1
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Crawford NG, McGreevy TJ, Mullen SP, Schneider CJ. The genetic basis of conspicuous coloration in the Guadeloupean anole: Evolution by sexual and ecological selection. Ecol Evol 2023; 13:e10266. [PMID: 37435022 PMCID: PMC10330958 DOI: 10.1002/ece3.10266] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 07/13/2023] Open
Abstract
Understanding how natural selection acts on the genome and contributes to the process of speciation is a primary aim of the study of evolution. Here we used natural variation in two subspecies of the Guadeloupean anole (Anolis marmoratus ssp.), from the island of Guadeloupe in the Lesser Antilles, to explore the genomic basis of adaptation and speciation in Anolis lizards. These subspecies inhabit distinct ecological environments and display marked differences in adult male color and pattern. We sequenced the complete genomes of 20 anoles, 10 from each subspecies, at 1.4× coverage. We used genome-wide scans of population differentiation, allele frequency spectrum, and linkage disequilibrium to characterize the genomic architecture within and between the subspecies. While most of the genome was undifferentiated, we observed five large divergent regions. Within these regions we identified blocks, 5 kb pairs in length, enriched for fixed single nucleotide polymorphisms. These blocks encompass 97 genes, two of which are candidate pigmentation genes. One is melanophilin (mlph), which helps transport melanosomes within melanocytes. The other is a cluster of differentiation 36 (cd36), which regulates carotenoid pigment sequestration. We used high-pressure liquid chromatography to confirm that carotenoid pigments are significantly more abundant in the conspicuous orange-pigmented skin of male A. m. marmoratus suggesting that cd36 may be regulating pigment deposition in this tissue. We identified for the first time a carotenoid gene that is a potential target of divergent sexual selection and may be contributing to the early stages of speciation in Anolis lizards.
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Affiliation(s)
| | - Thomas J. McGreevy
- Department of BiologyBoston UniversityBostonMassachusettsUSA
- Department of Natural Resources ScienceUniversity of Rhode IslandKingstonRhode IslandUSA
| | - Sean P. Mullen
- Department of BiologyBoston UniversityBostonMassachusettsUSA
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2
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O'Connell KA, Prates I, Scheinberg LA, Mulder KP, Bell RC. Speciation and secondary contact in a fossorial island endemic, the São Tomé caecilian. Mol Ecol 2021; 30:2859-2871. [PMID: 33969550 DOI: 10.1111/mec.15928] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 02/06/2023]
Abstract
A period of isolation in allopatry typically precedes local adaptation and subsequent divergence among lineages. Alternatively, locally adapted phenotypes may arise and persist in the face of gene flow, resulting in strong correlations between ecologically-relevant phenotypic variation and corresponding environmental gradients. Quantifying genetic, ecological, and phenotypic divergence in such lineages can provide insights into the abiotic and biotic mechanisms that structure populations and drive the accumulation of phenotypic and taxonomic diversity. Low-vagility organisms whose distributions span ephemeral geographic barriers present the ideal evolutionary context within which to address these questions. Here, we combine genetic (mtDNA and genome-wide SNPs) and phenotypic data to investigate the divergence history of caecilians (Amphibia: Gymnophiona) endemic to the oceanic island of São Tomé in the Gulf of Guinea archipelago. Consistent with a previous mtDNA study, we find two phenotypically and genetically distinct lineages that occur along a north-to-south axis with extensive admixture in the centre of the island. Demographic modelling supports divergence in allopatry (~300 kya) followed by secondary contact (~95 kya). Consequently, in contrast to a morphological study that interpreted latitudinal phenotypic variation in these caecilians as a cline within a single widespread species, our analyses suggest a history of allopatric lineage divergence and subsequent hybridization that may have blurred species boundaries. We propose that late Pleistocene volcanic activity favoured allopatric divergence between these lineages with local adaptation to climate maintaining a stable hybrid zone in the centre of São Tomé Island. Our study joins a growing number of systems demonstrating lineage divergence on volcanic islands with stark environmental transitions across small geographic distances.
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Affiliation(s)
- Kyle A O'Connell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Biological Sciences, George Washington University, Washington, DC, USA
| | - Ivan Prates
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Lauren A Scheinberg
- Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
| | - Kevin P Mulder
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, California Academy of Sciences, San Francisco, CA, USA
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3
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Burress ED, Muñoz MM. Ecological Opportunity from Innovation, not Islands, Drove the Anole Lizard Adaptive Radiation. Syst Biol 2021; 71:93-104. [PMID: 33956152 DOI: 10.1093/sysbio/syab031] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/28/2021] [Accepted: 05/03/2021] [Indexed: 12/15/2022] Open
Abstract
Islands are thought to facilitate adaptive radiation by providing release from competition and predation. Anole lizards are considered a classic example of this phenomenon: different ecological specialists ('ecomorphs') evolved in the Caribbean Greater Antilles (Cuba, Hispaniola, Jamaica, and Puerto Rico), resulting in convergent assemblages that are not observed in mainland Latin America. Yet, the role of islands in facilitating adaptive radiation is more often implied than directly tested, leaving uncertain the role of biogeography in stimulating diversification. Here, we assess the proposed "island effect" on anole diversification using Bayesian phylogenetic comparative methods that explicitly incorporate rate heterogeneity across the tree and demonstrate two cases of would-be false positives. We discovered that rates of speciation and morphological evolution of island and mainland anoles are equivalent, implying that islands provide no special context for exceptionally rapid diversification. Likewise, rates of evolution were equivalent between island anoles that arose via in situ versus dispersal-based mechanisms, and we found no evidence for island-specific rates of speciation or morphological evolution. Nonetheless, the origin of Anolis is characterized by a speciation pulse that slowed over time - a classic signature of waning ecological opportunity. Our findings cast doubt on the notion that islands catalyzed the anole adaptive radiation and instead point to a key innovation, adhesive toe pads, which facilitated the exploitation of many arboreal niches sparsely utilized by other iguanian lizards. The selective pressures responsible for arboreal niche diversification differ between islands and the mainland, but the tempo of diversification driven by these discordant processes is indistinguishable.
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Affiliation(s)
- Edward D Burress
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Martha M Muñoz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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4
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Prates I, D'Angiolella AB, Rodrigues MT, Melo-Sampaio PR, de Queiroz K, Bell RC. Evolutionary drivers of sexual signal variation in Amazon Slender Anoles. Evolution 2021; 75:1361-1376. [PMID: 33860933 DOI: 10.1111/evo.14230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 01/29/2023]
Abstract
Phenotypic variation among populations, as seen in the signaling traits of many species, provides an opportunity to test whether similar factors generate repeated phenotypic patterns in different parts of a species' range. We investigated whether genetic divergence, abiotic gradients, and sympatry with closely related species explain variation in the dewlap colors of Amazon Slender Anoles, Anolis fuscoauratus. To this aim, we characterized dewlap diversity in the field with respect to population genetic structure and evolutionary relationships, assessed whether dewlap phenotypes are associated with climate or landscape variables, and tested for nonrandom associations in the distributions of A. fuscoauratus phenotypes and sympatric Anolis species. We found that dewlap colors vary among but not within sites in A. fuscoauratus. Regional genetic clusters included multiple phenotypes, while populations with similar dewlaps were often distantly related. Phenotypes did not segregate in environmental space, providing no support for optimized signal transmission at a local scale. Instead, we found a negative association between certain phenotypes and sympatric Anolis species with similar dewlap color attributes, suggesting that interactions with closely related species promoted dewlap divergence among A. fuscoauratus populations. Amazon Slender Anoles emerge as a promising system to address questions about parallel trait evolution and the contribution of signaling traits to speciation.
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Affiliation(s)
- Ivan Prates
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, 20560.,Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, Michigan, 48109
| | | | - Miguel T Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Paulo R Melo-Sampaio
- Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, 20560
| | - Rayna C Bell
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, 20560.,Herpetology Department, California Academy of Sciences, San Francisco, California, 94118
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5
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Pérez‐Cembranos A, Pérez‐Mellado V, Alemany I, Bassitta M, Terrasa B, Picornell A, Castro JA, Brown RP, Ramon C. Morphological and genetic diversity of the Balearic lizard,
Podarcis lilfordi
(Günther, 1874): Is it relevant to its conservation? DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
| | | | - Iris Alemany
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Marta Bassitta
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Bàrbara Terrasa
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Antonia Picornell
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - José A. Castro
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
| | - Richard P. Brown
- School of Biological and Environmental Sciences Liverpool John Moores University Liverpool UK
| | - Cori Ramon
- Laboratori de Genètica Departament de Biologia Universitat de les Illes Balears Palma de Mallorca Spain
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6
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Wiens JJ, Tuschhoff E. Songs versus colours versus horns: what explains the diversity of sexually selected traits? Biol Rev Camb Philos Soc 2020; 95:847-864. [PMID: 32092241 DOI: 10.1111/brv.12593] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 01/25/2020] [Accepted: 02/10/2020] [Indexed: 01/14/2023]
Abstract
Papers on sexual selection often highlight the incredible diversity of sexually selected traits across animals. Yet, few studies have tried to explain why this diversity evolved. Animals use many different types of traits to attract mates and outcompete rivals, including colours, songs, and horns, but it remains unclear why, for example, some taxa have songs, others have colours, and others horns. Here, we first conduct a systematic survey of the basic diversity and distribution of different types of sexually selected signals and weapons across the animal Tree of Life. Based on this survey, we describe seven major patterns in trait diversity and distributions. We then discuss 10 unanswered questions raised by these patterns, and how they might be addressed. One major pattern is that most types of sexually selected signals and weapons are apparently absent from most animal phyla (88%), in contrast to the conventional wisdom that a diversity of sexually selected traits is present across animals. Furthermore, most trait diversity is clustered in Arthropoda and Chordata, but only within certain clades. Within these clades, many different types of traits have evolved, and many types appear to have evolved repeatedly. By contrast, other major arthropod and chordate clades appear to lack all or most trait types, and similar patterns are repeated at smaller phylogenetic scales (e.g. within insects). Although most research on sexual selection focuses on female choice, we find similar numbers of traits (among sampled species) are involved in male contests (44%) and female choice (55%). Overall, these patterns are largely unexplained and unexplored, as are many other fundamental questions about the evolution of these traits. We suggest that understanding the diversity of sexually selected traits may require a shift towards macroevolutionary studies at relatively deep timescales (e.g. tens to hundreds of millions of years ago).
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Affiliation(s)
- John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
| | - E Tuschhoff
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721-0088, U.S.A
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7
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Reynolds RG, Kolbe JJ, Glor RE, López-Darias M, Gómez Pourroy CV, Harrison AS, de Queiroz K, Revell LJ, Losos JB. Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation. J Evol Biol 2020; 33:468-494. [PMID: 31872929 DOI: 10.1111/jeb.13581] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 12/18/2019] [Indexed: 01/15/2023]
Abstract
Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis of representative populations across the entire native range of A. sagrei, finding that the species originated in the early Pliocene, with the deepest divergence occurring between western and eastern Cuba. Lineages from these two regions subsequently colonized the northern Caribbean. We find that at the broadest scale, populations colonizing areas with fewer closely related competitors tend to evolve larger body size and more lamellae on their toepads. This trend follows expectations for post-colonization divergence from progenitors and convergence in allopatry, whereby populations freed from competition with close relatives evolve towards common morphological and ecological optima. Taken together, our results show a complex history of ancient and recent Cuban diaspora with populations on competitor-poor islands evolving away from their ancestral Cuban populations regardless of their phylogenetic relationships, thus providing insight into the original diversification of colonist anoles at the beginning of the radiation. Our research also supplies an evolutionary framework for the many studies of this increasingly important species in ecological and evolutionary research.
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Affiliation(s)
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Richard E Glor
- Herpetology Division, Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KA, USA
| | | | | | - Alexis S Harrison
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Liam J Revell
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Jonathan B Losos
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO, USA
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8
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Wollenberg Valero KC, Marshall JC, Bastiaans E, Caccone A, Camargo A, Morando M, Niemiller ML, Pabijan M, Russello MA, Sinervo B, Werneck FP, Sites JW, Wiens JJ, Steinfartz S. Patterns, Mechanisms and Genetics of Speciation in Reptiles and Amphibians. Genes (Basel) 2019; 10:genes10090646. [PMID: 31455040 PMCID: PMC6769790 DOI: 10.3390/genes10090646] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/21/2019] [Accepted: 08/05/2019] [Indexed: 12/22/2022] Open
Abstract
In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in these groups. This study then reviews the research on different aspects of speciation in reptiles and amphibians, including biogeography and climatic niches, ecological speciation, the relationship between speciation rates and phenotypic traits, and genetics and genomics. Further, several case studies of speciation in reptiles and amphibians that exemplify many of these themes are discussed. These include studies of integrative taxonomy and biogeography in South American lizards, ecological speciation in European salamanders, speciation and phenotypic evolution in frogs and lizards. The final case study combines genomics and biogeography in tortoises. The field of amphibian and reptile speciation research has steadily moved forward from the assessment of geographic and ecological aspects, to incorporating other dimensions of speciation, such as genetic mechanisms and evolutionary forces. A higher degree of integration among all these dimensions emerges as a goal for future research.
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Affiliation(s)
| | - Jonathon C Marshall
- Department of Zoology, Weber State University, 1415 Edvalson Street, Dept. 2505, Ogden, UT 84401, USA
| | - Elizabeth Bastiaans
- Department of Biology, State University of New York, College at Oneonta, Oneonta, NY 13820, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
| | - Arley Camargo
- Centro Universitario de Rivera, Universidad de la República, Ituzaingó 667, Rivera 40000, Uruguay
| | - Mariana Morando
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales (IPEEC, CENPAT-CONICET) Bv. Brown 2915, Puerto Madryn U9120ACD, Argentina
| | - Matthew L Niemiller
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, USA
| | - Maciej Pabijan
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, ul. Gronostajowa 9, 30-387 Kraków, Poland
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Barry Sinervo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Coastal Biology Building, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Fernanda P Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus 69060-000, Brazil
| | - Jack W Sites
- Department of Biological and Marine Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, UK
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Sebastian Steinfartz
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, 04103 Leipzig, Germany
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9
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Hu CC, Wu YQ, Ma L, Chen YJ, Ji X. Genetic and morphological divergence among three closely related Phrynocephalus species (Agamidae). BMC Evol Biol 2019; 19:114. [PMID: 31170905 PMCID: PMC6551896 DOI: 10.1186/s12862-019-1443-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 05/27/2019] [Indexed: 11/25/2022] Open
Abstract
Background The Qinghai-Tibetan Plateau (QTP) is the world’s highest and largest plateau, but the role of its uplift in the evolution of species or biotas still remains poorly known. Toad-headed lizards of the reproductively bimodal genus Phrynocephalus are a clade of agamids, with all viviparous species restricted to the QTP and adjacent regions. The eastern part of the range of the viviparous taxa is occupied by three closely related but taxonomically controversial species, P. guinanensis, P. putjatia and P. vlangalii. Here, we combined genetic (mitochondrial ND4 gene and nine microsatellite loci), morphological (11 mensural and 11 meristic variables), and ecological (nine climatic variables) data to explore possible scenarios that may explain the discordance between genetic and morphological patterns, and to test whether morphological divergence is associated with local adaptation. Results We found weak genetic differentiation but pronounced morphological divergence, especially between P. guinanensis and P. vlangalii. Genetically, the species boundary was not so clear between any species pair. Morphologically, the species boundary was clear between P. guinanensis and P. vlangalii but not between other two species pairs. Body size and scale characters accounted best for morphological divergence between species. Morphological divergence was related to habitat types that differ climatically. Conclusions Our study provides evidence for genetic and morphological divergence among the three closely related viviparous species of Phrynocephalus lizards, and supports the idea that natural selection in spatially heterogeneous environments can lead to population divergence even in the presence of gene flow. Our study supports the hypothesis that the evolutionary divergence between viviparous Phrynocephalus species was a consequence of environmental change after the uplift of the QTP. Electronic supplementary material The online version of this article (10.1186/s12862-019-1443-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chao-Chao Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.,Analysis and Testing Center, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Yan-Qing Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.,Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, 210000, Jiangsu, China
| | - Li Ma
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Yi-Jing Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, Jiangsu, China.
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10
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Prates I, Penna A, Rodrigues MT, Carnaval AC. Local adaptation in mainland anole lizards: Integrating population history and genome-environment associations. Ecol Evol 2018; 8:11932-11944. [PMID: 30598788 PMCID: PMC6303772 DOI: 10.1002/ece3.4650] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 09/22/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
Environmental gradients constrain physiological performance and thus species' ranges, suggesting that species occurrence in diverse environments may be associated with local adaptation. Genome-environment association analyses (GEAA) have become central for studies of local adaptation, yet they are sensitive to the spatial orientation of historical range expansions relative to landscape gradients. To test whether potentially adaptive genotypes occur in varied climates in wide-ranged species, we implemented GEAA on the basis of genomewide data from the anole lizards Anolis ortonii and Anolis punctatus, which expanded from Amazonia, presently dominated by warm and wet settings, into the cooler and less rainy Atlantic Forest. To examine whether local adaptation has been constrained by population structure and history, we estimated effective population sizes, divergence times, and gene flow under a coalescent framework. In both species, divergence between Amazonian and Atlantic Forest populations dates back to the mid-Pleistocene, with subsequent gene flow. We recovered eleven candidate genes involved with metabolism, immunity, development, and cell signaling in A. punctatus and found no loci whose frequency is associated with environmental gradients in A. ortonii. Distinct signatures of adaptation between these species are not associated with historical constraints or distinct climatic space occupancies. Similar patterns of spatial structure between selected and neutral SNPs along the climatic gradient, as supported by patterns of genetic clustering in A. punctatus, may have led to conservative GEAA performance. This study illustrates how tests of local adaptation can benefit from knowledge about species histories to support hypothesis formulation, sampling design, and landscape gradient characterization.
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Affiliation(s)
- Ivan Prates
- Department of Vertebrate ZoologyNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Department of Biology, City College of New York and Graduate CenterCity University of New YorkNew YorkNew York
| | - Anna Penna
- Department of AnthropologyUniversity of Texas at San AntonioSan AntonioTexas
| | | | - Ana Carolina Carnaval
- Department of Biology, City College of New York and Graduate CenterCity University of New YorkNew YorkNew York
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11
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Yıldırım Y, Anderson MJ, Hansson B, Patel S, Millar CD, Rainey PB. Genetic structure of the grey side-gilled sea slug (Pleurobranchaea maculata) in coastal waters of New Zealand. PLoS One 2018; 13:e0202197. [PMID: 30114275 PMCID: PMC6095540 DOI: 10.1371/journal.pone.0202197] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 07/30/2018] [Indexed: 01/09/2023] Open
Abstract
Pleurobranchaea maculata is a rarely studied species of the Heterobranchia found throughout the south and western Pacific-and recently recorded in Argentina-whose population genetic structure is unknown. Interest in the species was sparked in New Zealand following a series of dog deaths caused by ingestions of slugs containing high levels of the neurotoxin tetrodotoxin. Here we describe the genetic structure and demographic history of P. maculata populations from five principle locations in New Zealand based on extensive analyses of 12 microsatellite loci and the COI and CytB regions of mitochondrial DNA (mtDNA). Microsatellite data showed significant differentiation between northern and southern populations with population structure being associated with previously described regional variations in tetrodotoxin concentrations. However, mtDNA sequence data did not support such structure, revealing a star-shaped haplotype network with estimates of expansion time suggesting a population expansion in the Pleistocene era. Inclusion of publicly available mtDNA sequence sea slugs from Argentina did not alter the star-shaped network. We interpret our data as indicative of a single founding population that fragmented following geographical changes that brought about the present day north-south divide in New Zealand waters. Lack of evidence of cryptic species supports data indicating that differences in toxicity of individuals among regions are a consequence of differences in diet.
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Affiliation(s)
- Yeşerin Yıldırım
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
| | - Marti J. Anderson
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Selina Patel
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Craig D. Millar
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, Paris, France
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12
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Cádiz A, Nagata N, Díaz LM, Suzuki-Ohno Y, Echenique-Díaz LM, Akashi HD, Makino T, Kawata M. Factors affecting interspecific differences in genetic divergence among populations of Anolis lizards in Cuba. ZOOLOGICAL LETTERS 2018; 4:21. [PMID: 30116552 PMCID: PMC6085692 DOI: 10.1186/s40851-018-0107-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Geographical patterns and degrees of genetic divergence among populations differ between species, reflecting relative potentials for speciation or cladogenesis and differing capacities for environmental adaptation. Identification of factors that contribute to genetic divergence among populations is important to the understanding of why some species exhibit greater interpopulation genetic divergence. In this study, we calculated the mean pairwise genetic distances among populations as species' average genetic divergence by a phylogeny using nuclear and mitochondrial genes of 303 individuals from 33 Cuban Anolis species and estimated species ages by another phylogeny using nuclear and mitochondrial genes of 51 Cuban and 47 non-Cuban Anolis species. We identified factors that influence species' differences in genetic divergence among 26 species of Anolis lizards from Cuba. Species ages, environmental heterogeneity within species ranges, and ecomorph types were considered as factors affecting average genetic divergences among populations. RESULTS The phylogenies presented in this study provide the most comprehensive sampling of Cuban Anolis species to date. The phylogeny showed more conservative evolution of Anolis ecomorphs within Cuba and identified twig anoles as a monophyletic group. Subsequent Phylogenetic Generalized Least Squares (PGLS) analyses showed that species age was positively correlated with species' average genetic divergence among populations. CONCLUSION Although previous studies have focused on factors affecting genetic divergence within species, the present study showed for the first time that species differences in genetic divergence could be largely affected by species age.
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Affiliation(s)
- Antonio Cádiz
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
- Faculty of Biology, Havana University, Havana, Cuba
| | - Nobuaki Nagata
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Luis M. Díaz
- National Museum of Natural History of Cuba, Havana, Cuba
| | | | | | | | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masakado Kawata
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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13
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Tamate S, Iwasaki WM, Krysko KL, Camposano BJ, Mori H, Funayama R, Nakayama K, Makino T, Kawata M. Inferring evolutionary responses of Anolis carolinensis introduced into the Ogasawara archipelago using whole genome sequence data. Sci Rep 2017; 7:18008. [PMID: 29269734 PMCID: PMC5740155 DOI: 10.1038/s41598-017-17852-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022] Open
Abstract
Invaded species often can rapidly expand and establish in novel environments through adaptive evolution, resulting in devastating effects on native communities. However, it is unclear if genetic variation at whole-genomic levels is actually reduced in the introduced populations and which genetic changes have occurred responding to adaptation to new environments. In the 1960s, Anolis carolinensis was introduced onto one of the Ogasawara Islands, Japan, and subsequently expanded its range rapidly throughout two of the islands. Morphological comparison showed that lower hindlimb length in the introduced populations tended to be longer than those in its native Florida populations. Using re-sequenced whole genomic data, we estimated that the effective population size at the time of introduction was actually small (less than 50). We also inferred putative genomic regions subject to natural selection after this introduction event using SweeD and a method based on Tajima's D, π and F ST . Five candidate genes that were potentially subject to selection were estimated by both methods. The results suggest that there were standing variations that could potentially contribute to adaptation to nonnative environments despite the founder population being small.
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Affiliation(s)
- Satoshi Tamate
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan
| | - Watal M Iwasaki
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan
| | - Kenneth L Krysko
- Division of Herpetology, Florida Museum of Natural History, 1659 Museum Road, University of Florida, Gainesville, FL, 32611, USA
| | - Brian J Camposano
- Forest Management Bureau, Florida Forest Service, Florida Department of Agriculture and Consumer Services, 3125 Conner Boulevard, I-255, Tallahassee, FL, 32399, USA
| | - Hideaki Mori
- Japan Wildlife Research Center, Ogasawara Division, Okumura, Chichijima, Ogasawara, Tokyo, 100-2101, Japan
| | - Ryo Funayama
- United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo, Aoba, Sendai, 980-8575, Japan
| | - Keiko Nakayama
- United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo, Aoba, Sendai, 980-8575, Japan
| | - Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan.
| | - Masakado Kawata
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8578, Japan.
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14
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Feiner N. Accumulation of transposable elements in Hox gene clusters during adaptive radiation of Anolis lizards. Proc Biol Sci 2017; 283:rspb.2016.1555. [PMID: 27733546 DOI: 10.1098/rspb.2016.1555] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/14/2016] [Indexed: 12/20/2022] Open
Abstract
Transposable elements (TEs) are DNA sequences that can insert elsewhere in the genome and modify genome structure and gene regulation. The role of TEs in evolution is contentious. One hypothesis posits that TE activity generates genomic incompatibilities that can cause reproductive isolation between incipient species. This predicts that TEs will accumulate during speciation events. Here, I tested the prediction that extant lineages with a relatively high rate of speciation have a high number of TEs in their genomes. I sequenced and analysed the TE content of a marker genomic region (Hox clusters) in Anolis lizards, a classic case of an adaptive radiation. Unlike other vertebrates, including closely related lizards, Anolis lizards have high numbers of TEs in their Hox clusters, genomic regions that regulate development of the morphological adaptations that characterize habitat specialists in these lizards. Following a burst of TE activity in the lineage leading to extant Anolis, TEs have continued to accumulate during or after speciation events, resulting in a positive relationship between TE density and lineage speciation rate. These results are consistent with the prediction that TE activity contributes to adaptive radiation by promoting speciation. Although there was no evidence that TE density per se is associated with ecological morphology, the activity of TEs in Hox clusters could have been a rich source for phenotypic variation that may have facilitated the rapid parallel morphological adaptation to microhabitats seen in extant Anolis lizards.
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Affiliation(s)
- Nathalie Feiner
- Department of Biology, Lund University, Sölvegatan 37, 223 62 Lund, Sweden Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
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15
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Inferring responses to climate dynamics from historical demography in neotropical forest lizards. Proc Natl Acad Sci U S A 2017; 113:7978-85. [PMID: 27432951 DOI: 10.1073/pnas.1601063113] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future.
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16
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de la Harpe M, Paris M, Karger DN, Rolland J, Kessler M, Salamin N, Lexer C. Molecular ecology studies of species radiations: current research gaps, opportunities and challenges. Mol Ecol 2017; 26:2608-2622. [PMID: 28316112 DOI: 10.1111/mec.14110] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 02/11/2017] [Accepted: 03/06/2017] [Indexed: 12/28/2022]
Abstract
Understanding the drivers and limits of species radiations is a crucial goal of evolutionary genetics and molecular ecology, yet research on this topic has been hampered by the notorious difficulty of connecting micro- and macroevolutionary approaches to studying the drivers of diversification. To chart the current research gaps, opportunities and challenges of molecular ecology approaches to studying radiations, we examine the literature in the journal Molecular Ecology and revisit recent high-profile examples of evolutionary genomic research on radiations. We find that available studies of radiations are highly unevenly distributed among taxa, with many ecologically important and species-rich organismal groups remaining severely understudied, including arthropods, plants and fungi. Most studies employed molecular methods suitable over either short or long evolutionary time scales, such as microsatellites or restriction site-associated DNA sequencing (RAD-seq) in the former case and conventional amplicon sequencing of organellar DNA in the latter. The potential of molecular ecology studies to address and resolve patterns and processes around the species level in radiating groups of taxa is currently limited primarily by sample size and a dearth of information on radiating nuclear genomes as opposed to organellar ones. Based on our literature survey and personal experience, we suggest possible ways forward in the coming years. We touch on the potential and current limitations of whole-genome sequencing (WGS) in studies of radiations. We suggest that WGS and targeted ('capture') resequencing emerge as the methods of choice for scaling up the sampling of populations, species and genomes, including currently understudied organismal groups and the genes or regulatory elements expected to matter most to species radiations.
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Affiliation(s)
- Marylaure de la Harpe
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
| | - Margot Paris
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland
| | - Dirk N Karger
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Jonathan Rolland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Michael Kessler
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, Zürich, CH-8008, Switzerland
| | - Nicolas Salamin
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, CH-1015, Switzerland.,Swiss Institute of Bioinformatics, Quartier Sorge, Lausanne, CH-1015, Switzerland
| | - Christian Lexer
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg, CH-1700, Switzerland.,Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, Vienna, A-1030, Austria
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17
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Yang M, He Z, Shi S, Wu CI. Can genomic data alone tell us whether speciation happened with gene flow? Mol Ecol 2017; 26:2845-2849. [PMID: 28345182 DOI: 10.1111/mec.14117] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/08/2017] [Accepted: 03/20/2017] [Indexed: 01/02/2023]
Abstract
The allopatric model, which requires a period of geographical isolation for speciation to complete, has been the standard model in the modern era. Recently, "speciation with gene flow" has been widely discussed in relation to the model of "strict allopatry" and the level of DNA divergence across genomic regions. We wish to caution that genomic data by themselves may only permit the rejection of the simplest form of allopatry. Even a slightly more complex and realistic model that starts with subdivided populations would be impossible to reject by the genomic data alone. To resolve this central issue of speciation, other forms of observations such as the sequencing of reproductive isolation genes or the identification of geographical barrier(s) will be necessary.
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Affiliation(s)
- Ming Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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18
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Ng J, Ossip-Klein AG, Glor RE. Adaptive signal coloration maintained in the face of gene flow in a Hispaniolan Anolis Lizard. BMC Evol Biol 2016; 16:193. [PMID: 27650469 PMCID: PMC5029017 DOI: 10.1186/s12862-016-0763-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 09/07/2016] [Indexed: 11/17/2022] Open
Abstract
Background Studies of geographic variation can provide insight into the evolutionary processes involved in the early stages of biological diversification. In particular, multiple, replicated cases of geographic trait divergence present a powerful approach to study how patterns of introgression and adaptive divergence can vary with geographic space and time. In this study, we conduct replicated, fine-scaled molecular genetic analyses of striking geographic dewlap color variation of a Hispaniolan Anolis lizard, Anolis distichus, to investigate whether adaptive trait divergence is consistently associated with speciation, whereby genetic divergence is observed with neutral markers, or whether locally adapted traits are maintained in the face of continued gene flow. Results We find instances where shifts in adaptive dewlap coloration across short geographic distances are associated with reproductive isolation as well as maintained in the face of gene flow, suggesting the importance of both processes in maintaining geographic dewlap variation. Conclusion Our study suggests that adaptive dewlap color differences are maintained under strong divergent natural selection, but this divergence does not necessarily lead to anole speciation. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0763-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
| | | | - Richard E Glor
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, 66045, USA
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19
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Prates I, Rivera D, Rodrigues MT, Carnaval AC. A mid‐
P
leistocene rainforest corridor enabled synchronous invasions of the
A
tlantic
F
orest by
A
mazonian anole lizards. Mol Ecol 2016; 25:5174-5186. [DOI: 10.1111/mec.13821] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 08/10/2016] [Accepted: 08/22/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Ivan Prates
- Department of Biology City College of New York 160 Convent Avenue Marshak Science Building, Room J‐526 New York NY 10031 USA
- Department of Biology Graduate Center City University of New York 365 Fifth Avenue, Room 4315 New York NY 10016 USA
| | - Danielle Rivera
- Department of Biology City College of New York 160 Convent Avenue Marshak Science Building, Room J‐526 New York NY 10031 USA
- Department of Biology University of Texas at Arlington 501 S. Nedderman Drive Arlington TX 76019 USA
| | - Miguel T. Rodrigues
- Departamento de Zoologia Instituto de Biociências Universidade de São Paulo Rua do Matão Travessa 14, n. 321 São Paulo SP 05508‐090 Brazil
| | - Ana C. Carnaval
- Department of Biology City College of New York 160 Convent Avenue Marshak Science Building, Room J‐526 New York NY 10031 USA
- Department of Biology Graduate Center City University of New York 365 Fifth Avenue, Room 4315 New York NY 10016 USA
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20
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Shaffer HB, Gidiş M, McCartney-Melstad E, Neal KM, Oyamaguchi HM, Tellez M, Toffelmier EM. Conservation genetics and genomics of amphibians and reptiles. Annu Rev Anim Biosci 2015; 3:113-38. [PMID: 25580719 DOI: 10.1146/annurev-animal-022114-110920] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.
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21
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Li LF, Wang HY, Pang D, Liu Y, Liu B, Xiao HX. Phenotypic and genetic evidence for ecological speciation of Aquilegia japonica and A. oxysepala. THE NEW PHYTOLOGIST 2014; 204:1028-1040. [PMID: 25117915 DOI: 10.1111/nph.12967] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
Natural selection is thought to be a driving force that can cause the evolution of reproductive isolation. The genus Aquilegia is a model system to address how natural selection promotes the process of speciation. Morphological differences between A. oxysepala, A. japonica and their hybrids were quantified for two vegetative (plant height and leaf area) and three floral morphological (sepal area, corolla length and diameter) traits. We also evaluated the genetic variability of the two species and their hybrids based on two chloroplast (1225 bp), four nuclear (5811 bp) genes and 15 microsatellites. Our results revealed that differentiation of A. japonica and A. oxysepala at the ecological and morphological levels also involved divergence at the genetic level. In addition, the analysis of nucleotide variation patterns showed that the two species possessed numerous fixation sites at nuclear genes gAA4, gA7 and gAA12. Furthermore, we found that all of the phenotypic hybrids also showed a genetically admixed ancestry. These findings suggest that natural selection has indeed facilitated the formation of distinct genetic variation patterns in the two Aquilegia species and habitat adaptation has been driving the ecologically based evolution of reproductive isolation.
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Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
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22
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Dalrymple RL, Hui FKC, Flores-Moreno H, Kemp DJ, Moles AT. Roses are red, violets are blue - so how much replication should you do? An assessment of variation in the colour of flowers and birds. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12402] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Rhiannon L. Dalrymple
- Evolution and Ecology Research Centre; School of Biological, Earth and Environmental Sciences; The University of New South Wales; Sydney NSW 2052 Australia
| | - Francis K. C. Hui
- Evolution and Ecology Research Centre; School of Biological, Earth and Environmental Sciences; The University of New South Wales; Sydney NSW 2052 Australia
- School of Mathematics and Statistics; University of New South Wales; Sydney NSW 2052 Australia
| | - Habacuc Flores-Moreno
- Evolution and Ecology Research Centre; School of Biological, Earth and Environmental Sciences; The University of New South Wales; Sydney NSW 2052 Australia
| | - Darrell J. Kemp
- Department of Biological Sciences; Macquarie University; Sydney NSW 2109 Australia
| | - Angela T. Moles
- Evolution and Ecology Research Centre; School of Biological, Earth and Environmental Sciences; The University of New South Wales; Sydney NSW 2052 Australia
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23
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Prates I, Rodrigues MT, Melo-Sampaio PR, Carnaval AC. Phylogenetic relationships of Amazonian anole lizards (Dactyloa): taxonomic implications, new insights about phenotypic evolution and the timing of diversification. Mol Phylogenet Evol 2014; 82 Pt A:258-68. [PMID: 25451806 DOI: 10.1016/j.ympev.2014.10.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/24/2014] [Accepted: 10/02/2014] [Indexed: 12/15/2022]
Abstract
The ecology and evolution of Caribbean anoles are well described, yet little is known about mainland anole species. Lack of phylogenetic information limits our knowledge about species boundaries, morphological evolution, and the biogeography of anoles in South America. To help fill this gap, we provide an updated molecular phylogeny of the Dactyloa (Dactyloidae), with emphasis on the punctata species group. By sampling understudied Amazonian taxa, we (i) assess the phylogenetic placement of the 'odd anole', D. dissimilis; (ii) infer the relationships of the proboscis-bearing D. phyllorhina, testing the hypothesis of independent nasal appendage evolution within the anole radiation; and (iii) examine genetic and dewlap color variation in D. punctata and D. philopunctata. Combining multiple nuclear loci with a review of the fossil record, we also (iv) estimate divergence times within the pleurodont iguanian clade of lizards, including Amazonian representatives of Dactyloa and Norops (Dactyloidae) and of Polychrus (Polychrotidae). We recover the five Dactyloa clades previously referred to as the aequatorialis, heteroderma, latifrons, punctata and roquet species groups, as well as a sixth clade composed of D. dissimilis and the non-Amazonian D. neblinina and D. calimae. We find D. phyllorhina to be nested within the punctata group, suggesting independent evolution of the anole proboscis. We consistently recover D. philopunctata nested within D. punctata, and report limited genetic divergence between distinct dewlap phenotypes. The most recent common ancestor of Dactyloa, Anolis and Norops dates back to the Eocene. Most Amazonian taxa within both Dactyloa and Norops diverged in the Miocene, but some diversification events were as old as the late Eocene and late Oligocene. Amazonian Polychrus diverged in the Pliocene. Our findings have broad implications for anole biogeography, disputing recent suggestions that modern dactyloid genera were present in the Caribbean region during the Cretaceous.
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Affiliation(s)
- Ivan Prates
- Department of Biology, City College of New York, New York, NY, USA; Graduate Center, City University of New York, New York, NY, USA.
| | - Miguel Trefaut Rodrigues
- Departamento de Zoologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Paulo Roberto Melo-Sampaio
- Programa de Pós-graduação em Ecologia e Manejo de Recursos Naturais and Laboratório de Herpetologia, Universidade Federal do Acre, Rio Branco, AC, Brazil; União Educacional do Norte, Rio Branco, AC, Brazil.
| | - Ana Carolina Carnaval
- Department of Biology, City College of New York, New York, NY, USA; Graduate Center, City University of New York, New York, NY, USA.
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24
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Cruickshank TE, Hahn MW. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol 2014; 23:3133-57. [DOI: 10.1111/mec.12796] [Citation(s) in RCA: 764] [Impact Index Per Article: 76.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/05/2014] [Accepted: 05/07/2014] [Indexed: 12/18/2022]
Affiliation(s)
| | - Matthew W. Hahn
- Department of Biology; Indiana University; Bloomington IN 47405 USA
- School of Informatics and Computing; Indiana University; Bloomington IN 47405 USA
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25
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Odendaal LJ, Jacobs DS, Bishop JM. Sensory trait variation in an echolocating bat suggests roles for both selection and plasticity. BMC Evol Biol 2014; 14:60. [PMID: 24674227 PMCID: PMC3986686 DOI: 10.1186/1471-2148-14-60] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 03/20/2014] [Indexed: 02/04/2023] Open
Abstract
Background Across heterogeneous environments selection and gene flow interact to influence the rate and extent of adaptive trait evolution. This complex relationship is further influenced by the rarely considered role of phenotypic plasticity in the evolution of adaptive population variation. Plasticity can be adaptive if it promotes colonization and survival in novel environments and in doing so may increase the potential for future population differentiation via selection. Gene flow between selectively divergent environments may favour the evolution of phenotypic plasticity or conversely, plasticity itself may promote gene flow, leading to a pattern of trait differentiation in the presence of gene flow. Variation in sensory traits is particularly informative in testing the role of environment in trait and population differentiation. Here we test the hypothesis of ‘adaptive differentiation with minimal gene flow’ in resting echolocation frequencies (RF) of Cape horseshoe bats (Rhinolophus capensis) across a gradient of increasingly cluttered habitats. Results Our analysis reveals a geographically structured pattern of increasing RF from open to highly cluttered habitats in R. capensis; however genetic drift appears to be a minor player in the processes influencing this pattern. Although Bayesian analysis of population structure uncovered a number of spatially defined mitochondrial groups and coalescent methods revealed regional-scale gene flow, phylogenetic analysis of mitochondrial sequences did not correlate with RF differentiation. Instead, habitat discontinuities between biomes, and not genetic and geographic distances, best explained echolocation variation in this species. We argue that both selection for increased detection distance in relatively less cluttered habitats and adaptive phenotypic plasticity may have influenced the evolution of matched echolocation frequencies and habitats across different populations. Conclusions Our study reveals significant sensory trait differentiation in the presence of historical gene flow and suggests roles for both selection and plasticity in the evolution of echolocation variation in R. capensis. These results highlight the importance of population level analyses to i) illuminate the subtle interplay between selection, plasticity and gene flow in the evolution of adaptive traits and ii) demonstrate that evolutionary processes may act simultaneously and that their relative influence may vary across different environments.
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Affiliation(s)
- Lizelle J Odendaal
- Department of Biological Sciences, University of Cape Town, 7701 Cape Town, South Africa.
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