1
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Vangestel C, Swaegers J, De Corte Z, Dekoninck W, Gharbi K, Gillespie R, Vandekerckhove M, Van Belleghem SM, Hendrickx F. Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles. SCIENCE ADVANCES 2024; 10:eadk7906. [PMID: 38820159 PMCID: PMC11141621 DOI: 10.1126/sciadv.adk7906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/30/2024] [Indexed: 06/02/2024]
Abstract
Island faunas exhibit some of the most iconic examples where similar forms repeatedly evolve within different islands. Yet, whether these deterministic evolutionary trajectories within islands are driven by an initial, singular divergence and the subsequent exchange of individuals and adaptive genetic variation between islands remains unclear. Here, we study a gradual, repeated evolution of low-dispersive highland ecotypes from a dispersive lowland ecotype of Calosoma beetles along the island progression of the Galápagos. We show that repeated highland adaptation involved selection on multiple shared alleles within extensive chromosomal inversions that originated from an initial adaptation event on the oldest island. These highland inversions first spread through dispersal of highland individuals. Subsequent admixture with the lowland ecotype resulted in polymorphic dispersive populations from which the highland populations evolved on the youngest islands. Our findings emphasize the significance of an ancient divergence in driving repeated evolution and highlight how a mixed contribution of inter-island colonization and within-island evolution can shape parallel species communities.
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Affiliation(s)
- Carl Vangestel
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | - Janne Swaegers
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Ecology, Evolution and Conservation Biology, Biology Department, University of Leuven, Leuven, Belgium
| | - Zoë De Corte
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | | | - Karim Gharbi
- Earlham Institute, Norwich Research Park, Norfolk, United Kingdom
| | - Rosemary Gillespie
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Matthias Vandekerckhove
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
| | - Steven M. Van Belleghem
- Ecology, Evolution and Conservation Biology, Biology Department, University of Leuven, Leuven, Belgium
| | - Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Terrestrial Ecology Unit, Biology Department, Ghent University, Gent, Belgium
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2
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Garrick RC. Genetic signatures of lineage fusion closely resemble population decline. Ecol Evol 2023; 13:e10725. [PMID: 37964788 PMCID: PMC10641302 DOI: 10.1002/ece3.10725] [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: 09/14/2023] [Revised: 10/24/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline-high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (F S and Z nS), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.
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Affiliation(s)
- Ryan C. Garrick
- Department of BiologyUniversity of MississippiOxfordMississippiUSA
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3
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Tozzi A. Non-ultrametric phylogenetic trees shed new light on Neanderthal introgression. ORG DIVERS EVOL 2023:1-9. [PMID: 37359819 PMCID: PMC10256575 DOI: 10.1007/s13127-023-00613-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: 05/06/2022] [Accepted: 04/28/2023] [Indexed: 06/28/2023]
Abstract
Ultrametric spaces are widely used to depict evolutionary times in phylogenetic trees since they assume that every population/species is located at the tips of bifurcating branches of the same length. The discrete branching of ultrametric trees permits the measurement of distances between pairs of individuals that are proportional to their divergence time. Here the traditional ultrametric concept of bifurcating and divergent phylogenetic tree is overturned and a new type of non-ultrametric diagram is introduced. The objective of this study is the description of gene flows in branching species/populations in terms of converging trees instead of bifurcating trees. To provide an operational example, the paleoanthropological issue of the date of Neanderthal genome's introgression in non-African humans is examined. Neanderthals and ancient humans are not anymore two species that exchange chunks of DNA, rather become a single, novel cluster of extant hominins that must be considered by itself. The novel converging, non-ultrametric phylogenetic trees permit the calibration of molecular clocks with a twofold benefit. When the date of the branching of two population/species from a common ancestor is known, the novel approach allows to calculate the time of subsequent introgressions. On the contrary, when the date of the introgression between two population/species is known, the novel approach allows to detect the time of their previous branching from a common ancestor.
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Affiliation(s)
- Arturo Tozzi
- Center for Nonlinear Science, Department of Physics, University of North Texas, 1155 Union Circle, Denton, TX #31142776203-5017 USA
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4
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Cerca J, Cotoras DD, Bieker VC, De-Kayne R, Vargas P, Fernández-Mazuecos M, López-Delgado J, White O, Stervander M, Geneva AJ, Guevara Andino JE, Meier JI, Roeble L, Brée B, Patiño J, Guayasamin JM, Torres MDL, Valdebenito H, Castañeda MDR, Chaves JA, Díaz PJ, Valente L, Knope ML, Price JP, Rieseberg LH, Baldwin BG, Emerson BC, Rivas-Torres G, Gillespie R, Martin MD. Evolutionary genomics of oceanic island radiations. Trends Ecol Evol 2023:S0169-5347(23)00032-0. [PMID: 36870806 DOI: 10.1016/j.tree.2023.02.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 01/26/2023] [Accepted: 02/02/2023] [Indexed: 03/06/2023]
Abstract
A recurring feature of oceanic archipelagos is the presence of adaptive radiations that generate endemic, species-rich clades that can offer outstanding insight into the links between ecology and evolution. Recent developments in evolutionary genomics have contributed towards solving long-standing questions at this interface. Using a comprehensive literature search, we identify studies spanning 19 oceanic archipelagos and 110 putative adaptive radiations, but find that most of these radiations have not yet been investigated from an evolutionary genomics perspective. Our review reveals different gaps in knowledge related to the lack of implementation of genomic approaches, as well as undersampled taxonomic and geographic areas. Filling those gaps with the required data will help to deepen our understanding of adaptation, speciation, and other evolutionary processes.
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Affiliation(s)
- José Cerca
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
| | - Darko D Cotoras
- Department of Terrestrial Zoology, Senckenberg Research Institute and Natural History Museum, Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Department of Entomology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA
| | - Vanessa C Bieker
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Rishi De-Kayne
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Pablo Vargas
- Biodiversity and Conservation, Real Jardín Botánico, 28014 Madrid, Spain
| | - Mario Fernández-Mazuecos
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, Calle Darwin 2, 28049 Madrid, Spain; Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid (CIBC-UAM), Calle Darwin 2, 28049 Madrid, Spain
| | - Julia López-Delgado
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Oliver White
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Martin Stervander
- Bird Group, Natural History Museum, Akeman Street, Tring, Hertfordshire HP23 6AP, UK
| | - Anthony J Geneva
- Department of Biology and Center for Computational and Integrative Biology, Rutgers University-Camden, Camden, NJ, USA
| | - Juan Ernesto Guevara Andino
- Grupo de Investigación en Biodiversidad Medio Ambiente y Salud (BIOMAS), Universidad de las Américas, Quito, Ecuador
| | - Joana Isabel Meier
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Lizzie Roeble
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700, 5 CC Groningen, The Netherlands
| | - Baptiste Brée
- Université de Pau et des Pays de l'Adour (UPPA), Energy Environment Solutions (E2S), Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Analytiques et de Physico-Chimie pour l'Environnement et les Matériaux (IPREM), 64000 Pau, France
| | - Jairo Patiño
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), Calle Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Juan M Guayasamin
- Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, 170901 Quito, Ecuador; Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador
| | - María de Lourdes Torres
- Laboratorio de Biotecnología Vegetal, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, Quito, Ecuador; Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador
| | - Hugo Valdebenito
- Galapagos Science Center, Universidad San Francisco de Quito (USFQ) and University of North Carolina (UNC) at Chapel Hill, San Cristobal, Galapagos, Ecuador; Herbarium of Economic Botany of Ecuador (Herabario QUSF), Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, Quito, Ecuador
| | | | - Jaime A Chaves
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA; Laboratorio de Biología Evolutiva, Instituto Biósfera, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Calle Diego de Robles y Avenida Pampite, Cumbayá, 170901 Quito, Ecuador
| | - Patricia Jaramillo Díaz
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador; Department of Botany and Plant Physiology, University of Málaga, Málaga, Spain
| | - Luis Valente
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Groningen Institute for Evolutionary Life Sciences, University of Groningen, Box 11103, 9700, 5 CC Groningen, The Netherlands
| | - Matthew L Knope
- Department of Biology, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, 96720, HI, USA
| | - Jonathan P Price
- Department of Biology, University of Hawai'i at Hilo, 200 West Kawili Street, Hilo, 96720, HI, USA
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Bruce G Baldwin
- Jepson Herbarium and Department of Integrative Biology, 1001 Valley Life Sciences Building 2465, University of California, Berkeley, CA 94720-2465, USA
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna, Spain
| | - Gonzalo Rivas-Torres
- Estación Científica Charles Darwin, Fundación Charles Darwin, Santa Cruz, Galápagos, Ecuador; Estación de Biodiversidad Tiputini, Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Rosemary Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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5
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Jensen EL, Quinzin MC, Miller JM, Russello MA, Garrick RC, Edwards DL, Glaberman S, Chiari Y, Poulakakis N, Tapia W, Gibbs JP, Caccone A. A new lineage of Galapagos giant tortoises identified from museum samples. Heredity (Edinb) 2022; 128:261-270. [PMID: 35217806 PMCID: PMC8987048 DOI: 10.1038/s41437-022-00510-8] [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: 11/10/2020] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
The Galapagos Archipelago is recognized as a natural laboratory for studying evolutionary processes. San Cristóbal was one of the first islands colonized by tortoises, which radiated from there across the archipelago to inhabit 10 islands. Here, we sequenced the mitochondrial control region from six historical giant tortoises from San Cristóbal (five long deceased individuals found in a cave and one found alive during an expedition in 1906) and discovered that the five from the cave are from a clade that is distinct among known Galapagos giant tortoises but closely related to the species from Española and Pinta Islands. The haplotype of the individual collected alive in 1906 is in the same clade as the haplotype in the contemporary population. To search for traces of a second lineage in the contemporary population on San Cristóbal, we closely examined the population by sequencing the mitochondrial control region for 129 individuals and genotyping 70 of these for both 21 microsatellite loci and >12,000 genome-wide single nucleotide polymorphisms [SNPs]. Only a single mitochondrial haplotype was found, with no evidence to suggest substructure based on the nuclear markers. Given the geographic and temporal proximity of the two deeply divergent mitochondrial lineages in the historical samples, they were likely sympatric, raising the possibility that the lineages coexisted. Without the museum samples, this important discovery of an additional lineage of Galapagos giant tortoise would not have been possible, underscoring the value of such collections and providing insights into the early evolution of this iconic radiation.
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Affiliation(s)
- Evelyn L Jensen
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA. .,School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK.
| | - Maud C Quinzin
- MIT Media Lab, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joshua M Miller
- Department of Biological Sciences, MacEwan University, Edmonton, AB, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Kelowna, BC, Canada
| | - Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, MS, 38677, USA
| | - Danielle L Edwards
- Department of Life & Environmental Sciences, University of California, Merced, CA, USA
| | - Scott Glaberman
- Department of Environmental Science and Policy, George Mason University, Fairfax, VA, USA
| | - Ylenia Chiari
- Department of Biology, George Mason University, Fairfax, VA, USA
| | - Nikos Poulakakis
- Department of Biology, School of Sciences and Engineering, University of Crete, Irakleio, Greece.,The Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Irakleio, Greece
| | - Washington Tapia
- Galapagos Conservancy, 11150 Fairfax Boulevard #408, Fairfax, VA, 22030, USA.,University of Málaga, Campus Teatinos, Apdo. 59, 29080, Málaga, Spain
| | - James P Gibbs
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, USA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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6
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Jensen EL, Gaughran SJ, Garrick RC, Russello MA, Caccone A. Demographic history and patterns of molecular evolution from whole genome sequencing in the radiation of Galapagos giant tortoises. Mol Ecol 2021; 30:6325-6339. [PMID: 34510620 DOI: 10.1111/mec.16176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 12/23/2022]
Abstract
Whole genome sequencing provides deep insights into the evolutionary history of a species, including patterns of diversity, signals of selection, and historical demography. When applied to closely related taxa with a wealth of background knowledge, population genomics provides a comparative context for interpreting population genetic summary statistics and comparing empirical results with the expectations of population genetic theory. The Galapagos giant tortoises (Chelonoidis spp.), an iconic rapid and recent radiation, offer such an opportunity. Here, we sequenced whole genomes from three individuals of the 12 extant lineages of Galapagos giant tortoise and estimate diversity measures and reconstruct changes in coalescent rate over time. We also compare the number of derived alleles in each lineage to infer how synonymous and nonsynonymous mutation accumulation rates correlate with population size and life history traits. Remarkably, we find that patterns of molecular evolution are similar within individuals of the same lineage, but can differ significantly among lineages, reinforcing the evolutionary distinctiveness of the Galapagos giant tortoise species. Notably, differences in mutation accumulation among lineages do not align with simple population genetic predictions, suggesting that the drivers of purifying selection are more complex than is currently appreciated. By integrating results from earlier population genetic and phylogeographic studies with new findings from the analysis of whole genomes, we provide the most in-depth insights to date on the evolution of Galapagos giant tortoises, and identify discrepancies between expectation from population genetic theory and empirical data that warrant further scrutiny.
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Affiliation(s)
- Evelyn L Jensen
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Stephen J Gaughran
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, Mississippi, USA
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, British Columbia, Canada
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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7
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Abstract
Many species of plants, animals, and microorganisms exchange genes well after the point of evolutionary divergence at which taxonomists recognize them as species. Genomes contain signatures of past gene exchange and, in some cases, they reveal a legacy of lineages that no longer exist. But genomic data are not available for many organisms, and particularly problematic for reconstructing and interpreting evolutionary history are communities that have been depleted by extinctions. For these, morphology may substitute for genes, as exemplified by the history of Darwin's finches on the Galápagos islands of Floreana and San Cristóbal. Darwin and companions collected seven specimens of a uniquely large form of Geospiza magnirostris in 1835. The populations became extinct in the next few decades, partly due to destruction of Opuntia cactus by introduced goats, whereas Geospiza fortis has persisted to the present. We used measurements of large samples of G. fortis collected for museums in the period 1891 to 1906 to test for unusually large variances and skewed distributions of beak and body size resulting from introgression. We found strong evidence of hybridization on Floreana but not on San Cristóbal. The skew is in the direction of the absent G. magnirostris We estimate introgression influenced 6% of the frequency distribution that was eroded by selection after G. magnirostris became extinct on these islands. The genetic residuum of an extinct species in an extant one has implications for its future evolution, as well as for a conservation program of reintroductions in extinction-depleted communities.
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8
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Dass K, Lewbart GA, Muñoz-Pérez JP, Yépez MI, Loyola A, Chen E, Páez-Rosas D. Whole blood fatty acid concentrations in the San Cristóbal Galápagos tortoise (Chelonoidis chathamensis). PeerJ 2021; 9:e11582. [PMID: 34249492 PMCID: PMC8254470 DOI: 10.7717/peerj.11582] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 05/19/2021] [Indexed: 11/24/2022] Open
Abstract
To continue releasing San Cristóbal Galápagos tortoises housed in managed-care facilities at the Giant Tortoise Breeding Center of Galápagos National Park (Galapaguera de Cerro Colorado) to the Otoy Ecological Farm, health assessments and physical examinations were conducted. As a part of these wellness examinations, blood was drawn from 11 tortoises to analyze fatty acid concentrations. Fatty acid levels can provide insight into the nutritional profiles, immune status, and reproductive health of vertebrates. To the co-author's knowledge, there is no current information about fatty acids in this species. It was hypothesized that there would be inherent differences based on the different geographic ranges, diets, sex, and age of turtles. It was noted that the ω-6/ω-3 ratio was higher for the breeding center than for the ecological farm and that overall polyunsaturated fatty acids (PUFAs) did not have any significant differences. The ω-6/ω-3 findings can contribute to a global picture of these fatty acids across taxa, as reptiles are underrepresented in this area of research. Additional results are a resourceful starting point for future investigations into how fatty acids are affected in Galápagos tortoises.
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Affiliation(s)
- Khushboo Dass
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States of America
| | - Gregory A. Lewbart
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States of America
| | - Juan Pablo Muñoz-Pérez
- Faculty of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
- USFQ & UNC-Chapel Hill Galápagos Science Center (GSC), Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Andrea Loyola
- Direcion Parque Nacional Galápagos, Islas Galápagos, Ecuador
| | - Emile Chen
- 9 Oneida Court, Chester Springs, PA, United States of America
| | - Diego Páez-Rosas
- USFQ & UNC-Chapel Hill Galápagos Science Center (GSC), Universidad San Francisco de Quito, Quito, Ecuador
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9
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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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10
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Milot E, Béchet A, Maris V. The dimensions of evolutionary potential in biological conservation. Evol Appl 2020; 13:1363-1379. [PMID: 32684964 PMCID: PMC7359841 DOI: 10.1111/eva.12995] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 04/13/2020] [Accepted: 04/17/2020] [Indexed: 01/05/2023] Open
Abstract
It is now well admitted by ecologists that the conservation of biodiversity should imply preserving the evolutionary processes that will permit its adaptation to ongoing and future environmental changes. This is attested by the ever-growing reference to the conservation of evolutionary potential in the scientific literature. The impression that one may have when reading papers is that conserving evolutionary potential can only be a good thing, whatever biological system is under scrutiny. However, different objectives, such as maintaining species richness versus ecosystem services, may express different, when not conflicting, underlying values attributed to biodiversity. For instance, biodiversity can be intrinsically valued, as worth it to be conserved per se, or it can be conserved as a means for human flourishing. Consequently, both the concept of evolutionary potential and the prescriptions derived from the commitment to conserve it remain problematic, due to a lack of explicit mention of the norms underlying different conservation visions. Here, we contend that those who advocate for the conservation of evolutionary potential should position their conception along four dimensions: what vehicles instantiate the evolutionary potential relevant to their normative commitment; what temporality is involved; how measurable evolutionary potential is, and what degree of human influence is tolerated. We need to address these dimensions if we are to determine why and when the maintenance of evolutionary potential is an appropriate target for the conservation of biodiversity.
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Affiliation(s)
- Emmanuel Milot
- Department of Chemistry, Biochemistry and Physics Université du Québec à Trois-Rivières Trois-Rivières Québec Canada
| | - Arnaud Béchet
- Tour du Valat Research Institute for the Conservation of Mediterranean Wetlands Arles France
| | - Virginie Maris
- Centre d'écologie fonctionnelle et évolutive, CNRS, EPHE, IRD Univ Montpellier Univ Paul Valéry Montpellier 3 Montpellier France
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11
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Friis G, Milá B. Change in sexual signalling traits outruns morphological divergence across an ecological gradient in the post-glacial radiation of the songbird genus Junco. J Evol Biol 2020; 33:1276-1293. [PMID: 32603490 DOI: 10.1111/jeb.13671] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 12/30/2022]
Abstract
The relative roles of natural and sexual selection in promoting evolutionary lineage divergence remains controversial and difficult to assess in natural systems. Local adaptation through natural selection is known to play a central role in promoting evolutionary divergence, yet secondary sexual traits can vary widely among species in recent radiations, suggesting that sexual selection may also be important in the early stages of speciation. Here, we compare rates of divergence in ecologically relevant traits (morphology) and sexually selected signalling traits (coloration) relative to neutral structure in genome-wide molecular markers and examine patterns of variation in sexual dichromatism to explore the roles of natural and sexual selection in the diversification of the songbird genus Junco (Aves: Passerellidae). Juncos include divergent lineages in Central America and several dark-eyed junco (J. hyemalis) lineages that diversified recently as the group recolonized North America following the last glacial maximum (ca. 18,000 years ago). We found an accelerated rate of divergence in sexually selected characters relative to ecologically relevant traits. Moreover, sexual dichromatism measurements suggested a positive relationship between the degree of colour divergence and the strength of sexual selection when controlling for neutral genetic distance. We also found a positive correlation between dichromatism and latitude, which coincides with the geographic axis of decreasing lineage age in juncos but also with a steep ecological gradient. Finally, we found significant associations between genome-wide variants linked to functional genes and proxies of both sexual and natural selection. These results suggest that the joint effects of sexual and ecological selection have played a prominent role in the junco radiation.
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Affiliation(s)
- Guillermo Friis
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Borja Milá
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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12
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Wogan GOU, Voelker G, Oatley G, Bowie RCK. Biome stability predicts population structure of a southern African aridland bird species. Ecol Evol 2020; 10:4066-4081. [PMID: 32489631 PMCID: PMC7244808 DOI: 10.1002/ece3.6175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 11/07/2022] Open
Abstract
Environments are heterogeneous in space and time, and the permeability of landscape and climatic barriers to gene flow may change over time. When barriers are present, they may start populations down the path toward speciation, but if they become permeable before the process of speciation is complete, populations may once more merge. In Southern Africa, aridland biomes play a central role in structuring the organization of biodiversity. These biomes were subject to substantial restructuring during Plio-Pleistocene climatic fluctuations, and the imprint of this changing environment should leave genetic signatures on the species living there. Here, we investigate the role of adjacent aridland biome boundaries in structuring the genetic diversity within a widespread generalist bird, the Cape Robin-chat (Cossypha caffra). We find evidence supporting a central role for aridland biomes in structuring populations across Southern Africa. Our findings support a scenario wherein populations were isolated in different biome refugia, due to separation by the exceptionally arid Nama Karoo biome. This biome barrier may have arisen through a combination of habitat instability and environmental unsuitability, and was highly unstable throughout the Plio-Pleistocene. However, we also recovered a pattern of extensive contemporary gene flow and admixture across the Nama Karoo, potentially driven by the establishment of homesteads over the past 200 years. Thus, the barrier has become permeable, and populations are currently merging. This represents an instance where initial formation of a barrier to gene flow enabled population differentiation, with subsequent gene flow and the merging of populations after the barrier became permeable.
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Affiliation(s)
- Guinevere O. U. Wogan
- Department of Integrative BiologyMuseum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCAUSA
| | - Gary Voelker
- Department of Wildlife and Fisheries SciencesBiodiversity Research and Teaching CollectionsTexas A&M UniversityCollege StationTXUSA
| | - Graeme Oatley
- Department of GeographyCollege of Life and Environmental SciencesUniversity of ExeterExeterUK
- DST/NRF Centre of Excellence at the Percy FitzPatrick InstituteUniversity of Cape TownRondeboschSouth Africa
| | - Rauri C. K. Bowie
- Department of Integrative BiologyMuseum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCAUSA
- DST/NRF Centre of Excellence at the Percy FitzPatrick InstituteUniversity of Cape TownRondeboschSouth Africa
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13
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Hedrick PW. Galapagos Islands Endemic Vertebrates: A Population Genetics Perspective. J Hered 2020; 110:137-157. [PMID: 30541084 DOI: 10.1093/jhered/esy066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 11/12/2022] Open
Abstract
The organisms of the Galapagos Islands played a central role in the development of the theory of evolution by Charles Darwin. Examination of the population genetics factors of many of these organisms with modern molecular methods has expanded our understanding of their evolution. Here, I provide a perspective on how selection, gene flow, genetic drift, mutation, and inbreeding have contributed to the evolution of 6 iconic Galapagos species: flightless cormorant, pink iguana, marine iguana, Galapagos hawk, giant tortoises, and Darwin's finches. Because of the inherent biological differences among these species that have colonized the Galapagos, different population genetic factors appear to be more or less important in these different species. For example, the Galapagos provided novel environments in which strong selection took place and the Darwin's finches diversified to produce new species and the cormorant adapted to the nutrient-rich western shores of the Galapagos by losing its ability to fly and genomic data have now identified candidate genes. In both the pink iguana, which exists in one small population, and the Galapagos hawk, which has small population sizes, genetic drift has been potentially quite important. There appears to be very limited interisland gene flow in the flightless cormorant and the Galapagos hawk. On the other hand, both the marine iguana and some of the Darwin's finches appear to have significant interisland gene flow. Hybridization between species and subspecies has also introduced new adaptive variation, and in some cases, hybridization might have resulted in despeciation. Overall, new population genetics and genomics research has provided additional insight into the evolution of vertebrate species in the Galapagos.
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14
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Reid K, Carlos Garza J, Gephard SR, Caccone A, Post DM, Palkovacs EP. Restoration-mediated secondary contact leads to introgression of alewife ecotypes separated by a colonial-era dam. Evol Appl 2020; 13:652-664. [PMID: 32211058 PMCID: PMC7086056 DOI: 10.1111/eva.12890] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/30/2019] [Accepted: 10/02/2019] [Indexed: 12/20/2022] Open
Abstract
Secondary contact may have important implications for ecological and evolutionary processes; however, few studies have tracked the outcomes of secondary contact from its onset in natural ecosystems. We evaluated an anadromous alewife (Alosa pseudoharengus ) reintroduction project in Rogers Lake (Connecticut, USA), which contains a landlocked alewife population that was isolated as a result of colonial-era damming. After access to the ocean was restored, adult anadromous alewife were stocked into the lake. We assessed anadromous juvenile production, the magnitude and direction of introgression, and the potential for competition between ecotypes. We obtained fin clips from all adult alewife stocked into the lake during the restoration and a sample of juveniles produced in the lake two years after the stocking began. We assessed the ancestry of juveniles using categorical assignment and pedigree reconstruction with newly developed microhaplotype genetic markers. Anadromous alewives successfully spawned in the lake and hybridized with the landlocked population. Parentage assignments revealed that male and female anadromous fish contributed equally to juvenile F1 hybrids. The presence of landlocked backcrosses shows that some hybrids were produced within the first two years of secondary contact, matured in the lake, and reproduced. Therefore, introgression appears directional, from anadromous into landlocked, in the lake environment. Differences in estimated abundance of juveniles of different ecotypes in different habitats were also detected, which may reduce competition between ecotypes as the restoration continues. Our results illustrate the utility of restoration projects to study the outcomes of secondary contact in real ecosystems.
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Affiliation(s)
- Kerry Reid
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCAUSA
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCAUSA
| | - John Carlos Garza
- Southwest Fisheries Science CenterNational Marine Fisheries ServiceSanta CruzCAUSA
- Department of Ocean SciencesUniversity of CaliforniaSanta CruzCAUSA
| | - Steven R. Gephard
- Fisheries DivisionConnecticut Department of Energy and Environmental ProtectionOld LymeCTUSA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - David M. Post
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Eric P. Palkovacs
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaSanta CruzCAUSA
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15
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Saarman NP, Opiro R, Hyseni C, Echodu R, Opiyo EA, Dion K, Johnson T, Aksoy S, Caccone A. The population genomics of multiple tsetse fly (Glossina fuscipes fuscipes) admixture zones in Uganda. Mol Ecol 2019; 28:66-85. [PMID: 30471158 DOI: 10.1111/mec.14957] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 10/26/2018] [Accepted: 11/05/2018] [Indexed: 11/28/2022]
Abstract
Understanding the mechanisms that enforce, maintain or reverse the process of speciation is an important challenge in evolutionary biology. This study investigates the patterns of divergence and discusses the processes that form and maintain divergent lineages of the tsetse fly Glossina fuscipes fuscipes in Uganda. We sampled 251 flies from 18 sites spanning known genetic lineages and the four admixture zones between them. We apply population genomics, hybrid zone and approximate Bayesian computation to the analysis of three types of genetic markers: 55,267 double-digest restriction site-associated DNA (ddRAD) SNPs to assess genome-wide admixture, 16 microsatellites to provide continuity with published data and accurate biogeographic modelling, and a 491-bp fragment of mitochondrial cytochrome oxidase I and II to infer maternal inheritance patterns. Admixture zones correspond with regions impacted by the reorganization of Uganda's river networks that occurred during the formation of the West African Rift system over the last several hundred thousand years. Because tsetse fly population distributions are defined by rivers, admixture zones likely represent both old and new regions of secondary contact. Our results indicate that older hybrid zones contain mostly parental types, while younger zones contain variable hybrid types resulting from multiple generations of interbreeding. These findings suggest that reproductive barriers are nearly complete in the older admixture zones, while nearly absent in the younger admixture zones. Findings are consistent with predictions of hybrid zone theory: Populations in zones of secondary contact transition rapidly from early to late stages of speciation or collapse all together.
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Affiliation(s)
- Norah P Saarman
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Robert Opiro
- Department of Biology, Faculty of Science, Gulu University, Uganda
| | - Chaz Hyseni
- Department of Biology, University of Mississippi, Oxford, Mississippi
| | - Richard Echodu
- Department of Biology, Faculty of Science, Gulu University, Uganda
| | | | - Kirstin Dion
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Thomas Johnson
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
| | - Serap Aksoy
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut
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16
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Maier PA, Vandergast AG, Ostoja SM, Aguilar A, Bohonak AJ. Pleistocene glacial cycles drove lineage diversification and fusion in the Yosemite toad (
Anaxyrus canorus
). Evolution 2019; 73:2476-2496. [DOI: 10.1111/evo.13868] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 09/18/2019] [Accepted: 10/14/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Paul A. Maier
- Department of BiologySan Diego State University 5500 Campanile Dr. San Diego CA 92182
- FamilyTreeDNA Gene by Gene, 1445 N Loop W Houston TX 77008
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research CenterSan Diego Field Station 4165 Spruance Road, Suite 200 San Diego CA 92101
| | - Steven M. Ostoja
- USDA California Climate Hub, Agricultural Research Service, John Muir Institute of the EnvironmentUniversity of California, Davis 1 Shields Ave. Davis CA 95616
| | - Andres Aguilar
- Department of Biological SciencesCalifornia State University, Los Angeles 5151 State University Dr Los Angeles CA 90032
| | - Andrew J. Bohonak
- Department of BiologySan Diego State University 5500 Campanile Dr. San Diego CA 92182
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17
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Miller JM, Quinzin MC, Edwards DL, Eaton DAR, Jensen EL, Russello MA, Gibbs JP, Tapia W, Rueda D, Caccone A. Genome-Wide Assessment of Diversity and Divergence Among Extant Galapagos Giant Tortoise Species. J Hered 2019; 109:611-619. [PMID: 29986032 DOI: 10.1093/jhered/esy031] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/04/2018] [Indexed: 12/19/2022] Open
Abstract
Genome-wide assessments allow for fuller characterization of genetic diversity, finer-scale population delineation, and better detection of demographically significant units to guide conservation compared with those based on "traditional" markers. Galapagos giant tortoises (Chelonoidis spp.) have long provided a case study for how evolutionary genetics may be applied to advance species conservation. Ongoing efforts to bolster tortoise populations, which have declined by 90%, have been informed by analyses of mitochondrial DNA sequence and microsatellite genotypic data, but could benefit from genome-wide markers. Taking this next step, we used double-digest restriction-site associated DNA sequencing to collect genotypic data at >26000 single nucleotide polymorphisms (SNPs) for 117 individuals representing all recognized extant Galapagos giant tortoise species. We then quantified genetic diversity, population structure, and compared results to estimates from mitochondrial DNA and microsatellite loci. Our analyses detected 12 genetic lineages concordant with the 11 named species as well as previously described structure within one species, C. becki. Furthermore, the SNPs provided increased resolution, detecting admixture in 4 individuals. SNP-based estimates of diversity and differentiation were significantly correlated with those derived from nuclear microsatellite loci and mitochondrial DNA sequences. The SNP toolkit presented here will serve as a resource for advancing efforts to understand tortoise evolution, species radiations, and aid conservation of the Galapagos tortoise species complex.
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Affiliation(s)
- Joshua M Miller
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Maud C Quinzin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Danielle L Edwards
- Life and Environmental Sciences, University of California, Merced, Merced, CA
| | - Deren A R Eaton
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT.,Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY
| | - Evelyn L Jensen
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC, Canada
| | - James P Gibbs
- College of Environmental Science & Forestry, State University of New York, Syracuse, NY
| | - Washington Tapia
- Galapagos Conservancy, Fairfax, VA.,Galápagos National Park Directorate, Puerto Ayora, Galápagos, Ecuador
| | - Danny Rueda
- Galápagos National Park Directorate, Puerto Ayora, Galápagos, Ecuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
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18
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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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19
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Widespread hybridization among native and invasive species of Operophtera moths (Lepidoptera: Geometridae) in Europe and North America. Biol Invasions 2019. [DOI: 10.1007/s10530-019-02054-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Hyseni C, Garrick RC. The role of glacial-interglacial climate change in shaping the genetic structure of eastern subterranean termites in the southern Appalachian Mountains, USA. Ecol Evol 2019; 9:4621-4636. [PMID: 31031931 PMCID: PMC6476779 DOI: 10.1002/ece3.5065] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/27/2019] [Accepted: 02/25/2019] [Indexed: 11/30/2022] Open
Abstract
The eastern subterranean termite, Reticulitermes flavipes, currently inhabits previously glaciated regions of the northeastern U.S., as well as the unglaciated southern Appalachian Mountains and surrounding areas. We hypothesized that Pleistocene climatic fluctuations have influenced the distribution of R. flavipes, and thus the evolutionary history of the species. We estimated contemporary and historical geographic distributions of R. flavipes by constructing Species Distribution Models (SDM). We also inferred the evolutionary and demographic history of the species using mitochondrial (cytochrome oxidase I and II) and nuclear (endo-beta-1,4-glucanase) DNA sequence data. To do this, genetic populations were delineated using Bayesian spatial-genetic clustering, competing hypotheses about population divergence were assessed using approximate Bayesian computation (ABC), and changes in population size were estimated using Bayesian skyline plots. SDMs identified areas in the north with suitable habitat during the transition from the Last Interglacial to the Last Glacial Maximum, as well as an expanding distribution from the mid-Holocene to the present. Genetic analyses identified three geographically cohesive populations, corresponding with northern, central, and southern portions of the study region. Based on ABC analyses, divergence between the Northern and Southern populations was the oldest, estimated to have occurred 64.80 thousand years ago (kya), which corresponds with the timing of available habitat in the north. The Central and Northern populations diverged in the mid-Holocene, 8.63 kya, after which the Central population continued to expand. Accordingly, phylogeographic patterns of R. flavipes in the southern Appalachians appear to have been strongly influenced by glacial-interglacial climate change. OPEN RESEARCH BADGES This article has been awarded Open Materials, Open Data Badges. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.5hr7f31.
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Affiliation(s)
- Chaz Hyseni
- Department of BiologyUniversity of MississippiOxfordMississippi
| | - Ryan C. Garrick
- Department of BiologyUniversity of MississippiOxfordMississippi
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21
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Gaughran SJ, Quinzin MC, Miller JM, Garrick RC, Edwards DL, Russello MA, Poulakakis N, Ciofi C, Beheregaray LB, Caccone A. Theory, practice, and conservation in the age of genomics: The Galápagos giant tortoise as a case study. Evol Appl 2018; 11:1084-1093. [PMID: 30026799 PMCID: PMC6050186 DOI: 10.1111/eva.12551] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/31/2017] [Indexed: 12/25/2022] Open
Abstract
High-throughput DNA sequencing allows efficient discovery of thousands of single nucleotide polymorphisms (SNPs) in nonmodel species. Population genetic theory predicts that this large number of independent markers should provide detailed insights into population structure, even when only a few individuals are sampled. Still, sampling design can have a strong impact on such inferences. Here, we use simulations and empirical SNP data to investigate the impacts of sampling design on estimating genetic differentiation among populations that represent three species of Galápagos giant tortoises (Chelonoidis spp.). Though microsatellite and mitochondrial DNA analyses have supported the distinctiveness of these species, a recent study called into question how well these markers matched with data from genomic SNPs, thereby questioning decades of studies in nonmodel organisms. Using >20,000 genomewide SNPs from 30 individuals from three Galápagos giant tortoise species, we find distinct structure that matches the relationships described by the traditional genetic markers. Furthermore, we confirm that accurate estimates of genetic differentiation in highly structured natural populations can be obtained using thousands of SNPs and 2-5 individuals, or hundreds of SNPs and 10 individuals, but only if the units of analysis are delineated in a way that is consistent with evolutionary history. We show that the lack of structure in the recent SNP-based study was likely due to unnatural grouping of individuals and erroneous genotype filtering. Our study demonstrates that genomic data enable patterns of genetic differentiation among populations to be elucidated even with few samples per population, and underscores the importance of sampling design. These results have specific implications for studies of population structure in endangered species and subsequent management decisions.
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Affiliation(s)
| | - Maud C. Quinzin
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Joshua M. Miller
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | | | | | - Michael A. Russello
- Department of BiologyUniversity of British Columbia, Okanagan CampusKelownaBCCanada
| | - Nikos Poulakakis
- Department of BiologySchool of Sciences and EngineeringUniversity of CreteHeraklion, CreteGreece
- Natural History Museum of CreteSchool of Sciences and EngineeringUniversity of CreteHeraklion, CreteGreece
| | - Claudio Ciofi
- Department of BiologyUniversity of FlorenceSesto Fiorentino (FI)Italy
| | - Luciano B. Beheregaray
- Molecular Ecology LabSchool of Biological SciencesFlinders UniversityAdelaideSAAustralia
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
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22
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Kearns AM, Restani M, Szabo I, Schrøder-Nielsen A, Kim JA, Richardson HM, Marzluff JM, Fleischer RC, Johnsen A, Omland KE. Genomic evidence of speciation reversal in ravens. Nat Commun 2018; 9:906. [PMID: 29500409 PMCID: PMC5834606 DOI: 10.1038/s41467-018-03294-w] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/01/2018] [Indexed: 01/10/2023] Open
Abstract
Many species, including humans, have emerged via complex reticulate processes involving hybridisation. Under certain circumstances, hybridisation can cause distinct lineages to collapse into a single lineage with an admixed mosaic genome. Most known cases of such 'speciation reversal' or 'lineage fusion' involve recently diverged lineages and anthropogenic perturbation. Here, we show that in western North America, Common Ravens (Corvus corax) have admixed mosaic genomes formed by the fusion of non-sister lineages ('California' and 'Holarctic') that diverged ~1.5 million years ago. Phylogenomic analyses and concordant patterns of geographic structuring in mtDNA, genome-wide SNPs and nuclear introns demonstrate long-term admixture and random interbreeding between the non-sister lineages. In contrast, our genomic data support reproductive isolation between Common Ravens and Chihuahuan Ravens (C. cryptoleucus) despite extensive geographic overlap and a sister relationship between Chihuahuan Ravens and the California lineage. These data suggest that the Common Raven genome was formed by secondary lineage fusion and most likely represents a case of ancient speciation reversal that occurred without anthropogenic causes.
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Affiliation(s)
- Anna M Kearns
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway.
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA.
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, 20013-7012, DC, USA.
| | - Marco Restani
- Department of Biological Sciences, St. Cloud State University, 720 Fourth Avenue, St. Cloud, MN, 56301-4498, USA
| | - Ildiko Szabo
- Cowan Tetrapod Collection, Beaty Biodiversity Museum, University of British Columbia, 2212 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | | | - Jin Ah Kim
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Hayley M Richardson
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - John M Marzluff
- School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, WA, 98195, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, 20013-7012, DC, USA
| | - Arild Johnsen
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318, Oslo, Norway
| | - Kevin E Omland
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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23
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Miller JM, Quinzin MC, Scheibe EH, Ciofi C, Villalva F, Tapia W, Caccone A. Genetic Pedigree Analysis of the Pilot Breeding Program for the Rediscovered Galapagos Giant Tortoise from Floreana Island. J Hered 2018; 109:620-630. [DOI: 10.1093/jhered/esy010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/25/2018] [Indexed: 12/16/2022] Open
Affiliation(s)
- Joshua M Miller
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Maud C Quinzin
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Elizabeth H Scheibe
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
| | - Claudio Ciofi
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Fredy Villalva
- Galapagos Galapagos National Park Directorate, Puerto Ayora, Ecuador
| | - Washington Tapia
- Galapagos Galapagos National Park Directorate, Puerto Ayora, Ecuador
- Galapagos Conservancy, Fairfax, VA
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
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24
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Tominaga A, Matsui M, Yoshikawa N, Eto K, Nishikawa K. Genomic Displacement and Shift of the Hybrid Zone in the Japanese Fire-Bellied Newt. J Hered 2017; 109:232-242. [DOI: 10.1093/jhered/esx085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 09/29/2017] [Indexed: 12/25/2022] Open
Affiliation(s)
- Atsushi Tominaga
- Department of Natural Sciences, Faculty of Education, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu, Sakyo, Kyoto, Japan
| | - Natsuhiko Yoshikawa
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, Tsukuba, Ibaraki, Japan
| | - Koshiro Eto
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu, Sakyo, Kyoto, Japan
- Kitakyushu Museum of Natural History and Human History, Higashida, Yahatahigashiku, Kitakyushu, Fukuoka, Japan
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu, Sakyo, Kyoto, Japan
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25
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Miller JM, Quinzin MC, Poulakakis N, Gibbs JP, Beheregaray LB, Garrick RC, Russello MA, Ciofi C, Edwards DL, Hunter EA, Tapia W, Rueda D, Carrión J, Valdivieso AA, Caccone A. Identification of Genetically Important Individuals of the Rediscovered Floreana Galápagos Giant Tortoise (Chelonoidis elephantopus) Provide Founders for Species Restoration Program. Sci Rep 2017; 7:11471. [PMID: 28904401 PMCID: PMC5597637 DOI: 10.1038/s41598-017-11516-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 08/25/2017] [Indexed: 11/09/2022] Open
Abstract
Species are being lost at an unprecedented rate due to human-driven environmental changes. The cases in which species declared extinct can be revived are rare. However, here we report that a remote volcano in the Galápagos Islands hosts many giant tortoises with high ancestry from a species previously declared as extinct: Chelonoidis elephantopus or the Floreana tortoise. Of 150 individuals with distinctive morphology sampled from the volcano, genetic analyses revealed that 65 had C. elephantopus ancestry and thirty-two were translocated from the volcano's slopes to a captive breeding center. A genetically informed captive breeding program now being initiated will, over the next decades, return C. elephantopus tortoises to Floreana Island to serve as engineers of the island's ecosystems. Ironically, it was the haphazard translocations by mariners killing tortoises for food centuries ago that created the unique opportunity to revive this "lost" species today.
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Affiliation(s)
- Joshua M Miller
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St. New Haven, Connecticut, 06520, United States of America.
| | - Maud C Quinzin
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St. New Haven, Connecticut, 06520, United States of America
| | - Nikos Poulakakis
- Department of Biology, School of Sciences and Engineering, University of Crete, Vasilika Vouton, Gr-71300, Heraklio, Crete, Greece.,Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Av., GR-71409, Heraklio, Crete, Greece
| | - James P Gibbs
- College of Environmental Science & Forestry, State University of New York, Syracuse, New York, 13210, United States of America
| | - Luciano B Beheregaray
- Molecular Ecology Lab, School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, SA, 5001, Australia
| | - Ryan C Garrick
- Department of Biology, University of Mississippi, Oxford, Mississippi, 38677, United States of America
| | - Michael A Russello
- Department of Biology, University of British Columbia, Okanagan Campus, Kelowna, BC V1V 1V7, Canada
| | - Claudio Ciofi
- Department Biology, University of Florence, 50019, Sesto Fiorentino (FI), Italy
| | - Danielle L Edwards
- Life and Environmental Sciences, University of California, Merced, 5200 N Lake Rd, Merced, California, 95343, United States of America
| | - Elizabeth A Hunter
- Department of Natural Resources and Environmental Science, University of Nevada - Reno, Max Fleischmann Agricultural Building, Reno, NV, 89557, USA
| | - Washington Tapia
- Galapagos Conservancy, Fairfax, Virginia, 22030, United States of America.,Galápagos National Park Directorate, Puerto Ayora, Galápagos, Ecuador
| | - Danny Rueda
- Galápagos National Park Directorate, Puerto Ayora, Galápagos, Ecuador
| | - Jorge Carrión
- Galápagos National Park Directorate, Puerto Ayora, Galápagos, Ecuador
| | - Andrés A Valdivieso
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St. New Haven, Connecticut, 06520, United States of America
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St. New Haven, Connecticut, 06520, United States of America.
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26
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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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27
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Jirsová D, Štefka J, Jirků M. Discordant population histories of host and its parasite: A role for ecological permeability of extreme environment? PLoS One 2017; 12:e0175286. [PMID: 28394904 PMCID: PMC5386267 DOI: 10.1371/journal.pone.0175286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 03/23/2017] [Indexed: 12/24/2022] Open
Abstract
Biogeographical and ecological barriers strongly affect the course of micro-evolutionary processes in free living organisms. Here we assess the impact of a recently emerged barrier on populations of limnic fauna. Genetic diversity and population structure in a host-parasite system (Wenyonia virilis tapeworm, Synodontis schall catfish) are analyzed in the recently divided Turkana and Nile basins. The two basins, were repeatedly connected during the Holocene wet/dry climatic oscillations, following late Pleistocene dessication of the Turkana basin. Mitochondrial DNA sequences for cytochrome oxidase I gene (cox I) and a whole genome scanning method—amplified fragment length polymorphism (AFLP) were employed. A total of 347 cox I sequences (representing 209 haplotypes) and 716 AFLP fragments, as well as 120 cox I sequences (20 haplotypes) and 532 AFLP fragments were obtained from parasites and hosts, respectively. Although results indicate that host and parasite populations share some formative traits (bottlenecks, Nilotic origin), their population histories/patterns differ markedly. Mitochondrial analysis revealed that parasite populations evolve significantly faster and show remarkably higher genetic variability. Analyses of both markers confirmed that the parasites undergo lineage fission, forming new clusters specific for either freshwater or saline parts of Lake Turkana. In congruence with the geological history, these clusters apparently indicate multiple colonisations of Lake Turkana from the Nile. In contrast, the host population pattern indicates fusion of different colonisation waves. Although fish host populations remain connected, saline habitats in Lake Turkana (absent in the Nile), apparently pose a barrier to the gene flow in the parasite, possibly due to its multihost lifecycle, which involves freshwater annelids. Despite partially corroborating mitochondrial results, AFLP data was not sufficiently informative for analyzing populations with recently mixed biogeographic histories.
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Affiliation(s)
- Dagmar Jirsová
- Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, České Budějovice, Czech Republic
- * E-mail:
| | - Jan Štefka
- Faculty of Science, University of South Bohemia, Branišovská, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, České Budějovice, Czech Republic
| | - Miloslav Jirků
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská, České Budějovice, Czech Republic
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28
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Willows-Munro S, Dowler RC, Jarcho MR, Phillips RB, Snell HL, Wilbert TR, Edwards CW. Cryptic diversity in Black rats Rattus rattus of the Galápagos Islands, Ecuador. Ecol Evol 2016; 6:3721-3733. [PMID: 27231528 PMCID: PMC4863831 DOI: 10.1002/ece3.2033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 01/29/2016] [Accepted: 02/02/2016] [Indexed: 11/30/2022] Open
Abstract
Human activity has facilitated the introduction of a number of alien mammal species to the Galápagos Archipelago. Understanding the phylogeographic history and population genetics of invasive species on the Archipelago is an important step in predicting future spread and designing effective management strategies. In this study, we describe the invasion pathway of Rattus rattus across the Galápagos using microsatellite data, coupled with historical knowledge. Microsatellite genotypes were generated for 581 R. rattus sampled from 15 islands in the archipelago. The genetic data suggest that there are at least three genetic lineages of R. rattus present on the Galápagos Islands. The spatial distributions of these lineages correspond to the main centers of human settlement in the archipelago. There was limited admixture among these three lineages, and these finding coupled with low rates of gene flow among island populations suggests that interisland movement of R. rattus is rare. The low migration among islands recorded for the species will have a positive impact on future eradication efforts.
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Affiliation(s)
- Sandi Willows-Munro
- School of Life Sciences University of Kwa Zulu-Natal PO Box X01 Scottsville 3209 South Africa
| | - Robert C Dowler
- Department of Biology Angelo State University San Angelo Texas
| | | | - Reese B Phillips
- U.S. Fish and Wildlife Service Pacific Islands Fish and Wildlife Office 300 Ala Moana Blvd Rm 3-122 Honolulu Hawaii
| | - Howard L Snell
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico
| | - Tammy R Wilbert
- Smithsonian Conservation Biology Institute National Zoological Park Washington District of Columbia
| | - Cody W Edwards
- Department of Biology George Mason University Fairfax Virginia 22030
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29
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MacLeod A, Rodríguez A, Vences M, Orozco-terWengel P, García C, Trillmich F, Gentile G, Caccone A, Quezada G, Steinfartz S. Hybridization masks speciation in the evolutionary history of the Galápagos marine iguana. Proc Biol Sci 2016; 282:20150425. [PMID: 26041359 DOI: 10.1098/rspb.2015.0425] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The effects of the direct interaction between hybridization and speciation-two major contrasting evolutionary processes--are poorly understood. We present here the evolutionary history of the Galápagos marine iguana (Amblyrhynchus cristatus) and reveal a case of incipient within--island speciation, which is paralleled by between-island hybridization. In-depth genome-wide analyses suggest that Amblyrhynchus diverged from its sister group, the Galápagos land iguanas, around 4.5 million years ago (Ma), but divergence among extant populations is exceedingly young (less than 50,000 years). Despite Amblyrhynchus appearing as a single long-branch species phylogenetically, we find strong population structure between islands, and one case of incipient speciation of sister lineages within the same island--ostensibly initiated by volcanic events. Hybridization between both lineages is exceedingly rare, yet frequent hybridization with migrants from nearby islands is evident. The contemporary snapshot provided by highly variable markers indicates that speciation events may have occurred throughout the evolutionary history of marine iguanas, though these events are not visible in the deeper phylogenetic trees. We hypothesize that the observed interplay of speciation and hybridization might be a mechanism by which local adaptations, generated by incipient speciation, can be absorbed into a common gene pool, thereby enhancing the evolutionary potential of the species as a whole.
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Affiliation(s)
- Amy MacLeod
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, Braunschweig 38106, Germany Department of Animal Behavior, University of Bielefeld, Bielefeld 33501, Germany
| | - Ariel Rodríguez
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, Braunschweig 38106, Germany
| | - Miguel Vences
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, Braunschweig 38106, Germany
| | | | - Carolina García
- Charles Darwin Foundation, Puerto Ayora, Santa Cruz Island, Galápagos, Ecuador
| | - Fritz Trillmich
- Department of Animal Behavior, University of Bielefeld, Bielefeld 33501, Germany
| | - Gabriele Gentile
- Laboratory of Experimental Ecology and Aquaculture, Department of Biology, University of Rome, Tor Vergata, Rome 0033, Italy
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT 06520-8106, USA
| | - Galo Quezada
- Galápagos National Park Authority, Central Office, Puerto Ayora, Santa Cruz Island, Galápagos, Ecuador
| | - Sebastian Steinfartz
- Zoological Institute, Technische Universität Braunschweig, Mendelssohnstrasse 4, Braunschweig 38106, Germany
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30
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Grant PR, Grant BR. Introgressive hybridization and natural selection in Darwin's finches. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12702] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Peter R. Grant
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton NJ 08544-1003 USA
| | - B. Rosemary Grant
- Department of Ecology and Evolutionary Biology; Princeton University; Princeton NJ 08544-1003 USA
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31
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Description of a New Galapagos Giant Tortoise Species (Chelonoidis; Testudines: Testudinidae) from Cerro Fatal on Santa Cruz Island. PLoS One 2015; 10:e0138779. [PMID: 26488886 PMCID: PMC4619298 DOI: 10.1371/journal.pone.0138779] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/03/2015] [Indexed: 11/20/2022] Open
Abstract
The taxonomy of giant Galapagos tortoises (Chelonoidis spp.) is currently based primarily on morphological characters and island of origin. Over the last decade, compelling genetic evidence has accumulated for multiple independent evolutionary lineages, spurring the need for taxonomic revision. On the island of Santa Cruz there is currently a single named species, C. porteri. Recent genetic and morphological studies have shown that, within this taxon, there are two evolutionarily and spatially distinct lineages on the western and eastern sectors of the island, known as the Reserva and Cerro Fatal populations, respectively. Analyses of DNA from natural populations and museum specimens, including the type specimen for C. porteri, confirm the genetic distinctiveness of these two lineages and support elevation of the Cerro Fatal tortoises to the rank of species. In this paper, we identify DNA characters that define this new species, and infer evolutionary relationships relative to other species of Galapagos tortoises.
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32
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Hendrickx F, Backeljau T, Dekoninck W, Van Belleghem SM, Vandomme V, Vangestel C. Persistent inter- and intraspecific gene exchange within a parallel radiation of caterpillar hunter beetles (Calosomasp.) from the Galápagos. Mol Ecol 2015; 24:3107-21. [DOI: 10.1111/mec.13233] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 01/17/2023]
Affiliation(s)
- Frederik Hendrickx
- Royal Belgian Institute of Natural Sciences; Vautierstraat 29 Brussels 1000 Belgium
- Terrestrial Ecology Unit (TEREC); Biology Department; Ghent University; K.L. Ledeganckstraat 35 Gent 9000 Belgium
| | - Thierry Backeljau
- Royal Belgian Institute of Natural Sciences; Vautierstraat 29 Brussels 1000 Belgium
- Evolutionary Ecology Group; Department of Biology; University of Antwerp; Groenenborgerlaan 171 Antwerp 2020 Belgium
| | - Wouter Dekoninck
- Royal Belgian Institute of Natural Sciences; Vautierstraat 29 Brussels 1000 Belgium
| | - Steven M. Van Belleghem
- Royal Belgian Institute of Natural Sciences; Vautierstraat 29 Brussels 1000 Belgium
- Terrestrial Ecology Unit (TEREC); Biology Department; Ghent University; K.L. Ledeganckstraat 35 Gent 9000 Belgium
| | - Viki Vandomme
- Terrestrial Ecology Unit (TEREC); Biology Department; Ghent University; K.L. Ledeganckstraat 35 Gent 9000 Belgium
| | - Carl Vangestel
- Royal Belgian Institute of Natural Sciences; Vautierstraat 29 Brussels 1000 Belgium
- Terrestrial Ecology Unit (TEREC); Biology Department; Ghent University; K.L. Ledeganckstraat 35 Gent 9000 Belgium
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33
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Garrick RC, Bonatelli IAS, Hyseni C, Morales A, Pelletier TA, Perez MF, Rice E, Satler JD, Symula RE, Thomé MTC, Carstens BC. The evolution of phylogeographic data sets. Mol Ecol 2015; 24:1164-71. [DOI: 10.1111/mec.13108] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 01/21/2015] [Accepted: 02/04/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Ryan C. Garrick
- Department of Biology; University of Mississippi; Oxford MS 38677 USA
| | - Isabel A. S. Bonatelli
- Departamento de Biologia; Universidade Federal de São Carlos; Campus Sorocaba Caixa Postal 18052780 Sorocaba São Paulo Brazil
| | - Chaz Hyseni
- Department of Biology; University of Mississippi; Oxford MS 38677 USA
| | - Ariadna Morales
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
| | - Tara A. Pelletier
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
| | - Manolo F. Perez
- Departamento de Biologia; Universidade Federal de São Carlos; Campus Sorocaba Caixa Postal 18052780 Sorocaba São Paulo Brazil
| | - Edwin Rice
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
| | - Jordan D. Satler
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
| | - Rebecca E. Symula
- Department of Biology; University of Mississippi; Oxford MS 38677 USA
| | - Maria Tereza C. Thomé
- Departamento de Zoologia; Instituto de Biociências; UNESP - Univ Estadual Paulista; Campus Rio Claro Caixa Postal 19913506-900 Rio Claro São Paulo Brazil
| | - Bryan C. Carstens
- Department of Evolution, Ecology and Organismal Biology; The Ohio State University; 318 W. 12th Avenue Columbus OH 43210-1293 USA
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34
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Garrick RC, Kajdacsi B, Russello MA, Benavides E, Hyseni C, Gibbs JP, Tapia W, Caccone A. Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises. Ecol Evol 2015; 5:676-94. [PMID: 25691990 PMCID: PMC4328771 DOI: 10.1002/ece3.1388] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 02/05/2023] Open
Abstract
Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (N e ) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ∽100 generations, ∽2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical N e of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary N e were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, N e generally represented ∽0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.
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Affiliation(s)
- Ryan C Garrick
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - Brittney Kajdacsi
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Michael A Russello
- Department of Biology, University of British ColumbiaOkanagan Campus, Kelowna, British Columbia, V1V 1V7, Canada
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
| | - Chaz Hyseni
- Department of Biology, University of MississippiOxford, Mississippi, 38677
| | - James P Gibbs
- College of Environmental Science and Forestry, State University of New YorkSyracuse, New York, 13210
| | - Washington Tapia
- Department of Applied Research, Galápagos National Park ServicePuerto Ayora, Galápagos, Ecuador
- Biodiver S.A. ConsultoresKm 5 Vía a Baltra, Isla Santa Cruz, Galápagos, Ecuador
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale UniversityNew Haven, Connecticut, 06520
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35
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Emerson BC, Faria CMA. Fission and fusion in island taxa--serendipity, or something to be expected? Mol Ecol 2014; 23:5132-4. [PMID: 25330853 DOI: 10.1111/mec.12951] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 09/25/2014] [Accepted: 09/29/2014] [Indexed: 11/30/2022]
Abstract
A well-used metaphor for oceanic islands is that they act as 'natural laboratories' for the study of evolution. But how can islands or archipelagos be considered analogues of laboratories for understanding the evolutionary process itself? It is not necessarily the case that just because two or more related species occur on an island or archipelago, somehow, this can help us understand more about their evolutionary history. But in some cases, it can. In this issue of Molecular Ecology, Garrick et al. () use population-level sampling within closely related taxa of Galapagos giant tortoises to reveal a complex demographic history of the species Chelonoidis becki - a species endemic to Isabela Island, and geographically restricted to Wolf Volcano. Using microsatellite genotyping and mitochondrial DNA sequencing, they provide a strong case for C. becki being derived from C. darwini from the neighbouring island of Santiago. But the interest here is that colonization did not happen only once. Garrick et al. () reveal C. becki to be the product of a double colonization event, and their data reveal these two founding lineages to be now fusing back into one. Their results are compelling and add to a limited literature describing the evolutionary consequences of double colonization events. Here, we look at the broader implications of the findings of Garrick et al. () and suggest genomic admixture among multiple founding populations may be a characteristic feature within insular taxa.
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Affiliation(s)
- Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, San Cristóbal de La Laguna, Santa Cruz de Tenerife, 38206, Spain
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