51
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Chhina AK, Thompson KA, Schluter D. Adaptive divergence and the evolution of hybrid trait mismatch in threespine stickleback. Evol Lett 2022; 6:34-45. [PMID: 35127136 PMCID: PMC8802241 DOI: 10.1002/evl3.264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 10/31/2021] [Indexed: 12/31/2022] Open
Abstract
Selection against mismatched traits in hybrids is the phenotypic analogue of intrinsic hybrid incompatibilities. Mismatch occurs when hybrids resemble one parent population for some phenotypic traits and the other parent population for other traits, and is caused by dominance in opposing directions or from segregation of alleles in recombinant hybrids. In this study, we used threespine stickleback fish (Gasterosteus aculeatus L.) to test the theoretical prediction that trait mismatch in hybrids should increase with the magnitude of phenotypic divergence between parent populations. We measured morphological traits in parents and hybrids in crosses between a marine population representing the ancestral form and twelve freshwater populations that have diverged from this ancestral state to varying degrees according to their environments. We found that trait mismatch was greater in more divergent crosses for both F1 and F2 hybrids. In the F1, the divergence–mismatch relationship was caused by traits having dominance in different directions, whereas it was caused by increasing segregating phenotypic variation in the F2. Our results imply that extrinsic hybrid incompatibilities accumulate as phenotypic divergence proceeds.
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Affiliation(s)
- Avneet K. Chhina
- Department of Zoology & Biodiversity Research Centre University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Ken A. Thompson
- Department of Zoology & Biodiversity Research Centre University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Dolph Schluter
- Department of Zoology & Biodiversity Research Centre University of British Columbia Vancouver BC V6T 1Z4 Canada
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52
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Coughlan J. One fish, two fish, red fish, dead fish: Detecting the genomic footprint of ecological incompatibilities. PLoS Biol 2022; 20:e3001504. [PMID: 35015759 PMCID: PMC8752012 DOI: 10.1371/journal.pbio.3001504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
As we uncover the ubiquity of hybridization in nature, determining how natural selection acts on hybrids has newfound importance for speciation. A study in PLOS Biology uses threespine stickleback to detect a genomic signature of ecological incompatibilities.
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Affiliation(s)
- Jenn Coughlan
- Biology Department, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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53
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Adaptive divergence in shoot gravitropism creates hybrid sterility in an Australian wildflower. Proc Natl Acad Sci U S A 2021; 118:2004901118. [PMID: 34789571 PMCID: PMC8617494 DOI: 10.1073/pnas.2004901118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2021] [Indexed: 11/18/2022] Open
Abstract
New species originate as populations become reproductively isolated from one another. Despite recent progress in uncovering the genetic basis of reproductive isolation, it remains unclear whether intrinsic reproductive barriers, such as hybrid sterility, can evolve as a by-product of local adaptation to contrasting environments. Here, we show that differences in a plant’s response to the pull of gravity have repeatedly evolved amongst coastal populations of an Australian wildflower, thus implicating a role of natural selection in their evolution. We found a strong genetic association between variation in this adaptive trait and hybrid sterility, suggesting that intrinsic reproductive barriers contribute to the origin of new species as populations adapt to heterogeneous environments. Natural selection is responsible for much of the diversity we see in nature. Just as it drives the evolution of new traits, it can also lead to new species. However, it is unclear whether natural selection conferring adaptation to local environments can drive speciation through the evolution of hybrid sterility between populations. Here, we show that adaptive divergence in shoot gravitropism, the ability of a plant’s shoot to bend upwards in response to the downward pull of gravity, contributes to the evolution of hybrid sterility in an Australian wildflower, Senecio lautus. We find that shoot gravitropism has evolved multiple times in association with plant height between adjacent populations inhabiting contrasting environments, suggesting that these traits have evolved by natural selection. We directly tested this prediction using a hybrid population subjected to eight rounds of recombination and three rounds of selection in the field. Our experiments revealed that shoot gravitropism responds to natural selection in the expected direction of the locally adapted population. Using the advanced hybrid population, we discovered that individuals with extreme differences in gravitropism had more sterile crosses than individuals with similar gravitropic responses, which were largely fertile, indicating that this adaptive trait is genetically correlated with hybrid sterility. Our results suggest that natural selection can drive the evolution of locally adaptive traits that also create hybrid sterility, thus revealing an evolutionary connection between local adaptation and the origin of new species.
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54
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Rosser N, Edelman NB, Queste LM, Nelson M, Seixas F, Dasmahapatra KK, Mallet J. Complex basis of hybrid female sterility and Haldane's rule in Heliconius butterflies: Z-linkage and epistasis. Mol Ecol 2021; 31:959-977. [PMID: 34779079 DOI: 10.1111/mec.16272] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/14/2021] [Accepted: 09/27/2021] [Indexed: 12/19/2022]
Abstract
Hybrids between species are often sterile or inviable. Hybrid unfitness usually evolves first in the heterogametic sex-a pattern known as Haldane's rule. The genetics of Haldane's rule have been extensively studied in species where the male is the heterogametic (XX/XY) sex, but its basis in taxa where the female is heterogametic (ZW/ZZ), such as Lepidoptera and birds, is largely unknown. Here, we analyse a new case of female hybrid sterility between geographic subspecies of Heliconius pardalinus. The two subspecies mate freely in captivity, but female F1 hybrids in both directions of cross are sterile. Sterility is due to arrested development of oocytes after they become differentiated from nurse cells, but before yolk deposition. We backcrossed fertile male F1 hybrids to parental females and mapped quantitative trait loci (QTLs) for female sterility. We also identified genes differentially expressed in the ovary as a function of oocyte development. The Z chromosome has a major effect, similar to the 'large X effect' in Drosophila, with strong epistatic interactions between loci at either end of the Z chromosome, and between the Z chromosome and autosomal loci on chromosomes 8 and 20. By intersecting the list of genes within these QTLs with those differentially expressed in sterile and fertile hybrids, we identified three candidate genes with relevant phenotypes. This study is the first to characterize hybrid sterility using genome mapping in the Lepidoptera and shows that it is produced by multiple complex epistatic interactions often involving the sex chromosome, as predicted by the dominance theory of Haldane's rule.
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Affiliation(s)
- Neil Rosser
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Department of Biology, University of York, York, UK
| | - Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Yale Institute for Biospheric Studies, Yale University, New Haven, Connecticut, USA.,Yale School for the Environment, Yale University, New Haven, Connecticut, USA
| | | | | | - Fernando Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | | | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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55
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Weber AAT, Rajkov J, Smailus K, Egger B, Salzburger W. Speciation dynamics and extent of parallel evolution along a lake-stream environmental contrast in African cichlid fishes. SCIENCE ADVANCES 2021; 7:eabg5391. [PMID: 34731007 PMCID: PMC8565912 DOI: 10.1126/sciadv.abg5391] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding the dynamics of speciation is a central topic in evolutionary biology. Here, we investigated how morphological and genomic differentiation accumulated along the speciation continuum in the African cichlid fish Astatotilapia burtoni. While morphological differentiation was continuously distributed across different lake-stream population pairs, we found that there were two categories with respect to genomic differentiation, suggesting a “gray zone” of speciation at ~0.1% net nucleotide divergence. Genomic differentiation was increased in the presence of divergent selection and drift compared to drift alone. The quantification of phenotypic and genetic parallelism in four cichlid species occurring along a lake-stream environmental contrast revealed parallel and antiparallel components in rapid adaptive divergence, and morphological convergence in species replicates inhabiting the same environments. Furthermore, we show that the extent of parallelism was higher when ancestral populations were more similar. Our study highlights the complementary roles of divergent selection and drift on speciation and parallel evolution.
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56
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Ito S, Hirano T, Chiba S, Konuma J. Shell colour diversification induced by ecological release: A shift in natural selection after a migration event. Ecol Evol 2021; 11:15534-15544. [PMID: 34824773 PMCID: PMC8601913 DOI: 10.1002/ece3.8080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 11/20/2022] Open
Abstract
Ecological release is often attributed to the rapid adaptive diversification of phenotypic traits. However, it is not well understood how natural selection changes its strength and direction through the process of ecological release. Herein, we demonstrated how shell colour of the Japanese land snail Euhadra peliomphala simodae has diversified via a shift in natural selection due to ecological release after migration from the mainland to an island. This snail's shell colour diversified on the island due to disruptive selection after migration from the mainland. We used trail camera traps to identify the cause of natural selection on both the mainland and the island. We then conducted a mark-recapture experiment while collecting microhabitat use data. In total, we captured and marked around 1,700 snails on the mainland, some of which were preyed upon by an unknown predator. The trail camera traps showed that the predator is the large Japanese field mouse Apodemus speciosus, and the predatory frequency was higher on the mainland than on the island. However, this predation did not correlate with shell colour. Microhabitat use on the island was more extensive than on the mainland, with snails on the island using both ground and arboreal microhabitats. A Bayesian estimation showed that the stabilizing selection on shell colour came from factors other than predation. Our results suggest that the course of natural selection was modified due to ecological release after migration from the mainland, explaining one cause of the phenotypic diversification.
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Affiliation(s)
- Shun Ito
- Graduate School of Life ScienceTohoku UniversityMiyagiJapan
| | - Takahiro Hirano
- Graduate School of Life ScienceTohoku UniversityMiyagiJapan
- Center for Northeast Asian StudiesTohoku UniversityMiyagiJapan
| | - Satoshi Chiba
- Graduate School of Life ScienceTohoku UniversityMiyagiJapan
- Center for Northeast Asian StudiesTohoku UniversityMiyagiJapan
| | - Junji Konuma
- Department of Biology, Faculty of ScienceToho UniversityChibaJapan
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57
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Changes in selection pressure can facilitate hybridization during biological invasion in a Cuban lizard. Proc Natl Acad Sci U S A 2021; 118:2108638118. [PMID: 34654747 DOI: 10.1073/pnas.2108638118] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2021] [Indexed: 11/18/2022] Open
Abstract
Hybridization is among the evolutionary mechanisms most frequently hypothesized to drive the success of invasive species, in part because hybrids are common in invasive populations. One explanation for this pattern is that biological invasions coincide with a change in selection pressures that limit hybridization in the native range. To investigate this possibility, we studied the introduction of the brown anole (Anolis sagrei) in the southeastern United States. We find that native populations are highly genetically structured. In contrast, all invasive populations show evidence of hybridization among native-range lineages. Temporal sampling in the invasive range spanning 15 y showed that invasive genetic structure has stabilized, indicating that large-scale contemporary gene flow is limited among invasive populations and that hybrid ancestry is maintained. Additionally, our results are consistent with hybrid persistence in invasive populations resulting from changes in natural selection that occurred during invasion. Specifically, we identify a large-effect X chromosome locus associated with variation in limb length, a well-known adaptive trait in anoles, and show that this locus is often under selection in the native range, but rarely so in the invasive range. Moreover, we find that the effect size of alleles at this locus on limb length is much reduced in hybrids among divergent lineages, consistent with epistatic interactions. Thus, in the native range, epistasis manifested in hybrids can strengthen extrinsic postmating isolation. Together, our findings show how a change in natural selection can contribute to an increase in hybridization in invasive populations.
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58
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Ottenburghs J. The genic view of hybridization in the Anthropocene. Evol Appl 2021; 14:2342-2360. [PMID: 34745330 PMCID: PMC8549621 DOI: 10.1111/eva.13223] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/24/2022] Open
Abstract
Human impact is noticeable around the globe, indicating that a new era might have begun: the Anthropocene. Continuing human activities, including land-use changes, introduction of non-native species and rapid climate change, are altering the distributions of countless species, often giving rise to human-mediated hybridization events. While the interbreeding of different populations or species can have detrimental effects, such as genetic extinction, it can be beneficial in terms of adaptive introgression or an increase in genetic diversity. In this paper, I first review the different mechanisms and outcomes of anthropogenic hybridization based on literature from the last five years (2016-2020). The most common mechanisms leading to the interbreeding of previously isolated taxa include habitat change (51% of the studies) and introduction of non-native species (34% intentional and 19% unintentional). These human-induced hybridization events most often result in introgression (80%). The high incidence of genetic exchange between the hybridizing taxa indicates that the application of a genic view of speciation (and introgression) can provide crucial insights on how to address hybridization events in the Anthropocene. This perspective considers the genome as a dynamic collection of genetic loci with distinct evolutionary histories, giving rise to a heterogenous genomic landscape in terms of genetic differentiation and introgression. First, understanding this genomic landscape can lead to a better selection of diagnostic genetic markers to characterize hybrid populations. Second, describing how introgression patterns vary across the genome can help to predict the likelihood of negative processes, such as demographic and genetic swamping, as well as positive outcomes, such as adaptive introgression. It is especially important to not only quantify how much genetic material introgressed, but also what has been exchanged. Third, comparing introgression patterns in pre-Anthropocene hybridization events with current human-induced cases might provide novel insights into the likelihood of genetic swamping or species collapse during an anthropogenic hybridization event. However, this comparative approach remains to be tested before it can be applied in practice. Finally, the genic view of introgression can be combined with conservation genomic studies to determine the legal status of hybrids and take appropriate measures to manage anthropogenic hybridization events. The interplay between evolutionary and conservation genomics will result in the constant exchange of ideas between these fields which will not only improve our knowledge on the origin of species, but also how to conserve and protect them.
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Affiliation(s)
- Jente Ottenburghs
- Wildlife Ecology and ConservationWageningen University & ResearchWageningenThe Netherlands
- Forest Ecology and Forest ManagementWageningen University & ResearchWageningenThe Netherlands
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59
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Miller AK, Westlake CS, Cross KL, Leigh BA, Bordenstein SR. The microbiome impacts host hybridization and speciation. PLoS Biol 2021; 19:e3001417. [PMID: 34699520 PMCID: PMC8547693 DOI: 10.1371/journal.pbio.3001417] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Microbial symbiosis and speciation profoundly shape the composition of life's biodiversity. Despite the enormous contributions of these two fields to the foundations of modern biology, there is a vast and exciting frontier ahead for research, literature, and conferences to address the neglected prospects of merging their study. Here, we survey and synthesize exemplar cases of how endosymbionts and microbial communities affect animal hybridization and vice versa. We conclude that though the number of case studies remain nascent, the wide-ranging types of animals, microbes, and isolation barriers impacted by hybridization will likely prove general and a major new phase of study that includes the microbiome as part of the functional whole contributing to reproductive isolation. Though microorganisms were proposed to impact animal speciation a century ago, the weight of the evidence supporting this view has now reached a tipping point.
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Affiliation(s)
- Asia K. Miller
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt University, Vanderbilt Microbiome Innovation Center, Nashville, Tennessee, United States of America
| | - Camille S. Westlake
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt University, Vanderbilt Microbiome Innovation Center, Nashville, Tennessee, United States of America
| | - Karissa L. Cross
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt University, Vanderbilt Microbiome Innovation Center, Nashville, Tennessee, United States of America
| | - Brittany A. Leigh
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt University, Vanderbilt Microbiome Innovation Center, Nashville, Tennessee, United States of America
| | - Seth R. Bordenstein
- Vanderbilt University, Department of Biological Sciences, Nashville, Tennessee, United States of America
- Vanderbilt University, Vanderbilt Microbiome Innovation Center, Nashville, Tennessee, United States of America
- Vanderbilt University Medical Center, Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, Tennessee, United States of America
- Vanderbilt University Medical Center, Department of Pathology, Microbiology & Immunology, Nashville, Tennessee, United States of America
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60
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Serrato-Capuchina A, D’Agostino ERR, Peede D, Roy B, Isbell K, Wang J, Matute DR. P-elements strengthen reproductive isolation within the Drosophila simulans species complex. Evolution 2021; 75:2425-2440. [PMID: 34463356 PMCID: PMC8772388 DOI: 10.1111/evo.14319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 04/29/2021] [Accepted: 05/06/2021] [Indexed: 11/28/2022]
Abstract
Determining mechanisms that underlie reproductive isolation (RI) is key to understanding how species boundaries are maintained in nature. Transposable elements (TEs) are ubiquitous across eukaryotic genomes. However, the role of TEs in modulating the strength of RI between species is poorly understood. Several species of Drosophila have been found to harbor P-elements (PEs), yet only D. simulans is known to be currently polymorphic for their presence in wild populations. PEs can cause RI between PE-containing (P) and PE-lacking (M) lineages of the same species. However, it is unclear whether they also contribute to the magnitude of RI between species. Here, we use the simulans species complex to assess whether differences in PE status between D. simulans and its sister species, which do not harbor PEs, contribute to multiple barriers to gene flow between species. We show that crosses involving a P D. simulans father and an M mother from a sister species exhibit lower F1 female fecundity than crosses involving an M D. simulans father and an M sister-species mother. We also find that another TE, I-element, might play a minor role in determining the frequency of dysgenesis between species. Our results suggest that the presence of PEs in a species can strengthen isolation from its sister species, providing evidence that TEs can play a role in RI.
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Affiliation(s)
- Antonio Serrato-Capuchina
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Emmanuel R. R. D’Agostino
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - David Peede
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Baylee Roy
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Kristin Isbell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Jeremy Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
| | - Daniel R. Matute
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514
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61
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Jofre GI, Rosenthal GG. A narrow window for geographic cline analysis using genomic data: Effects of age, drift, and migration on error rates. Mol Ecol Resour 2021; 21:2278-2287. [PMID: 33979028 DOI: 10.1111/1755-0998.13428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 01/11/2023]
Abstract
The use of genomic and phenotypic data to scan for outliers is a mainstay for studies of hybridization and speciation. Geographic cline analysis of natural hybrid zones is widely used to identify putative signatures of selection by detecting deviations from baseline patterns of introgression. As with other outlier-based approaches, demographic histories can make neutral regions appear to be under selection and vice versa. In this study, we use a forward-time individual-based simulation approach to evaluate the robustness of geographic cline analysis under different evolutionary scenarios. We modelled multiple stepping-stone hybrid zones with distinct age, deme sizes, and migration rates, and evolving under different types of selection. We found that drift distorts cline shapes and increases false positive rates for signatures of selection. This effect increases with hybrid zone age, particularly if migration between demes is low. Drift can also distort the signature of deleterious effects of hybridization, with genetic incompatibilities and particularly underdominance prone to spurious typing as adaptive introgression. Our results suggest that geographic clines are most useful for outlier analysis in young hybrid zones with large populations of hybrid individuals. Current approaches may overestimate adaptive introgression and underestimate selection against maladaptive genotypes.
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Affiliation(s)
- Gaston I Jofre
- Department of Biology, Texas A&M University, TAMU, College Station, TX, USA.,Centro de Investigaciones Cientıficas de las Huastecas "Aguazarca", Calnali Hidalgo, Mexico.,Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Gil G Rosenthal
- Department of Biology, Texas A&M University, TAMU, College Station, TX, USA.,Centro de Investigaciones Cientıficas de las Huastecas "Aguazarca", Calnali Hidalgo, Mexico
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62
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Against the Odds: Hybrid Zones between Mangrove Killifish Species with Different Mating Systems. Genes (Basel) 2021; 12:genes12101486. [PMID: 34680881 PMCID: PMC8535463 DOI: 10.3390/genes12101486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/21/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Different mating systems are expected to affect the extent and direction of hybridization. Due to the different levels of sexual conflict, the weak inbreeder/strong outbreeder (WISO) hypothesis predicts that gametes from self-incompatible (SI) species should outcompete gametes from self-compatible (SC) ones. However, other factors such as timing of selfing and unilateral incompatibilities may also play a role on the direction of hybridization. In addition, differential mating opportunities provided by different mating systems are also expected to affect the direction of introgression in hybrid zones involving outcrossers and selfers. Here, we explored these hypotheses with a unique case of recent hybridization between two mangrove killifish species with different mating systems, Kryptolebias ocellatus (obligately outcrossing) and K. hermaphroditus (predominantly self-fertilizing) in two hybrid zones in southeast Brazil. Hybridization rates were relatively high (~20%), representing the first example of natural hybridization between species with different mating systems in vertebrates. All F1 individuals were sired by the selfing species. Backcrossing was small, but mostly asymmetrical with the SI parental species, suggesting pattern commonly observed in plant hybrid zones with different mating systems. Our findings shed light on how contrasting mating systems may affect the direction and extent of gene flow between sympatric species, ultimately affecting the evolution and maintenance of hybrid zones.
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63
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Mass of genes rather than master genes underlie the genomic architecture of amphibian speciation. Proc Natl Acad Sci U S A 2021; 118:2103963118. [PMID: 34465621 DOI: 10.1073/pnas.2103963118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genetic architecture of speciation, i.e., how intrinsic genomic incompatibilities promote reproductive isolation (RI) between diverging lineages, is one of the best-kept secrets of evolution. To directly assess whether incompatibilities arise in a limited set of large-effect speciation genes, or in a multitude of loci, we examined the geographic and genomic landscapes of introgression across the hybrid zones of 41 pairs of frog and toad lineages in the Western Palearctic region. As the divergence between lineages increases, phylogeographic transitions progressively become narrower, and larger parts of the genome resist introgression. This suggests that anuran speciation proceeds through a gradual accumulation of multiple barrier loci scattered across the genome, which ultimately deplete hybrid fitness by intrinsic postzygotic isolation, with behavioral isolation being achieved only at later stages. Moreover, these loci were disproportionately sex linked in one group (Hyla) but not in others (Rana and Bufotes), implying that large X-effects are not necessarily a rule of speciation with undifferentiated sex chromosomes. The highly polygenic nature of RI and the lack of hemizygous X/Z chromosomes could explain why the speciation clock ticks slower in amphibians compared to other vertebrates. The clock-like dynamics of speciation combined with the analytical focus on hybrid zones offer perspectives for more standardized practices of species delimitation.
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64
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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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65
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Pereira RJ, Lima TG, Pierce-Ward NT, Chao L, Burton RS. Recovery from hybrid breakdown reveals a complex genetic architecture of mitonuclear incompatibilities. Mol Ecol 2021; 30:6403-6416. [PMID: 34003535 DOI: 10.1111/mec.15985] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/29/2021] [Accepted: 05/11/2021] [Indexed: 01/03/2023]
Abstract
Reproductive isolation is often achieved when genes that are neutral or beneficial in their genomic background become functionally incompatible in a foreign genomic background, causing inviability, sterility or other forms of low fitness in hybrids. Recent studies suggest that mitonuclear interactions are among the initial incompatibilities to evolve at early stages of population divergence across taxa. Yet, the genomic architecture of mitonuclear incompatibilities has rarely been elucidated. We employ an experimental evolution approach starting with low-fitness F2 interpopulation hybrids of the copepod Tigriopus californicus, in which frequencies of compatible and incompatible nuclear alleles change in response to an alternative mitochondrial background. After about nine generations, we observe a generalized increase in population size and in survivorship, suggesting efficiency of selection against maladaptive phenotypes. Whole genome sequencing of evolved populations showed some consistent allele frequency changes across three replicates of each reciprocal cross, but markedly different patterns between mitochondrial backgrounds. In only a few regions (~6.5% of the genome), the same parental allele was overrepresented irrespective of the mitochondrial background. About 33% of the genome showed allele frequency changes consistent with divergent selection, with the location of these genomic regions strongly differing between mitochondrial backgrounds. In 87% and 89% of these genomic regions, the dominant nuclear allele matched the associated mitochondrial background, consistent with mitonuclear co-adaptation. These results suggest that mitonuclear incompatibilities have a complex polygenic architecture that differs between populations, potentially generating genome-wide barriers to gene flow between closely related taxa.
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Affiliation(s)
- Ricardo J Pereira
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Thiago G Lima
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - N Tessa Pierce-Ward
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lin Chao
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
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66
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Kolora SRR, Gysi DM, Schaffer S, Grimm-Seyfarth A, Szabolcs M, Faria R, Henle K, Stadler PF, Schlegel M, Nowick K. Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards. Genome Biol Evol 2021; 13:6275683. [PMID: 33988711 PMCID: PMC8382678 DOI: 10.1093/gbe/evab109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 11/12/2022] Open
Abstract
The European green lizards of the Lacerta viridis complex consist of two closely related species, L. viridis and Lacerta bilineata that split less than 7 million years ago in the presence of gene flow. Recently, a third lineage, referred to as the “Adriatic” was described within the L. viridis complex distributed from Slovenia to Greece. However, whether gene flow between the Adriatic lineage and L. viridis or L. bilineata has occurred and the evolutionary processes involved in their diversification are currently unknown. We hypothesized that divergence occurred in the presence of gene flow between multiple lineages and involved tissue-specific gene evolution. In this study, we sequenced the whole genome of an individual of the Adriatic lineage and tested for the presence of gene flow amongst L. viridis, L. bilineata, and Adriatic. Additionally, we sequenced transcriptomes from multiple tissues to understand tissue-specific effects. The species tree supports that the Adriatic lineage is a sister taxon to L. bilineata. We detected gene flow between the Adriatic lineage and L. viridis suggesting that the evolutionary history of the L. viridis complex is likely shaped by gene flow. Interestingly, we observed topological differences between the autosomal and Z-chromosome phylogenies with a few fast evolving genes on the Z-chromosome. Genes highly expressed in the ovaries and strongly co-expressed in the brain experienced accelerated evolution presumably contributing to establishing reproductive isolation in the L. viridis complex.
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Affiliation(s)
- Sree Rohit Raj Kolora
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany.,Molecular Evolution & Animal Systematics, University of Leipzig, Leipzig, Germany.,Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Deisy Morselli Gysi
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany.,Swarm Intelligence and Complex Systems Group, Faculty of Mathematics and Computer Science, University of Leipzig, Leipzig, Germany.,Center for Complex Networks Research, Northeastern University, Boston, MA, USA
| | - Stefan Schaffer
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Leipzig, Germany.,Molecular Evolution & Animal Systematics, University of Leipzig, Leipzig, Germany
| | - Annegret Grimm-Seyfarth
- Department of Conservation Biology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Márton Szabolcs
- Department of Tisza River Research, Danube Research Institute, Centre for Ecological Research, Hungarian Academy of Sciences, Debrecen, Hungary
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Klaus Henle
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Leipzig, Germany.,Department of Conservation Biology, UFZ-Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Peter F Stadler
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Leipzig, Germany.,Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Leipzig, Germany.,Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Universität Leipzig, Leipzig, Germany.,Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Theoretical Chemistry, University of Vienna, Wien, Austria.,Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia.,Santa Fe Institute, New Mexico, USA
| | - Martin Schlegel
- German Centre for Integrative Biodiversity Research (iDiv) Halle Jena Leipzig, Leipzig, Germany.,Molecular Evolution & Animal Systematics, University of Leipzig, Leipzig, Germany
| | - Katja Nowick
- Institute for Biology, Freie Universität Berlin, Berlin, Germany
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67
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Vershinina AO, Heintzman PD, Froese DG, Zazula G, Cassatt-Johnstone M, Dalén L, Der Sarkissian C, Dunn SG, Ermini L, Gamba C, Groves P, Kapp JD, Mann DH, Seguin-Orlando A, Southon J, Stiller M, Wooller MJ, Baryshnikov G, Gimranov D, Scott E, Hall E, Hewitson S, Kirillova I, Kosintsev P, Shidlovsky F, Tong HW, Tiunov MP, Vartanyan S, Orlando L, Corbett-Detig R, MacPhee RD, Shapiro B. Ancient horse genomes reveal the timing and extent of dispersals across the Bering Land Bridge. Mol Ecol 2021; 30:6144-6161. [PMID: 33971056 DOI: 10.1111/mec.15977] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/24/2021] [Accepted: 04/27/2021] [Indexed: 01/02/2023]
Abstract
The Bering Land Bridge (BLB) last connected Eurasia and North America during the Late Pleistocene. Although the BLB would have enabled transfers of terrestrial biota in both directions, it also acted as an ecological filter whose permeability varied considerably over time. Here we explore the possible impacts of this ecological corridor on genetic diversity within, and connectivity among, populations of a once wide-ranging group, the caballine horses (Equus spp.). Using a panel of 187 mitochondrial and eight nuclear genomes recovered from present-day and extinct caballine horses sampled across the Holarctic, we found that Eurasian horse populations initially diverged from those in North America, their ancestral continent, around 1.0-0.8 million years ago. Subsequent to this split our mitochondrial DNA analysis identified two bidirectional long-range dispersals across the BLB ~875-625 and ~200-50 thousand years ago, during the Middle and Late Pleistocene. Whole genome analysis indicated low levels of gene flow between North American and Eurasian horse populations, which probably occurred as a result of these inferred dispersals. Nonetheless, mitochondrial and nuclear diversity of caballine horse populations retained strong phylogeographical structuring. Our results suggest that barriers to gene flow, currently unidentified but possibly related to habitat distribution across Beringia or ongoing evolutionary divergence, played an important role in shaping the early genetic history of caballine horses, including the ancestors of living horses within Equus ferus.
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Affiliation(s)
- Alisa O Vershinina
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Duane G Froese
- Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, AB, Canada
| | - Grant Zazula
- Collections and Research, Canadian Museum of Nature, Station D, Ottawa, ON, Canada.,Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | | | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Clio Der Sarkissian
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - Shelby G Dunn
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Luca Ermini
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark
| | - Cristina Gamba
- Lundbeck Foundation GeoGenetics Center, University of Copenhagen, Copenhagen, Denmark
| | - Pamela Groves
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, CA, USA
| | - Joshua D Kapp
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Daniel H Mann
- Institute of Arctic Biology, University of Alaska Fairbanks, Fairbanks, CA, USA
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | - John Southon
- Keck-CCAMS Group, Earth System Science Department, University of California, Irvine, CA, USA
| | - Mathias Stiller
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Division Molecular Pathology, Institute of Pathology, University Hospital Leipzig, Leipzig, Germany
| | - Matthew J Wooller
- Alaska Stable Isotope Facility, Water and Environmental Research Center, Institute of Northern Engineering, University of Alaska Fairbanks, Fairbanks, AK, USA.,Department of Marine Biology, College of Fisheries and Ocean Sciences, University of Alaska Fairbanks, Fairbanks, AK, USA
| | - Gennady Baryshnikov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, St. Petersburg, Russia
| | - Dmitry Gimranov
- Institute of Plant & Animal Ecology of the Russian Academy of Sciences, Ural Branch, Ekaterinburg, Russia.,Ural Federal University named after the first President of Russia B. N. Yeltsin, Ekaterinburg, Russia
| | - Eric Scott
- California State University, San Bernardino, CA, USA
| | - Elizabeth Hall
- Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | - Susan Hewitson
- Government of Yukon, Department of Tourism and Culture, Palaeontology Program, Whitehorse, YT, Canada
| | - Irina Kirillova
- Institute of Geography, Russian Academy of Sciences, Moscow, Russia
| | - Pavel Kosintsev
- Institute of Plant & Animal Ecology of the Russian Academy of Sciences, Ural Branch, Ekaterinburg, Russia
| | | | - Hao-Wen Tong
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China
| | - Mikhail P Tiunov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of Russian Academy of Sciences, Vladivostok, Russia
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A. Shilo, Far East Branch, Russian Academy of Sciences, Magadan, Russia
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse UMR5288, Faculté de Médecine Purpan, Université Paul Sabatier, Toulouse, France
| | | | | | - Beth Shapiro
- Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
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68
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Stankowski S, Ravinet M. Defining the speciation continuum. Evolution 2021; 75:1256-1273. [PMID: 33754340 DOI: 10.1111/evo.14215] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 03/01/2021] [Accepted: 03/13/2021] [Indexed: 02/06/2023]
Abstract
A primary roadblock to our understanding of speciation is that it usually occurs over a timeframe that is too long to study from start to finish. The idea of a speciation continuum provides something of a solution to this problem; rather than observing the entire process, we can simply reconstruct it from the multitude of speciation events that surround us. But what do we really mean when we talk about the speciation continuum, and can it really help us understand speciation? We explored these questions using a literature review and online survey of speciation researchers. Although most researchers were familiar with the concept and thought it was useful, our survey revealed extensive disagreement about what the speciation continuum actually tells us. This is due partly to the lack of a clear definition. Here, we provide an explicit definition that is compatible with the Biological Species Concept. That is, the speciation continuum is a continuum of reproductive isolation. After outlining the logic of the definition in light of alternatives, we explain why attempts to reconstruct the speciation process from present-day populations will ultimately fail. We then outline how we think the speciation continuum concept can continue to act as a foundation for understanding the continuum of reproductive isolation that surrounds us.
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Affiliation(s)
- Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, United Kingdom.,Current Address: Sean Stankowski, IST Austria, Klosterneuburg, 3400, Austria
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, 0316, Norway.,School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
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69
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Gu H, Wang Y, Wang H, He Y, Deng S, He X, Wu Y, Xing K, Gao X, He X, Wang Z. Contrasting ecological niches lead to great postzygotic ecological isolation: a case of hybridization between carnivorous and herbivorous cyprinid fishes. Front Zool 2021; 18:18. [PMID: 33882942 PMCID: PMC8059018 DOI: 10.1186/s12983-021-00401-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 03/21/2021] [Indexed: 11/18/2022] Open
Abstract
Background Postzygote isolation is an important part of species isolation, especially for fish, and it can be divided into two aspects: genetic isolation and ecological isolation. With the increase in parental genetic distance, the intensity of genetic isolation between them also increases. Will the increase in parental ecological niche differences also lead to the increase in ecological isolation intensity between them? This question is difficult to answer based on the current literature due to the lack of hybridization cases of contrasting ecological niche parents. Results Cyprinid fish parents (Schizothorax wangchiachii and Percocypris pingi) with contrasting ecological niches (herbivorous and carnivorous) and their F1 hybrids were used as research objects. Fish and periphytic algae were selected as food corresponding to different parental resources. The foraging-related traits of these hybrids are generally the same between parents; however, the intermediate foraging traits of hybrids did not result in intermediate foraging performance for parental resources, and these hybrids could hardly forage for parental resources. The poor foraging performance of these hybrids for parental resources was caused not only by the decline in the foraging ability of these hybrids but, more importantly, by the decrease in foraging activity. Interestingly, these hybrids initially showed a high interest in foraging small fishes; however, after the first successful capture, these hybrids had difficulty ingesting fish and spit them out, which led to the subsequent decrease in foraging activity. We designed a series of experiments to explore the mechanism of the fish spitting of these hybrids, excluding the taste and the size of prey, and found that the decrease in their pharyngeal tooth puncture ability may be the reason. Conclusions This study was the first to demonstrate that these parents with contrasting ecological niches will produce great postzygotic ecological isolation for parental resources. The poor foraging performance of these hybrids for parental resources is mainly due to the decrease in foraging activity. Interestingly, these hybrids have obvious fish-spitting behaviour, which is a typical example of the incompatibility between intermediate traits and genetic behaviors. Supplementary Information The online version contains supplementary material available at 10.1186/s12983-021-00401-4.
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Affiliation(s)
- Haoran Gu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Yuanfu Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Haoyu Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - You He
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Sihong Deng
- Liangshan Kehua Water Ecology Company Limited, Xichang, 615000, China
| | - Xingheng He
- Sichuan Lubei Biotechnology Company Limited, Chengdu, 610011, China
| | - Yi Wu
- Sichuan Lubei Biotechnology Company Limited, Chengdu, 610011, China
| | - Kaiyan Xing
- Xichang Agriculture and Rural Affairs Bureau, Xichang, 615000, China
| | - Xue Gao
- Xichang Agriculture and Rural Affairs Bureau, Xichang, 615000, China
| | - Xuefu He
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Zhijian Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing, 400715, China.
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70
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Christmas MJ, Jones JC, Olsson A, Wallerman O, Bunikis I, Kierczak M, Peona V, Whitley KM, Larva T, Suh A, Miller-Struttmann NE, Geib JC, Webster MT. Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics. Mol Biol Evol 2021; 38:3126-3143. [PMID: 33823537 PMCID: PMC8321533 DOI: 10.1093/molbev/msab086] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Evidence is accumulating that gene flow commonly occurs between recently diverged species, despite the existence of barriers to gene flow in their genomes. However, we still know little about what regions of the genome become barriers to gene flow and how such barriers form. Here, we compare genetic differentiation across the genomes of bumblebee species living in sympatry and allopatry to reveal the potential impact of gene flow during species divergence and uncover genetic barrier loci. We first compared the genomes of the alpine bumblebee Bombus sylvicola and a previously unidentified sister species living in sympatry in the Rocky Mountains, revealing prominent islands of elevated genetic divergence in the genome that colocalize with centromeres and regions of low recombination. This same pattern is observed between the genomes of another pair of closely related species living in allopatry (B. bifarius and B. vancouverensis). Strikingly however, the genomic islands exhibit significantly elevated absolute divergence (dXY) in the sympatric, but not the allopatric, comparison indicating that they contain loci that have acted as barriers to historical gene flow in sympatry. Our results suggest that intrinsic barriers to gene flow between species may often accumulate in regions of low recombination and near centromeres through processes such as genetic hitchhiking, and that divergence in these regions is accentuated in the presence of gene flow.
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Affiliation(s)
- Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Julia C Jones
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ola Wallerman
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ignas Bunikis
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Valentina Peona
- Department of Organismal Biology-Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Kaitlyn M Whitley
- Department of Biology, Appalachian State University, Boone, NC, USA.,U.S. Department of Agriculture, Agriculture Research Service, Charleston, SC, USA
| | - Tuuli Larva
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Alexander Suh
- Department of Organismal Biology-Systematic Biology, Uppsala University, Uppsala, Sweden.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | | | - Jennifer C Geib
- Department of Biology, Appalachian State University, Boone, NC, USA
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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71
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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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72
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Pfennig KS. Biased Hybridization and Its Impact on Adaptive Introgression. Trends Ecol Evol 2021; 36:488-497. [PMID: 33752896 DOI: 10.1016/j.tree.2021.02.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 02/20/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023]
Abstract
Gene exchange between species can influence ecological and evolutionary processes ranging from population rescue to adaptive radiation. Genomic tools have provided new insights into the prevalence and nature of gene exchange between species. However, much remains unknown of how ecological, behavioral, and evolutionary factors determine what genetic variation moves between species in the first place. In particular, more research is needed that evaluates whether such factors bias gene flow from one species to another, and whether any such biases affect how genetic variation from another species is ultimately retained in the genome of a given species. Addressing this issue is crucial in a changing world where hybridization and introgression might determine which species succeed and which become extinct.
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Affiliation(s)
- Karin S Pfennig
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599-3280, USA.
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73
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Brekke TD, Moore EC, Campbell-Staton SC, Callahan CM, Cheviron ZA, Good JM. X chromosome-dependent disruption of placental regulatory networks in hybrid dwarf hamsters. Genetics 2021; 218:6168998. [PMID: 33710276 DOI: 10.1093/genetics/iyab043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 02/16/2021] [Indexed: 11/14/2022] Open
Abstract
Embryonic development in mammals is highly sensitive to changes in gene expression within the placenta. The placenta is also highly enriched for genes showing parent-of-origin or imprinted expression, which is predicted to evolve rapidly in response to parental conflict. However, little is known about the evolution of placental gene expression, or if divergence of placental gene expression plays an important role in mammalian speciation. We used crosses between two species of dwarf hamsters (Phodopus sungorus and Phodopus campbelli) to examine the genetic and regulatory underpinnings of severe placental overgrowth in their hybrids. Using quantitative genetic mapping and mitochondrial substitution lines, we show that overgrowth of hybrid placentas was primarily caused by genetic differences on the maternally inherited P. sungorus X chromosome. Mitochondrial interactions did not contribute to abnormal hybrid placental development, and there was only weak correspondence between placental disruption and embryonic growth. Genome-wide analyses of placental transcriptomes from the parental species and first- and second-generation hybrids revealed a central group of co-expressed X-linked and autosomal genes that were highly enriched for maternally biased expression. Expression of this gene network was strongly correlated with placental size and showed widespread misexpression dependent on epistatic interactions with X-linked hybrid incompatibilities. Collectively, our results indicate that the X chromosome is likely to play a prominent role in the evolution of placental gene expression and the accumulation of hybrid developmental barriers between mammalian species.
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Affiliation(s)
- Thomas D Brekke
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.,School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Emily C Moore
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Shane C Campbell-Staton
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.,Department of Ecology and Evolutionary Biology; Institute for Society and Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Colin M Callahan
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Zachary A Cheviron
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Jeffrey M Good
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
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74
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Joffard N, Silva WTAF, Twyford AD. Digest: The role of postzygotic isolation in Mimulus speciation. Evolution 2021; 75:756-758. [PMID: 33469918 DOI: 10.1111/evo.14175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/30/2020] [Indexed: 01/08/2023]
Abstract
Recently diverged species often show incomplete reproductive isolation and subsequently experience hybridization and introgression. The plant genus Mimulus includes many such examples of closely related taxa that prove useful for studying incipient speciation. However, Sandstedt et al. show that in contrast to other Mimulus species, species of the M. tilingii complex are characterized by strong postzygotic isolation mediated by multiple barriers. This finding highlights the diverse speciation histories of related plant groups.
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Affiliation(s)
- Nina Joffard
- Evolutionary Biology Centre, Department of Ecology and Genetics, Plant Ecology and Evolution Program, Uppsala University, Uppsala, Sweden
| | - Willian T A F Silva
- Centre for Environmental and Climate Research, Lund University, Lund, Sweden
| | - Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh, UK.,Royal Botanic Garden Edinburgh, Edinburgh, UK
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López‐Delgado J, van Riemsdijk I, Arntzen JW. Tracing species replacement in Iberian marbled newts. Ecol Evol 2021; 11:402-414. [PMID: 33437438 PMCID: PMC7790658 DOI: 10.1002/ece3.7060] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 10/12/2020] [Accepted: 10/19/2020] [Indexed: 11/25/2022] Open
Abstract
Secondary contact between closely related species can lead to the formation of hybrid zones, allowing for interspecific gene flow. Hybrid zone movement can take place if one of the species possesses a competitive advantage over the other, ultimately resulting in species replacement. Such hybrid zone displacement is predicted to leave a genomic footprint across the landscape in the form of asymmetric gene flow (or introgression) of selectively neutral alleles from the displaced to the advancing species. Hybrid zone movement has been suggested for marbled newts in the Iberian Peninsula, supported by asymmetric gene flow and a distribution relict (i.e., an enclave) of Triturus marmoratus in the range of T. pygmaeus. We developed a panel of nuclear and mitochondrial SNP markers to test for the presence of a T. marmoratus genomic footprint in the Lisbon peninsula, south of the enclave. We found no additional populations of T. marmoratus. Analysis with the software Structure showed no genetic traces of T. marmoratus in T. pygmaeus. A principal component analysis showed some variation within the local T. pygmaeus, but it is unclear if this represents introgression from T. marmoratus. The results may be explained by (a) species replacement without introgressive hybridization and (b) displacement with hybridization followed by the near-complete erosion of the footprint by purifying selection. We predict that testing for a genomic footprint north of the reported enclave would confirm that species replacement in these marbled newts occurred with hybridization.
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Affiliation(s)
- Julia López‐Delgado
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Institute for BiologyLeiden UniversityLeidenThe Netherlands
- Present address:
University of LeedsLeedsUnited Kingdom
| | - Isolde van Riemsdijk
- Naturalis Biodiversity CenterLeidenThe Netherlands
- Present address:
Institute for Evolution and Ecology, Tübingen UniversityLeedsGermany
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Martin CH, Gould KJ. Surprising spatiotemporal stability of a multi-peak fitness landscape revealed by independent field experiments measuring hybrid fitness. Evol Lett 2020; 4:530-544. [PMID: 33312688 PMCID: PMC7719547 DOI: 10.1002/evl3.195] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 07/23/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022] Open
Abstract
The effect of the environment on fitness in natural populations is a fundamental question in evolutionary biology. However, experimental manipulations of both environment and phenotype at the same time are rare. Thus, the relative importance of the competitive environment versus intrinsic organismal performance in shaping the location, height, and fluidity of fitness peaks and valleys remains largely unknown. Here, we experimentally tested the effect of competitor frequency on the complex fitness landscape driving adaptive radiation of a generalist and two trophic specialist pupfishes, a scale-eater and molluscivore, endemic to hypersaline lakes on San Salvador Island (SSI), Bahamas. We manipulated phenotypes, by generating 3407 F4/F5 lab-reared hybrids, and competitive environment, by altering the frequency of rare transgressive hybrids between field enclosures in two independent lake populations. We then tracked hybrid survival and growth rates across these four field enclosures for 3-11 months. In contrast to competitive speciation theory, we found no evidence that the frequency of hybrid phenotypes affected their survival. Instead, we observed a strikingly similar fitness landscape to a previous independent field experiment, each supporting multiple fitness peaks for generalist and molluscivore phenotypes and a large fitness valley isolating the divergent scale-eater phenotype. These features of the fitness landscape were stable across manipulated competitive environments, multivariate trait axes, and spatiotemporal heterogeneity. We suggest that absolute performance constraints and divergent gene regulatory networks shape macroevolutionary (interspecific) fitness landscapes in addition to microevolutionary (intraspecific) competitive dynamics. This interplay between organism and environment underlies static and dynamic features of the adaptive landscape.
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Affiliation(s)
- Christopher H. Martin
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia94720
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia94720
| | - Katelyn J. Gould
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27515
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Kulmuni J, Butlin RK, Lucek K, Savolainen V, Westram AM. Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190528. [PMID: 32654637 PMCID: PMC7423269 DOI: 10.1098/rstb.2019.0528] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/21/2020] [Indexed: 12/12/2022] Open
Abstract
Speciation, that is, the evolution of reproductive barriers eventually leading to complete isolation, is a crucial process generating biodiversity. Recent work has contributed much to our understanding of how reproductive barriers begin to evolve, and how they are maintained in the face of gene flow. However, little is known about the transition from partial to strong reproductive isolation (RI) and the completion of speciation. We argue that the evolution of strong RI is likely to involve different processes, or new interactions among processes, compared with the evolution of the first reproductive barriers. Transition to strong RI may be brought about by changing external conditions, for example, following secondary contact. However, the increasing levels of RI themselves create opportunities for new barriers to evolve and, and interaction or coupling among barriers. These changing processes may depend on genomic architecture and leave detectable signals in the genome. We outline outstanding questions and suggest more theoretical and empirical work, considering both patterns and processes associated with strong RI, is needed to understand how speciation is completed. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Jonna Kulmuni
- Organismal and Evolutionary Biology, University of Helsinki, Finland
| | - Roger K. Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, 4056 Basel, Switzerland
| | - Vincent Savolainen
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK
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