1
|
Geng X, Summers J, Chen N. Ecological niche contributes to the persistence of the western × glaucous-winged gull hybrid zone. Ecol Evol 2024; 14:e11678. [PMID: 39005880 PMCID: PMC11239321 DOI: 10.1002/ece3.11678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/23/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024] Open
Abstract
Hybrid zones occur in nature when populations with limited reproductive barriers overlap in space. Many hybrid zones persist over time, and different models have been proposed to explain how selection can maintain hybrid zone stability. More empirical studies are needed to elucidate the role of ecological adaptation in maintaining stable hybrid zones. Here, we investigated the role of exogenous factors in maintaining a hybrid zone between western gulls (Larus occidentalis) and glaucous-winged gulls (L. glaucescens). We used ecological niche models (ENMs) and niche similarity tests to quantify and examine the ecological niches of western gulls, glaucous-winged gulls, and their hybrids. We found evidence of niche divergence between all three groups. Our results support the bounded superiority model, providing further evidence that exogenous selection favoring hybrids may be an important factor in maintaining this stable hybrid zone.
Collapse
Affiliation(s)
- Xuewen Geng
- Department of BiologyUniversity of RochesterRochesterNew YorkUSA
| | - Jeremy Summers
- Department of BiologyUniversity of RochesterRochesterNew YorkUSA
| | - Nancy Chen
- Department of BiologyUniversity of RochesterRochesterNew YorkUSA
| |
Collapse
|
2
|
Tataru D, De Leon M, Dutton S, Perez FM, Rendahl A, Ferris KG. Fluctuating selection in a Monkeyflower hybrid zone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599085. [PMID: 38948721 PMCID: PMC11212913 DOI: 10.1101/2024.06.14.599085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
While hybridization was viewed as a hindrance to adaptation and speciation by early evolutionary biologists, recent studies have demonstrated the importance of hybridization in facilitating evolutionary processes. However, it is still not well-known what role spatial and temporal variation in natural selection play in the maintenance of naturally occurring hybrid zones. To identify whether hybridization is adaptive between two closely related monkeyflower species, Mimulus guttatus and Mimulus laciniatus, we performed repeated reciprocal transplants between natural hybrid and pure species' populations. We planted parental genotypes along with multiple experimental hybrid generations in a dry (2021) and extremely wet (2023) year in the Sierra Nevada, CA. By taking fine scale environmental measurements, we found that the environment of the hybrid zone is more similar to M. laciniatus's seasonally dry rocky outcrop habitat than M. guttatus's moist meadows. In our transplants hybridization does not appear to be maintained by a consistent fitness advantage of hybrids over parental species in hybrid zones, but rather a lack of strong selection against hybrids. We also found higher fitness of the drought adapted species, M. laciniatus, than M. guttatus in both species' habitats, as well as phenotypic selection for M. laciniatus-like traits in the hybrid habitat in the dry year of our experiment. These findings suggest that in this system hybridization might function to introduce drought-adapted traits and genes from M. laciniatus into M. guttatus, specifically in years with limited soil moisture. However, we also find evidence of genetic incompatibilities in second generation hybrids in the wetter year, which may balance a selective advantage of M. laciniatus introgression. Therefore, we find that hybridization in this system is both potentially adaptive and costly, and that the interaction of positive and negative selection likely determines patterns of gene flow between these Mimulus species.
Collapse
Affiliation(s)
- Diana Tataru
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
| | - Max De Leon
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
| | - Spencer Dutton
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
| | - Fidel Machado Perez
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
- University of California Merced, Merced, CA
| | - Alexander Rendahl
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
| | - Kathleen G Ferris
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA
| |
Collapse
|
3
|
Martins ARP, Warren NB, McMillan WO, Barrett RDH. Spatiotemporal dynamics in butterfly hybrid zones. INSECT SCIENCE 2024; 31:328-353. [PMID: 37596954 DOI: 10.1111/1744-7917.13262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.
Collapse
Affiliation(s)
- Ananda R Pereira Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Natalie B Warren
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Rowan D H Barrett
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| |
Collapse
|
4
|
Geng X, Summers J, Chen N. Ecological niche contributes to the persistence of the Western x Glaucous-winged Gull hybrid zone. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.14.571742. [PMID: 38168246 PMCID: PMC10760172 DOI: 10.1101/2023.12.14.571742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Hybrid zones occur in nature when populations with limited reproductive barriers overlap in space. Many hybrid zones persist over time, and different models have been proposed to explain how selection can maintain hybrid zone stability. More empirical studies are needed to elucidate the role of ecological adaptation in maintaining stable hybrid zones. Here, we investigated the role of exogenous factors in maintaining a hybrid zone between western gulls (Larus occidentalis) and glaucous-winged gulls (L. glaucescens). We used ecological niche models (ENMs) and niche similarity tests to quantify and examine the ecological niches of western gulls, glaucous-winged gulls, and their hybrids. We found evidence of niche divergence between all three groups. Our results best support the bounded superiority model, providing further evidence that exogenous selection favoring hybrids may be an important factor in maintaining this stable hybrid zone.
Collapse
Affiliation(s)
- Xuewen Geng
- Department of Biology, University of Rochester
| | | | - Nancy Chen
- Department of Biology, University of Rochester
| |
Collapse
|
5
|
Patel JS, Chouvenc T, Wu CC, Li HF, Su NY. Soldier phenotypic differences among 2 invasive and destructive Coptotermes species and their hybrids (Blattodea: Isoptera: Rhinotermitidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2023; 23:2. [PMID: 37952215 PMCID: PMC10640870 DOI: 10.1093/jisesa/iead095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/16/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
With recent evidence of hybridization events in the field, the phenotypic traits of F1 hybrid colonies of 2 destructive subterranean termite species, Coptotermes formosanus Shiraki and Coptotermes gestroi (Wasmann) remain to be investigated. In this study, laboratory colonies of 2 conspecific pairings and 2 heterospecific pairings (hybrid F = ♀C. formosanus × ♂C. gestroi, hybrid G = ♀C. gestroi × ♂C. formosanus) were examined in Florida, USA, and in Taiwan. Colony nest architecture for both hybrids displayed disorganized carton materials compared to the defined trabecular carton of both parental species. Soldier head measurements were not a reliable approach for diagnostic purposes, as soldier morphometric traits widely overlapped across all mating combinations, except for hybrid F soldiers displaying abnormally long mandibles. Hybrid F soldiers' mandibles also remained parallel when at rest. However, 4 qualitative morphological differences in soldiers were determined for diagnostic purposes. First, the fontanelle in both hybrids is horizontally ellipsoid whereas subcircular in C. gestroi and trianguliform in C. formosanus. Second, sclerotized striations along the postmental sulcus are present in C. gestroi, absent in C. formosanus, and intermediate in both hybrid soldier types. Third, each lateral margin of the fontanelle is flanked by 2 setae in C. formosanus and both hybrids, while a single seta resides on each side of the fontanelle in C. gestroi. Finally, C. gestroi and hybrid soldiers' heads are characterized by a bulging vertex that is lacking in C. formosanus. Therefore, a combination of these 4 characteristics now allows for soldier identification of hybrid Coptotermes.
Collapse
Affiliation(s)
- Jayshree S Patel
- Department of Entomology and Nematology, Ft. Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Ft. Lauderdale, FL, USA
- Oncospark Inc., Jacksonville, FL, USA
| | - Thomas Chouvenc
- Department of Entomology and Nematology, Ft. Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Ft. Lauderdale, FL, USA
| | - Chia-Chien Wu
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan
| | - Hou-Feng Li
- Department of Entomology, National Chung Hsing University, Taichung, Taiwan
| | - Nan-Yao Su
- Department of Entomology and Nematology, Ft. Lauderdale Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Ft. Lauderdale, FL, USA
| |
Collapse
|
6
|
Preckler-Quisquater S, Kierepka EM, Reding DM, Piaggio AJ, Sacks BN. Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages? Mol Ecol 2023; 32:5323-5337. [PMID: 37632719 DOI: 10.1111/mec.17105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500-3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70-200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today's contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms.
Collapse
Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Elizabeth M Kierepka
- North Carolina Museum of Natural Sciences, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Dawn M Reding
- Department of Biology, Luther College, Decorah, Iowa, USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services, National Wildlife Research Center, Wildlife Genetics Lab, Fort Collins, Colorado, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
| |
Collapse
|
7
|
Andersen JC, Havill NP, Chandler JL, Boettner GH, Griffin BP, Elkinton JS. Seasonal differences in the timing of flight between the invasive winter moth and native Bruce spanworm promotes reproductive isolation. ENVIRONMENTAL ENTOMOLOGY 2023; 52:740-749. [PMID: 37459357 DOI: 10.1093/ee/nvad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/16/2023] [Accepted: 06/23/2023] [Indexed: 08/19/2023]
Abstract
The European winter moth, Operophtera brumata L. (Lepidoptera: Geometridae), was accidentally introduced to North America on at least 4 separate occasions, where it has been hybridizing with the native Bruce spanworm, O. bruceata Hulst, at rates up to 10% per year. Both species are known to respond to the same sex pheromones and to produce viable offspring, but whether they differ in the seasonal timing of their mating flights is unknown. Therefore, we collected adult male moths weekly along 2 transects in the northeastern United States and genotyped individuals using polymorphic microsatellite markers as males of these 2 species cannot be differentiated morphologically. Along each transect, we then estimated the cumulative proportions (i.e., the number of individuals out of the total collected) of each species on each calendar day. Our results indicate that there are significant differences between the species regarding their seasonal timing of flight, and these allochronic differences likely are acting to promote reproductive isolation between these 2 species. Lastly, our results suggest that the later flight observed by winter moth compared to Bruce spanworm may be limiting its inland spread in the northeastern United States because of increased exposure to extreme winter events.
Collapse
Affiliation(s)
- Jeremy C Andersen
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Nathan P Havill
- USDA-Forest Service, Northern Research Station, Hamden, CT 06514, USA
| | - Jennifer L Chandler
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - George H Boettner
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Brian P Griffin
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Joseph S Elkinton
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003, USA
| |
Collapse
|
8
|
Mallet J, Mullen SP. Reproductive isolation is a heuristic, not a measure: a commentary on Westram et al., 2022. J Evol Biol 2022; 35:1175-1182. [PMID: 36063161 DOI: 10.1111/jeb.14052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 12/17/2022]
Abstract
Reproductive isolation is the heuristic basis of the biological species concept, but what is it? Westram et al. (this issue) propose that it is a measurable quantity, "barrier strength," that prevents gene flow among populations. However, their attempt to make the concept of reproductive isolation more scientific is unlikely to satisfy the diverse opinions of all evolutionary biologists. There are many different opinions about the nature of species, even under the biological species concept. Complete reproductive isolation, where gene flow is effectively zero, is regarded by some biologists as an important end point of speciation. Others, including Westram et al., argue for a more nuanced approach, and they also suggest that reproductive isolation may differ in different parts of the genome due to variation in genetic linkage to divergently selected loci. In contrast to both these approaches, we favour as a key criterion of speciation the stable coexistence of divergent populations in sympatry. Obviously, such populations must be reproductively isolated in some sense, but neither the fraction of the genome that is exchanged, nor measures of overall barrier strength acting on neutral variation will yield very precise predictions as to species status. Although an overall measure of reproductive isolation is virtually unattainable for these reasons, its early generation components, such as assortative mating, divergent selection, or hybrid inviability and sterility are readily measurable and remain informative. For example, we can make the prediction that to remain divergent in sympatry, almost all sexual species will require strong assortative mating, as well as some sort of ecological or intrinsic selection against hybrids and introgressed variants.
Collapse
Affiliation(s)
- James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Sean P Mullen
- Department of Biology, Boston University, Boston, Massachusetts, USA
| |
Collapse
|
9
|
Beaudry FEG, Rifkin JL, Peake AL, Kim D, Jarvis-Cross M, Barrett SCH, Wright SI. Effects of the neo-X chromosome on genomic signatures of hybridization in Rumex hastatulus. Mol Ecol 2022; 31:3708-3721. [PMID: 35569016 DOI: 10.1111/mec.16496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022]
Abstract
Natural hybrid zones provide opportunities for studies of the evolution of reproductive isolation in wild populations. Although recent investigations have found that the formation of neo-sex chromosomes is associated with reproductive isolation, the mechanisms remain unclear in most cases. Here, we assess the contemporary structure of gene flow in the contact zone between largely allopatric cytotypes of the dioecious plant Rumex hastatulus, a species with evidence of sex chromosome turn-over. Males to the west of the Mississippi river, USA, have an X and a single Y chromosome, whereas populations to the east of the river have undergone a chromosomal rearrangement giving rise to a larger X and two Y chromosomes. Using reduced-representation sequencing, we provide evidence that hybrids form readily and survive multiple backcross generations in the field, demonstrating the potential for ongoing gene flow between the cytotypes. Cline analysis of each chromosome separately captured no signals of difference in cline shape between chromosomes. However, principal component regression revealed a significant increase in the contribution of individual SNPs to inter-cytotype differentiation on the neo-X chromosome, but no correlation with recombination rate. Cline analysis revealed that the only SNPs with significantly steeper clines than the genome average were located on the neo-X. Our data are consistent with a role for neo-sex chromosomes in reproductive isolation between R. hastatulus cytotypes. Our investigation highlights the importance of studying plant hybrid zones for understanding the evolution of sex chromosomes.
Collapse
Affiliation(s)
- Felix E G Beaudry
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Joanna L Rifkin
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Amanda L Peake
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Deanna Kim
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Madeline Jarvis-Cross
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Spencer C H Barrett
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| | - Stephen I Wright
- The University of Toronto, Department of Ecology and Evolutionary Biology, Toronto, ON, Canada
| |
Collapse
|
10
|
Aguillon SM, Rohwer VG. Revisiting a classic hybrid zone: Movement of the northern flicker hybrid zone in contemporary times. Evolution 2022; 76:1082-1090. [PMID: 35318662 DOI: 10.1111/evo.14474] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 01/22/2023]
Abstract
Natural hybrid zones have provided important insights into the evolutionary process, and their geographic dynamics over time can help to disentangle the underlying biological processes that maintain them. Here, we leverage replicated sampling of an identical transect across the hybrid zone between yellow-shafted and red-shafted flickers in the Great Plains to assess its stability over ∼60 years (1955-1957 to 2016-2018). We identify a ∼73-km westward shift in the hybrid zone center toward the range of the red-shafted flicker, but find no associated changes in width over our sampling period. In fact, the hybrid zone remains remarkably narrow, suggesting some kind of selective pressure maintains the zone. By comparing to previous work in the same geographic region, it appears likely that the movement in the hybrid zone has occurred in the years since the early 1980s. This recent movement may be related to changes in climate or land management practices that have allowed westward movement of yellow-shafted flickers into the Great Plains.
Collapse
Affiliation(s)
- Stepfanie M Aguillon
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, New York, 14850.,Current Address: Department of Biology, Stanford University, Stanford, California, 94305
| | - Vanya G Rohwer
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853.,Cornell University Museum of Vertebrates, Ithaca, New York, 14850
| |
Collapse
|
11
|
Del-Rio G, Rego MA, Whitney BM, Schunck F, Silveira LF, Faircloth BC, Brumfield RT. Displaced clines in an avian hybrid zone (Thamnophilidae: Rhegmatorhina) within an Amazonian interfluve. Evolution 2021; 76:455-475. [PMID: 34626500 DOI: 10.1111/evo.14377] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 12/24/2022]
Abstract
Secondary contact between species often results in the formation of a hybrid zone, with the eventual fates of the hybridizing species dependent on evolutionary and ecological forces. We examine this process in the Amazon Basin by conducting the first genomic and phenotypic characterization of the hybrid zone formed after secondary contact between two obligate army-ant-followers: the White-breasted Antbird (Rhegmatorhina hoffmannsi) and the Harlequin Antbird (Rhegmatorhina berlepschi). We found a major geographic displacement (∼120 km) between the mitochondrial and nuclear clines, and we explore potential hypotheses for the displacement, including sampling error, genetic drift, and asymmetric cytonuclear incompatibilities. We cannot exclude roles for sampling error and genetic drift in contributing to the discordance; however, the data suggest expansion and unidirectional introgression of hoffmannsi into the distribution of berlepschi.
Collapse
Affiliation(s)
- Glaucia Del-Rio
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Marco A Rego
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Bret M Whitney
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Fabio Schunck
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Luís F Silveira
- Museu de Zoologia, Universidade de São Paulo, São Paulo, SP, 04263-000, Brazil
| | - Brant C Faircloth
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| | - Robb T Brumfield
- Museum of Natural Science, Louisiana State University, Baton Rouge, Louisiana, 70803.,Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, 70803
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Caeiro-Dias G, Rocha S, Couto A, Pereira C, Brelsford A, Crochet PA, Pinho C. Nuclear phylogenies and genomics of a contact zone establish the species rank of Podarcis lusitanicus (Squamata, Lacertidae). Mol Phylogenet Evol 2021; 164:107270. [PMID: 34352374 DOI: 10.1016/j.ympev.2021.107270] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 05/19/2021] [Accepted: 07/26/2021] [Indexed: 11/27/2022]
Abstract
Unravelling when divergent lineages constitute distinct species can be challenging, particularly in complex scenarios combining cryptic diversity and phylogenetic discordances between different types of molecular markers. Combining a phylogenetic approach with the study of contact zones can help to overcome such difficulties. The Podarcis hispanicus species complex has proven to be prosperous in independent evolutionary units, sometimes associated with cryptic diversity. Previous studies have revealed that one of the species of this complex, P. guadarramae, comprises two deeply divergent yet morphologically indistinguishable evolutionary units, currently regarded as subspecies (P. g. guadarramae and P. g. lusitanicus). In this study we used molecular data to address the systematics of the two lineages of Podarcis guadarramae and the closely related P. bocagei. Firstly, we reconstructed the species tree of these three and two additional taxa based on 30 nuclear loci using the multispecies coalescent with and without gene flow. Secondly, we used SNPs obtained from RADseq data to analyze the population structure across the distribution limits P. g. lusitanicus and P. g. guadarramae, and for comparison, a contact zone between P. bocagei and P. g. lusitanicus. Nuclear phylogenetic relationships between these three taxa are clearly difficult to determine due to the influence of gene flow, but our results give little support to the monophyly of P. guadarramae, potentially due to a nearly simultaneous divergence between them. Genetic structure and geographic cline analysis revealed that the two lineages of P. guadarramae replace each other abruptly across the sampled region and that gene flow is geographically restricted, implying the existence of strong reproductive isolation. Podarcis bocagei and P. g. lusitanicus show a similar degree of genetic differentiation and reproductive isolation, with very low levels of admixture in syntopy. These results support that all three forms are equally differentiated and reproductively isolated. In consequence, we conclude that the two former subspecies of Podarcis guadarramae constitute valid, yet cryptic species, that should be referred to as P. lusitanicus and P. guadarramae.
Collapse
Affiliation(s)
- Guilherme Caeiro-Dias
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBio, Vairão, Portugal.
| | - Sara Rocha
- CINBIO, Universidade de Vigo, 36310 Vigo, España; Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, España
| | - Alvarina Couto
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBio, Vairão, Portugal
| | - Carolina Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBio, Vairão, Portugal
| | - Alan Brelsford
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland; Biology Department, University of California Riverside, CA, USA
| | | | - Catarina Pinho
- Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO/InBio, Vairão, Portugal
| |
Collapse
|
14
|
Faust E, Jansson E, André C, Halvorsen KT, Dahle G, Knutsen H, Quintela M, Glover KA. Not that clean: Aquaculture-mediated translocation of cleaner fish has led to hybridization on the northern edge of the species' range. Evol Appl 2021; 14:1572-1587. [PMID: 34178105 PMCID: PMC8210792 DOI: 10.1111/eva.13220] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Translocation and introduction of non-native organisms can have major impacts on local populations and ecosystems. Nevertheless, translocations are common practices in agri- and aquaculture. Each year, millions of wild-caught wrasses are transported large distances to be used as cleaner fish for parasite control in marine salmon farms. Recently, it was documented that translocated cleaner fish are able to escape and reproduce with local wild populations. This is especially a challenge in Norway, which is the world's largest salmon producer. Here, a panel of 84 informative SNPs was developed to identify the presence of nonlocal corkwing wrasse (Symphodus melops) escapees and admixed individuals in wild populations in western Norway. Applying this panel to ~2000 individuals, escapees and hybrids were found to constitute up to 20% of the local population at the northern edge of the species' distribution. The introduction of southern genetic material at the northern edge of the species distribution range has altered the local genetic composition and could obstruct local adaptation and further range expansion. Surprisingly, in other parts of the species distribution where salmon farming is also common, few escapees and hybrids were found. Why hybridization seems to be common only in the far north is discussed in the context of demographic and transport history. However, the current lack of reporting of escapes makes it difficult to evaluate possible causes for why some aquaculture-dense areas have more escapees and hybrids than others. The results obtained in this study, and the observed high genomic divergence between the main export and import regions, puts the sustainability of mass translocation of nonlocal wild wrasse into question and suggests that the current management regime needs re-evaluation.
Collapse
Affiliation(s)
- Ellika Faust
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | | | - Carl André
- Department of Marine Sciences – TjärnöUniversity of GothenburgStrömstadSweden
| | | | - Geir Dahle
- Institute of Marine ResearchBergenNorway
| | - Halvor Knutsen
- Institute of Marine ResearchHisNorway
- Centre of Coastal ResearchUniversity of AgderKristiansandNorway
| | | | - Kevin A. Glover
- Institute of Marine ResearchBergenNorway
- Institute of BiologyUniversity of BergenBergenNorway
| |
Collapse
|
15
|
Stankowski S, Ravinet M. Defining the speciation continuum. Evolution 2021; 75:1256-1273. [PMID: 33754340 DOI: 10.1111/evo.14215] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [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.
Collapse
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
| |
Collapse
|
16
|
Olofsson JK, Curran EV, Nyirenda F, Bianconi ME, Dunning LT, Milenkovic V, Sotelo G, Hidalgo O, Powell RF, Lundgren MR, Leitch IJ, Nosil P, Osborne CP, Christin PA. Low dispersal and ploidy differences in a grass maintain photosynthetic diversity despite gene flow and habitat overlap. Mol Ecol 2021; 30:2116-2130. [PMID: 33682242 DOI: 10.1111/mec.15871] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022]
Abstract
Geographical isolation facilitates the emergence of distinct phenotypes within a single species, but reproductive barriers or selection are needed to maintain the polymorphism after secondary contact. Here, we explore the processes that maintain intraspecific variation of C4 photosynthesis, a complex trait that results from the combined action of multiple genes. The grass Alloteropsis semialata includes C4 and non-C4 populations, which have coexisted as a polyploid series for more than 1 million years in the miombo woodlands of Africa. Using population genomics, we show that there is genome-wide divergence for the photosynthetic types, but the current geographical distribution does not reflect a simple habitat displacement scenario as the genetic clusters overlap, being occasionally mixed within a given habitat. Despite evidence of recurrent introgression between non-C4 and C4 groups, in both diploids and polyploids, the distinct genetic lineages retain their identity, potentially because of selection against hybrids. Coupled with strong isolation by distance within each genetic group, this selection created a geographical mosaic of photosynthetic types. Diploid C4 and non-C4 types never grew together, and the C4 type from mixed populations constantly belonged to the hexaploid lineage. By limiting reproductive interactions between photosynthetic types, the ploidy difference probably allows their co-occurrence, reinforcing the functional diversity within this species. Together, these factors enabled the persistence of divergent physiological traits of ecological importance within a single species despite gene flow and habitat overlap.
Collapse
Affiliation(s)
- Jill K Olofsson
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Emma V Curran
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Florence Nyirenda
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Matheus E Bianconi
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Luke T Dunning
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Vanja Milenkovic
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Graciela Sotelo
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | | | | - Marjorie R Lundgren
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | | - Patrik Nosil
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | - Colin P Osborne
- Department of Animal and Plant Science, University of Sheffield, Sheffield, UK
| | | |
Collapse
|
17
|
Pflugbeil G, Affenzeller M, Tribsch A, Comes HP. Primary hybrid zone formation in Tephroseris helenitis (Asteraceae), following postglacial range expansion along the central Northern Alps. Mol Ecol 2021; 30:1704-1720. [PMID: 33548078 PMCID: PMC8048512 DOI: 10.1111/mec.15832] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 11/26/2022]
Abstract
Distinguishing between secondary versus primary hybrid zone formation remains a challenging task as, for instance, the time window in which these historical (vicariant) versus contemporary (environmental-selective) processes are distinguishable may be relatively narrow. Here, we examine the origin and structure of a transition zone between two subspecies of Tephroseris helenitis along the central Northern Alps, using molecular (AFLP) and morphological (achene type) data in combination with ecological niche models (ENMs) to hindcast ranges at the Last Glacial Maximum (LGM) and mid-Holocene. Samples were collected over a c. 350 km long transect, largely covered by ice during the LGM. Genetically nonadmixed individuals of subspp. helenitis versus salisburgensis dominated the westernmost versus eastern transect areas, with admixed individuals occurring in between. Clines for achene morphology and outlier loci potentially under climate-driven selection were steep, largely noncoincidental, and displaced to the east of the cline centre for neutral AFLPs. During the LGM, ssp. helenitis should have been able to persist in a refugium southwest of the transect, while suitable habitat for ssp. salisburgensis was apparently absent at this time. Together with patterns of genetic and clinal variation, our ENM data are suggestive of a primary hybrid zone that originated after the species' postglacial, eastward expansion. The observed clinal changes may thus reflect random/nonadaptive processes during expansion and selection on particular loci, and possibly achene type, in response to a long-term, west-to-east climate gradient in the direction of more stressful (e.g., wetter/cooler) conditions. Overall, this study adds to the vast hybrid zone literature a rare example of a hybrid zone caused by primary differentiation within a plant species, underlaid by historical range expansion.
Collapse
Affiliation(s)
- Georg Pflugbeil
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | | | - Andreas Tribsch
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Hans Peter Comes
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| |
Collapse
|
18
|
Burbrink FT, Gehara M, McKelvy AD, Myers EA. Resolving spatial complexities of hybridization in the context of the gray zone of speciation in North American ratsnakes (Pantherophis obsoletus complex). Evolution 2021; 75:260-277. [PMID: 33346918 DOI: 10.1111/evo.14141] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 10/01/2020] [Accepted: 11/17/2020] [Indexed: 01/04/2023]
Abstract
Inferring the history of divergence between species in a framework that permits the presence of gene flow has been crucial for characterizing the "gray zone" of speciation, which is the period of time where lineages have diverged but have not yet achieved strict reproductive isolation. However, estimates of both divergence times and rates of gene flow often ignore spatial information, for example when considering the location and width of hybrid zones with respect to changes in the environment between lineages. Using population genomic data from the North American ratsnake complex (Pantherophis obsoletus), we connected phylogeographic estimates of lineage structure, migration, historical demography, and timing of divergence with hybrid zone dynamics. We examined the spatial context of diversification by linking migration and timing of divergence to the location and widths of hybrid zones. Artificial neural network approaches were applied to understand how landscape features and past climate have influenced population genetic structure among these lineages. We found that rates of migration between lineages were associated with the overall width of hybrid zones. Timing of divergence was not related to migration rate or hybrid zone width across species pairs but may be related to the number of alleles weakly introgressing through hybrid zones. This research underscores how incomplete reproductive isolation can be better understood by considering differential allelic introgression and the effects of historical and contemporary landscape features on the formation of lineages as well as overall genomic estimates of migration rates through time.
Collapse
Affiliation(s)
- Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024
| | - Marcelo Gehara
- Department of Biological Sciences, Rutgers University Newark, 195 University Ave, Newark, New Jersey, 07102
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, New York, 10016
| | - Edward A Myers
- Department of Herpetology, The American Museum of Natural History, Central Park West and 79th Street, New York, New York, 10024.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC
| |
Collapse
|
19
|
Araki Y, Sota T. Population genetic structure underlying the geographic variation in beetle structural colour with multiple transition zones. Mol Ecol 2020; 30:670-684. [PMID: 33253446 DOI: 10.1111/mec.15758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/12/2020] [Accepted: 11/24/2020] [Indexed: 11/27/2022]
Abstract
We studied the population genetic structure underlying the geographic variation in the structural colour of the geotrupid dung beetle, Phelotrupes auratus, which exhibits metallic body colours of different reflectance wavelengths perceived as red, green and indigo. These forms occur parapatrically in an area of Japan. The colour variation was not related to variation in climatic factors. Using single nucleotide polymorphisms (SNPs) from restriction-site-associated DNA sequences, we discriminated five groups of populations (west/red, south/green, south/indigo, south/red and east/red) by a combination of genetic clusters (west, south and east) and three colour forms. There were three transition zones for the colour forms: two between the red and green forms were hybrid zones with steep genetic clines, which implies the existence of barriers to gene flow between regions with different colours. The remaining transition zone between the green and indigo forms lacked genetic differentiation, despite the evident colour changes, which implies regionally specific selection on the different colours. In a genomewide association study, we identified four SNPs that were associated with the red/green or indigo colour and were not linked with one another, which implies that the coloration was controlled by multiple loci, each affecting the expression of a different colour range. These loci may have controlled the transitions between different combinations of colours. Our study demonstrates that geographic colour variation within a species can be maintained by nonuniform interactions among barriers to gene flow, locally specific selection on different colours, and the effects of different colour loci.
Collapse
Affiliation(s)
- Yoshifumi Araki
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Teiji Sota
- Department of Zoology, Graduate School of Science, Kyoto University, Kyoto, Japan
| |
Collapse
|
20
|
Wang S, Rohwer S, de Zwaan DR, Toews DPL, Lovette IJ, Mackenzie J, Irwin D. Selection on a small genomic region underpins differentiation in multiple color traits between two warbler species. Evol Lett 2020; 4:502-515. [PMID: 33312686 PMCID: PMC7719548 DOI: 10.1002/evl3.198] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 09/20/2020] [Accepted: 09/30/2020] [Indexed: 11/18/2022] Open
Abstract
Speciation is one of the most important processes in biology, yet the study of the genomic changes underlying this process is in its infancy. North American warbler species Setophaga townsendi and Setophaga occidentalis hybridize in a stable hybrid zone, following a period of geographic separation. Genomic differentiation accumulated during geographic isolation can be homogenized by introgression at secondary contact, whereas genetic regions that cause low hybrid fitness can be shielded from such introgression. Here, we examined the genomic underpinning of speciation by investigating (1) the genetic basis of divergent pigmentation traits between species, (2) variation in differentiation across the genome, and (3) the evidence for selection maintaining differentiation in the pigmentation genes. Using tens of thousands of single nucleotide polymorphisms (SNPs) genotyped in hundreds of individuals within and near the hybrid zone, genome-wide association mapping revealed a single SNP associated with cheek, crown, breast coloration, and flank streaking, reflecting pleiotropy (one gene affecting multiple traits) or close physical linkage of different genes affecting different traits. This SNP is within an intron of the RALY gene, hence we refer to it as the RALY SNP. We then examined between-species genomic differentiation, using both genotyping-by-sequencing and whole genome sequencing. We found that the RALY SNP is within one of the highest peaks of differentiation, which contains three genes known to influence pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). Heterozygotes at this gene block are likely of reduced fitness, as the geographic cline of the RALY SNP has been narrow over two decades. Together, these results reflect at least one barrier to gene flow within this narrow (∼200 kb) genomic region that modulates plumage difference between species. Despite extensive gene flow between species across the genome, this study provides evidence that selection on a phenotype-associated genomic region maintains a stable species boundary.
Collapse
Affiliation(s)
- Silu Wang
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T1Z4Canada
| | - Sievert Rohwer
- Department of Biology and Burke MuseumUniversity of WashingtonSeattleWashington98195
| | - Devin R. de Zwaan
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCV6T1Z4Canada
| | - David P. L. Toews
- Department of Biology619 Mueller LaboratoryPennsylvania State UniversityUniversity ParkPennsylvania16802
| | - Irby J. Lovette
- Fuller Evolutionary Biology ProgramCornell Lab of OrnithologyIthacaNew York14850
| | - Jacqueline Mackenzie
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T1Z4Canada
| | - Darren Irwin
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T1Z4Canada
| |
Collapse
|
21
|
Barreto SB, Knowles LL, Affonso PRADM, Batalha-Filho H. Riverscape properties contribute to the origin and structure of a hybrid zone in a Neotropical freshwater fish. J Evol Biol 2020; 33:1530-1542. [PMID: 32862491 DOI: 10.1111/jeb.13689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 11/28/2022]
Abstract
Understanding the structure of hybrid zones provides valuable insights about species boundaries and speciation, such as the evolution of barriers to gene flow and the strength of selection. In river networks, studying evolutionary processes in hybrid zones can be especially challenging, given the influence of past and current river properties along with biological species-specific traits. Here, we suggest that a natural hybrid zone between two divergent lineages of the sexually dimorphic Neotropical fish Nematocharax venustus was probably established by secondary contact as a result of a river capture event between the Contas and Pardo river basins. This putative river capture is supported by hydrogeological evidence of elbows of capture, wind gaps and geological faults. The morphological (colour pattern) and genetic (mtDNA and RADseq) variation reveal a clinal transition between parental lineages along the main river, with predominance of F2 hybrids at the centre of the hybrid zone, absence of early generation backcrosses and different levels of hybridization in the tributaries. We highlight that different sources of information are crucial for understanding how the riverscape spatial history influences the connectivity between and within river systems and, consequently, the dynamics of gene flow between freshwater lineages/species.
Collapse
Affiliation(s)
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | | | | |
Collapse
|
22
|
Stankowski S, Westram AM, Zagrodzka ZB, Eyres I, Broquet T, Johannesson K, Butlin RK. The evolution of strong reproductive isolation between sympatric intertidal snails. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190545. [PMID: 32654639 DOI: 10.1098/rstb.2019.0545] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The evolution of strong reproductive isolation (RI) is fundamental to the origins and maintenance of biological diversity, especially in situations where geographical distributions of taxa broadly overlap. But what is the history behind strong barriers currently acting in sympatry? Using whole-genome sequencing and single nucleotide polymorphism genotyping, we inferred (i) the evolutionary relationships, (ii) the strength of RI, and (iii) the demographic history of divergence between two broadly sympatric taxa of intertidal snail. Despite being cryptic, based on external morphology, Littorina arcana and Littorina saxatilis differ in their mode of female reproduction (egg-laying versus brooding), which may generate a strong post-zygotic barrier. We show that egg-laying and brooding snails are closely related, but genetically distinct. Genotyping of 3092 snails from three locations failed to recover any recent hybrid or backcrossed individuals, confirming that RI is strong. There was, however, evidence for a very low level of asymmetrical introgression, suggesting that isolation remains incomplete. The presence of strong, asymmetrical RI was further supported by demographic analysis of these populations. Although the taxa are currently broadly sympatric, demographic modelling suggests that they initially diverged during a short period of geographical separation involving very low gene flow. Our study suggests that some geographical separation may kick-start the evolution of strong RI, facilitating subsequent coexistence of taxa in sympatry. The strength of RI needed to achieve sympatry and the subsequent effect of sympatry on RI remain open questions. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
Collapse
Affiliation(s)
- Sean Stankowski
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Anja M Westram
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Zuzanna B Zagrodzka
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Isobel Eyres
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Thomas Broquet
- CNRS and Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden
| |
Collapse
|
23
|
Capblancq T, Després L, Mavárez J. Genetic, morphological and ecological variation across a sharp hybrid zone between two alpine butterfly species. Evol Appl 2020; 13:1435-1450. [PMID: 32684968 PMCID: PMC7359832 DOI: 10.1111/eva.12925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 12/02/2019] [Accepted: 12/09/2019] [Indexed: 11/26/2022] Open
Abstract
Identifying the mechanisms involved in the formation and maintenance of species is a central question in evolutionary biology, and distinguishing the selective drivers of populations' divergence from demographic processes is of particular interest to better understand the speciation process. Hybrid zones are recognized to provide ideal places to investigate the genetic architecture of speciation and to identify the mechanisms allowing diverging species to maintain their integrity in the face of gene flow. Here, we studied two alpine butterfly species, Coenonympha macromma and C. gardetta, which can be found flying together and hybridizing in narrow contact zones in the southern French Alps. We characterized the genomic composition of individuals, their morphology and their local habitat requirements, within and around a hybrid zone. Genetic diversity analysis at 794 SNPs revealed that all individuals within the hybrid zone were highly admixed, which was not the case outside the hybrid zone. Cline analysis showed that, despite ongoing hybridization, 56 out of 122 loci differentially fixed or nearly so between the two species were impermeable to introgression across the sharp hybrid zone (9 km wide). We also found concordance in cline position and width among genetic, morphological and environmental variation, suggesting a coupling of different reproductive barriers. Habitat characteristics such as the presence of trees and shrubs and the start of the growing season were strongly associated with the genetic variation, and we found evidence of divergence at genetic markers associated with morphology and physiology, putatively involved in visual or environmental reproductive isolation. We discuss the various behavioural and ecological factors that might interplay to maintain current levels of divergence and gene flow between this species pair.
Collapse
Affiliation(s)
- Thibaut Capblancq
- Laboratoire d’Écologie AlpineUMR UGA‐USMB‐CNRS 5553Université Grenoble AlpesGrenobleFrance
- Department of Plant BiologyUniversity of VermontBurlingtonVTUSA
| | - Laurence Després
- Laboratoire d’Écologie AlpineUMR UGA‐USMB‐CNRS 5553Université Grenoble AlpesGrenobleFrance
| | - Jesús Mavárez
- Laboratoire d’Écologie AlpineUMR UGA‐USMB‐CNRS 5553Université Grenoble AlpesGrenobleFrance
- Departamento de Ciencias Biológicas y AmbientalesUniversidad Jorge Tadeo LozanoBogotáColombia
| |
Collapse
|
24
|
Mimura M, Suga M. Ambiguous species boundaries: Hybridization and morphological variation in two closely related Rubus species along altitudinal gradients. Ecol Evol 2020; 10:7476-7486. [PMID: 32760542 PMCID: PMC7391560 DOI: 10.1002/ece3.6473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/11/2020] [Accepted: 05/13/2020] [Indexed: 11/23/2022] Open
Abstract
Although hybridization frequently occurs among plant species, hybrid zones of divergent lineages formed at species boundaries are less common and may not be apparent in later generations of hybrids with more parental-like phenotypes, as a consequence of backcrossing. To determine the effects of dispersal and selection on species boundaries, we compared clines in leaf traits and molecular hybrid index along two hybrid zones on Yakushima Island, Japan, in which a temperate (Rubus palmatus) and subtropical (Rubus grayanus) species of wild raspberry are found. Leaf sinus depth in the two hybrid zones had narrower clines at 600 m a.s.l. than the molecular hybrid index and common garden tests confirmed that some leaf traits, including leaf sinus depth that is a major trait used in species identification, are genetically divergent between these closely related species. The sharp transition in leaf phenotypic traits compared to molecular markers indicated divergent selection pressure on the hybrid zone structure. We suggest that species boundaries based on neutral molecular data may differ from those based on observed morphological traits.
Collapse
Affiliation(s)
- Makiko Mimura
- Department of BiologyGraduate School of Natural Science and TechnologyOkayama UniversityOkayamaJapan
| | - Mihoko Suga
- Graduate School of AgricultureTamagawa UniversityTokyoJapan
- Present address:
Sacred Heart SchoolTokyoJapan
| |
Collapse
|
25
|
Irwin DE. Assortative Mating in Hybrid Zones Is Remarkably Ineffective in Promoting Speciation. Am Nat 2020; 195:E150-E167. [DOI: 10.1086/708529] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
26
|
McEntee JP, Burleigh JG, Singhal S. Dispersal Predicts Hybrid Zone Widths across Animal Diversity: Implications for Species Borders under Incomplete Reproductive Isolation. Am Nat 2020; 196:9-28. [PMID: 32552108 DOI: 10.1086/709109] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hybrid zones occur as range boundaries for many animal taxa. One model for how hybrid zones form and stabilize is the tension zone model, a version of which predicts that hybrid zone widths are determined by a balance between random dispersal into hybrid zones and selection against hybrids. Here, we examine whether random dispersal and proxies for selection against hybrids (genetic distances between hybridizing pairs) can explain variation in hybrid zone widths across 131 hybridizing pairs of animals. We show that these factors alone can explain ∼40% of the variation in zone width among animal hybrid zones, with dispersal explaining far more of the variation than genetic distances. Patterns within clades were idiosyncratic. Genetic distances predicted hybrid zone widths particularly well for reptiles, while this relationship was opposite tension zone predictions in birds. Last, the data suggest that dispersal and molecular divergence set lower bounds on hybrid zone widths in animals, indicating that there are geographic restrictions on hybrid zone formation. Overall, our analyses reinforce the fundamental importance of dispersal in hybrid zone formation and more generally in the ecology of range boundaries.
Collapse
|
27
|
Menon M, Landguth E, Leal‐Saenz A, Bagley JC, Schoettle AW, Wehenkel C, Flores‐Renteria L, Cushman SA, Waring KM, Eckert AJ. Tracing the footprints of a moving hybrid zone under a demographic history of speciation with gene flow. Evol Appl 2020; 13:195-209. [PMID: 31892952 PMCID: PMC6935588 DOI: 10.1111/eva.12795] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/20/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023] Open
Abstract
A lack of optimal gene combinations, as well as low levels of genetic diversity, is often associated with the formation of species range margins. Conservation efforts rely on predictive modelling using abiotic variables and assessments of genetic diversity to determine target species and populations for controlled breeding, germplasm conservation and assisted migration. Biotic factors such as interspecific competition and hybridization, however, are largely ignored, despite their prevalence across diverse taxa and their role as key evolutionary forces. Hybridization between species with well-developed barriers to reproductive isolation often results in the production of offspring with lower fitness. Generation of novel allelic combinations through hybridization, however, can also generate positive fitness consequences. Despite this possibility, hybridization-mediated introgression is often considered a threat to biodiversity as it can blur species boundaries. The contribution of hybridization towards increasing genetic diversity of populations at range margins has only recently gathered attention in conservation studies. We assessed the extent to which hybridization contributes towards range dynamics by tracking spatio-temporal changes in the central location of a hybrid zone between two recently diverged species of pines: Pinus strobiformis and P. flexilis. By comparing geographic cline centre estimates for global admixture coefficient with morphological traits associated with reproductive output, we demonstrate a northward shift in the hybrid zone. Using a combination of spatially explicit, individual-based simulations and linkage disequilibrium variance partitioning, we note a significant contribution of adaptive introgression towards this northward movement, despite the potential for differences in regional population size to aid hybrid zone movement. Overall, our study demonstrates that hybridization between recently diverged species can increase genetic diversity and generate novel allelic combinations. These novel combinations may allow range margin populations to track favourable climatic conditions or facilitate adaptive evolution to ongoing and future climate change.
Collapse
Affiliation(s)
- Mitra Menon
- Integrative Life SciencesVirginia Commonwealth UniversityRichmondVirginia
| | - Erin Landguth
- School of Public and Community Health SciencesUniversity of MontanaMissoulaMontana
| | - Alejandro Leal‐Saenz
- Programa Institucional de Doctorado en Ciencias Agropecuarias y ForestalesUniversidad Juárez del Estado de DurangoDurangoMexico
| | - Justin C. Bagley
- Department of BiologyVirginia Commonwealth UniversityRichmondVirginia
| | - Anna W. Schoettle
- Rocky Mountain Research StationUSDA Forest ServiceFort CollinsColorado
| | - Christian Wehenkel
- Instituto de Silvicultura e Industria de la MaderaUniversidad Juarez del Estado de DurangoDurangoMexico
| | | | | | | | - Andrew J. Eckert
- Department of BiologyVirginia Commonwealth UniversityRichmondVirginia
| |
Collapse
|
28
|
Fustier MA, Martínez-Ainsworth NE, Aguirre-Liguori JA, Venon A, Corti H, Rousselet A, Dumas F, Dittberner H, Camarena MG, Grimanelli D, Ovaskainen O, Falque M, Moreau L, de Meaux J, Montes-Hernández S, Eguiarte LE, Vigouroux Y, Manicacci D, Tenaillon MI. Common gardens in teosintes reveal the establishment of a syndrome of adaptation to altitude. PLoS Genet 2019; 15:e1008512. [PMID: 31860672 PMCID: PMC6944379 DOI: 10.1371/journal.pgen.1008512] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 01/06/2020] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
In plants, local adaptation across species range is frequent. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Genome scans are popular to uncover outlier loci potentially involved in the genetic architecture of local adaptation, however links between outliers and phenotypic variation are rarely addressed. Here we focused on adaptation of teosinte populations along two elevation gradients in Mexico that display continuous environmental changes at a short geographical scale. We used two common gardens, and phenotyped 18 traits in 1664 plants from 11 populations of annual teosintes. In parallel, we genotyped these plants for 38 microsatellite markers as well as for 171 outlier single nucleotide polymorphisms (SNPs) that displayed excess of allele differentiation between pairs of lowland and highland populations and/or correlation with environmental variables. Our results revealed that phenotypic differentiation at 10 out of the 18 traits was driven by local selection. Trait covariation along the elevation gradient indicated that adaptation to altitude results from the assembly of multiple co-adapted traits into a complex syndrome: as elevation increases, plants flower earlier, produce less tillers, display lower stomata density and carry larger, longer and heavier grains. The proportion of outlier SNPs associating with phenotypic variation, however, largely depended on whether we considered a neutral structure with 5 genetic groups (73.7%) or 11 populations (13.5%), indicating that population stratification greatly affected our results. Finally, chromosomal inversions were enriched for both SNPs whose allele frequencies shifted along elevation as well as phenotypically-associated SNPs. Altogether, our results are consistent with the establishment of an altitudinal syndrome promoted by local selective forces in teosinte populations in spite of detectable gene flow. Because elevation mimics climate change through space, SNPs that we found underlying phenotypic variation at adaptive traits may be relevant for future maize breeding.
Collapse
Affiliation(s)
- Margaux-Alison Fustier
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Natalia E. Martínez-Ainsworth
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Jonás A. Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Anthony Venon
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Hélène Corti
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Agnès Rousselet
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Fabrice Dumas
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Hannes Dittberner
- Institute of Botany, University of Cologne Biocenter, Cologne, Germany
| | - María G. Camarena
- Campo Experimental Bajío, InstitutoNacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Mexico
| | - Daniel Grimanelli
- UMR Diversité, Adaptation et Développement des plantes, Université de Montpellier, Institut de Recherche pour le développement, Montpellier, France
| | - Otso Ovaskainen
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Matthieu Falque
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Laurence Moreau
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Juliette de Meaux
- Institute of Botany, University of Cologne Biocenter, Cologne, Germany
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, InstitutoNacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, Mexico
| | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Yves Vigouroux
- UMR Diversité, Adaptation et Développement des plantes, Université de Montpellier, Institut de Recherche pour le développement, Montpellier, France
| | - Domenica Manicacci
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - Maud I. Tenaillon
- Génétique Quantitative et Evolution – Le Moulon, Université Paris-Saclay, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| |
Collapse
|
29
|
van Riemsdijk I, Butlin RK, Wielstra B, Arntzen JW. Testing an hypothesis of hybrid zone movement for toads in France. Mol Ecol 2019; 28:1070-1083. [PMID: 30609055 DOI: 10.1111/mec.15005] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/08/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Hybrid zone movement may result in substantial unidirectional introgression of selectively neutral material from the local to the advancing species, leaving a genetic footprint. This genetic footprint is represented by a trail of asymmetric tails and displaced cline centres in the wake of the moving hybrid zone. A peak of admixture linkage disequilibrium is predicted to exist ahead of the centre of the moving hybrid zone. We test these predictions of the movement hypothesis in a hybrid zone between common (Bufo bufo) and spined toads (B. spinosus), using 31 nuclear and one mtDNA SNPs along a transect in the northwest of France. Average effective selection in Bufo hybrids is low and clines vary in shape and centre. A weak pattern of asymmetric introgression is inferred from cline discordance of seven nuclear markers. The dominant direction of gene flow is from B. spinosus to B. bufo and is in support of southward movement of the hybrid zone. Conversely, a peak of admixture linkage disequilibrium north of the hybrid zone suggests northward movement. These contrasting results can be explained by reproductive isolation of the B. spinosus and B. bufo gene pools at the southern (B. spinosus) side of the hybrid zone. The joint occurrence of asymmetric introgression and admixture linkage disequilibrium can also be explained by the combination of low dispersal and random genetic drift due to low effective population sizes.
Collapse
Affiliation(s)
- Isolde van Riemsdijk
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
| | - Roger K Butlin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Ben Wielstra
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands.,Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.,Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California
| | - Jan W Arntzen
- Taxonomy and Systematics, Naturalis Biodiversity Center, Leiden, The Netherlands
| |
Collapse
|
30
|
Scordato ESC, Smith CCR, Semenov GA, Liu Y, Wilkins MR, Liang W, Rubtsov A, Sundev G, Koyama K, Turbek SP, Wunder MB, Stricker CA, Safran RJ. Migratory divides coincide with reproductive barriers across replicated avian hybrid zones above the Tibetan Plateau. Ecol Lett 2019; 23:231-241. [DOI: 10.1111/ele.13420] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/25/2019] [Accepted: 10/15/2019] [Indexed: 01/02/2023]
Affiliation(s)
- Elizabeth S. C. Scordato
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- Department of Biological Sciences California State Polytechnic University Pomona CA USA
| | - Chris C. R. Smith
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Georgy A. Semenov
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- Institute of Ecology and Systematics of Animals Novosibirsk Russia
| | - Yu Liu
- Queen Mary University of London London England
- Beijing Normal University Beijing China
| | - Matthew R. Wilkins
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- Vanderbilt University Center for Science Outreach Nashville TN37212 USA
| | - Wei Liang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands College of Life Sciences Hainan Normal University Haikou571158 China
| | | | - Gomboobaatar Sundev
- National University of Mongolia P. O. Box 537 Ulaanbaatar210646 Mongolia
- Mongolian Ornithological Society P. O. Box 537 Ulaanbaatar210646 Mongolia
| | - Kazuo Koyama
- Japan Bird Research Association Tokyo Japan183‐0034
| | - Sheela P. Turbek
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Michael B. Wunder
- Department of Integrative Biology University of Colorado Denver Denver CO USA
| | | | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| |
Collapse
|
31
|
Sequeira F, Bessa-Silva A, Tarroso P, Sousa-Neves T, Vallinoto M, Gonçalves H, Martínez-Solano I. Discordant patterns of introgression across a narrow hybrid zone between two cryptic lineages of an Iberian endemic newt. J Evol Biol 2019; 33:202-216. [PMID: 31677317 DOI: 10.1111/jeb.13562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 10/15/2019] [Accepted: 10/25/2019] [Indexed: 11/30/2022]
Abstract
The study of natural hybrid zones can illuminate aspects of lineage divergence and speciation in morphologically cryptic taxa. We studied a hybrid zone between two highly divergent but morphologically similar lineages (south-western and south-eastern) of the Iberian endemic Bosca's newt (Lissotriton boscai) in SW Iberia with a multilocus dataset (microsatellites, nuclear and mitochondrial genes). STRUCTURE and NEWHYBRIDS analyses retrieved few admixed individuals, which classified as backcrosses involving parental individuals of the south-western lineage. Our results show asymmetric introgression of mtDNA beyond the contact from this lineage into the south-eastern lineage. Analysis of nongeographic introgression patterns revealed asymmetries in the direction of introgression, but except for mtDNA, we did not find evidence for nonconcordant introgression patterns across nuclear loci. Analysis of a 150-km transect across the hybrid zone showed broadly coincident cline widths (ca. 3.2-27.9 km), and concordant cline centres across all markers, except for mtDNA that is displaced ca. 60 km northward. Results from ecological niche modelling show that the hybrid zone is in a climatically homogenous area with suitable habitat for the species, suggesting that contact between the two lineages is unlikely to occur further south as their distributions are currently separated by an extensive area of unfavourable habitat. Taken together, our findings suggest the genetic structure of this hybrid zone results from the interplay of historical (biogeographic) and population-level processes. The narrowness and coincidence of genetic clines can be explained by weak selection against hybrids and reflect a degree of reproductive isolation that is consistent with cryptic speciation.
Collapse
Affiliation(s)
- Fernando Sequeira
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal
| | - Adam Bessa-Silva
- Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Pará, Brasil
| | - Pedro Tarroso
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal
| | - Tiago Sousa-Neves
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Museu Paraense Emílio Goeldi, Coordenação de Zoologia, Pará, Brasil
| | - Marcelo Vallinoto
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Laboratório de Evolução (LEVO), Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Pará, Brasil
| | - Helena Gonçalves
- Laboratorio Associado, CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal.,Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Iñigo Martínez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC (MNCN-CSIC), Madrid, Spain
| |
Collapse
|
32
|
Wang S, Rohwer S, Delmore K, Irwin DE. Cross-decades stability of an avian hybrid zone. J Evol Biol 2019; 32:1242-1251. [PMID: 31430391 DOI: 10.1111/jeb.13524] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/06/2019] [Accepted: 08/13/2019] [Indexed: 01/04/2023]
Abstract
Hybrid zones are particularly valuable for understanding the evolution of partial reproductive isolation between differentiated populations. An increasing number of hybrid zones have been inferred to move over time, but in most such cases zone movement has not been tested with long-term genomic data. The hybrid zone between Townsend's Warblers (Setophaga townsendi) and Hermit Warblers (S. occidentalis) in the Washington Cascades was previously inferred to be moving from northern S. townsendi southwards towards S. occidentalis, based on plumage and behavioural patterns as well as a 2000-km genetic wake of hermit mitochondrial DNA (mtDNA) in coastal Townsend's Warblers. We directly tested whether hybrid zone position has changed over 2-3 decades by tracking plumage, mtDNA and nuclear genomic variation across the hybrid zone over two sampling periods (1987-94 and 2015-16). Surprisingly, there was no significant movement in genomic or plumage cline centres between the two time periods. Plumage cline widths were narrower than expected by neutral diffusion, consistent with a 'tension zone' model, in which selection against hybrids is balanced by movement of parental forms into the zone. Our results indicate that this hybrid zone is either stable in its location or moving at a rate that is not detectable over 2-3 decades. Despite considerable gene flow, the stable clines in multiple phenotypic and genotypic characters over decades suggest evolutionary stability of this young pair of sister species, allowing divergence to continue. We propose a novel biogeographic scenario to explain these patterns: rather than the hybrid zone having moved thousands of kilometres to its current position, inland Townsend's met coastal Hermit Warbler populations along a broad front of the British Columbia and Alaska coast and hybridization led to replacement of the Hermit Warbler plumage with Townsend's Warbler plumage patterns along this coastline. Hence, hybrid zones along British Columbia and Alaska moved only a short distance from the inland to the coast, whereas the Hermit Warbler phenotype appears stable in Washington and further south. This case provides an example of the complex biogeographic processes that have led to the distribution of current phenotypes within and among closely related species.
Collapse
Affiliation(s)
- Silu Wang
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Sievert Rohwer
- Department of Biology and Burke Museum, University of Washington, Seattle, WA, USA
| | - Kira Delmore
- Department of Biology, Texas A & M, College Station, TX, USA
| | - Darren E Irwin
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| |
Collapse
|
33
|
Thurman TJ, Szejner-Sigal A, McMillan WO. Movement of a Heliconius hybrid zone over 30 years: A Bayesian approach. J Evol Biol 2019; 32:974-983. [PMID: 31216075 DOI: 10.1111/jeb.13499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/29/2019] [Accepted: 06/10/2019] [Indexed: 11/27/2022]
Abstract
Hybrid zones have long been of interest to biologists as natural laboratories where we can gain insight into the processes of adaptation and speciation. Repeated sampling of individual hybrid zones has been particularly useful in elucidating the dynamic balance between selection and dispersal that maintains most hybrid zones. Here, we revisit a hybrid zone between Heliconius erato butterflies in Panamá for a third time over more than 30 years. We combine a novel Bayesian extension of stepped-cline hybrid zone models with environmental data to understand the genetic and environmental causes of cline dynamics in this species. The cline has continued to move west, likely due to dominance drive, but has slowed and broadened. Environmental analyses suggest that widespread deforestation in Panamá could be leading to decreased avian predation and relaxed selection, causing the observed changes in cline dynamics.
Collapse
Affiliation(s)
- Timothy J Thurman
- Smithsonian Tropical Research Institute, Panamá, República de Panamá.,Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada
| | - Andre Szejner-Sigal
- Smithsonian Tropical Research Institute, Panamá, República de Panamá.,Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
| |
Collapse
|
34
|
Inman R, Fotheringham AS, Franklin J, Esque T, Edwards T, Nussear K. Local niche differences predict genotype associations in sister taxa of desert tortoise. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Richard Inman
- School of Geographical Sciences and Urban Planning Arizona State University Tempe Arizona
- U.S. Geological Survey Western Ecological Research Center Henderson Nevada
| | | | - Janet Franklin
- Department of Botany and Plant Sciences University of California – Riverside Riverside California
| | - Todd Esque
- U.S. Geological Survey Western Ecological Research Center Henderson Nevada
| | - Taylor Edwards
- University of Arizona Genetics Core, University of Arizona Tucson Arizona
| | - Kenneth Nussear
- Department of Geography University of Nevada – Reno Reno Nevada
| |
Collapse
|
35
|
Wennevik V, Quintela M, Skaala Ø, Verspoor E, Prusov S, Glover KA. Population genetic analysis reveals a geographically limited transition zone between two genetically distinct Atlantic salmon lineages in Norway. Ecol Evol 2019; 9:6901-6921. [PMID: 31380023 PMCID: PMC6662299 DOI: 10.1002/ece3.5258] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/24/2019] [Accepted: 04/26/2019] [Indexed: 12/17/2022] Open
Abstract
Atlantic salmon is characterized by a high degree of population genetic structure throughout its native range. However, while populations inhabiting rivers in Norway and Russia make up a significant proportion of salmon in the Atlantic, thus far, genetic studies in this region have only encompassed low to modest numbers of populations. Here, we provide the first "in-depth" investigation of population genetic structuring in the species in this region. Analysis of 18 microsatellites on >9,000 fish from 115 rivers revealed highly significant population genetic structure throughout, following a hierarchical pattern. The highest and clearest level of division separated populations north and south of the Lofoten region in northern Norway. In this region, only a few populations displayed intermediate genetic profiles, strongly indicating a geographically limited transition zone. This was further supported by a dedicated cline analysis. Population genetic structure was also characterized by a pattern of isolation by distance. A decline in overall genetic diversity was observed from the south to the north, and two of the microsatellites showed a clear decrease in number of alleles across the observed transition zone. Together, these analyses support results from previous studies, that salmon in Norway originate from two main genetic lineages, one from the Barents-White Sea refugium that recolonized northern Norwegian and adjacent Russian rivers, and one from the eastern Atlantic that recolonized the rest of Norway. Furthermore, our results indicate that local conditions in the limited geographic transition zone between the two observed lineages, characterized by open coastline with no obvious barriers to gene flow, are strong enough to maintain the genetic differentiation between them.
Collapse
Affiliation(s)
| | | | | | - Eric Verspoor
- Rivers and Lochs Institute, Inverness CollegeUniversity of the Highlands and IslandsInvernessUK
| | - Sergey Prusov
- The Knipovich Polar Research Institute of Marine Fisheries and Oceanography (PINRO)MurmanskRussia
| | | |
Collapse
|
36
|
Bourgeois Y, Boissinot S. On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements. Genes (Basel) 2019; 10:genes10060419. [PMID: 31151307 PMCID: PMC6627506 DOI: 10.3390/genes10060419] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/05/2019] [Accepted: 05/21/2019] [Indexed: 01/18/2023] Open
Abstract
Transposable elements (TEs) play an important role in shaping genomic organization and structure, and may cause dramatic changes in phenotypes. Despite the genetic load they may impose on their host and their importance in microevolutionary processes such as adaptation and speciation, the number of population genetics studies focused on TEs has been rather limited so far compared to single nucleotide polymorphisms (SNPs). Here, we review the current knowledge about the dynamics of transposable elements at recent evolutionary time scales, and discuss the mechanisms that condition their abundance and frequency. We first discuss non-adaptive mechanisms such as purifying selection and the variable rates of transposition and elimination, and then focus on positive and balancing selection, to finally conclude on the potential role of TEs in causing genomic incompatibilities and eventually speciation. We also suggest possible ways to better model TEs dynamics in a population genomics context by incorporating recent advances in TEs into the rich information provided by SNPs about the demography, selection, and intrinsic properties of genomes.
Collapse
Affiliation(s)
- Yann Bourgeois
- New York University Abu Dhabi, P.O. 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
| | - Stéphane Boissinot
- New York University Abu Dhabi, P.O. 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
37
|
Batalha-Filho H, Maldonado-Coelho M, Miyaki CY. Historical climate changes and hybridization shaped the evolution of Atlantic Forest spinetails (Aves: Furnariidae). Heredity (Edinb) 2019; 123:675-693. [PMID: 31123344 DOI: 10.1038/s41437-019-0234-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/04/2019] [Accepted: 05/09/2019] [Indexed: 01/23/2023] Open
Abstract
Combining phylogeographic approaches and hybrid zone inference in a single framework is a robust way to depict respectively the biogeographic history of lineages and the evolutionary processes responsible for speciation. Here, we studied the spatiotemporal patterns of diversification and characterize the hybrid zone between two Atlantic Forest spinetails (Synallaxis ruficapilla and Synallaxis cinerea) using mitochondrial DNA and nuclear (autosomal and Z-linked) genes. We consistently recovered divergence between and within the two species during the late Pliocene and Pleistocene using an isolation with migration model. Also, our results indicate distinct levels of introgression among lineages. Ecological niche models and demographic inferences, used to infer range distributions throughout the late Quaternary, were not consistent with the hypothesis of a large river as a primary barrier responsible for the divergence of the two species. Instead, a scenario of isolation and divergence followed by geographic expansion and admixture as a consequence of Quaternary climatic oscillations was supported. Paleomodels also were not consistent with the idea that the hybrid zone originated in primary differentiation and favor a secondary contact scenario. Model fitting indicated that clines of different loci spanning the hybrid zone are coincident and concordant. The narrow cline for one Z-linked locus could be indicative of some form of post-zygotic selection hindering genetic homogenization between the two species.
Collapse
Affiliation(s)
| | | | - Cristina Yumi Miyaki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| |
Collapse
|
38
|
Genetic Analysis of a Cryptic Contact Zone between Mitochondrial Clades of the Eastern Red-Backed Salamander, Plethodon cinereus. J HERPETOL 2019. [DOI: 10.1670/18-088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
39
|
Hooper DM, Griffith SC, Price TD. Sex chromosome inversions enforce reproductive isolation across an avian hybrid zone. Mol Ecol 2018; 28:1246-1262. [PMID: 30230092 DOI: 10.1111/mec.14874] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/23/2018] [Accepted: 08/27/2018] [Indexed: 12/11/2022]
Abstract
Across hybrid zones, the sex chromosomes are often more strongly differentiated than the autosomes. This is regularly attributed to the greater frequency of reproductive incompatibilities accumulating on sex chromosomes and their exposure in the heterogametic sex. Working within an avian hybrid zone, we explore the possibility that chromosome inversions differentially accumulate on the Z chromosome compared to the autosomes and thereby contribute to Z chromosome differentiation. We analyse the northern Australian hybrid zone between two subspecies of the long-tailed finch (Poephila acuticauda), first described based on differences in bill colour, using reduced-representation genomic sequencing for 293 individuals over a 1,530-km transect. Autosomal differentiation between subspecies is minimal. In contrast, 75% of the Z chromosome is highly differentiated and shows a steep genomic cline, which is displaced 350 km to the west of the cline in bill colour. Differentiation is associated with two or more putative chromosomal inversions, each predominating in one subspecies. If inversions reduce recombination between hybrid incompatibilities, they are selectively favoured and should therefore accumulate in hybrid zones. We argue that this predisposes inversions to differentially accumulate on the Z chromosome. One genomic region affecting bill colour is on the Z, but the main candidates are on chromosome 8. This and the displacement of the bill colour and Z chromosome cline centres suggest that bill colour has not strongly contributed to inversion accumulation. Based on cline width, however, the Z chromosome and bill colour both contribute to reproductive isolation established between this pair of subspecies.
Collapse
Affiliation(s)
- Daniel M Hooper
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York.,Committe on Evolutionary Biology, University of Chicago, Chicago, Illinois
| | - Simon C Griffith
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Trevor D Price
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois
| |
Collapse
|
40
|
Dyer KA, Bewick ER, White BE, Bray MJ, Humphreys DP. Fine-scale geographic patterns of gene flow and reproductive character displacement in Drosophila subquinaria and Drosophila recens. Mol Ecol 2018; 27:10.1111/mec.14825. [PMID: 30074656 PMCID: PMC6360132 DOI: 10.1111/mec.14825] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/12/2022]
Abstract
When two species are incompletely isolated, strengthening premating isolation barriers in response to the production of low fitness hybrids may complete the speciation process. Here, we use the sister species Drosophila subquinaria and Drosophila recens to study the conditions under which this reinforcement of species boundaries occurs in natural populations. We first extend the region of known sympatry between these species, and then we conduct a fine-scale geographic survey of mate discrimination coupled with estimates of gene flow within and admixture between species. Within D. subquinaria, reinforcement is extremely effective: we find variation in mate discrimination both against D. recens males and against conspecific allopatric males on the scale of a few kilometres and in the face of gene flow both from conspecific populations and introgression from D. recens. In D. recens, we do not find evidence for increased mate discrimination in sympatry, even where D. recens is rare, consistent with substantial gene flow throughout the species' range. Finally, we find that introgression between species is asymmetric, with more from D. recens into D. subquinaria than vice versa. Within each species, admixture is highest in the geographic region where it is rare relative to the other species, suggesting that when hybrids are produced they are of low fitness. In sum, reinforcement within D. subquinaria is effective at maintaining species boundaries, but even when reinforcing selection is strong it may not always result in a pattern of strong reproductive character displacement due to variation in the frequency of hybridization and gene flow from neighbouring populations.
Collapse
Affiliation(s)
- Kelly A. Dyer
- Department of Genetics; University of Georgia; Athens, GA 30602; USA
| | | | - Brooke E. White
- Department of Genetics; University of Georgia; Athens, GA 30602; USA
| | | | | |
Collapse
|
41
|
Lin D, Bi K, Conroy CJ, Lacey EA, Schraiber JG, Bowie RCK. Mito-nuclear discordance across a recent contact zone for California voles. Ecol Evol 2018; 8:6226-6241. [PMID: 29988439 PMCID: PMC6024151 DOI: 10.1002/ece3.4129] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 11/17/2022] Open
Abstract
To examine the processes that maintain genetic diversity among closely related taxa, we investigated the dynamics of introgression across a contact zone between two lineages of California voles (Microtus californicus). We tested the prediction that introgression of nuclear loci would be greater than that for mitochondrial loci, assuming ongoing gene flow across the contact zone. We also predicted that genomic markers would show a mosaic pattern of differentiation across this zone, consistent with genomes that are semi-permeable. Using mitochondrial cytochrome b sequences and genome-wide loci developed via ddRAD-seq, we analyzed genetic variation for 10 vole populations distributed along the central California coast; this transect included populations from within the distributions of both parental lineages as well as the putative contact zone. Our analyses revealed that (1) the two lineages examined are relatively young, having diverged ca. 8.5-54 kya, (2) voles from the contact zone in Santa Barbara County did not include F1 or early generation backcrossed individuals, and (3) there appeared to be little to no recurrent gene flow across the contact zone. Introgression patterns for mitochondrial and nuclear markers were not concordant; only mitochondrial markers revealed evidence of introgression, putatively due to historical hybridization. These differences in genetic signatures are intriguing given that the contact zone occurs in a region of continuous vole habitat, with no evidence of past or present physical barriers. Future studies that examine specific isolating mechanisms, such as microhabitat use and mate choice, will facilitate our understanding of how genetic boundaries are maintained in this system.
Collapse
Affiliation(s)
- Dana Lin
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia
| | - Ke Bi
- Computational Genomics Resource LaboratoryCalifornia Institute for Quantitative BiosciencesUniversity of California, BerkeleyBerkeleyCalifornia
| | - Christopher J. Conroy
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia
| | - Eileen A. Lacey
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia
| | - Joshua G. Schraiber
- Department of BiologyCenter for Computational Genetics and GenomicsTemple UniversityPhiladelphiaPennsylvania
- Institute for Genomics and Evolutionary MedicineTemple UniversityPhiladelphiaPennsylvania
| | - Rauri C. K. Bowie
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia
- Department of Integrative BiologyUniversity of California, BerkeleyBerkeleyCalifornia
| |
Collapse
|
42
|
Rafati N, Blanco-Aguiar JA, Rubin CJ, Sayyab S, Sabatino SJ, Afonso S, Feng C, Alves PC, Villafuerte R, Ferrand N, Andersson L, Carneiro M. A genomic map of clinal variation across the European rabbit hybrid zone. Mol Ecol 2018; 27:1457-1478. [PMID: 29359877 DOI: 10.1111/mec.14494] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 01/02/2023]
Abstract
Speciation is a process proceeding from weak to complete reproductive isolation. In this continuum, naturally hybridizing taxa provide a promising avenue for revealing the genetic changes associated with the incipient stages of speciation. To identify such changes between two subspecies of rabbits that display partial reproductive isolation, we studied patterns of allele frequency change across their hybrid zone using whole-genome sequencing. To connect levels and patterns of genetic differentiation with phenotypic manifestations of subfertility in hybrid rabbits, we further investigated patterns of gene expression in testis. Geographic cline analysis revealed 253 regions characterized by steep changes in allele frequency across their natural region of contact. This catalog of regions is likely to be enriched for loci implicated in reproductive barriers and yielded several insights into the evolution of hybrid dysfunction in rabbits: (i) incomplete reproductive isolation is likely governed by the effects of many loci, (ii) protein-protein interaction analysis suggest that genes within these loci interact more than expected by chance, (iii) regulatory variation is likely the primary driver of incompatibilities, and (iv) large chromosomal rearrangements appear not to be a major mechanism underlying incompatibilities or promoting isolation in the face of gene flow. We detected extensive misregulation of gene expression in testis of hybrid males, but not a statistical overrepresentation of differentially expressed genes in candidate regions. Our results also did not support an X chromosome-wide disruption of expression as observed in mice and cats, suggesting variation in the mechanistic basis of hybrid male reduced fertility among mammals.
Collapse
Affiliation(s)
- Nima Rafati
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - José A Blanco-Aguiar
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Instituto de Investigacion en Recursos Cinegéticos (IREC-CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Carl J Rubin
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Shumaila Sayyab
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Research Center for Modeling and Simulation, National University of Sciences and Technology, Islamabad, Pakistan
| | - Stephen J Sabatino
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Chungang Feng
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | | | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland, South Africa
| | - Leif Andersson
- Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| |
Collapse
|
43
|
|
44
|
Morales-Rozo A, Tenorio EA, Carling MD, Cadena CD. Origin and cross-century dynamics of an avian hybrid zone. BMC Evol Biol 2017; 17:257. [PMID: 29246108 PMCID: PMC5732383 DOI: 10.1186/s12862-017-1096-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 11/27/2017] [Indexed: 01/07/2023] Open
Abstract
Background Characterizations of the dynamics of hybrid zones in space and time can give insights about traits and processes important in population divergence and speciation. We characterized a hybrid zone between tanagers in the genus Ramphocelus (Aves, Thraupidae) located in southwestern Colombia. We evaluated whether this hybrid zone originated as a result of secondary contact or of primary differentiation, and described its dynamics across time using spatial analyses of molecular, morphological, and coloration data in combination with paleodistribution modeling. Results Models of potential historical distributions based on climatic data and genetic signatures of demographic expansion suggested that the hybrid zone likely originated following secondary contact between populations that expanded their ranges out of isolated areas in the Quaternary. Concordant patterns of variation in phenotypic characters across the hybrid zone and its narrow extent are suggestive of a tension zone, maintained by a balance between dispersal and selection against hybrids. Estimates of phenotypic cline parameters obtained using specimens collected over nearly a century revealed that, in recent decades, the zone appears to have moved to the east and to higher elevations, and may have become narrower. Genetic variation was not clearly structured along the hybrid zone, but comparisons between historical and contemporary specimens suggested that temporal changes in its genetic makeup may also have occurred. Conclusions Our data suggest that the hybrid zone likey resulted from secondary contact between populations. The observed changes in the hybrid zone may be a result of sexual selection, asymmetric gene flow, or environmental change. Electronic supplementary material The online version of this article (doi: 10.1186/s12862-017-1096-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Andrea Morales-Rozo
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia.,Programa de Biología y Museo de Historia Natural, Universidad de los Llanos, Sede Barcelona, Villavicencio, Colombia
| | - Elkin A Tenorio
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia.,Calima: Fundación para la Investigación de la Biodiversidad y Conservación en el Trópico, Cali, Colombia
| | - Matthew D Carling
- Cornell Laboratory of Ornithology, Cornell University, Ithaca, NY, USA.,Department of Zoology and Physiology, University of Wyoming, Laramie, WY, USA
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas, Universidad de Los Andes, Bogotá, Colombia.
| |
Collapse
|
45
|
Ding S, Mishra M, Wu H, Liang S, Miyamoto MM. Characterization of hybridization within a secondary contact region of the inshore fish, Bostrychus sinensis, in the East China Sea. Heredity (Edinb) 2017; 120:51-62. [PMID: 29234169 DOI: 10.1038/s41437-017-0011-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 08/30/2017] [Accepted: 09/22/2017] [Indexed: 11/09/2022] Open
Abstract
The northwest Pacific marginal seas are a primary center of phylogeographic and evolutionary research, because of their dynamic geographic history of falling and rising sea levels during the glaciations and interglaciations of the last one million years. Here we present new molecular and morphological data for geographic samples of the four-eyed sleeper (Bostrychus sinensis), which reinforce the evidence for secondary contact and hybridization between two phylogeographic lineages in the East China Sea. Specifically, we find that the secondary contact region is characterized by a low frequency of hybridization, where mitochondrial DNA introgression is relatively common, whereas F1 hybrids are correspondingly scarce. Furthermore, the adult standard lengths of the two phylogeographic lineages vary geographically in a manner that is consistent with reproductive character displacement. Collectively, the molecular and morphological data document that sleeper hybridization conforms to the classic "tension zone" model, where alleles are lost via reduced hybrid viability and/or positive assortative mating but are then replenished by dispersal from south of the secondary contact region. They also indicate that the two phylogeographic lineages are at an incipient stage of the speciation process. These results and conclusions for the four-eyed sleeper are presented as a case study for future research on the vicariance, secondary contact, and hybridization of marine groups in the northwest Pacific marginal seas.
Collapse
Affiliation(s)
- Shaoxiong Ding
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361012, China. .,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, 361012, China.
| | - Mrinal Mishra
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611-8525, USA
| | - Haohao Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361012, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, 361012, China
| | - Shuang Liang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361012, China.,Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, Xiamen University, Xiamen, 361012, China
| | - Michael M Miyamoto
- Department of Biology, University of Florida, Box 118525, Gainesville, FL, 32611-8525, USA
| |
Collapse
|
46
|
Semenov GA, Scordato ESC, Khaydarov DR, Smith C, Kane NC, Safran RJ. Effects of assortative mate choice on the genomic and morphological structure of a hybrid zone between two bird subspecies. Mol Ecol 2017; 26:6430-6444. [DOI: 10.1111/mec.14376] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 08/15/2017] [Accepted: 09/27/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Georgy A. Semenov
- Department of Ecology & Evolutionary Biology The University of Arizona Tucson AZ USA
- Institute of Systematics and Ecology of Animals Novosibirsk Russia
| | | | | | - Chris C. R. Smith
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| |
Collapse
|
47
|
Delahaie B, Cornuault J, Masson C, Bertrand JAM, Bourgeois YXC, Milá B, Thébaud C. Narrow hybrid zones in spite of very low population differentiation in neutral markers in an island bird species complex. J Evol Biol 2017; 30:2132-2145. [DOI: 10.1111/jeb.13177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/26/2017] [Accepted: 09/07/2017] [Indexed: 02/06/2023]
Affiliation(s)
- B. Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
- Centre d'Ecologie Fonctionnelle et Evolutive; CNRS-UMR5175 CEFE; Montpellier France
| | - J. Cornuault
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - C. Masson
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - J. A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - Y. X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - B. Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | - C. Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| |
Collapse
|
48
|
MacGregor HEA, Lewandowsky RAM, d'Ettorre P, Leroy C, Davies NW, While GM, Uller T. Chemical communication, sexual selection, and introgression in wall lizards. Evolution 2017; 71:2327-2343. [DOI: 10.1111/evo.13317] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Hannah E. A. MacGregor
- School of Biological Sciences; University of Tasmania; Hobart Tasmania 7001 Australia
- Department of Zoology, Edward Grey Institute; University of Oxford; Oxford OX1 3PS United Kingdom
| | - Rachel A. M. Lewandowsky
- School of Biological Sciences; University of Tasmania; Hobart Tasmania 7001 Australia
- Department of Zoology, Edward Grey Institute; University of Oxford; Oxford OX1 3PS United Kingdom
| | - Patrizia d'Ettorre
- Laboratory of Experimental and Comparative Ethology; University of Paris 13; Sorbonne Paris Cité 93430 Villetaneuse Paris France
| | - Chloé Leroy
- Laboratory of Experimental and Comparative Ethology; University of Paris 13; Sorbonne Paris Cité 93430 Villetaneuse Paris France
| | - Noel W. Davies
- Central Science Laboratory; University of Tasmania; Hobart, Tasmania 7001 Australia
| | - Geoffrey M. While
- School of Biological Sciences; University of Tasmania; Hobart Tasmania 7001 Australia
- Department of Zoology, Edward Grey Institute; University of Oxford; Oxford OX1 3PS United Kingdom
| | - Tobias Uller
- Department of Zoology, Edward Grey Institute; University of Oxford; Oxford OX1 3PS United Kingdom
- Department of Biology; Lund University; Sölvegatan 37 223 62 Lund Sweden
| |
Collapse
|
49
|
Scordato ESC, Wilkins MR, Semenov G, Rubtsov AS, Kane NC, Safran RJ. Genomic variation across two barn swallow hybrid zones reveals traits associated with divergence in sympatry and allopatry. Mol Ecol 2017; 26:5676-5691. [DOI: 10.1111/mec.14276] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 12/31/2022]
Affiliation(s)
| | - Matthew R. Wilkins
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
- School of Biological Sciences University of Nebraska‐Lincoln Lincoln NE USA
| | - Georgy Semenov
- Department of Ecology & Evolutionary Biology University of Arizona Tucson AZ USA
- Institute of Systematics and Ecology of Animals Novosibirsk Russia
| | | | - Nolan C. Kane
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology The University of Colorado Boulder CO USA
| |
Collapse
|
50
|
Britton-Davidian J, Caminade P, Davidian E, Pagès M. Does chromosomal change restrict gene flow between house mouse populations (Mus musculus domesticus)? Evidence from microsatellite polymorphisms. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|