1
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Janko K, Eisner J, Cigler P, Tichopád T. Unifying framework explaining how parental regulatory divergence can drive gene expression in hybrids and allopolyploids. Nat Commun 2024; 15:8714. [PMID: 39379366 PMCID: PMC11461870 DOI: 10.1038/s41467-024-52546-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 09/12/2024] [Indexed: 10/10/2024] Open
Abstract
Hybridization and polyploidy are powerful evolutionary forces, inducing a range of phenotypic outcomes, including non-additive expression, subgenome dominance, deviations in genomic dosage, and transcriptome downsizing. The reasons for these patterns and whether they are universal adaptive responses to genome merging and doubling remain debated. To address this, we develop a thermodynamic model of gene expression based on transcription factor (TF)-promoter binding. Applied to hybridization between species with divergent gene expression levels, cell volumes, or euchromatic ratios, this model distinguishes the effects of hybridization from those of polyploidy. Our results align with empirical observations, suggesting that gene regulation patterns in hybrids and polyploids often stem from the constrained interplay between inherited diverged regulatory networks rather than from subsequent adaptive evolution. In addition, occurrence of certain phenotypic traits depend on specific assumptions about promoter-TF coevolution and their distribution within the hybrid's nucleoplasm, offering new research avenues to understand the underlying mechanisms. In summary, our model explains how the legacy of divergent species directly influences the phenotypic traits of hybrids and allopolyploids.
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Affiliation(s)
- Karel Janko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the Czech Aacademy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic.
| | - Jan Eisner
- Department of Mathematics, Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1760, 370 05, České Budějovice, Czech Republic
- Department of Biology and Ecology, Faculty of Natural Sciences, University of Ostrava, Chittussiho 10, Ostrava, Czech Republic
| | - Petr Cigler
- Institute of Organic Chemistry and Biochemistry of the CAS, 166 10, Prague, Czech Republic.
| | - Tomáš Tichopád
- Department of Biology and Ecology, Faculty of Natural Sciences, University of Ostrava, Chittussiho 10, Ostrava, Czech Republic
- University of South Bohemia in České Budějovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Zátiší 728/II, 389 25, Vodňany, Czech Republic
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2
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Long Z, Rieseberg LH. Documenting homoploid hybrid speciation. Mol Ecol 2024:e17412. [PMID: 38780141 DOI: 10.1111/mec.17412] [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: 01/29/2024] [Revised: 04/11/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Homoploid hybrid speciation is challenging to document because hybridization can lead to outcomes other than speciation. Thus, some authors have argued that establishment of homoploid hybrid speciation should include evidence that reproductive barriers isolating the hybrid neo-species from its parental species were derived from hybridization. While this criterion is difficult to satisfy, several recent papers have successfully employed a common pipeline to identify candidate genes underlying such barriers and (in one case) to validate their function. We describe this pipeline, its application to several plant and animal species and what we have learned about homoploid hybrid speciation as a consequence. We argue that - given the ubiquity of admixture and the polygenic basis of reproductive isolation - homoploid hybrid speciation could be much more common and more protracted than suggested by earlier conceptual arguments and theoretical studies.
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Affiliation(s)
- Zhiqin Long
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Nieto Feliner G, Criado Ruiz D, Álvarez I, Villa-Machío I. The puzzle of plant hybridisation: a high propensity to hybridise but few hybrid zones reported. Heredity (Edinb) 2023; 131:307-315. [PMID: 37884616 PMCID: PMC10673867 DOI: 10.1038/s41437-023-00654-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 10/13/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
An interesting conundrum was recently revealed by R. Abbott when he found that the number of hybrid zones reported in the literature for plants is very low, given the propensity of plants to hybridise. In another literature survey on hybrid zones performed over the period 1970-2022, we found that the number of hybrid zones reported for vertebrates was 2.3 times greater than that reported for vascular plants, even though there are about six times more vascular plant species than vertebrates. Looking at the number of papers reporting hybrid zones, there are 4.9 times more on vertebrates than on vascular plants. These figures support the relevance of this conundrum. In this paper we aim to shed light on this question by providing a structured discussion of the causes that may underlie this conundrum. We propose six non-mutually exclusive factors, namely lack or deficit of spatial structure, lack or deficit of genetic structure, effects of hybridisation between non-closely related species, lability of plant hybrid zones over time, botanists' perception of hybridisation, and deficit of population genetic data. There does not appear to be a single factor that explains our puzzle, which applies to all cases of plants where hybridisation is detected but no hybrid zone is reported. It is argued that some plant features suggest that the puzzle is not, at least entirely, due to insufficient knowledge of the specific cases, a hypothesis that should be addressed with a wider range of empirical data across different taxonomic groups.
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Affiliation(s)
| | - David Criado Ruiz
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | - Inés Álvarez
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
| | - Irene Villa-Machío
- Real Jardín Botánico (RJB), CSIC, Plaza de Murillo 2, 28014, Madrid, Spain
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4
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Marta A, Tichopád T, Bartoš O, Klíma J, Shah MA, Bohlen VŠ, Bohlen J, Halačka K, Choleva L, Stöck M, Dedukh D, Janko K. Genetic and karyotype divergence between parents affect clonality and sterility in hybrids. eLife 2023; 12:RP88366. [PMID: 37930936 PMCID: PMC10627513 DOI: 10.7554/elife.88366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
Asexual reproduction can be triggered by interspecific hybridization, but its emergence is supposedly rare, relying on exceptional combinations of suitable genomes. To examine how genomic and karyotype divergence between parental lineages affect the incidence of asexual gametogenesis, we experimentally hybridized fishes (Cobitidae) across a broad phylogenetic spectrum, assessed by whole exome data. Gametogenic pathways generally followed a continuum from sexual reproduction in hybrids between closely related evolutionary lineages to sterile or inviable crosses between distant lineages. However, most crosses resulted in a combination of sterile males and asexually reproducing females. Their gametes usually experienced problems in chromosome pairing, but females also produced a certain proportion of oocytes with premeiotically duplicated genomes, enabling their development into clonal eggs. Interspecific hybridization may thus commonly affect cell cycles in a specific way, allowing the formation of unreduced oocytes. The emergence of asexual gametogenesis appears tightly linked to hybrid sterility and constitutes an inherent part of the extended speciation continuum.
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Affiliation(s)
- Anatolie Marta
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CASLibechovCzech Republic
| | - Tomáš Tichopád
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CASLibechovCzech Republic
| | - Oldřich Bartoš
- Military Health Institute, Military Medical AgencyPragueCzech Republic
| | - Jiří Klíma
- Laboratory of Cell Regeneration and Plasticity, Institute of Animal Physiology and Genetics of the CASLiběchovCzech Republic
| | - Mujahid Ali Shah
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in Ceske BudejoviceVodnanyCzech Republic
| | - Vendula Šlechtová Bohlen
- Laboratory of Fish genetics, Institute of Animal Physiology and Genetics of the CASLiběchovCzech Republic
| | - Joerg Bohlen
- Laboratory of Fish genetics, Institute of Animal Physiology and Genetics of the CASLiběchovCzech Republic
| | - Karel Halačka
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CASLibechovCzech Republic
| | - Lukáš Choleva
- Department of Biology and Ecology, Faculty of Science, University of OstravaOstravaCzech Republic
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries - IGBBerlinGermany
| | - Dmitrij Dedukh
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CASLibechovCzech Republic
| | - Karel Janko
- Laboratory of Non-Mendelian Evolution, Institute of Animal Physiology and Genetics of the CASLibechovCzech Republic
- Department of Biology and Ecology, Faculty of Science, University of OstravaOstravaCzech Republic
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5
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Blanckaert A, Sriram V, Bank C. In search of the Goldilocks zone for hybrid speciation II: hard times for hybrid speciation? Evolution 2023; 77:2162-2172. [PMID: 37459183 PMCID: PMC10547126 DOI: 10.1093/evolut/qpad125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/24/2023] [Accepted: 06/30/2023] [Indexed: 07/28/2023]
Abstract
Hybridization opens a unique window for observing speciation mechanisms and is a potential engine of speciation. One controversially discussed outcome of hybridization is homoploid hybrid speciation by reciprocal sorting, where a hybrid population maintains a mixed combination of the parental genetic incompatibilities, preventing further gene exchange between the newly formed population and the two parental sources. Previous work showed that, for specific linkage architectures (i.e., the genomic location and order of hybrid incompatibilities), reciprocal sorting could reliably result in hybrid speciation. Yet, the sorting of incompatibilities creates a risk of population extinction. To understand how the demographic consequences of the purging of incompatibilities interact with the formation of a hybrid species, we model an isolated hybrid population resulting from a single admixture event. We study how population size, linkage architecture, and the strength of the incompatibility affect survival of the hybrid population, resolution/purging of the genetic incompatibilities and the probability of observing hybrid speciation. We demonstrate that the extinction risk is highest for intermediately strong hybrid incompatibilities. In addition, the linkage architecture displaying the highest hybrid speciation probabilities changes drastically with population size. Overall, this indicates that population dynamics can strongly affect the outcome of hybridization and the hybrid speciation probability.
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Affiliation(s)
- Alexandre Blanckaert
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal
| | | | - Claudia Bank
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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6
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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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7
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Blanckaert A, Sriram V, Bank C. In search of the Goldilocks zone for hybrid speciation II: hard times for hybrid speciation? BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528680. [PMID: 36824868 PMCID: PMC9948988 DOI: 10.1101/2023.02.15.528680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Hybridization opens a unique window for observing speciation mechanisms and is a potential engine of speciation. One controversially discussed outcome of hybridization is homoploid hybrid speciation by reciprocal sorting, where a hybrid population maintains a mixed combination of the parental genetic incompatibilities, preventing further gene exchange between the newly formed population and the two parental sources. Previous work showed that, for specific linkage architectures (i.e., the genomic location and order of hybrid incompatibilities), reciprocal sorting could reliably result in hybrid speciation. Yet, the sorting of incompatibilities creates a risk of population extinction. To understand how demographic consequences of the purging of incompatibilities interact with the formation of a hybrid species, we model an isolated hybrid population resulting from a single admixture event. We study how population size, linkage architecture and the strength of the incompatibility affect survival of the hybrid population, resolution/purging of the genetic incompatibilities and the probability of observing hybrid speciation. We demonstrate that the extinction risk is highest for intermediately strong hybrid incompatibilities. In addition, the linkage architecture displaying the highest hybrid speciation probabilities changes drastically with population size. Overall, this indicates that population dynamics can strongly affect the outcome of hybridization and the hybrid speciation probability.
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Affiliation(s)
- Alexandre Blanckaert
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
- cE3c - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Portugal
| | | | - Claudia Bank
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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8
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Grossfurthner LP, Milano ER, Hohenlohe PA, Waits LP, Richardson BA. Population structure and hybridization under contemporary and future climates in a heteroploid foundational shrub species ( Artemisia tridentata). FRONTIERS IN PLANT SCIENCE 2023; 14:1155868. [PMID: 37284723 PMCID: PMC10239881 DOI: 10.3389/fpls.2023.1155868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/20/2023] [Indexed: 06/08/2023]
Abstract
Current and past climatic changes can shift plant climatic niches, which may cause spatial overlap or separation between related taxa. The former often leads to hybridization and introgression, which may generate novel variation and influence the adaptive capacity of plants. An additional mechanism facilitating adaptations to novel environments and an important evolutionary driver in plants is polyploidy as the result of whole genome duplication. Artemisia tridentata (big sagebrush) is a landscape-dominating foundational shrub in the western United States which occupies distinct ecological niches, exhibiting diploid and tetraploid cytotypes. Tetraploids have a large impact on the species' landscape dominance as they occupy a preponderance of the arid spectrum of A. tridentata range. Three distinct subspecies are recognized, which co-occur in ecotones - the transition zone between two or more distinct ecological niches - allowing for hybridization and introgression. Here we assess the genomic distinctiveness and extent of hybridization among subspecies at different ploidies under both contemporary and predicted future climates. We sampled five transects throughout the western United States where a subspecies overlap was predicted using subspecies-specific climate niche models. Along each transect, we sampled multiple plots representing the parental and the potential hybrid habitats. We performed reduced representation sequencing and processed the data using a ploidy-informed genotyping approach. Population genomic analyses revealed distinct diploid subspecies and at least two distinct tetraploid gene pools, indicating independent origins of the tetraploid populations. We detected low levels of hybridization (2.5%) between the diploid subspecies, while we found evidence for increased admixture between ploidy levels (18%), indicating hybridization has an important role in the formation of tetraploids. Our analyses highlight the importance of subspecies co-occurrence within these ecotones to maintain gene exchange and potential formation of tetraploid populations. Genomic confirmations of subspecies in the ecotones support the subspecies overlap predicted by the contemporary climate niche models. However, future mid-century projections of subspecies niches predict a substantial loss in range and subspecies overlap. Thus, reductions in hybridization potential could affect new recruitment of genetically variable tetraploids that are vital to this species' ecological role. Our results underscore the importance of ecotone conservation and restoration.
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Affiliation(s)
- Lukas P. Grossfurthner
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, United States
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Elizabeth R. Milano
- Rocky Mountain Research Station, United States Department of Agriculture (USDA) Forest Service, Moscow, ID, United States
| | - Paul A. Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, United States
| | - Bryce A. Richardson
- Rocky Mountain Research Station, United States Department of Agriculture (USDA) Forest Service, Moscow, ID, United States
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9
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Jia Y, Liu ML, López-Pujol J, Jia RW, Kou YX, Yue M, Guan TX, Li ZH. The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis. Mol Phylogenet Evol 2023; 182:107736. [PMID: 36805473 DOI: 10.1016/j.ympev.2023.107736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/03/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023]
Abstract
Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.
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Affiliation(s)
- Yun Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Mi-Li Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Jordi López-Pujol
- Botanic Institute of Barcelona (IBB), CSIC-Ajuntament de Barcelona, Barcelona 08038, Catalonia, Spain; Escuela de Ciencias Ambientales, Universidad Espíritu Santo (UEES), Samborondón 091650, Ecuador
| | - Rui-Wen Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Yi-Xuan Kou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, Shaanxi, China
| | - Tian-Xia Guan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China; Key Laboratory of Hexi Corridor Resources Utilization of Gansu, College of Life Sciences and Engineering, Hexi University, Zhangye 734000, Gansu, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, Shaanxi, China.
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10
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Nali RC, Zamudio KR, Prado CPA. Hybridization despite elaborate courtship behavior and female choice in Neotropical tree frogs. Integr Zool 2023; 18:208-224. [PMID: 35041294 DOI: 10.1111/1749-4877.12628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanisms of hybridization can be elucidated by analyzing genotypes as well as phenotypes that could act as premating barriers, as the reproductive interactions among heterospecifics can alter the evolutionary history of species. In frogs, hybrids typically occur among species that reproduce explosively (in dense aggregations) with few opportunities for mate selection but are rare in species with elaborate courtship behaviors that may prevent erroneous mating. Using 21 microsatellite markers, we examined hybridization in the prolonged-breeding tree frogs Bokermannohyla ibitiguara and B. sazimai sampled within a contact zone in the Brazilian savanna (72 tadpoles; 74 adults). We also compared acoustic and morphological data. We confirmed both parental species genetically; STRUCTURE results confirmed 14 hybrids, 11 of which were second-generation according to NEWHYBRIDS, all with intermediate values of genetic dissimilarities compared to the parentals. Morphological and acoustic analyses revealed that hybrids showed variable but not necessarily intermediate phenotypes. Moreover, 2 hybrids exhibited call types different from parentals. The reproduction of B. ibitiguara involves territorial and aggressive males, elaborate courtships with acoustic and tactile stimuli, choosy females, and opportunistic strategies. Our study uncovers a rare case of viable hybridization among closely related frogs with such a combination of complex courtship behaviors and mate choice. We discuss the likely directionality and mechanisms behind this phenomenon, and highlight the importance of investigating hybridization even in species that show elaborate reproduction and female choice to advance our understanding of animal diversification.
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Affiliation(s)
- Renato C Nali
- Programa de Pós-Graduação em Ecologia, Evolução e Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Kelly R Zamudio
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA.,Department of Integrative Biology, University of Texas, Austin, Texas, USA
| | - Cynthia P A Prado
- Programa de Pós-Graduação em Ecologia, Evolução e Biodiversidade, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, São Paulo, Brazil.,Departamento de Morfologia e Fisiologia Animal, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, São Paulo, Brazil
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11
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Klápště J, Jaquish B, Porth I. Building resiliency in conifer forests: Interior spruce crosses among weevil resistant and susceptible parents produce hybrids appropriate for multi-trait selection. PLoS One 2022; 17:e0263488. [PMID: 36459506 PMCID: PMC9718410 DOI: 10.1371/journal.pone.0263488] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 11/08/2022] [Indexed: 12/03/2022] Open
Abstract
Tree planting programs now need to consider climate change increasingly, therefore, the resistance to pests plays an essential role in enabling tree adaptation to new ranges through tree population movement. The weevil Pissodes strobi (Peck) is a major pest of spruces and substantially reduces lumber quality. We revisited a large Interior spruce provenance/progeny trial (2,964 genotypes, 42 families) of varying susceptibility, established in British Columbia. We employed multivariate mixed linear models to estimate covariances between, and genetic control of, juvenile height growth and resistance traits. We performed linear regressions and ordinal logistic regressions to test for impact of parental origin on growth and susceptibility to the pest, respectively. A significant environmental component affected the correlations between resistance and height, with outcomes dependent on families. Parents sourced from above 950 m a.s.l. elevation negatively influenced host resistance to attacks, probably due to higher P. engelmannii proportion. For the genetic contribution of parents sourced from above 1,200 m a.s.l., however, we found less attack severity, probably due to a marked mismatch in phenologies. This clearly highlights that interspecific hybrid status might be a good predictor for weevil attacks and delineates the boundaries of successful spruce population movement. Families resulting from crossing susceptible parents generally showed fast-growing trees were the most affected by weevil attacks. Such results indicate that interspecific 'hybrids' with a higher P. glauca ancestry might be genetically better equipped with an optimized resource allocation between defence and growth and might provide the solution for concurrent improvement in resistance against weevil attacks, whilst maintaining tree productivity.
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Affiliation(s)
- Jaroslav Klápště
- Scion (New Zealand Forest Research Institute Ltd.), Rotorua, New Zealand
| | - Barry Jaquish
- BC Ministry of Forests, Lands, Natural Resource Operations and Rural Development, Vernon, B.C., Canada
| | - Ilga Porth
- Department of Wood and Forest Sciences, Université Laval, Québec City, Québec, Canada
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec City, Québec, Canada
- Centre for Forest Research, Université Laval, Québec City, Québec, Canada
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12
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David JR, Ferreira EA, Jabaud L, Ogereau D, Bastide H, Yassin A. Evolution of assortative mating following selective introgression of pigmentation genes between two Drosophila species. Ecol Evol 2022; 12:e8821. [PMID: 35432924 PMCID: PMC9006235 DOI: 10.1002/ece3.8821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/24/2022] [Indexed: 12/03/2022] Open
Abstract
Adaptive introgression is ubiquitous in animals, but experimental support for its role in driving speciation remains scarce. In the absence of conscious selection, admixed laboratory strains of Drosophila asymmetrically and progressively lose alleles from one parental species and reproductive isolation against the predominant parent ceases after 10 generations. Here, we selectively introgressed during 1 year light pigmentation genes of D. santomea into the genome of its dark sibling D. yakuba, and vice versa. We found that the pace of phenotypic change differed between the species and the sexes and identified through genome sequencing common as well as distinct introgressed loci in each species. Mating assays showed that assortative mating between introgressed flies and both parental species persisted even after 4 years (~60 generations) from the end of the selection. Those results indicate that selective introgression of as low as 0.5% of the genome can beget morphologically distinct and reproductively isolated strains, two prerequisites for the delimitation of new species. Our findings hence represent a significant step toward understanding the genome-wide dynamics of speciation-through-introgression.
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Affiliation(s)
- Jean R. David
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Erina A. Ferreira
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Laure Jabaud
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - David Ogereau
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Héloïse Bastide
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
| | - Amir Yassin
- Laboratoire Évolution, Génomes, Comportement et ÉcologieCNRSIRDUniversité Paris‐Saclay – Institut DiversitéEcologie et Evolution du Vivant (IDEEV)Gif‐sur‐YvetteFrance
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13
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Gu Q, Wang S, Zhong H, Yuan H, Yang J, Yang C, Huang X, Xu X, Wang Y, Wei Z, Wang J, Liu S. Phylogeographic relationships and the evolutionary history of the Carassius auratus complex with a newly born homodiploid raw fish (2nNCRC). BMC Genomics 2022; 23:242. [PMID: 35350975 PMCID: PMC8962218 DOI: 10.1186/s12864-022-08468-x] [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: 06/09/2021] [Accepted: 03/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
An important aspect of studying evolution is to understand how new species are formed and their uniqueness is maintained. Hybridization can lead to the formation of new species through reorganization of the adaptive system and significant changes in phenotype. Interestingly, eight stable strains of 2nNCRC derived from interspecies hybridization have been established in our laboratory. To examine the phylogeographical pattern of the widely distributed genus Carassius across Eurasia and investigate the possible homoploid hybrid origin of the Carassius auratus complex lineage in light of past climatic events, the mitochondrial genome (mtDNA) and one nuclear DNA were used to reconstruct the phylogenetic relationship between the C. auratus complex and 2nNCRC and to assess how demographic history, dispersal and barriers to gene flow have led to the current distribution of the C. auratus complex.
Results
As expected, 2nNCRC had a very close relationship with the C. auratus complex and similar morphological characteristics to those of the C. auratus complex, which is genetically distinct from the other three species of Carassius. The estimation of divergence time and ancestral state demonstrated that the C. auratus complex possibly originated from the Yangtze River basin in China. There were seven sublineages of the C. auratus complex across Eurasia and at least four mtDNA lineages endemic to particular geographical regions in China. The primary colonization route from China to Mongolia and the Far East (Russia) occurred during the Late Pliocene, and the diversification of other sublineages of the C. auratus complex specifically coincided with the interglacial stage during the Early and Mid-Pleistocene in China.
Conclusion
Our results support the origin of the C. auratus complex in China, and its wide distribution across Eurasia was mainly due to natural Pleistocene dispersal and recent anthropogenic translocation. The sympatric distribution of the ancestral area for both parents of 2nNCRC and the C. auratus complex, as well as the significant changes in the structure of pharyngeal teeth and morphological characteristics between 2nNCRC and its parents, imply that homoploid hybrid speciation (HHS) for C. auratus could likely have occurred in nature. The diversification pattern indicated an independent evolutionary history of the C. auratus complex, which was not separated from the most recent common ancestor of C. carassius or C. cuvieri. Considering that the paleoclimate oscillation and the development of an eastward-flowing drainage system during the Pliocene and Pleistocene in China provided an opportunity for hybridization between divergent lineages, the formation of 2nNCRC in our laboratory could be a good candidate for explaining the HHS of C. auratus in nature.
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14
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Michelotti LA, Sun S, Heitman J, James TY. Clonal evolution in serially passaged Cryptococcus neoformans × deneoformans hybrids reveals a heterogenous landscape of genomic change. Genetics 2022; 220:iyab142. [PMID: 34849836 PMCID: PMC8733418 DOI: 10.1093/genetics/iyab142] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/25/2021] [Indexed: 11/14/2022] Open
Abstract
Cryptococcus neoformans × deneoformans hybrids (also known as serotype AD hybrids) are basidiomycete yeasts that are common in a clinical setting. Like many hybrids, the AD hybrids are largely locked at the F1 stage and are mostly unable to undergo normal meiotic reproduction. However, these F1 hybrids, which display a high (∼10%) sequence divergence are known to genetically diversify through mitotic recombination and aneuploidy, and this diversification may be adaptive. In this study, we evolved a single AD hybrid genotype in six diverse environments by serial passaging and then used genome resequencing of evolved clones to determine evolutionary mechanisms of adaptation. The evolved clones generally increased fitness after passaging, accompanied by an average of 3.3 point mutations, 2.9 loss of heterozygosity (LOH) events, and 0.7 trisomic chromosomes per clone. LOH occurred through nondisjunction of chromosomes, crossing over consistent with break-induced replication, and gene conversion, in that order of prevalence. The breakpoints of these recombination events were significantly associated with regions of the genome with lower sequence divergence between the parents and clustered in sub-telomeric regions, notably in regions that had undergone introgression between the two parental species. Parallel evolution was observed, particularly through repeated homozygosity via nondisjunction, yet there was little evidence of environment-specific parallel change for either LOH, aneuploidy, or mutations. These data show that AD hybrids have both a remarkable genomic plasticity and yet are challenged in the ability to recombine through sequence divergence and chromosomal rearrangements, a scenario likely limiting the precision of adaptive evolution to novel environments.
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Affiliation(s)
- Lucas A Michelotti
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sheng Sun
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
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15
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Buck LT, Katz DC, Ackermann RR, Hlusko LJ, Kanthaswamy S, Weaver TD. Effects of hybridization on pelvic morphology: A macaque model. J Hum Evol 2021; 159:103049. [PMID: 34455262 DOI: 10.1016/j.jhevol.2021.103049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/28/2022]
Abstract
Ancient DNA analyses have shown that interbreeding between hominin taxa occurred multiple times. Although admixture is often reflected in skeletal phenotype, the relationship between the two remains poorly understood, hampering interpretation of the hominin fossil record. Direct study of this relationship is often impossible due to the paucity of hominin fossils and difficulties retrieving ancient genetic material. Here, we use a sample of known ancestry hybrids between two closely related nonhuman primate taxa (Indian and Chinese Macaca mulatta) to investigate the effect of admixture on skeletal morphology. We focus on pelvic shape, which has potential fitness implications in hybrids, as mismatches between maternal pelvic and fetal cranial morphology are often fatal to mother and offspring. As the pelvis is also one of the skeletal regions that differs most between Homo sapiens and Neanderthals, investigating the pelvic consequences of interbreeding could be informative regarding the viability of their hybrids. We find that the effect of admixture in M. mulatta is small and proportional to the relatively small morphological difference between the parent taxa. Sexual dimorphism appears to be the main determinant of pelvic shape in M. mulatta. The lack of difference in pelvic shape between Chinese and Indian M. mulatta is in contrast to that between Neanderthals and H. sapiens, despite a similar split time (in generations) between the hybridizing pairs. Greater phenotypic divergence between hominins may relate to adaptations to disparate environments but may also highlight how the unique degree of cultural buffering in hominins allowed for greater neutral divergence. In contrast to some previous work identifying extreme morphologies in first- and second-generation hybrids, here the relationship between pelvic shape and admixture is linear. This linearity may be because most sampled animals have a multigenerational admixture history or because of relatively high constraints on the pelvis compared with other skeletal regions.
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Affiliation(s)
- Laura T Buck
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK; Department of Anthropology, University of California Davis, USA.
| | - David C Katz
- Department of Anthropology, University of California Davis, USA; University of Calgary, Cumming School of Medicine, Canada
| | - Rebecca Rogers Ackermann
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley, USA; Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Sree Kanthaswamy
- School of Natural and Mathematical Sciences, Arizona State University, USA
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16
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Moran BM, Payne C, Langdon Q, Powell DL, Brandvain Y, Schumer M. The genomic consequences of hybridization. eLife 2021; 10:e69016. [PMID: 34346866 PMCID: PMC8337078 DOI: 10.7554/elife.69016] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/09/2021] [Indexed: 12/29/2022] Open
Abstract
In the past decade, advances in genome sequencing have allowed researchers to uncover the history of hybridization in diverse groups of species, including our own. Although the field has made impressive progress in documenting the extent of natural hybridization, both historical and recent, there are still many unanswered questions about its genetic and evolutionary consequences. Recent work has suggested that the outcomes of hybridization in the genome may be in part predictable, but many open questions about the nature of selection on hybrids and the biological variables that shape such selection have hampered progress in this area. We synthesize what is known about the mechanisms that drive changes in ancestry in the genome after hybridization, highlight major unresolved questions, and discuss their implications for the predictability of genome evolution after hybridization.
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Affiliation(s)
- Benjamin M Moran
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Cheyenne Payne
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Quinn Langdon
- Department of Biology, Stanford UniversityStanfordUnited States
| | - Daniel L Powell
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
| | - Yaniv Brandvain
- Department of Ecology, Evolution & Behavior and Plant and Microbial Biology, University of MinnesotaMinneapolisUnited States
| | - Molly Schumer
- Department of Biology, Stanford UniversityStanfordUnited States
- Centro de Investigaciones Científicas de las Huastecas “Aguazarca”HidalgoMexico
- Hanna H. Gray Fellow, Howard Hughes Medical InstituteStanfordUnited States
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17
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Janzen T, Diaz F. Individual‐based simulations of genome evolution with ancestry: The
GenomeAdmixR
R package. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thijs Janzen
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands
- Carl von Ossietzky University Oldenburg Germany
| | - Fernando Diaz
- Department of Entomology University of Arizona Tucson AZ USA
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18
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Brice C, Zhang Z, Bendixsen D, Stelkens R. Hybridization Outcomes Have Strong Genomic and Environmental Contingencies. Am Nat 2021; 198:E53-E67. [PMID: 34403309 DOI: 10.1086/715356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractExtreme F2 phenotypes known as transgressive segregants can cause increased or decreased fitness in hybrids beyond the ranges seen in parental populations. Despite the usefulness of transgression for plant and animal breeding and its potential role in hybrid speciation, the genetic mechanisms and predictors of transgressive segregation remain largely untested. We generated seven hybrid crosses between five widely divergent Saccharomyces yeast species and measured the fitness of the parents and their viable F1 and F2 hybrids in seven stressful environments. We found that on average 16.6% of all replicate F2 hybrids had higher fitness than both parents. Against our predictions, transgression frequency was not a function of parental genetic and phenotypic distances across test environments. Within environments, some relationships were significant, but not in the predicted direction; for example, genetic distance was negatively related to transgression in ethanol and hydrogen peroxide. Significant effects of hybrid cross, test environment, and cross × environment interactions suggest that the amount of transgression produced in a hybrid cross is highly context specific and that outcomes of hybridization differ even among crosses made from the same two parents. If the goal is to reliably predict hybrid fitness and forecast the evolutionary potential of admixed populations, we need more efforts to identify patterns beyond the idiosyncrasies caused by specific genomic or environmental contexts.
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19
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Serrato-Capuchina A, Schwochert TD, Zhang S, Roy B, Peede D, Koppelman C, Matute DR. Pure species discriminate against hybrids in the Drosophila melanogaster species subgroup. Evolution 2021; 75:1753-1774. [PMID: 34043234 DOI: 10.1111/evo.14259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 01/20/2021] [Accepted: 02/09/2021] [Indexed: 12/11/2022]
Abstract
Introgression, the exchange of alleles between species, is a common event in nature. This transfer of alleles between species must happen through fertile hybrids. Characterizing the traits that cause defects in hybrids illuminates how and when gene flow is expected to occur. Inviability and sterility are extreme examples of fitness reductions but are not the only type of defects in hybrids. Some traits specific to hybrids are more subtle but are important to determine their fitness. In this report, we study whether F1 hybrids between two species pairs of Drosophila are as attractive as the parental species. We find that in both species pairs, the sexual attractiveness of the F1 hybrids is reduced and that pure species discriminate strongly against them. We also find that the cuticular hydrocarbon (CHC) profile of the female hybrids is intermediate between the parental species. Perfuming experiments show that modifying the CHC profile of the female hybrids to resemble pure species improves their chances of mating. Our results show that behavioral discrimination against hybrids might be an important component of the persistence of species that can hybridize.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Timothy D Schwochert
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Stephania Zhang
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Baylee Roy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - David Peede
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Caleigh Koppelman
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
| | - Daniel R Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599
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20
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Richards EJ, McGirr JA, Wang JR, St John ME, Poelstra JW, Solano MJ, O'Connell DC, Turner BJ, Martin CH. A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape. Proc Natl Acad Sci U S A 2021; 118:e2011811118. [PMID: 33990463 PMCID: PMC8157919 DOI: 10.1073/pnas.2011811118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to the novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid swarm origins and temporal stages of adaptation. Using a combination of population genomics, transcriptomics, and genome-wide association mapping, we demonstrate that this microendemic adaptive radiation of novel trophic specialists on San Salvador Island, Bahamas experienced twice as much adaptive introgression as generalist populations on neighboring islands and that adaptive divergence occurred in stages. First, standing regulatory variation in genes associated with feeding behavior (prlh, cfap20, and rmi1) were swept to fixation by selection, then standing regulatory variation in genes associated with craniofacial and muscular development (itga5, ext1, cyp26b1, and galr2) and finally the only de novo nonsynonymous substitution in an osteogenic transcription factor and oncogene (twist1) swept to fixation most recently. Our results demonstrate how ancient alleles maintained in distinct environmental refugia can be assembled into new adaptive combinations and provide a framework for reconstructing the spatiotemporal landscape of adaptation and speciation.
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Affiliation(s)
- Emilie J Richards
- Department of Integrative Biology, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Joseph A McGirr
- Department of Environmental Toxicology, University of California, Davis, CA 95616
| | - Jeremy R Wang
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514
| | - Michelle E St John
- Department of Integrative Biology, University of California, Berkeley, CA 94720
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
| | - Jelmer W Poelstra
- Molecular and Cellular Imaging Center, Ohio State University, Columbus, OH 43210
| | - Maria J Solano
- Department of Biology, University of North Carolina, Chapell Hill, NC 27514
| | | | - Bruce J Turner
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24601
| | - Christopher H Martin
- Department of Integrative Biology, University of California, Berkeley, CA 94720;
- Museum of Vertebrate Zoology, University of California, Berkeley, CA 94720
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21
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Ponnanna K, DSouza SM, Ramachandra NB. De novo assembly, annotation and gene expression profiles of gonads of Cytorace-3, a hybrid lineage of Drosophila nasuta nasuta and D. n. albomicans. Genomics Inform 2021; 19:e8. [PMID: 33840172 PMCID: PMC8042302 DOI: 10.5808/gi.20051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/19/2020] [Indexed: 11/26/2022] Open
Abstract
Cytorace-3 is a laboratory evolved hybrid lineage of Drosophila nasuta nasuta males and Drosophila nasuta albomicans females currently passing ~850 generations. To assess interracial hybridization effects on gene expression in Cytorace-3 we profiled the transcriptomes of mature ovaries and testes by employing Illumina sequencing technology and de novo transcriptome assembling strategies. We found 26% of the ovarian, and 14% of testis genes to be differentially expressed in Cytorace-3 relative to the expressed genes in the parental gonadal transcriptomes. About 5% of genes exhibited additive gene expression pattern in the ovary and 3% in the testis, while the remaining genes were misexpressed in Cytorace-3. Nearly 772 of these misexpressed genes in the ovary and 413 in the testis were either over- or under-dominant. Genes following D. n. nasuta dominance was twice (270 genes) than D. n. albomicans dominance (133 genes) in the ovary. In contrast, only 105 genes showed D. n. nasuta dominance and 207 showed D. n. albomicans dominance in testis transcriptome. Of the six expression inheritance patterns, conserved inheritance pattern was predominant for both ovary (73%) and testis (85%) in Cytorace-3. This study is the first to provide an overview of the expression divergence and inheritance patterns of the transcriptomes in an independently evolving distinct hybrid lineage of Drosophila. This recorded expression divergence in Cytorace-3 surpasses that between parental lineages illustrating the strong impact of hybridization driving rapid gene expression changes.
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Affiliation(s)
- Koushik Ponnanna
- Department of Studies in Genetics and Genomics, University of Mysore, Mysuru 570006, India
| | - Stafny M DSouza
- Department of Studies in Genetics and Genomics, University of Mysore, Mysuru 570006, India
| | - Nallur B Ramachandra
- Department of Studies in Genetics and Genomics, University of Mysore, Mysuru 570006, India
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22
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Matute DR, Cooper BS. Comparative studies on speciation: 30 years since Coyne and Orr. Evolution 2021; 75:764-778. [PMID: 33491225 PMCID: PMC8247902 DOI: 10.1111/evo.14181] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/16/2020] [Accepted: 12/22/2020] [Indexed: 12/28/2022]
Abstract
Understanding the processes of population divergence and speciation remains a core question in evolutionary biology. For nearly a hundred years evolutionary geneticists have characterized reproductive isolation (RI) mechanisms and specific barriers to gene flow required for species formation. The seminal work of Coyne and Orr provided the first comprehensive comparative analysis of speciation. By combining phylogenetic hypotheses and species range data with estimates of genetic divergence and multiple mechanisms of RI across Drosophila, Coyne and Orr's influential meta-analyses answered fundamental questions and motivated new analyses that continue to push the field forward today. Now 30 years later, we revisit the five questions addressed by Coyne and Orr, identifying results that remain well supported and others that seem less robust with new data. We then consider the future of speciation research, with emphasis on areas where novel methods and data motivate potential progress. While the literature remains biased towards Drosophila and other model systems, we are enthusiastic about the future of the field.
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Affiliation(s)
- Daniel R. Matute
- Biology DepartmentUniversity of North CarolinaChapel HillNorth Carolina27510
| | - Brandon S. Cooper
- Division of Biological SciencesUniversity of MontanaMissoulaMontana59812
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23
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Casas L, Saenz-Agudelo P, Villegas-Ríos D, Irigoien X, Saborido-Rey F. Genomic landscape of geographically structured colour polymorphism in a temperate marine fish. Mol Ecol 2021; 30:1281-1296. [PMID: 33455028 PMCID: PMC7986630 DOI: 10.1111/mec.15805] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 01/06/2021] [Accepted: 01/08/2021] [Indexed: 12/14/2022]
Abstract
The study of phenotypic variation patterns among populations is fundamental to elucidate the drivers of evolutionary processes. Empirical evidence that supports ongoing genetic divergence associated with phenotypic variation remains very limited for marine species where larval dispersal is a common homogenizing force. We present a genome‐wide analysis of a marine fish, Labrus bergylta, comprising 144 samples distributed from Norway to Spain, a large geographical area that harbours a gradient of phenotypic differentiation. We analysed 39,602 biallelic single nucleotide polymorphisms and found a clear latitudinal gradient of genomic differentiation strongly correlated with the variation in phenotypic morph frequencies observed across the North Atlantic. We also detected a strong association between the latitude and the number of loci that appear to be under divergent selection, which increased with differences in coloration but not with overall genetic differentiation. Our results demonstrate that strong reproductive isolation is occurring between sympatric colour morphs of L. bergylta found at the southern areas and provide important new insights into the genomic changes shaping early stages of differentiation that might precede speciation with gene flow.
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Affiliation(s)
- Laura Casas
- Institute of Marine Research (IIM-CSIC), Vigo, Spain
| | - Pablo Saenz-Agudelo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - David Villegas-Ríos
- Institute of Marine Research (IIM-CSIC), Vigo, Spain.,Instituto Mediterráneo de Estudios Avanzados (IMEDEA-CSIC-UiB), Esporles, Mallorca, Spain
| | - Xabier Irigoien
- AZTI - Marine Research, Herrera Kaia, Pasaia (Gipuzkoa), Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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24
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Wang Z, Jiang Y, Bi H, Lu Z, Ma Y, Yang X, Chen N, Tian B, Liu B, Mao X, Ma T, DiFazio SP, Hu Q, Abbott RJ, Liu J. Hybrid speciation via inheritance of alternate alleles of parental isolating genes. MOLECULAR PLANT 2021; 14:208-222. [PMID: 33220509 DOI: 10.1016/j.molp.2020.11.008] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/11/2020] [Accepted: 11/13/2020] [Indexed: 05/21/2023]
Abstract
It is increasingly realized that homoploid hybrid speciation (HHS), which involves no change in chromosome number, is an important mechanism of speciation. HHS will likely increase in frequency as ecological and geographical barriers between species are continuing to be disrupted by human activities. HHS requires the establishment of reproductive isolation between a hybrid and its parents, but the underlying genes and genetic mechanisms remain largely unknown. In this study, we reveal by integrated approaches that reproductive isolation originates in one homoploid hybrid plant species through the inheritance of alternate alleles at genes that determine parental premating isolation. The parent species of this hybrid species are reproductively isolated by differences in flowering time and survivorship on soils containing high concentrations of iron. We found that the hybrid species inherits alleles of parental isolating major genes related to flowering time from one parent and alleles of major genes related to iron tolerance from the other parent. In this way, it became reproductively isolated from one parent by the difference in flowering time and from the other by habitat adaptation (iron tolerance). These findings and further modeling results suggest that HHS may occur relatively easily via the inheritance of alternate parental premating isolating genes and barriers.
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Affiliation(s)
- Zefu Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Hao Bi
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Zhiqiang Lu
- State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China; CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Yazhen Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Xiaoyue Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Ningning Chen
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Bin Tian
- State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China; Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry and Grassland Administration, Southwest Forestry University, Kunming 650224, China
| | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan 030006, China
| | - Xingxing Mao
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 25606, USA
| | - Quanjun Hu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China.
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews KY16 9TH, UK.
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences & State Key Lab of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu 610065, China; State Key Laboratory of Grassland Agro-Ecosystem, Innovation Institute of Ecology and Life Sciences, Lanzhou University, Lanzhou 730000, China.
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25
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Mating behavior of house mice of Trans-Caucasian hybrid zone: a comparative study with parent species Mus musculus. RUSSIAN JOURNAL OF THERIOLOGY 2020. [DOI: 10.15298/rusjtheriol.19.2.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Abstract
Introgressive hybridization can affect the evolution of populations in several important ways. It may retard or reverse divergence of species, enable the development of novel traits, enhance the potential for future evolution by elevating levels of standing variation, create new species, and alleviate inbreeding depression in small populations. Most of what is known of contemporary hybridization in nature comes from the study of pairs of species, either coexisting in the same habitat or distributed parapatrically and separated by a hybrid zone. More rarely, three species form an interbreeding complex (triad), reported in vertebrates, insects, and plants. Often, one species acts as a genetic link or conduit for the passage of genes (alleles) between two others that rarely, if ever, hybridize. Demographic and genetic consequences are unknown. Here we report results of a long-term study of interbreeding Darwin's finches on Daphne Major island, Galápagos. Geospiza fortis acted as a conduit for the passage of genes between two others that have never been observed to interbreed on Daphne: Geospiza fuliginosa, a rare immigrant, and Geospiza scandens, a resident. Microsatellite gene flow from G. fortis into G. scandens increased in frequency during 30 y of favorable ecological conditions, resulting in genetic and morphological convergence. G. fortis, G. scandens, and the derived dihybrids and trihybrids experienced approximately equal fitness. Especially relevant to young adaptive radiations, where species differ principally in ecology and behavior, these findings illustrate how new combinations of genes created by hybridization among three species can enhance the potential for evolutionary change.
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27
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Lavania UC. Plant speciation and polyploidy: in habitat divergence and environmental perspective. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00311-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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28
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Gillespie RG, Bennett GM, De Meester L, Feder JL, Fleischer RC, Harmon LJ, Hendry AP, Knope ML, Mallet J, Martin C, Parent CE, Patton AH, Pfennig KS, Rubinoff D, Schluter D, Seehausen O, Shaw KL, Stacy E, Stervander M, Stroud JT, Wagner C, Wogan GOU. Comparing Adaptive Radiations Across Space, Time, and Taxa. J Hered 2020; 111:1-20. [PMID: 31958131 PMCID: PMC7931853 DOI: 10.1093/jhered/esz064] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 10/28/2019] [Indexed: 01/02/2023] Open
Abstract
Adaptive radiation plays a fundamental role in our understanding of the evolutionary process. However, the concept has provoked strong and differing opinions concerning its definition and nature among researchers studying a wide diversity of systems. Here, we take a broad view of what constitutes an adaptive radiation, and seek to find commonalities among disparate examples, ranging from plants to invertebrate and vertebrate animals, and remote islands to lakes and continents, to better understand processes shared across adaptive radiations. We surveyed many groups to evaluate factors considered important in a large variety of species radiations. In each of these studies, ecological opportunity of some form is identified as a prerequisite for adaptive radiation. However, evolvability, which can be enhanced by hybridization between distantly related species, may play a role in seeding entire radiations. Within radiations, the processes that lead to speciation depend largely on (1) whether the primary drivers of ecological shifts are (a) external to the membership of the radiation itself (mostly divergent or disruptive ecological selection) or (b) due to competition within the radiation membership (interactions among members) subsequent to reproductive isolation in similar environments, and (2) the extent and timing of admixture. These differences translate into different patterns of species accumulation and subsequent patterns of diversity across an adaptive radiation. Adaptive radiations occur in an extraordinary diversity of different ways, and continue to provide rich data for a better understanding of the diversification of life.
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Affiliation(s)
- Rosemary G Gillespie
- University of California, Berkeley, Essig Museum of Entomology & Department of Environmental Science, Policy, and Management, Berkeley, CA
| | - Gordon M Bennett
- University of California Merced, Life and Environmental Sciences Unit, Merced, CA
| | - Luc De Meester
- University of Leuven, Laboratory of Aquatic Ecology, Evolution and Conservation, Leuven, Belguim
| | - Jeffrey L Feder
- University of Notre Dame, Dept. of Biological Sciences, Notre Dame, IN
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC
| | - Luke J Harmon
- University of Idaho, Dept. of Biological Sciences, Moscow, ID
| | | | | | | | - Christopher Martin
- University of California Berkeley, Integrative Biology and Museum of Vertebrate Zoology, Berkeley, CA
| | | | - Austin H Patton
- Washington State University, School of Biological Sciences, Pullman, WA
| | - Karin S Pfennig
- University of North Carolina at Chapel Hill, Department of Biology, Chapel Hill, NC
| | - Daniel Rubinoff
- University of Hawaiʻi at Manoa, Department of Plant and Environmental Protection Sciences, Honolulu, HI
| | | | - Ole Seehausen
- Institute of Ecology & Evolution, University of Bern, Bern, BE, Switzerland
- Center for Ecology, Evolution & Biogeochemistry, Eawag, Kastanienbaum, LU, Switzerland
| | - Kerry L Shaw
- Cornell University, Neurobiology and Behavior, Tower Road,, Ithaca, NY
| | - Elizabeth Stacy
- University of Nevada Las Vegas, School of Life Sciences, Las Vegas, NV
| | - Martin Stervander
- University of Oregon, Institute of Ecology and Evolution, Eugene, OR
| | - James T Stroud
- Washington University in Saint Louis, Biology, Saint Louis, MO
| | | | - Guinevere O U Wogan
- University of California Berkeley, Environmental Science Policy, and Management, Berkeley, CA
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29
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Matute DR, Comeault AA, Earley E, Serrato-Capuchina A, Peede D, Monroy-Eklund A, Huang W, Jones CD, Mackay TFC, Coyne JA. Rapid and Predictable Evolution of Admixed Populations Between Two Drosophila Species Pairs. Genetics 2020; 214:211-230. [PMID: 31767631 PMCID: PMC6944414 DOI: 10.1534/genetics.119.302685] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022] Open
Abstract
The consequences of hybridization are varied, ranging from the origin of new lineages, introgression of some genes between species, to the extinction of one of the hybridizing species. We generated replicate admixed populations between two pairs of sister species of Drosophila: D. simulans and D. mauritiana; and D. yakuba and D. santomea Each pair consisted of a continental species and an island endemic. The admixed populations were maintained by random mating in discrete generations for over 20 generations. We assessed morphological, behavioral, and fitness-related traits from each replicate population periodically, and sequenced genomic DNA from the populations at generation 20. For both pairs of species, species-specific traits and their genomes regressed to those of the continental species. A few alleles from the island species persisted, but they tended to be proportionally rare among all sites in the genome and were rarely fixed within the populations. This paucity of alleles from the island species was particularly pronounced on the X-chromosome. These results indicate that nearly all foreign genes were quickly eliminated after hybridization and that selection against the minor species genome might be similar across experimental replicates.
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Affiliation(s)
- Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Aaron A Comeault
- School of Natural Sciences, Bangor University, Wales, UK LL57 2EN
| | - Eric Earley
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | | | - David Peede
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Anaïs Monroy-Eklund
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Wen Huang
- Program in Genetics and Department of Biological Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Corbin D Jones
- Biology Department, University of North Carolina, Chapel Hill, North Carolina
| | - Trudy F C Mackay
- Program in Genetics and Department of Biological Science, North Carolina State University, Raleigh, North Carolina 27695
| | - Jerry A Coyne
- Ecology and Evolution, University of Chicago, Illinois 60637
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30
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Meier JI, Stelkens RB, Joyce DA, Mwaiko S, Phiri N, Schliewen UK, Selz OM, Wagner CE, Katongo C, Seehausen O. The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes. Nat Commun 2019; 10:5391. [PMID: 31796733 PMCID: PMC6890737 DOI: 10.1038/s41467-019-13278-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 10/22/2019] [Indexed: 01/26/2023] Open
Abstract
The process of adaptive radiation was classically hypothesized to require isolation of a lineage from its source (no gene flow) and from related species (no competition). Alternatively, hybridization between species may generate genetic variation that facilitates adaptive radiation. Here we study haplochromine cichlid assemblages in two African Great Lakes to test these hypotheses. Greater biotic isolation (fewer lineages) predicts fewer constraints by competition and hence more ecological opportunity in Lake Bangweulu, whereas opportunity for hybridization predicts increased genetic potential in Lake Mweru. In Lake Bangweulu, we find no evidence for hybridization but also no adaptive radiation. We show that the Bangweulu lineages also colonized Lake Mweru, where they hybridized with Congolese lineages and then underwent multiple adaptive radiations that are strikingly complementary in ecology and morphology. Our data suggest that the presence of several related lineages does not necessarily prevent adaptive radiation, although it constrains the trajectories of morphological diversification. It might instead facilitate adaptive radiation when hybridization generates genetic variation, without which radiation may start much later, progress more slowly or never occur.
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Affiliation(s)
- Joana I Meier
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street, Cambridge, CB2 1TP, UK
| | - Rike B Stelkens
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Division of Population Genetics, Department of Zoology, Stockholm University, Svante Arrheniusväg 18 B, 106 91, Stockholm, Sweden
| | - Domino A Joyce
- Evolutionary and Ecological Genomics Group, Department of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Salome Mwaiko
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Numel Phiri
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Ulrich K Schliewen
- SNSB-Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, Munich, Germany
| | - Oliver M Selz
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Catherine E Wagner
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Biodiversity Institute and Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Cyprian Katongo
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Ole Seehausen
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland.
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.
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31
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Abstract
Interspecific hybridization is the process where closely related species mate and produce offspring with admixed genomes. The genomic revolution has shown that hybridization is common, and that it may represent an important source of novel variation. Although most interspecific hybrids are sterile or less fit than their parents, some may survive and reproduce, enabling the transfer of adaptive variants across the species boundary, and even result in the formation of novel evolutionary lineages. There are two main variants of hybrid species genomes: allopolyploid, which have one full chromosome set from each parent species, and homoploid, which are a mosaic of the parent species genomes with no increase in chromosome number. The establishment of hybrid species requires the development of reproductive isolation against parental species. Allopolyploid species often have strong intrinsic reproductive barriers due to differences in chromosome number, and homoploid hybrids can become reproductively isolated from the parent species through assortment of genetic incompatibilities. However, both types of hybrids can become further reproductively isolated, gaining extrinsic isolation barriers, by exploiting novel ecological niches, relative to their parents. Hybrids represent the merging of divergent genomes and thus face problems arising from incompatible combinations of genes. Thus hybrid genomes are highly dynamic and undergo rapid evolutionary change, including genome stabilization in which selection against incompatible combinations results in fixation of compatible ancestry block combinations within the hybrid species. The potential for rapid adaptation or speciation makes hybrid genomes a particularly exciting subject of in evolutionary biology. Here we summarize how introgressed alleles or hybrid species can establish and how the resulting hybrid genomes evolve.
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Affiliation(s)
- Anna Runemark
- Department of Biology, Lund University, Lund, Sweden
- * E-mail:
| | - Mario Vallejo-Marin
- Biological and Environmental Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Joana I. Meier
- St John's College, Cambridge, Cambridge, United Kingdom
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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32
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White NJ, Snook RR, Eyres I. The Past and Future of Experimental Speciation. Trends Ecol Evol 2019; 35:10-21. [PMID: 31522756 DOI: 10.1016/j.tree.2019.08.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/08/2019] [Accepted: 08/14/2019] [Indexed: 12/22/2022]
Abstract
Speciation is the result of evolutionary processes that generate barriers to gene flow between populations, facilitating reproductive isolation. Speciation is typically studied via theoretical models and snapshot tests in natural populations. Experimental speciation enables real-time direct tests of speciation theory and has been long touted as a critical complement to other approaches. We argue that, despite its promise to elucidate the evolution of reproductive isolation, experimental speciation has been underutilised and lags behind other contributions to speciation research. We review recent experiments and outline a framework for how experimental speciation can be implemented to address current outstanding questions that are otherwise challenging to answer. Greater uptake of this approach is necessary to rapidly advance understanding of speciation.
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Affiliation(s)
- Nathan J White
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm 106-91, Sweden
| | - Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK.
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33
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Dean LL, Magalhaes IS, Foote A, D'Agostino D, McGowan S, MacColl ADC. Admixture between ancient lineages, selection, and the formation of sympatric stickleback species-pairs. Mol Biol Evol 2019; 36:2481-2497. [PMID: 31297536 PMCID: PMC6805233 DOI: 10.1093/molbev/msz161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/02/2019] [Accepted: 07/07/2019] [Indexed: 12/14/2022] Open
Abstract
Ecological speciation has become a popular model for the development and maintenance of reproductive isolation in closely related sympatric pairs of species or ecotypes. An implicit assumption has been that such pairs originate (possibly with gene flow) from a recent, genetically homogeneous ancestor. However, recent genomic data has revealed that currently sympatric taxa are often a result of secondary contact between ancestrally allopatric lineages. This has sparked an interest in the importance of initial hybridization upon secondary contact, with genomic re-analysis of classic examples of ecological speciation often implicating admixture in speciation. We describe a novel occurrence of unusually well-developed reproductive isolation in a model system for ecological speciation: the three-spined stickleback (Gasterosteus aculeatus), breeding sympatrically in multiple lagoons on the Scottish island of North Uist. Using morphological data, targeted genotyping and genome-wide single nucleotide polymorphism (SNP) data we show that lagoon resident and anadromous ecotypes are strongly reproductively isolated with an estimated hybridization rate of only ∼1%. We use palaeoecological and genetic data to test three hypotheses to explain the existence of these species-pairs. Our results suggest that recent, purely ecological speciation from a genetically homogeneous ancestor is probably not solely responsible for the evolution of species-pairs. Instead we reveal a complex colonisation history with multiple ancestral lineages contributing to the genetic composition of species-pairs, alongside strong disruptive selection. Our results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Isabel S Magalhaes
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK.,Department of Life Sciences, Whitelands College, University of Roehampton, London, UK
| | - Andrew Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd, UK
| | - Daniele D'Agostino
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Suzanne McGowan
- School of Geography, The University of Nottingham, University Park, Nottingham, UK
| | - Andrew D C MacColl
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
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34
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Zhang BW, Xu LL, Li N, Yan PC, Jiang XH, Woeste KE, Lin K, Renner SS, Zhang DY, Bai WN. Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut. Mol Biol Evol 2019; 36:2451-2461. [PMID: 31163451 DOI: 10.1093/molbev/msz112] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/13/2019] [Accepted: 04/16/2019] [Indexed: 01/25/2023] Open
Abstract
Abstract
Persian walnut (Juglans regia) is cultivated worldwide for its high-quality wood and nuts, but its origin has remained mysterious because in phylogenies it occupies an unresolved position between American black walnuts and Asian butternuts. Equally unclear is the origin of the only American butternut, J. cinerea. We resequenced the whole genome of 80 individuals from 19 of the 22 species of Juglans and assembled the genome of its relatives Pterocarya stenoptera and Platycarya strobilacea. Using phylogenetic-network analysis of single-copy nuclear genes, genome-wide site pattern probabilities, and Approximate Bayesian Computation, we discovered that J. regia (and its landrace J. sigillata) arose as a hybrid between the American and the Asian lineages and that J. cinerea resulted from massive introgression from an immigrating Asian butternut into the genome of an American black walnut. Approximate Bayesian Computation modeling placed the hybrid origin in the late Pliocene, ∼3.45 My, with both parental lineages since having gone extinct in Europe.
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Affiliation(s)
- Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lin-Lin Xu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Nan Li
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Peng-Cheng Yan
- Beijing Key Laboratory of Cloud Computing Key Technology and Application, Beijing Computing Center, Beijing, China
| | - Xin-Hua Jiang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Keith E Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN
| | - Kui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Susanne S Renner
- Department of Biology, Systematic Botany and Mycology, University of Munich (LMU), Munich, Germany
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
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35
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Marques DA, Meier JI, Seehausen O. A Combinatorial View on Speciation and Adaptive Radiation. Trends Ecol Evol 2019; 34:531-544. [DOI: 10.1016/j.tree.2019.02.008] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 02/07/2019] [Accepted: 02/13/2019] [Indexed: 01/28/2023]
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