1
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Augustijnen H, Lucek K. Beyond gene flow: (non)-parallelism of secondary contact in a pair of highly differentiated sibling species. Mol Ecol 2024:e17488. [PMID: 39119885 DOI: 10.1111/mec.17488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/01/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024]
Abstract
Replicated secondary contact zones can provide insights into the barriers to gene flow that are important during speciation and can reveal to which degree secondary contact may result in similar evolutionary outcomes. Here, we studied two secondary contact zones between highly differentiated Alpine butterflies of the genus Erebia using whole-genome resequencing data. We assessed the genomic relationships between populations and species and found hybridization to be rare, with no to little current or historical introgression in either contact zone. There are large similarities between contact zones, consistent with an allopatric origin of interspecific differentiation, with no indications for ongoing reinforcing selection. Consistent with expected reduced effective population size, we further find that scaffolds related to the Z-chromosome show increased differentiation compared to the already high levels across the entire genome, which could also hint towards a contribution of the Z chromosome to species divergence in this system. Finally, we detected the presence of the endosymbiont Wolbachia, which can cause reproductive isolation between its hosts, in all E. cassioides, while it appears to be fully or largely absent in contact zone populations of E. tyndarus. We discuss how this rare pattern may have arisen and how it may have affected the dynamics of speciation upon secondary contact.
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Affiliation(s)
- Hannah Augustijnen
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Kay Lucek
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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2
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Garner AG, Goulet-Scott BE, Hopkins R. Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers. THE NEW PHYTOLOGIST 2024; 243:451-465. [PMID: 38764373 DOI: 10.1111/nph.19802] [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: 10/06/2023] [Accepted: 03/22/2024] [Indexed: 05/21/2024]
Abstract
The tree of life is riddled with reticulate evolutionary histories, and some clades, such as the eastern standing Phlox, appear to be hotspots of hybridization. In this group, there are two cases of reinforcement and nine hypothesized hybrid species. Given their historical importance in our understanding of plant speciation, the relationships between these taxa and the role of hybridization in their diversification require genomic validation. Using phylogenomic analyses, we resolve the evolutionary relationships of the eastern standing Phlox and evaluate hypotheses about whether and how hybridization and gene flow played a role in their diversification. Our results provide novel resolution of the phylogenetic relationships in this group, including paraphyly across some taxa. We identify gene flow during one case of reinforcement and find genomic support for a hybrid lineage underlying one of the five hypothesized homoploid hybrid speciation events. Additionally, we estimate the ancestries of four allotetraploid hybrid species. Our results are consistent with hybridization contributing to diverse evolutionary outcomes within this group; although, not as extensively as previously hypothesized. This study demonstrates the importance of phylogenomics in evaluating hypothesized evolutionary histories of non-model systems and adds to the growing support of interspecific genetic exchange in the generation of biodiversity.
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Affiliation(s)
- Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
| | - Benjamin E Goulet-Scott
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- The Arnold Arboretum, Harvard University, Boston, MA, 02131, USA
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3
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Bailey N, Ruiz C, Tosi A, Stevison L. Genomic analysis of the rhesus macaque ( Macaca mulatta) and the cynomolgus macaque ( Macaca fascicularis) uncover polygenic signatures of reinforcement speciation. Ecol Evol 2023; 13:e10571. [PMID: 37849934 PMCID: PMC10577069 DOI: 10.1002/ece3.10571] [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: 06/21/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/19/2023] Open
Abstract
Speciation can involve phases of divergent adaptation in allopatry and ecological/reproductive character displacement in sympatry or parapatry. Reproductive character displacement can result as a means of preventing hybridization, a process known as reinforcement speciation. In this study, we use whole-genome sequencing (WGS) of two closely related primate species that have experienced introgression in their history, the rhesus (Macaca mulatta) and cynomolgus (M. fascicularis) macaques, to identify genes exhibiting reproductive character displacement and other patterns consistent with reinforcement speciation. Using windowed scans of various population genetic statistics to identify signatures of reinforcement, we find 184 candidate genes associated with a variety of functions, including an overrepresentation of multiple neurological functions and several genes involved in sexual development and gametogenesis. These results are consistent with a variety of genes acting in a reinforcement process between these species. We also find signatures of introgression of the Y-chromosome that confirm previous studies suggesting male-driven introgression of M. mulatta into M. fascicularis populations. This study uses WGS to find evidence of the process of reinforcement in primates that have medical and conservation relevance.
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Affiliation(s)
- Nick Bailey
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
| | - Cody Ruiz
- Department of AnthropologyKent State UniversityKentOhioUSA
| | - Anthony Tosi
- Department of AnthropologyKent State UniversityKentOhioUSA
| | - Laurie Stevison
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
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4
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Giesen A, Blanckenhorn WU, Schäfer MA, Shimizu KK, Shimizu-Inatsugi R, Misof B, Podsiadlowski L, Niehuis O, Lischer HEL, Aeschbacher S, Kapun M. Geographic Variation in Genomic Signals of Admixture Between Two Closely Related European Sepsid Fly Species. Evol Biol 2023; 50:395-412. [PMID: 37854269 PMCID: PMC10579158 DOI: 10.1007/s11692-023-09612-5] [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: 01/16/2023] [Accepted: 07/28/2023] [Indexed: 10/20/2023]
Abstract
The extent of interspecific gene flow and its consequences for the initiation, maintenance, and breakdown of species barriers in natural systems remain poorly understood. Interspecific gene flow by hybridization may weaken adaptive divergence, but can be overcome by selection against hybrids, which may ultimately promote reinforcement. An informative step towards understanding the role of gene flow during speciation is to describe patterns of past gene flow among extant species. We investigate signals of admixture between allopatric and sympatric populations of the two closely related European dung fly species Sepsis cynipsea and S. neocynipsea (Diptera: Sepsidae). Based on microsatellite genotypes, we first inferred a baseline demographic history using Approximate Bayesian Computation. We then used genomic data from pooled DNA of natural and laboratory populations to test for past interspecific gene flow based on allelic configurations discordant with the inferred population tree (ABBA-BABA test with D-statistic). Comparing the detected signals of gene flow with the contemporary geographic relationship among interspecific pairs of populations (sympatric vs. allopatric), we made two contrasting observations. At one site in the French Cevennes, we detected an excess of past interspecific gene flow, while at two sites in Switzerland we observed lower signals of past microsatellite genotypes gene flow among populations in sympatry compared to allopatric populations. These results suggest that the species boundaries between these two species depend on the past and/or present eco-geographic context in Europe, which indicates that there is no uniform link between contemporary geographic proximity and past interspecific gene flow in natural populations. Supplementary Information The online version contains supplementary material available at 10.1007/s11692-023-09612-5.
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Affiliation(s)
- Athene Giesen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Wolf U. Blanckenhorn
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin A. Schäfer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Bernhard Misof
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | | | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University, Freiburg, Germany
| | - Heidi E. L. Lischer
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland
| | - Simon Aeschbacher
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Kapun
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Division of Cell & Developmental Biology, Medical University of Vienna, Vienna, Austria
- Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
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5
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Giles‐Pérez GI, Aguirre‐Planter E, Eguiarte LE, Jaramillo‐Correa JP. Demographic modelling helps track the rapid and recent divergence of a conifer species pair from Central Mexico. Mol Ecol 2022; 31:5074-5088. [PMID: 35951172 PMCID: PMC9804182 DOI: 10.1111/mec.16646] [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: 04/29/2021] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 01/05/2023]
Abstract
Secondary contact of recently diverged species may have several outcomes, ranging from rampant hybridization to reinforced reproductive isolation. In plants, selfing tolerance and disjunct reproductive phenology may lead to reproductive isolation at contact zones. However, they may also evolve under both allopatric or parapatric frameworks and originate from adaptive and/or neutral forces. Inferring the historical demography of diverging taxa is thus a crucial step to identify factors that may have led to putative reproductive isolation. We explored various competing demographypotheses to account for the rapid divergence of a fir species complex (Abies flinckii-A. religiosa) distributed in "sky-islands" across central Mexico (i.e., along the Trans-Mexican Volcanic Belt; TMVB). Despite co-occurring in two independent sympatric regions (west and centre), these taxa rarely interbreed because of disjunct reproductive phenologies. We genotyped 1147 single nucleotide polymorphisms, generated by GBS (genotyping by sequencing), across 23 populations, and compared multiple scenarios based on the geological history of the TMVB. The best-fitting model revealed one of the most rapid and complete speciation cases for a conifer species-pair, dating back to ~1.2 million years ago. Coupled with the lack of support for stepwise colonization, our coalescent inferences point to an early cessation of interspecific gene flow under parapatric speciation; ancestral gene flow during divergence was asymmetrical (mostly from western firs into A. religiosa) and exclusive to the most ancient (i.e., central) contact zone. Factors promoting rapid reproductive isolation should be explored in other slowly evolving species complexes as they may account for the large tropical and subtropical diversity.
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Affiliation(s)
- Gustavo I. Giles‐Pérez
- Programa de Doctorado en Ciencias BiomédicasUniversidad Nacional Autónoma de MéxicoCDMXMexico,Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCDMXMexico
| | - Erika Aguirre‐Planter
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCDMXMexico
| | - Luis E. Eguiarte
- Departamento de Ecología EvolutivaInstituto de Ecología, Universidad Nacional Autónoma de MéxicoCDMXMexico
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6
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Buck R, Flores-Rentería L. The Syngameon Enigma. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11070895. [PMID: 35406874 PMCID: PMC9002738 DOI: 10.3390/plants11070895] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 05/17/2023]
Abstract
Despite their evolutionary relevance, multispecies networks or syngameons are rarely reported in the literature. Discovering how syngameons form and how they are maintained can give insight into processes such as adaptive radiations, island colonizations, and the creation of new hybrid lineages. Understanding these complex hybridization networks is even more pressing with anthropogenic climate change, as syngameons may have unique synergistic properties that will allow participating species to persist. The formation of a syngameon is not insurmountable, as several ways for a syngameon to form have been proposed, depending mostly on the magnitude and frequency of gene flow events, as well as the relatedness of its participants. Episodic hybridization with small amounts of introgression may keep syngameons stable and protect their participants from any detrimental effects of gene flow. As genomic sequencing becomes cheaper and more species are included in studies, the number of known syngameons is expected to increase. Syngameons must be considered in conservation efforts as the extinction of one participating species may have detrimental effects on the survival of all other species in the network.
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7
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Liu Y, Henkel J, Beaurepaire A, Evans JD, Neumann P, Huang Q. Comparative genomics suggests local adaptations in the invasive small hive beetle. Ecol Evol 2021; 11:15780-15791. [PMID: 34824789 PMCID: PMC8601931 DOI: 10.1002/ece3.8242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 01/01/2023] Open
Abstract
Invasive species are a major driver of ecological and environmental changes that affect human health, food security, and natural biodiversity. The success and impact of biological invasions depend on adaptations to novel abiotic and biotic selective pressures. However, the molecular mechanisms underlying adaptations in invasive parasitic species are inadequately understood. Small hive beetles, Aethina tumida, are parasites of bee nests. Originally endemic to sub-Saharan Africa, they are now found nearly globally. Here, we investigated the molecular bases of the adaptations to novel environments underlying their invasion routes. Genomes of historic and recent adults A. tumida from both the endemic and introduced ranges were compared. Analysis of gene-environment association identified 3049 candidate loci located in 874 genes. Functional annotation showed a significant bias toward genes linked to growth and reproduction. One of the genes from the apoptosis pathway encodes an "ecdysone-related protein," which is a crucial regulator in controlling body size in response to environmental cues for holometabolous insects during cell death and renewal. Genes whose proteins regulate organ size, ovary activation, and oviposition were also detected. Functions of these enriched pathways parallel behavioral differences between introduced and native A. tumida populations, which may reflect patterns of local adaptation. The results considerably improve our understanding of the underlying mechanisms and ecological factors driving adaptations of invasive species. Deep functional investigation of these identified loci will help clarify the mechanisms of local adaptation in A. tumida.
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Affiliation(s)
- Yuanzhen Liu
- Vetsuisse FacultyInstitute of Bee HealthUniversity of BernBernSwitzerland
| | - Jan Henkel
- Vetsuisse FacultyInstitute of GeneticsUniversity of BernBernSwitzerland
| | - Alexis Beaurepaire
- Vetsuisse FacultyInstitute of Bee HealthUniversity of BernBernSwitzerland
| | - Jay D. Evans
- USDA‐ARS Beltsville Bee Research LaboratoryBeltsvilleMarylandUSA
| | - Peter Neumann
- Vetsuisse FacultyInstitute of Bee HealthUniversity of BernBernSwitzerland
- AgroscopeSwiss Bee Research CentreBernSwitzerland
| | - Qiang Huang
- Honeybee Research InstituteJiangxi Agricultural UniversityNanchangChina
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8
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Ospina OE, Lemmon AR, Dye M, Zdyrski C, Holland S, Stribling D, Kortyna ML, Lemmon EM. Neurogenomic divergence during speciation by reinforcement of mating behaviors in chorus frogs (Pseudacris). BMC Genomics 2021; 22:711. [PMID: 34600496 PMCID: PMC8487493 DOI: 10.1186/s12864-021-07995-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 09/10/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Species interactions can promote mating behavior divergence, particularly when these interactions are costly due to maladaptive hybridization. Selection against hybridization can indirectly cause evolution of reproductive isolation within species, a process termed cascade reinforcement. This process can drive incipient speciation by generating divergent selection pressures among populations that interact with different species assemblages. Theoretical and empirical studies indicate that divergent selection on gene expression networks has the potential to increase reproductive isolation among populations. After identifying candidate synaptic transmission genes derived from neurophysiological studies in anurans, we test for divergence of gene expression in a system undergoing cascade reinforcement, the Upland Chorus Frog (Pseudacris feriarum). RESULTS Our analyses identified seven candidate synaptic transmission genes that have diverged between ancestral and reinforced populations of P. feriarum, including five that encode synaptic vesicle proteins. Our gene correlation network analyses revealed four genetic modules that have diverged between these populations, two possessing a significant concentration of neurotransmission enrichment terms: one for synaptic membrane components and the other for metabolism of the neurotransmitter nitric oxide. We also ascertained that a greater number of genes have diverged in expression by geography than by sex. Moreover, we found that more genes have diverged within females as compared to males between populations. Conversely, we observed no difference in the number of differentially-expressed genes within the ancestral compared to the reinforced population between the sexes. CONCLUSIONS This work is consistent with the idea that divergent selection on mating behaviors via cascade reinforcement contributed to evolution of gene expression in P. feriarum. Although our study design does not allow us to fully rule out the influence of environment and demography, the fact that more genes diverged in females than males points to a role for cascade reinforcement. Our discoveries of divergent candidate genes and gene networks related to neurotransmission support the idea that neural mechanisms of acoustic mating behaviors have diverged between populations, and agree with previous neurophysiological studies in frogs. Increasing support for this hypothesis, however, will require additional experiments under common garden conditions. Our work points to the importance of future replicated and tissue-specific studies to elucidate the relative contribution of gene expression divergence to the evolution of reproductive isolation during incipient speciation.
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Affiliation(s)
- Oscar E Ospina
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Drive, 50011, Ames, IA, USA
- Present address: Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, 13131 USF Magnolia Drive, Tampa, FL, 33612, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, 400 Dirac Science Library, Tallahassee, FL, 32306, USA
| | - Mysia Dye
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Drive, 50011, Ames, IA, USA
| | - Christopher Zdyrski
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Drive, 50011, Ames, IA, USA
- Present address: Genetics and Genomics Program, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA
| | - Sean Holland
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Drive, 50011, Ames, IA, USA
| | - Daniel Stribling
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Drive, 50011, Ames, IA, USA
- Present address: Department of Molecular Genetics and Microbiology, Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
| | - Michelle L Kortyna
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Drive, 50011, Ames, IA, USA
| | - Emily Moriarty Lemmon
- Department of Biomedical Sciences, College of Veterinary Medicine, Iowa State University, 1800 Christensen Drive, 50011, Ames, IA, USA.
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9
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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10
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Goulet-Scott BE, Garner AG, Hopkins R. Genomic analyses overturn two long-standing homoploid hybrid speciation hypotheses. Evolution 2021; 75:1699-1710. [PMID: 34101168 DOI: 10.1111/evo.14279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/27/2021] [Accepted: 05/11/2021] [Indexed: 01/21/2023]
Abstract
The importance of hybridization in generating biological diversity has been historically controversial. Previously, inference about hybridization was limited by dependence on morphological data; with the advent of the next-generation sequencing tools for nonmodel organisms, the evolutionary significance of hybridization is more evident. Here, we test classic hypotheses of hybrid origins of two species in the Phlox pilosa complex. Morphological intermediacy motivated the hypotheses that Phlox amoena lighthipei and Phlox pilosa deamii were independent homoploid hybrid lineages derived from P. amoena amoena and P. pilosa pilosa. We use double-digest restriction site-associated DNA sequencing of individuals from throughout the range of these taxa to conduct the most thorough analysis of evolutionary history in this system to date. Surprisingly, we find no support for the hybrid origin of P. pilosa deamii or P. amoena lighthipei. Our data do identify a history of admixture in individuals collected at a contemporary hybrid zone between the putative parent lineages. We show that three very different evolutionary histories, only one of which involves hybrid origin, have produced intermediate or recombinant morphological traits between P. amoena amoena and P. pilosa pilosa. Although morphological data are still an efficient means of generating hypotheses about past gene flow, genomic data are now the standard of evidence for elucidating evolutionary history.
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Affiliation(s)
- Benjamin E Goulet-Scott
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138.,Arnold Arboretum of Harvard University, Boston, Massachusetts, 02131
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11
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Orsucci M, Sicard A. Flower evolution in the presence of heterospecific gene flow and its contribution to lineage divergence. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:971-989. [PMID: 33537708 DOI: 10.1093/jxb/eraa549] [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: 08/10/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
The success of species depends on their ability to exploit ecological resources in order to optimize their reproduction. However, species are not usually found within single-species ecosystems but in complex communities. Because of their genetic relatedness, closely related lineages tend to cluster within the same ecosystem, rely on the same resources, and be phenotypically similar. In sympatry, they will therefore compete for the same resources and, in the case of flowering plants, exchange their genes through heterospecific pollen transfer. These interactions, nevertheless, pose significant challenges to species co-existence because they can lead to resource limitation and reproductive interference. In such cases, divergent selective pressures on floral traits will favour genotypes that isolate or desynchronize the reproduction of sympatric lineages. The resulting displacement of reproductive characters will, in turn, lead to pre-mating isolation and promote intraspecific divergence, thus initiating or reinforcing the speciation process. In this review, we discuss the current theoretical and empirical knowledge on the influence of heterospecific pollen transfer on flower evolution, highlighting its potential to uncover the ecological and genomic constraints shaping the speciation process.
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Affiliation(s)
- Marion Orsucci
- Department of Plant Biology, Swedish University of Agricultural, Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Adrien Sicard
- Department of Plant Biology, Swedish University of Agricultural, Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
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12
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Härer A, Bolnick DI, Rennison DJ. The genomic signature of ecological divergence along the benthic-limnetic axis in allopatric and sympatric threespine stickleback. Mol Ecol 2020; 30:451-463. [PMID: 33222348 DOI: 10.1111/mec.15746] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/21/2020] [Accepted: 11/09/2020] [Indexed: 12/23/2022]
Abstract
The repeated occurrence of similar phenotypes in independent lineages (i.e., parallel evolution) in response to similar ecological conditions can provide compelling insights into the process of adaptive evolution. An intriguing question is to what extent repeated phenotypic changes are underlain by repeated changes at the genomic level and whether patterns of genomic divergence differ with the geographic context in which populations evolve. Here, we combined genomic, morphological and ecological data sets to investigate the genomic signatures of divergence across populations of threespine stickleback (Gasterosteus aculeatus) that adapted to contrasting ecological niches (benthic or limnetic) in either sympatry or allopatry. We found that genome-wide differentiation (FST ) was an order of magnitude higher and substantially more repeatable for sympatric benthic and limnetic specialists compared to allopatric populations with similar levels of ecological divergence. We identified genomic regions consistently differentiated between sympatric ecotypes that were also differentiated between or associated with benthic vs. limnetic niche in allopatric populations. These candidate regions were enriched on three chromosomes known to be involved in the benthic-limnetic divergence of threespine stickleback. Some candidate regions overlapped with QTL for body shape and trophic traits such as gill raker number, traits that strongly differ between benthic and limnetic ecotypes. In summary, our study shows that magnitude and repeatability of genomic signatures of ecological divergence in threespine stickleback highly depend on the geographic context. The identified candidate regions provide starting points to identify functionally important genes for the adaptation to benthic and limnetic niches.
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Affiliation(s)
- Andreas Härer
- Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, USA
| | - Daniel I Bolnick
- Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Diana J Rennison
- Division of Biological Sciences, Section of Ecology, Behavior, & Evolution, University of California San Diego, La Jolla, CA, USA
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13
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Hinojosa JC, Koubínová D, Dincă V, Hernández-Roldán J, Munguira ML, García-Barros E, Vila M, Alvarez N, Mutanen M, Vila R. Rapid colour shift by reproductive character displacement in Cupido butterflies. Mol Ecol 2020; 29:4942-4955. [PMID: 33051915 DOI: 10.1111/mec.15682] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 12/27/2022]
Abstract
Reproductive character displacement occurs when competition for successful breeding imposes a divergent selection on the interacting species, causing a divergence of reproductive traits. Here, we show that a disputed butterfly taxon is actually a case of male wing colour shift, apparently produced by reproductive character displacement. Using double digest restriction-site associated DNA sequencing and mitochondrial DNA sequencing we studied four butterfly taxa of the subgenus Cupido (Lepidoptera: Lycaenidae): Cupido minimus and the taxon carswelli, both characterized by brown males and females, plus C. lorquinii and C. osiris, both with blue males and brown females. Unexpectedly, taxa carswelli and C. lorquinii were close to indistinguishable based on our genomic and mitochondrial data, despite displaying strikingly different male coloration. In addition, we report and analysed a brown male within the C. lorquinii range, which demonstrates that the brown morph occurs at very low frequency in C. lorquinii. Such evidence strongly suggests that carswelli is conspecific with C. lorquinii and represents populations with a fixed male brown colour morph. Considering that these brown populations occur in sympatry with or very close to the blue C. osiris, and that the blue C. lorquinii populations never do, we propose that the taxon carswelli could have lost the blue colour due to reproductive character displacement with C. osiris. Since male colour is important for conspecific recognition during courtship, we hypothesize that the observed colour shift may eventually trigger incipient speciation between blue and brown populations. Male colour seems to be an evolutionarily labile character in the Polyommatinae, and the mechanism described here might be at work in the wide diversification of this subfamily of butterflies.
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Affiliation(s)
| | | | - Vlad Dincă
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Juan Hernández-Roldán
- Departamento de Biología - Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel L Munguira
- Departamento de Biología - Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Enrique García-Barros
- Departamento de Biología - Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Vila
- GIBE Research Group, Universidade da Coruña, A Coruña, Spain
| | | | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Barcelona, Spain
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14
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North HL, Caminade P, Severac D, Belkhir K, Smadja CM. The role of copy-number variation in the reinforcement of sexual isolation between the two European subspecies of the house mouse. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190540. [PMID: 32654648 PMCID: PMC7423270 DOI: 10.1098/rstb.2019.0540] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2020] [Indexed: 12/24/2022] Open
Abstract
Reinforcement has the potential to generate strong reproductive isolation through the evolution of barrier traits as a response to selection against maladaptive hybridization, but the genetic changes associated with this process remain largely unexplored. Building upon the increasing evidence for a role of structural variants in adaptation and speciation, we addressed the role of copy-number variation in the reinforcement of sexual isolation evidenced between the two European subspecies of the house mouse. We characterized copy-number divergence between populations of Mus musculus musculus that display assortative mate choice, and those that do not, using whole-genome resequencing data. Updating methods to detect deletions and tandem duplications (collectively: copy-number variants, CNVs) in Pool-Seq data, we developed an analytical pipeline dedicated to identifying genomic regions showing the expected pattern of copy-number displacement under a reinforcement scenario. This strategy allowed us to detect 1824 deletions and seven tandem duplications that showed extreme differences in frequency between behavioural classes across replicate comparisons. A subset of 480 deletions and four tandem duplications were specifically associated with the derived trait of assortative mate choice. These 'Choosiness-associated' CNVs occur in hundreds of genes. Consistent with our hypothesis, such genes included olfactory receptors potentially involved in the olfactory-based assortative mate choice in this system as well as one gene, Sp110, that is known to show patterns of differential expression between behavioural classes in an organ used in mate choice-the vomeronasal organ. These results demonstrate that fine-scale structural changes are common and highly variable within species, despite being under-studied, and may be important targets of reinforcing selection in this system and others. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Henry L. North
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
| | - Pierre Caminade
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 rue de la cardonille, 34094 Montpellier Cedex 5, France
| | - Khalid Belkhir
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
| | - Carole M. Smadja
- Institut des Sciences de l'Evolution (UMR 5554 CNRS, IRD, EPHE, Université de Montpellier), Université de Montpellier, Campus Triolet, Place Eugène Bataillon, 34095 Montpellier, France
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15
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Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190528. [PMID: 32654637 PMCID: PMC7423269 DOI: 10.1098/rstb.2019.0528] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Jonna Kulmuni
- Organismal and Evolutionary Biology, University of Helsinki, Finland
| | - Roger K. Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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16
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Lucek K, Butlin RK, Patsiou T. Secondary contact zones of closely-related Erebia butterflies overlap with narrow phenotypic and parasitic clines. J Evol Biol 2020; 33:1152-1163. [PMID: 32573833 DOI: 10.1111/jeb.13669] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/05/2020] [Accepted: 06/16/2020] [Indexed: 11/30/2022]
Abstract
Zones of secondary contact between closely related taxa are a common legacy of the Quaternary ice ages. Despite their abundance, the factors that keep species apart and prevent hybridization are often unknown. Here, we study a very narrow contact zone between three closely related butterfly species of the Erebia tyndarus species complex. Using genomic data, we first determined whether gene flow occurs and then assessed whether it might be hampered by differences in chromosome number between some species. We found interspecific gene flow between sibling species that differ in karyotype by one chromosome. Conversely, only F1 hybrids occurred between two species that have the same karyotype, forming a steep genomic cline. In a second step, we fitted clines to phenotypic, ecological and parasitic data to identify the factors associated with the genetic cline. We found clines for phenotypic data and the prevalence of the endosymbiont parasite Wolbachia to overlap with the genetic cline, suggesting that they might be drivers for separating the two species. Overall, our results highlight that some gene flow is possible between closely related species despite different chromosome numbers, but that other barriers restrict such gene flow.
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Affiliation(s)
- Kay Lucek
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, Tjärnö, University of Gothenburg, Strömstad, Sweden
| | - Theofania Patsiou
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.,Institute of Plant Sciences, Department of Biology, University of Bern, Bern, Switzerland
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17
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Ravinet M, Kume M, Ishikawa A, Kitano J. Patterns of genomic divergence and introgression between Japanese stickleback species with overlapping breeding habitats. J Evol Biol 2020; 34:114-127. [PMID: 32557887 DOI: 10.1111/jeb.13664] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 11/26/2022]
Abstract
With only a few absolute geographic barriers in marine environments, the factors maintaining reproductive isolation among marine organisms remain elusive. However, spatial structuring in breeding habitat can contribute to reproductive isolation. This is particularly important for marine organisms that migrate to use fresh- or brackish water environments to breed. The Japanese Gasterosteus stickleback species, the Pacific Ocean three-spined stickleback (G. aculeatus) and the Japan Sea stickleback (G. nipponicus) overwinter in the sea, but migrate to rivers for spawning. Although they co-occur at several locations across the Japanese islands, they are reproductively isolated. Our previous studies in Bekanbeushi River showed that the Japan Sea stickleback spawns in the estuary, while the Pacific Ocean stickleback mainly spawns further upstream in freshwater. Overall genomic divergence was very high with many interspersed regions of introgression. Here, we investigated genomic divergence and introgression between the sympatric species in the much shorter Tokotan River, where they share spawning sites. The levels of genome-wide divergence were reduced and introgression was increased, suggesting that habitat isolation substantially contributes to a reduction in gene flow. We also found that genomic regions of introgression were largely shared between the two systems. Furthermore, some regions of introgression were located near loci with a heterozygote advantage for juvenile survival. Taken together, introgression may be partially driven by adaptation in this system. Although, the two species remain clearly genetically differentiated. Regions with low recombination rates showed especially low introgression. Speciation reversal is therefore likely prevented by barriers other than habitat isolation.
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Affiliation(s)
- Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Manabu Kume
- Kyoto University Field Science Education and Research Center, Kyoto, Japan
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Japan
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18
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Tonzo V, Papadopoulou A, Ortego J. Genomic footprints of an old affair: Single nucleotide polymorphism data reveal historical hybridization and the subsequent evolution of reproductive barriers in two recently diverged grasshoppers with partly overlapping distributions. Mol Ecol 2020; 29:2254-2268. [DOI: 10.1111/mec.15475] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Vanina Tonzo
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
| | - Anna Papadopoulou
- Department of Biological Sciences University of Cyprus Nicosia Cyprus
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD‐CSIC) Seville Spain
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19
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Moran RL, Catchen JM, Fuller RC. Genomic Resources for Darters (Percidae: Etheostominae) Provide Insight into Postzygotic Barriers Implicated in Speciation. Mol Biol Evol 2020; 37:711-729. [PMID: 31688927 PMCID: PMC7038671 DOI: 10.1093/molbev/msz260] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Comparative genomic approaches are increasingly being used to study the evolution of reproductive barriers in nonmodel species. Although numerous studies have examined prezygotic isolation in darters (Percidae), investigations into postzygotic barriers have remained rare due to long generation times and a lack of genomic resources. Orangethroat and rainbow darters naturally hybridize and provide a remarkable example of male-driven speciation via character displacement. Backcross hybrids suffer from high mortality, which appears to promote behavioral isolation in sympatry. To investigate the genomic architecture of postzygotic isolation, we used Illumina and PacBio sequencing to generate a chromosome-level, annotated assembly of the orangethroat darter genome and high-density linkage maps for orangethroat and rainbow darters. We also analyzed genome-wide RADseq data from wild-caught adults of both species and laboratory-generated backcrosses to identify genomic regions associated with hybrid incompatibles. Several putative chromosomal translocations and inversions were observed between orangethroat and rainbow darters, suggesting structural rearrangements may underlie postzygotic isolation. We also found evidence of selection against recombinant haplotypes and transmission ratio distortion in backcross hybrid genomes, providing further insight into the genomic architecture of genetic incompatibilities. Notably, regions with high levels of genetic divergence between species were enriched for genes associated with developmental and meiotic processes, providing strong candidates for postzygotic isolating barriers. These findings mark significant contributions to our understanding of the genetic basis of reproductive isolation between species undergoing character displacement. Furthermore, the genomic resources presented here will be instrumental for studying speciation in darters, the most diverse vertebrate group in North America.
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Affiliation(s)
- Rachel L Moran
- Program in Ecology, Evolution, and Conservation Biology, Department of Animal Biology, University of Illinois at Urbana-Champaign, Champaign, IL
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN
| | - Julian M Catchen
- Program in Ecology, Evolution, and Conservation Biology, Department of Animal Biology, University of Illinois at Urbana-Champaign, Champaign, IL
| | - Rebecca C Fuller
- Program in Ecology, Evolution, and Conservation Biology, Department of Animal Biology, University of Illinois at Urbana-Champaign, Champaign, IL
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20
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Montero-Mendieta S, Tan K, Christmas MJ, Olsson A, Vilà C, Wallberg A, Webster MT. The genomic basis of adaptation to high-altitude habitats in the eastern honey bee (Apis cerana). Mol Ecol 2019; 28:746-760. [PMID: 30576015 DOI: 10.1111/mec.14986] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 01/30/2023]
Abstract
The eastern honey bee (Apis cerana) is of central importance for agriculture in Asia. It has adapted to a wide variety of environmental conditions across its native range in southern and eastern Asia, which includes high-altitude regions. eastern honey bees inhabiting mountains differ morphologically from neighbouring lowland populations and may also exhibit differences in physiology and behaviour. We compared the genomes of 60 eastern honey bees collected from high and low altitudes in Yunnan and Gansu provinces, China, to infer their evolutionary history and to identify candidate genes that may underlie adaptation to high altitude. Using a combination of FST -based statistics, long-range haplotype tests and population branch statistics, we identified several regions of the genome that appear to have been under positive selection. These candidate regions were strongly enriched for coding sequences and had high haplotype homozygosity and increased divergence specifically in highland bee populations, suggesting they have been subjected to recent selection in high-altitude habitats. Candidate loci in these genomic regions included genes related to reproduction and feeding behaviour in honey bees. Functional investigation of these candidate loci is necessary to fully understand the mechanisms of adaptation to high-altitude habitats in the eastern honey bee.
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Affiliation(s)
| | - Ken Tan
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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