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Leitwein M, Durif G, Delpuech E, Gagnaire PA, Ernande B, Vandeputte M, Vergnet A, Duranton M, Clota F, Allal F. The Fate of a Polygenic Phenotype Within the Genomic Landscapes of Introgression in the European Seabass Hybrid Zone. Mol Biol Evol 2024; 41:msae194. [PMID: 39271153 PMCID: PMC11430266 DOI: 10.1093/molbev/msae194] [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: 02/07/2024] [Revised: 08/26/2024] [Accepted: 09/06/2024] [Indexed: 09/15/2024] Open
Abstract
Unraveling the evolutionary mechanisms and consequences of hybridization is a major concern in biology. Many studies have documented the interplay between recombination and selection in modulating the genomic landscape of introgression, but few have considered how associations with phenotype may affect this landscape. Here, we use the European seabass (Dicentrarchus labrax), a key species in marine aquaculture that undergoes natural hybridization, to determine how selection on phenotype modulates the introgression landscape between Atlantic and Mediterranean lineages. We use a high-density single nucleotide polymorphism array to assess individual local ancestry along the genome and improve the mapping of muscle fat content, a polygenic trait that is divergent between lineages. Taking into account variation in recombination rates, we reveal a purging of Atlantic ancestry in the admixed Mediterranean populations. While Atlantic individuals had higher muscle fat content, we observed that genomic regions associated with this trait in Mediterranean populations displayed reduced introgression of Atlantic ancestry. These results emphasize how selection against maladapted alleles shapes the genomic landscape of introgression.
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Affiliation(s)
- Maeva Leitwein
- UMR Marbec, Université Montpellier, CNRS, Ifremer, IRD, INRAE, 34000 Montpellier, France
| | - Ghislain Durif
- IMAG-Institut Montpelliérain Alexander Grothendieck, 34000 Montpellier, France
| | - Emilie Delpuech
- UMR Marbec, Université Montpellier, CNRS, Ifremer, IRD, INRAE, 34000 Montpellier, France
| | | | - Bruno Ernande
- UMR Marbec, Université Montpellier, CNRS, Ifremer, IRD, INRAE, 34000 Montpellier, France
| | - Marc Vandeputte
- UMR Marbec, Université Montpellier, CNRS, Ifremer, IRD, INRAE, 34000 Montpellier, France
| | - Alain Vergnet
- UMR Marbec, Université Montpellier, CNRS, Ifremer, IRD, INRAE, 34000 Montpellier, France
| | - Maud Duranton
- UMR Marbec, Université Montpellier, CNRS, Ifremer, IRD, INRAE, 34000 Montpellier, France
| | - Frederic Clota
- UMR Marbec, Université Montpellier, CNRS, Ifremer, IRD, INRAE, 34000 Montpellier, France
| | - François Allal
- UMR Marbec, Université Montpellier, CNRS, Ifremer, IRD, INRAE, 34000 Montpellier, France
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2
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Tseng YH, Kuo LY, Borokini I, Fawcett S. The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae. AMERICAN JOURNAL OF BOTANY 2024; 111:e16388. [PMID: 39135339 DOI: 10.1002/ajb2.16388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 07/15/2024] [Accepted: 07/15/2024] [Indexed: 08/24/2024]
Abstract
PREMISE Hybridization is recognized as an important mechanism in fern speciation, with many allopolyploids known among congeners, as well as evidence of ancient genome duplications. Several contemporary instances of deep (intergeneric) hybridization have been noted, invariably resulting in sterile progeny. We chose the christelloid lineage of the family Thelypteridaceae, recognized for its high frequency of both intra- and intergeneric hybrids, to investigate recent hybrid speciation between deeply diverged lineages. We also seek to understand the ecological and evolutionary outcomes of resulting lineages across the landscape. METHODS By phasing captured reads within a phylogenomic data set of GoFlag 408 nuclear loci using HybPhaser, we investigated candidate hybrids to identify parental lineages. We estimated divergence ages by inferring a dated phylogeny using fossil calibrations with treePL. We investigated ecological niche conservatism between one confirmed intergeneric allotetraploid and its diploid progenitors using the centroid, overlap, unfilling, and expansion (COUE) framework. RESULTS We provide evidence for at least six instances of intergeneric hybrid speciation within the christelloid clade and estimate up to 45 million years of divergence between progenitors. The niche quantification analysis showed moderate niche overlap between an allopolyploid species and its progenitors, with significant divergence from the niche of one progenitor and conservatism to the other. CONCLUSIONS The examples provided here highlight the overlooked role that allopolyploidization following intergeneric hybridization may play in fern diversification and range and niche expansions. Applying this approach to other fern taxa may reveal a similar pattern of deep hybridization resulting in highly successful novel lineages.
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Affiliation(s)
- Yu-Hsin Tseng
- Department of Life Sciences, National Chung Hsing University, no. 145 Xingda Rd., South District, 40227, Taichung, Taiwan
| | - Li-Yaung Kuo
- College of Life Science, National Tsing Hua University, No. 101, Section 2, Kuang Fu Road, Hsinchu, 30044, Taiwan
| | - Israel Borokini
- Department of Ecology, Montana State University, 310 Lewis Hall, Bozeman, 59717, MT, USA
- University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building, Berkeley, 94720-2465, CA, USA
| | - Susan Fawcett
- University and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building, Berkeley, 94720-2465, CA, USA
- National Tropical Botanical Garden, 3530 Papālina Road, Kalāheo, 96741, HI, USA
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3
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Gawrońska B, Marszałek M, Kosiński P, Podsiedlik M, Bednorz L, Zeyland J. No wonder, it is a hybrid. Natural hybridization between Jacobaea vulgaris and J. erucifolia revealed by molecular marker systems and its potential ecological impact. Ecol Evol 2023; 13:e10467. [PMID: 37664498 PMCID: PMC10468328 DOI: 10.1002/ece3.10467] [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: 03/07/2023] [Revised: 08/09/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
Progressive changes in the environment are related to modifications of the habitat. Introducing exotic species, and interbreeding between species can lead to processes that in the case of rare species or small populations threatens their integrity. Given the declining trends of many populations due to increased hybridization, early recognition of hybrids becomes important in conservation management. Natural hybridization is prevalent in Jacobaea. There are many naturally occurring interspecific hybrids in this genus, including those between Jacobaea vulgaris and its relatives. Although Jacobaea erucifolia and J. vulgaris often co-occur and are considered closely related, apart from the few reports of German botanists on the existence of such hybrids, there is no information on research confirming hybridization between them. Morphologically intermediate individuals, found in the sympatric distributions of J. vulgaris and J. erucifolia, were hypothesized to be their hybrids. Two molecular marker systems (nuclear and chloroplast DNA markers) were employed to test this hypothesis and characterize putative hybrids. Nuclear and chloroplast DNA sequencing results and taxon-specific amplified fragment length polymorphism (AFLP) fragment distribution analysis confirmed the hybrid nature of all 25 putative hybrids. The AFLP patterns of most hybrids demonstrated a closer relationship to J. erucifolia, suggesting frequent backcrossing. Moreover, they showed that several individuals previously described as pure were probably also of hybrid origin, backcrosses to J. erucifolia and J. vulgaris. This study provides the first molecular confirmation that natural hybrids between J. vulgaris and J. erucifolia occur in Poland. Hybridization appeared to be bidirectional but asymmetrical with J. vulgaris as the usual maternal parent.
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Affiliation(s)
- Barbara Gawrońska
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
| | - Małgorzata Marszałek
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
| | - Piotr Kosiński
- Department of Botany, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
- Institute of DendrologyPolish Academy of SciencesKórnikPoland
| | - Marek Podsiedlik
- Natural History Collections, Faculty of BiologyAdam Mickiewicz University in PoznańPoznańPoland
| | - Leszek Bednorz
- Department of Botany, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
| | - Joanna Zeyland
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and BioengineeringPoznań University of Life SciencesPoznańPoland
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4
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Staude IR, Ebersbach J. Neophytes may promote hybridization and adaptations to a changing planet. Ecol Evol 2023; 13:e10405. [PMID: 37593753 PMCID: PMC10427993 DOI: 10.1002/ece3.10405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/14/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023] Open
Abstract
Human activities erode geographic barriers, facilitating hybridization among previously isolated taxa. However, limited empirical research exists on the consequences of introduced species (neophytes) for hybridization and subsequent evolutionary outcomes. To address this knowledge gap, we employed a macroecological approach. First, we examined the spatial and phylogenetic overlap between neophytes and hybrids by integrating the Plants of the World Online database with the Global Naturalized Alien Flora database. Second, leveraging the largest dated plant phylogeny available, we compared diversification rates between genera containing hybrids and neophytes versus those without. Third, focusing on the extensively studied hybrid flora of Britain, we studied the spatial distributions of hybrids in relation to neophyte and native parents, assessing potential adaptations to anthropogenic disturbances and impacts on native species. Overall, our findings highlight positive ties between contemporary biodiversity redistribution and hybridization. Spatially (across countries) and phylogenetically (across genera), neophyte incidence was positively associated with hybrid incidence. Genera comprising both hybrids and neophytes displayed significantly higher diversification rates. Neophyte hybrids primarily occupied areas with a higher human footprint, with limited evidence of hybrids threatening native species throughout their range in more natural habitats. These results challenge the notion that species naturalizations and hybridizations exclusively yield negative outcomes for biodiversity. While it is conceivable that anthropogenic hybridization may facilitate recombination of genetic variation and contribute to conserving genetic diversity in disturbed environments, further research is needed to fully understand these processes.
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Affiliation(s)
- Ingmar R. Staude
- Institute of BiologyLeipzig UniversityLeipzigGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Jana Ebersbach
- Institute of BiologyLeipzig UniversityLeipzigGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
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5
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Stone BW, Rodríguez-Peña RA, Wolfe AD. Testing hypotheses of hybrid taxon formation in the shrubby beardtongues (Penstemon subgenus Dasanthera). AMERICAN JOURNAL OF BOTANY 2023; 110:e16118. [PMID: 36480414 DOI: 10.1002/ajb2.16118] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Hybridization is increasingly being identified in the genomes of species across the tree of life, leading to a general recognition that hybridization plays an important role in the generation of species diversity. While hybridization may increase species diversity directly via the formation of new taxa through hybrid speciation, it may also act indirectly via the exchange of phenotypic and genetic variance between species, which may in turn stimulate future speciation events. METHODS Using high-throughput sequence data, we resolved phylogenetic relationships and investigated the role of hybridization as a diversification mechanism in the shrubby beardtongues (Penstemon subgenus Dasanthera), a group of North American wildflowers that has undergone a recent and rapid adaptive radiation. Specifically, we tested four hypotheses of hybrid taxon formation resulting from hybridization between P. davidsonii and P. fruticosus. RESULTS Species tree inference supports the monophyly of subgenus Dasanthera and elucidates relationships between taxa distributed in the Cascades and Sierra Nevada Mountains. Results also provide evidence of gene flow between P. davidsonii and P. fruticosus and support at least one hybrid origin hypothesis (P. davidsonii var. menziesii) in a region of contemporary distributional overlap. Hybridization may have also been facilitated by historical overlap in geographic distribution caused by species' responses to climatic changes during the Pleistocene. CONCLUSIONS Our results support a history of hybridization between focal taxa in a rapidly radiating clade of plants and more broadly contribute to our growing understanding of the role of hybridization as a diversification mechanism in plants.
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Affiliation(s)
- Benjamin W Stone
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | | | - Andrea D Wolfe
- Department of Evolution, Ecology, & Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
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6
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Encinas‐Viso F, Morin L, Sathyamurthy R, Knerr N, Roux C, Broadhurst L. Population genomics reveal multiple introductions and admixture of
Sonchus oleraceus
in Australia. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Francisco Encinas‐Viso
- Centre for Australian National Biodiversity Research Commonwealth Scientific and Industrial Research Organisation (CSIRO) Canberra Australian Capital Territory Australia
| | - Louise Morin
- CSIRO Health and Biosecurity Canberra Australian Capital Territory Australia
| | | | - Nunzio Knerr
- Centre for Australian National Biodiversity Research Commonwealth Scientific and Industrial Research Organisation (CSIRO) Canberra Australian Capital Territory Australia
| | - Camille Roux
- UMR 8198 – Evo‐Eco‐Paleo CNRS – Univ Lille Lille France
| | - Linda Broadhurst
- Centre for Australian National Biodiversity Research Commonwealth Scientific and Industrial Research Organisation (CSIRO) Canberra Australian Capital Territory Australia
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7
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Mitchell N, Luu H, Owens GL, Rieseberg LH, Whitney KD. Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus). Evolution 2022; 76:1512-1528. [PMID: 35665925 PMCID: PMC9544064 DOI: 10.1111/evo.14536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 01/22/2023]
Abstract
To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than that of nonhybrids. We used field experimental evolution in annual sunflowers (Helianthus) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to nonhybrid controls. We created hybrids between Helianthus annuus (L.) and H. debilis (Nutt.) and grew plots of both hybrids and nonhybrid controls through eight generations at three sites in Texas. We collected seeds from each generation and grew each generation × treatment × home site combination at two final common gardens. We estimated the strength and direction of evolution in terms of fitness and 24 traits, tested for repeated versus nonrepeated evolution, and assessed overall phenotypic evolution across lineages and in relation to a locally adapted phenotype. Hybrids consistently evolved higher fitness over time, while controls did not, although trait evolution varied in strength across home sites. Repeated evolution was more evident in hybrids versus nonhybrid controls, and hybrid evolution was often in the direction of the locally adapted phenotype. Our findings have implications for both the nature of repeatability in evolution and the contribution of hybridization to evolution across environmental contexts.
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Affiliation(s)
- Nora Mitchell
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA,Department of BiologyUniversity of Wisconsin – Eau ClaireEau ClaireWisconsinUSA
| | - Hoang Luu
- Department of Environmental and Plant BiologyOhio UniversityAthensOhioUSA
| | - Gregory L. Owens
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaBritish ColumbiaCanada
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8
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Introgressive hybridisation between domestic pigs (Sus scrofa domesticus) and endemic Corsican wild boars (S. s. meridionalis): effects of human-mediated interventions. Heredity (Edinb) 2022; 128:279-290. [PMID: 35273382 PMCID: PMC8986821 DOI: 10.1038/s41437-022-00517-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
Owing to the intensified domestication process with artificial trait selection, introgressive hybridisation between domestic and wild species poses a management problem. Traditional free-range livestock husbandry, as practiced in Corsica and Sardinia, is known to facilitate hybridisation between wild boars and domestic pigs (Sus scrofa). Here, we assessed the genetic distinctness and genome-wide domestic pig ancestry levels of the Corsican wild boar subspecies S. s. meridionalis, with reference to its Sardinian conspecifics, employing a genome-wide single nucleotide polymorphism (SNP) assay and mitochondrial control region (mtCR) haplotypes. We also assessed the reliance of morphological criteria and the melanocortin-1 receptor (MC1R) coat colour gene to identify individuals with domestic introgression. While Corsican wild boars showed closest affinity to Sardinian and Italian wild boars compared to other European populations based on principal component analysis, the observation of previously undescribed mtCR haplotypes and high levels of nuclear divergence (Weir’s θ > 0.14) highlighted the genetic distinctness of Corsican S. s. meridionalis. Across three complementary analyses of mixed ancestry (i.e., STRUCTURE, PCADMIX, and ELAI), proportions of domestic pig ancestry were estimated at 9.5% in Corsican wild boars, which was significantly higher than in wild boars in Sardinia, where free-range pig keeping was banned in 2012. Comparison of morphologically pure- and hybrid-looking Corsican wild boars suggested a weak correlation between morphological criteria and genome-wide domestic pig ancestry. The study highlights the usefulness of molecular markers to assess the direct impacts of management practices on gene flow between domestic and wild species.
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9
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Shapiro JA. What we have learned about evolutionary genome change in the past 7 decades. Biosystems 2022; 215-216:104669. [DOI: 10.1016/j.biosystems.2022.104669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/12/2022]
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10
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Clark MI, Bradburd GS, Akopyan M, Vega A, Rosenblum EB, Robertson JM. Genetic isolation by distance underlies colour pattern divergence in red-eyed treefrogs (Agalychnis callidryas). Mol Ecol 2022; 31:1666-1681. [PMID: 35034406 PMCID: PMC8923152 DOI: 10.1111/mec.16350] [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: 05/22/2021] [Revised: 10/21/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
Investigating the spatial distribution of genetic and phenotypic variation can provide insights into the evolutionary processes that shape diversity in natural systems. We characterized patterns of genetic and phenotypic diversity to learn about drivers of colour-pattern diversification in red-eyed treefrogs (Agalychnis callidryas) in Costa Rica. Along the Pacific coast, red-eyed treefrogs have conspicuous leg colour patterning that transitions from orange in the north to purple in the south. We measured phenotypic variation of frogs, with increased sampling at sites where the orange-to-purple transition occurs. At the transition zone, we discovered the co-occurrence of multiple colour-pattern morphs. To explore possible causes of this variation, we generated a single nucleotide polymorphism data set to analyse population genetic structure, measure genetic diversity and infer the processes that mediate genotype-phenotype dynamics. We investigated how patterns of genetic relatedness correspond to individual measures of colour pattern along the coast, including testing for the role of hybridization in geographic regions where orange and purple phenotypic groups co-occur. We found no evidence that colour-pattern polymorphism in the transition zone arose through recent hybridization. Instead, a strong pattern of genetic isolation by distance indicates that colour-pattern variation was either retained through other processes such as ancestral colour polymorphisms or ancient secondary contact, or else it was generated by novel mutations. We found that phenotype changes along the Pacific coast more than would be expected based on genetic divergence and geographic distance alone. Combined, our results suggest the possibility of selective pressures acting on colour pattern at a small geographic scale.
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Affiliation(s)
- Meaghan I. Clark
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of integrative Biology, Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, Michigan, USA,W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, USA
| | - Gideon S. Bradburd
- Department of integrative Biology, Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Maria Akopyan
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | | | - Erica Bree Rosenblum
- Department of Environmental Science, Policy, and Management, University of California Berkeley, Berkeley, California, USA,Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, California, USA
| | - Jeanne M. Robertson
- Department of Biology, California State University Northridge, Northridge, California, USA,Department of Herpetology, Natural History Museum of Los Angeles County, Los Angeles, California, USA
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11
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Whiteman NK. Evolution in small steps and giant leaps. Evolution 2022; 76:67-77. [PMID: 35040122 PMCID: PMC9387839 DOI: 10.1111/evo.14432] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/28/2021] [Accepted: 01/03/2022] [Indexed: 02/03/2023]
Abstract
The first Editor of Evolution was Ernst Mayr. His foreword to the first issue of Evolution published in 1947 framed evolution as a "problem of interaction" that was just beginning to be studied in this broad context. First, I explore progress and prospects on understanding the subsidiary interactions identified by Mayr, including interactions between parts of organisms, between individuals and populations, between species, and between the organism and its abiotic environment. Mayr's overall "problem of interaction" framework is examined in the context of coevolution within and among levels of biological organization. This leads to a comparison in the relative roles of biotic versus abiotic agents of selection and fluctuating versus directional selection, followed by stabilizing selection in shaping the genomic architecture of adaptation. Oligogenic architectures may be typical for traits shaped more by fluctuating selection and biotic selection. Conversely, polygenic architectures may be typical for traits shaped more by directional followed by stabilizing selection and abiotic selection. The distribution of effect sizes and turnover dynamics of adaptive alleles in these scenarios deserves further study. Second, I review two case studies on the evolution of acquired toxicity in animals, one involving cardiac glycosides obtained from plants and one involving bacterial virulence factors horizontally transferred to animals. The approaches used in these studies and the results gained directly flow from Mayr's vision of an evolutionary biology that revolves around the "problem of interaction."
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Affiliation(s)
- Noah K. Whiteman
- Department of Integrative Biology, University of California, Berkeley, California 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720
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12
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Wong ELY, Hiscock SJ, Filatov DA. The Role of Interspecific Hybridisation in Adaptation and Speciation: Insights From Studies in Senecio. FRONTIERS IN PLANT SCIENCE 2022; 13:907363. [PMID: 35812981 PMCID: PMC9260247 DOI: 10.3389/fpls.2022.907363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/03/2022] [Indexed: 05/08/2023]
Abstract
Hybridisation is well documented in many species, especially plants. Although hybrid populations might be short-lived and do not evolve into new lineages, hybridisaiton could lead to evolutionary novelty, promoting adaptation and speciation. The genus Senecio (Asteraceae) has been actively used to unravel the role of hybridisation in adaptation and speciation. In this article, we first briefly describe the process of hybridisation and the state of hybridisation research over the years. We then discuss various roles of hybridisation in plant adaptation and speciation illustrated with examples from different Senecio species, but also mention other groups of organisms whenever necessary. In particular, we focus on the genomic and transcriptomic consequences of hybridisation, as well as the ecological and physiological aspects from the hybrids' point of view. Overall, this article aims to showcase the roles of hybridisation in speciation and adaptation, and the research potential of Senecio, which is part of the ecologically and economically important family, Asteraceae.
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Affiliation(s)
- Edgar L. Y. Wong
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- *Correspondence: Edgar L. Y. Wong,
| | - Simon J. Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
- Oxford Botanic Garden and Arboretum, Oxford, United Kingdom
| | - Dmitry A. Filatov
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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14
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Adavoudi R, Pilot M. Consequences of Hybridization in Mammals: A Systematic Review. Genes (Basel) 2021; 13:50. [PMID: 35052393 PMCID: PMC8774782 DOI: 10.3390/genes13010050] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Hybridization, defined as breeding between two distinct taxonomic units, can have an important effect on the evolutionary patterns in cross-breeding taxa. Although interspecific hybridization has frequently been considered as a maladaptive process, which threatens species genetic integrity and survival via genetic swamping and outbreeding depression, in some cases hybridization can introduce novel adaptive variation and increase fitness. Most studies to date focused on documenting hybridization events and analyzing their causes, while relatively little is known about the consequences of hybridization and its impact on the parental species. To address this knowledge gap, we conducted a systematic review of studies on hybridization in mammals published in 2010-2021, and identified 115 relevant studies. Of 13 categories of hybridization consequences described in these studies, the most common negative consequence (21% of studies) was genetic swamping and the most common positive consequence (8%) was the gain of novel adaptive variation. The total frequency of negative consequences (49%) was higher than positive (13%) and neutral (38%) consequences. These frequencies are biased by the detection possibilities of microsatellite loci, the most common genetic markers used in the papers assessed. As negative outcomes are typically easier to demonstrate than positive ones (e.g., extinction vs hybrid speciation), they may be over-represented in publications. Transition towards genomic studies involving both neutral and adaptive variation will provide a better insight into the real impacts of hybridization.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, ul. Nadwiślańska 108, 80-680 Gdańsk, Poland;
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15
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O'Donnell ST, Fitz-Gibbon ST, Sork VL. Ancient Introgression Between Distantly Related White Oaks (Quercus sect. Quercus) Shows Evidence of Climate-Associated Asymmetric Gene Exchange. J Hered 2021; 112:663-670. [PMID: 34508641 DOI: 10.1093/jhered/esab053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 09/10/2021] [Indexed: 12/14/2022] Open
Abstract
Ancient introgression can be an important source of genetic variation that shapes the evolution and diversification of many taxa. Here, we estimate the timing, direction, and extent of gene flow between two distantly related oak species in the same section (Quercus sect. Quercus). We estimated these demographic events using genotyping by sequencing data, which generated 25 702 single nucleotide polymorphisms for 24 individuals of California scrub oak (Quercus berberidifolia) and 23 individuals of Engelmann oak (Quercus engelmannii). We tested several scenarios involving gene flow between these species using the diffusion approximation-based population genetic inference framework and model-testing approach of the Python package DaDi. We found that the most likely demographic scenario includes a bottleneck in Q. engelmannii that coincides with asymmetric gene flow from Q. berberidifolia into Q. engelmannii. Given that the timing of this gene flow coincides with the advent of a Mediterranean-type climate in the California Floristic Province, we propose that changing precipitation patterns and seasonality may have favored the introgression of climate-associated genes from the endemic into the non-endemic California oak.
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Affiliation(s)
- Scott T O'Donnell
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Sorel T Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Victoria L Sork
- Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
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16
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Abstract
Alleles that introgress between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments.
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Affiliation(s)
- Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA; .,Current affiliation: Yale Institute for Biospheric Studies and Yale School of the Environment, Yale University, New Haven, Connecticut 06511, USA;
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA;
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17
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Myers EA, Mulcahy DG, Falk B, Johnson K, Carbi M, de Queiroz K. Interspecific Gene Flow and Mitochondrial Genome Capture During the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae). Syst Biol 2021; 71:501-511. [PMID: 34735007 DOI: 10.1093/sysbio/syab089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 11/12/2022] Open
Abstract
Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean Anolis lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, A. opalinus, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting. Here we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene-tree, species-tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene-tree recovers the same relationships previously inferred for this group, which is strikingly different from the species-tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model, so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group, however coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of Anolis is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent adaptive radiations.
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Affiliation(s)
- Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Bryan Falk
- Division of Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Kiyomi Johnson
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Marina Carbi
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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18
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Zalmat AS, Sotola VA, Nice CC, Martin NH. Genetic structure in Louisiana Iris species reveals patterns of recent and historical admixture. AMERICAN JOURNAL OF BOTANY 2021; 108:2257-2268. [PMID: 34618352 DOI: 10.1002/ajb2.1758] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 06/13/2023]
Abstract
PREMISE When divergent lineages come into secondary contact, reproductive isolation may be incomplete, thus providing an opportunity to investigate how speciation is manifested in the genome. The Louisiana Irises (Iris, series Hexagonae) comprise a group of three or more ecologically and reproductively divergent lineages that can produce hybrids where they come into contact. We estimated standing genetic variation to understand the current distribution of population structure in the Louisiana Irises. METHODS We used genotyping-by-sequencing techniques to sample the genomes of Louisiana Iris species across their ranges. We sampled 20 populations (n = 632 individuals) across 11,249 loci and used Entropy and PCA models to assess population genetic data. RESULTS We discovered evidence for interspecific gene flow in parts of the range. Our analysis revealed patterns of population structure at odds with widely accepted nominal taxonomy. We discovered undescribed hybrid populations, designated as belonging to the I. brevicaulis lineage. Iris nelsonii shared significant ancestry with only one of the purported parent species, I. fulva, evidence inconsistent with a hybrid origin. CONCLUSIONS This study provides several key findings important to the investigation of standing genetic variation in the Louisiana Iris species complex. Compared to the other nominal species, I. brevicaulis contains a large amount of genetic diversity. In addition, we discovered a previously unknown hybrid zone between I. brevicaulis and I. hexagona along the Texas coast. Finally, our results do not support the long-standing hypothesis that I. nelsonii has mixed ancestry from three parental taxa.
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Affiliation(s)
- Alexander S Zalmat
- Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
| | - V Alex Sotola
- Department of Genetics, University of Georgia, Athens, Georgia, 30602-7223, USA
| | - Chris C Nice
- Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
| | - Noland H Martin
- Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
- Director of the Population and Conservation Biology Program, Department of Biology, Texas State University, San Marcos, Texas, 78666-0202, USA
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19
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Blischak PD, Barker MS, Gutenkunst RN. Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks. Mol Ecol Resour 2021; 21:2676-2688. [PMID: 33682305 PMCID: PMC8675098 DOI: 10.1111/1755-0998.13355] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 01/26/2021] [Accepted: 02/05/2021] [Indexed: 11/30/2022]
Abstract
Inferring the frequency and mode of hybridization among closely related organisms is an important step for understanding the process of speciation and can help to uncover reticulated patterns of phylogeny more generally. Phylogenomic methods to test for the presence of hybridization come in many varieties and typically operate by leveraging expected patterns of genealogical discordance in the absence of hybridization. An important assumption made by these tests is that the data (genes or SNPs) are independent given the species tree. However, when the data are closely linked, it is especially important to consider their nonindependence. Recently, deep learning techniques such as convolutional neural networks (CNNs) have been used to perform population genetic inferences with linked SNPs coded as binary images. Here, we use CNNs for selecting among candidate hybridization scenarios using the tree topology (((P1 , P2 ), P3 ), Out) and a matrix of pairwise nucleotide divergence (dXY ) calculated in windows across the genome. Using coalescent simulations to train and independently test a neural network showed that our method, HyDe-CNN, was able to accurately perform model selection for hybridization scenarios across a wide breath of parameter space. We then used HyDe-CNN to test models of admixture in Heliconius butterflies, as well as comparing it to phylogeny-based introgression statistics. Given the flexibility of our approach, the dropping cost of long-read sequencing and the continued improvement of CNN architectures, we anticipate that inferences of hybridization using deep learning methods like ours will help researchers to better understand patterns of admixture in their study organisms.
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Affiliation(s)
- Paul D. Blischak
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Michael S. Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Ryan N. Gutenkunst
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, 85721, USA
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20
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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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21
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Mendes SL, Machado MP, Coelho MM, Sousa VC. Genomic data and multi-species demographic modelling uncover past hybridization between currently allopatric freshwater species. Heredity (Edinb) 2021; 127:401-412. [PMID: 34462578 PMCID: PMC8478877 DOI: 10.1038/s41437-021-00466-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023] Open
Abstract
Evidence for ancient interspecific gene flow through hybridization has been reported in many animal and plant taxa based on genetic markers. The study of genomic patterns of closely related species with allopatric distributions allows the assessment of the relative importance of vicariant isolating events and past gene flow. Here, we investigated the role of gene flow in the evolutionary history of four closely related freshwater fish species with currently allopatric distributions in western Iberian rivers-Squalius carolitertii, S. pyrenaicus, S. torgalensis and S. aradensis-using a population genomics dataset of 23,562 SNPs from 48 individuals, obtained through genotyping by sequencing (GBS). We uncovered a species tree with two well-differentiated clades: (i) S. carolitertii and S. pyrenaicus; and (ii) S. torgalensis and S. aradensis. By using D-statistics and demographic modelling based on the site frequency spectrum, comparing alternative demographic scenarios of hybrid origin, secondary contact and isolation, we found that the S. pyrenaicus North lineage is likely the result of an ancient hybridization event between S. carolitertii (contributing ~84%) and S. pyrenaicus South lineage (contributing ~16%), consistent with a hybrid speciation scenario. Furthermore, in the hybrid lineage, we identify outlier loci potentially affected by selection favouring genes from each parental lineage at different genomic regions. Our results suggest that ancient hybridization can affect speciation and that freshwater fish species currently in allopatry are useful to study these processes.
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Affiliation(s)
- Sofia L. Mendes
- grid.9983.b0000 0001 2181 4263cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Miguel P. Machado
- grid.9983.b0000 0001 2181 4263cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Maria M. Coelho
- grid.9983.b0000 0001 2181 4263cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Vitor C. Sousa
- grid.9983.b0000 0001 2181 4263cE3c—Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
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22
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Köhler M, Oakley LJ, Font F, Peñas MLL, Majure LC. On the continuum of evolution: a putative new hybrid speciation event in Opuntia (Cactaceae) between a native and an introduced species in southern South America. SYST BIODIVERS 2021. [DOI: 10.1080/14772000.2021.1967510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Matias Köhler
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
| | - Luis J. Oakley
- Cátedra de Botánica, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Santa Fe, Argentina
- Red List Authority Coordinator for the Temperate South American Plant Specialist Groups – International Union for Conservation of Nature (IUCN), Gland, Switzerland
| | - Fabián Font
- Herbario Museo de Farmacobotánica “Juan A. Domínguez” (BAF), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - M. Laura Las Peñas
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), Facultas de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba – CONICET, Córdoba, Argentina
| | - Lucas C. Majure
- University of Florida Herbarium (FLAS), Florida Museum of Natural History, Gainesville, FL, USA
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23
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Li M, Zheng Z, Liu J, Yang Y, Ren G, Ru D, Zhang S, Du X, Ma T, Milne R, Liu J. Evolutionary origin of a tetraploid Allium species on the Qinghai-Tibet Plateau. Mol Ecol 2021; 30:5780-5795. [PMID: 34487579 DOI: 10.1111/mec.16168] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 08/09/2021] [Accepted: 08/31/2021] [Indexed: 12/30/2022]
Abstract
Extinct taxa may be detectable if they were ancestors to extant hybrid species, which retain their genetic signature. In this study, we combined phylogenomics, population genetics and fluorescence in situ hybridization (GISH and FISH) analyses to trace the origin of the alpine tetraploid Allium tetraploideum (2n = 4x = 32), one of the five known members in the subgenus Cyathophora. We found that A. tetraploideum was an obvious allotetrapoploid derived from ancestors including at least two closely related diploid species, A. farreri and A. cyathophorum, from which it differs by multiple ecological and genomic attributes. However, these two species cannot account for the full genome of A. tetraploideum, indicating that at least one extinct diploid is also involved in its ancestry. Furthermore, A. tetraploideum appears to have arisen via homoploid hybrid speciation (HHS) from two extinct allotetraploid parents, which derived in turn from the aforementioned diploids. Other modes of origin were possible, but all were even more complex and involved additional extinct ancestors. Our study together highlights how some polyploid species might have very complex origins, involving both HHS and polyploid speciation and also extinct ancestors.
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Affiliation(s)
- Minjie Li
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Juncheng Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guangpeng Ren
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shangzhe Zhang
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Edinburgh, UK.,Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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24
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Morales-Cruz A, Aguirre-Liguori JA, Zhou Y, Minio A, Riaz S, Walker AM, Cantu D, Gaut BS. Introgression among North American wild grapes (Vitis) fuels biotic and abiotic adaptation. Genome Biol 2021; 22:254. [PMID: 34479604 PMCID: PMC8414701 DOI: 10.1186/s13059-021-02467-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/12/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Introgressive hybridization can reassort genetic variants into beneficial combinations, permitting adaptation to new ecological niches. To evaluate evolutionary patterns and dynamics that contribute to introgression, we investigate six wild Vitis species that are native to the Southwestern United States and useful for breeding grapevine (V. vinifera) rootstocks. RESULTS By creating a reference genome assembly from one wild species, V. arizonica, and by resequencing 130 accessions, we focus on identifying putatively introgressed regions (pIRs) between species. We find six species pairs with signals of introgression between them, comprising up to ~ 8% of the extant genome for some pairs. The pIRs tend to be gene poor, located in regions of high recombination and enriched for genes implicated in disease resistance functions. To assess potential pIR function, we explore SNP associations to bioclimatic variables and to bacterial levels after infection with the causative agent of Pierce's disease (Xylella fastidiosa). pIRs are enriched for SNPs associated with both climate and bacterial levels, suggesting that introgression is driven by adaptation to biotic and abiotic stressors. CONCLUSIONS Altogether, this study yields insights into the genomic extent of introgression, potential pressures that shape adaptive introgression, and the evolutionary history of economically important wild relatives of a critical crop.
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Affiliation(s)
- Abraham Morales-Cruz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | | | - Yongfeng Zhou
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
| | - Andrea Minio
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Summaira Riaz
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Andrew M. Walker
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, Davis, CA USA
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA USA
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25
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Mitchell N, Whitney KD. Limited evidence for a positive relationship between hybridization and diversification across seed plant families. Evolution 2021; 75:1966-1982. [PMID: 34156712 DOI: 10.1111/evo.14291] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 01/09/2023]
Abstract
Hybridization has experimental and observational ties to evolutionary processes and outcomes such as adaptation, speciation, and radiation. Although it has been hypothesized that hybridization and diversification are positively correlated, this idea remains largely untested empirically, and hybridization can also potentially reduce diversity. Here, we use a hybridization database on 170 seed plant families, life history information, and a time-calibrated phylogeny to test for phylogenetically-corrected associations between hybridization and diversification rates, while also taking into account life-history traits that may be correlated with both processes. We use three methods to estimate diversification rates and two metrics of hybridization. Although hybridization explains only a small amount of overall variation in diversification rates, we show that diversification and hybridization are sometimes positively correlated, although the effect sizes are very small. Moreover, the relationship remains detectable when incorporating the correlations between diversification and two other life history characteristics, perenniality and woodiness. We discuss potential mechanisms for this association under four different scenarios: hybridization may drive diversification, diversification may drive hybridization, both hybridization and diversification may jointly be driven by other factors, or, as an alternative, that there is in fact no relationship between the two. We suggest future studies to disentangle the causal structure.
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Affiliation(s)
- Nora Mitchell
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, 87131.,Department of Biology, University of Wisconsin - Eau Claire, Eau Claire, Wisconsin, 54701
| | - Kenneth D Whitney
- Department of Biology, University of New Mexico, Albuquerque, New Mexico, 87131
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26
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Goulet-Scott BE, Garner AG, Hopkins R. Genomic analyses overturn two long-standing homoploid hybrid speciation hypotheses. Evolution 2021; 75:1699-1710. [PMID: 34101168 DOI: 10.1111/evo.14279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/27/2021] [Accepted: 05/11/2021] [Indexed: 01/21/2023]
Abstract
The importance of hybridization in generating biological diversity has been historically controversial. Previously, inference about hybridization was limited by dependence on morphological data; with the advent of the next-generation sequencing tools for nonmodel organisms, the evolutionary significance of hybridization is more evident. Here, we test classic hypotheses of hybrid origins of two species in the Phlox pilosa complex. Morphological intermediacy motivated the hypotheses that Phlox amoena lighthipei and Phlox pilosa deamii were independent homoploid hybrid lineages derived from P. amoena amoena and P. pilosa pilosa. We use double-digest restriction site-associated DNA sequencing of individuals from throughout the range of these taxa to conduct the most thorough analysis of evolutionary history in this system to date. Surprisingly, we find no support for the hybrid origin of P. pilosa deamii or P. amoena lighthipei. Our data do identify a history of admixture in individuals collected at a contemporary hybrid zone between the putative parent lineages. We show that three very different evolutionary histories, only one of which involves hybrid origin, have produced intermediate or recombinant morphological traits between P. amoena amoena and P. pilosa pilosa. Although morphological data are still an efficient means of generating hypotheses about past gene flow, genomic data are now the standard of evidence for elucidating evolutionary history.
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Affiliation(s)
- Benjamin E Goulet-Scott
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Austin G Garner
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138.,Arnold Arboretum of Harvard University, Boston, Massachusetts, 02131
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27
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Stone BW, Wolfe AD. Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization. Mol Ecol 2021; 30:3826-3839. [PMID: 34013537 DOI: 10.1111/mec.15992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 12/26/2022]
Abstract
Quaternary glacial cycles often altered species' geographic distributions, which in turn altered the geographic structure of species' genetic diversity. In many cases, glacial expansion forced species in temperate climates to contract their ranges and reside in small pockets of suitable habitat (refugia), where they were likely to interact closely with other species, setting the stage for potential gene exchange. These introgression events, in turn, would have degraded species boundaries, making the inference of phylogenetic relationships challenging. Using high-throughput sequence data, we employed a combination of species distribution models and hybridization tests to assess the effect of glaciation on the geographic distributions, phylogenetic relationships, and patterns of gene flow of five species of Penstemon subgenus Dasanthera, long-lived shrubby angiosperms distributed throughout the Pacific Northwest of North America. Surprisingly, we found that rather than reducing their ranges to small refugia, most Penstemon subgenus Dasanthera species experienced increased suitable habitat during the Last Glacial Maximum relative to the present day. We also found substantial evidence for gene exchange between species, with the bulk of introgression events occurring in or near the Klamath Mountains of southwestern Oregon and northwestern California. Subsequently, our phylogenetic inference reveals blurred taxonomic boundaries in the Klamath Mountains, where introgression is most prevalent. Our results question the classical paradigm of temperate species' responses to glaciation and highlight the importance of contextualizing phylogenetic inference with species' histories of introgression.
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Affiliation(s)
- Benjamin W Stone
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Andrea D Wolfe
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
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Singhal S, Roddy AB, DiVittorio C, Sanchez-Amaya A, Henriquez CL, Brodersen CR, Fehlberg S, Zapata F. Diversification, disparification and hybridization in the desert shrubs Encelia. THE NEW PHYTOLOGIST 2021; 230:1228-1241. [PMID: 33460447 DOI: 10.1111/nph.17212] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/10/2021] [Indexed: 05/28/2023]
Abstract
There are multiple hypotheses for the spectacular plant diversity found in deserts. We explore how different factors, including the roles of ecological opportunity and selection, promote diversification and disparification in Encelia, a lineage of woody plants in the deserts of the Americas. Using a nearly complete species-level phylogeny based on double-digest restriction-aided sequencing along with a broad set of phenotypic traits, we estimate divergence times and diversification rates, identify instances of hybridization, quantify trait disparity and assess phenotypic divergence across environmental gradients. We show that Encelia originated and diversified recently (mid-Pleistocene) and rapidly, with rates comparable to notable adaptive radiations in plants. Encelia probably originated in the hot deserts of North America, with subsequent diversification across steep environmental gradients. We uncover multiple instances of gene flow between species. The radiation of Encelia is characterized by fast rates of phenotypic evolution, trait lability and extreme disparity across environments and between species pairs with overlapping geographic ranges. Encelia exemplifies how interspecific gene flow in combination with high trait lability can enable exceptionally fast diversification and disparification across steep environmental gradients.
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Affiliation(s)
- Sonal Singhal
- Department of Biology, CSU Dominguez Hills, 1000 E Victoria Street, Carson, CA, 90747, USA
| | - Adam B Roddy
- Institute of Environment, Department of Biological Sciences, Florida International University, Miami, FL, 33133, USA
| | - Christopher DiVittorio
- University of California Institute for México and the United States, University of California, 3324 Olmsted Hall, Riverside, CA, 92521, USA
- Pinecrest Research Corporation, 5627 Telegraph Avenue, Suite 420, Oakland, CA, 94609, USA
| | - Ary Sanchez-Amaya
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Dr. South, Los Angeles, CA, 90095, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Dr. South, Los Angeles, CA, 90095, USA
| | - Craig R Brodersen
- School of the Environment, Yale University, New Haven, CT, 06511, USA
| | - Shannon Fehlberg
- Research, Conservation, and Collections, Desert Botanical Garden, 1201 N Galvin Parkway, Phoenix, AZ, 85008, USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, 612 Charles E. Young Dr. South, Los Angeles, CA, 90095, USA
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29
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Discovery of a dune‐building hybrid beachgrass (
Ammophila arenaria
×
A. breviligulata
) in the U.S. Pacific Northwest. Ecosphere 2021. [DOI: 10.1002/ecs2.3501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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30
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Wood AW, Duda TF. Reticulate evolution in Conidae: Evidence of nuclear and mitochondrial introgression. Mol Phylogenet Evol 2021; 161:107182. [PMID: 33892099 DOI: 10.1016/j.ympev.2021.107182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/07/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
Conidae is a hyperdiverse family of marine snails that has many hallmarks of adaptive radiation. Hybridization and introgression may contribute to such instances of rapid diversification by generating novel gene combinations that facilitate exploitation of distinct niches. Here we evaluated whether or not these mechanisms may have contributed to the evolutionary history of a subgenus of Conidae (Virroconus). Several observations hint at evidence of past introgression for members of this group, including incongruence between phylogenetic relationships inferred from mitochondrial gene sequences and morphology and widespread sympatry of many Virroconus species in the Indo-West Pacific. We generated and analyzed transcriptome data of Virroconus species to (i) infer a robust nuclear phylogeny, (ii) assess mitochondrial and nuclear gene tree discordance, and (iii) formally test for introgression of nuclear loci. We identified introgression of mitochondrial genomes and nuclear gene regions between ancestors of one pair of Virroconus species, and mitochondrial introgression between another pair. We also found evidence of adaptive introgression of conotoxin venom loci between a third pair of species. Together, our results demonstrate that hybridization and introgression impacted the evolutionary history of Virroconus and hence may have contributed to the adaptive radiation of Conidae.
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Affiliation(s)
- Andrew W Wood
- University of Michigan, Department of Ecology & Evolutionary Biology, 1105 North University Avenue, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA.
| | - Thomas F Duda
- University of Michigan, Department of Ecology & Evolutionary Biology, 1105 North University Avenue, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA.
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31
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Chen D, Yan PC, Guo YP. Imprints of independent allopolyploid formations on patterns of gene expression in two sibling yarrow species (Achillea, Asteraceae). BMC Genomics 2021; 22:264. [PMID: 33849436 PMCID: PMC8045213 DOI: 10.1186/s12864-021-07566-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 03/30/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polyploid species often originate recurrently. While this is well known, there is little information on the extent to which distinct allotetraploid species formed from the same parent species differ in gene expression. The tetraploid yarrow species Achillea alpina and A. wilsoniana arose independently from allopolyploidization between diploid A. acuminata and A. asiatica. The genetics and geography of these origins are clear from previous studies, providing a solid basis for comparing gene expression patterns of sibling allopolyploid species that arose independently. RESULTS We conducted comparative RNA-sequencing analyses on the two Achillea tetraploid species and their diploid progenitors to evaluate: 1) species-specific gene expression and coexpression across the four species; 2) patterns of inheritance of parental gene expression; 3) parental contributions to gene expression in the allotetraploid species, and homeolog expression bias. Diploid A. asiatica showed a higher contribution than diploid A. acuminata to the transcriptomes of both tetraploids and also greater homeolog bias in these transcriptomes, possibly reflecting a maternal effect. Comparing expressed genes in the two allotetraploids, we found expression of ca. 30% genes were species-specific in each, which were most enriched for GO terms pertaining to "defense response". Despite species-specific and differentially expressed genes between the two allotetraploids, they display similar transcriptome changes in comparison to their diploid progenitors. CONCLUSION Two independently originated Achillea allotetraploid species exhibited difference in gene expression, some of which must be related to differential adaptation during their post-speciation evolution. On the other hand, they showed similar expression profiles when compared to their progenitors. This similarity might be expected when pairs of merged diploid genomes in tetraploids are similar, as is the case in these two particular allotetraploids.
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Affiliation(s)
- Duo Chen
- Key Laboratory of Biodiversity Science and Ecological Engineering of the Ministry of Education, and College of Life Sciences, Beijing Normal University, Beijing, China
| | - Peng-Cheng Yan
- Beijing Tangtang Tianxia Biotechnology Co., Ltd, Beijing, China
| | - Yan-Ping Guo
- Key Laboratory of Biodiversity Science and Ecological Engineering of the Ministry of Education, and College of Life Sciences, Beijing Normal University, Beijing, China.
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32
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Hirashiki C, Kareiva P, Marvier M. Concern over hybridization risks should not preclude conservation interventions. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.424] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Claire Hirashiki
- Institute of the Environment and Sustainability University of California, Los Angeles Los Angeles California USA
| | | | - Michelle Marvier
- Department of Environmental Studies and Sciences Santa Clara University Santa Clara California USA
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33
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Bird KA, Niederhuth CE, Ou S, Gehan M, Pires JC, Xiong Z, VanBuren R, Edger PP. Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus. THE NEW PHYTOLOGIST 2021; 230:354-371. [PMID: 33280122 PMCID: PMC7986222 DOI: 10.1111/nph.17137] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 11/30/2020] [Indexed: 05/03/2023]
Abstract
Allopolyploidisation merges evolutionarily distinct parental genomes (subgenomes) into a single nucleus. A frequent observation is that one subgenome is 'dominant' over the other subgenome, often being more highly expressed. Here, we 'replayed the evolutionary tape' with six isogenic resynthesised Brassica napus allopolyploid lines and investigated subgenome dominance patterns over the first 10 generations postpolyploidisation. We found that the same subgenome was consistently more dominantly expressed in all lines and generations and that >70% of biased gene pairs showed the same dominance patterns across all lines and an in silico hybrid of the parents. Gene network analyses indicated an enrichment for network interactions and several biological functions for the Brassica oleracea subgenome biased pairs, but no enrichment was identified for Brassica rapa subgenome biased pairs. Furthermore, DNA methylation differences between subgenomes mirrored the observed gene expression bias towards the dominant subgenome in all lines and generations. Many of these differences in gene expression and methylation were also found when comparing the progenitor genomes, suggesting that subgenome dominance is partly related to parental genome differences rather than just a byproduct of allopolyploidisation. These findings demonstrate that 'replaying the evolutionary tape' in an allopolyploid results in largely repeatable and predictable subgenome expression dominance patterns.
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Affiliation(s)
- Kevin A. Bird
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
- Ecology, Evolutionary Biology and BehaviorMichigan State UniversityEast LansingMI48824USA
| | - Chad E. Niederhuth
- Department of Plant BiologyMichigan State UniversityEast LansingMI48824USA
| | - Shujun Ou
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIA50011USA
| | - Malia Gehan
- Donald Danforth Plant Science CenterSt LouisMO63123USA
| | - J. Chris Pires
- Division of Biological SciencesUniversity of MissouriColumbiaMO65211USA
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop BiotechnologyInner Mongolia UniversityHohhot010070China
| | - Robert VanBuren
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
- Plant Resilience InstituteMichigan State UniversityEast LansingMI48824USA
| | - Patrick P. Edger
- Department of HorticultureMichigan State UniversityEast LansingMI48824USA
- Ecology, Evolutionary Biology and BehaviorMichigan State UniversityEast LansingMI48824USA
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34
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Fabritzek AG, Griebeler EM, Kadereit JW. Hybridization, ecogeographical displacement and the emergence of new lineages - A genotyping-by-sequencing and ecological niche and species distribution modelling study of Sempervivum tectorum L. (Houseleek). J Evol Biol 2021; 34:830-844. [PMID: 33714223 DOI: 10.1111/jeb.13784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/18/2021] [Accepted: 03/03/2021] [Indexed: 11/28/2022]
Abstract
Ecogeographical displacement of homoploid hybrid lineages from their parents is well documented and considered an important mechanism to achieve reproductive isolation. In this study, we investigated the origin of the flowering plant species Sempervivum tectorum in the Massif Central (France) through homoploid hybridization between lineages of the species from the Rhine Gorge area (Germany) and the Pyrenees (France). We used genotyping-by-sequencing genetic data as evidence for the hybrid origin of the Massif Central lineage, and WorldClim climatic data and soil pH and soil temperature data collected by us for ecological niche and species distribution modelling. We could show that the Massif Central lineage shows hybrid admixture and that the niche of this lineage is significantly different from those of the parental lineages. In comparison with the parental niches, different variables of the niche of the hybrid lineage are intermediate, parental-combined or extreme. The different niche of the Massif Central populations thus can plausibly be interpreted as hybridization-derived. Our species distribution modelling for the Last Glacial Maximum and Mid-Holocene showed that the potential distribution of the hybrid lineage at the likely time of its origin in the Quaternary possibly was parapatric in relation to the largely sympatric distributions of the parental lineages. We hypothesize that reproductive isolation of the hybrid lineage from the parental lineages resulted from the segregation of distribution ranges by a differential response of the three lineages to a warming climate.
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Affiliation(s)
- Armin G Fabritzek
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Eva Maria Griebeler
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Joachim W Kadereit
- Institut für Organismische und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
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35
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Spengler RN, Petraglia M, Roberts P, Ashastina K, Kistler L, Mueller NG, Boivin N. Exaptation Traits for Megafaunal Mutualisms as a Factor in Plant Domestication. FRONTIERS IN PLANT SCIENCE 2021; 12:649394. [PMID: 33841476 PMCID: PMC8024633 DOI: 10.3389/fpls.2021.649394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/25/2021] [Indexed: 05/26/2023]
Abstract
Megafaunal extinctions are recurring events that cause evolutionary ripples, as cascades of secondary extinctions and shifting selective pressures reshape ecosystems. Megafaunal browsers and grazers are major ecosystem engineers, they: keep woody vegetation suppressed; are nitrogen cyclers; and serve as seed dispersers. Most angiosperms possess sets of physiological traits that allow for the fixation of mutualisms with megafauna; some of these traits appear to serve as exaptation (preadaptation) features for farming. As an easily recognized example, fleshy fruits are, an exaptation to agriculture, as they evolved to recruit a non-human disperser. We hypothesize that the traits of rapid annual growth, self-compatibility, heavy investment in reproduction, high plasticity (wide reaction norms), and rapid evolvability were part of an adaptive syndrome for megafaunal seed dispersal. We review the evolutionary importance that megafauna had for crop and weed progenitors and discuss possible ramifications of their extinction on: (1) seed dispersal; (2) population dynamics; and (3) habitat loss. Humans replaced some of the ecological services that had been lost as a result of late Quaternary extinctions and drove rapid evolutionary change resulting in domestication.
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Affiliation(s)
- Robert N. Spengler
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kseniia Ashastina
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Logan Kistler
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
| | - Natalie G. Mueller
- Department of Archaeology, Washington University in St. Louis, St. Louis, MO, United States
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, DC, United States
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada
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36
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Moore AJ, Messick JA, Kadereit JW. Range and niche expansion through multiple interspecific hybridization: a genotyping by sequencing analysis of Cherleria (Caryophyllaceae). BMC Ecol Evol 2021; 21:40. [PMID: 33691632 PMCID: PMC7945309 DOI: 10.1186/s12862-020-01721-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 11/10/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Cherleria (Caryophyllaceae) is a circumboreal genus that also occurs in the high mountains of the northern hemisphere. In this study, we focus on a clade that diversified in the European High Mountains, which was identified using nuclear ribosomal (nrDNA) sequence data in a previous study. With the nrDNA data, all but one species was monophyletic, with little sequence variation within most species. Here, we use genotyping by sequencing (GBS) data to determine whether the nrDNA data showed the full picture of the evolution in the genomes of these species. RESULTS The overall relationships found with the GBS data were congruent with those from the nrDNA study. Most of the species were still monophyletic and many of the same subclades were recovered, including a clade of three narrow endemic species from Greece and a clade of largely calcifuge species. The GBS data provided additional resolution within the two species with the best sampling, C. langii and C. laricifolia, with structure that was congruent with geography. In addition, the GBS data showed significant hybridization between several species, including species whose ranges did not currently overlap. CONCLUSIONS The hybridization led us to hypothesize that lineages came in contact on the Balkan Peninsula after they diverged, even when those lineages are no longer present on the Balkan Peninsula. Hybridization may also have helped lineages expand their niches to colonize new substrates and different areas. Not only do genome-wide data provide increased phylogenetic resolution of difficult nodes, they also give evidence for a more complex evolutionary history than what can be depicted by a simple, branching phylogeny.
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Affiliation(s)
- Abigail J. Moore
- Department of Microbiology and Plant Biology and Oklahoma Biological Survey, University of Oklahoma, 770 Van Vleet Oval, Norman, OK 73019 USA
| | - Jennifer A. Messick
- Department of Biology, University of Central Oklahoma, Howell Hall, Room 220, Edmond, OK 73034 USA
| | - Joachim W. Kadereit
- Fachbereich Biologie, Institut Für Organismische Und Molekulare Evolutionsbiologie, Johannes Gutenberg-Universität Mainz, Anselm-Franz-von-Bentzel-Weg 9a, 55099 Mainz, Germany
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Menon M, Bagley JC, Page GFM, Whipple AV, Schoettle AW, Still CJ, Wehenkel C, Waring KM, Flores-Renteria L, Cushman SA, Eckert AJ. Adaptive evolution in a conifer hybrid zone is driven by a mosaic of recently introgressed and background genetic variants. Commun Biol 2021; 4:160. [PMID: 33547394 PMCID: PMC7864969 DOI: 10.1038/s42003-020-01632-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 11/18/2020] [Indexed: 01/30/2023] Open
Abstract
Extant conifer species may be susceptible to rapid environmental change owing to their long generation times, but could also be resilient due to high levels of standing genetic diversity. Hybridisation between closely related species can increase genetic diversity and generate novel allelic combinations capable of fuelling adaptive evolution. Our study unravelled the genetic architecture of adaptive evolution in a conifer hybrid zone formed between Pinus strobiformis and P. flexilis. Using a multifaceted approach emphasising the spatial and environmental patterns of linkage disequilibrium and ancestry enrichment, we identified recently introgressed and background genetic variants to be driving adaptive evolution along different environmental gradients. Specifically, recently introgressed variants from P. flexilis were favoured along freeze-related environmental gradients, while background variants were favoured along water availability-related gradients. We posit that such mosaics of allelic variants within conifer hybrid zones will confer upon them greater resilience to ongoing and future environmental change and can be a key resource for conservation efforts.
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Affiliation(s)
- Mitra Menon
- grid.27860.3b0000 0004 1936 9684Department of Evolution and Ecology, University of California, Davis, CA USA
| | - Justin C. Bagley
- grid.257992.20000 0001 0019 1845Department of Biology, Jacksonville State University, Jacksonville, AL USA
| | - Gerald F. M. Page
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Amy V. Whipple
- grid.261120.60000 0004 1936 8040Department of Biological Sciences and Merriam Powel Center for Environmental Research, Northern Arizona University, Flagstaff, AZ USA
| | - Anna W. Schoettle
- grid.497401.f0000 0001 2286 5230Rocky Mountain Research Station, USDA Forest Service, Fort Collins, CO USA
| | - Christopher J. Still
- grid.4391.f0000 0001 2112 1969Forest Ecosystems and Society, Oregon State University, Corvallis, OR USA
| | - Christian Wehenkel
- grid.412198.70000 0000 8724 8383Instituto de Silvicultura e Industria de la Madera, Universidad Juarez del Estado de Durango, Durango, Mexico
| | - Kristen M. Waring
- grid.261120.60000 0004 1936 8040School of Forestry, Northern Arizona University, Flagstaff, AZ USA
| | - Lluvia Flores-Renteria
- grid.263081.e0000 0001 0790 1491Department of Biology, San Diego State University, San Diego, CA USA
| | - Samuel A. Cushman
- grid.472551.00000 0004 0404 3120Rocky Mountain Research Station, USDA Forest Service, Flagstaff, AZ USA
| | - Andrew J. Eckert
- grid.224260.00000 0004 0458 8737Department of Biology, Virginia Commonwealth University, Richmond, VA USA
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Conservation in the face of hybridisation: genome-wide study to evaluate taxonomic delimitation and conservation status of a threatened orchid species. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01325-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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39
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Hudson CM, Lucek K, Marques DA, Alexander TJ, Moosmann M, Spaak P, Seehausen O, Matthews B. Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.611672] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.
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Nge FJ, Biffin E, Thiele KR, Waycott M. Reticulate Evolution, Ancient Chloroplast Haplotypes, and Rapid Radiation of the Australian Plant Genus Adenanthos (Proteaceae). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.616741] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cytonuclear discordance, commonly detected in phylogenetic studies, is often attributed to hybridization and/or incomplete lineage sorting (ILS). New sequencing technologies and analytical approaches can provide new insights into the relative importance of these processes. Hybridization has previously been reported in the Australian endemic plant genus Adenanthos (Proteaceae). Like many Australian genera, Adenanthos is of relatively ancient origin, and provides an opportunity to examine long-term evolutionary consequences of gene flow between lineages. Using a hybrid capture approach, we assembled densely sampled low-copy nuclear and plastid DNA sequences for Adenanthos, inferred its evolutionary history, and used a Bayesian posterior predictive approach and coalescent simulations to assess relative contributions of hybridization and ILS to cytonuclear discordance. Our analyses indicate that strong incongruence detected between our plastid and nuclear phylogenies is not only the result of ILS, but also results from extensive ancient introgression as well as recent chloroplast capture and introgression between extant Adenanthos species. The deep reticulation was also detected from long-persisting chloroplast haplotypes shared between evolutionarily distant species. These haplotypes may have persisted for over 12 Ma in localized populations across southwest Western Australia, indicating that the region is not only an important area for old endemic lineages and accumulation of species, but is also characterized by persistence of high genetic diversity. Deep introgression in Adenanthos coincided with the rapid radiation of the genus during the Miocene, a time when many Australian temperate plant groups radiated in response to large-scale climatic change. This study suggests that ancient introgression may play an important role in the evolution of the Australian flora more broadly.
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Natural hybridization between pen shell species: Pinna rudis and the critically endangered Pinna nobilis may explain parasite resistance in P. nobilis. Mol Biol Rep 2021; 48:997-1004. [PMID: 33394229 DOI: 10.1007/s11033-020-06063-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/03/2020] [Indexed: 10/22/2022]
Abstract
Recently, Pinna nobilis pen shells population in Mediterranean Sea has plummeted due to a Mass Mortality Event caused by an haplosporidian parasite. In consequence, this bivalve species has been included in the IUCN Red List as "Critically Endangered". In the current scenario, several works are in progress to protect P. nobilis from extinction, being identification of hybrids (P. nobilis x P. rudis) among survivors extremely important for the conservation of the species.Morphological characteristics and molecular analyses were used to identify putative hybrids. A total of 10 individuals of each species (P. nobilis and P. rudis) and 3 doubtful individuals were considered in this study. The putative hybrids showed shell morphology and mantle coloration intermingled exhibiting both P. nobilis and P. rudis traits. Moreover, the analyses of 1150 bp of the 28S gene showed 9 diagnostic sites between P. rudis and P. nobilis, whereas hybrids showed both parental diagnostic alleles at the diagnostic loci. Regarding the multilocus genotypes from the 8 microsatellite markers, the segregation of two Pinna species was clearly detected on the PCoA plot and the 3 hybrids showed intermediate positions.This is the first study evidencing the existence of hybrids P. nobilis x P. rudis, providing molecular methodology for a proper identification of new hybrids. Further studies testing systematically all parasite-resisting isolated P. nobilis should be undertaken to determine if the resistance is resulting from introgression of P. rudis into P. nobilis genome and identifying aspects related to resistance.
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Rutherford S, Wan JSH, Cohen JM, Benson D, Rossetto M. Looks can be deceiving: speciation dynamics of co-distributed Angophora (Myrtaceae) species in a varying landscape. Evolution 2020; 75:310-329. [PMID: 33325041 DOI: 10.1111/evo.14140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/05/2020] [Accepted: 11/24/2020] [Indexed: 11/30/2022]
Abstract
Understanding the mechanisms underlying species divergence remains a central goal in evolutionary biology. Landscape genetics can be a powerful tool for examining evolutionary processes. We used genome-wide scans to genotype samples from populations of eight Angophora species. Angophora is a small genus within the eucalypts comprising common and rare species in a heterogeneous landscape, making it an appropriate group to study speciation. We found A. hispida was highly differentiated from the other species. Two subspecies of A. costata (subsp. costata and subsp. euryphylla) formed a group, while the third (subsp. leiocarpa, which is only distinguished by its smooth fruits and provenance) was supported as a distinct pseudocryptic species. Other species that are morphologically distinct could not be genetically differentiated (e.g., A. floribunda and A. subvelutina). Distribution and genetic differentiation within Angophora were strongly influenced by temperature and humidity, as well as biogeographic barriers, particularly rivers and higher elevation regions. While extensive introgression was found between many populations of some species (e.g., A. bakeri and A. floribunda), others only hybridized at certain locations. Overall, our findings suggest multiple mechanisms drove evolutionary diversification in Angophora and highlight how genome-wide analyses of related species in a diverse landscape can provide insights into speciation.
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Affiliation(s)
- Susan Rutherford
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China.,Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Justin S H Wan
- Institute of Environment and Ecology, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, China.,Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Joel M Cohen
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Doug Benson
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
| | - Maurizio Rossetto
- Research Centre for Ecosystem Resilience, Australian Institute of Botanic Science, Sydney, Australia
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Vila-Viçosa C, Gonçalves J, Honrado J, Lomba Â, Almeida RS, Vázquez FM, Garcia C. Late Quaternary range shifts of marcescent oaks unveil the dynamics of a major biogeographic transition in southern Europe. Sci Rep 2020; 10:21598. [PMID: 33298997 PMCID: PMC7726089 DOI: 10.1038/s41598-020-78576-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 11/26/2020] [Indexed: 11/09/2022] Open
Abstract
Marcescent forests are ecotones distributed across southern Europe that host increased levels of biodiversity but their persistence is threatened by global change. Here we study the range dynamics of these forests in the Iberian Peninsula (IP) during the Late Quaternary, a period of profound climate and anthropic changes. We modeled and compared the distribution of eight oak taxa for the present and two paleoclimatic environments, the Last Glacial Maximum (LGM, ~ 21 kya) and the Mid-Holocene (MH, ~ 6 kya). Presence records were combined with bioclimatic and topographic data in an ensemble modelling framework to obtain spatial projections for present and past conditions across taxa. Substantial distribution shifts were projected between the three studied periods, that were explained by precipitation, winter cold and terrain ruggedness. Results were congruent with paleoclimatic records of the IP and showed that range shifts of these contact zones concurred with range dynamics of both Submediterranean and Temperate oaks. Notably, the distribution ranges of hybrid oaks and marcescent forests matched throughout the late Quaternary. This study contributes to unveil the complex Late-Quaternary biogeography of the ecotone belt occupied by marcescent forests and, more broadly, of Mediterranean oaks. Improved knowledge of species' responses to climate dynamics will allow us to anticipate and manage future range shifts driven by climate change.
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Affiliation(s)
- Carlos Vila-Viçosa
- CIBIO (Research Center in Biodiversity and Genetic Resources) - InBIO (Research Network in Biodiversity and Evolutionary Biology), University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal. .,MHNC-UP - Museum of Natural History and Science of the University of Porto - PO Herbarium, University of Porto, Praça Gomes Teixeira, 4099-002, Porto, Portugal. .,Biology Department, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, s/n, 4169-007, Porto, Portugal.
| | - João Gonçalves
- CIBIO (Research Center in Biodiversity and Genetic Resources) - InBIO (Research Network in Biodiversity and Evolutionary Biology), University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - João Honrado
- CIBIO (Research Center in Biodiversity and Genetic Resources) - InBIO (Research Network in Biodiversity and Evolutionary Biology), University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Biology Department, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Ângela Lomba
- CIBIO (Research Center in Biodiversity and Genetic Resources) - InBIO (Research Network in Biodiversity and Evolutionary Biology), University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal
| | - Rubim S Almeida
- CIBIO (Research Center in Biodiversity and Genetic Resources) - InBIO (Research Network in Biodiversity and Evolutionary Biology), University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,MHNC-UP - Museum of Natural History and Science of the University of Porto - PO Herbarium, University of Porto, Praça Gomes Teixeira, 4099-002, Porto, Portugal.,Biology Department, Faculty of Sciences, University of Porto, Rua Do Campo Alegre, s/n, 4169-007, Porto, Portugal
| | - Francisco Maria Vázquez
- Agricultural Research Centre, Finca La Orden, Valdesequera, CICYTEX - Centro de Investigaciones Científicas Y Tecnológicas de Extremadura, Ctra. A-V, Km 372, 06187, Guadajira, Badajoz, Spain
| | - Cristina Garcia
- CIBIO (Research Center in Biodiversity and Genetic Resources) - InBIO (Research Network in Biodiversity and Evolutionary Biology), University of Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-661, Vairão, Portugal.,Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology (IIB), University of Liverpool, Bioscience Building, Liverpool, L69 7ZB, UK
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Combining Satellite Remote Sensing and Climate Data in Species Distribution Models to Improve the Conservation of Iberian White Oaks (Quercus L.). ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION 2020. [DOI: 10.3390/ijgi9120735] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Iberian Peninsula hosts a high diversity of oak species, being a hot-spot for the conservation of European White Oaks (Quercus) due to their environmental heterogeneity and its critical role as a phylogeographic refugium. Identifying and ranking the drivers that shape the distribution of White Oaks in Iberia requires that environmental variables operating at distinct scales are considered. These include climate, but also ecosystem functioning attributes (EFAs) related to energy–matter exchanges that characterize land cover types under various environmental settings, at finer scales. Here, we used satellite-based EFAs and climate variables in species distribution models (SDMs) to assess how variables related to ecosystem functioning improve our understanding of current distributions and the identification of suitable areas for White Oak species in Iberia. We developed consensus ensemble SDMs targeting a set of thirteen oaks, including both narrow endemic and widespread taxa. Models combining EFAs and climate variables obtained a higher performance and predictive ability (true-skill statistic (TSS): 0.88, sensitivity: 99.6, specificity: 96.3), in comparison to the climate-only models (TSS: 0.86, sens.: 96.1, spec.: 90.3) and EFA-only models (TSS: 0.73, sens.: 91.2, spec.: 82.1). Overall, narrow endemic species obtained higher predictive performance using combined models (TSS: 0.96, sens.: 99.6, spec.: 96.3) in comparison to widespread oaks (TSS: 0.80, sens.: 92.6, spec.: 87.7). The Iberian White Oaks show a high dependence on precipitation and the inter-quartile range of Normalized Difference Water Index (NDWI) (i.e., seasonal water availability) which appears to be the most important EFA variable. Spatial projections of climate–EFA combined models contribute to identify the major diversity hotspots for White Oaks in Iberia, holding higher values of cumulative habitat suitability and species richness. We discuss the implications of these findings for guiding the long-term conservation of Iberian White Oaks and provide spatially explicit geospatial information about each oak species (or set of species) relevant for developing biogeographic conservation frameworks.
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Folk RA, Siniscalchi CM, Soltis DE. Angiosperms at the edge: Extremity, diversity, and phylogeny. PLANT, CELL & ENVIRONMENT 2020; 43:2871-2893. [PMID: 32926444 DOI: 10.1111/pce.13887] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/21/2020] [Accepted: 08/13/2020] [Indexed: 05/26/2023]
Abstract
A hallmark of flowering plants is their ability to invade some of the most extreme and dynamic habitats, including cold and dry biomes, to a far greater extent than other land plants. Recent work has provided insight to the phylogenetic distribution and evolutionary mechanisms which have enabled this success, yet needed is a synthesis of evolutionary perspectives with plant physiological traits, morphology, and genomic diversity. Linking these disparate components will not only lead to better understand the evolutionary parallelism and diversification of plants with these two strategies, but also to provide the framework needed for directing future research. We summarize the primary physiological and structural traits involved in response to cold- and drought stress, outline the phylogenetic distribution of these adaptations, and describe the recurring association of these changes with rapid diversification events that occurred in multiple lineages over the past 15 million years. Across these threefold facets of dry-cold correlation (traits, phylogeny, and time) we stress the contrast between (a) the amazing diversity of solutions flowering plants have developed in the face of extreme environments and (b) a broad correlation between cold and dry adaptations that in some cases may hint at deep common origins.
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Affiliation(s)
- Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Carolina M Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, Mississippi, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
- Biodiversity Institute, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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46
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Parker VT, Rodriguez CY, Wechsler G, Vasey MC. Allopatry, hybridization, and reproductive isolation in Arctostaphylos. AMERICAN JOURNAL OF BOTANY 2020; 107:1798-1814. [PMID: 33274449 DOI: 10.1002/ajb2.1576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/09/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Hybridization plays a key role in introgressive adaptation, speciation, and adaptive radiation as a source of evolutionary innovation. Hybridization is considered common in Arctostaphylos, yet species boundaries are retained in stands containing multiple species. Arctostaphylos contains diploids and tetraploids, and recent phylogenies indicate two clades; we hypothesize combinations of these traits limit or promote hybridization rates. METHODS We statistically analyzed co-occurrence patterns of species by clade membership and ploidy level from 87 random 0.1 ha plots. We sampled multiple sites to analyze for percent hybridization based on morphology. Finally, phenophases were analyzed by scoring herbarium sheets for a large number of taxa from both clades as well as tetraploids, and second, surveying three field sites over two years for divergence in phenological stages between co-occurring taxa. RESULTS Most taxa in Arctostaphylos are allopatric relative to other congenerics. When two taxa co-occur, the patterns are a diploid with a tetraploid, or two diploids from different clades. When three taxa co-occur, the pattern is two diploids from different clades and a tetraploid. Field and herbarium data both indicate flowering phenology is displaced between diploids from the two clades; one of the diploid clades and tetraploids overlap considerably. CONCLUSIONS The two deep clades in Arctostaphylos are genetically distant, with hybrids rare or non-existent when taxa co-occur. Reproductive isolation between clades is enhanced by displaced flowering phenology for co-occurring species. Within clades, taxa appear to have few reproductive barriers other than an allopatric distribution or different ploidy levels.
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Affiliation(s)
- V Thomas Parker
- Department of Biology, San Francisco State University, San Francisco, California, 94132, USA
| | - Christina Y Rodriguez
- Department of Biology, San Francisco State University, San Francisco, California, 94132, USA
| | - Gail Wechsler
- Department of Biology, San Francisco State University, San Francisco, California, 94132, USA
| | - Michael C Vasey
- Department of Biology, San Francisco State University, San Francisco, California, 94132, USA
- San Francisco Bay National Estuarine Research Reserve, Estuary & Ocean Science Center, San Francisco State University, Romberg Tiburon Campus, 3150 Paradise Drive, Tiburon, California, 94920, USA
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Coppi A, Baker AJM, Bettarini I, Colzi I, Echevarria G, Pazzagli L, Gonnelli C, Selvi F. Population Genetics of Odontarrhena (Brassicaceae) from Albania: The Effects of Anthropic Habitat Disturbance, Soil, and Altitude on a Ni-Hyperaccumulator Plant Group from a Major Serpentine Hotspot. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1686. [PMID: 33271845 PMCID: PMC7759883 DOI: 10.3390/plants9121686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 11/22/2022]
Abstract
Albanian taxa and populations of the genus Odontarrhena are most promising candidates for research on metal tolerance and Ni-agromining, but their genetic structure remains unknown. We investigated phylogenetic relationships and genetic differentiation in relation to distribution and ploidy of the taxa, anthropic site disturbance, elevation, soil type, and trace metals at each population site. After performing DNA sequencing of selected accessions, we applied DNA-fingerprinting to analyze the genetic structure of 32 populations from ultramafic and non-ultramafic outcrops across Albania. Low sequence divergence resulted in poorly resolved phylograms, but supported affinity between the two diploid serpentine endemics O. moravensis and O. rigida. Analysis of molecular variance (AMOVA) revealed significant population differentiation, but no isolation by distance. Among-population variation was higher in polyploids than in diploids, in which genetic distances were lower. Genetic admixing at population and individual level occurred especially in the polyploids O. chalcidica, O. decipiens, and O. smolikana. Admixing increased with site disturbance. Outlier loci were higher in serpentine populations but decreased along altitude with lower drought and heat stress. Genetic variability gained by gene flow and hybridization at contact zones with "resident" species of primary ultramafic habitats promoted expansion of the tetraploid O. chalcidica across anthropogenic sites.
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Affiliation(s)
- Andrea Coppi
- Department of Biology, University of Firenze, 50121 Firenze, Italy;
| | - Alan J. M. Baker
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane QLD 4072, Australia; (A.J.M.B.); (G.E.)
- Laboratoire Sols et Environnement, Université de Lorraine/INRA, F-54000 Vandoeuvre-lès-Nancy, France
| | - Isabella Bettarini
- Department of Biomedical Experimental and Clinical Sciences, University of Firenze, 50121 Firenze, Italy; (I.B.); (L.P.)
| | - Ilaria Colzi
- Department of Biology, University of Firenze, 50121 Firenze, Italy;
| | - Guillaume Echevarria
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, Brisbane QLD 4072, Australia; (A.J.M.B.); (G.E.)
- Laboratoire Sols et Environnement, Université de Lorraine/INRA, F-54000 Vandoeuvre-lès-Nancy, France
| | - Luigia Pazzagli
- Department of Biomedical Experimental and Clinical Sciences, University of Firenze, 50121 Firenze, Italy; (I.B.); (L.P.)
| | | | - Federico Selvi
- Department of Agriculture, Food, Environment and Forestry, Laboratories of Botany, 50121 Firenze, Italy;
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Wagner MR, Roberts JH, Balint-Kurti P, Holland JB. Heterosis of leaf and rhizosphere microbiomes in field-grown maize. THE NEW PHYTOLOGIST 2020; 228:1055-1069. [PMID: 32521050 DOI: 10.1111/nph.16730] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/28/2020] [Indexed: 05/21/2023]
Abstract
Macroorganisms' genotypes shape their phenotypes, which in turn shape the habitat available to potential microbial symbionts. This influence of host genotype on microbiome composition has been demonstrated in many systems; however, most previous studies have either compared unrelated genotypes or delved into molecular mechanisms. As a result, it is currently unclear whether the heritability of host-associated microbiomes follows similar patterns to the heritability of other complex traits. We take a new approach to this question by comparing the microbiomes of diverse maize inbred lines and their F1 hybrid offspring, which we quantified in both rhizosphere and leaves of field-grown plants using 16S-v4 and ITS1 amplicon sequencing. We show that inbred lines and hybrids differ consistently in the composition of bacterial and fungal rhizosphere communities, as well as leaf-associated fungal communities. A wide range of microbiome features display heterosis within individual crosses, consistent with patterns for nonmicrobial maize phenotypes. For leaf microbiomes, these results were supported by the observation that broad-sense heritability in hybrids was substantially higher than narrow-sense heritability. Our results support our hypothesis that at least some heterotic host traits affect microbiome composition in maize.
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Affiliation(s)
- Maggie R Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
- Kansas Biological Survey, University of Kansas, Lawrence, KS, 66045, USA
| | - Joseph H Roberts
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Peter Balint-Kurti
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
- Plant Science Research Unit, Agricultural Research Service, United States Department of Agriculture, Raleigh, NC, 27695, USA
| | - James B Holland
- Plant Science Research Unit, Agricultural Research Service, United States Department of Agriculture, Raleigh, NC, 27695, USA
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
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Scarrow M, Wang Y, Sun G. Molecular regulatory mechanisms underlying the adaptability of polyploid plants. Biol Rev Camb Philos Soc 2020; 96:394-407. [PMID: 33098261 DOI: 10.1111/brv.12661] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022]
Abstract
Polyploidization influences the genetic composition and gene expression of an organism. This multi-level genetic change allows the formation of new regulatory pathways leading to increased adaptability. Although both forms of polyploidization provide advantages, autopolyploids were long thought to have little impact on plant divergence compared to allopolyploids due to their formation through genome duplication only, rather than in combination with hybridization. Recent advances have begun to clarify the molecular regulatory mechanisms such as microRNAs, alternative splicing, RNA-binding proteins, histone modifications, chromatin remodelling, DNA methylation, and N6 -methyladenosine (m6A) RNA methylation underlying the evolutionary success of polyploids. Such research is expanding our understanding of the evolutionary adaptability of polyploids and the regulatory pathways that allow adaptive plasticity in a variety of plant species. Herein we review the roles of individual molecular regulatory mechanisms and their potential synergistic pathways underlying plant evolution and adaptation. Notably, increasing interest in m6A methylation has provided a new component in potential mechanistic coordination that is still predominantly unexplored. Future research should attempt to identify and functionally characterize the evolutionary impact of both individual and synergistic pathways in polyploid plant species.
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Affiliation(s)
- Margaret Scarrow
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
| | - Yiling Wang
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, 041000, China
| | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, B3H 3C3, Canada
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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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