mol Ecol 2022; 31:4688-4706. [PMID: 35861579 DOI: 10.1111/mec.16625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 06/22/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022]
Abstract
Sympatric adaptive phenotypic divergence should be underlain by genomic differentiation between sub-populations. When divergence drives similar patterns of phenotypic and ecological variation within species we expect evolution to draw on common allelic variation. We investigated divergence histories and genomic signatures of adaptive divergence between benthic and pelagic morphs of Icelandic Arctic charr. Divergence histories for each of four populations were reconstructed using coalescent modelling and 14,187 single nucleotide polymorphisms. Sympatric divergence with continuous gene flow was supported in two populations while allopatric divergence with secondary contact was supported in one population; we could not differentiate between demographic models in the fourth population. We detected parallel patterns of phenotypic divergence along benthic-pelagic evolutionary trajectories among populations. Patterns of genomic differentiation between benthic and pelagic morphs were characterized by outlier loci in many narrow peaks of differentiation throughout the genome, which may reflect the eroding effects of gene flow on nearby neutral loci. We then used genome-wide association analyses to relate both phenotypic (body shape and size) and ecological (carbon and nitrogen stable isotopes) variation to patterns of genomic differentiation. Many peaks of genomic differentiation were associated with phenotypic and ecological variation in the three highly divergent populations, suggesting a genomic basis for adaptive divergence. We detected little evidence for a parallel genomic basis of differentiation as most regions and outlier loci were not shared among populations. Our results show that adaptive divergence can have varied genomic consequences in populations with relatively recent common origins, similar divergence histories, and parallel phenotypic divergence.
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Affiliation(s)
| | - Kevin Parsons
- Institute of Biodiversity, Animal Health and Comparative Medicine, School of Life Science, University of Glasgow, Glasgow, UK
| | - Skúli Skúlason
- Department of Aquaculture and Fish Biology, Hólar University, Saudárkrókur, Iceland.,Icelandic Museum of Natural History, Reykjavik, Iceland
| | - Oscar Gaggiotti
- School of biology, Scottish Oceans Institute, University of St. Andrews, St. Andrews, UK
| | - Moira Ferguson
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
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31
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Hou Z, Li A. Genomic Differentiation and Demographic Histories of Two Closely Related Salicaceae Species. FRONTIERS IN PLANT SCIENCE 2022; 13:911467. [PMID: 35747877 PMCID: PMC9210983 DOI: 10.3389/fpls.2022.911467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Populus alba (P. alba) and Populus davidiana (P. davidiana) are important plant species for answering a variety of issues on species evolution due to their wide distribution and ability to adapt to a variety of environments and climates. Even though P. alba and P. davidiana belong to ecologically and economically important forest trees in the Northern Hemisphere, little is known about their genomic landscape and genome divergence during speciation. We re-sequenced 20 and 19 members of P. davidiana and P. alba, respectively, and found that the Dxy value between P. alba and P. davidiana was 0.2658, whereas the F ST values were 0.2988, indicating that the genetic divergence was fairly clear. Populus davidiana and P. alba diverged from the ancestor in the middle Pleistocene, c. 0.80 Ma (95% HPD: 0.79-0.81 Ma). The population sizes of P. davidiana increased ~20,000 years ago after a considerable long-term decline following divergence. However, after differentiation, the effective population size of P. alba expanded slightly before experiencing a long-term bottleneck effect. According to the expectation of allopatric speciation, we found a significant number of genomic differentiation sites in both species' speciation events, and the majority of these genomic differentiation regions can be attributed to neutral evolutionary processes. Nevertheless, the regions with extreme divergence exist in abundance, indicating that natural selection has had an impact. Positive selection can be found in highly differentiated regions, while long-term balancing selection traits can be easily observed in low differentiated regions. According to these findings, climate differences over the Quaternary, as well as variance in linked selection and recombination, all contributed significantly to genomic divergence during allopatric speciation of the two aspens.
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32
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Neo-sex chromosome evolution shapes sex-dependent asymmetrical introgression barrier. Proc Natl Acad Sci U S A 2022; 119:e2119382119. [PMID: 35512091 PMCID: PMC9171612 DOI: 10.1073/pnas.2119382119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
It is increasingly recognized that sex chromosomes are not only the battlegrounds between sexes but also the Great Walls fencing off introgression between diverging lineages. Here we dissect the multifaceted roles of sex chromosomes using experimental evolution, whole-genome resequencing, and theoretical modeling, taking advantage of hybrid populations between a Drosophila sister species pair in the early stage of speciation that have different sex chromosome systems. Our work sheds light onto the complex roles of neo-sex chromosome evolution in creating a sex-dependent asymmetrical introgression barrier at a species boundary, and we show how diverse population genetic forces act in concert to explain observed patterns of introgression across the genome. Sex chromosomes play a special role in the evolution of reproductive barriers between species. Here we describe conflicting roles of nascent sex chromosomes on patterns of introgression in an experimental hybrid swarm. Drosophila nasuta and Drosophila albomicans are recently diverged, fully fertile sister species that have different sex chromosome systems. The fusion between an autosome (Muller CD) with the ancestral X and Y gave rise to neo-sex chromosomes in D. albomicans, while Muller CD remains unfused in D. nasuta. We found that a large block containing overlapping inversions on the neo-sex chromosome stood out as the strongest barrier to introgression. Intriguingly, the neo-sex chromosome introgression barrier is asymmetrical and sex-dependent. Female hybrids showed significant D. albomicans–biased introgression on Muller CD (neo-X excess), while males showed heterosis with excessive (neo-X, D. nasuta Muller CD) genotypes. We used a population genetic model to dissect the interplay of sex chromosome drive, heterospecific pairing incompatibility between the neo-sex chromosomes and unfused Muller CD, neo-Y disadvantage, and neo-X advantage in generating the observed sex chromosome genotypes in females and males. We show that moderate neo-Y disadvantage and D. albomicans specific meiotic drive are required to observe female-specific D. albomicans–biased introgression in this system, together with pairing incompatibility and neo-X advantage. In conclusion, this hybrid swarm between a young species pair sheds light onto the multifaceted roles of neo-sex chromosomes in a sex-dependent asymmetrical introgression barrier at a species boundary.
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33
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Gao W, Yu CX, Zhou WW, Zhang BL, Chambers EA, Dahn HA, Jin JQ, Murphy RW, Zhang YP, Che J. Species persistence with hybridization in toad-headed lizards driven by divergent selection and low recombination. Mol Biol Evol 2022; 39:6561330. [PMID: 35356979 PMCID: PMC9007161 DOI: 10.1093/molbev/msac064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Speciation plays a central role in evolutionary studies, and particularly how reproductive isolation (RI) evolves. The origins and persistence of RI are distinct processes that require separate evaluations. Treating them separately clarifies the drivers of speciation and then it is possible to link the processes to understand large-scale patterns of diversity. Recent genomic studies have focused predominantly on how species or RI originate. However, we know little about how species persist in face of gene flow. Here, we evaluate a contact zone of two closely related toad-headed lizards (Phrynocephalus) using a chromosome-level genome assembly and population genomics. To some extent, recent asymmetric introgression from Phrynocephalus putjatai to P. vlangalii reduces their genomic differences. However, their highly divergent regions (HDRs) have heterogeneous distributions across the genomes. Functional gene annotation indicates that many genes within HDRs are involved in reproduction and RI. Compared with allopatric populations, contact areas exhibit recent divergent selection on the HDRs and a lower population recombination rate. Taken together, this implies that divergent selection and low genetic recombination help maintain RI. This study provides insights into the genomic mechanisms that drive RI and two species persistence in the face of gene flow during the late stage of speciation.
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Affiliation(s)
- Wei Gao
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Chuan-Xin Yu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Wei-Wei Zhou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, University of Texas at Austin, Austin, USA.,Department of Environmental Science, Policy, and Management, Univerity of California, Berkeley, USA
| | - Hollis A Dahn
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Jie-Qiong Jin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Robert W Murphy
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, Ontario, Canada
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Jing Che
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Key Laboratory of Biodiversity and Ecological Security of Gaoligong Mountain, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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34
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Bendall EE, Bagley RK, Sousa VC, Linnen CR. Faster-haplodiploid evolution under divergence-with-gene-flow: simulations and empirical data from pine-feeding hymenopterans. Mol Ecol 2022; 31:2348-2366. [PMID: 35231148 DOI: 10.1111/mec.16410] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 11/28/2022]
Abstract
Although haplodiploidy is widespread in nature, the evolutionary consequences of this mode of reproduction are not well characterized. Here, we examine how genome-wide hemizygosity and a lack of recombination in haploid males affects genomic differentiation in populations that diverge via natural selection while experiencing gene flow. First, we simulated diploid and haplodiploid "genomes" (500-kb loci) evolving under an isolation-with-migration model with mutation, drift, selection, migration, and recombination; and examined differentiation at neutral sites both tightly and loosely linked to a divergently selected site. So long as there is divergent selection and migration, sex-limited hemizygosity and recombination cause elevated differentiation (i.e., produce a "faster-haplodiploid effect") in haplodiploid populations relative to otherwise equivalent diploid populations, for both recessive and codominant mutations. Second, we used genome-wide SNP data to model divergence history and describe patterns of genomic differentiation between sympatric populations of Neodiprion lecontei and N. pinetum, a pair of pine sawfly species (order: Hymenoptera; family: Diprionidae) that are specialized on different pine hosts. These analyses support a history of continuous gene exchange throughout divergence and reveal a pattern of heterogeneous genomic differentiation that is consistent with divergent selection on many unlinked loci. Third, using simulations of haplodiploid and diploid populations evolving according to the estimated divergence history of N. lecontei and N. pinetum, we found that divergent selection would lead to higher differentiation in haplodiploids. Based on these results, we hypothesize that haplodiploids undergo divergence-with-gene-flow and sympatric speciation more readily than diploids.
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Affiliation(s)
- Emily E Bendall
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Robin K Bagley
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA.,Department of Evolution, Ecology, and Organismal Biology, The Ohio State University at Lima, Lima, OH, 45804, USA
| | - Vitor C Sousa
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Campo Grande 1749-016, Lisboa, Portugal
| | - Catherine R Linnen
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA
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35
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Shaker Al-Rubaiee Z, Salh Hussin M, Baho S. Evolutionary Relationship and the Sequence Similarities among Different Fungal Species Infecting Birds Captured from Different Areas in Denmark. ARCHIVES OF RAZI INSTITUTE 2022; 77:491-496. [PMID: 35891731 PMCID: PMC9288641 DOI: 10.22092/ari.2021.356858.1929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 12/19/2021] [Indexed: 06/15/2023]
Abstract
Fungal diseases are the common cause of death in wild animals and birds of prey. This study was designed to investigate the development of fungal infections among wild birds in Denmark. In this study, fungal samples were isolated from such sources as Barn swallows' feathers, White stork, and birds of prey. The fungal species were isolated by direct culture of feathers on SD Agar with chloramphenicol and incubated at 28±2ºC. The fungal genomic DNA was isolated from each species, PCR reaction was performed, and the resulting fragments of the 18S rRNA DNA were sequenced and used for identification. A comparison between the resulting fragments was made to find out the percentage of similarity among the different fungal species. The multiple sequence alignment showed percentages of similarities ranging from 39% to 99%. To sum up, the 18S rRNA DNA sequence has been evolved dramatically even within the same species, while still conserved in others. It is a useful tool to be used for the identification of fungal species as it reduces time. Moreover, according to the results, there were no comprehensive high homology percentages among the species infecting the same bird.
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Affiliation(s)
- Z Shaker Al-Rubaiee
- Biological Department, College of Science, Mustansiriya University, Baghdad, Iraq
| | - M Salh Hussin
- Biological Department, College of Science, Mustansiriya University, Baghdad, Iraq
| | - S Baho
- Biological Department, College of Science, Mustansiriya University, Baghdad, Iraq
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36
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Finger N, Farleigh K, Bracken JT, Leaché AD, François O, Yang Z, Flouri T, Charran T, Jezkova T, Williams DA, Blair C. Genome-scale data reveal deep lineage divergence and a complex demographic history in the Texas horned lizard (Phrynosoma cornutum) throughout the southwestern and central US. Genome Biol Evol 2021; 14:6443127. [PMID: 34849831 PMCID: PMC8735750 DOI: 10.1093/gbe/evab260] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2021] [Indexed: 12/03/2022] Open
Abstract
The southwestern and central United States serve as an ideal region to test alternative hypotheses regarding biotic diversification. Genomic data can now be combined with sophisticated computational models to quantify the impacts of paleoclimate change, geographic features, and habitat heterogeneity on spatial patterns of genetic diversity. In this study, we combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA sequences (ND1) from the Texas horned lizard (Phrynosoma cornutum) to quantify relative support for different catalysts of diversification. Phylogenetic and clustering analyses of the GBS data indicate support for at least three primary populations. The spatial distribution of populations appears concordant with habitat type, with desert populations in AZ and NM showing the largest genetic divergence from the remaining populations. The mtDNA data also support a divergent desert population, but other relationships differ and suggest mtDNA introgression. Genotype–environment association with bioclimatic variables supports divergence along precipitation gradients more than along temperature gradients. Demographic analyses support a complex history, with introgression and gene flow playing an important role during diversification. Bayesian multispecies coalescent analyses with introgression (MSci) analyses also suggest that gene flow occurred between populations. Paleo-species distribution models support two southern refugia that geographically correspond to contemporary lineages. We find that divergence times are underestimated and population sizes are overestimated when introgression occurred and is ignored in coalescent analyses, and furthermore, inference of ancient introgression events and demographic history is sensitive to inclusion of a single recently admixed sample. Our analyses cannot refute the riverine barrier or glacial refugia hypotheses. Results also suggest that populations are continuing to diverge along habitat gradients. Finally, the strong evidence of admixture, gene flow, and mtDNA introgression among populations suggests that P. cornutum should be considered a single widespread species under the General Lineage Species Concept.
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Affiliation(s)
- Nicholas Finger
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY, 11201, USA
| | - Keaka Farleigh
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA
| | - Jason T Bracken
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA
| | - Adam D Leaché
- Department of Biology & Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, 98195, USA
| | - Olivier François
- Faculty of Medicine, University Grenoble-Alpes, TIMC-IMAG UMR 5525, Grenoble, La Tronche, F38706, France 38000
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Tomas Flouri
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Tristan Charran
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY, 11201, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA
| | - Dean A Williams
- Department of Biology, Texas Christian University, 2800 S University Dr, Fort Worth, TX, 76129, USA
| | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY, 11201, USA.,Biology PhD Program, CUNY Graduate Center, 365 5th Ave, New York, NY, 10016, USA
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37
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Burbrink FT, Bernstein JM, Kuhn A, Gehara M, Ruane S. Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulum Complex). Syst Biol 2021; 71:839-858. [PMID: 35043210 DOI: 10.1093/sysbio/syab093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/13/2022] Open
Abstract
Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with geographic space, contemporary and historical climate, and biogeographic barriers have complex effects on contemporary population genetic structure and processes of speciation. While allopatric speciation at biogeographic barriers is considered the primary mechanism for generating species, more recently it has been shown that parapatric modes of divergence may be equally or even more common. With genomic data and better modeling capabilities, we can more clearly define causes of speciation in relation to biogeography and migration between lineages, the location of hybrid zones with respect to the ecology of parental lineages, and differential introgression of genes between taxa. Here, we examine the origins of three Nearctic milksnakes (Lampropeltis elapsoides, Lampropeltis triangulum and Lampropeltis gentilis) using genome-scale data to better understand species diversification. Results from artificial neural networks show that a mix of a strong biogeographic barrier, environmental changes, and physical space has affected genetic structure in these taxa. These results underscore conspicuous environmental changes that occur as the sister taxa L. triangulum and L. gentilis diverged near the Great Plains into the forested regions of the Eastern Nearctic. This area has been recognized as a region for turnover for many vertebrate species, but as we show here the contemporary boundary does not isolate these sister species. These two species likely formed in the mid-Pleistocene and have remained partially reproductively isolated over much of this time, showing differential introgression of loci. We also demonstrate that when L. triangulum and L. gentilis are each in contact with the much older L. elapsoides, some limited gene flow has occurred. Given the strong agreement between nuclear and mtDNA genomes, along with estimates of ecological niche, we suggest that all three lineages should continue to be recognized as unique species. Furthermore, this work emphasizes the importance of considering complex modes of divergence and differential allelic introgression over a complex landscape when testing mechanisms of speciation. [Cline; delimitation; Eastern Nearctic; Great Plains; hybrids; introgression; speciation.].
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Justin M Bernstein
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Arianna Kuhn
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA
| | - Sara Ruane
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ 07102, USA.,Amphibian and Reptile Collection, Negaunee Integrative Research Center, Field Museum of Natural History, 1400 S Lake Shore Dr, Chicago, IL 60605, USA
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38
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St John CA, Buser TJ, Kee VE, Kirilchik S, Bogdanov B, Neely D, Sandel M, Aguilar A. Diversification along a benthic to pelagic gradient contributes to fish diversity in the world's largest lake (Lake Baikal, Russia). Mol Ecol 2021; 31:238-251. [PMID: 34614231 DOI: 10.1111/mec.16209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 09/03/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022]
Abstract
Insights into the generation of diversity in both plants and animals have relied heavily on studying speciation in adaptive radiations. Russia's Lake Baikal has facilitated a putative adaptive radiation of cottid fishes (sculpins), some of which are highly specialized to inhabit novel niches created by the lake's unique geology and ecology. Here, we test evolutionary relationships and novel morphological adaptation in a piece of this radiation: the Baikal cottid genus, Cottocomephorus, a morphologically derived benthopelagic genus of three described species. We used a combination of mitochondrial DNA and restriction site associated DNA sequencing from all Cottocomephorus species. Analysis of mitochondrial cytochrome b haplotypes was only able to two resolve two lineages: C. grewingkii and C. comephoroides/inermis. Phylogenetic inference, principal component analysis, and faststructure of genome-wide SNPs uncovered three lineages within Cottocomephorus: C. comephoroides, C. inermis and C. grewingkii. We found recent divergence and admixture between C. comephoroides and C. inermis and deep divergence between these two species and C. grewingkii. Contrasting other fish radiations, we found no evidence of ancient hybridization among Cottocomephorus species. Digital morphology revealed highly derived pelagic phenotypes that reflect divergence by specialization to the benthopelagic niche in Cottocomephorus. Among Cottocomephorus species, we found evidence of ongoing adaptation to the pelagic zone. This pattern highlights the importance of speciation along a benthic-pelagic gradient seen in Cottocomephorus and across other adaptive fish radiations.
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Affiliation(s)
- Carl A St John
- Department of Biological Science, California State University Los Angeles, Los Angeles, California, USA
| | - Thaddaeus J Buser
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, USA
| | - Victoria E Kee
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, USA
| | - Sergei Kirilchik
- Limnological Institute, Russian Academy of Sciences, Irkutsk, Russia
| | - Bakhtiar Bogdanov
- Limnological Institute, Russian Academy of Sciences, Irkutsk, Russia
| | - David Neely
- Tennessee Aquarium Conservation Institute, Chattanooga, Tennessee, USA
| | - Michael Sandel
- Biological and Environmental Sciences, University of Western Alabama, Livingston, Alabama, USA
| | - Andres Aguilar
- Department of Biological Science, California State University Los Angeles, Los Angeles, California, USA
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39
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Chafin TK, Regmi B, Douglas MR, Edds DR, Wangchuk K, Dorji S, Norbu P, Norbu S, Changlu C, Khanal GP, Tshering S, Douglas ME. Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210727. [PMID: 34729207 PMCID: PMC8548808 DOI: 10.1098/rsos.210727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological 'ecotypes' observed in polyploid snowtrout (Cyprinidae: Schizothorax). However, parallel patterns of differential introgression during secondary contact are a viable alternative hypothesis. Here, we used ddRADseq (N = 35 319 de novo and N = 10 884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples (N = 48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational 'ecotypes' were consistent in geometric morphometric space, but with phylogenetic relationships at the drainage level, sustaining a hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively 'masks' previous isolation. Our results underscore two salient factors: (i) morphological adaptations are retained despite hybridization and (ii) the degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.
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Affiliation(s)
- Tyler K. Chafin
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder 80309, USA
| | - Binod Regmi
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS), National Institutes of Health, Bethesda, MD 20892, USA
| | - Marlis R. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - David R. Edds
- Department of Biological Sciences, Emporia State University, Emporia, KS 66801, USA
| | - Karma Wangchuk
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Sonam Dorji
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Pema Norbu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Sangay Norbu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Changlu Changlu
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Gopal Prasad Khanal
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Singye Tshering
- National Research and Development Centre for Riverine and Lake Fisheries, Ministry of Agriculture and Forests, Royal Government of Bhutan, Haa, Bhutan
| | - Michael E. Douglas
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
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40
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Myers EA. Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Mol Phylogenet Evol 2021; 165:107313. [PMID: 34537323 DOI: 10.1016/j.ympev.2021.107313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/28/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group.
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Affiliation(s)
- Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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41
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Mass of genes rather than master genes underlie the genomic architecture of amphibian speciation. Proc Natl Acad Sci U S A 2021; 118:2103963118. [PMID: 34465621 DOI: 10.1073/pnas.2103963118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic architecture of speciation, i.e., how intrinsic genomic incompatibilities promote reproductive isolation (RI) between diverging lineages, is one of the best-kept secrets of evolution. To directly assess whether incompatibilities arise in a limited set of large-effect speciation genes, or in a multitude of loci, we examined the geographic and genomic landscapes of introgression across the hybrid zones of 41 pairs of frog and toad lineages in the Western Palearctic region. As the divergence between lineages increases, phylogeographic transitions progressively become narrower, and larger parts of the genome resist introgression. This suggests that anuran speciation proceeds through a gradual accumulation of multiple barrier loci scattered across the genome, which ultimately deplete hybrid fitness by intrinsic postzygotic isolation, with behavioral isolation being achieved only at later stages. Moreover, these loci were disproportionately sex linked in one group (Hyla) but not in others (Rana and Bufotes), implying that large X-effects are not necessarily a rule of speciation with undifferentiated sex chromosomes. The highly polygenic nature of RI and the lack of hemizygous X/Z chromosomes could explain why the speciation clock ticks slower in amphibians compared to other vertebrates. The clock-like dynamics of speciation combined with the analytical focus on hybrid zones offer perspectives for more standardized practices of species delimitation.
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42
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Campbell MA, Anderson EC, Garza JC, Pearse DE. Polygenic basis and the role of genome duplication in adaptation to similar selective environments. J Hered 2021; 112:614-625. [PMID: 34420047 DOI: 10.1093/jhered/esab049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 08/20/2021] [Indexed: 02/02/2023] Open
Abstract
Genetic changes underlying adaptation vary greatly in terms of complexity and, within the same species, genetic responses to similar selective pressures may or may not be the same. We examine both complex (supergene) and simple (SNP) genetic variants occurring in populations of rainbow trout (Oncorhynchus mykiss) independently isolated from ocean access and compared them to each other and to an anadromous below-barrier population representing their ancestral source to search for signatures of both parallel and non-parallel adaptation. All landlocked populations displayed an increased frequency of a large inversion on chromosome Omy05, while three of the four populations exhibited elevated frequencies of another inversion located on chromosome Omy20. In addition, we identified numerous regions outside these two inversions that also show significant shifts in allele frequencies consistent with adaptive evolution. However, there was little concordance among above-barrier populations in these specific genomic regions under selection. In part, the lack of concordance appears to arise from ancestral autopolyploidy in rainbow trout that provides duplicate genomic regions of similar functional composition for selection to act upon. Thus, while selection acting on landlocked populations universally favors the resident ecotype, outside of the major chromosomal inversions, the resulting genetic changes are largely distinct among populations. Our results indicate that selection on standing genetic variation is likely the primary mode of rapid adaptation, and that both supergene complexes and individual loci contribute to adaptive evolution, further highlighting the diversity of adaptive genomic variation involved in complex phenotypic evolution.
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Affiliation(s)
- Matthew A Campbell
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Eric C Anderson
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - John Carlos Garza
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
| | - Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, USA
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43
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Manthey JD, Klicka J, Spellman GM. The Genomic Signature of Allopatric Speciation in a Songbird Is Shaped by Genome Architecture (Aves: Certhia americana). Genome Biol Evol 2021; 13:evab120. [PMID: 34042960 PMCID: PMC8364988 DOI: 10.1093/gbe/evab120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 12/31/2022] Open
Abstract
The genomic signature of speciation with gene flow is often attributed to the strength of divergent selection and recombination rate in regions harboring targets for selection. In contrast, allopatric speciation provides a different geographic context and evolutionary scenario, whereby introgression is limited by isolation rather than selection against gene flow. Lacking shared divergent selection or selection against hybridization, we would predict the genomic signature of allopatric speciation would largely be shaped by genomic architecture-the nonrandom distribution of functional elements and chromosomal characteristics-through its role in affecting the processes of selection and drift. Here, we built and annotated a chromosome-scale genome assembly for a songbird (Passeriformes: Certhia americana). We show that the genomic signature of allopatric speciation between its two primary lineages is largely shaped by genomic architecture. Regionally, gene density and recombination rate variation explain a large proportion of variance in genomic diversity, differentiation, and divergence. We identified a heterogeneous landscape of selection and neutrality, with a large portion of the genome under the effects of indirect selection. We found higher proportions of small chromosomes under the effects of indirect selection, likely because they have relatively higher gene density. At the chromosome scale, differential genomic architecture of macro- and microchromosomes shapes the genomic signatures of speciation: chromosome size has: 1) a positive relationship with genetic differentiation, genetic divergence, rate of lineage sorting in the contact zone, and proportion neutral evolution and 2) a negative relationship with genetic diversity and recombination rate.
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Affiliation(s)
- Joseph D Manthey
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - John Klicka
- Burke Museum of Natural History, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, Colorado, USA
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44
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Porter CK, Confer JL, Aldinger KR, Canterbury RA, Larkin JL, McNeil DJ. Strong yet incomplete reproductive isolation in Vermivora is not contradicted by other lines of evidence: A reply to Toews et al. Ecol Evol 2021; 11:10724-10730. [PMID: 34367609 PMCID: PMC8328446 DOI: 10.1002/ece3.7763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 11/16/2022] Open
Abstract
Toews et al. assert that strong reproductive isolation in Vermivora is inconsistent with other lines of evidence. Here, we discuss how strong yet incomplete reproductive isolation is consistent with other results from this system.
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Affiliation(s)
- Cody K. Porter
- Wildlife Biology ProgramLees‐McRae CollegeBanner ElkNCUSA
| | | | - Kyle R. Aldinger
- West Virginia Cooperative Fish and Wildlife Research UnitDivision of Forestry and Natural ResourcesWest Virginia UniversityMorgantownWVUSA
| | | | | | - Darin J. McNeil
- Department of EntomologyThe Pennsylvania State UniversityUniversity ParkPAUSA
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45
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Behrens KA, Girasek QL, Sickler A, Hyde J, Buonaccorsi VP. Regions of genetic divergence in depth-separated Sebastes rockfish species pairs: Depth as a potential driver of speciation. Mol Ecol 2021; 30:4259-4275. [PMID: 34181798 DOI: 10.1111/mec.16046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/20/2022]
Abstract
Depth separation is a proposed driver of speciation in marine fishes, with marine rockfish (genus Sebastes) providing a potentially informative study system. Sebastes rockfishes are commercially and ecologically important. This genus encompasses more than one hundred species and the ecological and morphological variance between these species provides opportunity for identifying speciation-driving adaptations, particularly along a depth gradient. A reduced-representation sequencing method (ddRADseq) was used to compare 95 individuals encompassing six Sebastes species. In this study, we sought to identify regions of divergence between species that were indicative of divergent adaptation and reproductive barriers leading to speciation. A pairwise comparison of S. chrysomelas (black-and-yellow rockfish) and S. carnatus (gopher rockfish) FST values revealed three major regions of elevated genomic divergence, two of which were also present in the S. miniatus (vermilion rockfish) and S. crocotulus (sunset rockfish) comparison. These corresponded with regions of both elevated DXY values and reduced nucleotide diversity in two cases, suggesting a speciation-with-gene-flow evolutionary model followed by post-speciation selective sweeps within each species. Limited whole-genome resequencing was also performed to identify mutations with predicted effects between S. chrysomelas and S. carnatus. Within these islands, we identified important SNPs in genes involved in immune function and vision. This supports their potential role in speciation, as these are adaptive vectors noted in other organisms. Additionally, changes to genes involved in pigment expression and mate recognition shed light on how S. chrysomelas and S. carnatus may have become reproductively isolated.
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Affiliation(s)
- Kristen A Behrens
- Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA
| | - Quinn L Girasek
- Department of Biology, Juniata College, Huntingdon, Pennsylvania, USA
| | - Alex Sickler
- Center for Data Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - John Hyde
- Fisheries Resources Division, Southwest Fisheries Science Center, NOAA Fisheries, La Jolla, California, USA
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46
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Chabot AA, Lougheed SC. Integrative assessment of intraspecific diversification in Loggerhead Shrike ( Lanius ludovicianus) provides insight on the geographic pattern of phenotypic divergence and process of speciation. CAN J ZOOL 2021. [DOI: 10.1139/cjz-2020-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Integrated studies of the geographical, ecological, and historical factors that shape intraspecific phenotypic and genetic variation can help us to decipher the processes leading to geographic patterns of population divergence and speciation. We quantify and compare morphological and genetic variation in the Loggerhead Shrike (Lanius ludovicianus Linnaeus, 1766), a broadly distributed passerine in North America with both migratory and non-migratory populations that occupy a diversity of habitats and topographies. The geographic distributions and patterns of differentiation among subspecies suggest that migration has strongly impacted population divergence, including the habit of migrating itself, but also dispersal. Patterns of mitochondrial and nuclear genetic differentiation can be attributed to female-biased dispersal and to increased dispersal rates and distances in migratory populations. Weak phenotypic differentiation among migratory versus migratory and non-migratory populations suggest that migration may more strongly affect morphology than adaptation to local habitats. Our results generally support previous subspecific designations with two notable exceptions. We found little genetic differentiation between two subspecies (Lanius ludovicianus gambeli Ridgway, 1887 and Lanius ludovicianus mexicanus C.L. Brehm, 1854), but identify a new, distinct subspecies, which we refer to as Lanius ludovicianus centralis ssp. nov.
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Affiliation(s)
- Amy A. Chabot
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
- African Lion Safari, Cambridge, ON N1R 5S2, Canada
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47
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Jermy T, Szentesi Á. Why are there not more herbivorous insect species? ACTA ZOOL ACAD SCI H 2021. [DOI: 10.17109/azh.67.2.119.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Insect species richness is estimated to exceed three million species, of which roughly half is herbivorous. Despite the vast number of species and varied life histories, the proportion of herbivorous species among plant-consuming organisms is lower than it could be due to constraints that impose limits to their diversification. These include ecological factors, such as vague interspecific competition; anatomical and physiological limits, such as neural limits and inability of handling a wide range of plant allelochemicals; phylogenetic constraints, like niche conservatism; and most importantly, a low level of concerted genetic variation necessary to a phyletic conversion. It is suggested that diversification ultimately depends on what we call the intrinsic trend of diversification of the insect genome. In support of the above, we survey the major types of host-specificity, the mechanisms and constraints of host specialization, possible pathways of speciation, and hypotheses concerning insect diversification.
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48
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Vershinina AO, Heintzman PD, Froese DG, Zazula G, Cassatt-Johnstone M, Dalén L, Der Sarkissian C, Dunn SG, Ermini L, Gamba C, Groves P, Kapp JD, Mann DH, Seguin-Orlando A, Southon J, Stiller M, Wooller MJ, Baryshnikov G, Gimranov D, Scott E, Hall E, Hewitson S, Kirillova I, Kosintsev P, Shidlovsky F, Tong HW, Tiunov MP, Vartanyan S, Orlando L, Corbett-Detig R, MacPhee RD, Shapiro B. Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge. Mol Ecol 2021; 30:6144-6161. [PMID: 33971056 DOI: 10.1111/mec.15977] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/24/2021] [Accepted: 04/27/2021] [Indexed: 01/02/2023]
Abstract
The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.
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Affiliation(s)
- Alisa O Vershinina
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Duane G Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada
| | - Grant Zazula
- Collections and Research, Canadian Museum of Nature, Station D, Ottawa, ON, Canada.,Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Clio Der Sarkissian
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Shelby G Dunn
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Luca Ermini
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark
| | - Cristina Gamba
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark
| | - Pamela Groves
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, CA, USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Daniel H Mann
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, CA, USA
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - John Southon
- Keck-CCAMS Group, Earth System Science Department, University of California, Irvine, CA, USA
| | - Mathias Stiller
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Division Molecular Pathology, Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, Fairbanks, AK, USA.,Department of Marine Biology, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Gennady Baryshnikov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Dmitry Gimranov
- Institute of Plant & Animal Ecology of the Russian Academy of Sciences, Ural Branch, Ekaterinburg, Russia.,Ural Federal University named after the first President of Russia B. N. Yeltsin, Ekaterinburg, Russia
| | - Eric Scott
- California State University, San Bernardino, CA, USA
| | - Elizabeth Hall
- Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | - Susan Hewitson
- Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | - Irina Kirillova
- Institute of Geography, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Kosintsev
- Institute of Plant & Animal Ecology of the Russian Academy of Sciences, Ural Branch, Ekaterinburg, Russia
| | | | - Hao-Wen Tong
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Mikhail P Tiunov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russia
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A. Shilo, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | | | | | - Beth Shapiro
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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49
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Stankowski S, Ravinet M. Defining the speciation continuum. Evolution 2021; 75:1256-1273. [PMID: 33754340 DOI: 10.1111/evo.14215] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/01/2021] [Accepted: 03/13/2021] [Indexed: 02/06/2023]
Abstract
A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present-day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.
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Affiliation(s)
- Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Current Address: Sean Stankowski, IST Austria, Klosterneuburg, 3400, Austria
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, 0316, Norway.,School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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50
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Vogt G. Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance. J Biosci 2021. [DOI: 10.1007/s12038-021-00138-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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