1
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Long KM, Rivera-Colón AG, Bennett KFP, Catchen JM, Braun MJ, Brawn JD. Ongoing introgression of a secondary sexual plumage trait in a stable avian hybrid zone. Evolution 2024; 78:1539-1553. [PMID: 38753474 DOI: 10.1093/evolut/qpae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 05/14/2024] [Indexed: 05/18/2024]
Abstract
Hybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus, including bright yellow collar and olive belly color, have introgressed ~50 km asymmetrically across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei, suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989-1994) and contemporary (2017-2020) transect samples to survey both morphological and genetic variation. Genome-wide single nucleotide polymorphism data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species.
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Affiliation(s)
- Kira M Long
- Program in Ecology, Evolution and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, United States
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
| | - Kevin F P Bennett
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, United States
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Julian M Catchen
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, United States
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
| | - Jeffrey D Brawn
- Department of Natural Resources & Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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2
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Vernasco BJ, Long KM, Braun MJ, Brawn JD. Genetic and telomeric variability: Insights from a tropical avian hybrid zone. Mol Ecol 2024:e17491. [PMID: 39192633 DOI: 10.1111/mec.17491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 07/01/2024] [Accepted: 07/09/2024] [Indexed: 08/29/2024]
Abstract
Telomere lengths and telomere dynamics can correlate with lifespan, behaviour and individual quality. Such relationships have spurred interest in understanding variation in telomere lengths and their dynamics within and between populations. Many studies have identified how environmental processes can influence telomere dynamics, but the role of genetic variation is much less well characterized. To provide a novel perspective on how telomeric variation relates to genetic variability, we longitudinally sampled individuals across a narrow hybrid zone (n = 127 samples), wherein two Manacus species characterized by contrasting genome-wide heterozygosity interbreed. We measured individual (n = 66) and population (n = 3) differences in genome-wide heterozygosity and, among hybrids, amount of genetic admixture using RADseq-generated SNPs. We tested for population differences in telomere lengths and telomere dynamics. We then examined how telomere lengths and telomere dynamics covaried with genome-wide heterozygosity within populations. Hybrid individuals exhibited longer telomeres, on average, than individuals sampled in the adjacent parental populations. No population differences in telomere dynamics were observed. Within the parental population characterized by relatively low heterozygosity, higher genome-wide heterozygosity was associated with shorter telomeres and higher rates of telomere shortening-a pattern that was less apparent in the other populations. All of these relationships were independent of sex, despite the contrasting life histories of male and female manakins. Our study highlights how population comparisons can reveal interrelationships between genetic variation and telomeres, and how naturally occurring hybridization and genome-wide heterozygosity can relate to telomere lengths and telomere dynamics.
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Affiliation(s)
- Ben J Vernasco
- School of Biological Sciences, Washington State University, Pullman, Washington, USA
| | - Kira M Long
- Program in Ecology, Evolution and Conservation Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Michael J Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Department of Biology and Biology Graduate Program, University of Maryland, College Park, Maryland, USA
| | - Jeffrey D Brawn
- Department of Natural Resources and Environmental Sciences, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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3
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Horníková M, Lanier HC, Marková S, Escalante MA, Searle JB, Kotlík P. Genetic admixture drives climate adaptation in the bank vole. Commun Biol 2024; 7:863. [PMID: 39009753 PMCID: PMC11251159 DOI: 10.1038/s42003-024-06549-z] [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: 07/20/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Genetic admixture introduces new variants at relatively high frequencies, potentially aiding rapid responses to environmental changes. Here, we evaluate its role in adaptive variation related to climatic conditions in bank voles (Clethrionomys glareolus) in Britain, using whole-genome data. Our results reveal loci showing excess ancestry from one of the two postglacial colonist populations inconsistent with overall admixture patterns. Notably, loci associated with climate adaptation exhibit disproportionate amounts of excess ancestry, highlighting the impact of admixture between colonist populations on local adaptation. The results suggest strong and localized selection on climate-adaptive loci, as indicated by steep clines and/or shifted cline centres, during population replacement. A subset, including a haemoglobin gene, is associated with oxidative stress responses, underscoring a role of oxidative stress in local adaptation. Our study highlights the important contribution of admixture during secondary contact between populations from distinct climatic refugia enriching adaptive diversity. Understanding these dynamics is crucial for predicting future adaptive capacity to anthropogenic climate change.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
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4
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Delmore K, Justen H, Kay KM, Kitano J, Moyle LC, Stelkens R, Streisfeld MA, Yamasaki YY, Ross J. Genomic Approaches Are Improving Taxonomic Representation in Genetic Studies of Speciation. Cold Spring Harb Perspect Biol 2024; 16:a041438. [PMID: 37848243 PMCID: PMC10835617 DOI: 10.1101/cshperspect.a041438] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Until recently, our understanding of the genetics of speciation was limited to a narrow group of model species with a specific set of characteristics that made genetic analysis feasible. Rapidly advancing genomic technologies are eliminating many of the distinctions between laboratory and natural systems. In light of these genomic developments, we review the history of speciation genetics, advances that have been gleaned from model and non-model organisms, the current state of the field, and prospects for broadening the diversity of taxa included in future studies. Responses to a survey of speciation scientists across the world reveal the ongoing division between the types of questions that are addressed in model and non-model organisms. To bridge this gap, we suggest integrating genetic studies from model systems that can be reared in the laboratory or greenhouse with genomic studies in related non-models where extensive ecological knowledge exists.
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Affiliation(s)
- Kira Delmore
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Hannah Justen
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Rike Stelkens
- Division of Population Genetics, Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Joseph Ross
- Department of Biology, California State University, Fresno, California 93740, USA
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5
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Villa-Machío I, Heuertz M, Álvarez I, Nieto Feliner G. Demography-driven and adaptive introgression in a hybrid zone of the Armeria syngameon. Mol Ecol 2023. [PMID: 37837272 DOI: 10.1111/mec.17167] [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: 07/18/2022] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023]
Abstract
Syngameons represent networks of otherwise distinct species connected by limited gene exchange. Although most studies have focused on how species maintain their cohesiveness despite gene flow, there are additional relevant questions regarding the evolutionary dynamics of syngameons and their drivers, as well as the success of their members and the network as a whole. Using a ddRADseq approach, we analysed the genetic structure, genomic clines and demographic history of a coastal hybrid zone involving two species of the Armeria (Plumbaginaceae) syngameon in southern Spain. We inferred that a peripheral population of the sand dune-adapted A. pungens diverged from the rest of the conspecific populations and subsequently hybridized with a locally more abundant pinewood congener, A. macrophylla. Both species display extensive plastid DNA haplotype sharing. Genomic cline analysis identified bidirectional introgression, but more outlier loci with excess A. pungens than A. macrophylla ancestry, suggesting the possibility of selection for A. pungens alleles. This is consistent with the finding that the A. pungens phenotype is selected for in open habitats, and with the strong correlation found between ancestry and phenotype. Taken together, our analyses suggest an intriguing scenario in which bidirectional introgression may, on the one hand, help to avoid reduced levels of genetic diversity due to the small size and isolated location of the A. pungens range-edge population, thereby minimizing demographic risks of stochastic extinction. On the other hand, the data also suggest that introgression into A. macrophylla may allow individuals to grow in open, highly irradiated, deep sandy, salt-exposed habitats.
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Affiliation(s)
- Irene Villa-Machío
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | | | - Inés Álvarez
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
| | - Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB), CSIC, Madrid, Spain
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6
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Duvernell DD, Remex NS, Miller JT, Schaefer JF. Variable rates of hybridization among contact zones between a pair of topminnow species, Fundulus notatus and F. olivaceus. Ecol Evol 2023; 13:e10399. [PMID: 37560181 PMCID: PMC10408002 DOI: 10.1002/ece3.10399] [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: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
Pairs of species that exhibit broadly overlapping distributions, and multiple geographically isolated contact zones, provide opportunities to investigate the mechanisms of reproductive isolation. Such naturally replicated systems have demonstrated that hybridization rates can vary substantially among populations, raising important questions about the genetic basis of reproductive isolation. The topminnows, Fundulus notatus and F. olivaceus, are reciprocally monophyletic, and co-occur in drainages throughout much of the central and southern United States. Hybridization rates vary substantially among populations in isolated drainage systems. We employed genome-wide sampling to investigate geographic variation in hybridization, and to assess the possible importance of chromosome fusions to reproductive isolation among nine separate contact zones. The species differ by chromosomal rearrangements resulting from Robertsonian (Rb) fusions, so we hypothesized that Rb fusion chromosomes would serve as reproductive barriers, exhibiting steeper genomic clines than the rest of the genome. We observed variation in hybridization dynamics among drainages that ranged from nearly random mating to complete absence of hybridization. Contrary to predictions, our use of genomic cline analyses on mapped species-diagnostic SNP markers did not indicate consistent patterns of variable introgression across linkage groups, or an association between Rb fusions and genomic clines that would be indicative of reproductive isolation. We did observe a relationship between hybridization rates and population phylogeography, with the lowest rates of hybridization tending to be found in populations inferred to have had the longest histories of drainage sympatry. Our results, combined with previous studies of contact zones between the species, support population history as an important factor in explaining variation in hybridization rates.
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Affiliation(s)
- David D. Duvernell
- Department of Biological SciencesMissouri University of Science and TechnologyRollaMissouriUSA
| | - Naznin S. Remex
- Department of Biological SciencesMissouri University of Science and TechnologyRollaMissouriUSA
- Present address:
Department of Molecular and Cellular PhysiologyLouisiana State University Health Sciences CenterShreveportLouisianaUSA
| | - Jeffrey T. Miller
- Molecular, Cellular, and Biomedical SciencesUniversity of New HampshireDurhamNew HampshireUSA
| | - Jacob F. Schaefer
- Department of Biological SciencesUniversity of Southern MississippiHattiesburgMississippiUSA
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7
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van Riemsdijk I, Arntzen JW, Bucciarelli GM, McCartney-Melstad E, Rafajlović M, Scott PA, Toffelmier E, Shaffer HB, Wielstra B. Two transects reveal remarkable variation in gene flow on opposite ends of a European toad hybrid zone. Heredity (Edinb) 2023; 131:15-24. [PMID: 37106116 PMCID: PMC10313803 DOI: 10.1038/s41437-023-00617-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Speciation entails a reduction in gene flow between lineages. The rates at which genomic regions become isolated varies across space and time. Barrier markers are linked to putative genes involved in (processes of) reproductive isolation, and, when observed over two transects, indicate species-wide processes. In contrast, transect-specific putative barrier markers suggest local processes. We studied two widely separated transects along the 900 km hybrid zone between Bufo bufo and B. spinosus, in northern and southern France, for ~1200 RADseq markers. We used genomic and geographic cline analyses to identify barrier markers based on their restricted introgression, and found that some markers are transect-specific, while others are shared between transects. Twenty-six barrier markers were shared across both transects, of which some are clustered in the same chromosomal region, suggesting that their associated genes are involved in reduced gene flow across the entire hybrid zone. Transect-specific barrier markers were twice as numerous in the southern than in the northern transect, suggesting that the overall barrier effect is weaker in northern France. We hypothesize that this is consistent with a longer period of secondary contact in southern France. The smaller number of introgressed genes in the northern transect shows considerably more gene flow towards the southern (B. spinosus) than the northern species (B. bufo). We hypothesize that hybrid zone movement in northern France and hybrid zone stability in southern France explain this pattern. The Bufo hybrid zone provides an excellent opportunity to separate a general barrier effect from localized gene flow-reducing conditions.
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Affiliation(s)
- I van Riemsdijk
- Naturalis Biodiversity Center, Leiden, the Netherlands.
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands.
- Institute for Evolution and Ecology, Plant Evolutionary Ecology, Tübingen University, Tübingen, Germany.
| | - J W Arntzen
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - G M Bucciarelli
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
- Institute of the Environment, UC Davis, Davis, CA, USA
- Department of Wildlife, Fish, and Conservation Biology, UC Davis, Davis, CA, USA
| | - E McCartney-Melstad
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - M Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - P A Scott
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Natural Sciences Collegium, Eckerd College, 4200 54 Ave S, St Petersburg, FL, 33711, USA
| | - E Toffelmier
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - H B Shaffer
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - B Wielstra
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
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8
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Caeiro-Dias G, Brelsford A, Meneses-Ribeiro M, Crochet PA, Pinho C. Hybridization in late stages of speciation: Strong but incomplete genome-wide reproductive isolation and 'large Z-effect' in a moving hybrid zone. Mol Ecol 2023. [PMID: 37316984 DOI: 10.1111/mec.17035] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 06/16/2023]
Abstract
In organisms reproducing sexually, speciation occurs when increasing divergence results in pre- or post-zygotic reproductive isolation between lineages. Studies focusing on reproductive isolation origin in early stages of speciation are common and many rely on genomic scans to infer introgression providing limited information on the genomic architecture of reproductive isolation long-term maintenance. This study analyses a natural hybrid zone between two species in a late stage of speciation. We used ddRADseq genotyping in the contact between Podarcis bocagei and P. carbonelli to examine admixture extent, analyse hybrid zone stability and assess genome-wide variation in selection against introgression. We confirmed strong but incomplete reproductive isolation in a bimodal hybrid zone. New findings revealed population genetic structure within P. carbonelli in the contact zone; geographical and genomic clines analysis suggested strong selection against gene flow, but a relatively small proportion of the loci can introgress, mostly within the narrow contact zone. However, geographical clines revealed that a few introgressed loci show signs of potential positive selection, particularly into P. bocagei. Geographical clines also detected a signal of hybrid zone movement towards P. bocagei distribution. Genomic cline analysis revealed heterogeneous patterns of introgression among loci within the syntopy zone, but the majority maintain a strong association with the genomic background of origin. However, incongruences between both cline approaches were found, potentially driven by confounding effects on genomic clines. Last, an important role of the Z chromosome in reproductive isolation is suggested. Importantly, overall patterns of restricted introgression seem to result from numerous strong intrinsic barriers across the genome.
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Affiliation(s)
- Guilherme Caeiro-Dias
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Biology Department, University of California Riverside, Riverside, California, USA
| | - Mariana Meneses-Ribeiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Pierre-André Crochet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Catarina Pinho
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
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9
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Zhang L, Chaturvedi S, Nice CC, Lucas LK, Gompert Z. Population genomic evidence of selection on structural variants in a natural hybrid zone. Mol Ecol 2023; 32:1497-1514. [PMID: 35398939 DOI: 10.1111/mec.16469] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/18/2022] [Accepted: 03/28/2022] [Indexed: 12/01/2022]
Abstract
Structural variants (SVs) can promote speciation by directly causing reproductive isolation or by suppressing recombination across large genomic regions. Whereas examples of each mechanism have been documented, systematic tests of the role of SVs in speciation are lacking. Here, we take advantage of long-read (Oxford nanopore) whole-genome sequencing and a hybrid zone between two Lycaeides butterfly taxa (L. melissa and Jackson Hole Lycaeides) to comprehensively evaluate genome-wide patterns of introgression for SVs and relate these patterns to hypotheses about speciation. We found >100,000 SVs segregating within or between the two hybridizing species. SVs and SNPs exhibited similar levels of genetic differentiation between species, with the exception of inversions, which were more differentiated. We detected credible variation in patterns of introgression among SV loci in the hybrid zone, with 562 of 1419 ancestry-informative SVs exhibiting genomic clines that deviated from null expectations based on genome-average ancestry. Overall, hybrids exhibited a directional shift towards Jackson Hole Lycaeides ancestry at SV loci, consistent with the hypothesis that these loci experienced more selection on average than SNP loci. Surprisingly, we found that deletions, rather than inversions, showed the highest skew towards excess ancestry from Jackson Hole Lycaeides. Excess Jackson Hole Lycaeides ancestry in hybrids was also especially pronounced for Z-linked SVs and inversions containing many genes. In conclusion, our results show that SVs are ubiquitous and suggest that SVs in general, but especially deletions, might disproportionately affect hybrid fitness and thus contribute to reproductive isolation.
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Affiliation(s)
- Linyi Zhang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biology, Utah State University, Logan, Utah, USA
| | - Samridhi Chaturvedi
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Chris C Nice
- Department of Biology, Texas State University, San Marcos, Texas, USA
| | - Lauren K Lucas
- Department of Biology, Utah State University, Logan, Utah, USA
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10
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Barske J, Fuxjager MJ, Ciofi C, Natali C, Schlinger BA, Billo T, Fusani L. Beyond plumage: acrobatic courtship displays show intermediate patterns in manakin hybrids. Anim Behav 2023. [DOI: 10.1016/j.anbehav.2023.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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11
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Hodel RGJ, Massatti R, Knowles LL. Hybrid enrichment of adaptive variation revealed by genotype-environment associations in montane sedges. Mol Ecol 2022; 31:3722-3737. [PMID: 35560840 PMCID: PMC9327521 DOI: 10.1111/mec.16502] [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: 05/19/2021] [Revised: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 12/04/2022]
Abstract
The role of hybridization in diversification is complex and may result in many possible outcomes. Not only can hybridization produce new lineages, but those lineages may contain unique combinations of adaptive genetic variation derived from parental taxa that allow hybrid‐origin lineages to occupy unique environmental space relative to one (or both) parent(s). We document such a case of hybridization between two sedge species, Carex nova and Carex nelsonii (Cyperaceae), that occupy partially overlapping environmental space in the southern Rocky Mountains, USA. In the region hypothesized to be the origin of the hybrid lineage, one parental taxon (C. nelsonii) is at the edge of its environmental tolerance. Hybrid‐origin individuals display mixed ancestry between the parental taxa—of nearly 7000 unlinked loci sampled, almost 30% showed evidence of excess ancestry from one parental lineage—approximately half displayed a genomic background skewed towards one parent, and half skewed towards the other. To test whether excess ancestry loci may have conferred an adaptive advantage to the hybrid‐origin lineage, we conducted genotype–environment association analyses on different combinations of loci—with and without excess ancestry—and with multiple contrasts between the hybrids and parental taxa. Loci with skewed ancestry showed significant environmental associations distinguishing the hybrid lineage from one parent (C. nelsonii), whereas loci with relatively equal representation of parental ancestries showed no such environmental associations. Moreover, the overwhelming majority of candidate adaptive loci with respect to environmental gradients also had excess ancestry from a parental lineage, implying these loci have facilitated the persistence of the hybrid lineage in an environment unsuitable to at least one parent.
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Affiliation(s)
- Richard G J Hodel
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, USA
| | - Rob Massatti
- U.S. Geological Survey, Southwest Biological Science Center, Flagstaff, AZ, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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12
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Wolfgramm H, Martens J, Töpfer T, Vamberger M, Pathak A, Stuckas H, Päckert M. Asymmetric allelic introgression across a hybrid zone of the coal tit ( Periparus ater) in the central Himalayas. Ecol Evol 2021; 11:17332-17351. [PMID: 34938512 PMCID: PMC8668783 DOI: 10.1002/ece3.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/07/2022] Open
Abstract
In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (Periparus ater) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western "spot-winged tit" (P. a. melanolophus) and Eastern Himalayan coal tits (P. a. aemodius) occur across a narrow range of <100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern P. a. aemodius into far western populations of phenotypic P. a. melanolophus but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.
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Affiliation(s)
- Hannes Wolfgramm
- Senckenberg Natural History Collections DresdenDresdenGermany
- Present address:
Department of Functional GenomicsInterfaculty Institute of Genetics and Functional GenomicsUniversity Medicine GreifswaldGreifswaldGermany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution (iomE)Johannes Gutenberg UniversityMainzGermany
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity ChangeZoological Research Museum Alexander KoenigBonnGermany
| | | | - Abhinaya Pathak
- Department of National Parks and Wildlife ConservationKathmanduNepal
| | - Heiko Stuckas
- Senckenberg Natural History Collections DresdenDresdenGermany
| | - Martin Päckert
- Senckenberg Natural History Collections DresdenDresdenGermany
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13
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Martin BT, Chafin TK, Douglas MR, Douglas ME. ClineHelpR: an R package for genomic cline outlier detection and visualization. BMC Bioinformatics 2021; 22:501. [PMID: 34656096 PMCID: PMC8520269 DOI: 10.1186/s12859-021-04423-x] [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: 07/27/2021] [Accepted: 10/04/2021] [Indexed: 11/30/2022] Open
Abstract
Background Patterns of multi-locus differentiation (i.e., genomic clines) often extend broadly across hybrid zones and their quantification can help diagnose how species boundaries are shaped by adaptive processes, both intrinsic and extrinsic. In this sense, the transitioning of loci across admixed individuals can be contrasted as a function of the genome-wide trend, in turn allowing an expansion of clinal theory across a much wider array of biodiversity. However, computational tools that serve to interpret and consequently visualize ‘genomic clines’ are limited, and users must often write custom, relatively complex code to do so. Results Here, we introduce the ClineHelpR R-package for visualizing genomic clines and detecting outlier loci using output generated by two popular software packages, bgc and Introgress. ClineHelpR bundles both input generation (i.e., filtering datasets and creating specialized file formats) and output processing (e.g., MCMC thinning and burn-in) with functions that directly facilitate interpretation and hypothesis testing. Tools are also provided for post-hoc analyses that interface with external packages such as ENMeval and RIdeogram. Conclusions Our package increases the reproducibility and accessibility of genomic cline methods, thus allowing an expanded user base and promoting these methods as mechanisms to address diverse evolutionary questions in both model and non-model organisms. Furthermore, the ClineHelpR extended functionality can evaluate genomic clines in the context of spatial and environmental features, allowing users to explore underlying processes potentially contributing to the observed patterns and helping facilitate effective conservation management strategies.
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Affiliation(s)
- Bradley T Martin
- Arkansas Conservation and Molecular Ecology Laboratory, Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA. .,University of Arkansas Global Campus, Fayetteville, AR, 72701, USA.
| | - Tyler K Chafin
- Arkansas Conservation and Molecular Ecology Laboratory, Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.,Ecology and Evolutionary Biology Department, University of Colorado, Boulder, CO, USA
| | - Marlis R Douglas
- Arkansas Conservation and Molecular Ecology Laboratory, Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Michael E Douglas
- Arkansas Conservation and Molecular Ecology Laboratory, Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
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14
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Jahner JP, Parchman TL, Matocq MD. Multigenerational backcrossing and introgression between two woodrat species at an abrupt ecological transition. Mol Ecol 2021; 30:4245-4258. [PMID: 34219316 DOI: 10.1111/mec.16056] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/28/2021] [Indexed: 12/27/2022]
Abstract
When organisms experience secondary contact after allopatric divergence, genomic regions can introgress differentially depending on their relationships with adaptation, reproductive isolation, recombination, and drift. Analyses of genome-wide patterns of divergence and introgression could provide insight into the outcomes of hybridization and the potential relationship between allopatric divergence and reproductive isolation. Here, we generate population genetic data (26,262 SNPs; 353 individuals) using a reduced-representation sequencing approach to quantify patterns of ancestry, differentiation, and introgression between a pair of ecologically distinct mammals-the desert woodrat (N. lepida) and Bryant's woodrat (N. bryanti)-that hybridize at a sharp ecotone in southern California. Individual ancestry estimates confirmed that hybrids were rare in this bimodal hybrid zone, and entirely consisted of a few F1 individuals and a broad range of multigenerational backcrosses. Genomic cline analyses indicated more than half of loci had elevated introgression from one genomic background into the other. However, introgression was not associated with relative or absolute measures of divergence, and loci with extreme values for both were not typically found near detoxification enzymes previously implicated in dietary specialization for woodrats. The decoupling of differentiation and introgression suggests that processes other than adaptation, such as drift, may underlie the extreme clines at this contact zone.
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Affiliation(s)
- Joshua P Jahner
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Department of Botany, University of Wyoming, Laramie, Wyoming, USA
| | - Thomas L Parchman
- Department of Biology, University of Nevada, Reno, Nevada, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA
| | - Marjorie D Matocq
- Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, Nevada, USA.,Department of Natural Resources and Environmental Science, University of Nevada, Reno, Nevada, USA
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15
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Bennett KFP, Lim HC, Braun MJ. Sexual selection and introgression in avian hybrid zones: Spotlight on Manacus. Integr Comp Biol 2021; 61:1291-1309. [PMID: 34128981 DOI: 10.1093/icb/icab135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybrid zones offer a window into the processes and outcomes of evolution, from species formation or fusion to genomic underpinnings of specific traits and isolating mechanisms. Sexual selection is believed to be an important factor in speciation processes, and hybrid zones present special opportunities to probe its impact. The manakins (Aves, Pipridae) are a promising group in which to study the interplay of sexual selection and natural hybridization: they show substantial variation across the family in the strength of sexual selection they experience, they readily hybridize within and between genera, and they appear to have formed hybrid species, a rare event in birds. A hybrid zone between two manakins in the genus Manacus is unusual in that plumage and behavioral traits of one species have introgressed asymmetrically into populations of the second species through positive sexual selection, then apparently stalled at a river barrier. This is one of a handful of documented examples of asymmetric sexual trait introgression with a known selective mechanism. It offers opportunities to examine reproductive isolation, introgression, plumage color evolution, and natural factors enhancing or constraining the effects of sexual selection in real time. Here, we review previous work in this system, propose new hypotheses for observed patterns, and recommend approaches to test them.
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Affiliation(s)
- Kevin F P Bennett
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Haw Chuan Lim
- Department of Biology, George Mason University, Manassas, VA, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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16
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McFarlane SE, Senn HV, Smith SL, Pemberton JM. Locus-specific introgression in young hybrid swarms: Drift may dominate selection. Mol Ecol 2021; 30:2104-2115. [PMID: 33638185 DOI: 10.1111/mec.15862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/01/2021] [Accepted: 02/17/2021] [Indexed: 12/17/2022]
Abstract
Closely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These human-mediated hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44,997 SNPs to identify loci introgressing more or less when compared to the genome wide expectation in a human-mediated hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centres that were significantly different from the genome wide expectation, and 17.6% of all SNPs had excess rates of introgression. Based on simulations, we believe that many of these markers have diverged from the genome-wide average due to drift, rather than because of selection, and we suggest that these simulations can be useful as a null distribution for future studies of genomic clines. Future work on red deer and sika could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are responding to selection.
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Affiliation(s)
- S Eryn McFarlane
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,Department of Biology, Lund University, Lund, Sweden
| | - Helen V Senn
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Stephanie L Smith
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.,The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Edinburgh, UK
| | - Josephine M Pemberton
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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17
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Shastry V, Adams PE, Lindtke D, Mandeville EG, Parchman TL, Gompert Z, Buerkle CA. Model-based genotype and ancestry estimation for potential hybrids with mixed-ploidy. Mol Ecol Resour 2021; 21:1434-1451. [PMID: 33482035 DOI: 10.1111/1755-0998.13330] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/11/2020] [Accepted: 01/11/2021] [Indexed: 11/29/2022]
Abstract
Non-random mating among individuals can lead to spatial clustering of genetically similar individuals and population stratification. This deviation from panmixia is commonly observed in natural populations. Consequently, individuals can have parentage in single populations or involving hybridization between differentiated populations. Accounting for this mixture and structure is important when mapping the genetics of traits and learning about the formative evolutionary processes that shape genetic variation among individuals and populations. Stratified genetic relatedness among individuals is commonly quantified using estimates of ancestry that are derived from a statistical model. Development of these models for polyploid and mixed-ploidy individuals and populations has lagged behind those for diploids. Here, we extend and test a hierarchical Bayesian model, called entropy, which can use low-depth sequence data to estimate genotype and ancestry parameters in autopolyploid and mixed-ploidy individuals (including sex chromosomes and autosomes within individuals). Our analysis of simulated data illustrated the trade-off between sequencing depth and genome coverage and found lower error associated with low-depth sequencing across a larger fraction of the genome than with high-depth sequencing across a smaller fraction of the genome. The model has high accuracy and sensitivity as verified with simulated data and through analysis of admixture among populations of diploid and tetraploid Arabidopsis arenosa.
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Affiliation(s)
| | - Paula E Adams
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA
| | - Dorothea Lindtke
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | | | | | | | - C Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, WY, USA
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18
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Nieto Feliner G, Casacuberta J, Wendel JF. Genomics of Evolutionary Novelty in Hybrids and Polyploids. Front Genet 2020; 11:792. [PMID: 32849797 PMCID: PMC7399645 DOI: 10.3389/fgene.2020.00792] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/03/2020] [Indexed: 12/15/2022] Open
Abstract
It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.
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Affiliation(s)
- Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico, CSIC, Madrid, Spain
| | - Josep Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Barcelona, Spain
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, United States
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19
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Liberles DA, Chang B, Geiler-Samerotte K, Goldman A, Hey J, Kaçar B, Meyer M, Murphy W, Posada D, Storfer A. Emerging Frontiers in the Study of Molecular Evolution. J Mol Evol 2020; 88:211-226. [PMID: 32060574 PMCID: PMC7386396 DOI: 10.1007/s00239-020-09932-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A collection of the editors of Journal of Molecular Evolution have gotten together to pose a set of key challenges and future directions for the field of molecular evolution. Topics include challenges and new directions in prebiotic chemistry and the RNA world, reconstruction of early cellular genomes and proteins, macromolecular and functional evolution, evolutionary cell biology, genome evolution, molecular evolutionary ecology, viral phylodynamics, theoretical population genomics, somatic cell molecular evolution, and directed evolution. While our effort is not meant to be exhaustive, it reflects research questions and problems in the field of molecular evolution that are exciting to our editors.
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Affiliation(s)
- David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
| | - Belinda Chang
- Department of Ecology and Evolutionary Biology and Department of Cell and Systems Biology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada
| | - Kerry Geiler-Samerotte
- Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Aaron Goldman
- Department of Biology, Oberlin College and Conservatory, K123 Science Center, 119 Woodland Street, Oberlin, OH, 44074, USA
| | - Jody Hey
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA
| | - Betül Kaçar
- Department of Molecular and Cell Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michelle Meyer
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA
| | - William Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77843, USA
| | - David Posada
- Biomedical Research Center (CINBIO), University of Vigo, Vigo, Spain
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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20
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Abstract
Introgressive hybridization can affect the evolution of populations in several important ways. It may retard or reverse divergence of species, enable the development of novel traits, enhance the potential for future evolution by elevating levels of standing variation, create new species, and alleviate inbreeding depression in small populations. Most of what is known of contemporary hybridization in nature comes from the study of pairs of species, either coexisting in the same habitat or distributed parapatrically and separated by a hybrid zone. More rarely, three species form an interbreeding complex (triad), reported in vertebrates, insects, and plants. Often, one species acts as a genetic link or conduit for the passage of genes (alleles) between two others that rarely, if ever, hybridize. Demographic and genetic consequences are unknown. Here we report results of a long-term study of interbreeding Darwin's finches on Daphne Major island, Galápagos. Geospiza fortis acted as a conduit for the passage of genes between two others that have never been observed to interbreed on Daphne: Geospiza fuliginosa, a rare immigrant, and Geospiza scandens, a resident. Microsatellite gene flow from G. fortis into G. scandens increased in frequency during 30 y of favorable ecological conditions, resulting in genetic and morphological convergence. G. fortis, G. scandens, and the derived dihybrids and trihybrids experienced approximately equal fitness. Especially relevant to young adaptive radiations, where species differ principally in ecology and behavior, these findings illustrate how new combinations of genes created by hybridization among three species can enhance the potential for evolutionary change.
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21
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Ebersbach J, Posso-Terranova A, Bogdanowicz S, Gómez-Díaz M, García-González MX, Bolívar-García W, Andrés J. Complex patterns of differentiation and gene flow underly the divergence of aposematic phenotypes in Oophaga poison frogs. Mol Ecol 2020; 29:1944-1956. [PMID: 31971303 DOI: 10.1111/mec.15360] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/11/2019] [Accepted: 01/04/2020] [Indexed: 12/16/2022]
Abstract
Hybridization and introgression can have complex consequences for both species evolution and conservation. Here, we investigated the origin and characteristics of a putative hybrid zone between two South American poison dart frog species, Oophaga anchicayensis and the critically endangered Oophaga lehmanni, which are heavily sought after on the illegal pet market. Using a combination of phenotypic (49 traits) and genomic (ddRADseq) data, we found that the putative hybrids are morphologically distinct from their parental species and confirmed genomic signatures of admixture in these populations. Several lines of evidence (hybrid indices, interspecific hybrid heterozygosity, genomic clines, comparisons with simulated hybrids and demographic modelling) support the conclusion that these populations are not comprised of early-generation hybrids and thus, they probably did not arise as a result of illegal translocations associated with wildlife trafficking. Instead, they probably represent an independent lineage which has persisted through isolation and has only relatively recently re-established gene flow with both parental species. Furthermore, we detected signals of differential introgression from parental species into these hybrid populations which suggest relaxed stabilizing selection on these aposematic colour morphs, potentially via context-dependent female choice. These populations thus provide a fascinating window into the role of hybridization, isolation and female choice in the diversification of South American poison dart frogs. In addition, our results underline the importance of landscape conservation measures to protect, not only known localities of nominal species, but also the phenotypic and genomic variation harbored by admixed lineages which represent crucial repositories for the impressive diversity in this system.
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Affiliation(s)
- Jana Ebersbach
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Andrés Posso-Terranova
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Facultad de Ciencias Agropecuarias, Universidad Nacional de Colombia sede Palmira, Palmira, Colombia
| | - Steven Bogdanowicz
- Department of Ecology and Evolution, Cornell University, Ithaca, NY, USA
| | - Mónica Gómez-Díaz
- Research Group in Animal Ecology, Department of Biology, Universidad del Valle, Cali, Colombia
| | | | - Wilmar Bolívar-García
- Research Group in Animal Ecology, Department of Biology, Universidad del Valle, Cali, Colombia
| | - José Andrés
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada.,Department of Ecology and Evolution, Cornell University, Ithaca, NY, USA
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22
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Rahman S, Schmidt D, Hughes JM. Genetic structure of Australian glass shrimp, Paratya australiensis, in relation to altitude. PeerJ 2020; 8:e8139. [PMID: 31942250 PMCID: PMC6955102 DOI: 10.7717/peerj.8139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 11/01/2019] [Indexed: 11/29/2022] Open
Abstract
Paratya australiensis Kemp (Decapoda: Atyidae) is a widely distributed freshwater shrimp in eastern Australia. The species has been considered as an important stream organism for studying genetics, dispersal, biology, behaviour and evolution in atyids and is a major food source for stream dwelling fishes. Paratya australiensis is a cryptic species complex consisting of nine highly divergent mitochondrial DNA lineages. Previous studies in southeast Queensland showed that “lineage 4” favours upstream sites at higher altitudes, with cooler water temperatures. This study aims to identify putative selection and population structure between high elevation and low elevation populations of this lineage at relatively small spatial scales. Sample localities were selected from three streams: Booloumba Creek, Broken Bridge Creek and Obi Obi Creek in the Conondale Range, southeast Queensland. Six sample localities, consisting of 142 individuals in total were sequenced using double digest Restriction Site Associated DNA-sequencing (ddRAD-seq) technique. Among the 142 individuals, 131 individuals shared 213 loci. Outlier analysis on 213 loci showed that 27 loci were putatively under selection between high elevation and low elevation populations. Outlier analysis on individual streams was also done to test for parallel patterns of adaptation, but there was no evidence of a parallel pattern. Population structure was observed using both the 27 outliers and 186 neutral loci and revealed similar population structure in both cases. Therefore, we cannot differentiate between selection and drift here. The highest genetic differentiation was observed between high elevation and low elevation populations of Booloumba Creek, with small levels of differentiation in the other two streams.
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Affiliation(s)
- Sharmeen Rahman
- Griffith School of Environment and Australian Rivers Institute, Griffith University, Brisbane, QLD, Australia
| | - Daniel Schmidt
- Griffith School of Environment and Australian Rivers Institute, Griffith University, Brisbane, QLD, Australia
| | - Jane M Hughes
- Griffith School of Environment and Australian Rivers Institute, Griffith University, Brisbane, QLD, Australia
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23
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Hybridization increases population variation during adaptive radiation. Proc Natl Acad Sci U S A 2019; 116:23216-23224. [PMID: 31659024 DOI: 10.1073/pnas.1913534116] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Adaptive radiations are prominent components of the world's biodiversity. They comprise many species derived from one or a small number of ancestral species in a geologically short time that have diversified into a variety of ecological niches. Several authors have proposed that introgressive hybridization has been important in the generation of new morphologies and even new species, but how that happens throughout evolutionary history is not known. Interspecific gene exchange is expected to have greatest impact on variation if it occurs after species have diverged genetically and phenotypically but before genetic incompatibilities arise. We use a dated phylogeny to infer that populations of Darwin's finches in the Galápagos became more variable in morphological traits through time, consistent with the hybridization hypothesis, and then declined in variation after reaching a peak. Some species vary substantially more than others. Phylogenetic inferences of hybridization are supported by field observations of contemporary hybridization. Morphological effects of hybridization have been investigated on the small island of Daphne Major by documenting changes in hybridizing populations of Geospiza fortis and Geospiza scandens over a 30-y period. G. scandens showed more evidence of admixture than G. fortis Beaks of G. scandens became progressively blunter, and while variation in length increased, variation in depth decreased. These changes imply independent effects of introgression on 2, genetically correlated, beak dimensions. Our study shows how introgressive hybridization can alter ecologically important traits, increase morphological variation as a radiation proceeds, and enhance the potential for future evolution in changing environments.
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24
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Zieliński P, Dudek K, Arntzen JW, Palomar G, Niedzicka M, Fijarczyk A, Liana M, Cogǎlniceanu D, Babik W. Differential introgression across newt hybrid zones: Evidence from replicated transects. Mol Ecol 2019; 28:4811-4824. [DOI: 10.1111/mec.15251] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Piotr Zieliński
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | | | - Gemma Palomar
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Marta Niedzicka
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
| | - Anna Fijarczyk
- Département de Biologie Faculté des Sciences et de génie Université Laval Québec QC Canada
| | | | - Dan Cogǎlniceanu
- Faculty of Natural Sciences and Agricultural Sciences University Ovidius Constanţa Constanţa Romania
| | - Wiesław Babik
- Institute of Environmental Sciences Faculty of Biology Jagiellonian University Kraków Poland
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25
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Rifkin JL, Castillo AS, Liao IT, Rausher MD. Gene flow, divergent selection and resistance to introgression in two species of morning glories (Ipomoea). Mol Ecol 2019; 28:1709-1729. [PMID: 30451335 DOI: 10.1111/mec.14945] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 09/03/2018] [Accepted: 11/01/2018] [Indexed: 02/03/2023]
Abstract
Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergent SNPs in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the result of divergent selection in the face of gene flow. We analysed a SNP data set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater from I. lacunosa to I. cordatotriloba than in the reverse direction, resulting in sympatric and allopatric I. cordatotriloba being substantially more different than sympatric and allopatric I. lacunosa. Many SNPs highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow, I. cordatotriloba traits become much more like those of I. lacunosa than the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.
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Affiliation(s)
- Joanna L Rifkin
- Department of Biology, Duke University, Durham, North Carolina
| | | | - Irene T Liao
- Department of Biology, Duke University, Durham, North Carolina
| | - Mark D Rausher
- Department of Biology, Duke University, Durham, North Carolina
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26
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Oswald JA, Harvey MG, Remsen RC, Foxworth DU, Dittmann DL, Cardiff SW, Brumfield RT. Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves:Plegadis falcinellus) into the New World. Mol Ecol 2019; 28:1675-1691. [DOI: 10.1111/mec.15008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 12/07/2018] [Accepted: 12/19/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Jessica A. Oswald
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana
- Florida Museum of Natural History University of Florida Gainesville Florida
| | - Michael G. Harvey
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana
| | - Rosalind C. Remsen
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana
| | - DePaul U. Foxworth
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana
| | - Donna L. Dittmann
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana
| | - Steven W. Cardiff
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana
| | - Robb T. Brumfield
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana
- Department of Biological Sciences Louisiana State University Baton Rouge Louisiana
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27
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Baiz MD, Tucker PK, Cortés-Ortiz L. Multiple forms of selection shape reproductive isolation in a primate hybrid zone. Mol Ecol 2019; 28:1056-1069. [PMID: 30582763 PMCID: PMC6888905 DOI: 10.1111/mec.14966] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 10/22/2018] [Indexed: 01/02/2023]
Abstract
Speciation occurs when populations diverge and become reproductively isolated from each other. Natural selection is commonly accepted to play a large role in this process, and it has been widely assumed that reproductive isolation often results as a by-product of divergence driven by adaptation in allopatry. When such populations come into secondary contact, reinforcement can act to strengthen reproductive isolation, but the frequency and importance of this process are still unknown. Here, we explored genomic signatures of selection in allopatry and sympatry for loci associated with reproductive isolation using a natural primate hybrid zone. By analysing reduced-representation sequencing data, we quantified admixture and population structure across a howler monkey hybrid zone and examined the relationship between locus-specific differentiation and introgression. We detected extensive admixture that was mostly limited to the narrow contact zone. Loci with reduced introgression into the heterospecific genomic background (the pattern expected for loci associated with reproductive isolation due to selection against hybrids) were significantly more differentiated between allopatric parental populations than loci with neutral and increased introgression, supporting the hypothesis that reproductive isolation is a by-product of divergence in allopatry. Further, loci with reduced introgression showed greater differentiation in sympatry than in allopatry, suggesting a role for reinforcement. Thus, our results reflect multiple forms of selection that have shaped reproductive isolation in this system. We conclude that reproductive isolation may have initially been driven by divergence in allopatry, but later reinforced by divergent selection in sympatry.
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Affiliation(s)
- Marcella D Baiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Priscilla K Tucker
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - Liliana Cortés-Ortiz
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
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28
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Scott PA, Glenn TC, Rissler LJ. Formation of a recent hybrid zone offers insight into the geographic puzzle and maintenance of species boundaries in musk turtles. Mol Ecol 2019; 28:761-771. [DOI: 10.1111/mec.14983] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/11/2018] [Accepted: 12/17/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Peter A. Scott
- Department of Biological Sciences University of Alabama Tuscaloosa Alabama
| | - Travis C. Glenn
- Department of Environmental Health Science and Institute of Bioinformatics University of Georgia Athens Georgia
| | - Leslie J. Rissler
- Department of Biological Sciences University of Alabama Tuscaloosa Alabama
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29
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Alex Sotola V, Ruppel DS, Bonner TH, Nice CC, Martin NH. Asymmetric introgression between fishes in the Red River basin of Texas is associated with variation in water quality. Ecol Evol 2019; 9:2083-2095. [PMID: 30847094 PMCID: PMC6392354 DOI: 10.1002/ece3.4901] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/05/2018] [Accepted: 12/13/2018] [Indexed: 01/01/2023] Open
Abstract
When ecologically divergent taxa encounter one another, hybrid zones can form when reproductive isolation is incomplete. The location of such hybrid zones can be influenced by environmental variables, and an ecological context can provide unique insights into the mechanisms by which species diverge and are maintained. Two ecologically differentiated species of small benthic fishes, the endemic and imperiled prairie chub, Macrhybopsis australis, and the shoal chub, Macrhybopsis hyostoma, are locally sympatric within the upper Red River Basin of Texas. We integrated population genomic data and environmental data to investigate species divergence and the maintenance of species boundaries in these two species. We found evidence of advanced-generation asymmetric hybridization and introgression, with shoal chub alleles introgressing more frequently into prairie chubs than the reciprocal. Using a Bayesian Genomic Cline framework, patterns of genomic introgression were revealed to be quite heterogeneous, yet shoal chub alleles were found to have likely selectively introgressed across species boundaries significantly more often than prairie chub alleles, potentially explaining some of the observed asymmetry in hybridization. These patterns were remarkably consistent across two sampled geographic regions of hybridization. Several environmental variables were found to significantly predict individual admixture, suggesting ecological isolation might maintain species boundaries.
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Affiliation(s)
| | | | | | - Chris C. Nice
- Biology DepartmentTexas State UniversitySan MarcosTexas
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30
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Pulido-Santacruz P, Aleixo A, Weir JT. Morphologically cryptic Amazonian bird species pairs exhibit strong postzygotic reproductive isolation. Proc Biol Sci 2019. [PMID: 29514967 DOI: 10.1098/rspb.2017.2081] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We possess limited understanding of how speciation unfolds in the most species-rich region of the planet-the Amazon basin. Hybrid zones provide valuable information on the evolution of reproductive isolation, but few studies of Amazonian vertebrate hybrid zones have rigorously examined the genome-wide underpinnings of reproductive isolation. We used genome-wide genetic datasets to show that two deeply diverged, but morphologically cryptic sister species of forest understorey birds show little evidence for prezygotic reproductive isolation, but substantial postzygotic isolation. Patterns of heterozygosity and hybrid index revealed that hybrid classes with heavily recombined genomes are rare and closely match simulations with high levels of selection against hybrids. Genomic and geographical clines exhibit a remarkable similarity across loci in cline centres, and have exceptionally narrow cline widths, suggesting that postzygotic isolation is driven by genetic incompatibilities at many loci, rather than a few loci of strong effect. We propose Amazonian understorey forest birds speciate slowly via gradual accumulation of postzygotic genetic incompatibilities, with prezygotic barriers playing a less important role. Our results suggest old, cryptic Amazonian taxa classified as subspecies could have substantial postzygotic isolation deserving species recognition and that species richness is likely to be substantially underestimated in Amazonia.
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Affiliation(s)
| | - Alexandre Aleixo
- Department of Zoology, Museu Paraense Emílio Goeldi, Belém, Brazil
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada .,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada
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31
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Cortés-Ortiz L, Baiz MD, Hermida-Lagunes J, García-Orduña F, Rangel-Negrín A, Kitchen DM, Bergman TJ, Dias PAD, Canales-Espinosa D. Reduced Introgression of Sex Chromosome Markers in the Mexican Howler Monkey ( Alouatta palliata × A. pigra) Hybrid Zone. INT J PRIMATOL 2019; 40:114-131. [PMID: 30880850 PMCID: PMC6394575 DOI: 10.1007/s10764-018-0056-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 06/07/2018] [Indexed: 01/12/2023]
Abstract
Interspecific hybridization allows the introgression or movement of alleles from one genome to another. While some genomic regions freely exchange alleles during hybridization, loci associated with reproductive isolation do not intermix. In many model organisms, the X chromosome displays limited introgression compared to autosomes owing to the presence of multiple loci associated with hybrid sterility or inviability (the "large X-effect"). Similarly, if hybrids are produced, the heterogametic sex is usually inviable or sterile, a pattern known as Haldane's rule. We analyzed the patterns of introgression of genetic markers located in the mitochondrial (control region) and nuclear (autosomal microsatellites and sex chromosome genes) genomes of two howler monkey species (Alouatta palliata and A. pigra) that form a natural hybrid zone in southern Mexico, to evaluate whether the large X-effect and Haldane's rule affect the outcomes of hybridization between these sister species. To identify the level of admixture of each individual in the hybrid zone (N = 254) we analyzed individuals sampled outside the hybrid zone (109 A. pigra and 39 A. palliata) to determine allele frequencies of parental species and estimated a hybrid index based on nuclear markers. We then performed a cline analysis using individuals in the hybrid zone to determine patterns of introgression for each locus. Our analyses show that although the hybrid zone is bimodal (with no known F1 s and few recent generation hybrids) and quite narrow, there has been extensive introgression in both directions, and there is a large array of admixed individuals in the hybrid zone. Mitochondrial and most autosomal markers showed bidirectional introgression, but some had biased introgression toward one species or the other. All markers on the sex chromosomes and a few autosomal markers showed highly restricted introgression. This pattern is consistent with the hypothesis that the sex chromosomes make a disproportionate contribution to reproductive isolation, and our results broaden the taxonomic representation of these patterns across animal taxa.
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Affiliation(s)
- Liliana Cortés-Ortiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA
| | - Marcella D Baiz
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA
| | | | | | | | - Dawn M Kitchen
- Department of Anthropology, The Ohio State University, Columbus, OH 43210 USA
| | - Thore J Bergman
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103 USA.,Department of Psychology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Pedro A D Dias
- Instituto de Neuroetología, Universidad Veracruzana, Xalapa, Veracruz, Mexico
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32
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Friis G, Fandos G, Zellmer AJ, McCormack JE, Faircloth BC, Milá B. Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird. Mol Ecol 2018; 27:5137-5153. [PMID: 30451354 DOI: 10.1111/mec.14946] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 09/26/2018] [Accepted: 10/15/2018] [Indexed: 12/25/2022]
Abstract
The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic-environment association analyses (GEA) while controlling for population structure. Analysis of genome-wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation-by-adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci.
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Affiliation(s)
- Guillermo Friis
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Guillermo Fandos
- Department of Biodiversity, Ecology and Evolution, Complutense University of Madrid, Madrid, Spain
| | - Amanda J Zellmer
- Department of Biology, Occidental College, Los Angeles, California
| | - John E McCormack
- Department of Biology, Occidental College, Los Angeles, California.,Moore Laboratory of Zoology and Department of Biology, Occidental College, Los Angeles, California
| | - Brant C Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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33
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Miles MC, Goller F, Fuxjager MJ. Physiological constraint on acrobatic courtship behavior underlies rapid sympatric speciation in bearded manakins. eLife 2018; 7:e40630. [PMID: 30375331 PMCID: PMC6207423 DOI: 10.7554/elife.40630] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 10/11/2018] [Indexed: 12/28/2022] Open
Abstract
Physiology's role in speciation is poorly understood. Motor systems, for example, are widely thought to shape this process because they can potentiate or constrain the evolution of key traits that help mediate speciation. Previously, we found that Neotropical manakin birds have evolved one of the fastest limb muscles on record to support innovations in acrobatic courtship display (Fuxjager et al., 2016a). Here, we show how this modification played an instrumental role in the sympatric speciation of a manakin genus, illustrating that muscle specializations fostered divergence in courtship display speed, which may generate assortative mating. However, innovations in contraction-relaxation cycling kinetics that underlie rapid muscle performance are also punctuated by a severe speed-endurance trade-off, blocking further exaggeration of display speed. Sexual selection therefore potentiated phenotypic displacement in a trait critical to mate choice, all during an extraordinarily fast species radiation-and in doing so, pushed muscle performance to a new boundary altogether.
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Affiliation(s)
| | - Franz Goller
- University of UtahSalt Lake CityUnited States
- Institute for ZoophysiologyUniversity of MünsterGermany
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34
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Dissection by genomic and plumage variation of a geographically complex hybrid zone between two Australian non-sister parrot species, Platycercus adscitus and Platycercus eximius. Heredity (Edinb) 2018; 122:402-416. [PMID: 30082918 PMCID: PMC6460760 DOI: 10.1038/s41437-018-0127-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 06/23/2018] [Accepted: 06/27/2018] [Indexed: 01/27/2023] Open
Abstract
The study of hybrid zones advances understanding of the speciation process, and approaches incorporating genomic data are increasingly used to draw significant conclusions about the impact of hybridisation. Despite the progress made, the complex interplay of factors that can lead to substantially variable hybridisation outcomes are still not well understood, and many systems and/or groups remain comparatively poorly studied. Our study aims to broaden the literature on avian hybrid zones, investigating a potentially geographically and temporally complex putative hybrid zone between two native Australian non-sister parrot species, the pale-headed and eastern rosellas (Platycercus adscitus and Platycercus eximius, respectively). We analysed six plumage traits and >1400 RADseq loci and detected hybrid individuals and an unexpectedly complex geographic structure. The hybrid zone is larger than previously described due to either observer bias or its movement over recent decades. It comprises different subregions where genetic and plumage signals of admixture vary markedly in their concordance. Evidence of contemporary hybridisation (later generation and backcrossed individuals) both within and beyond the previously defined zone, when coupled with a lack of F1 hybrids and differential patterns of introgression among potentially diagnostic loci, indicates a lack of post-zygotic barriers to gene flow between species. Despite ongoing gene flow, species boundaries are likely maintained largely by strong pre-mating barriers. These findings are discussed in detail and future avenues for research into this system are proposed, which would be of benefit to the speciation and hybrid zone literature.
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35
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Westram AM, Rafajlović M, Chaube P, Faria R, Larsson T, Panova M, Ravinet M, Blomberg A, Mehlig B, Johannesson K, Butlin R. Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow. Evol Lett 2018; 2:297-309. [PMID: 30283683 PMCID: PMC6121805 DOI: 10.1002/evl3.74] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 06/14/2018] [Accepted: 06/29/2018] [Indexed: 12/16/2022] Open
Abstract
Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.
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Affiliation(s)
- Anja M. Westram
- Department of Animal and Plant SciencesUniversity of SheffieldUK
- Current address: IST AustriaAm Campus 13400KlosterneuburgAustria
| | - Marina Rafajlović
- Department of Marine SciencesUniversity of Gothenburg40530GothenburgSweden
- Department of PhysicsUniversity of Gothenburg41296GothenburgSweden
| | - Pragya Chaube
- Department of Animal and Plant SciencesUniversity of SheffieldUK
| | - Rui Faria
- Department of Animal and Plant SciencesUniversity of SheffieldUK
| | - Tomas Larsson
- Department of Marine SciencesUniversity of Gothenburg40530GothenburgSweden
| | - Marina Panova
- Department of Marine Sciences ‐ TjärnöUniversity of Gothenburg45296StrömstadSweden
| | - Mark Ravinet
- CEES (Centre for Ecological and Evolutionary Synthesis)University of OsloOslo0316Norway
| | - Anders Blomberg
- Department of Chemistry and Molecular BiologyUniversity of Gothenburg40530GothenburgSweden
| | - Bernhard Mehlig
- Department of PhysicsUniversity of Gothenburg41296GothenburgSweden
| | - Kerstin Johannesson
- Department of Marine Sciences ‐ TjärnöUniversity of Gothenburg45296StrömstadSweden
| | - Roger Butlin
- Department of Animal and Plant SciencesUniversity of SheffieldUK
- Department of Marine Sciences ‐ TjärnöUniversity of Gothenburg45296StrömstadSweden
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36
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Menon M, Bagley JC, Friedline CJ, Whipple AV, Schoettle AW, Leal‐Sàenz A, Wehenkel C, Molina‐Freaner F, Flores‐Rentería L, Gonzalez‐Elizondo MS, Sniezko RA, Cushman SA, Waring KM, Eckert AJ. The role of hybridization during ecological divergence of southwestern white pine (
Pinus strobiformis
) and limber pine (
P. flexilis
). Mol Ecol 2018; 27:1245-1260. [DOI: 10.1111/mec.14505] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/19/2017] [Accepted: 12/21/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Mitra Menon
- Integrative Life Sciences Virginia Commonwealth University Richmond VA USA
- Department of Biology Virginia Commonwealth University Richmond VA USA
| | - Justin C. Bagley
- Department of Biology Virginia Commonwealth University Richmond VA USA
- Departamento de Zoologia Universidade de Brasília Brasília DF Brazil
| | | | - Amy V. Whipple
- Department of Biological Sciences and Merriam Powel Center for Environmental Research Northern Arizona University Flagstaff AZ USA
| | - Anna W. Schoettle
- Rocky Mountain Research Station USDA Forest Service Ft. Collins CO USA
| | - Alejandro Leal‐Sàenz
- Programa Institucional de Doctorado en Ciencias Agropecuarias y Forestales Universidad Juárez del Estado de Durango Durango Mexico
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la Madera Universidad Juarez del Estado de Durango Durango Mexico
| | - Francisco Molina‐Freaner
- Institutos de Geologia y Ecologia Universidad Nacional Autónoma de Mexico, Estación Regional del Noroeste Hermosillo Sonora Mexico
| | | | | | | | - Samuel A. Cushman
- Rocky Mountain Research Station USDA Forest Service Flagstaff AZ USA
| | | | - Andrew J. Eckert
- Department of Biology Virginia Commonwealth University Richmond VA USA
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37
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Sung C, Bell KL, Nice CC, Martin NH. Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone. Mol Ecol 2018; 27:959-978. [DOI: 10.1111/mec.14481] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 12/14/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Cheng‐Jung Sung
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Katherine L. Bell
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Chris C. Nice
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
| | - Noland H. Martin
- Population and Conservation Biology Program Department of Biology Texas State University San Marcos TX USA
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38
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Rafati N, Blanco-Aguiar JA, Rubin CJ, Sayyab S, Sabatino SJ, Afonso S, Feng C, Alves PC, Villafuerte R, Ferrand N, Andersson L, Carneiro M. A genomic map of clinal variation across the European rabbit hybrid zone. Mol Ecol 2018; 27:1457-1478. [PMID: 29359877 DOI: 10.1111/mec.14494] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 01/02/2023]
Abstract
Speciation is a process proceeding from weak to complete reproductive isolation. In this continuum, naturally hybridizing taxa provide a promising avenue for revealing the genetic changes associated with the incipient stages of speciation. To identify such changes between two subspecies of rabbits that display partial reproductive isolation, we studied patterns of allele frequency change across their hybrid zone using whole-genome sequencing. To connect levels and patterns of genetic differentiation with phenotypic manifestations of subfertility in hybrid rabbits, we further investigated patterns of gene expression in testis. Geographic cline analysis revealed 253 regions characterized by steep changes in allele frequency across their natural region of contact. This catalog of regions is likely to be enriched for loci implicated in reproductive barriers and yielded several insights into the evolution of hybrid dysfunction in rabbits: (i) incomplete reproductive isolation is likely governed by the effects of many loci, (ii) protein-protein interaction analysis suggest that genes within these loci interact more than expected by chance, (iii) regulatory variation is likely the primary driver of incompatibilities, and (iv) large chromosomal rearrangements appear not to be a major mechanism underlying incompatibilities or promoting isolation in the face of gene flow. We detected extensive misregulation of gene expression in testis of hybrid males, but not a statistical overrepresentation of differentially expressed genes in candidate regions. Our results also did not support an X chromosome-wide disruption of expression as observed in mice and cats, suggesting variation in the mechanistic basis of hybrid male reduced fertility among mammals.
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Affiliation(s)
- Nima Rafati
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - José A Blanco-Aguiar
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Instituto de Investigacion en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Carl J Rubin
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Shumaila Sayyab
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Stephen J Sabatino
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Chungang Feng
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | | | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland, South Africa
| | - Leif Andersson
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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39
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Lee SR, Jo YS, Park CH, Friedman JM, Olson MS. Population genomic analysis suggests strong influence of river network on spatial distribution of genetic variation in invasive saltcedar across the southwestern United States. Mol Ecol 2018; 27:636-646. [PMID: 29274176 DOI: 10.1111/mec.14468] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 11/22/2017] [Accepted: 12/04/2017] [Indexed: 01/19/2023]
Abstract
Understanding the complex influences of landscape and anthropogenic elements that shape the population genetic structure of invasive species provides insight into patterns of colonization and spread. The application of landscape genomics techniques to these questions may offer detailed, previously undocumented insights into factors influencing species invasions. We investigated the spatial pattern of genetic variation and the influences of landscape factors on population similarity in an invasive riparian shrub, saltcedar (Tamarix L.) by analysing 1,997 genomewide SNP markers for 259 individuals from 25 populations collected throughout the southwestern United States. Our results revealed a broad-scale spatial genetic differentiation of saltcedar populations between the Colorado and Rio Grande river basins and identified potential barriers to population similarity along both river systems. River pathways most strongly contributed to population similarity. In contrast, low temperature and dams likely served as barriers to population similarity. We hypothesize that large-scale geographic patterns in genetic diversity resulted from a combination of early introductions from distinct populations, the subsequent influence of natural selection, dispersal barriers and founder effects during range expansion.
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Affiliation(s)
- Soo-Rang Lee
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Yeong-Seok Jo
- National Institute of Biological Resources, Seo-gu, Incheon, Korea
| | - Chan-Ho Park
- National Institute of Biological Resources, Seo-gu, Incheon, Korea
| | | | - Matthew S Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
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40
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41
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Uy JAC, Cooper EA, Cutie S, Concannon MR, Poelstra JW, Moyle RG, Filardi CE. Mutations in different pigmentation genes are associated with parallel melanism in island flycatchers. Proc Biol Sci 2017; 283:rspb.2016.0731. [PMID: 27412275 DOI: 10.1098/rspb.2016.0731] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/21/2016] [Indexed: 12/17/2022] Open
Abstract
The independent evolution of similar traits across multiple taxa provides some of the most compelling evidence of natural selection. Little is known, however, about the genetic basis of these convergent or parallel traits: are they mediated by identical or different mutations in the same genes, or unique mutations in different genes? Using a combination of candidate gene and reduced representation genomic sequencing approaches, we explore the genetic basis of and the evolutionary processes that mediate similar plumage colour shared by isolated populations of the Monarcha castaneiventris flycatcher of the Solomon Islands. A genome-wide association study (GWAS) that explicitly controlled for population structure revealed that mutations in known pigmentation genes are the best predictors of parallel plumage colour. That is, entirely black or melanic birds from one small island share an amino acid substitution in the melanocortin-1 receptor (MC1R), whereas similarly melanic birds from another small island over 100 km away share an amino acid substitution in a predicted binding site of agouti signalling protein (ASIP). A third larger island, which separates the two melanic populations, is inhabited by birds with chestnut bellies that lack the melanic MC1R and ASIP allelic variants. Formal FST outlier tests corroborated the results of the GWAS and suggested that strong, directional selection drives the near fixation of the MC1R and ASIP variants across islands. Our results, therefore, suggest that selection acting on different mutations with large phenotypic effects can drive the evolution of parallel melanism, despite the relatively small population size on islands.
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Affiliation(s)
- J Albert C Uy
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Elizabeth A Cooper
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Stephen Cutie
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Moira R Concannon
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Jelmer W Poelstra
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Robert G Moyle
- Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - Christopher E Filardi
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY 10024, USA
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42
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Blackburn GS, Brunet BMT, Muirhead K, Cusson M, Béliveau C, Levesque RC, Lumley LM, Sperling FAH. Distinct sources of gene flow produce contrasting population genetic dynamics at different range boundaries of aChoristoneurabudworm. Mol Ecol 2017; 26:6666-6684. [DOI: 10.1111/mec.14386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 09/26/2017] [Accepted: 10/07/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Gwylim S. Blackburn
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Bryan M. T. Brunet
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| | - Kevin Muirhead
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
| | - Michel Cusson
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Catherine Béliveau
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Roger C. Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec QC Canada
| | - Lisa M. Lumley
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
- Laurentian Forestry Centre; Natural Resources Canada; Canadian Forest Service; Quebec City QC Canada
| | - Felix A. H. Sperling
- Department of Biological Sciences; CW405 Biosciences Centre; University of Alberta; Edmonton AB Canada
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43
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Gompert Z, Mandeville EG, Buerkle CA. Analysis of Population Genomic Data from Hybrid Zones. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2017. [DOI: 10.1146/annurev-ecolsys-110316-022652] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zachariah Gompert
- Department of Biology and Ecology Center, Utah State University, Logan, Utah 84322
| | - Elizabeth G. Mandeville
- Department of Botany and Wyoming Cooperative Fish and Wildlife Research Unit, University of Wyoming, Laramie, Wyoming 82071
| | - C. Alex Buerkle
- Department of Botany and Program in Ecology, University of Wyoming, Laramie, Wyoming 82071
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44
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Fouet C, Kamdem C, Gamez S, White BJ. Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group. Evol Appl 2017; 10:897-906. [PMID: 29151881 PMCID: PMC5680430 DOI: 10.1111/eva.12492] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 04/27/2017] [Indexed: 01/16/2023] Open
Abstract
Ongoing speciation in the most important African malaria vectors gives rise to cryptic populations, which differ remarkably in their behavior, ecology, and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is crucial for effective disease control because heterogeneity within vector species contributes to variability in malaria cases and allow fractions of populations to escape control efforts. To examine population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group-a large taxonomic group that diverged ~3 Myr ago. Using 4,343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high-FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA, and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.
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Affiliation(s)
- Caroline Fouet
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Colince Kamdem
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Stephanie Gamez
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Bradley J. White
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
- Center for Disease Vector ResearchInstitute for Integrative Genome BiologyUniversity of CaliforniaRiversideCAUSA
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45
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Scordato ESC, Wilkins MR, Semenov G, Rubtsov AS, Kane NC, Safran RJ. Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry. Mol Ecol 2017; 26:5676-5691. [DOI: 10.1111/mec.14276] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Matthew R. Wilkins
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - Georgy Semenov
- Department of Ecology & Evolutionary Biology University of Arizona Tucson AZ USA
- Institute of Systematics and Ecology of Animals Novosibirsk Russia
| | | | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
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46
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Singhal S, Bi K. History cleans up messes: The impact of time in driving divergence and introgression in a tropical suture zone. Evolution 2017; 71:1888-1899. [DOI: 10.1111/evo.13278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 05/04/2017] [Indexed: 02/01/2023]
Affiliation(s)
- Sonal Singhal
- Department of Ecology and Evolutionary Biology University of Michigan, 830 North University Ann Arbor Michigan 48109
- Museum of Zoology University of Michigan, 1109 Geddes Avenue Ann Arbor Michigan 48109
| | - Ke Bi
- Museum of Vertebrate Zoology University of California, Berkeley, 3101 Valley Life Sciences Building Berkeley California 94720
- Computational Genomics Resource Laboratory, California Institute for Quantitative Biosciences University of California Berkeley California 94720
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47
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Schield DR, Adams RH, Card DC, Perry BW, Pasquesi GM, Jezkova T, Portik DM, Andrew AL, Spencer CL, Sanchez EE, Fujita MK, Mackessy SP, Castoe TA. Insight into the roles of selection in speciation from genomic patterns of divergence and introgression in secondary contact in venomous rattlesnakes. Ecol Evol 2017; 7:3951-3966. [PMID: 28616190 PMCID: PMC5468163 DOI: 10.1002/ece3.2996] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 03/21/2017] [Indexed: 01/03/2023] Open
Abstract
Investigating secondary contact of historically isolated lineages can provide insight into how selection and drift influence genomic divergence and admixture. Here, we studied the genomic landscape of divergence and introgression following secondary contact between lineages of the Western Diamondback Rattlesnake (Crotalus atrox) to determine whether genomic regions under selection in allopatry also contribute to reproductive isolation during introgression. We used thousands of nuclear loci to study genomic differentiation between two lineages that have experienced recent secondary contact following isolation, and incorporated sampling from a zone of secondary contact to identify loci that are resistant to gene flow in hybrids. Comparisons of patterns of divergence and introgression revealed a positive relationship between allelic differentiation and resistance to introgression across the genome, and greater‐than‐expected overlap between genes linked to lineage‐specific divergence and loci that resist introgression. Genes linked to putatively selected markers were related to prominent aspects of rattlesnake biology that differ between populations of Western Diamondback rattlesnakes (i.e., venom and reproductive phenotypes). We also found evidence for selection against introgression of genes that may contribute to cytonuclear incompatibility, consistent with previously observed biased patterns of nuclear and mitochondrial alleles suggestive of partial reproductive isolation due to cytonuclear incompatibilities. Our results provide a genome‐scale perspective on the relationships between divergence and introgression in secondary contact that is relevant for understanding the roles of selection in maintaining partial isolation of lineages, causing admixing lineages to not completely homogenize.
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Affiliation(s)
- Drew R Schield
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Richard H Adams
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Daren C Card
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Blair W Perry
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Giulia M Pasquesi
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Tereza Jezkova
- Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ USA
| | - Daniel M Portik
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Audra L Andrew
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Carol L Spencer
- Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Elda E Sanchez
- National Natural Toxins Research Center and Department of Chemistry Texas A&M University Kingsville Kingsville TX USA
| | - Matthew K Fujita
- Department of Biology The University of Texas at Arlington Arlington TX USA
| | - Stephen P Mackessy
- School of Biological Sciences University of Northern Colorado Greeley CO USA
| | - Todd A Castoe
- Department of Biology The University of Texas at Arlington Arlington TX USA
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48
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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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49
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Branch CL, Jahner JP, Kozlovsky DY, Parchman TL, Pravosudov VV. Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees ( Poecile gambeli). ROYAL SOCIETY OPEN SCIENCE 2017; 4:170057. [PMID: 28405402 PMCID: PMC5383859 DOI: 10.1098/rsos.170057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/16/2017] [Indexed: 06/07/2023]
Abstract
Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed, on average, two weeks later than low elevation birds, the extent of gene flow between elevations is unknown. Despite phenotypic variation and indirect evidence for local adaptation, population genetic analyses based on 18 073 single nucleotide polymorphisms across three transects of high and low elevation populations provided no evidence for genetic differentiation. Analyses based on individual genotypes revealed no patterns of clustering, pairwise estimates of genetic differentiation (FST, Nei's D) were very low, and AMOVA revealed no evidence for genetic variation structured by transect or by low and high elevation sites within transects. In addition, we found no consistent evidence for strong parallel allele frequency divergence between low and high elevation sites within the three transects. Large elevation-related phenotypic variation may be maintained by strong selection despite gene flow and future work should focus on the mechanisms underlying such variation.
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50
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Holliday JA, Aitken SN, Cooke JEK, Fady B, González-Martínez SC, Heuertz M, Jaramillo-Correa JP, Lexer C, Staton M, Whetten RW, Plomion C. Advances in ecological genomics in forest trees and applications to genetic resources conservation and breeding. Mol Ecol 2017; 26:706-717. [PMID: 27997049 DOI: 10.1111/mec.13963] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 12/07/2016] [Accepted: 12/14/2016] [Indexed: 12/25/2022]
Abstract
Forest trees are an unparalleled group of organisms in their combined ecological, economic and societal importance. With widespread distributions, predominantly random mating systems and large population sizes, most tree species harbour extensive genetic variation both within and among populations. At the same time, demographic processes associated with Pleistocene climate oscillations and land-use change have affected contemporary range-wide diversity and may impinge on the potential for future adaptation. Understanding how these adaptive and neutral processes have shaped the genomes of trees species is therefore central to their management and conservation. As for many other taxa, the advent of high-throughput sequencing methods is expected to yield an understanding of the interplay between the genome and environment at a level of detail and depth not possible only a few years ago. An international conference entitled 'Genomics and Forest Tree Genetics' was held in May 2016, in Arcachon (France), and brought together forest geneticists with a wide range of research interests to disseminate recent efforts that leverage contemporary genomic tools to probe the population, quantitative and evolutionary genomics of trees. An important goal of the conference was to discuss how such data can be applied to both genome-enabled breeding and the conservation of forest genetic resources under land use and climate change. Here, we report discoveries presented at the meeting and discuss how the ecological genomic toolkit can be used to address both basic and applied questions in tree biology.
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Affiliation(s)
- Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, 304 Cheatham Hall, Blacksburg, VA 24061, USA
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T1Z4, Canada
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, 5-108 Centennial Centre for Interdisciplinary Science, Edmonton, AB T6G2E9, Canada
| | - Bruno Fady
- Mediterranean Forest Ecology (URFM), Institut National de la Recherche Agronomique (INRA), Domaine St Paul, Site Agroparc, 84914 Avignon, France
| | | | - Myriam Heuertz
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Juan-Pablo Jaramillo-Correa
- Institute of Ecology, Universidad Nacional Autonoma de Mexico (UNAM) Circuito Exterior s/n, Apartado Postal 70-275, 04510 Ciudad de México, Mexico City, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna Faculty of Life SciencesRennweg 14, Room 217, A-1030, Vienna, Austria
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, 370 Plant Biotechnology Building, 2505 EJ Chapman Drive, Knoxville, TN 37996, USA
| | - Ross W Whetten
- Department of Forestry and Environmental Resources, North Carolina State University Jordan Hall Addition 5231, Raleigh, NC 27695, USA
| | - Christophe Plomion
- BIOGECO, INRA, Universite de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
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