1
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Huang Z, Liu Q, Zeng X, Ni G. High-quality chromosome-level genome assembly of the Northern Pacific sea star Asterias amurensis. DNA Res 2024; 31:dsae007. [PMID: 38416146 PMCID: PMC11090083 DOI: 10.1093/dnares/dsae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 02/29/2024] Open
Abstract
Asterias amurensis, a starfish species that is native to countries such as China and Japan, as well as non-native regions like Australia, has raised serious concerns in terms of its impact on ecology and economy. To gain a better understanding of its population genomics and dynamics, we successfully assembled a high-quality chromosome-level genome of A. amurensis using PacBio and Hi-C sequencing technologies. A total of 87 scaffolds assembly with contig N50 length of 10.85 Mb and scaffold N50 length of 23.34 Mb were obtained, with over 98.80% (0.48 Gb) of them anchored to 22 pseudochromosomes. We predicted 16,673 protein-coding genes, 95.19% of which were functionally annotated. Our phylogenetic analysis revealed that A. amurensis and Asterias rubens formed a clade, and their divergence time was estimated ~ 28 million years ago (Mya). The significantly enriched pathways and Gene Ontology terms related to the amplified gene family were mainly associated with immune response and energy metabolism, suggesting that these factors might have contributed to the adaptability of A. amurensis to its environment. This study provides valuable genomic resources for comprehending the genetics, dynamics, and evolution of A. amurensis, especially when population outbreaks or invasions occur.
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Affiliation(s)
- Zhichao Huang
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China
| | - Qi Liu
- Wuhan Onemore-tech Co., Ltd, Wuhan 430000, China
| | - Xiaoqi Zeng
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
| | - Gang Ni
- Ministry of Education Key Laboratory of Mariculture, Ocean University of China, Qingdao 266003, China
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2
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Martins ARP, Warren NB, McMillan WO, Barrett RDH. Spatiotemporal dynamics in butterfly hybrid zones. INSECT SCIENCE 2024; 31:328-353. [PMID: 37596954 DOI: 10.1111/1744-7917.13262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.
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Affiliation(s)
- Ananda R Pereira Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Natalie B Warren
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Rowan D H Barrett
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
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3
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Sianta SA, Moeller DA, Brandvain Y. The extent of introgression between incipient Clarkia species is determined by temporal environmental variation and mating system. Proc Natl Acad Sci U S A 2024; 121:e2316008121. [PMID: 38466849 PMCID: PMC10963018 DOI: 10.1073/pnas.2316008121] [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: 09/18/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Introgression is pervasive across the tree of life but varies across taxa, geography, and genomic regions. However, the factors modulating this variation and how they may be affected by global change are not well understood. Here, we used 200 genomes and a 15-y site-specific environmental dataset to investigate the effects of environmental variation and mating system divergence on the magnitude of introgression between a recently diverged outcrosser-selfer pair of annual plants in the genus Clarkia. These sister taxa diverged very recently and subsequently came into secondary sympatry where they form replicated contact zones. Consistent with observations of other outcrosser-selfer pairs, we found that introgression was asymmetric between taxa, with substantially more introgression from the selfer to the outcrosser. This asymmetry was caused by a bias in the direction of initial F1 hybrid formation and subsequent backcrossing. We also found extensive variation in the outcrosser's admixture proportion among contact zones, which was predicted nearly entirely by interannual variance in spring precipitation. Greater fluctuations in spring precipitation resulted in higher admixture proportions, likely mediated by the effects of spring precipitation on the expression of traits that determine premating reproductive isolation. Climate-driven hybridization dynamics may be particularly affected by global change, potentially reshaping species boundaries and adaptation to novel environments.
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Affiliation(s)
- Shelley A. Sianta
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - David A. Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
| | - Yaniv Brandvain
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN55108
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4
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Diz AP, Skibinski DOF. Patterns of admixture and introgression in a mosaic Mytilus galloprovincialis and Mytilus edulis hybrid zone in SW England. Mol Ecol 2024; 33:e17233. [PMID: 38063472 DOI: 10.1111/mec.17233] [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] [Revised: 11/21/2023] [Accepted: 11/24/2023] [Indexed: 01/25/2024]
Abstract
The study of hybrid zones offers important insights into speciation. Earlier studies on hybrid populations of the marine mussel species Mytilus edulis and Mytilus galloprovincialis in SW England provided evidence of admixture but were constrained by the limited number of molecular markers available. We use 57 ancestry-informative SNPs, most of which have been mapped genetically, to provide evidence of distinctive differences between admixed populations in SW England and asymmetrical introgression from M. edulis to M. galloprovincialis. We combine the genetic study with analysis of phenotypic traits of potential ecological and adaptive significance. We demonstrate that hybrid individuals have brown mantle edges unlike the white or purple in the parental species, suggesting allelic or non-allelic genomic interactions. We report differences in gonad development stage between the species consistent with a prezygotic barrier between the species. By incorporating results from publications dating back to 1980, we confirm the long-term stability of the hybrid zone despite higher viability of M. galloprovincialis. This stability coincides with a dramatic change in temperature of UK coastal waters and suggests that these hybrid populations might be resisting the effects of global warming. However, a single SNP locus associated with the Notch transmembrane signalling protein shows a markedly different pattern of variation to the others and might be associated with adaptation of M. galloprovincialis to colder northern temperatures.
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Affiliation(s)
- Angel P Diz
- Centro de Investigación Mariña, Universidade de Vigo (CIM-UVIGO), Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
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5
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Graham BA, Szabo I, Cicero C, Strickland D, Woods J, Coneybeare H, Dohms KM, Burg TM. Habitat and climate influence hybridization among three genetically distinct Canada jay (Perisoreus canadensis) morphotypes in an avian hybrid zone complex. Heredity (Edinb) 2023; 131:361-373. [PMID: 37813941 PMCID: PMC10674025 DOI: 10.1038/s41437-023-00652-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023] Open
Abstract
Examining the frequency and distribution of hybrids across contact zones provide insights into the factors mediating hybridization. In this study, we examined the effect of habitat and climate on hybridization patterns for three phenotypically, genetically, and ecologically distinct groups of the Canada jay (Perisoreus canadensis) in a secondary contact zone in western North America. Additionally, we tested whether the frequency of hybridization involving the three groups (referred to as Boreal, Pacific and Rocky Mountain morphotypes) is similar across the hybrid zones or whether some pairs have hybridized more frequently than others. We reanalyzed microsatellite, mtDNA and plumage data, and new microsatellite and plumage data for 526 individuals to identify putative genetic and phenotypic hybrids. The genetically and phenotypically distinct groups are associated with different habitats and occupy distinct climate niches across the contact zone. Most putative genetic hybrids (86%) had Rocky Mountain ancestry. Hybrids were observed most commonly in intermediate climate niches and in habitats where Engelmann spruce (Picea engelmannii) overlaps broadly with boreal and subalpine tree species. Our finding that hybrids occupy intermediate climate niches relative to parental morphotypes matches patterns for other plant and animal species found in this region. This study demonstrates how habitat and climate influence hybridization patterns in areas of secondary contact and adds to the growing body of research on tri-species hybrid zones.
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Affiliation(s)
- B A Graham
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada.
| | - I Szabo
- Beaty Biodiversity Museum, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - C Cicero
- Museum of Vertebrate Zoology, University of California, 3101 Valley Life Sciences Building, Berkeley, CA, 94720-3160, USA
| | - D Strickland
- 1063 Oxtongue Lake Road, Dwight, ON, P0A 1H0, Canada
| | - J Woods
- 1221 23rd Avenue SW, Salmon Arm, BC, V1E 0A9, Canada
| | - H Coneybeare
- 5210 Frederick Road, Armstrong, BC, V0E 1B4, Canada
| | - K M Dohms
- Canadian Wildlife Services, Environment and Climate Change Canada, 5421 Robertson Road, Delta, BC, V4K 3N2, Canada
| | - T M Burg
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive W, Lethbridge, AB, T1K 3M4, Canada
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6
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Firneno TJ, Semenov G, Dopman EB, Taylor SA, Larson EL, Gompert Z. Quantitative Analyses of Coupling in Hybrid Zones. Cold Spring Harb Perspect Biol 2023; 15:a041434. [PMID: 37739809 PMCID: PMC10691479 DOI: 10.1101/cshperspect.a041434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
In hybrid zones, whether barrier loci experience selection mostly independently or as a unit depends on the ratio of selection to recombination as captured by the coupling coefficient. Theory predicts a sharper transition between an uncoupled and coupled system when more loci affect hybrid fitness. However, the extent of coupling in hybrid zones has rarely been quantified. Here, we use simulations to characterize the relationship between the coupling coefficient and variance in clines across genetic loci. We then reanalyze 25 hybrid zone data sets and find that cline variances and estimated coupling coefficients form a smooth continuum from high variance and weak coupling to low variance and strong coupling. Our results are consistent with low rates of hybridization and a strong genome-wide barrier to gene flow when the coupling coefficient is much greater than 1, but also suggest that this boundary might be approached gradually and at a near constant rate over time.
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Affiliation(s)
- Thomas J Firneno
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Georgy Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80211, USA
| | - Erica L Larson
- Department of Biology, University of Denver, Denver, Colorado 80208, USA
| | - Zachariah Gompert
- Department of Biology, Utah State University, Logan, Utah 84321, USA
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7
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Coimbra RTF, Winter S, Muneza A, Fennessy S, Otiende M, Mijele D, Masiaine S, Stacy-Dawes J, Fennessy J, Janke A. Genomic analysis reveals limited hybridization among three giraffe species in Kenya. BMC Biol 2023; 21:215. [PMID: 37833744 PMCID: PMC10576358 DOI: 10.1186/s12915-023-01722-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND In the speciation continuum, the strength of reproductive isolation varies, and species boundaries are blurred by gene flow. Interbreeding among giraffe (Giraffa spp.) in captivity is known, and anecdotal reports of natural hybrids exist. In Kenya, Nubian (G. camelopardalis camelopardalis), reticulated (G. reticulata), and Masai giraffe sensu stricto (G. tippelskirchi tippelskirchi) are parapatric, and thus, the country might be a melting pot for these taxa. We analyzed 128 genomes of wild giraffe, 113 newly sequenced, representing these three taxa. RESULTS We found varying levels of Nubian ancestry in 13 reticulated giraffe sampled across the Laikipia Plateau most likely reflecting historical gene flow between these two lineages. Although comparatively weaker signs of ancestral gene flow and potential mitochondrial introgression from reticulated into Masai giraffe were also detected, estimated admixture levels between these two lineages are minimal. Importantly, contemporary gene flow between East African giraffe lineages was not statistically significant. Effective population sizes have declined since the Late Pleistocene, more severely for Nubian and reticulated giraffe. CONCLUSIONS Despite historically hybridizing, these three giraffe lineages have maintained their overall genomic integrity suggesting effective reproductive isolation, consistent with the previous classification of giraffe into four species.
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Affiliation(s)
- Raphael T F Coimbra
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
| | - Sven Winter
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | | | | | | | | | | | - Julian Fennessy
- Giraffe Conservation Foundation, Windhoek, Namibia
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt, Germany.
- Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt, Germany.
- LOEWE Centre for Translational Biodiversity Genomics, Frankfurt, Germany.
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8
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Garcia-Erill G, Hanghøj K, Heller R, Wiuf C, Albrechtsen A. Estimating admixture pedigrees of recent hybrids without a contiguous reference genome. Mol Ecol Resour 2023; 23:1604-1619. [PMID: 37400991 DOI: 10.1111/1755-0998.13830] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 07/05/2023]
Abstract
The genome of recently admixed individuals or hybrids has characteristic genetic patterns that can be used to learn about their recent admixture history. One of these are patterns of interancestry heterozygosity, which can be inferred from SNP data from either called genotypes or genotype likelihoods, without the need for information on genomic location. This makes them applicable to a wide range of data that are often used in evolutionary and conservation genomic studies, such as low-depth sequencing mapped to scaffolds and reduced representation sequencing. Here we implement maximum likelihood estimation of interancestry heterozygosity patterns using two complementary models. We furthermore develop apoh (Admixture Pedigrees of Hybrids), a software that uses estimates of paired ancestry proportions to detect recently admixed individuals or hybrids, and to suggest possible admixture pedigrees. It furthermore calculates several hybrid indices that make it easier to identify and rank possible admixture pedigrees that could give rise to the estimated patterns. We implemented apoh both as a command line tool and as a Graphical User Interface that allows the user to automatically and interactively explore, rank and visualize compatible recent admixture pedigrees, and calculate the different summary indices. We validate the performance of the method using admixed family trios from the 1000 Genomes Project. In addition, we show its applicability on identifying recent hybrids from RAD-seq data of Grant's gazelle (Nanger granti and Nanger petersii) and whole genome low-depth data of waterbuck (Kobus ellipsiprymnus) which shows complex admixture of up to four populations.
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Affiliation(s)
| | - Kristian Hanghøj
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Heller
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Carsten Wiuf
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
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9
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Evans SA, Whigham DF, Hartvig I, McCormick MK. Hybridization in the Fringed Orchids: An Analysis of Species Boundaries in the Face of Gene Flow. DIVERSITY 2023. [DOI: 10.3390/d15030384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Natural hybridization between closely related species in sympatry is an evolutionary process that is common in orchids. Once seen as a threat to parent species, interspecific genetic change is increasingly viewed as a source of novel variation in some ecological contexts. Terrestrial fringed orchids in the genus Platanthera contain several clades with high genetic compatibility among species and many putative hybrids. We used biallelic SNPs generated with 3RAD sequencing to study the hybrid complex formed from the parent species P. blephariglottis, P. ciliaris, and P. cristata with high resolution. The genetic structure and phylogenetic relationship of the hybrid complex revealed site-dependent gene flow between species. We documented extensive hybridization and cryptic hybrids in sympatric sites. Interspecific genetic exchange is particularly common between P. blephariglottis and P. ciliaris, with cryptic hybrids among putative P. ciliaris samples being more common than parental assignments in sympatric sites. Hybridization across the triad species complex can reticulate lineages and introduce adaptive alleles. Conversely, it can reduce diversification rates and introduce maladaptive alleles. Investigation into whether anthropogenic forces are eroding species boundaries, particularly the permeable P. blephariglottis and P. ciliaris boundary, is appropriate for conservation efforts.
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10
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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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11
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McFarlane SE, Mandeville EG. Diverse data sources and new statistical models offer prospects for improving the predictability of anthropogenic hybridization. GLOBAL CHANGE BIOLOGY 2023; 29:923-925. [PMID: 36409147 DOI: 10.1111/gcb.16527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Human disturbance can theoretically influence the rates of hybridization, but few studies have convincingly identified a causal link. Grabenstein et al. (2022) used a genomic and phenotypic study of chickadees to associate hybridization with human disturbance. Additionally, this is consistent with citizen science reports of chickadee hybrids across the range. We highlight the exciting aspects of this work and make suggestions about a role for broad geographic and genomic sampling, and new statistical methods to better connect hybridization outcomes to anthropogenic disturbance in diverse study systems.
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Affiliation(s)
- S Eryn McFarlane
- Department of Botany, University of Wyoming, Laramie, Wyoming, USA
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12
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Alexander A, Robbins MB, Holmes J, Moyle RG, Peterson AT. Limited movement of an avian hybrid zone in relation to regional variation in magnitude of climate change. Mol Ecol 2022; 31:6634-6648. [PMID: 36210655 PMCID: PMC9729445 DOI: 10.1111/mec.16727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 01/13/2023]
Abstract
Studies of natural hybrid zones can provide documentation of range shifts in response to climate change and identify loci important to reproductive isolation. Using a temporal (36-38 years) comparison of the black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee hybrid zone, we investigated movement of the western portion of the zone (western Missouri) and assessed whether loci and pathways underpinning reproductive isolation were similar to those in the eastern portion of the hybrid zone. Using 92 birds sampled along the hybrid zone transect in 2016 and 68 birds sampled between 1978 and 1980, we generated 11,669 SNPs via ddRADseq. These SNPs were used to assess movement of the hybrid zone through time and to evaluate variation in introgression among loci. We demonstrate that the interface has moved ~5 km to the northwest over the last 36-38 years, that is, at only one-fifth the rate at which the eastern portion (e.g., Pennsylvania, Ohio) of the hybrid zone has moved. Temperature trends over the last 38 years reveal that eastern areas have warmed 50% more than western areas in terms of annual mean temperature, possibly providing an explanation for the slower movement of the hybrid zone in Missouri. Our results suggest hybrid zone movement in broadly distributed species, such as chickadees, will vary between areas in response to local differences in the impacts of climate change.
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Affiliation(s)
- Alana Alexander
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.,Department of Anatomy, University of Otago, Dunedin 9016, New Zealand.,Corresponding author.
| | - Mark B. Robbins
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA
| | - Jesse Holmes
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.,Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| | - Robert G. Moyle
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.,Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
| | - A. Townsend Peterson
- Biodiversity Institute, University of Kansas, Lawrence, Kansas 66045, USA.,Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045, USA
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13
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Baird SJE, Petružela J, Jaroň I, Škrabánek P, Martínková N. Genome polarisation for detecting barriers to geneflow. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Jan Petružela
- Institute of Vertebrate Biology Czech Academy of Sciences Brno Czechia
- Department of Botany and Zoology Masaryk University Brno Czechia
| | - Izar Jaroň
- Institute of Vertebrate Biology Czech Academy of Sciences Brno Czechia
| | - Pavel Škrabánek
- Institute of Automation and Computer Science Brno University of Technology Brno Czechia
| | - Natália Martínková
- Institute of Vertebrate Biology Czech Academy of Sciences Brno Czechia
- RECETOX, Masaryk University Brno Czechia
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14
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Mandeville EG, Hall RO, Buerkle CA. Ecological outcomes of hybridization vary extensively in Catostomus fishes. Evolution 2022; 76:2697-2711. [PMID: 36097356 PMCID: PMC9801484 DOI: 10.1111/evo.14624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 07/20/2022] [Accepted: 07/26/2022] [Indexed: 01/22/2023]
Abstract
Hybridization outcomes vary geographically and can depend on the environment. Hybridization can also reshape biotic interactions, leading to ecological shifts. If hybrids function differently ecologically in ways that enhance or reduce fitness, and those ecological roles vary geographically, ecological factors might explain variation in hybridization outcomes. However, relatively few studies have focused on ecological traits of hybrids. We compared the feeding ecology of Catostomus fish species and hybrids by using stable isotopes (δ13 C and δ15 N) as a proxy for diet and habitat use, and compared two native species, an introduced species, and three interspecific hybrid crosses. We included hybrids and parental species from seven rivers where hybridization outcomes vary. Relative isotopic niches of native species varied geographically, but native species did not fully overlap in isotopic space in any river sampled, suggesting little overlap of resource use between historically sympatric species. The introduced species overlapped with one or both native species in every river, suggesting similar resource use and potential competition. Hybrids occupied intermediate, matching, or more transgressive isotopic niches, and varied within and among rivers. Ecological outcomes of hybridization varied across locations, implying that hybridization might have unpredictable, idiosyncratic ecological effects.
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Affiliation(s)
- Elizabeth G. Mandeville
- Department of Integrative Biology, University of Guelph, Guelph, Ontario Canada
- Department of Botany, University of Wyoming, Laramie, Wyoming USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming USA
| | - Robert O. Hall
- Program in Ecology, University of Wyoming, Laramie, Wyoming USA
- Flathead Lake Biological Station, University of Montana, Polson, Montana USA (present address)
- Department of Zoology and Physiology, University of Wyoming, Laramie, Wyoming USA
| | - C. Alex Buerkle
- Department of Botany, University of Wyoming, Laramie, Wyoming USA
- Program in Ecology, University of Wyoming, Laramie, Wyoming USA
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15
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Nikolakis ZL, Schield DR, Westfall AK, Perry BW, Ivey KN, Orton RW, Hales NR, Adams RH, Meik JM, Parker JM, Smith CF, Gompert Z, Mackessy SP, Castoe TA. Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone. Evolution 2022; 76:2513-2530. [PMID: 36111705 DOI: 10.1111/evo.14612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 01/22/2023]
Abstract
Hybrid zones provide valuable opportunities to understand the genomic mechanisms that promote speciation by providing insight into factors involved in intermediate stages of speciation. Here, we investigate introgression in a hybrid zone between two rattlesnake species (Crotalus viridis and Crotalus oreganus concolor) that have undergone historical allopatric divergence and recent range expansion and secondary contact. We use Bayesian genomic cline models to characterize genomic patterns of introgression between these lineages and identify loci potentially subject to selection in hybrids. We find evidence for a large number of genomic regions with biased ancestry that deviate from the genomic background in hybrids (i.e., excess ancestry loci), which tend to be associated with genomic regions with higher recombination rates. We also identify suites of excess ancestry loci that show highly correlated allele frequencies (including conspecific and heterospecific combinations) across physically unlinked genomic regions in hybrids. Our findings provide evidence for multiple multilocus evolutionary processes impacting hybrid fitness in this system.
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Affiliation(s)
- Zachary L Nikolakis
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Kathleen N Ivey
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Richard W Orton
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Nicole R Hales
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
| | - Richard H Adams
- Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, Georgia, 31061
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, Texas, 76402
| | - Joshua M Parker
- Department of Life Sciences, Fresno City College, Fresno, California, 93741
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, 80639
| | | | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, 80639
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, 76019
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16
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Augustijnen H, Patsiou T, Lucek K. Secondary contact rather than coexistence-Erebia butterflies in the Alps. Evolution 2022; 76:2669-2686. [PMID: 36117267 PMCID: PMC9828779 DOI: 10.1111/evo.14615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 08/05/2022] [Accepted: 08/30/2022] [Indexed: 01/22/2023]
Abstract
Secondary contact zones are ideal systems to study the processes that govern the evolution of reproductive barriers, especially at advanced stages of the speciation process. An increase in reproductive isolation resulting from selection against maladaptive hybrids is thought to contribute to reproductive barrier buildup in secondary contact zones. Although such processes have been invoked for many systems, it remains unclear to which extent they influence contact zone dynamics in nature. Here, we study a very narrow contact zone between the butterfly species Erebia cassioides and Erebia tyndarus in the Swiss Alps. We quantified phenotypic traits related to wing shape and reproduction as well as ecology to compare the degree of intra- and interspecific differentiation. Even though only very few first-generation hybrids occur, we find no strong indications for current reinforcing selection, suggesting that if reinforcement occurred in our system, it likely operated in the past. Additionally, we show that both species differ less in their ecological niche at the contact zone than elsewhere, which could explain why coexistence between these butterflies may currently not be possible.
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Affiliation(s)
- Hannah Augustijnen
- Department of Environmental SciencesUniversity of BaselBaselCH‐4056Switzerland
| | - Theofania Patsiou
- Institute of Plant SciencesUniversity of BernBernCH‐3013Switzerland,Department of BiologyUniversity of FribourgFribourgCH‐1700Switzerland
| | - Kay Lucek
- Department of Environmental SciencesUniversity of BaselBaselCH‐4056Switzerland
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17
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Fang B, Momigliano P, Kahilainen KK, Merilä J. Allopatric origin of sympatric whitefish morphs with insights on the genetic basis of their reproductive isolation. Evolution 2022; 76:1905-1913. [PMID: 35797649 DOI: 10.1111/evo.14559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 06/13/2022] [Accepted: 06/22/2022] [Indexed: 01/22/2023]
Abstract
The European whitefish (Coregonus lavaretus) species complex is a classic example of recent adaptive radiation. Here, we examine a whitefish population introduced to northern Finnish Lake Tsahkal in the late 1960s, where three divergent morphs (viz. littoral, pelagic, and profundal feeders) were found 10 generations after. Using demographic modeling based on genomic data, we show that whitefish morphs evolved during a phase of strict isolation, refuting a rapid sympatric divergence scenario. The lake is now an artificial hybrid zone between morphs originated in allopatry. Despite their current syntopy, clear genetic differentiation remains between two of the three morphs. Using admixture mapping, we identify five SNPs associated with gonad weight variation, a proxy for sexual maturity and spawning time. We suggest that ecological adaptations in spawning time evolved in allopatry are currently maintaining partial reproductive isolation in the absence of other barriers to gene flow.
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Affiliation(s)
- Bohao Fang
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Paolo Momigliano
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo, 36310, Spain
| | - Kimmo K Kahilainen
- Lammi Biological Station, University of Helsinki, Lammi, 16900, Finland.,Kilpisjärvi Biological Station, University of Helsinki, Kilpisjärvi, 99490, Finland
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, 00014, Finland.,Area of Ecology and Biodiversity, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
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18
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Swaegers J, Sánchez-Guillén RA, Chauhan P, Wellenreuther M, Hansson B. Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies. Proc Biol Sci 2022; 289:20220968. [PMID: 35855603 PMCID: PMC9297008 DOI: 10.1098/rspb.2022.0968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Contemporary hybrid zones act as natural laboratories for the investigation of species boundaries and may shed light on the little understood roles of sex chromosomes in species divergence. Sex chromosomes are considered to function as a hotspot of genetic divergence between species; indicated by less genomic introgression compared to autosomes during hybridization. Moreover, they are thought to contribute to Haldane's rule, which states that hybrids of the heterogametic sex are more likely to be inviable or sterile. To test these hypotheses, we used contemporary hybrid zones of Ischnura elegans, a damselfly species that has been expanding its range into the northern and western regions of Spain, leading to chronic hybridization with its sister species Ischnura graellsii. We analysed genome-wide SNPs in the Spanish I. elegans and I. graellsii hybrid zone and found (i) that the X chromosome shows less genomic introgression compared to autosomes, and (ii) that males are underrepresented among admixed individuals, as predicted by Haldane's rule. This is the first study in Odonata that suggests a role of the X chromosome in reproductive isolation. Moreover, our data add to the few studies on species with X0 sex determination system and contradict the hypothesis that the absence of a Y chromosome causes exceptions to Haldane's rule.
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Affiliation(s)
- Janne Swaegers
- Department of Biology, Lund University, Ecology Building, Lund 22362, Sweden,Evolutionary Stress Ecology and Ecotoxicology, KU Leuven, Leuven, Belgium
| | | | - Pallavi Chauhan
- Department of Biology, Lund University, Ecology Building, Lund 22362, Sweden
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson, New Zealand,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Bengt Hansson
- Department of Biology, Lund University, Ecology Building, Lund 22362, Sweden
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19
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Burbrink FT, Crother BI, Murray CM, Smith BT, Ruane S, Myers EA, Pyron RA. Empirical and philosophical problems with the subspecies rank. Ecol Evol 2022; 12:e9069. [PMID: 35845367 PMCID: PMC9271888 DOI: 10.1002/ece3.9069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/01/2022] [Accepted: 06/10/2022] [Indexed: 11/12/2022] Open
Abstract
Species‐level taxonomy derives from empirical sources (data and techniques) that assess the existence of spatiotemporal evolutionary lineages via various species “concepts.” These concepts determine if observed lineages are independent given a particular methodology and ontology, which relates the metaphysical species concept to what “kind” of thing a species is in reality. Often, species concepts fail to link epistemology back to ontology. This lack of coherence is in part responsible for the persistence of the subspecies rank, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse of incipient species. Thus, prospective events like lineages merging or diverging require information from unknowable future information. This is also conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies can seem attractive given that many lineages do not exhibit intrinsic reproductive isolation. We argue that using subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatiotemporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from evolutionary ontology and do not consider genealogy. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.
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Affiliation(s)
- Frank T Burbrink
- Department of Herpetology American Museum of Natural History New York New York USA
| | - Brian I Crother
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Christopher M Murray
- Department of Biological Sciences Southeastern Louisiana University Hammond Louisiana USA
| | - Brian Tilston Smith
- Department of Ornithology American Museum of Natural History New York New York USA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research Center Field Museum of Natural History Chicago Illinois USA
| | - Edward A Myers
- Department of Herpetology American Museum of Natural History New York New York USA.,Department of Biological Sciences Clemson University Clemson South Carolina USA.,Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA
| | - Robert Alexander Pyron
- Department of Vertebrate Zoology Smithsonian Institution, National Museum of Natural History Washington District of Columbia USA.,Department of Biological Sciences The George Washington University Washington District of Columbia USA
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20
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Beaudry FEG, Rifkin JL, Peake AL, Kim D, Jarvis-Cross M, Barrett SCH, Wright SI. Effects of the neo-X chromosome on genomic signatures of hybridization in Rumex hastatulus. Mol Ecol 2022; 31:3708-3721. [PMID: 35569016 DOI: 10.1111/mec.16496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
Natural hybrid zones provide opportunities for studies of the evolution of reproductive isolation in wild populations. Although recent investigations have found that the formation of neo-sex chromosomes is associated with reproductive isolation, the mechanisms remain unclear in most cases. Here, we assess the contemporary structure of gene flow in the contact zone between largely allopatric cytotypes of the dioecious plant Rumex hastatulus, a species with evidence of sex chromosome turn-over. Males to the west of the Mississippi river, USA, have an X and a single Y chromosome, whereas populations to the east of the river have undergone a chromosomal rearrangement giving rise to a larger X and two Y chromosomes. Using reduced-representation sequencing, we provide evidence that hybrids form readily and survive multiple backcross generations in the field, demonstrating the potential for ongoing gene flow between the cytotypes. Cline analysis of each chromosome separately captured no signals of difference in cline shape between chromosomes. However, principal component regression revealed a significant increase in the contribution of individual SNPs to inter-cytotype differentiation on the neo-X chromosome, but no correlation with recombination rate. Cline analysis revealed that the only SNPs with significantly steeper clines than the genome average were located on the neo-X. Our data are consistent with a role for neo-sex chromosomes in reproductive isolation between R. hastatulus cytotypes. Our investigation highlights the importance of studying plant hybrid zones for understanding the evolution of sex chromosomes.
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Affiliation(s)
- Felix E G Beaudry
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Joanna L Rifkin
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Amanda L Peake
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Deanna Kim
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Madeline Jarvis-Cross
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Spencer C H Barrett
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Stephen I Wright
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
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21
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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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22
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Wu Z, Wang Z, Xie D, Zhang J, Cai P, Li X, Xu X, Li T, Zhao J. Extensive Sympatry and Frequent Hybridization of Ecologically Divergent Aquatic Plants on the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:851151. [PMID: 35646042 PMCID: PMC9135455 DOI: 10.3389/fpls.2022.851151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 04/13/2022] [Indexed: 06/15/2023]
Abstract
Hybridization has fascinated biologists in recent centuries for its evolutionary importance, especially in plants. Hybrid zones are commonly located in regions across environmental gradients due to more opportunities to contact and ecological heterogeneity. For aquatic taxa, intrazonal character makes broad overlapping regions in intermediate environments between related species. However, we have limited information on the hybridization pattern of aquatic taxa in alpines, especially submerged macrophytes. In this study, we aimed to test the hypotheses that niche overlap and hybridization might be extensive in related aquatic plants across an altitudinal gradient. We evaluated the niche overlap in three related species pairs on the Qinghai-Tibetan Plateau and assessed the spatial pattern of hybrid populations. Obvious niche overlap and common hybridization were revealed in all three pairs of related aquatic plants. The plateau edge and river basins were broad areas for the sympatry of divergent taxa, where a large proportion of hybrid populations occurred. Hybrids are also discretely distributed in diverse habitats on the plateau. Differences in the extent of niche overlap, genetic incompatibility and phylogeographic history might lead to variation differences in hybridization patterns among the three species pairs. Our results suggested that plateau areas are a hotspot for ecologically divergent aquatic species to contact and mate and implied that hybridization may be important for the freshwater biodiversity of highlands.
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Affiliation(s)
- Zhigang Wu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Zhong Wang
- Department of Ecology, College of Life Science, Wuhan University, Wuhan, China
| | - Dong Xie
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- National Wetland Ecosystem Field Station of Taihu Lake, National Forestry Administration, Suzhou, China
| | - Juan Zhang
- Department of Ecology, College of Life Science, Wuhan University, Wuhan, China
| | - Pengsen Cai
- Department of Ecology, College of Life Science, Wuhan University, Wuhan, China
| | - Xing Li
- Department of Ecology, College of Life Science, Wuhan University, Wuhan, China
| | - Xinwei Xu
- Department of Ecology, College of Life Science, Wuhan University, Wuhan, China
| | - Tao Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Jindong Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Protein and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
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23
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Shepherd L, Simon C, Langton-Myers S, Morgan-Richards M. Insights into Aotearoa New Zealand’s biogeographic history provided by the study of natural hybrid zones. J R Soc N Z 2022. [DOI: 10.1080/03036758.2022.2061020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Lara Shepherd
- Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand
| | - Chris Simon
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
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24
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Irwin D, Schluter D. Hybridization and the Coexistence of Species. Am Nat 2022; 200:E93-E109. [DOI: 10.1086/720365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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25
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Moran RL, Jaggard JB, Roback EY, Kenzior A, Rohner N, Kowalko JE, Ornelas-García CP, McGaugh SE, Keene AC. Hybridization underlies localized trait evolution in cavefish. iScience 2022; 25:103778. [PMID: 35146393 PMCID: PMC8819016 DOI: 10.1016/j.isci.2022.103778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/13/2021] [Accepted: 01/12/2022] [Indexed: 11/04/2022] Open
Abstract
Introgressive hybridization may play an integral role in local adaptation and speciation (Taylor and Larson, 2019). In the Mexican tetra Astyanax mexicanus, cave populations have repeatedly evolved traits including eye loss, sleep loss, and albinism. Of the 30 caves inhabited by A. mexicanus, Chica cave is unique because it contains multiple pools inhabited by putative hybrids between surface and cave populations (Mitchell et al., 1977), providing an opportunity to investigate the impact of hybridization on complex trait evolution. We show that hybridization between cave and surface populations may contribute to localized variation in traits associated with cave evolution, including pigmentation, eye development, and sleep. We also uncover an example of convergent evolution in a circadian clock gene in multiple cavefish lineages and burrowing mammals, suggesting a shared genetic mechanism underlying circadian disruption in subterranean vertebrates. Our results provide insight into the role of hybridization in facilitating phenotypic evolution. Hybridization leads to a localized difference in sleep duration within a single cave Genomic analysis identifies coding differences in Cry1A across cave pools Changes in Cry1A appear to be conserved in cavefish and burrowing mammals
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26
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Li Y, Zhang X, Wang L, Sork VL, Mao L, Fang Y. Influence of Pliocene and Pleistocene climates on hybridization patterns between two closely related oak species in China. ANNALS OF BOTANY 2022; 129:231-245. [PMID: 34893791 PMCID: PMC8796672 DOI: 10.1093/aob/mcab140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/31/2021] [Accepted: 11/26/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND AIMS Contemporary patterns of genetic admixture reflect imprints of both ancient and recent gene flow, which can provide us with valuable information on hybridization history in response to palaeoclimate change. Here, we examine the relationships between present admixture patterns and past climatic niche suitability of two East Asian Cerris oaks (Quercus acutissima and Q. chenii) to test the hypothesis that the mid-Pliocene warm climate promoted while the Pleistocene cool climate limited hybridization among local closely related taxa. METHODS We analyse genetic variation at seven nuclear microsatellites (1111 individuals) and three chloroplast intergenic spacers (576 individuals) to determine the present admixture pattern and ancient hybridization history. We apply an information-theoretic model selection approach to explore the associations of genetic admixture degree with past climatic niche suitability at multiple spatial scales. KEY RESULTS More than 70 % of the hybrids determined by Bayesian clustering analysis and more than 90 % of the individuals with locally shared chloroplast haplotypes are concentrated within a mid-Pliocene contact zone between ~30°N and 35°N. Climatic niche suitabilities for Q. chenii during the mid-Pliocene Warm Period [mPWP, ~3.264-3.025 million years ago (mya)] and during the Last Glacial Maximum (LGM, ~0.022 mya) best explain the admixture patterns across all Q. acutissima populations and across those within the ancient contact zone, respectively. CONCLUSIONS Our results highlight that palaeoclimate change shapes present admixture patterns by influencing the extent of historical range overlap. Specifically, the mid-Pliocene warm climate promoted ancient contact, allowing widespread hybridization throughout central China. In contrast, the Pleistocene cool climate caused the local extinction of Q. chenii, reducing the probability of interspecific gene flow in most areas except those sites having a high level of ecological stability.
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Affiliation(s)
- Yao Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Xingwang Zhang
- School of Life Sciences, Huaibei Normal University, Huaibei, Anhui 235000, China
| | - Lu Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, USA
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - Lingfeng Mao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
- Laboratory of Biodiversity and Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Yanming Fang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
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27
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Ottenburghs J. Digest: Following clines along an Amazonian hybrid zone. Evolution 2022; 76:677-678. [PMID: 35083752 PMCID: PMC9305588 DOI: 10.1111/evo.14437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/07/2022] [Indexed: 11/29/2022]
Abstract
The shape and position of clines can provide crucial insights into the evolutionary forces at work in hybrid zones. In this issue, Del‐Rio and colleagues applied cline theory to a hybrid zone between two antbird species in Amazonia. A narrow and displaced mitochondrial cline suggests that the selected genetic marker failed to track the northward movement of this hybrid zone, possibly due to reduced fitness of female hybrids.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and Conservation, Wageningen University, the Netherlands.,Forest Ecology and Forest Management, Wageningen University, the Netherlands
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28
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Sequeira F, Arntzen JW, van Gulik D, Hajema S, Diaz RL, Wagt M, van Riemsdijk I. Genetic traces of hybrid zone movement across a fragmented habitat. J Evol Biol 2022; 35:400-412. [PMID: 35043504 DOI: 10.1111/jeb.13982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/27/2022]
Abstract
Theoretical and empirical studies suggest that the structure and position of hybrid zones can change over time. Evidence for moving hybrid zones has been directly inferred by repeated sampling over time, or indirectly through the detection of genetic footprints left by the receding species and the resulting asymmetric patterns of introgression across markers. We here investigate a hybrid zone formed by two subspecies of the Iberian golden-striped salamander, Chioglossa lusitanica, using a panel of 35 nuclear loci (31 SNPs and 4 allozymes) and one mitochondrial locus in a transect in central Portugal. We found concordant and coincident clines for most of the nuclear loci (n=22, 63%), defining a narrow hybrid zone of ca. 6 km wide, with the centre positioned ca. 15 km south of the Mondego river. Asymmetric introgression was observed at another 14 loci. Their clines are displaced towards the north, with positions located either close to the Mondego river (n=6), or further northwards (n=8). We interpret these profiles as genetic traces of the southward displacement of C. lusitanica lusitanica by C. l. longipes over the wider Mondego river valley. We noted the absence of significant linkage disequilibrium and we inferred low levels of effective selection per locus against hybrids, suggesting that introgression in the area of species replacement occurred under a neutral diffusion process. A species distribution model suggests that the C. lusitanica hybrid zone coincides with a narrow corridor of fragmented habitat. From the position of the displaced clines, we infer that patches of locally suitable habitat trapped some genetic variants that became disassociated from the southward moving hybrid zone. This study highlights the influence of habitat availability on hybrid zone movement.
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Affiliation(s)
- Fernando Sequeira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Jan W Arntzen
- Institute of Biology, Leiden University, Leiden, The Netherlands.,Naturalis Biodiversity Centre, P. O. Box 9517, 2300 RA, Leiden, The Netherlands
| | - Davy van Gulik
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Steven Hajema
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Ruben Lopez Diaz
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Mattijn Wagt
- Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
| | - Isolde van Riemsdijk
- Naturalis Biodiversity Centre, P. O. Box 9517, 2300 RA, Leiden, The Netherlands.,Hogeschool Leiden, P. O. Box 382, 2300 AJ, Leiden, The Netherlands
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29
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Muniz AC, Pimenta RJG, Cruz MV, Rodrigues JG, Buzatti RSDO, Heuertz M, Lemos‐Filho JP, Lovato MB. Hybrid zone of a tree in a Cerrado/Atlantic Forest ecotone as a hotspot of genetic diversity and conservation. Ecol Evol 2022; 12:e8540. [PMID: 35127043 PMCID: PMC8803295 DOI: 10.1002/ece3.8540] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 12/17/2021] [Indexed: 01/10/2023] Open
Abstract
The Cerrado, the largest Neotropical savanna, and the Brazilian Atlantic Forest form large ecotonal areas where savanna and forest habitats occupy adjacent patches with closely related species occurring side by side, providing opportunities for hybridization. Here, we investigated the evolutionary divergence between the savanna and forest ecotypes of the widely distributed tree Plathymenia reticulata (n = 233 individuals). Genetic structure analysis of P. reticulata was congruent with the recognition of two ecotypes, whose divergence captured the largest proportion of genetic variance in the data (F CT = 0.222 and F ST = 0.307). The ecotonal areas between the Cerrado and the Atlantic Forest constitute a hybrid zone in which a diversity of hybrid classes was observed, most of them corresponding to second-generation hybrids (F2) or backcrosses. Gene flow occurred mainly toward the forest ecotype. The genetic structure was congruent with isolation by environment, and environmental correlates of divergence were identified. The observed pattern of high genetic divergence between ecotypes may reflect an incipient speciation process in P. reticulata. The low genetic diversity of the P. reticulata forest ecotype indicate that it is threatened in areas with high habitat loss on Atlantic Forest. In addition, the high divergence from the savanna ecotype suggests it should be treated as a different unit of management. The high genetic diversity found in the ecotonal hybrid zone supports the view of ecotones as important areas for the origin and conservation of biodiversity in the Neotropics.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | - Mariana Vargas Cruz
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | | | | | | | - José P. Lemos‐Filho
- Departamento de BotânicaUniversidade Federal de Minas GeraisBelo HorizonteBrazil
| | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e EvoluçãoUniversidade Federal de Minas GeraisBelo HorizonteBrazil
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30
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Silliman K, Zhao H, Justice M, Thongda W, Bowen B, Peatman E. Complex introgression among three diverged largemouth bass lineages. Evol Appl 2021; 14:2815-2830. [PMID: 34950231 PMCID: PMC8674896 DOI: 10.1111/eva.13314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/21/2021] [Accepted: 10/14/2021] [Indexed: 12/30/2022] Open
Abstract
Hybrid zones between diverged lineages offer a unique opportunity to study evolutionary processes related to speciation. Natural and anthropogenic hybridization in the black basses (Micropterus spp.) is well documented, including an extensive intergrade zone between the widespread northern Largemouth Bass (M. salmoides) and the Florida Bass (M. floridanus). Phenotypic surveys have identified an estuarine population of Largemouth Bass (M. salmoides) in the Mobile-Tensaw Delta, with larger relative weight and smaller adult size compared to inland populations, suggesting a potential third lineage of largemouth bass. To determine the evolutionary relationships among these Mobile Delta bass populations, M. salmoides and M. floridanus, putative pure and intergrade populations of all three groups were sampled across the eastern United States. Phylogenetic analyses of 8582 nuclear SNPs derived from genotype-by-sequencing and the ND2 mitochondrial gene determined that Delta bass populations stem from a recently diverged lineage of Largemouth Bass. Using a novel quantitative pipeline, a panel of 73 diagnostic SNPs was developed for the three lineages, evaluated for accuracy, and then used to screen 881 samples from 52 sites for genetic integrity and hybridization on the Agena MassARRAY platform. These results strongly support a redrawing of native ranges for both the intergrade zone and M. floridanus, which has significant implications for current fisheries management. Furthermore, Delta bass ancestry was shown to contribute significantly to the previously described intergrade zone between northern Largemouth Bass and Florida Bass, suggesting a more complex pattern of secondary contact and introgression among these diverged Micropterus lineages.
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Affiliation(s)
- Katherine Silliman
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - Honggang Zhao
- Department of Natural ResourcesCornell UniversityIthacaNew YorkUSA
| | - Megan Justice
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
| | - Wilawan Thongda
- Center of Excellence for Shrimp Molecular Biology and Biology (CENTEX Shrimp)Faculty of ScienceMahidol UniversityBangkokThailand
- National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development Agency (NSTDA)Pathum ThaniThailand
| | - Bryant Bowen
- Georgia Department of Natural ResourcesSocial CircleGeorgiaUSA
| | - Eric Peatman
- School of Fisheries, Aquaculture, and Aquatic SciencesAuburn UniversityAuburnAlabamaUSA
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31
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Justyn NM, Callaghan CT, Hill GE. A response to estimating hybridization in the wild using community science data: a path forward. Evolution 2021; 76:359-361. [PMID: 34705282 DOI: 10.1111/evo.14390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/17/2021] [Accepted: 09/01/2021] [Indexed: 11/27/2022]
Abstract
When working with a citizen science database like eBird, there are many possible ways to filter or subsample observations. Here, we discuss the potential biases and assumptions that surround different subsampling approaches or filtering that can be done to the eBird database. Restricting observations to species that are known to frequently hybridize, a specific time of the year, or a specific location, has the potential to greatly inflate the calculated per individual rate of hybridization. Such filtering also assumes that researchers know a birds' capacity to hybridize with all other species in its range, which we argue is an unfounded assumption. We ultimately conclude that a limited filtering approach is ideal when using a citizen science database to attempt to address a broad question such as: what is the per individual rate of hybridization across all of the bird species in the United States? This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nicholas M Justyn
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States, 36849
| | - Corey T Callaghan
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig, 04103, Germany
| | - Geoffrey E Hill
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States, 36849
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32
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Cruzan MB, Thompson PG, Diaz NA, Hendrickson EC, Gerloff KR, Kline KA, Machiorlete HM, Persinger JM. Weak coupling among barrier loci and waves of neutral and adaptive introgression across an expanding hybrid zone. Evolution 2021; 75:3098-3114. [PMID: 34668193 PMCID: PMC9298192 DOI: 10.1111/evo.14381] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 09/14/2021] [Accepted: 09/19/2021] [Indexed: 01/02/2023]
Abstract
Hybridization can serve as an evolutionary stimulus, but we have little understanding of introgression at early stages of hybrid zone formation. We analyze reproductive isolation and introgression between a range‐limited and a widespread species. Reproductive barriers are estimated based on differences in flowering time, ecogeographic distributions, and seed set from crosses. We find an asymmetrical mating barrier due to cytonuclear incompatibility that is consistent with observed clusters of coincident and concordant tension zone clines (barrier loci) for mtDNA haplotypes and nuclear SNPs. These groups of concordant clines are spread across the hybrid zone, resulting in weak coupling among barrier loci and extensive introgression. Neutral clines had nearly equal introgression into both species’ ranges, whereas putative cases of adaptive introgression had exceptionally wide clines with centers shifted toward one species. Analyses of cline shape indicate that secondary contact was initiated within the last 800 generations with the per‐generation dispersal between 200 and 400 m, and provide some of the first estimates of the strength of selection required to account for observed levels of adaptive introgression. The weak species boundary between these species appears to be in early stages of dissolution, and ultimately will precipitate genetic swamping of the range‐limited species.
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Affiliation(s)
- Mitchell B Cruzan
- Department of Biology, Portland State University, Portland, Oregon, 97201
| | - Pamela G Thompson
- Department of Biology, Portland State University, Portland, Oregon, 97201
| | - Nicolas A Diaz
- Department of Biology, Portland State University, Portland, Oregon, 97201
| | | | - Katie R Gerloff
- Department of Biology, Portland State University, Portland, Oregon, 97201
| | - Katie A Kline
- Department of Biology, Portland State University, Portland, Oregon, 97201
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33
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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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34
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Ottenburghs J. The genic view of hybridization in the Anthropocene. Evol Appl 2021; 14:2342-2360. [PMID: 34745330 PMCID: PMC8549621 DOI: 10.1111/eva.13223] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
Human impact is noticeable around the globe, indicating that a new era might have begun: the Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering the distributions of countless species, often giving rise to human-mediated hybridization events. While the interbreeding of different populations or species can have detrimental effects, such as genetic extinction, it can be beneficial in terms of adaptive introgression or an increase in genetic diversity. In this paper, I first review the different mechanisms and outcomes of anthropogenic hybridization based on literature from the last five years (2016-2020). The most common mechanisms leading to the interbreeding of previously isolated taxa include habitat change (51% of the studies) and introduction of non-native species (34% intentional and 19% unintentional). These human-induced hybridization events most often result in introgression (80%). The high incidence of genetic exchange between the hybridizing taxa indicates that the application of a genic view of speciation (and introgression) can provide crucial insights on how to address hybridization events in the Anthropocene. This perspective considers the genome as a dynamic collection of genetic loci with distinct evolutionary histories, giving rise to a heterogenous genomic landscape in terms of genetic differentiation and introgression. First, understanding this genomic landscape can lead to a better selection of diagnostic genetic markers to characterize hybrid populations. Second, describing how introgression patterns vary across the genome can help to predict the likelihood of negative processes, such as demographic and genetic swamping, as well as positive outcomes, such as adaptive introgression. It is especially important to not only quantify how much genetic material introgressed, but also what has been exchanged. Third, comparing introgression patterns in pre-Anthropocene hybridization events with current human-induced cases might provide novel insights into the likelihood of genetic swamping or species collapse during an anthropogenic hybridization event. However, this comparative approach remains to be tested before it can be applied in practice. Finally, the genic view of introgression can be combined with conservation genomic studies to determine the legal status of hybrids and take appropriate measures to manage anthropogenic hybridization events. The interplay between evolutionary and conservation genomics will result in the constant exchange of ideas between these fields which will not only improve our knowledge on the origin of species, but also how to conserve and protect them.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and ConservationWageningen University & ResearchWageningenThe Netherlands
- Forest Ecology and Forest ManagementWageningen University & ResearchWageningenThe Netherlands
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35
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Burbrink FT, Ruane S. Contemporary Philosophy and Methods for Studying Speciation and Delimiting Species. ICHTHYOLOGY & HERPETOLOGY 2021. [DOI: 10.1643/h2020073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024; . Send reprint requests to this address
| | - Sara Ruane
- Earth and Environmental Sciences: Ecology and Evolution, Rutgers University–Newark, 195 University Avenue, Newark, New Jersey 07102
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36
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Frayer ME, Payseur BA. Demographic history shapes genomic ancestry in hybrid zones. Ecol Evol 2021; 11:10290-10302. [PMID: 34367575 PMCID: PMC8328415 DOI: 10.1002/ece3.7833] [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: 03/25/2021] [Revised: 06/03/2021] [Accepted: 06/08/2021] [Indexed: 12/26/2022] Open
Abstract
Demographic factors such as migration rate and population size can impede or facilitate speciation. In hybrid zones, reproductive boundaries between species are tested and demography mediates the opportunity for admixture between lineages that are partially isolated. Genomic ancestry is a powerful tool for revealing the history of admixed populations, but models and methods based on local ancestry are rarely applied to structured hybrid zones. To understand the effects of demography on ancestry in hybrids zones, we performed individual-based simulations under a stepping-stone model, treating migration rate, deme size, and hybrid zone age as parameters. We find that the number of ancestry junctions (the transition points between genomic regions with different ancestries) and heterogenicity (the genomic proportion heterozygous for ancestry) are often closely connected to demographic history. Reducing deme size reduces junction number and heterogenicity. Elevating migration rate increases heterogenicity, but migration affects junction number in more complex ways. We highlight the junction frequency spectrum as a novel and informative summary of ancestry that responds to demographic history. A substantial proportion of junctions are expected to fix when migration is limited or deme size is small, changing the shape of the spectrum. Our findings suggest that genomic patterns of ancestry could be used to infer demographic history in hybrid zones.
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Affiliation(s)
- Megan E. Frayer
- Laboratory of GeneticsUniversity of Wisconsin MadisonMadisonWIUSA
| | - Bret A. Payseur
- Laboratory of GeneticsUniversity of Wisconsin MadisonMadisonWIUSA
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37
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How Important Are Structural Variants for Speciation? Genes (Basel) 2021; 12:genes12071084. [PMID: 34356100 PMCID: PMC8305853 DOI: 10.3390/genes12071084] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/04/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
Understanding the genetic basis of reproductive isolation is a central issue in the study of speciation. Structural variants (SVs); that is, structural changes in DNA, including inversions, translocations, insertions, deletions, and duplications, are common in a broad range of organisms and have been hypothesized to play a central role in speciation. Recent advances in molecular and statistical methods have identified structural variants, especially inversions, underlying ecologically important traits; thus, suggesting these mutations contribute to adaptation. However, the contribution of structural variants to reproductive isolation between species—and the underlying mechanism by which structural variants most often contribute to speciation—remain unclear. Here, we review (i) different mechanisms by which structural variants can generate or maintain reproductive isolation; (ii) patterns expected with these different mechanisms; and (iii) relevant empirical examples of each. We also summarize the available sequencing and bioinformatic methods to detect structural variants. Lastly, we suggest empirical approaches and new research directions to help obtain a more complete assessment of the role of structural variants in speciation.
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38
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Diz AP, Romero MR, Galindo J, Saura M, Skibinski DOF, Rolán-Alvarez E. Proteomic analysis of F1 hybrids and intermediate variants in a littorina saxatilis hybrid zone. Curr Zool 2021; 68:351-359. [PMID: 35592345 PMCID: PMC9113252 DOI: 10.1093/cz/zoab054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/03/2021] [Indexed: 11/22/2022] Open
Abstract
Proteomic analysis was carried out on the Crab (upper-shore) and Wave (lower-shore) ecotypes of Littorina saxatilis from a hybrid zone at Silleiro Cape, Spain. Proteome profiles of individual snails were obtained. Protein expression in F1 hybrid snails bred in the laboratory and snails with intermediate shell phenotypes collected from the mid-shore were compared with Crab and Wave ecotypes using analytical approaches used to study dominance. Multivariate analysis over many protein spots showed that the F1 snails are distinct from both ecotypes but closer to the Wave ecotype. The intermediate snails are highly variable, some closer to the Crab and others to the Wave ecotype. Considered on a protein by protein basis, some proteins are significantly closer in expression to the Crab and others to the Wave ecotype for both F1 and intermediate snails. Furthermore, a significant majority of proteins were closer in expression to the Wave ecotype for the F1, consistent with the multivariate analysis. No such significant majority toward either the Crab or Wave ecotype was observed for the intermediate snails. The closer similarity of F1 and Wave ecotype expression patterns could be the result of similar selective pressures in the similar mid-shore and low-shore environments. For a significantly larger number of proteins, intermediate snails were closer in expression to the ecotype having the lower expression, for both Crab and Wave ecotypes. This is somewhat unexpected as lower expression might be expected to be an indication of impairment of function and lower fitness. Proteomic analysis could be important for the identification of candidate proteins useful for gaining improved understanding of adaptation and barriers to gene flow in hybrid zones.
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Affiliation(s)
- Angel P Diz
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
- Address Correspondence to Angel P. Diz. E-mail:
| | - Mónica R Romero
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
| | - Juan Galindo
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
| | - María Saura
- Departamento de Mejora Genética Animal, INIA, Madrid 28040, Spain
| | - David O F Skibinski
- Institute of Life Science, Swansea University Medical School, Swansea SA2 8PP, UK
| | - Emilio Rolán-Alvarez
- Centro de Investigación Mariña (CIM-UVIGO), Universidade de Vigo, Vigo 36310, Spain
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39
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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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40
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Brice C, Zhang Z, Bendixsen D, Stelkens R. Hybridization Outcomes Have Strong Genomic and Environmental Contingencies. Am Nat 2021; 198:E53-E67. [PMID: 34403309 DOI: 10.1086/715356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractExtreme F2 phenotypes known as transgressive segregants can cause increased or decreased fitness in hybrids beyond the ranges seen in parental populations. Despite the usefulness of transgression for plant and animal breeding and its potential role in hybrid speciation, the genetic mechanisms and predictors of transgressive segregation remain largely untested. We generated seven hybrid crosses between five widely divergent Saccharomyces yeast species and measured the fitness of the parents and their viable F1 and F2 hybrids in seven stressful environments. We found that on average 16.6% of all replicate F2 hybrids had higher fitness than both parents. Against our predictions, transgression frequency was not a function of parental genetic and phenotypic distances across test environments. Within environments, some relationships were significant, but not in the predicted direction; for example, genetic distance was negatively related to transgression in ethanol and hydrogen peroxide. Significant effects of hybrid cross, test environment, and cross × environment interactions suggest that the amount of transgression produced in a hybrid cross is highly context specific and that outcomes of hybridization differ even among crosses made from the same two parents. If the goal is to reliably predict hybrid fitness and forecast the evolutionary potential of admixed populations, we need more efforts to identify patterns beyond the idiosyncrasies caused by specific genomic or environmental contexts.
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41
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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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Porto-Hannes I, Burlakova LE, Zanatta DT, Lasker HR. Boundaries and hybridization in a secondary contact zone between freshwater mussel species (Family:Unionidae). Heredity (Edinb) 2021; 126:955-973. [PMID: 33883699 PMCID: PMC8178349 DOI: 10.1038/s41437-021-00424-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 02/02/2023] Open
Abstract
Correct species identification and delineation are crucial for effective conservation and management. However, species delineation can be problematic in the presence of morphological ambiguities due to phenotypic plasticity, convergence, and/or interspecific hybridization. Here, we investigated the degree of hybridization between two closely related freshwater mussel species [Bivalvia: Unionidae; Lampsilis siliquoidea (Barnes) and L. radiata (Gmelin)] that present intermediate forms in areas of sympatry. Unionids have a distinct form of mitochondrial DNA (mtDNA) inheritance, termed doubly uniparental inheritance (DUI) where female mtDNA (F-type) is transmitted to all progeny but male mtDNA (M-type) is mostly inherited by the males resulting in mostly homoplasmic females and heteroplasmic males. An individual was identified as hybrid when F-type and M-type mtDNA of the two different species were found in the same individual. Twelve out of 116 sequenced males were identified as hybrids indicating that these species hybridize where their geographic range overlaps in the lower Great Lakes and St. Lawrence basins. Microsatellite analyses further support the occurrence of hybridization but at a larger spatial scale than indicated by the mitochondrial analyses. We also found that strong within-species population genetic structure affects the detection of purebred individuals overestimating the number of hybrids. Given the large geographic scale and proportion of hybrids found in this study, natural hybridization and introgression need to be considered when implementing local biodiversity inventories, identifying waterbodies as source of organisms for relocation and restoration projects and when setting appropriate conservation policies.
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Affiliation(s)
- Isabel Porto-Hannes
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo, Buffalo, NY, USA.
| | | | - David T Zanatta
- Institute for Great Lakes Research, Biology Department, Central Michigan University, Mount Pleasant, MI, USA
| | - Howard R Lasker
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo, Buffalo, NY, USA
- Department of Environment and Sustainability, University at Buffalo, Buffalo, NY, USA
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43
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Velo-Antón G, Lourenço A, Galán P, Nicieza A, Tarroso P. Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander. Sci Rep 2021; 11:9259. [PMID: 33927228 PMCID: PMC8085075 DOI: 10.1038/s41598-021-88349-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 02/02/2023] Open
Abstract
Explicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.
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Affiliation(s)
- Guillermo Velo-Antón
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.6312.60000 0001 2097 6738Universidade de Vigo, Grupo de Ecoloxía Animal, Departamento de Ecoloxía e Bioloxía Animal, Torre Cacti (Lab 97), 36310 Vigo, Spain
| | - André Lourenço
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.5808.50000 0001 1503 7226Departamento de Biologia da Faculdade de Ciências, Universidade do Porto. Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro Galán
- grid.8073.c0000 0001 2176 8535Grupo de Investigación en Bioloxía Evolutiva (GIBE), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n, 15071 A Coruña, Spain
| | - Alfredo Nicieza
- grid.10863.3c0000 0001 2164 6351Departamento de Biologıa de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain ,grid.10863.3c0000 0001 2164 6351Unidad Mixta de Investigacion en Biodiversidad (UMIB), CSIC-Universidad de Oviedo-Principado de Asturias, Mieres, Spain
| | - Pedro Tarroso
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal
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Kakioka R, Kume M, Ishikawa A, Ansai S, Hosoki TK, Yamasaki YY, Nagano AJ, Toyoda A, Kitano J. Genetic basis for variation in the number of cephalic pores in a hybrid zone between closely related species of goby, Gymnogobius breunigii and Gymnogobius castaneus. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blab033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Populations or species exploiting different habitats can differ in sensory perception as a result of divergent adaptation. In bony fish, the water current is perceived via neuromasts, the end organ of the lateral line system. Although fish in different habitats are known to vary in neuromasts, we know little about the genetic basis for such variation. Here, we investigate the genetic basis for variation in supraorbital neuromasts in a hybrid zone between the Japanese gobies Gymnogobius breunigii and Gymnogobius castaneus. The former has supraorbital canal neuromasts with six cephalic pores, whereas the latter has only superficial neuromasts with no canals or pores in the supraorbital region. Our genomic analysis showed that G. breunigii and G. castaneus occur mainly in the lower and mid/upper reaches, respectively. In a river in northern Japan, hybrids were found at the sites between the habitats of the two species. These hybrids exhibited anomalies of cephalic pores. Using this hybrid zone, we conducted genome-wide association studies and identified one locus significantly associated with the number of pores. Genomic cline analysis in the hybrid zone demonstrated that this locus exhibited a higher introgression rate compared with the genomic background, indicating the possibility of adaptive introgression.
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Affiliation(s)
- Ryo Kakioka
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Manabu Kume
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Asano Ishikawa
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540,Japan
| | - Satoshi Ansai
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takuya K Hosoki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540,Japan
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194,Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540,Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies, Mishima, Shizuoka 411-8540,Japan
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45
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Pfennig KS. Biased Hybridization and Its Impact on Adaptive Introgression. Trends Ecol Evol 2021; 36:488-497. [PMID: 33752896 DOI: 10.1016/j.tree.2021.02.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Gene exchange between species can influence ecological and evolutionary processes ranging from population rescue to adaptive radiation. Genomic tools have provided new insights into the prevalence and nature of gene exchange between species. However, much remains unknown of how ecological, behavioral, and evolutionary factors determine what genetic variation moves between species in the first place. In particular, more research is needed that evaluates whether such factors bias gene flow from one species to another, and whether any such biases affect how genetic variation from another species is ultimately retained in the genome of a given species. Addressing this issue is crucial in a changing world where hybridization and introgression might determine which species succeed and which become extinct.
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Affiliation(s)
- Karin S Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
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46
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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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Thompson KA, Urquhart-Cronish M, Whitney KD, Rieseberg LH, Schluter D. Patterns, Predictors, and Consequences of Dominance in Hybrids. Am Nat 2021; 197:E72-E88. [PMID: 33625966 DOI: 10.1086/712603] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractCompared to those of their parents, are the traits of first-generation (F1) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? To address this empirical gap, we compiled data from 233 crosses in which traits were measured in a common environment for two parent taxa and their F1 hybrids. We find that individual traits in F1s are halfway between the parental midpoint and one parental value. Considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (parent bias) about 50% more than the other, while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that parent bias improves fitness, whereas mismatch reduces fitness. Our study has three major conclusions. First, hybrids are not phenotypically intermediate but rather exhibit substantial mismatch. Second, dominance is likely determined by the idiosyncratic evolutionary trajectories of individual traits and populations. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.
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48
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Araki Y, Sota T. Population genetic structure underlying the geographic variation in beetle structural colour with multiple transition zones. Mol Ecol 2020; 30:670-684. [PMID: 33253446 DOI: 10.1111/mec.15758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/12/2020] [Accepted: 11/24/2020] [Indexed: 11/27/2022]
Abstract
We studied the population genetic structure underlying the geographic variation in the structural colour of the geotrupid dung beetle, Phelotrupes auratus, which exhibits metallic body colours of different reflectance wavelengths perceived as red, green and indigo. These forms occur parapatrically in an area of Japan. The colour variation was not related to variation in climatic factors. Using single nucleotide polymorphisms (SNPs) from restriction-site-associated DNA sequences, we discriminated five groups of populations (west/red, south/green, south/indigo, south/red and east/red) by a combination of genetic clusters (west, south and east) and three colour forms. There were three transition zones for the colour forms: two between the red and green forms were hybrid zones with steep genetic clines, which implies the existence of barriers to gene flow between regions with different colours. The remaining transition zone between the green and indigo forms lacked genetic differentiation, despite the evident colour changes, which implies regionally specific selection on the different colours. In a genomewide association study, we identified four SNPs that were associated with the red/green or indigo colour and were not linked with one another, which implies that the coloration was controlled by multiple loci, each affecting the expression of a different colour range. These loci may have controlled the transitions between different combinations of colours. Our study demonstrates that geographic colour variation within a species can be maintained by nonuniform interactions among barriers to gene flow, locally specific selection on different colours, and the effects of different colour loci.
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Affiliation(s)
- Yoshifumi Araki
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
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49
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Asztalos M, Schultze N, Ihlow F, Geniez P, Berroneau M, Delmas C, Guiller G, Legentilhomme J, Kindler C, Fritz U. How often do they do it? An in-depth analysis of the hybrid zone of two grass snake species (Natrix astreptophora and Natrix helvetica). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
We examined the contact zone of two parapatric species of grass snake (Natrix astreptophora and Natrix helvetica) in southern France. To this end, we used comprehensive sampling, analysed mtDNA sequences and microsatellite loci, and built Species Distribution Models for current and past climatic conditions. The contact zone had established by the mid-Holocene during range expansions from glacial refuges in the Iberian Peninsula (N. astreptophora) and southern or western France (N. helvetica). The contact zone represents a narrow bimodal hybrid zone, with steep genetic transition from one taxon to the other and rare hybridization, supporting species status for N. astreptophora and N. helvetica. Our results suggest that the steepness of the clines is a more robust tool for species delimitation than cline width. In addition, we discovered in western France, beyond the hybrid zone, a remote population of N. helvetica with genetic signatures of hybridization with N. astreptophora, most likely the result of human-mediated long-distance dispersal. For N. helvetica, we identified a southern and a northern population cluster, connected by broad-scale gene flow in a unimodal hybrid zone running across France. This pattern either reflects genetic divergence caused by allopatry in two microrefuges and subsequent secondary contact or introgression of foreign alleles into the southern cluster.
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Affiliation(s)
- Marika Asztalos
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Nadine Schultze
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Flora Ihlow
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Philippe Geniez
- UMR 5175 CEFE, Biogéographie et Ecologie des Vertébrés, EPHE, PSL Université Recherche, Montpellier, Cedex 5, France
| | | | - Claudine Delmas
- NEO/ANA-CEN Ariège, 18 Impasse Denis Papin, Lavelanet, France
| | | | | | - Carolin Kindler
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, Dresden, Germany
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50
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Akopyan M, Gompert Z, Klonoski K, Vega A, Kaiser K, Mackelprang R, Rosenblum EB, Robertson JM. Genetic and phenotypic evidence of a contact zone between divergent colour morphs of the iconic red-eyed treefrog. Mol Ecol 2020; 29:4442-4456. [PMID: 32945036 DOI: 10.1111/mec.15639] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/21/2020] [Accepted: 09/03/2020] [Indexed: 12/28/2022]
Abstract
Hybrid zones act as natural laboratories where divergent genomes interact, providing powerful systems for examining the evolutionary processes underlying biological diversity. In this study, we characterized patterns of genomic and phenotypic variation resulting from hybridization between divergent intraspecific lineages of the Neotropical red-eyed treefrog (Agalychnis callidryas). We found genetic evidence of a newly discovered contact zone and phenotypic novelty in leg colour-a trait suspected to play a role in mediating assortative mating in this species. Analysis of hybrid ancestry revealed an abundance of later-generation Fn individuals, suggesting persistence of hybrids in the contact zone. Hybrids are predominantly of southern ancestry but are phenotypically more similar to northern populations. Genome-wide association mapping revealed QTL with measurable effects on leg-colour variation, but further work is required to dissect the architecture of this trait and establish causal links. Further, genomic cline analyses indicated substantial variation in patterns of introgression across the genome. Directional introgression of loci associated with different aspects of leg colour are inherited from each parental lineage, creating a distinct hybrid colour pattern. We show that hybridization can generate new phenotypes, revealing the evolutionary processes that potentially underlie patterns of phenotypic diversity in this iconic polytypic frog. Our study is consistent with a role of hybridization and sexual selection in lineage diversification, evolutionary processes that have been implicated in accelerating divergence in the most phenotypically diverse species.
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Affiliation(s)
- Maria Akopyan
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA.,Department of Biology, California State University, Northridge, CA, USA
| | | | - Karina Klonoski
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | | | - Kristine Kaiser
- Department of Biology, California State University, Northridge, CA, USA
| | | | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
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