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Innes PA, Goebl AM, Smith CCR, Rosenberger K, Kane NC. Gene expression and alternative splicing contribute to adaptive divergence of ecotypes. Heredity (Edinb) 2024; 132:120-132. [PMID: 38071268 PMCID: PMC10924094 DOI: 10.1038/s41437-023-00665-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 03/10/2024] Open
Abstract
Regulation of gene expression is a critical link between genotype and phenotype explaining substantial heritable variation within species. However, we are only beginning to understand the ways that specific gene regulatory mechanisms contribute to adaptive divergence of populations. In plants, the post-transcriptional regulatory mechanism of alternative splicing (AS) plays an important role in both development and abiotic stress response, making it a compelling potential target of natural selection. AS allows organisms to generate multiple different transcripts/proteins from a single gene and thus may provide a source of evolutionary novelty. Here, we examine whether variation in alternative splicing and gene expression levels might contribute to adaptation and incipient speciation of dune-adapted prairie sunflowers in Great Sand Dunes National Park, Colorado, USA. We conducted a common garden experiment to assess transcriptomic variation among ecotypes and analyzed differential expression, differential splicing, and gene coexpression. We show that individual genes are strongly differentiated for both transcript level and alternative isoform proportions, even when grown in a common environment, and that gene coexpression networks are disrupted between ecotypes. Furthermore, we examined how genome-wide patterns of sequence divergence correspond to divergence in transcript levels and isoform proportions and find evidence for both cis and trans-regulation. Together, our results emphasize that alternative splicing has been an underappreciated mechanism providing source material for natural selection at short evolutionary time scales.
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Affiliation(s)
- Peter A Innes
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA.
| | - April M Goebl
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
- Research and Conservation Department, Denver Botanic Gardens, Denver, CO, USA
| | - Chris C R Smith
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Kaylee Rosenberger
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
| | - Nolan C Kane
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
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2
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Goebl AM, Kane NC, Doak DF, Rieseberg LH, Ostevik KL. Adaptation to distinct habitats is maintained by contrasting selection at different life stages in sunflower ecotypes. Mol Ecol 2024; 33:e16785. [PMID: 36374153 DOI: 10.1111/mec.16785] [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: 07/12/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Conspecific populations living in adjacent but contrasting microenvironments represent excellent systems for studying natural selection. These systems are valuable because gene flow is expected to force genetic homogeneity except at loci experiencing divergent selection. A history of reciprocal transplant and common garden studies in such systems, and a growing number of genomic studies, have contributed to understanding how selection operates in natural populations. While selection can vary across different fitness components and life stages, few studies have investigated how this ultimately affects allele frequencies and the maintenance of divergence between populations. Here, we study two sunflower ecotypes in distinct, adjacent habitats by combining demographic models with genome-wide sequence data to estimate fitness and allele frequency change at multiple life stages. This framework allows us to estimate that only local ecotypes are likely to experience positive population growth (λ > 1) and that the maintenance of divergent adaptation appears to be mediated via habitat- and life stage-specific selection. We identify genetic variation, significantly driven by loci in chromosomal inversions, associated with different life history strategies in neighbouring ecotypes that optimize different fitness components and may contribute to the maintenance of distinct ecotypes.
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Affiliation(s)
- April M Goebl
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Nolan C Kane
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Daniel F Doak
- Environmental Studies Programme, University of Colorado, Boulder, Colorado, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kate L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Evolution, Ecology and Organismal Biology, University of California Riverside, Riverside, California, USA
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3
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Jadhao KR, Kale SS, Chavan NS, Janjal PH. Genome-wide analysis of the SPL transcription factor family and its response to water stress in sunflower (Helianthus annuus). Cell Stress Chaperones 2023; 28:943-958. [PMID: 37938528 PMCID: PMC10746691 DOI: 10.1007/s12192-023-01388-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 11/09/2023] Open
Abstract
SPL (SQUAMOSA promoter binding proteins-like) are plant-specific transcription factors that play essential roles in a variety of developmental processes as well as the ability to withstand biotic and abiotic stresses. To date, numerous species have been investigated for the SPL gene family, but so far, no SPL family genes have been thoroughly identified and characterized in the sunflower (Helianthus annuus). In this study, 25 SPL genes were identified in the sunflower genome and were unevenly distributed on 11 chromosomes. According to phylogeny analysis, 59 SPL genes from H. annuus, O. sativa, and A. thaliana were clustered into seven groups. Furthermore, the SPL genes in groups-I and II were demonstrated to be potential targets of miR156. Synteny analysis showed that 7 paralogous gene pairs exist in HaSPL genes and 26 orthologous gene pairs exist between sunflower and rice, whereas 21 orthologous gene pairs were found between sunflower and Arabidopsis. Segmental duplication appears to have played a vital role in the expansion processes of sunflower SPL genes, and because of selection pressure, all duplicated genes have undergone purifying selection. Tissue-specific gene expression analysis of the HaSBP genes proved their diverse spatiotemporal expression patterns, which were predominantly expressed in floral organs and differentially expressed in stem, axil, and root tissues. The expression pattern of HaSPL genes under water stress showed broad involvement of HaSPLs in the response to flood and drought stresses. This genome-wide identification investigation provides detailed information on the sunflower SPL transcription factor gene family and establishes a strong platform for future research on sunflower responses to abiotic stress tolerance.
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Affiliation(s)
- Kundansing R Jadhao
- Department of Bioinformatics, MGM College of Agricultural Biotechnology, Aurangabad, 431007, India.
| | - Sonam S Kale
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431003, India
| | - Nilesh S Chavan
- Department of Microbiology and Environmental Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, 431003, India
| | - Pandharinath H Janjal
- Department of Bioinformatics, MGM College of Agricultural Biotechnology, Aurangabad, 431007, India
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4
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Carvalho J, Morales HE, Faria R, Butlin RK, Sousa VC. Integrating Pool-seq uncertainties into demographic inference. Mol Ecol Resour 2023; 23:1737-1755. [PMID: 37475177 DOI: 10.1111/1755-0998.13834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 07/22/2023]
Abstract
Next-generation sequencing of pooled samples (Pool-seq) is a popular method to assess genome-wide diversity patterns in natural and experimental populations. However, Pool-seq is associated with specific sources of noise, such as unequal individual contributions. Consequently, using Pool-seq for the reconstruction of evolutionary history has remained underexplored. Here we describe a novel Approximate Bayesian Computation (ABC) method to infer demographic history, explicitly modelling Pool-seq sources of error. By jointly modelling Pool-seq data, demographic history and the effects of selection due to barrier loci, we obtain estimates of demographic history parameters accounting for technical errors associated with Pool-seq. Our ABC approach is computationally efficient as it relies on simulating subsets of loci (rather than the whole-genome) and on using relative summary statistics and relative model parameters. Our simulation study results indicate Pool-seq data allows distinction between general scenarios of ecotype formation (single versus parallel origin) and to infer relevant demographic parameters (e.g. effective sizes and split times). We exemplify the application of our method to Pool-seq data from the rocky-shore gastropod Littorina saxatilis, sampled on a narrow geographical scale at two Swedish locations where two ecotypes (Wave and Crab) are found. Our model choice and parameter estimates show that ecotypes formed before colonization of the two locations (i.e. single origin) and are maintained despite gene flow. These results indicate that demographic modelling and inference can be successful based on pool-sequencing using ABC, contributing to the development of suitable null models that allow for a better understanding of the genetic basis of divergent adaptation.
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Affiliation(s)
- João Carvalho
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Portugal
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui Faria
- 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
| | - Roger K Butlin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Vítor C Sousa
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Portugal
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5
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Mascarenhas R, Meirelles PM, Batalha-Filho H. Urbanization drives adaptive evolution in a Neotropical bird. Curr Zool 2023; 69:607-619. [PMID: 37637315 PMCID: PMC10449428 DOI: 10.1093/cz/zoac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/16/2022] [Indexed: 08/29/2023] Open
Abstract
Urbanization has dramatic impacts on natural habitats and such changes may potentially drive local adaptation of urban populations. Behavioral change has been specifically shown to facilitate the fast adaptation of birds to changing environments, but few studies have investigated the genetic mechanisms of this process. Such investigations could provide insights into questions about both evolutionary theory and management of urban populations. In this study, we investigated whether local adaptation has occurred in urban populations of a Neotropical bird species, Coereba flaveola, specifically addressing whether observed behavioral adaptations are correlated to genetic signatures of natural selection. To answer this question, we sampled 24 individuals in urban and rural environments, and searched for selected loci through a genome-scan approach based on RADseq genomic data, generated and assembled using a reference genome for the species. We recovered 46 loci as putative selection outliers, and 30 of them were identified as associated with biological processes possibly related to urban adaptation, such as the regulation of energetic metabolism, regulation of genetic expression, and changes in the immunological system. Moreover, genes involved in the development of the nervous system showed signatures of selection, suggesting a link between behavioral and genetic adaptations. Our findings, in conjunction with similar results in previous studies, support the idea that cities provide a similar selective pressure on urban populations and that behavioral plasticity may be enhanced through genetic changes in urban populations.
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Affiliation(s)
- Rilquer Mascarenhas
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Pedro Milet Meirelles
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
| | - Henrique Batalha-Filho
- National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Instituto de Biologia, Universidade Federal da Bahia, 40170-115 Salvador, Bahia, Brazil
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6
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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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7
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Massive haplotypes underlie ecotypic differentiation in sunflowers. Nature 2020; 584:602-607. [PMID: 32641831 DOI: 10.1038/s41586-020-2467-6] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/16/2020] [Indexed: 12/22/2022]
Abstract
Species often include multiple ecotypes that are adapted to different environments1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2-4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1-100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other-possibly now-extinct-congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation.
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8
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Huang K, Andrew RL, Owens GL, Ostevik KL, Rieseberg LH. Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype. Mol Ecol 2020; 29:2535-2549. [PMID: 32246540 DOI: 10.1111/mec.15428] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 03/19/2020] [Indexed: 12/19/2022]
Abstract
Both models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencing data and newly developed population genomic approaches to identify putative inversions that differentiate a sand dune ecotype of the prairie sunflower (Helianthus petiolaris) from populations found on the adjacent sand sheet. We detected seven large genomic regions that exhibit a different population structure than the rest of the genome and that vary in frequency between dune and nondune populations. These regions also show high linkage disequilibrium and high heterozygosity between, but not within, arrangements, consistent with the behaviour of large inversions, an inference subsequently validated in part by comparative genetic mapping. Genome-environment association analyses show that key environmental variables, including vegetation cover and soil nitrogen, are significantly associated with inversions. The inversions colocate with previously described "islands of differentiation," and appear to play an important role in adaptive divergence and incipient speciation within H. petiolaris.
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Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Rose L Andrew
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - Gregory L Owens
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Kate L Ostevik
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada.,Department of Biology, Duke University, Durham, NC, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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9
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Lucek K, Hohmann N, Willi Y. Postglacial ecotype formation under outcrossing and self-fertilization in Arabidopsis lyrata. Mol Ecol 2019; 28:1043-1055. [PMID: 30719799 DOI: 10.1111/mec.15035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/18/2019] [Accepted: 01/28/2019] [Indexed: 12/01/2022]
Abstract
The formation of ecotypes has been invoked as an important driver of postglacial biodiversity, because many species colonized heterogeneous habitats and experienced divergent selection. Ecotype formation has been predominantly studied in outcrossing taxa, while far less attention has been paid to the implications of mating system shifts. Here, we addressed whether substrate-related ecotypes exist in selfing and outcrossing populations of Arabidopsis lyrata subsp. lyrata and whether the genomic footprint differs between mating systems. The North American subspecies colonized both rocky and sandy habitats during postglacial range expansion and shifted the mating system from predominantly outcrossing to predominantly selfing in a number of regions. We performed an association study on pooled whole-genome sequence data of 20 selfing or outcrossing populations, which suggested genes involved in adaptation to substrate. Motivated by enriched gene ontology terms, we compared root growth between plants from the two substrates in a common environment and found that plants originating from sand grew roots faster and produced more side roots, independent of mating system. Furthermore, single nucleotide polymorphisms associated with substrate-related ecotypes were more clustered among selfing populations. Our study provides evidence for substrate-related ecotypes in A. lyrata and divergence in the genomic footprint between mating systems. The latter is the likely result of selfing populations having experienced divergent selection on larger genomic regions due to higher genome-wide linkage disequilibrium.
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Affiliation(s)
- Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Nora Hohmann
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Yvonne Willi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
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10
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Moreira-Hernández JI, Muchhala N. Importance of Pollinator-Mediated Interspecific Pollen Transfer for Angiosperm Evolution. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2019. [DOI: 10.1146/annurev-ecolsys-110218-024804] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding how pollen moves between species is critical to understanding speciation, diversification, and evolution of flowering plants. For co-flowering species that share pollinators, competition through interspecific pollen transfer (IPT) can profoundly impact floral evolution, decreasing female fitness via heterospecific pollen deposition on stigmas and male fitness via pollen misplacement during visits to heterospecific flowers. The pollination literature demonstrates that such reproductive interference frequently selects for reproductive character displacement in floral traits linked to pollinator attraction, pollen placement, and mating systems and has also revealed that IPT between given pairs of species is typically asymmetric. More recent work is starting to elucidate its importance to the speciation process, clarifying the link between IPT and current and historical patterns of hybridization, the evolution of phenotypic novelty through adaptive introgression, and the rise of reproductive isolation. Our review aims to stimulate further research on IPT as a ubiquitous mechanism that plays a central role in angiosperm diversification.
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Affiliation(s)
- Juan Isaac Moreira-Hernández
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri–St. Louis, St. Louis, Missouri 63121, USA;,
| | - Nathan Muchhala
- Department of Biology and Whitney R. Harris World Ecology Center, University of Missouri–St. Louis, St. Louis, Missouri 63121, USA;,
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11
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Zhang JQ, Imerovski I, Borkowski K, Huang K, Burge D, Rieseberg LH. Intraspecific genetic divergence within Helianthus niveus and the status of two new morphotypes from Mexico. AMERICAN JOURNAL OF BOTANY 2019; 106:1229-1239. [PMID: 31461165 DOI: 10.1002/ajb2.1349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/17/2019] [Indexed: 05/12/2023]
Abstract
PREMISE Collecting and characterizing the genetic diversity of wild relatives of crops can contribute importantly to sustainable crop production and food security. Wild sunflower, Helianthus niveus, occurs in arid regions in western North America and is partially cross-compatible with the cultivated sunflower (H. annuus). We assessed phylogenetic relationships and patterns of genetic divergence among three previously described subspecies (subsp. niveus, subsp. canescens, and subsp. tephrodes) as well as two new morphotypes of H. niveus recently discovered in extreme drought and dune habitats in Baja California, Mexico. METHODS We measured 50 plants growing in a common garden for 27 morphological traits and conducted principal component analysis to assess patterns of phenotypic variation. Genome size of each accession was determined using flow cytometry. Pollen viability of first generation hybrids between taxa was tested to infer the strength of intrinsic postzygotic reproductive barriers. Finally, genotyping-by-sequencing data were used to investigate the genetic structure and phylogenetic relationships among the previously described subspecies and new morphotypes. RESULTS The intraspecific genetic and phenotypic divergence of H. niveus populations closely tracks their geographical distribution. Subspecies niveus is phenotypically, genetically, and reproductively distinct from the other two subspecies and has a larger genome. Therefore, H. niveus as currently circumscribed should be considered to contain two distinct species, H. niveus and H. tephrodes. ABBA-BABA tests revealed substantial introgression between subsp. canescens and its sympatric congener H. petiolaris, which might contribute to their morphological similarities. The two new morphotypes collected in Mexico represent local ecotypes of subsp. niveus that occur in extreme drought and dune environments. Mantel tests showed a strong positive correlation between genetic and geographic distances. CONCLUSIONS We conclude that geographic isolation is primarily responsible for intraspecific genomic divergence within H. niveus, while patterns of phenotypic variation appear to have been shaped by ecological selection and interspecific introgression.
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Affiliation(s)
- Jian-Qiang Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T1Z4, Canada
| | - Ivana Imerovski
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T1Z4, Canada
| | - Kelly Borkowski
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T1Z4, Canada
| | - Kaichi Huang
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T1Z4, Canada
| | - Dylan Burge
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T1Z4, Canada
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T1Z4, Canada
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12
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Said Gutiérrez-Ortega J, Yamamoto T, Vovides AP, Angel Pérez-Farrera M, Martínez JF, Molina-Freaner F, Watano Y, Kajita T. Aridification as a driver of biodiversity: a case study for the cycad genus Dioon (Zamiaceae). ANNALS OF BOTANY 2018; 121:47-60. [PMID: 29155921 PMCID: PMC5786249 DOI: 10.1093/aob/mcx123] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 09/13/2017] [Indexed: 05/19/2023]
Abstract
Background and Aims Aridification is considered a selective pressure that might have influenced plant diversification. It is suggested that plants adapted to aridity diversified during the Miocene, an epoch of global aridification (≈15 million years ago). However, evidence supporting diversification being a direct response to aridity is scarce, and multidisciplinary evidence, besides just phylogenetic estimations, is necessary to support the idea that aridification has driven diversification. The cycad genus Dioon (Zamiaceae), a tropical group including species occurring from humid forests to arid zones, was investigated as a promising study system to understand the associations among habitat shifts, diversification times, the evolution of leaf epidermal adaptations, and aridification of Mexico. Methods A phylogenetic tree was constructed from seven chloroplast DNA sequences and the ITS2 spacer to reveal the relationships among 14 Dioon species from habitats ranging from humid forests to deserts. Divergence times were estimated and the habitat shifts throughout Dioon phylogeny were detected. The epidermal anatomy among Dioon species was compared and correlation tests were performed to associate the epidermal variations with habitat parameters. Key Results Events of habitat shifts towards arid zones happened exclusively in one of the two main clades of Dioon. Such habitat shifts happened during the species diversification of Dioon, mainly during the Miocene. Comparative anatomy showed epidermal differences between species from arid and mesic habitats. The variation of epidermal structures was found to be correlated with habitat parameters. Also, most of the analysed epidermal traits showed significant phylogenetic signals. Conclusions The diversification of Dioon has been driven by the aridification of Mexico. The Miocene timing corresponds to the expansion of arid zones that embedded the ancestral Dioon populations. As response, species in arid zones evolved epidermal traits to counteract aridity stress. This case study provides a robust body of evidence supporting the idea that aridification is an important driver of biodiversity.
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Affiliation(s)
| | - Takashi Yamamoto
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa, Japan
| | - Andrew P Vovides
- Departamento de Biología Evolutiva, Instituto de Ecología, A.C., Xalapa, Mexico
| | - Miguel Angel Pérez-Farrera
- Laboratorio de Ecología Evolutiva, Herbario Eizi Matuda, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Tuxtla Gutiérrez, Mexico
| | - José F Martínez
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Mexico
| | - Francisco Molina-Freaner
- Departamento de Ecología de la Biodiversidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Hermosillo, Mexico
- Instituto de Geología, Estación Regional del Noroeste, Universidad Nacional Autónoma de México, Hermosillo, Mexico
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Chiba, Japan
| | - Tadashi Kajita
- Iriomote Station, Tropical Biosphere Research Center, University of the Ryukyus, Uehara, Yaeyama, Okinawa, Japan
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13
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Turner KG, Huang DI, Cronk QCB, Rieseberg LH. Homogenization of Populations in the Wildflower, Texas Bluebonnet (Lupinus texensis). J Hered 2017; 109:152-161. [DOI: 10.1093/jhered/esx094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 10/26/2017] [Indexed: 11/13/2022] Open
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14
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Dillenberger MS, Kadereit JW. Simultaneous speciation in the European high mountain flowering plant genus Facchinia (Minuartia s.l., Caryophyllaceae) revealed by genotyping-by-sequencing. Mol Phylogenet Evol 2017; 112:23-35. [PMID: 28433621 DOI: 10.1016/j.ympev.2017.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/12/2017] [Accepted: 04/17/2017] [Indexed: 11/18/2022]
Abstract
Understanding the relative importance of different mechanisms of speciation in a given lineage requires fully resolved interspecific relationships. Using Facchinia, a genus of seven species centred in the European Alps, we explore whether the polytomy found by Sanger sequencing analyses of standard nuclear (ITS) and plastid markers (trnQ-rps16) is a hard or soft polytomy by substantially increasing the amount of DNA sequence data, generated by genotyping-by-sequencing. In comparison to 142 phylogenetically informative sites in the Sanger sequences the GBS sequences yielded 3363 phylogenetically informative sites after exclusion of apparently oversaturated SNPs. Maximum parsimony, maximum likelihood, NeighborNet, SVDquartets and Astral-II analyses all resulted in phylogenetic trees (and networks) in which interspecific relationships were largely unresolved. After excluding incomplete lineage sorting, hybridisation and oversaturation of characters as possible causes for lack of phylogenetic resolution, we conclude that the polytomy obtained most likely represents a hard polytomy. We hypothesize that diversification of Facchinia is best interpreted as the result of multiple simultaneous vicariance in response to climatic changes during the Early Quaternary.
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Affiliation(s)
- Markus S Dillenberger
- Department of Botany & Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.
| | - Joachim W Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
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15
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Cooper EA, Uy JAC. Genomic evidence for convergent evolution of a key trait underlying divergence in island birds. Mol Ecol 2017; 26:3760-3774. [DOI: 10.1111/mec.14116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/06/2017] [Accepted: 03/16/2017] [Indexed: 01/13/2023]
Affiliation(s)
| | - J. Albert C. Uy
- Department of Biology University of MiamiCoral Gables FL USA
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16
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Hamon P, Grover CE, Davis AP, Rakotomalala JJ, Raharimalala NE, Albert VA, Sreenath HL, Stoffelen P, Mitchell SE, Couturon E, Hamon S, de Kochko A, Crouzillat D, Rigoreau M, Sumirat U, Akaffou S, Guyot R. Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content. Mol Phylogenet Evol 2017; 109:351-361. [PMID: 28212875 DOI: 10.1016/j.ympev.2017.02.009] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 02/06/2017] [Accepted: 02/07/2017] [Indexed: 12/30/2022]
Abstract
A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate.
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Affiliation(s)
- Perla Hamon
- UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.
| | - Aaron P Davis
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AB, United Kingdom.
| | | | | | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA.
| | - Hosahalli L Sreenath
- Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Manasagangothri, Mysore 570006, India.
| | - Piet Stoffelen
- Herbarium Plantentuin Meise, Nieuwelaan 38, 1860 Meise, Belgium.
| | - Sharon E Mitchell
- Cornell University, Institute of Biotechnology, Genomic Diversity Facility, Ithaca, NY, USA.
| | | | - Serge Hamon
- UMR DIADE, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
| | | | | | - Michel Rigoreau
- Nestlé Centre R&D Tours, BP 49716, F-37097 Tours cedex 2, France.
| | - Ucu Sumirat
- Indonesian Coffee and Cocoa Research Institute Jl. PB Sudirman 90, Jember 68118, Indonesia.
| | | | - Romain Guyot
- UMR IPME, IRD, BP 64501, F-34394 Montpellier cedex 5, France.
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17
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Gould BA, Chen Y, Lowry DB. Pooled ecotype sequencing reveals candidate genetic mechanisms for adaptive differentiation and reproductive isolation. Mol Ecol 2016; 26:163-177. [DOI: 10.1111/mec.13881] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/22/2016] [Accepted: 08/29/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Billie A. Gould
- Department of Plant Biology; Michigan State University; Plant Biology Laboratories; 612 Wilson Road Room 166 East Lansing MI 48824 USA
| | - Yani Chen
- Department of Plant Biology; Michigan State University; Plant Biology Laboratories; 612 Wilson Road Room 166 East Lansing MI 48824 USA
| | - David B. Lowry
- Department of Plant Biology; Michigan State University; Plant Biology Laboratories; 612 Wilson Road Room 166 East Lansing MI 48824 USA
- Program in Ecology, Evolutionary Biology and Behavior; Michigan State University; Giltner Hall 293 Farm Ln Rm 103 East Lansing MI 48824 USA
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18
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Complete Mitochondrial Genome Sequence of Sunflower (Helianthus annuus L.). GENOME ANNOUNCEMENTS 2016; 4:4/5/e00981-16. [PMID: 27635002 PMCID: PMC5026442 DOI: 10.1128/genomea.00981-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This is the first complete mitochondrial genome sequence for sunflower and the first complete mitochondrial genome for any member of Asteraceae, the largest plant family, which includes over 23,000 named species. The master circle is 300,945-bp long and includes 27 protein-coding sequences, 18 tRNAs, and the 26S, 5S, and 18S rRNAs.
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19
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Ostevik KL, Andrew RL, Otto SP, Rieseberg LH. Multiple reproductive barriers separate recently diverged sunflower ecotypes. Evolution 2016; 70:2322-2335. [PMID: 27479368 DOI: 10.1111/evo.13027] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 06/12/2016] [Accepted: 06/27/2016] [Indexed: 01/17/2023]
Abstract
Measuring reproductive barriers between groups of organisms is an effective way to determine the traits and mechanisms that impede gene flow. However, to understand the ecological and evolutionary factors that drive speciation, it is important to distinguish between the barriers that arise early in the speciation process and those that arise after speciation is largely complete. In this article, we comprehensively test for reproductive isolation between recently diverged (<10,000 years bp) dune and nondune ecotypes of the prairie sunflower, Helianthus petiolaris. We find reproductive barriers acting at multiple stages of hybridization, including premating, postmating-prezygotic, and postzygotic barriers, despite the recent divergence. Barriers include extrinsic selection against immigrants and hybrids, a shift in pollinator assemblage, and postpollination assortative mating. Together, these data suggest that multiple barriers can be important for reducing gene flow in the earliest stages of speciation.
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Affiliation(s)
- Katherine L Ostevik
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Rose L Andrew
- School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
| | - Sarah P Otto
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Biology, Indiana University, Bloomington, Indiana
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20
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Payseur BA, Rieseberg LH. A genomic perspective on hybridization and speciation. Mol Ecol 2016; 25:2337-60. [PMID: 26836441 PMCID: PMC4915564 DOI: 10.1111/mec.13557] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/18/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022]
Abstract
Hybridization among diverging lineages is common in nature. Genomic data provide a special opportunity to characterize the history of hybridization and the genetic basis of speciation. We review existing methods and empirical studies to identify recent advances in the genomics of hybridization, as well as issues that need to be addressed. Notable progress has been made in the development of methods for detecting hybridization and inferring individual ancestries. However, few approaches reconstruct the magnitude and timing of gene flow, estimate the fitness of hybrids or incorporate knowledge of recombination rate. Empirical studies indicate that the genomic consequences of hybridization are complex, including a highly heterogeneous landscape of differentiation. Inferred characteristics of hybridization differ substantially among species groups. Loci showing unusual patterns - which may contribute to reproductive barriers - are usually scattered throughout the genome, with potential enrichment in sex chromosomes and regions of reduced recombination. We caution against the growing trend of interpreting genomic variation in summary statistics across genomes as evidence of differential gene flow. We argue that converting genomic patterns into useful inferences about hybridization will ultimately require models and methods that directly incorporate key ingredients of speciation, including the dynamic nature of gene flow, selection acting in hybrid populations and recombination rate variation.
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Affiliation(s)
- Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Loren H. Rieseberg
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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21
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Vera M, Díez-del-Molino D, García-Marín JL. Genomic survey provides insights into the evolutionary changes that occurred during European expansion of the invasive mosquitofish (Gambusia holbrooki). Mol Ecol 2016; 25:1089-105. [PMID: 26825431 DOI: 10.1111/mec.13545] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 12/10/2015] [Accepted: 01/15/2016] [Indexed: 01/26/2023]
Abstract
Biological invasions rank among the main global threats for biodiversity. The Eastern mosquitofish (Gambusia holbrooki) is considered one of the 100 world worst invasive species due to its high adaptation capability to new environments. Using the restriction-site-associated DNA tags (RADtags), introduced European locations were compared against native US mosquitofish populations to analyse genomic changes that occurred during invasive process of European locations. After filtering, 7724 RADtags containing only one SNP were retained for population studies. Comparative genomics indicated that 186 of these RADtags matched sequences in the transcriptome of Xyphophorus maculatus, the most closely related genome available. Genomic analyses showed that invasive populations show high reductions in diversity. Further, analyses of population structuring based on these data are concordant with previous analyses based on microsatellites. It is concluded that during the invasion process genetic drift was the main evolutionary force affecting patterns of diversity and population structure. While recognizing that positive selection could be masked by the strong drift during founder events, adaptive processes were evidenced in a reduced number of RADtags (<2%), with only one of these in a putative coding region. Surprisingly, balancing selection was detected in several coding RADtags, suggesting that the preservation of polymorphism in specific genes could be more important than the average population diversity for the population maintenance at any location, particularly for the survival of introduced populations.
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Affiliation(s)
- Manuel Vera
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
| | - David Díez-del-Molino
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
| | - José-Luis García-Marín
- LIG-UdG, Department of Biology, Faculty of Sciences, Universitat de Girona, Campus of Montilivi, 17071, Girona, Spain
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22
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Lowry DB, Hernandez K, Taylor SH, Meyer E, Logan TL, Barry KW, Chapman JA, Rokhsar DS, Schmutz J, Juenger TE. The genetics of divergence and reproductive isolation between ecotypes of Panicum hallii. THE NEW PHYTOLOGIST 2015; 205:402-14. [PMID: 25252269 PMCID: PMC4265272 DOI: 10.1111/nph.13027] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 07/31/2014] [Indexed: 05/08/2023]
Abstract
The process of plant speciation often involves the evolution of divergent ecotypes in response to differences in soil water availability between habitats. While the same set of traits is frequently associated with xeric/mesic ecotype divergence, it is unknown whether those traits evolve independently or if they evolve in tandem as a result of genetic colocalization either by pleiotropy or genetic linkage. The self-fertilizing C4 grass species Panicum hallii includes two major ecotypes found in xeric (var. hallii) or mesic (var. filipes) habitats. We constructed the first linkage map for P. hallii by genotyping a reduced representation genomic library of an F2 population derived from an intercross of var. hallii and filipes. We then evaluated the genetic architecture of divergence between these ecotypes through quantitative trait locus (QTL) mapping. Overall, we mapped QTLs for nine morphological traits that are involved in the divergence between the ecotypes. QTLs for five key ecotype-differentiating traits all colocalized to the same region of linkage group five. Leaf physiological traits were less divergent between ecotypes, but we still mapped five physiological QTLs. We also discovered a two-locus Dobzhansky-Muller hybrid incompatibility. Our study suggests that ecotype-differentiating traits may evolve in tandem as a result of genetic colocalization.
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Affiliation(s)
- David B Lowry
- Department of Integrative Biology and Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station C0990, Austin, TX, 78712, USA; Division of Science and Environmental Policy, California State University, Monterey Bay, 100 Campus Center, Seaside, CA, 93955, USA
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23
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McCluskey BM, Postlethwait JH. Phylogeny of zebrafish, a "model species," within Danio, a "model genus". Mol Biol Evol 2014; 32:635-52. [PMID: 25415969 DOI: 10.1093/molbev/msu325] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Zebrafish (Danio rerio) is an important model for vertebrate development, genomics, physiology, behavior, toxicology, and disease. Additionally, work on numerous Danio species is elucidating evolutionary mechanisms for morphological development. Yet, the relationships of zebrafish and its closest relatives remain unclear possibly due to incomplete lineage sorting, speciation with gene flow, and interspecies hybridization. To clarify these relationships, we first constructed phylogenomic data sets from 30,801 restriction-associated DNA (RAD)-tag loci (483,026 variable positions) with clear orthology to a single location in the sequenced zebrafish genome. We then inferred a well-supported species tree for Danio and tested for gene flow during the diversification of the genus. An approach independent of the sequenced zebrafish genome verified all inferred relationships. Although identification of the sister taxon to zebrafish has been contentious, multiple RAD-tag data sets and several analytical methods provided strong evidence for Danio aesculapii as the most closely related extant zebrafish relative studied to date. Data also displayed patterns consistent with gene flow during speciation and postspeciation introgression in the lineage leading to zebrafish. The incorporation of biogeographic data with phylogenomic analyses put these relationships in a phylogeographic context and supplied additional support for D. aesculapii as the sister species to D. rerio. The clear resolution of this study establishes a framework for investigating the evolutionary biology of Danio and the heterogeneity of genome evolution in the recent history of a model organism within an emerging model genus for genetics, development, and evolution.
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24
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Pan J, Wang B, Pei ZY, Zhao W, Gao J, Mao JF, Wang XR. Optimization of the genotyping-by-sequencing strategy for population genomic analysis in conifers. Mol Ecol Resour 2014; 15:711-22. [DOI: 10.1111/1755-0998.12342] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Jin Pan
- Department of Ecology and Environmental Science; Umeå University; Umeå SE-90187 Sweden
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Baosheng Wang
- Department of Ecology and Environmental Science; Umeå University; Umeå SE-90187 Sweden
| | - Zhi-Yong Pei
- Beijing Computing Centre; Beijing 100094 China
- Beijing Institute of Genomics; Chinese Academy of Sciences; Beijing 100101 China
| | - Wei Zhao
- State Key Laboratory of Systematic and Evolutionary Botany; Institute of Botany; Chinese Academy of Sciences; Beijing 100093 China
| | - Jie Gao
- Key Laboratory of Tropical Forest Ecology; Xishuangbanna Tropical Botanical Garden; Chinese Academy of Sciences; Menglun Yunnan 666303 China
| | - Jian-Feng Mao
- National Engineering Laboratory for Forest Tree Breeding; Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education; Beijing Forestry University; Beijing 100083 China
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science; Umeå University; Umeå SE-90187 Sweden
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25
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Kantar MB, Baute GJ, Bock DG, Rieseberg LH. Genomic variation in Helianthus: learning from the past and looking to the future. Brief Funct Genomics 2014; 13:328-40. [DOI: 10.1093/bfgp/elu004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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26
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Severns PM, Breed GA. Behavioral consequences of exotic host plant adoption and the differing roles of male harassment on female movement in two checkerspot butterflies. Behav Ecol Sociobiol 2014. [DOI: 10.1007/s00265-014-1693-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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27
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Martin CH, Feinstein LC. Novel trophic niches drive variable progress towards ecological speciation within an adaptive radiation of pupfishes. Mol Ecol 2014; 23:1846-62. [PMID: 24393262 DOI: 10.1111/mec.12658] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 12/09/2013] [Accepted: 12/20/2013] [Indexed: 01/15/2023]
Abstract
Adaptive radiation is recognized by a rapid burst of phenotypic, ecological and species diversification. However, it is unknown whether different species within an adaptive radiation evolve reproductive isolation at different rates. We compared patterns of genetic differentiation between nascent species within an adaptive radiation of Cyprinodon pupfishes using genotyping by sequencing. Similar to classic adaptive radiations, this clade exhibits rapid morphological diversification rates and two species are novel trophic specialists, a scale-eater and hard-shelled prey specialist (durophage), yet the radiation is <10 000 years old. Both specialists and an abundant generalist species all coexist in the benthic zone of lakes on San Salvador Island, Bahamas. Based on 13 912 single-nucleotide polymorphisms (SNPs), we found consistent differences in genetic differentiation between each specialist species and the generalist across seven lakes. The scale-eater showed the greatest genetic differentiation and clustered by species across lakes, whereas durophage populations often clustered with sympatric generalist populations, consistent with parallel speciation across lakes. However, we found strong evidence of admixture between durophage populations in different lakes, supporting a single origin of this species and genome-wide introgression with sympatric generalist populations. We conclude that the scale-eater is further along the speciation-with-gene-flow continuum than the durophage and suggest that different adaptive landscapes underlying these two niche environments drive variable progress towards speciation within the same habitat. Our previous measurements of fitness surfaces in these lakes support this conclusion: the scale-eating fitness peak may be more distant than the durophage peak on the complex adaptive landscape driving adaptive radiation.
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Affiliation(s)
- Christopher H Martin
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, 94720, USA; Department of Evolution & Ecology, University of California, Davis, CA, 94616, USA
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28
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Rieseberg L, Vines T, Gow J, Kane N. Molecular Ecology continues to perform well according to the major publication metrics. Introduction. Mol Ecol 2014; 23:1-15. [PMID: 24372750 DOI: 10.1111/mec.12586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/06/2013] [Indexed: 11/28/2022]
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29
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Wang XQ, Zhao L, Eaton DAR, Li DZ, Guo ZH. Identification of
SNP
markers for inferring phylogeny in temperate bamboos (
P
oaceae:
B
ambusoideae) using
RAD
sequencing. Mol Ecol Resour 2013; 13:938-45. [DOI: 10.1111/1755-0998.12136] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 06/08/2013] [Accepted: 06/10/2013] [Indexed: 12/29/2022]
Affiliation(s)
- X. Q. Wang
- Plant Germplasm and Genomics Center Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
- College of Life Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - L. Zhao
- Plant Germplasm and Genomics Center Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| | - D. A. R. Eaton
- Committee on Evolutionary Biology University of Chicago Chicago IL 60637 USA
| | - D. Z. Li
- Key Laboratory of Biodiversity and Biogeography Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
| | - Z. H. Guo
- Plant Germplasm and Genomics Center Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming 650201 China
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30
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Affiliation(s)
- Luisa Orsini
- Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Leuven, Belgium.
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31
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Catchen J, Hohenlohe PA, Bassham S, Amores A, Cresko WA. Stacks: an analysis tool set for population genomics. Mol Ecol 2013; 22:3124-40. [PMID: 23701397 DOI: 10.1111/mec.12354] [Citation(s) in RCA: 2101] [Impact Index Per Article: 191.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 04/16/2013] [Accepted: 04/16/2013] [Indexed: 02/06/2023]
Abstract
Massively parallel short-read sequencing technologies, coupled with powerful software platforms, are enabling investigators to analyse tens of thousands of genetic markers. This wealth of data is rapidly expanding and allowing biological questions to be addressed with unprecedented scope and precision. The sizes of the data sets are now posing significant data processing and analysis challenges. Here we describe an extension of the Stacks software package to efficiently use genotype-by-sequencing data for studies of populations of organisms. Stacks now produces core population genomic summary statistics and SNP-by-SNP statistical tests. These statistics can be analysed across a reference genome using a smoothed sliding window. Stacks also now provides several output formats for several commonly used downstream analysis packages. The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
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Affiliation(s)
- Julian Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA
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32
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Andrew RL, Rieseberg LH. DIVERGENCE IS FOCUSED ON FEW GENOMIC REGIONS EARLY IN SPECIATION: INCIPIENT SPECIATION OF SUNFLOWER ECOTYPES. Evolution 2013; 67:2468-82. [DOI: 10.1111/evo.12106] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 02/20/2013] [Indexed: 12/18/2022]
Affiliation(s)
- Rose L. Andrew
- Department of Botany, University of British Columbia, 3529-6270 University Blvd; Vancouver; British Columbia; V6T 1Z4; Canada
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