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Ghimire P, Palacios C, Trimble J, Lamichhaney S. Museum genomics approach to study the taxonomy and evolution of Woolly-necked storks using historic specimens. G3 (BETHESDA, MD.) 2024; 14:jkae081. [PMID: 38626302 DOI: 10.1093/g3journal/jkae081] [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: 01/05/2024] [Revised: 03/16/2024] [Accepted: 04/05/2024] [Indexed: 04/18/2024]
Abstract
The accessibility of genomic tools in evolutionary biology has allowed for a thorough exploration of various evolutionary processes associated with adaptation and speciation. However, genomic studies in natural systems present numerous challenges, reflecting the inherent complexities of studying organisms in their native habitats. The utilization of museum specimens for genomics research has received increased attention in recent times, facilitated by advancements in ancient DNA techniques. In this study, we have utilized a museum genomics approach to analyze historic specimens of Woolly-necked storks (Ciconia spp.) and examine their genetic composition and taxonomic status and explore the evolutionary and adaptive trajectories of populations over the years. The Woolly-necked storks are distributed in Asia and Africa with a taxonomic classification that has been a matter of ambiguity. Asian and African Woollynecks were recently recognized as different species based on their morphological differences; however, their genomic validation was lacking. In this study, we have used ∼70-year-old museum samples for whole-genome population-scale sequencing. Our study has revealed that Asian and African Woollynecks are genetically distinct, consistent with the current taxonomic classification based on morphological features. However, we also found a high genetic divergence between the Asian subspecies Ciconia episcopus neglecta and Ciconia episcopus episcopus, suggesting this classification requires a detailed examination to explore processes of ongoing speciation. Because taxonomic classification directly impacts conservation efforts, and there is evidence of declining populations of Asian Woollynecks in Southeast Asia, our results highlight that population-scale studies are urgent to determine the genetic, ecological, and phylogenetic diversity of these birds.
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Affiliation(s)
- Prashant Ghimire
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
| | - Catalina Palacios
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
| | - Jeremiah Trimble
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Sangeet Lamichhaney
- Department of Biological Sciences, Kent State University, Kent, OH 44240, USA
- School of Biomedical Sciences, Kent State University, Kent, OH 44240, USA
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2
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Geng FD, Liu MQ, Zhang XD, Wang LZ, Lei MF. Genomics of hybrid parallel origin in Aquilegia ecalcarata. BMC Ecol Evol 2024; 24:75. [PMID: 38844857 PMCID: PMC11155106 DOI: 10.1186/s12862-024-02266-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND The parallel evolution of similar traits or species provides strong evidence for the role of natural selection in evolution. Traits or species that evolved repeatedly can be driven by separate de novo mutations or interspecific gene flow. Although parallel evolution has been reported in many studies, documented cases of parallel evolution caused by gene flow are scarce by comparison. Aquilegia ecalcarata and A. kansuensis belong to the genus of Aquilegia, and are the closest related sister species. Mutiple origins of A. ecalcarata have been reported in previous studies, but whether they have been driven by separate de novo mutations or gene flow remains unclear. RESULTS In this study, We conducted genomic analysis from 158 individuals of two repeatedly evolving pairs of A. ecalcarata and A. kansuensis. All samples were divided into two distinct clades with obvious geographical distribution based on phylogeny and population structure. Demographic modeling revealed that the origin of the A. ecalcarata in the Eastern of China was caused by gene flow, and the Eastern A. ecalcarata occurred following introgression from Western A. ecalcarata population. Analysis of Treemix and D-statistic also revealed that a strong signal of gene flow was detected from Western A. ecalcarata to Eastern A. ecalcarata. Genetic divergence and selective sweep analyses inferred parallel regions of genomic divergence and identified many candidate genes associated with ecologically adaptive divergence between species pair. Comparative analysis of parallel diverged regions and gene introgression confirms that gene flow contributed to the parallel evolution of A. ecalcarata. CONCLUSIONS Our results further confirmed the multiple origins of A. ecalcarata and highlighted the roles of gene flow. These findings provide new evidence for parallel origin after hybridization as well as insights into the ecological adaptation mechanisms underlying the parallel origins of species.
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Affiliation(s)
- Fang-Dong Geng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
| | - Miao-Qing Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Xue-Dong Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Lu-Zhen Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Meng-Fan Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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3
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Imamoto M, Nakamura H, Aibara M, Hatashima R, Kimirei IA, Kashindye BB, Itoh T, Nikaido M. Severe Bottleneck Impacted the Genomic Structure of Egg-Eating Cichlids in Lake Victoria. Mol Biol Evol 2024; 41:msae093. [PMID: 38782570 PMCID: PMC11166178 DOI: 10.1093/molbev/msae093] [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: 08/04/2023] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Within 15,000 years, the explosive adaptive radiation of haplochromine cichlids in Lake Victoria, East Africa, generated 500 endemic species. In the 1980s, the upsurge of Nile perch, a carnivorous fish artificially introduced to the lake, drove the extinction of more than 200 endemic cichlids. The Nile perch predation particularly harmed piscivorous cichlids, including paedophages, cichlids eat eggs and fries, which is an example of the unique trophic adaptation seen in African cichlids. Here, aiming to investigate past demographic events possibly triggered by the invasion of Nile perch and the subsequent impacts on the genetic structure of cichlids, we conducted large-scale comparative genomics. We discovered evidence of recent bottleneck events in 4 species, including 2 paedophages, which began during the 1970s to 1980s, and population size rebounded during the 1990s to 2000s. The timing of the bottleneck corresponded to the historical records of endemic haplochromines" disappearance and later resurgence, which is likely associated with the introduction of Nile perch by commercial demand to Lake Victoria in the 1950s. Interestingly, among the 4 species that likely experienced bottleneck, Haplochromis sp. "matumbi hunter," a paedophagous cichlid, showed the most severe bottleneck signatures. The components of shared ancestry inferred by ADMIXTURE suggested a high genetic differentiation between matumbi hunter and other species. In contrast, our phylogenetic analyses highly supported the monophyly of the 5 paedophages, consistent with the results of previous studies. We conclude that high genetic differentiation of matumbi hunter occurred due to the loss of shared genetic components among haplochromines in Lake Victoria caused by the recent severe bottleneck.
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Affiliation(s)
- Minami Imamoto
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Haruna Nakamura
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies, SOKENDAI, Kanagawa, Japan
| | - Mitsuto Aibara
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ryo Hatashima
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Ismael A Kimirei
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | | | - Takehiko Itoh
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Masato Nikaido
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
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Teixeira H, Le Corre M, Michon L, Nicoll MAC, Jaeger A, Nikolic N, Pinet P, Couzi FX, Humeau L. Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts. Sci Rep 2024; 14:1960. [PMID: 38263429 PMCID: PMC10805739 DOI: 10.1038/s41598-024-52556-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.
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Affiliation(s)
- Helena Teixeira
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France.
| | - Matthieu Le Corre
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | - Laurent Michon
- Université de La Réunion, Laboratoire Géosciences Réunion, 97744, Saint Denis, France
- Université Paris Cité, Institut de physique du globe de Paris, CNRS, 75005, Paris, France
| | - Malcolm A C Nicoll
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Audrey Jaeger
- UMR ENTROPIE (Université de La Réunion, IRD, CNRS, IFREMER, Université de Nouvelle-Calédonie), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
| | | | - Patrick Pinet
- Parc National de La Réunion, Life+ Pétrels, 258 Rue de la République, 97431, Plaine des Palmistes, Réunion Island, France
| | - François-Xavier Couzi
- Société d'Etudes Ornithologiques de La Réunion (SEOR), 13 ruelle des Orchidées, 97440, Saint André, Réunion Island, France
| | - Laurence Humeau
- UMR PVBMT (Université de La Réunion, CIRAD), 15 Avenue René Cassin, CS 92003, 97744, Saint Denis Cedex 9, Ile de La Réunion, France
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5
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Irazábal-González L, Wright DS, Maan ME. Developmental and environmental plasticity in opsin gene expression in Lake Victoria cichlid fish. Evol Dev 2024; 26:e12465. [PMID: 38041513 DOI: 10.1111/ede.12465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/03/2023]
Abstract
In many organisms, sensory abilities develop and evolve according to the changing demands of navigating, foraging, and communication across different environments and life stages. Teleost fish inhabit heterogeneous light environments and exhibit a large diversity in visual system properties among species. Cichlids are a classic example of this diversity; visual system variation is generated by different tuning mechanisms that involve both genetic factors and phenotypic plasticity. Here, we document the developmental progression of visual pigment gene expression in Lake Victoria cichlids and test if these patterns are influenced by variation in light conditions. We reared two sister species of Pundamilia to adulthood in two distinct visual conditions that resemble the light environments that they naturally inhabit in Lake Victoria. We also included interspecific first-generation hybrids. We focused on the four opsins that are expressed in Pundamilia adults (using real-time quantitative polymerase chain reaction (RT-qPCR)) (SWS2B, SWS2A, RH2A, and LWS) at 17 time points. We find that opsin expression profiles progress from shorter-wavelength sensitive opsins to longer-wavelength sensitive opsins with increasing age, in both species and their hybrids. The developmental trajectories of opsin expression also responded plastically to the visual conditions. Developmental and environmental plasticity in opsin expression may provide an important stepping stone in the evolution of cichlid visual system diversity.
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Affiliation(s)
- Lucia Irazábal-González
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Daniel S Wright
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Martine E Maan
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
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6
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Cerca J. Understanding natural selection and similarity: Convergent, parallel and repeated evolution. Mol Ecol 2023; 32:5451-5462. [PMID: 37724599 DOI: 10.1111/mec.17132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/26/2023] [Accepted: 08/30/2023] [Indexed: 09/21/2023]
Abstract
Parallel and convergent evolution offer some of the most compelling evidence for the significance of natural selection in evolution, as the emergence of similar adaptive solutions is unlikely to occur by random chance alone. However, these terms are often employed inconsistently, leading to misinterpretation and confusion, and recently proposed definitions have unintentionally diminished the emphasis on the evolution of similar adaptive solutions. Here, I examine various conceptual frameworks and definitions related to parallel and convergent evolution and propose a consolidated framework that enhances our comprehension of these evolutionary patterns. The primary aim of this framework is to harmonize the concepts of parallel and convergent evolution together with natural selection and the idea of similarity. Both concepts involve the evolution of similar adaptive solutions as a result of environmental challenges. The distinction lies in ancestral phenotypes. Parallel evolution takes place when the ancestral phenotypes (before selection) of the lineages are similar. Convergent evolution happens when the lineages have distinct ancestral phenotypes (before selection). Because an ancestral-based distinction will inevitably lead to cases where uncertainty in the distinction may arise, the framework includes a general term, repeated evolution, which can be used as a term applying to the evolution of similar phenotypes and genotypes as well as similar responses to environmental pressures. Based on the argument that genetic similarity may frequently arise without selection, the framework posits that the similarity of genetic sequences is not of great interest unless linked to the actions of natural selection or to the origins (mutation, standing genetic variation, gene flow) and locations of the similar sequences.
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Affiliation(s)
- José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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7
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Meier JI, McGee MD, Marques DA, Mwaiko S, Kishe M, Wandera S, Neumann D, Mrosso H, Chapman LJ, Chapman CA, Kaufman L, Taabu-Munyaho A, Wagner CE, Bruggmann R, Excoffier L, Seehausen O. Cycles of fusion and fission enabled rapid parallel adaptive radiations in African cichlids. Science 2023; 381:eade2833. [PMID: 37769075 DOI: 10.1126/science.ade2833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/21/2023] [Indexed: 09/30/2023]
Abstract
Although some lineages of animals and plants have made impressive adaptive radiations when provided with ecological opportunity, the propensities to radiate vary profoundly among lineages for unknown reasons. In Africa's Lake Victoria region, one cichlid lineage radiated in every lake, with the largest radiation taking place in a lake less than 16,000 years old. We show that all of its ecological guilds evolved in situ. Cycles of lineage fusion through admixture and lineage fission through speciation characterize the history of the radiation. It was jump-started when several swamp-dwelling refugial populations, each of which were of older hybrid descent, met in the newly forming lake, where they fused into a single population, resuspending old admixture variation. Each population contributed a different set of ancient alleles from which a new adaptive radiation assembled in record time, involving additional fusion-fission cycles. We argue that repeated fusion-fission cycles in the history of a lineage make adaptive radiation fast and predictable.
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Affiliation(s)
- Joana I Meier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Cambridge, UK
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D McGee
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - David A Marques
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
- Natural History Museum Basel, Basel, Switzerland
| | - Salome Mwaiko
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
| | - Mary Kishe
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Sylvester Wandera
- National Fisheries Resources Research Institute (NAFIRRI), Jinja, Uganda
| | - Dirk Neumann
- Leipniz Institute for Biodiversity Change, Hamburg, Germany
| | - Hilary Mrosso
- Tanzania Fisheries Research Institute (TAFIRI), Dar es Salaam, Tanzania
| | - Lauren J Chapman
- Department of Biology, McGill University, Montreal, Quebec, Canada
| | - Colin A Chapman
- Wilson Center, Washington, DC, USA
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
- School of Life Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi'an, China
- Biology Department, Vancouver Island University, Nanaimo, British Columbia, Canada
| | - Les Kaufman
- Boston University Marine Program, Department of Biology, Boston University, Boston, MA, USA
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ole Seehausen
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland
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8
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van Rijssel JC, Moser FN, Mwaiko S, Seehausen O. Strong species structure but weak geographical structure in demersal Lake Victoria cichlids. Ecol Evol 2022; 12:e9669. [PMID: 36582774 PMCID: PMC9790821 DOI: 10.1002/ece3.9669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/27/2022] Open
Abstract
Studying phenotypic and genetic differentiation between very young species can be very informative with regard to learning about processes of speciation. Identifying and characterizing genetic species structure and distinguishing it from spatial genetic structure within a species is a prerequisite for this and is often not given sufficient attention. Young radiations of cichlid fish are classical speciation study systems. However, it is only during the past decade that population genomics based on next-generation sequencing has begun to provide the power to resolve species and distinguish speciation from spatial population structure for the youngest of these radiations. The Lake Victoria haplochromine cichlids constitute the youngest large cichlid fish radiation, probably <20,000 years old. Earlier work showed that communities of rocky reef cichlids are composed of many reciprocally monophyletic species despite their very recent origins. Here, we build on this work by studying assemblages of offshore demersal cichlids, adding analyses of within-species spatial structure to the sympatric species structure. We sampled seven multispecies communities along a 6-km-long transect from one side of the Mwanza Gulf to the other side. We investigated whether phenotypically diagnosed putative species are reciprocally monophyletic and whether such monophyly is stable across species geographic ranges. We show that all species are genetically strongly differentiated in sympatry, that they are reciprocally monophyletic, and that monophyly is stable across distribution ranges. We found significant differentiation between geographically distinct populations in two species, but no or weak isolation by distance. We further found subtle but significant morphological differences between all species and a linear relationship between genomic and morphological distance which suggests that differences in morphology begin to accumulate after speciation has already affected genome-wide restrictions of gene flow.
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Affiliation(s)
- Jacco C. van Rijssel
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland,Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland,Wageningen Marine ResearchWageningen UniversityIJmuidenThe Netherlands
| | - Florian N. Moser
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland,Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
| | - Salome Mwaiko
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland,Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
| | - Ole Seehausen
- Department of Fish Ecology & EvolutionEAWAG Centre for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland,Institute of Ecology and Evolution, Aquatic EcologyUniversity of BernBernSwitzerland
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9
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Lesturgie P, Lainé H, Suwalski A, Chifflet-Belle P, Maisano Delser P, Clua E, Jaquemet S, Magalon H, Mona S. Ecological and biogeographic features shaped the complex evolutionary history of an iconic apex predator (Galeocerdo cuvier). BMC Ecol Evol 2022; 22:147. [PMID: 36526977 PMCID: PMC9758794 DOI: 10.1186/s12862-022-02100-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The tiger shark (Galeocerdo cuvier) is a large iconic marine predator inhabiting worldwide tropical and subtropical waters. So far, only mitochondrial markers and microsatellites studies have investigated its worldwide historical demography with inconclusive outcomes. Here, we assessed for the first time the genomic variability of tiger shark based on RAD-seq data for 50 individuals from five sampling sites in the Indo-Pacific (IP) and one in the Atlantic Ocean (AO) to decipher the extent of the species' global connectivity and its demographic history. RESULTS Clustering algorithms (PCA and NMF), FST and an approximate Bayesian computation framework revealed the presence of two clusters corresponding to the two oceanic basins. By modelling the two-dimensional site frequency spectrum, we tested alternative isolation/migration scenarios between these two identified populations. We found the highest support for a divergence time between the two ocean basins of ~ 193,000 years before present (B.P) and an ongoing but limited asymmetric migration ~ 176 times larger from the IP to the AO (Nm ~ 3.9) than vice versa (Nm ~ 0.02). CONCLUSIONS The two oceanic regions are isolated by a strong barrier to dispersal more permeable from the IP to the AO through the Agulhas leakage. We finally emphasized contrasting recent demographic histories for the two regions, with the IP characterized by a recent bottleneck around 2000 years B.P. and the AO by an expansion starting 6000 years B.P. The large differentiation between the two oceanic regions and the absence of population structure within each ocean basin highlight the need for two large management units and call for future conservation programs at the oceanic rather than local scale, particularly in the Indo-Pacific where the population is declining.
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Affiliation(s)
- Pierre Lesturgie
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France
| | - Hugo Lainé
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France
| | - Arnaud Suwalski
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France ,grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France
| | - Pascaline Chifflet-Belle
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France ,grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France
| | | | - Eric Clua
- grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France ,Laboratoire d’Excellence CORAIL, Papetoai, French Polynesia
| | - Sébastien Jaquemet
- grid.11642.300000 0001 2111 2608UMR ENTROPIE (Université de La Réunion/IRD/CNRS), Université de La Réunion, Saint Denis, France
| | - Hélène Magalon
- Laboratoire d’Excellence CORAIL, Papetoai, French Polynesia ,grid.11642.300000 0001 2111 2608UMR ENTROPIE (Université de La Réunion/IRD/CNRS), Université de La Réunion, Saint Denis, France
| | - Stefano Mona
- grid.503191.f0000 0001 0143 5055Institut de Systématique, Evolution, Biodiversité (ISYEB), EPHE-PSL, Université PSL, MNHN, CNRS, SU, UA, Paris, France ,grid.424469.90000 0001 2195 5365EPHE, PSL Research University, Paris, France ,Laboratoire d’Excellence CORAIL, Papetoai, French Polynesia
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Muto N, Kai Y. Allopatric origin, secondary contact and subsequent isolation of sympatric rockfishes (Sebastidae: Sebastes) in the north-western Pacific. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Understanding how speciation occurs is central to biology. Gene flow between diverging taxa is correlated with geography and other aspects of speciation; therefore, the examination of gene flow during divergence is a potent approach to understanding the nature of speciation. Here, we inferred the speciation process of the sympatric rockfishes Sebastes steindachneri and Sebastes wakiyai in the north-western Pacific and its marginal seas based on genome-wide single nucleotide polymorphism and mitochondrial DNA data. Model-based demographic inference showed that gene flow between the two species was absent in the initial and late stages of divergence and present only in the middle stage. Population expansion occurred before or during the period of gene flow. The estimated timings of the initial divergence and population expansion fell within the Pleistocene, during which the seas currently inhabited by the two species were repeatedly isolated and reconnected. Contemporary isolation was supported by the absence of hybrids and the shared mitochondrial DNA haplotypes. Our results suggest that the two species initially diverged in allopatry, followed by secondary contact and introgression and by the completion of reproductive isolation. Given that complete isolation following secondary contact has rarely been tested or documented in marine organisms, we highlight the importance of careful consideration of alternative divergence scenarios to be tested, which should take into account the geological and environmental settings.
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Affiliation(s)
- Nozomu Muto
- Department of Marine Biology and Sciences, School of Biological Sciences, Tokai University , 5-1-1-1 Minamisawa, Minami-Ku, Sapporo, Hokkaido 005-8601 , Japan
| | - Yoshiaki Kai
- Maizuru Fisheries Research Station, Field Science Education and Research Center, Kyoto University , Nagahama, Maizuru, Kyoto 625-0086 , Japan
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11
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Noguerales V, Ortego J. Genomic evidence of speciation by fusion in a recent radiation of grasshoppers. Evolution 2022; 76:2618-2633. [PMID: 35695020 PMCID: PMC9796961 DOI: 10.1111/evo.14508] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/22/2022] [Accepted: 04/02/2022] [Indexed: 01/22/2023]
Abstract
Postdivergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (i.e., adaptive introgression) to the formation of new species (i.e., hybrid speciation). Although neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both scrub legumes and gramineous herbs) of the taxonomically controversial grasshopper Chorthippus saulcyi algoaldensis resulted from hybridization between the sister taxa C. binotatus (that exclusively feeds on scrub legumes) and C. saulcyi (that only feeds on gramineous herbs). Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that C. s. algoaldensis represents an independently evolving lineage and support the ancient hybrid origin of this taxon (about 1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate their long-term persistence through geographic isolation from parental forms in topographically complex landscapes.
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Affiliation(s)
- Víctor Noguerales
- Department of Biological SciencesUniversity of CyprusNicosia1678Cyprus,Island Ecology and Evolution GroupInstituto de Productos Naturales y Agrobiología (IPNA‐CSIC)San Cristóbal de La Laguna38206Spain
| | - Joaquín Ortego
- Department of Integrative EcologyEstación Biológica de Doñana (EBD‐CSIC)Sevilla41092Spain
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12
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Wilwert E, Etienne RS, van de Zande L, Maan ME. Contribution of opsins and chromophores to cone pigment variation across populations of Lake Victoria cichlids. JOURNAL OF FISH BIOLOGY 2022; 101:365-377. [PMID: 34860424 PMCID: PMC9543281 DOI: 10.1111/jfb.14969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/24/2021] [Accepted: 11/25/2021] [Indexed: 06/13/2023]
Abstract
Adaptation to heterogeneous sensory environments has been implicated as a key parameter in speciation. Cichlid fish are a textbook example of divergent visual adaptation, mediated by variation in the sequences and expression levels of cone opsin genes (encoding the protein component of visual pigments). In some vertebrates including fish, visual sensitivity is also tuned by the ratio of vitamin A1 /A2 -derived chromophores (i.e., the light-sensitive component of the visual pigment bound to the opsin protein), where higher proportions of A2 cause a more red-shifted wavelength absorbance. This study explores the variation in chromophore ratios across multiple cichlid populations in Lake Victoria, using as a proxy the expression of the gene Cyp27c1, which has been shown to regulate the conversion of vitamin A1 into vitamin A2 in several vertebrates. This study focuses on sympatric Pundamilia cichlids, where species with blue or red male coloration co-occur at multiple islands but occupy different depths and consequently different visual habitats. In the red species, we found higher cyp27c1 expression in populations from turbid waters than from clear waters, but there was no such pattern in the blue species. Across populations, differences between the sympatric species in cyp27c1 expression had a consistent relationship with species differences in opsin expression patterns, but the red/blue identity reversed between clear and turbid waters. To assess the contribution of heritable vs. environmental causes of variation, we tested whether light manipulations induce a change in cyp27c1 expression in the laboratory. We found that cyp27c1 expression was not influenced by experimental light conditions, suggesting that the observed variation in the wild is due to genetic differences. Nonetheless, compared to other cichlid species, cyp27c1 is expressed at very low levels in Pundamilia, suggesting that it may not be relevant for visual adaptation in this species. Conclusively, establishing the biological importance of this variation requires testing of actual A1 /A2 ratios in the eye, as well as its consequences for visual performance.
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Affiliation(s)
- Elodie Wilwert
- Groningen Institute for Evolutionary Life Sciences (GELIFES)GroningenThe Netherlands
| | - Rampal S. Etienne
- Groningen Institute for Evolutionary Life Sciences (GELIFES)GroningenThe Netherlands
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences (GELIFES)GroningenThe Netherlands
| | - Martine E. Maan
- Groningen Institute for Evolutionary Life Sciences (GELIFES)GroningenThe Netherlands
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13
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Lewanski AL, Golcher-Benavides J, Rick JA, Wagner CE. Variable hybridization between two Lake Tanganyikan cichlid species in recent secondary contact. Mol Ecol 2022; 31:5041-5059. [PMID: 35913373 DOI: 10.1111/mec.16636] [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: 12/06/2021] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 12/01/2022]
Abstract
Closely related taxa frequently exist in sympatry before the evolution of robust reproductive barriers, which can lead to substantial gene flow. Post-divergence gene flow can promote several disparate trajectories of divergence ranging from the erosion of distinctiveness and eventual collapse of the taxa to the strengthening of reproductive isolation. Among many relevant factors, understanding the demographic history of divergence (e.g. divergence time, extent of historical gene flow) can be particularly informative when examining contemporary gene flow between closely related taxa because this history can influence gene flow's prevalence and consequences. Here, we used genotyping-by-sequencing data to investigate speciation and contemporary hybridization in two closely related and sympatrically distributed Lake Tanganyikan cichlid species in the genus Petrochromis. Demographic modeling supported a speciation scenario involving divergence in isolation followed by secondary contact with bidirectional gene flow. Further investigation of this recent gene flow found evidence of ongoing hybridization between the species that varied in extent between different co-occurring populations. Relationships between abundance and the degree of admixture across populations suggest that the availability of conspecific mates may influence patterns of hybridization. These results, together with the observation that sets of recently diverged cichlid taxa are generally geographically separated in the lake, suggest that ongoing speciation in Lake Tanganyikan cichlids relies on initial spatial isolation. Additionally, the spatially heterogeneous patterns of admixture between the Petrochromis species illustrates the complexities of hybridization when species are in recent secondary contact.
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Affiliation(s)
| | - Jimena Golcher-Benavides
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Jessica A Rick
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Catherine E Wagner
- Department of Botany, University of Wyoming, Laramie, WY, USA.,Program in Ecology, University of Wyoming, Laramie, WY, USA.,Biodiversity Institute, University of Wyoming, Laramie, WY, USA
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14
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Mitchell N, Luu H, Owens GL, Rieseberg LH, Whitney KD. Hybrid evolution repeats itself across environmental contexts in Texas sunflowers (Helianthus). Evolution 2022; 76:1512-1528. [PMID: 35665925 PMCID: PMC9544064 DOI: 10.1111/evo.14536] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 01/22/2023]
Abstract
To what extent is evolution repeatable? Little is known about whether the evolution of hybrids is more (or less) repeatable than that of nonhybrids. We used field experimental evolution in annual sunflowers (Helianthus) in Texas to ask the extent to which hybrid evolution is repeatable across environments compared to nonhybrid controls. We created hybrids between Helianthus annuus (L.) and H. debilis (Nutt.) and grew plots of both hybrids and nonhybrid controls through eight generations at three sites in Texas. We collected seeds from each generation and grew each generation × treatment × home site combination at two final common gardens. We estimated the strength and direction of evolution in terms of fitness and 24 traits, tested for repeated versus nonrepeated evolution, and assessed overall phenotypic evolution across lineages and in relation to a locally adapted phenotype. Hybrids consistently evolved higher fitness over time, while controls did not, although trait evolution varied in strength across home sites. Repeated evolution was more evident in hybrids versus nonhybrid controls, and hybrid evolution was often in the direction of the locally adapted phenotype. Our findings have implications for both the nature of repeatability in evolution and the contribution of hybridization to evolution across environmental contexts.
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Affiliation(s)
- Nora Mitchell
- Department of BiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA,Department of BiologyUniversity of Wisconsin – Eau ClaireEau ClaireWisconsinUSA
| | - Hoang Luu
- Department of Environmental and Plant BiologyOhio UniversityAthensOhioUSA
| | - Gregory L. Owens
- Department of BiologyUniversity of VictoriaVictoriaBritish ColumbiaCanada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaBritish ColumbiaCanada
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15
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RADseq Data Suggest Occasional Hybridization between Microcebus murinus and M. ravelobensis in Northwestern Madagascar. Genes (Basel) 2022; 13:genes13050913. [PMID: 35627298 PMCID: PMC9140448 DOI: 10.3390/genes13050913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/29/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022] Open
Abstract
The occurrence of natural hybridization has been reported in a wide range of organisms, including primates. The present study focuses on the endemic lemurs of Madagascar, primates for which only a few species occur in sympatry or parapatry with congeners, thereby creating limited opportunity for natural hybridization. This study examines RADseq data from 480 individuals to investigate whether the recent expansion of Microcebus murinus towards the northwest and subsequent secondary contact with Microcebus ravelobensis has resulted in the occurrence of hybridization between the two species. Admixture analysis identified one individual with 26% of nuclear admixture, which may correspond to an F2- or F3-hybrid. A composite-likelihood approach was subsequently used to test the fit of alternative phylogeographic scenarios to the genomic data and to date introgression. The simulations yielded support for low levels of gene flow (2Nm0 = 0.063) between the two species starting before the Last Glacial Maximum (between 54 and 142 kyr). Since M. murinus most likely colonized northwestern Madagascar during the Late Pleistocene, the rather recent secondary contact with M. ravelobensis has likely created the opportunity for occasional hybridization. Although reproductive isolation between these distantly related congeners is not complete, it is effective in maintaining species boundaries.
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16
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Feller AF, Seehausen O. Genetic architecture of adaptive radiation across two trophic levels. Proc Biol Sci 2022; 289:20220377. [PMID: 35506225 PMCID: PMC9065965 DOI: 10.1098/rspb.2022.0377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Evolution of trophic diversity is a hallmark of adaptive radiation. Yet, transitions between carnivory and herbivory are rare in young adaptive radiations. Haplochromine cichlid fish of the African Great Lakes are exceptional in this regard. Lake Victoria was colonized by an insectivorous generalist and in less than 20 000 years, several clades of specialized herbivores evolved. Carnivorous versus herbivorous lifestyles in cichlids require many different adaptations in functional morphology, physiology and behaviour. Ecological transitions in either direction thus require many traits to change in a concerted fashion, which could be facilitated if genomic regions underlying these traits were physically linked or pleiotropic. However, linkage/pleiotropy could also constrain evolvability. To investigate components of the genetic architecture of a suite of traits that distinguish invertivores from algae scrapers, we performed quantitative trait locus (QTL) mapping using a second-generation hybrid cross. While we found indications of linkage/pleiotropy within trait complexes, QTLs for distinct traits were distributed across several unlinked genomic regions. Thus, a mixture of independently segregating variation and some pleiotropy may underpin the rapid trophic transitions. We argue that the emergence and maintenance of associations between the different genomic regions underpinning co-adapted traits that evolved and persist against some gene flow required reproductive isolation.
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Affiliation(s)
- Anna F. Feller
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Ole Seehausen
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
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17
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Teixeira H, Salmona J, Arredondo A, Mourato B, Manzi S, Rakotondravony R, Mazet O, Chikhi L, Metzger J, Radespiel U. Impact of model assumptions on demographic inferences: the case study of two sympatric mouse lemurs in northwestern Madagascar. BMC Ecol Evol 2021; 21:197. [PMID: 34727890 PMCID: PMC8561976 DOI: 10.1186/s12862-021-01929-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/18/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Quaternary climate fluctuations have been acknowledged as major drivers of the geographical distribution of the extraordinary biodiversity observed in tropical biomes, including Madagascar. The main existing framework for Pleistocene Malagasy diversification assumes that forest cover was strongly shaped by warmer Interglacials (leading to forest expansion) and by cooler and arid glacials (leading to forest contraction), but predictions derived from this scenario for forest-dwelling animals have rarely been tested with genomic datasets. RESULTS We generated genomic data and applied three complementary demographic approaches (Stairway Plot, PSMC and IICR-simulations) to infer population size and connectivity changes for two forest-dependent primate species (Microcebus murinus and M. ravelobensis) in northwestern Madagascar. The analyses suggested major demographic changes in both species that could be interpreted in two ways, depending on underlying model assumptions (i.e., panmixia or population structure). Under panmixia, the two species exhibited larger population sizes across the Last Glacial Maximum (LGM) and towards the African Humid Period (AHP). This peak was followed by a population decline in M. ravelobensis until the present, while M. murinus may have experienced a second population expansion that was followed by a sharp decline starting 3000 years ago. In contrast, simulations under population structure suggested decreasing population connectivity between the Last Interglacial and the LGM for both species, but increased connectivity during the AHP exclusively for M. murinus. CONCLUSION Our study shows that closely related species may differ in their responses to climatic events. Assuming that Pleistocene climatic conditions in the lowlands were similar to those in the Malagasy highlands, some demographic dynamics would be better explained by changes in population connectivity than in population size. However, changes in connectivity alone cannot be easily reconciled with a founder effect that was shown for M. murinus during its colonization of the northwestern Madagascar in the late Pleistocene. To decide between the two alternative models, more knowledge about historic forest dynamics in lowland habitats is necessary. Altogether, our study stresses that demographic inferences strongly depend on the underlying model assumptions. Final conclusions should therefore be based on a comparative evaluation of multiple approaches.
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Affiliation(s)
- Helena Teixeira
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
| | - Jordi Salmona
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
| | - Armando Arredondo
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Beatriz Mourato
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Sophie Manzi
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
| | - Romule Rakotondravony
- Ecole Doctorale Ecosystèmes Naturels (EDEN), University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, 401, Mahajanga, Madagascar
- Faculté des Sciences, de Technologies et de l'Environnement, University of Mahajanga, 5 Rue Georges V - Immeuble KAKAL, Mahajanga Be, B.P. 652, 401, Mahajanga, Madagascar
| | - Olivier Mazet
- Université de Toulouse, Institut National des Sciences Appliquées, Institut de Mathématiques de Toulouse, Toulouse, France
| | - Lounès Chikhi
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 Route de Narbonne, Bât. 4R1, 31062, Toulouse cedex 9, France
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Julia Metzger
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17p, 30559, Hannover, Germany
- Veterinary Functional Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195, Berlin, Germany
| | - Ute Radespiel
- Institute of Zoology, University of Veterinary Medicine Hannover, Foundation, Bünteweg 17, 30559, Hannover, Germany.
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18
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Hirase S, Yamasaki YY, Sekino M, Nishisako M, Ikeda M, Hara M, Merilä J, Kikuchi K. Genomic Evidence for Speciation with Gene Flow in Broadcast Spawning Marine Invertebrates. Mol Biol Evol 2021; 38:4683-4699. [PMID: 34311468 PMCID: PMC8557453 DOI: 10.1093/molbev/msab194] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
How early stages of speciation in free-spawning marine invertebrates proceed is poorly understood. The Western Pacific abalones, Haliotis discus, H. madaka, and H. gigantea, occur in sympatry with shared breeding season and are capable of producing viable F1 hybrids in spite of being ecologically differentiated. Population genomic analyses revealed that although the three species are genetically distinct, there is evidence for historical and ongoing gene flow among these species. Evidence from demographic modeling suggests that reproductive isolation among the three species started to build in allopatry and has proceeded with gene flow, possibly driven by ecological selection. We identified 27 differentiation islands between the closely related H. discus and H. madaka characterized by high FST and dA, but not high dXY values, as well as high genetic diversity in one H. madaka population. These genomic signatures suggest differentiation driven by recent ecological divergent selection in presence of gene flow outside of the genomic islands of differentiation. The differentiation islands showed low polymorphism in H. gigantea, and both high FST, dXY, and dA values between H. discus and H. gigantea, as well as between H. madaka and H. gigantea. Collectively, the Western Pacific abalones appear to occupy the early stages speciation continuum, and the differentiation islands associated with ecological divergence among the abalones do not appear to have acted as barrier loci to gene flow in the younger divergences but appear to do so in older divergences.
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Affiliation(s)
- Shotaro Hirase
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Maisaka, Hamamatsu, Shizuoka, Japan
| | - Yo Y Yamasaki
- Ecological Genetics Laboratory, Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masashi Sekino
- Bioinformatics and Biosciences Division, Fisheries Resources Institute, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Masato Nishisako
- Laboratory of Integrative Aquatic Biology, Graduate School of Agricultural Sciences, Tohoku University, Onagawa, Miyagi, Japan
| | - Minoru Ikeda
- Laboratory of Integrative Aquatic Biology, Graduate School of Agricultural Sciences, Tohoku University, Onagawa, Miyagi, Japan
| | - Motoyuki Hara
- Tohoku Ecosystem-Associated Marine Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Juha Merilä
- Ecological Genetics Research Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Research Division of Ecology and Biodiversity, Faculty of Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Kiyoshi Kikuchi
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Maisaka, Hamamatsu, Shizuoka, Japan
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19
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James ME, Arenas-Castro H, Groh JS, Allen SL, Engelstädter J, Ortiz-Barrientos D. Highly Replicated Evolution of Parapatric Ecotypes. Mol Biol Evol 2021; 38:4805-4821. [PMID: 34254128 PMCID: PMC8557401 DOI: 10.1093/molbev/msab207] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Parallel evolution of ecotypes occurs when selection independently drives the evolution of similar traits across similar environments. The multiple origins of ecotypes are often inferred based on a phylogeny that clusters populations according to geographic location and not by the environment they occupy. However, the use of phylogenies to infer parallel evolution in closely related populations is problematic because gene flow and incomplete lineage sorting can uncouple the genetic structure at neutral markers from the colonization history of populations. Here, we demonstrate multiple origins within ecotypes of an Australian wildflower, Senecio lautus. We observed strong genetic structure as well as phylogenetic clustering by geography and show that this is unlikely due to gene flow between parapatric ecotypes, which was surprisingly low. We further confirm this analytically by demonstrating that phylogenetic distortion due to gene flow often requires higher levels of migration than those observed in S. lautus. Our results imply that selection can repeatedly create similar phenotypes despite the perceived homogenizing effects of gene flow.
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Affiliation(s)
- Maddie E James
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Henry Arenas-Castro
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Jeffrey S Groh
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Scott L Allen
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
| | - Jan Engelstädter
- School of Biological Sciences, The University of Queensland,St. Lucia, QLD, Australia
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20
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Bemmels JB, Bramwell AC, Anderson SAS, Luzuriaga-Aveiga VE, Mikkelsen EK, Weir JT. Geographic contact drives increased reproductive isolation in two cryptic Empidonax flycatchers. Mol Ecol 2021; 30:4833-4844. [PMID: 34347907 DOI: 10.1111/mec.16105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/05/2021] [Accepted: 07/28/2021] [Indexed: 01/02/2023]
Abstract
Geographic contact between sister lineages often occurs near the final stages of speciation, but its role in speciation's completion remains debated. Reproductive isolation may be essentially complete prior to secondary contact. Alternatively, costly interactions between partially reproductively isolated species - such as maladaptive hybridization or competition for resources - may select for divergence, increasing reproductive isolation and driving speciation toward completion. Here, we use coalescent demographic modelling and whole-genome data sets to show that a period of contact and elevated hybridization between sympatric eastern North American populations of two cryptic bird species preceded a major increase in reproductive isolation between these populations within the last 10,000 years. In contrast, substantial introgression continues to the present in a western contact zone where geographic overlap is much narrower and probably of more recent origin. In the sympatric eastern region where reproductive isolation has increased, it is not accompanied by character displacement in key morphometric traits, plumage coloration, or ecological traits. While the precise trait and underlying mechanism driving increased reproductive isolation remains unknown, we discuss several possibilities and outline avenues for future research. Overall, our results highlight how demographic models can reveal the geographic context in which reproductive isolation was completed, and demonstrate how contact can accelerate the final stages of speciation.
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Affiliation(s)
- Jordan B Bemmels
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Ashley C Bramwell
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sean A S Anderson
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Vanessa E Luzuriaga-Aveiga
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Else K Mikkelsen
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Jason T Weir
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
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21
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Manthey JD, Klicka J, Spellman GM. The Genomic Signature of Allopatric Speciation in a Songbird Is Shaped by Genome Architecture (Aves: Certhia americana). Genome Biol Evol 2021; 13:evab120. [PMID: 34042960 PMCID: PMC8364988 DOI: 10.1093/gbe/evab120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 12/31/2022] Open
Abstract
The genomic signature of speciation with gene flow is often attributed to the strength of divergent selection and recombination rate in regions harboring targets for selection. In contrast, allopatric speciation provides a different geographic context and evolutionary scenario, whereby introgression is limited by isolation rather than selection against gene flow. Lacking shared divergent selection or selection against hybridization, we would predict the genomic signature of allopatric speciation would largely be shaped by genomic architecture-the nonrandom distribution of functional elements and chromosomal characteristics-through its role in affecting the processes of selection and drift. Here, we built and annotated a chromosome-scale genome assembly for a songbird (Passeriformes: Certhia americana). We show that the genomic signature of allopatric speciation between its two primary lineages is largely shaped by genomic architecture. Regionally, gene density and recombination rate variation explain a large proportion of variance in genomic diversity, differentiation, and divergence. We identified a heterogeneous landscape of selection and neutrality, with a large portion of the genome under the effects of indirect selection. We found higher proportions of small chromosomes under the effects of indirect selection, likely because they have relatively higher gene density. At the chromosome scale, differential genomic architecture of macro- and microchromosomes shapes the genomic signatures of speciation: chromosome size has: 1) a positive relationship with genetic differentiation, genetic divergence, rate of lineage sorting in the contact zone, and proportion neutral evolution and 2) a negative relationship with genetic diversity and recombination rate.
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Affiliation(s)
- Joseph D Manthey
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - John Klicka
- Burke Museum of Natural History, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Garth M Spellman
- Department of Zoology, Denver Museum of Nature & Science, Denver, Colorado, USA
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22
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Manipulation of the Tyrosinase gene permits improved CRISPR/Cas editing and neural imaging in cichlid fish. Sci Rep 2021; 11:15138. [PMID: 34302019 PMCID: PMC8302579 DOI: 10.1038/s41598-021-94577-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/13/2021] [Indexed: 12/12/2022] Open
Abstract
Direct tests of gene function have historically been performed in a limited number of model organisms. The CRISPR/Cas system is species-agnostic, offering the ability to manipulate genes in a range of models, enabling insights into evolution, development, and physiology. Astatotilapia burtoni, a cichlid fish from the rivers and shoreline around Lake Tanganyika, has been extensively studied in the laboratory to understand evolution and the neural control of behavior. Here we develop protocols for the creation of CRISPR-edited cichlids and create a broadly useful mutant line. By manipulating the Tyrosinase gene, which is necessary for eumelanin pigment production, we describe a fast and reliable approach to quantify and optimize gene editing efficiency. Tyrosinase mutants also remove a major obstruction to imaging, enabling visualization of subdermal structures and fluorophores in situ. These protocols will facilitate broad application of CRISPR/Cas9 to studies of cichlids as well as other non-traditional model aquatic species.
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23
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Excofffier L, Marchi N, Marques DA, Matthey-Doret R, Gouy A, Sousa VC. fastsimcoal2: demographic inference under complex evolutionary scenarios. Bioinformatics 2021; 37:4882-4885. [PMID: 34164653 PMCID: PMC8665742 DOI: 10.1093/bioinformatics/btab468] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/11/2021] [Accepted: 06/22/2021] [Indexed: 01/25/2023] Open
Abstract
Motivation fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework. Results Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured populations and of large chromosomes. Availability and implementation fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.
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Affiliation(s)
- Laurent Excofffier
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Nina Marchi
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - David Alexander Marques
- Life Science Division, Natural History Museum Basel, 4051 Basel, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG swiss Federal institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, 6047 Kastanienbaum, Switzerland
| | - Remi Matthey-Doret
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Alexandre Gouy
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Gouy Data Consulting, 1026 Denges, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics Lab, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
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24
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Phylogeographic and demographic modeling analyses of the multiple origins of the rheophytic goldenrod Solidago yokusaiana Makino. Heredity (Edinb) 2021; 126:831-845. [PMID: 33510467 PMCID: PMC8102582 DOI: 10.1038/s41437-021-00408-x] [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: 07/17/2020] [Revised: 01/11/2021] [Accepted: 01/11/2021] [Indexed: 01/30/2023] Open
Abstract
Understanding adaptation mechanisms is important in evolutionary biology. Parallel adaptation provides good opportunities to investigate adaptive evolution. To confirm parallel adaptation, it is effective to examine whether the phenotypic similarity has one or multiple origins and to use demographic modeling to consider the gene flow between ecotypes. Solidago yokusaiana is a rheophyte endemic to the Japanese Archipelago that diverged from Solidago virgaurea. This study examined the parallel origins of S. yokusaiana by distinguishing between multiple and single origins and subsequent gene flow. The haplotypes of noncoding chloroplast DNA and genotypes at 14 nuclear simple sequence repeat (nSSR) loci and single-nucleotide polymorphisms (SNPs) revealed by double-digest restriction-associated DNA sequencing (ddRADseq) were used for phylogeographic analysis; the SNPs were also used to model population demographics. Some chloroplast haplotypes were common to S. yokusaiana and its ancestor S. virgaurea. Also, the population genetic structures revealed by nSSR and SNPs did not correspond to the taxonomic species. The demographic modeling supported the multiple origins of S. yokusaiana in at least four districts and rejected a single origin with ongoing gene flow between the two species, implying that S. yokusaiana independently and repeatedly adapted to frequently flooding riversides.
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25
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Urban S, Nater A, Meyer A, Kratochwil CF. Different Sources of Allelic Variation Drove Repeated Color Pattern Divergence in Cichlid Fishes. Mol Biol Evol 2021; 38:465-477. [PMID: 32941629 PMCID: PMC7826197 DOI: 10.1093/molbev/msaa237] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The adaptive radiations of East African cichlid fish in the Great Lakes Victoria, Malawi, and Tanganyika are well known for their diversity and repeatedly evolved phenotypes. Convergent evolution of melanic horizontal stripes has been linked to a single locus harboring the gene agouti-related peptide 2 (agrp2). However, where and when the causal variants underlying this trait evolved and how they drove phenotypic divergence remained unknown. To test the alternative hypotheses of standing genetic variation versus de novo mutations (independently originating in each radiation), we searched for shared signals of genomic divergence at the agrp2 locus. Although we discovered similar signatures of differentiation at the locus level, the haplotypes associated with stripe patterns are surprisingly different. In Lake Malawi, the highest associated alleles are located within and close to the 5' untranslated region of agrp2 and likely evolved through recent de novo mutations. In the younger Lake Victoria radiation, stripes are associated with two intronic regions overlapping with a previously reported cis-regulatory interval. The origin of these segregating haplotypes predates the Lake Victoria radiation because they are also found in more basal riverine and Lake Kivu species. This suggests that both segregating haplotypes were present as standing genetic variation at the onset of the Lake Victoria adaptive radiation with its more than 500 species and drove phenotypic divergence within the species flock. Therefore, both new (Lake Malawi) and ancient (Lake Victoria) allelic variation at the same locus fueled rapid and convergent phenotypic evolution.
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Affiliation(s)
- Sabine Urban
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Alexander Nater
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Konstanz, Germany
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26
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Feller AF, Ogi V, Seehausen O, Meier JI. Identification of a novel sex determining chromosome in cichlid fishes that acts as XY or ZW in different lineages. HYDROBIOLOGIA 2021; 848:3727-3745. [PMID: 34720170 PMCID: PMC8550731 DOI: 10.1007/s10750-021-04560-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 02/02/2021] [Accepted: 02/23/2021] [Indexed: 05/02/2023]
Abstract
UNLABELLED Sex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid fishes from Lakes Victoria and Malawi. We find evidence for different sex determiners in each cross. In the Malawi cross and one Victoria cross the same chromosome is sex-linked but while females are the heterogametic sex in the Malawi species, males are the heterogametic sex in the Victoria species. This chromosome has not previously been reported to be sex determining in cichlids, increasing the number of different chromosomes shown to be sex determining in cichlids to 12. All Lake Victoria species of our crosses are less than 15,000 years divergent, and we identified different sex determiners among them. Our study provides further evidence for the diversity and evolutionary flexibility of sex determination in cichlids, factors which might contribute to their rapid adaptive radiations. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10750-021-04560-7.
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Affiliation(s)
- Anna F. Feller
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Vera Ogi
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Ole Seehausen
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
| | - Joana I. Meier
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ UK
- St John’s College, University of Cambridge, St John’s Street, Cambridge, CB2 1TP UK
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27
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Nolen ZJ, Yildirim B, Irisarri I, Liu S, Groot Crego C, Amby DB, Mayer F, Gilbert MTP, Pereira RJ. Historical isolation facilitates species radiation by sexual selection: Insights from
Chorthippus
grasshoppers. Mol Ecol 2020; 29:4985-5002. [DOI: 10.1111/mec.15695] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/29/2020] [Accepted: 10/05/2020] [Indexed: 01/01/2023]
Affiliation(s)
- Zachary J. Nolen
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München München Germany
- Department of Biology Lund University Lund Sweden
| | - Burcin Yildirim
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München München Germany
| | - Iker Irisarri
- Department of Biodiversity and Evolutionary Biology Museo Nacional de Ciencias Naturales (MNCN‐CSIC) Madrid Spain
- Department of Organismal Biology (Systematic Biology) Uppsala University Uppsala Sweden
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics University of Goettingen, Campus Institute Data Science Goettingen Germany
| | - Shanlin Liu
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- College of Plant Protection China Agricultural University Beijing China
| | - Clara Groot Crego
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München München Germany
| | | | - Frieder Mayer
- Museum für Naturkunde – Leibniz Institute for Evolution and Biodiversity Science Berlin Germany
| | | | - Ricardo J. Pereira
- Division of Evolutionary Biology Faculty of Biology II Ludwig‐ Maximilians‐Universität München München Germany
- Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
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28
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Svardal H, Salzburger W, Malinsky M. Genetic Variation and Hybridization in Evolutionary Radiations of Cichlid Fishes. Annu Rev Anim Biosci 2020; 9:55-79. [PMID: 33197206 DOI: 10.1146/annurev-animal-061220-023129] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Evolutionary radiations are responsible for much of the variation in biodiversity across taxa. Cichlid fishes are well known for spectacular evolutionary radiations, as they have repeatedly evolved into large and phenotypically diverse arrays of species. Cichlid genomes carry signatures of past events and, at the same time, are the substrate for ongoing evolution. We survey genome-wide data and the available literature covering 438 cichlid populations (412 species) across multiple radiations to synthesize information about patterns and sharing of genetic variation. Nucleotide diversity within species is low in cichlids, with 92% of surveyed populations having less diversity than the median value found in other vertebrates. Divergence within radiations is also low, and a large proportion of variation is shared among species due to incomplete lineage sorting and widespread hybridization. Population genetics therefore provides a suitable conceptual framework for evolutionary genomic studies of cichlid radiations. We focus in detail on the roles of hybridization in shaping the patterns of genetic variation and in promoting cichlid diversification.
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Affiliation(s)
- Hannes Svardal
- Department of Biology, University of Antwerp, 2020 Antwerp, Belgium; .,Naturalis Biodiversity Center, 2333 Leiden, The Netherlands
| | - Walter Salzburger
- Zoological Institute, University of Basel, 4051 Basel, Switzerland; ,
| | - Milan Malinsky
- Zoological Institute, University of Basel, 4051 Basel, Switzerland; ,
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29
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Carleton KL, Conte MA, Malinsky M, Nandamuri SP, Sandkam BA, Meier JI, Mwaiko S, Seehausen O, Kocher TD. Movement of transposable elements contributes to cichlid diversity. Mol Ecol 2020; 29:4956-4969. [PMID: 33049090 DOI: 10.1111/mec.15685] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/11/2022]
Abstract
African cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates. These shifts arise primarily from differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi cichlids, we previously identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or an opsin gene. In this comprehensive study, we show that these indels are the result of the movement of transposable elements (TEs) that correlate with opsin expression variation across the Malawi flock. In tracking the evolutionary history of these particular indels, we found they are endemic to Lake Malawi, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. However, an independent indel has arisen at a similar genomic location in one locus outside of the Malawi flock. The convergence in TE movement suggests these loci are primed for TE insertion and subsequent deletions. Increased TE mobility may be associated with interspecific hybridization, which disrupts mechanisms of TE suppression. This might provide a link between cichlid hybridization and accelerated regulatory variation. Overall, our study suggests that TEs may be an important driver of key regulatory changes, facilitating rapid phenotypic change and possibly speciation in African cichlids.
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Affiliation(s)
- Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Milan Malinsky
- Wellcome Sanger Institute, Cambridge, UK.,Zoological Institute, University of Basel, Basel, Switzerland
| | | | | | - Joana I Meier
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics Laboratory, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Salome Mwaiko
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution & Biogeochemistry, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
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30
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Manceau M, Marin J, Morlon H, Lambert A. Model-Based Inference of Punctuated Molecular Evolution. Mol Biol Evol 2020; 37:3308-3323. [PMID: 32521005 DOI: 10.1093/molbev/msaa144] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In standard models of molecular evolution, DNA sequences evolve through asynchronous substitutions according to Poisson processes with a constant rate (called the molecular clock) or a rate that can vary (relaxed clock). However, DNA sequences can also undergo episodes of fast divergence that will appear as synchronous substitutions affecting several sites simultaneously at the macroevolutionary timescale. Here, we develop a model, which we call the Relaxed Clock with Spikes model, combining basal, clock-like molecular substitutions with episodes of fast divergence called spikes arising at speciation events. Given a multiple sequence alignment and its time-calibrated species phylogeny, our model is able to detect speciation events (including hidden ones) cooccurring with spike events and to estimate the probability and amplitude of these spikes on the phylogeny. We identify the conditions under which spikes can be distinguished from the natural variance of the clock-like component of molecular substitutions and from variations of the clock. We apply the method to genes underlying snake venom proteins and identify several spikes at gene-specific locations in the phylogeny. This work should pave the way for analyses relying on whole genomes to inform on modes of species diversification.
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Affiliation(s)
- Marc Manceau
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, PSL Research University, Paris, France.,IBENS, Ecole Normale Supérieure, UMR 8197 CNRS, Paris, France.,DBSSE, ETH Zürich, Basel, Switzerland
| | - Julie Marin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, PSL Research University, Paris, France
| | - Hélène Morlon
- IBENS, Ecole Normale Supérieure, UMR 8197 CNRS, Paris, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U 1050, PSL Research University, Paris, France.,Laboratoire de Probabilités, Statistique et Modélisation (LPSM), Sorbonne Université, CNRS UMR 8001, Paris, France
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31
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Gainsford A, Jones GP, Hobbs JA, Heindler FM, van Herwerden L. Species integrity, introgression, and genetic variation across a coral reef fish hybrid zone. Ecol Evol 2020; 10:11998-12014. [PMID: 33209265 PMCID: PMC7663085 DOI: 10.1002/ece3.6769] [Citation(s) in RCA: 4] [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: 03/05/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 11/10/2022] Open
Abstract
Hybridization and introgression are evolutionarily significant phenomena breaking down species boundaries. "Hybrid zones" (regions of species overlap and hybridization) enable quantification of hybridization frequency and examination of mechanisms driving and maintaining gene flow. The hybrid anemonefish Amphiprion leucokranos is found where parent species (A. chrysopterus; A. sandaracinos) distributions overlap. Here, we examine geographic variation in hybridization and introgression, and potential impacts on parent species integrity through assessing relative abundance, social group composition, and genetic structure (mtDNA cytochrome b, 21 microsatellite loci) of taxa at three hybrid zone locations: Kimbe Bay (KB) and Kavieng (KA), Papua New Guinea; the Solomon Islands (SO). Relative abundances of and size disparities between parent species apparently drive hybridization frequency, introgression patterns, and genetic composition of taxa. Conspecific groups are most common in KB (65%) where parent species are similarly abundant. Conversely, mixed species groups dominate SO (82%), where A. chrysopterus is more abundant. Hybrids most commonly cohabit with A. sandaracinos in KB (17%), but with A. chrysopterus in KA (22%) and SO (50%). Genetic differentiation (nDNA) analyses indicate that parent species remain distinct, despite ongoing hybridization and hybrids are genetically similar to A. sandaracinos-resulting from persistent backcrossing with this smallest species. This study shows that hybridization outcomes may depend on the social and ecological context in which taxa hybridize, where relative abundance and disparate size of parent species explain the frequency and patterns of hybridization and introgression in the A. leucokranos hybrid zone, reflecting size-based dominance behaviors of anemonefish social groups.
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Affiliation(s)
- Ashton Gainsford
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQLDAustralia
- Faculty of Science and EngineeringJames Cook UniversityTownsvilleAustraliaAustralia
| | - Geoffrey P. Jones
- ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQLDAustralia
- Faculty of Science and EngineeringJames Cook UniversityTownsvilleAustraliaAustralia
| | - Jean‐Paul A. Hobbs
- School of Biological SciencesThe University of QueenslandBrisbaneQLDAustralia
| | | | - Lynne van Herwerden
- Faculty of Science and EngineeringJames Cook UniversityTownsvilleAustraliaAustralia
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32
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Gobbin TP, Tiemersma R, Leone G, Seehausen O, Maan ME. Patterns of ectoparasite infection in wild-caught and laboratory-bred cichlid fish, and their hybrids, implicate extrinsic rather than intrinsic causes of species differences in infection. HYDROBIOLOGIA 2020; 848:3817-3831. [PMID: 34720171 PMCID: PMC8550742 DOI: 10.1007/s10750-020-04423-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/07/2020] [Accepted: 09/22/2020] [Indexed: 06/13/2023]
Abstract
Parasite-mediated selection may initiate or enhance differentiation between host populations that are exposed to different parasite infections. Variation in infection among populations may result from differences in host ecology (thereby exposure to certain parasites) and/or intrinsic immunological traits. Species of cichlid fish, even when recently diverged, often differ in parasite infection, but the contributions of intrinsic and extrinsic causes are unknown. Here, we compare infection patterns between two closely related host species from Lake Victoria (genus Pundamilia), using wild-caught and first-generation laboratory-reared fish, as well as laboratory-reared hybrids. Three of the commonest ectoparasite species observed in the wild were also present in the laboratory populations. However, the infection differences between the host species as observed in the wild were not maintained in laboratory conditions. In addition, hybrids did not differ in infection from either parental species. These findings suggest that the observed species differences in infection in the wild might be mainly driven by ecology-related effects (i.e. differential exposure), rather than by intrinsic species differences in immunological traits. Thus, while there is scope for parasite-mediated selection in Pundamilia in the wild, it has apparently not yet generated divergent evolutionary responses and may not enhance assortative mating among closely related species.
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Affiliation(s)
- Tiziana P. Gobbin
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, Universitat Bern, Bern, Switzerland
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Ron Tiemersma
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Giulia Leone
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Ole Seehausen
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, Universitat Bern, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Martine E. Maan
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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33
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Aguirre-Liguori JA, Luna-Sánchez JA, Gasca-Pineda J, Eguiarte LE. Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize. Front Genet 2020; 11:870. [PMID: 33193568 PMCID: PMC7531271 DOI: 10.3389/fgene.2020.00870] [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: 05/13/2020] [Accepted: 07/16/2020] [Indexed: 12/21/2022] Open
Abstract
Massive parallel sequencing (MPS) is revolutionizing the field of molecular ecology by allowing us to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the economic and computational resources needed generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two simulated genomic datasets fitting a hierarchical structure, two extensive empirical genomic datasets, and a dataset comprising microsatellite information. For all datasets, we generated different subsampling designs by changing the number of loci, individuals, populations, and individuals per population to test for deviations in classic population genetics parameters (HS, FIS, FST). For the empirical datasets we also analyzed the effect of sampling design on landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling a different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. FIS was particularly sensitive to a low sampling of individuals in the simulated, genomic, and microsatellite datasets. For the empirical and simulated genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For the empirical datasets, we found that increasing the number of populations sampled was important in obtaining precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.
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Affiliation(s)
- Jonás A Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, United States
| | - Javier A Luna-Sánchez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jaime Gasca-Pineda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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34
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The ecological and genomic basis of explosive adaptive radiation. Nature 2020; 586:75-79. [DOI: 10.1038/s41586-020-2652-7] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/22/2020] [Indexed: 12/22/2022]
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35
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Yamasaki YY, Kakioka R, Takahashi H, Toyoda A, Nagano AJ, Machida Y, Møller PR, Kitano J. Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190548. [PMID: 32654635 DOI: 10.1098/rstb.2019.0548] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Speciation is a continuous process. Although it is known that differential adaptation can initiate divergence even in the face of gene flow, we know relatively little about the mechanisms driving complete reproductive isolation and the genomic patterns of divergence and introgression at the later stages of speciation. Sticklebacks contain many pairs of sympatric species differing in levels of reproductive isolation and divergence history. Nevertheless, most previous studies have focused on young species pairs. Here, we investigated two sympatric stickleback species, Pungitius pungitius and P. sinensis, whose habitats overlap in eastern Hokkaido; these species show hybrid male sterility, suggesting that they may be at a late stage of speciation. Our demographic analysis using whole-genome sequence data showed that these species split 1.73 Ma and came into secondary contact 37 200 years ago after a period of allopatry. This long period of allopatry might have promoted the evolution of intrinsic incompatibility. Although we detected on-going gene flow and signatures of introgression, overall genomic divergence was high, with considerable heterogeneity across the genome. The heterogeneity was significantly associated with variation in recombination rate. This sympatric pair provides new avenues to investigate the late stages of the stickleback speciation continuum. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Yo Y Yamasaki
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Ryo Kakioka
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Hiroshi Takahashi
- National Fisheries University, 2-7-1 Nagata-honmachi, Shimonoseki, Yamaguchi 759-6595, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Yoshiyasu Machida
- Bihoro Museum, Midori 253-4, Bihoro, Abashiri, Hokkaido 092-0002, Japan
| | - Peter R Møller
- Natural History Museum of Denmark, University of Copenhagen, Universitatetsparken 15, Copenhagen 2100, Denmark
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
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36
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Feller AF, Haesler MP, Peichel CL, Seehausen O. Genetic architecture of a key reproductive isolation trait differs between sympatric and non-sympatric sister species of Lake Victoria cichlids. Proc Biol Sci 2020; 287:20200270. [PMID: 32259470 PMCID: PMC7209058 DOI: 10.1098/rspb.2020.0270] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
One hallmark of the East African cichlid radiations is the rapid evolution of reproductive isolation that is robust to full sympatry of many closely related species. Theory predicts that species persistence and speciation in sympatry with gene flow are facilitated if loci of large effect or physical linkage (or pleiotropy) underlie traits involved in reproductive isolation. Here, we investigate the genetic architecture of a key trait involved in behavioural isolation, male nuptial coloration, by crossing two sister species pairs of Lake Victoria cichlids of the genus Pundamilia and mapping nuptial coloration in the F2 hybrids. One is a young sympatric species pair, representative of an axis of colour motif differentiation, red-dorsum versus blue, that is highly recurrent in closely related sympatric species. The other is a species pair representative of colour motifs, red-chest versus blue, that are common in allopatric but uncommon in sympatric closely related species. We find significant quantitative trait loci (QTLs) with moderate to large effects (some overlapping) for red and yellow in the sympatric red-dorsum × blue cross, whereas we find no significant QTLs in the non-sympatric red-chest × blue cross. These findings are consistent with theory predicting that large effect loci or linkage/pleiotropy underlying mating trait differentiation could facilitate speciation and species persistence with gene flow in sympatry.
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Affiliation(s)
- Anna F Feller
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Marcel P Haesler
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Ole Seehausen
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
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37
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Wright DS, van Eijk R, Schuart L, Seehausen O, Groothuis TGG, Maan ME. Testing sensory drive speciation in cichlid fish: Linking light conditions to opsin expression, opsin genotype and female mate preference. J Evol Biol 2019; 33:422-434. [PMID: 31820840 PMCID: PMC7187155 DOI: 10.1111/jeb.13577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 12/04/2019] [Indexed: 12/15/2022]
Abstract
Ecological speciation is facilitated when divergent adaptation has direct effects on selective mating. Divergent sensory adaptation could generate such direct effects, by mediating both ecological performance and mate selection. In aquatic environments, light attenuation creates distinct photic environments, generating divergent selection on visual systems. Consequently, divergent sensory drive has been implicated in the diversification of several fish species. Here, we experimentally test whether divergent visual adaptation explains the divergence of mate preferences in Haplochromine cichlids. Blue and red Pundamilia co‐occur across south‐eastern Lake Victoria. They inhabit different photic conditions and have distinct visual system properties. Previously, we documented that rearing fish under different light conditions influences female preference for blue versus red males. Here, we examine to what extent variation in female mate preference can be explained by variation in visual system properties, testing the causal link between visual perception and preference. We find that our experimental light manipulations influence opsin expression, suggesting a potential role for phenotypic plasticity in optimizing visual performance. However, variation in opsin expression does not explain species differences in female preference. Instead, female preference covaries with allelic variation in the long‐wavelength‐sensitive opsin gene (LWS), when assessed under broad‐spectrum light. Taken together, our study presents evidence for environmental plasticity in opsin expression and confirms the important role of colour perception in shaping female mate preferences in Pundamilia. However, it does not constitute unequivocal evidence for the direct effects of visual adaptation on assortative mating.
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Affiliation(s)
- Daniel Shane Wright
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Roel van Eijk
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Lisa Schuart
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands.,University of Applied Sciences van Hall Larenstein, Leeuwarden, The Netherlands
| | - Ole Seehausen
- Institute of Ecology & Evolution, University of Bern, Bern, Switzerland.,Department Fish Ecology & Evolution, Eawag, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
| | - Ton G G Groothuis
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Martine E Maan
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands.,Institute of Ecology & Evolution, University of Bern, Bern, Switzerland.,Department Fish Ecology & Evolution, Eawag, Center for Ecology, Evolution and Biogeochemistry, Kastanienbaum, Switzerland
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38
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Meier JI, Stelkens RB, Joyce DA, Mwaiko S, Phiri N, Schliewen UK, Selz OM, Wagner CE, Katongo C, Seehausen O. The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes. Nat Commun 2019; 10:5391. [PMID: 31796733 PMCID: PMC6890737 DOI: 10.1038/s41467-019-13278-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 10/22/2019] [Indexed: 01/26/2023] Open
Abstract
The process of adaptive radiation was classically hypothesized to require isolation of a lineage from its source (no gene flow) and from related species (no competition). Alternatively, hybridization between species may generate genetic variation that facilitates adaptive radiation. Here we study haplochromine cichlid assemblages in two African Great Lakes to test these hypotheses. Greater biotic isolation (fewer lineages) predicts fewer constraints by competition and hence more ecological opportunity in Lake Bangweulu, whereas opportunity for hybridization predicts increased genetic potential in Lake Mweru. In Lake Bangweulu, we find no evidence for hybridization but also no adaptive radiation. We show that the Bangweulu lineages also colonized Lake Mweru, where they hybridized with Congolese lineages and then underwent multiple adaptive radiations that are strikingly complementary in ecology and morphology. Our data suggest that the presence of several related lineages does not necessarily prevent adaptive radiation, although it constrains the trajectories of morphological diversification. It might instead facilitate adaptive radiation when hybridization generates genetic variation, without which radiation may start much later, progress more slowly or never occur.
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Affiliation(s)
- Joana I Meier
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
- St John's College, University of Cambridge, St John's Street, Cambridge, CB2 1TP, UK
| | - Rike B Stelkens
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Division of Population Genetics, Department of Zoology, Stockholm University, Svante Arrheniusväg 18 B, 106 91, Stockholm, Sweden
| | - Domino A Joyce
- Evolutionary and Ecological Genomics Group, Department of Biological and Marine Sciences, University of Hull, Hull, HU6 7RX, UK
| | - Salome Mwaiko
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Numel Phiri
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Ulrich K Schliewen
- SNSB-Bavarian State Collection of Zoology, Münchhausenstrasse 21, 81247, Munich, Germany
| | - Oliver M Selz
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
| | - Catherine E Wagner
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland
- Biodiversity Institute and Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Cyprian Katongo
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Ole Seehausen
- Division of Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstr. 6, CH-3012, Bern, Switzerland.
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry (CEEB), Eawag Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.
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39
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Selz OM, Seehausen O. Interspecific hybridization can generate functional novelty in cichlid fish. Proc Biol Sci 2019; 286:20191621. [PMID: 31640510 DOI: 10.1098/rspb.2019.1621] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The role of interspecific hybridization in evolution is still being debated. Interspecific hybridization has been suggested to facilitate the evolution of ecological novelty, and hence the invasion of new niches and adaptive radiation when ecological opportunity is present beyond the parental species niches. On the other hand, hybrids between two ecologically divergent species may perform less well than parental species in their respective niches because hybrids would be intermediate in performance in both niches. The evolutionary consequences of hybridization may hence be context-dependent, depending on whether ecological opportunities, beyond those of the parental species, do or do not exist. Surprisingly, these complementary predictions may never have been tested in the same experiment in animals. To do so, we investigate if hybrids between ecologically distinct cichlid species perform less well than the parental species when feeding on food either parent is adapted to, and if the same hybrids perform better than their parents when feeding on food none of the species are adapted to. We generated two first-generation hybrid crosses between species of African cichlids. In feeding efficiency experiments we measured the performance of hybrids and parental species on food types representing both parental species niches and additional 'novel' niches, not used by either of the parental species but by other species in the African cichlid radiations. We found that hybrids can have higher feeding efficiencies on the 'novel' food types but typically have lower efficiencies on parental food types when compared to parental species. This suggests that hybridization can generate functional variation that can be of ecological relevance allowing the access to resources outside of either parental species niche. Hence, we provide support for the hypothesis of ecological context-dependency of the evolutionary impact of interspecific hybridization.
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Affiliation(s)
- O M Selz
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
| | - O Seehausen
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, 6047 Kastanienbaum, Switzerland.,Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland
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40
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Rougeux C, Gagnaire P, Praebel K, Seehausen O, Bernatchez L. Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex. Mol Ecol 2019; 28:4388-4403. [DOI: 10.1111/mec.15226] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Clément Rougeux
- Département de biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec City QC Canada
| | | | - Kim Praebel
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Ole Seehausen
- Aquatic Ecology and Evolution Institute of Ecology & Evolution University of Bern Bern Switzerland
| | - Louis Bernatchez
- Département de biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec City QC Canada
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41
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Marques DA, Lucek K, Sousa VC, Excoffier L, Seehausen O. Admixture between old lineages facilitated contemporary ecological speciation in Lake Constance stickleback. Nat Commun 2019; 10:4240. [PMID: 31534121 PMCID: PMC6751218 DOI: 10.1038/s41467-019-12182-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 08/27/2019] [Indexed: 01/25/2023] Open
Abstract
Ecological speciation can sometimes rapidly generate reproductively isolated populations coexisting in sympatry, but the origin of genetic variation permitting this is rarely known. We previously explored the genomics of very recent ecological speciation into lake and stream ecotypes in stickleback from Lake Constance. Here, we reconstruct the origin of alleles underlying ecological speciation by combining demographic modelling on genome-wide single nucleotide polymorphisms, phenotypic data and mitochondrial sequence data in the wider European biogeographical context. We find that parallel differentiation between lake and stream ecotypes across replicate lake-stream ecotones resulted from recent secondary contact and admixture between old East and West European lineages. Unexpectedly, West European alleles that introgressed across the hybrid zone at the western end of the lake, were recruited to genomic islands of differentiation between ecotypes at the eastern end of the lake. Our results highlight an overlooked outcome of secondary contact: ecological speciation facilitated by admixture variation. Ecological speciation can proceed rapidly, but the origin of genetic variation facilitating it has remained elusive. Here, the authors show that secondary contact and introgression between deeply diverged lineages of stickleback fish facilitated rapid ecological speciation into lake and stream ecotypes in Lake Constance.
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Affiliation(s)
- David A Marques
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.,Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland
| | - Kay Lucek
- Department of Environmental Sciences, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland
| | - Vitor C Sousa
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Campo Grande 016, 1749-016, Lisbon, Portugal
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland.,Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
| | - Ole Seehausen
- Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, CH-3012, Bern, Switzerland. .,Department of Fish Ecology and Evolution, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Center for Ecology, Evolution and Biogeochemistry, Seestrasse 79, CH-6047, Kastanienbaum, Switzerland.
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42
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Wright DS, Meijer R, van Eijk R, Vos W, Seehausen O, Maan ME. Geographic variation in opsin expression does not align with opsin genotype in Lake Victoria cichlid populations. Ecol Evol 2019; 9:8676-8689. [PMID: 31410271 PMCID: PMC6686298 DOI: 10.1002/ece3.5411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/09/2019] [Accepted: 05/19/2019] [Indexed: 12/27/2022] Open
Abstract
Sensory adaptation to the local environment can contribute to speciation. Aquatic environments are well suited for studying this process: The natural attenuation of light through water results in heterogeneous light environments, to which vision-dependent species must adapt for communication and survival. Here, we study visual adaptation in sympatric Pundamilia cichlids from southeastern Lake Victoria. Species with blue or red male nuptial coloration co-occur at many rocky islands but tend to be depth-differentiated, entailing different visual habitats, more strongly at some islands than others. Divergent visual adaptation to these environments has been implicated as a major factor in the divergence of P. pundamilia and P. nyererei, as they show consistent differentiation in the long-wavelength-sensitive visual pigment gene sequence (LWS opsin). In addition to sequence variation, variation in the opsin gene expression levels may contribute to visual adaptation. We characterized opsin gene expression and LWS genotype across Pundamilia populations inhabiting turbid and clear waters, to examine how different mechanisms of visual tuning contribute to visual adaptation. As predicted, the short-wavelength-sensitive opsin (SWS2b) was expressed exclusively in a population from clear water. Contrary to prediction however, expression levels of the other opsins were species- and island-dependent and did not align with species differences in LWS genotype. Specifically, in two locations with turbid water, the shallow-water dwelling blue species expressed more LWS and less RH2A than the deeper-dwelling red species, while the opposite pattern occurred in the two locations with clear water. Visual modeling suggests that the observed distribution of opsin expression profiles and LWS genotypes does not maximize visual performance, implying the involvement of additional visual tuning mechanisms and/or incomplete adaptation. OPEN RESEARCH BADGE This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://hdl.handle.net/10411/I1IUUQ.
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Affiliation(s)
- Daniel Shane Wright
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Roy Meijer
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
- University of Applied Sciences van Hall LarensteinLeeuwardenThe Netherlands
| | - Roel van Eijk
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Wicher Vos
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Ole Seehausen
- Institute of Ecology & EvolutionUniversity of BernBernSwitzerland
- Department Fish Ecology & EvolutionEawag, Center for Ecology, Evolution and BiogeochemistryKastanienbaumSwitzerland
| | - Martine E. Maan
- Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
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43
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Dean LL, Magalhaes IS, Foote A, D'Agostino D, McGowan S, MacColl ADC. Admixture between ancient lineages, selection, and the formation of sympatric stickleback species-pairs. Mol Biol Evol 2019; 36:2481-2497. [PMID: 31297536 PMCID: PMC6805233 DOI: 10.1093/molbev/msz161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/02/2019] [Accepted: 07/07/2019] [Indexed: 12/14/2022] Open
Abstract
Ecological speciation has become a popular model for the development and maintenance of reproductive isolation in closely related sympatric pairs of species or ecotypes. An implicit assumption has been that such pairs originate (possibly with gene flow) from a recent, genetically homogeneous ancestor. However, recent genomic data has revealed that currently sympatric taxa are often a result of secondary contact between ancestrally allopatric lineages. This has sparked an interest in the importance of initial hybridization upon secondary contact, with genomic re-analysis of classic examples of ecological speciation often implicating admixture in speciation. We describe a novel occurrence of unusually well-developed reproductive isolation in a model system for ecological speciation: the three-spined stickleback (Gasterosteus aculeatus), breeding sympatrically in multiple lagoons on the Scottish island of North Uist. Using morphological data, targeted genotyping and genome-wide single nucleotide polymorphism (SNP) data we show that lagoon resident and anadromous ecotypes are strongly reproductively isolated with an estimated hybridization rate of only ∼1%. We use palaeoecological and genetic data to test three hypotheses to explain the existence of these species-pairs. Our results suggest that recent, purely ecological speciation from a genetically homogeneous ancestor is probably not solely responsible for the evolution of species-pairs. Instead we reveal a complex colonisation history with multiple ancestral lineages contributing to the genetic composition of species-pairs, alongside strong disruptive selection. Our results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin.
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Affiliation(s)
- Laura L Dean
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Isabel S Magalhaes
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK.,Department of Life Sciences, Whitelands College, University of Roehampton, London, UK
| | - Andrew Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd, UK
| | - Daniele D'Agostino
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
| | - Suzanne McGowan
- School of Geography, The University of Nottingham, University Park, Nottingham, UK
| | - Andrew D C MacColl
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, UK
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44
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Cai Z, Zhou L, Ren NN, Xu X, Liu R, Huang L, Zheng XM, Meng QL, Du YS, Wang MX, Geng MF, Chen WL, Jing CY, Zou XH, Guo J, Chen CB, Zeng HZ, Liang YT, Wei XH, Guo YL, Zhou HF, Zhang FM, Ge S. Parallel Speciation of Wild Rice Associated with Habitat Shifts. Mol Biol Evol 2019; 36:875-889. [PMID: 30861529 PMCID: PMC6501882 DOI: 10.1093/molbev/msz029] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon. We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a “magic” trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.
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Affiliation(s)
- Zhe Cai
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Lian Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ning-Ning Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xun Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Lei Huang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Ming Zheng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Qing-Lin Meng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Su Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Xia Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Fan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Li Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Chun-Yan Jing
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Hui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jie Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Cheng-Bin Chen
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Hua-Zhong Zeng
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Yun-Tao Liang
- Guangxi Academy Agricultural Sciences, Nanning, Guangxi, China
| | - Xing-Hua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hai-Fei Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Fu-Min Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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45
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Aguirre-Liguori JA, Gaut BS, Jaramillo-Correa JP, Tenaillon MI, Montes-Hernández S, García-Oliva F, Hearne SJ, Eguiarte LE. Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies (Zea mays parviglumis and Zea mays mexicana). Mol Ecol 2019; 28:2814-2830. [PMID: 30980686 DOI: 10.1111/mec.15098] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 03/27/2019] [Accepted: 04/08/2019] [Indexed: 01/03/2023]
Abstract
Patterns of genomic divergence between hybridizing taxa can be heterogeneous along the genome. Both differential introgression and local adaptation may contribute to this pattern. Here, we analysed two teosinte subspecies, Zea mays ssp. parviglumis and ssp. mexicana, to test whether their divergence has occurred in the face of gene flow and to infer which environmental variables have been important drivers of their ecological differentiation. We generated 9,780 DArTseqTM SNPs for 47 populations, and used an additional data set containing 33,454 MaizeSNP50 SNPs for 49 populations. With these data, we inferred features of demographic history and performed genome wide scans to determine the number of outlier SNPs associated with climate and soil variables. The two data sets indicate that divergence has occurred or been maintained despite continuous gene flow and/or secondary contact. Most of the significant SNP associations were to temperature and to phosphorus concentration in the soil. A large proportion of these candidate SNPs were located in regions of high differentiation that had been identified previously as putative inversions. We therefore propose that genomic differentiation in teosintes has occurred by a process of adaptive divergence, with putative inversions contributing to reduced gene flow between locally adapted populations.
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Affiliation(s)
- Jonás A Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California
| | - Juan Pablo Jaramillo-Correa
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maud I Tenaillon
- Génétique Quantitative et Evolution- Le Moulon, INRA, Gif-sur-Yvette, France
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Celaya, México
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Morelia, México
| | - Sarah J Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, México
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46
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Adams RH, Schield DR, Castoe TA. Recent Advances in the Inference of Gene Flow from Population Genomic Data. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s40610-019-00120-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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47
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Brock CD, Wagner CE. The smelly path to sympatric speciation? Mol Ecol 2019; 27:4153-4156. [PMID: 30375091 DOI: 10.1111/mec.14845] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/28/2023]
Abstract
In this issue of Molecular Ecology, Poelstra et al. () use genomic data to show that cichlid species in the adaptive radiation in Lake Ejagham, Cameroon, experienced gene flow with a riverine relative, primarily prior to their diversification. Intriguingly, this introgression brought with it olfactory alleles that the authors suggest may play a sensory role in speciation. As a classic example of sympatric speciation due to the highly restricted geography of this small (0.49 km2 ) crater lake (Schliewen et al., ), this result sheds new light on the history of this fascinating radiation. As genomic data for cichlid radiations accumulate, finding evidence of introgression increasingly appears to be the rule rather than the exception (Kautt et al., ; Meier et al., , ). However, two points are pressing as evidence for introgression mounts: (a) It is crucial to understand the assumptions of analytical approaches used and (b) it is important to think clearly about the divergent contexts in which evidence for introgression has been invoked as an important feature of adaptive radiation.
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Affiliation(s)
- Chad D Brock
- Department of Botany and Biodiversity Institute, University of Wyoming, Laramie, Wyoming
| | - Catherine E Wagner
- Department of Botany and Biodiversity Institute, University of Wyoming, Laramie, Wyoming
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48
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Benham PM, Cheviron ZA. Divergent mitochondrial lineages arose within a large, panmictic population of the Savannah sparrow (Passerculus sandwichensis). Mol Ecol 2019; 28:1765-1783. [PMID: 30770598 DOI: 10.1111/mec.15049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 02/06/2019] [Accepted: 02/12/2019] [Indexed: 12/24/2022]
Abstract
Unusual patterns of mtDNA diversity can reveal interesting aspects of a species' biology. However, making such inferences requires discerning among the many alternative scenarios that could underlie any given mtDNA pattern. Next-generation sequencing methods provide large, multilocus data sets with increased power to resolve unusual mtDNA patterns. A mtDNA-based phylogeography of the Savannah sparrow (Passerculus sandwichensis) previously identified two sympatric, but divergent (~2%) clades within the nominate subspecies group and a third clade that consisted of birds sampled from northwest Mexico. We revisited the phylogeography of this species using a population genomic data set to resolve the processes leading to the evolution of sympatric and divergent mtDNA lineages. We identified two genetic clusters in the genomic data set corresponding to (a) the nominate subspecies group and (b) northwestern Mexico birds. Following divergence, the nominate clade maintained a large, stable population, indicating that divergent mitochondrial lineages arose within a panmictic population. Simulations based on parameter estimates from this model further confirmed that this demographic history could produce observed levels of mtDNA diversity. Patterns of divergent, sympatric mtDNA lineages are frequently interpreted as admixture of historically isolated lineages. Our analyses reject this interpretation for Savannah sparrows and underscore the need for genomic data sets to resolve the evolutionary mechanisms behind anomalous, locus-specific patterns.
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Affiliation(s)
- Phred M Benham
- Division of Biological Sciences, University of Montana, Missoula, Montana
| | - Zachary A Cheviron
- Division of Biological Sciences, University of Montana, Missoula, Montana
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49
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Conte MA, Joshi R, Moore EC, Nandamuri SP, Gammerdinger WJ, Roberts RB, Carleton KL, Lien S, Kocher TD. Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. Gigascience 2019; 8:giz030. [PMID: 30942871 PMCID: PMC6447674 DOI: 10.1093/gigascience/giz030] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/11/2019] [Accepted: 03/07/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. RESULTS We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage. CONCLUSION This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
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Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Rajesh Joshi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Emily C Moore
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | - Reade B Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA
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50
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Barth JMI, Villegas-Ríos D, Freitas C, Moland E, Star B, André C, Knutsen H, Bradbury I, Dierking J, Petereit C, Righton D, Metcalfe J, Jakobsen KS, Olsen EM, Jentoft S. Disentangling structural genomic and behavioural barriers in a sea of connectivity. Mol Ecol 2019; 28:1394-1411. [PMID: 30633410 PMCID: PMC6518941 DOI: 10.1111/mec.15010] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/21/2018] [Accepted: 12/27/2018] [Indexed: 12/17/2022]
Abstract
Genetic divergence among populations arises through natural selection or drift and is counteracted by connectivity and gene flow. In sympatric populations, isolating mechanisms are thus needed to limit the homogenizing effects of gene flow to allow for adaptation and speciation. Chromosomal inversions act as an important mechanism maintaining isolating barriers, yet their role in sympatric populations and divergence with gene flow is not entirely understood. Here, we revisit the question of whether inversions play a role in the divergence of connected populations of the marine fish Atlantic cod (Gadus morhua), by exploring a unique data set combining whole‐genome sequencing data and behavioural data obtained with acoustic telemetry. Within a confined fjord environment, we find three genetically differentiated Atlantic cod types belonging to the oceanic North Sea population, the western Baltic population and a local fjord‐type cod. Continuous behavioural tracking over 4 year revealed temporally stable sympatry of these types within the fjord. Despite overall weak genetic differentiation consistent with high levels of gene flow, we detected significant frequency shifts of three previously identified inversions, indicating an adaptive barrier to gene flow. In addition, behavioural data indicated that North Sea cod and individuals homozygous for the LG12 inversion had lower fitness in the fjord environment. However, North Sea and fjord‐type cod also occupy different depths, possibly contributing to prezygotic reproductive isolation and representing a behavioural barrier to gene flow. Our results provide the first insights into a complex interplay of genomic and behavioural isolating barriers in Atlantic cod and establish a new model system towards an understanding of the role of genomic structural variants in adaptation and diversification.
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Affiliation(s)
- Julia M I Barth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Zoological Institute, University of Basel, Basel, Switzerland
| | - David Villegas-Ríos
- Department of Ecology and Marine Resources, Mediterranean Institute for Advanced Studies, IMEDEA CSIC-UIB, Esporles, Spain.,Department of Ecology and Marine Resources, Institute of Marine Research, (IIM CSIC), Vigo, Spain
| | - Carla Freitas
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway.,Oceanic Observatory of Madeira, Funchal, Portugal
| | - Even Moland
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Carl André
- Department of Marine Sciences - Tjärnö, University of Gothenburg, Gothenburg, Sweden
| | - Halvor Knutsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.,Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Ian Bradbury
- Science Branch, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Jan Dierking
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | | | - David Righton
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Julian Metcalfe
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, UK
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Esben M Olsen
- Institute for Marine Research, Flødevigen, Norway.,Centre for Coastal Research, University of Agder, Agder, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway
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