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Tharakan S, Shepherd N, Gower DJ, Stanley EL, Felice RN, Goswami A, Watanabe A. High-Density Geometric Morphometric Analysis of Intraspecific Cranial Integration in the Barred Grass Snake ( Natrix helvetica) and Green Anole ( Anolis carolinensis). Integr Org Biol 2023; 5:obad022. [PMID: 37397233 PMCID: PMC10311474 DOI: 10.1093/iob/obad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/30/2023] [Accepted: 06/02/2023] [Indexed: 07/04/2023] Open
Abstract
How do phenotypic associations intrinsic to an organism, such as developmental and mechanical processes, direct morphological evolution? Comparisons of intraspecific and clade-wide patterns of phenotypic covariation could inform how population-level trends ultimately dictate macroevolutionary changes. However, most studies have focused on analyzing integration and modularity either at macroevolutionary or intraspecific levels, without a shared analytical framework unifying these temporal scales. In this study, we investigate the intraspecific patterns of cranial integration in two squamate species: Natrix helvetica and Anolis carolinensis. We analyze their cranial integration patterns using the same high-density three-dimensional geometric morphometric approach used in a prior squamate-wide evolutionary study. Our results indicate that Natrix and Anolis exhibit shared intraspecific cranial integration patterns, with some differences, including a more integrated rostrum in the latter. Notably, these differences in intraspecific patterns correspond to their respective interspecific patterns in snakes and lizards, with few exceptions. These results suggest that interspecific patterns of cranial integration reflect intraspecific patterns. Hence, our study suggests that the phenotypic associations that direct morphological variation within species extend across micro- and macroevolutionary levels, bridging these two scales.
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Affiliation(s)
- S Tharakan
- Department of Anatomy, New York Institute of Technology, College of Osteopathic Medicine, 100 Northern Boulevard, Old Westbury, NY 11568, USA
| | - N Shepherd
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - D J Gower
- Life Sciences Division, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - E L Stanley
- Digital Imaging Division, Florida Museum of Natural History, University of Florida, Gainesville, FL 32611-0001, USA
| | - R N Felice
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- Life Sciences Division, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
- Centre for Integrative Anatomy, Department of Cell and Developmental Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - A Goswami
- Department of Genetics, Evolution, and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- Life Sciences Division, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
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Toyama KS, Mahler DL, Goodman RM. Climate shapes patterns of sexual size and shape dimorphism across the native range of the green anole lizard, Anolis carolinensis (Squamata: Dactyloidae). Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract
Geographical variation in sexual size dimorphism (SSD) can result from the combined effects of environmental and sexual selection. To understand the determinants of SSD across geographical landscapes, we tested for relationships between SSD and climatic variables in the widespread lizard Anolis carolinensis. To distinguish alternative hypotheses for observed patterns of variation in SSD, we also examined sex-specific patterns of body size evolution and asked whether SSD was associated with certain patterns of sexual shape dimorphism. We found strong evidence for Rensch’s rule (an increase in male-biased SSD with average body size) in A. carolinensis and evidence for the reversed version of Bergmann’s rule (an increase in body size towards warmer environments) in males. Across populations, SSD was positively related to temperature; however, female body size was not related to any climatic variable, suggesting that the latitudinal gradient of SSD might be driven by a gradient in the intensity of sexual selection acting on males. Sexual size dimorphism was positively correlated with sexual dimorphism in head shape and negatively correlated with limb length dimorphism, suggesting that sexual selection in males might drive the evolution of SSD and that differences in size and limb shape between sexes might represent alternative strategies to avoid competition for the same resources.
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Affiliation(s)
- Ken S Toyama
- Department of Ecology and Evolutionary Biology, University of Toronto , ON , Canada M5S 3B2
| | - D Luke Mahler
- Department of Ecology and Evolutionary Biology, University of Toronto , ON , Canada M5S 3B2
| | - Rachel M Goodman
- Biology Department, Hampden-Sydney College , Hampden-Sydney, VA , USA
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3
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Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species. Commun Biol 2022; 5:1126. [PMID: 36284162 PMCID: PMC9596491 DOI: 10.1038/s42003-022-04074-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 10/06/2022] [Indexed: 12/12/2022] Open
Abstract
Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei – a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei. A highly-complete chromosome-scale genome assembly of the brown anole, Anolis sagrei, provides insight into the evolution of sex chromosomes and is a crucial resource for this model lizard species.
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Mayer GC, Lazell J. The identity of the introduced green anole (Reptilia: Squamata) of Hawaii and other Pacific islands. P BIOL SOC WASH 2021. [DOI: 10.2988/0006-324x-134.1.294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Gregory C. Mayer
- (GCM) Department of Biological Sciences, University of Wisconsin-Parkside, Kenosha, WI, 53405, USA, e-mail:
| | - James Lazell
- (JL) The Conservation Agency, 6 Swinburne Street, Jamestown, RI, 02835, USA
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Corbett-Detig RB, Russell SL, Nielsen R, Losos J. Phenotypic Convergence Is Not Mirrored at the Protein Level in a Lizard Adaptive Radiation. Mol Biol Evol 2021; 37:1604-1614. [PMID: 32027369 DOI: 10.1093/molbev/msaa028] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
There are many compelling examples of molecular convergence at individual genes. However, the prevalence and the relative importance of adaptive genome-wide convergence remain largely unknown. Many recent works have reported striking examples of excess genome-wide convergence, but some of these studies have been called into question because of the use of inappropriate null models. Here, we sequenced and compared the genomes of 12 species of anole lizards that have independently converged on suites of adaptive behavioral and morphological traits. Despite extensive searches for a genome-wide signature of molecular convergence, we found no evidence supporting molecular convergence at specific amino acids either at individual genes or at genome-wide comparisons; we also uncovered no evidence supporting an excess of adaptive convergence in the rates of amino acid substitutions within genes. Our findings indicate that comprehensive phenotypic convergence is not mirrored at genome-wide protein-coding levels in anoles, and therefore, that adaptive phenotypic convergence is likely not constrained by the evolution of many specific protein sequences or structures.
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Affiliation(s)
- Russell B Corbett-Detig
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA.,Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA
| | - Shelbi L Russell
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA.,Centre for GeoGenetics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Losos
- Department of Biology and Living Earth Collaborative, Washington University, Saint Louis, MO
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Abstract
Background and aims Wildlife conservation has focused primarily on species for the last decades. Recently, popular perception and laws have begun to recognize the central importance of genetic diversity in the conservation of biodiversity. How to incorporate genetic diversity in ongoing monitoring and management of wildlife is still an open question. Methods We tested a panel of multiplexed, high-throughput sequenced introns in the small mammal communities of two UNESCO World Heritage Sites on different continents to assess their viability for large-scale monitoring of genetic variability in a spectrum of diverse species. To enhance applicability across other systems, the bioinformatic pipeline for primer design was outlined. Results The number of loci amplified and amplification evenness decreased as phylogenetic distance increased from the reference taxa, yet several loci were still variable across multiple mammal orders. Conclusions Genetic variability found is informative for population genetic analyses and for addressing phylogeographic and phylogenetic questions, illustrated by small mammal examples here.
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Ryan LM, Gunderson AR. Competing native and invasive Anolis lizards exhibit thermal preference plasticity in opposite directions. JOURNAL OF EXPERIMENTAL ZOOLOGY PART 2020; 335:118-125. [PMID: 33052040 DOI: 10.1002/jez.2420] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/04/2020] [Accepted: 09/17/2020] [Indexed: 12/29/2022]
Abstract
Invasive species have emerged as a significant problem in the age of anthropogenic change. Behavior can be key to invasive species success and is strongly affected by temperature. Therefore, knowledge of the temperature dependence of behavior is likely critical to understand invasive species dynamics and their interactions with native species. In this study, we tested for differences in thermal preference plasticity and temperature-dependent activity levels in a pair of congeneric lizards found in the United States: the invasive Anolis sagrei and the native A. carolinensis. We predicted that A. sagrei would demonstrate greater thermal preference plasticity and would utilize a higher and/or wider range of activity temperatures than A. carolinensis. Both would point to plasticity allowing A. sagrei to behaviorally exploiting thermal conditions that A. carolinensis cannot. We found that both species exhibited plasticity in thermal preference, but in opposite directions: preferred temperatures of A. carolinensis increased with acclimation temperature, while those of A. sagrei decreased. As a result, which species had a higher thermal preference changed with acclimation conditions. We saw no difference in overall field activity rates between the species, but that A. sagrei did tend to be active over a broader range of body temperatures. In sum, we found little evidence that differences in thermal preference plasticity between the species allow A. sagrei to remain active at a higher or broader temperature range than A. carolinensis. Nonetheless, the thermal preference data suggest complementary thermal preferences between the species that could promote microclimatic partitioning, though more work is required to test this idea.
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Affiliation(s)
- Lucy M Ryan
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA
| | - Alex R Gunderson
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, Louisiana, USA
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Reynolds RG, Kolbe JJ, Glor RE, López-Darias M, Gómez Pourroy CV, Harrison AS, de Queiroz K, Revell LJ, Losos JB. Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation. J Evol Biol 2020; 33:468-494. [PMID: 31872929 DOI: 10.1111/jeb.13581] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 12/18/2019] [Indexed: 01/15/2023]
Abstract
Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis of representative populations across the entire native range of A. sagrei, finding that the species originated in the early Pliocene, with the deepest divergence occurring between western and eastern Cuba. Lineages from these two regions subsequently colonized the northern Caribbean. We find that at the broadest scale, populations colonizing areas with fewer closely related competitors tend to evolve larger body size and more lamellae on their toepads. This trend follows expectations for post-colonization divergence from progenitors and convergence in allopatry, whereby populations freed from competition with close relatives evolve towards common morphological and ecological optima. Taken together, our results show a complex history of ancient and recent Cuban diaspora with populations on competitor-poor islands evolving away from their ancestral Cuban populations regardless of their phylogenetic relationships, thus providing insight into the original diversification of colonist anoles at the beginning of the radiation. Our research also supplies an evolutionary framework for the many studies of this increasingly important species in ecological and evolutionary research.
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Affiliation(s)
| | - Jason J Kolbe
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Richard E Glor
- Herpetology Division, Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KA, USA
| | | | | | - Alexis S Harrison
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Liam J Revell
- Department of Biology, University of Massachusetts Boston, Boston, MA, USA.,Departamento de Ecología, Facultad de Ciencias, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Jonathan B Losos
- Department of Biology, Washington University in Saint Louis, Saint Louis, MO, USA
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9
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Bourgeois Y, Boissinot S. Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer. Mol Ecol 2019; 28:3523-3543. [PMID: 31233650 DOI: 10.1111/mec.15162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/28/2019] [Indexed: 02/06/2023]
Abstract
What makes a species able to colonize novel environments? This question is key to understand the dynamics of adaptive radiations and ecological niche shifts, but the mechanisms that underlie expansion into novel habitats remain poorly understood at a genomic scale. Lizards from the genus Anolis are typically tropical, and the green anole (Anolis carolinensis) constitutes an exception since it expanded into temperate North America from subtropical Florida. Thus, we used the green anole as a model to investigate signatures of selection associated with colonization of a new environment, namely temperate North America. To this end, we analysed 29 whole-genome sequences, covering the entire native range of the species. We used a combination of recent methods to quantify both positive and balancing selection in northern populations, including FST outlier methods, machine learning and ancestral recombination graphs. We naively scanned for genes of interest and assessed the overlap between multiple tests. Strikingly, we identified many genes involved in behaviour, suggesting that the recent successful colonization of northern environments may have been linked to behavioural shifts as well as physiological adaptation. Using a candidate genes strategy, we determined that genes involved in response to cold or behaviour displayed more frequently signals of selection, while controlling for local recombination rate, gene clustering and gene length. In addition, we found signatures of balancing selection at immune genes in all investigated genetic groups, but also at genes involved in neuronal and anatomical development.
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Affiliation(s)
- Yann Bourgeois
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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10
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Bourgeois Y, Ruggiero RP, Manthey JD, Boissinot S. Recent Secondary Contacts, Linked Selection, and Variable Recombination Rates Shape Genomic Diversity in the Model Species Anolis carolinensis. Genome Biol Evol 2019; 11:2009-2022. [PMID: 31134281 PMCID: PMC6681179 DOI: 10.1093/gbe/evz110] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/23/2019] [Indexed: 12/14/2022] Open
Abstract
Gaining a better understanding on how selection and neutral processes affect genomic diversity is essential to gain better insights into the mechanisms driving adaptation and speciation. However, the evolutionary processes affecting variation at a genomic scale have not been investigated in most vertebrate lineages. Here, we present the first population genomics survey using whole genome resequencing in the green anole (Anolis carolinensis). Anoles have been intensively studied to understand mechanisms underlying adaptation and speciation. The green anole in particular is an important model to study genome evolution. We quantified how demography, recombination, and selection have led to the current genetic diversity of the green anole by using whole-genome resequencing of five genetic clusters covering the entire species range. The differentiation of green anole's populations is consistent with a northward expansion from South Florida followed by genetic isolation and subsequent gene flow among adjacent genetic clusters. Dispersal out-of-Florida was accompanied by a drastic population bottleneck followed by a rapid population expansion. This event was accompanied by male-biased dispersal and/or selective sweeps on the X chromosome. We show that the interaction between linked selection and recombination is the main contributor to the genomic landscape of differentiation in the anole genome.
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Affiliation(s)
| | | | - Joseph D Manthey
- New York University Abu Dhabi, United Arab Emirates
- Department of Biological Sciences, Texas Tech University
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11
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Kolora SRR, Weigert A, Saffari A, Kehr S, Walter Costa MB, Spröer C, Indrischek H, Chintalapati M, Lohse K, Doose G, Overmann J, Bunk B, Bleidorn C, Grimm-Seyfarth A, Henle K, Nowick K, Faria R, Stadler PF, Schlegel M. Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation. Gigascience 2019; 8:giy160. [PMID: 30535196 PMCID: PMC6381762 DOI: 10.1093/gigascience/giy160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 09/19/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Lacerta viridis and Lacerta bilineata are sister species of European green lizards (eastern and western clades, respectively) that, until recently, were grouped together as the L. viridis complex. Genetic incompatibilities were observed between lacertid populations through crossing experiments, which led to the delineation of two separate species within the L. viridis complex. The population history of these sister species and processes driving divergence are unknown. We constructed the first high-quality de novo genome assemblies for both L. viridis and L. bilineata through Illumina and PacBio sequencing, with annotation support provided from transcriptome sequencing of several tissues. To estimate gene flow between the two species and identify factors involved in reproductive isolation, we studied their evolutionary history, identified genomic rearrangements, detected signatures of selection on non-coding RNA, and on protein-coding genes. FINDINGS Here we show that gene flow was primarily unidirectional from L. bilineata to L. viridis after their split at least 1.15 million years ago. We detected positive selection of the non-coding repertoire; mutations in transcription factors; accumulation of divergence through inversions; selection on genes involved in neural development, reproduction, and behavior, as well as in ultraviolet-response, possibly driven by sexual selection, whose contribution to reproductive isolation between these lacertid species needs to be further evaluated. CONCLUSION The combination of short and long sequence reads resulted in one of the most complete lizard genome assemblies. The characterization of a diverse array of genomic features provided valuable insights into the demographic history of divergence among European green lizards, as well as key species differences, some of which are candidates that could have played a role in speciation. In addition, our study generated valuable genomic resources that can be used to address conservation-related issues in lacertids.
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Affiliation(s)
- Sree Rohit Raj Kolora
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Amin Saffari
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Human Biology Group, Institute for Zoology, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 1–3, Berlin, D-14195, Germany
| | - Stephanie Kehr
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
| | - Maria Beatriz Walter Costa
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Embrapa Agroenergia, Parque Estacaeo Biologica (PqEB), Asa Norte, Brasilia/DF, 70770-901, Brazil
| | - Cathrin Spröer
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Henrike Indrischek
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, Dresden, 01307, Germany
- Max Planck Institute for Physics of Complex Systems, Noethnitzerstrasse 38, 01187 Dresden, Germany
- Center for Systems Biology Dresden, Pfotenhauerstrasse 108, 01397 Dresden, Germany
| | - Manjusha Chintalapati
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany
| | - Konrad Lohse
- Institute of Evolutionary Biology, University of Edinburgh, King's Buildings, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom
| | - Gero Doose
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
| | - Jörg Overmann
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Boyke Bunk
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, Braunschweig, 38124, Germany
| | - Christoph Bleidorn
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Department of Animal Evolution and Biodiversity, University of Göttingen, Untere Karspüle 2, Göttingen, 37073, Germany
- Museo Nacional de Ciencias Naturales, Spanish National Research Council (CSIC), Madrid, 28006, Spain
| | - Annegret Grimm-Seyfarth
- Department of Conservation Biology, UFZ - Helmholtz Center for Environmental Research, Permoserstrasse 15, Leipzig, 04318, Germany
- Plant Ecology and Nature Conservation, University of Potsdam, Am Mühlenberg 3, Potsdam, 14476, Germany
| | - Klaus Henle
- Department of Conservation Biology, UFZ - Helmholtz Center for Environmental Research, Permoserstrasse 15, Leipzig, 04318, Germany
| | - Katja Nowick
- Human Biology Group, Institute for Zoology, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 1–3, Berlin, D-14195, Germany
| | - Rui Faria
- Department of Animal and Plant Sciences, Alfred Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Peter F Stadler
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstrasse 16-18, Leipzig, 04107, Germany
- Competence Center for Scalable Data Services and Solutions Dresden/Leipzig, Universität Leipzig, Augustusplatz 12, Leipzig, 04107, Germany
- Max-Planck-Institute for Mathematics in the Sciences, Inselstrasse 22, Leipzig, 04103, Germany
- Fraunhofer Institut Für Zelltherapie Und Immunologie, Perlickstrasse 1, Leipzig, 04103, Germany
- Department of Theoretical Chemistry, University of Vienna, Währinger strasse 17, Wien, 1090, Austria
- Center for non-Coding RNA in Technology and Health, University of Copenhagen, Gronnegardsvej 3, Frederiksberg C, 1870, Denmark
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico, 87501, USA
| | - Martin Schlegel
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, Leipzig, 04103, Germany
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstrasse 33, Leipzig, 04103, Germany
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Prates I, Penna A, Rodrigues MT, Carnaval AC. Local adaptation in mainland anole lizards: Integrating population history and genome-environment associations. Ecol Evol 2018; 8:11932-11944. [PMID: 30598788 PMCID: PMC6303772 DOI: 10.1002/ece3.4650] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 09/22/2018] [Accepted: 09/24/2018] [Indexed: 12/21/2022] Open
Abstract
Environmental gradients constrain physiological performance and thus species' ranges, suggesting that species occurrence in diverse environments may be associated with local adaptation. Genome-environment association analyses (GEAA) have become central for studies of local adaptation, yet they are sensitive to the spatial orientation of historical range expansions relative to landscape gradients. To test whether potentially adaptive genotypes occur in varied climates in wide-ranged species, we implemented GEAA on the basis of genomewide data from the anole lizards Anolis ortonii and Anolis punctatus, which expanded from Amazonia, presently dominated by warm and wet settings, into the cooler and less rainy Atlantic Forest. To examine whether local adaptation has been constrained by population structure and history, we estimated effective population sizes, divergence times, and gene flow under a coalescent framework. In both species, divergence between Amazonian and Atlantic Forest populations dates back to the mid-Pleistocene, with subsequent gene flow. We recovered eleven candidate genes involved with metabolism, immunity, development, and cell signaling in A. punctatus and found no loci whose frequency is associated with environmental gradients in A. ortonii. Distinct signatures of adaptation between these species are not associated with historical constraints or distinct climatic space occupancies. Similar patterns of spatial structure between selected and neutral SNPs along the climatic gradient, as supported by patterns of genetic clustering in A. punctatus, may have led to conservative GEAA performance. This study illustrates how tests of local adaptation can benefit from knowledge about species histories to support hypothesis formulation, sampling design, and landscape gradient characterization.
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Affiliation(s)
- Ivan Prates
- Department of Vertebrate ZoologyNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Department of Biology, City College of New York and Graduate CenterCity University of New YorkNew YorkNew York
| | - Anna Penna
- Department of AnthropologyUniversity of Texas at San AntonioSan AntonioTexas
| | | | - Ana Carolina Carnaval
- Department of Biology, City College of New York and Graduate CenterCity University of New YorkNew YorkNew York
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Reeves LE, Gillett-Kaufman JL, Kawahara AY, Kaufman PE. Barcoding blood meals: New vertebrate-specific primer sets for assigning taxonomic identities to host DNA from mosquito blood meals. PLoS Negl Trop Dis 2018; 12:e0006767. [PMID: 30161128 PMCID: PMC6135518 DOI: 10.1371/journal.pntd.0006767] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 09/12/2018] [Accepted: 08/20/2018] [Indexed: 12/22/2022] Open
Abstract
The transmission dynamics of mosquito-vectored pathogens are, in part, mediated by mosquito host-feeding patterns. These patterns are elucidated using blood meal analysis, a collection of serological and molecular techniques that determine the taxonomic identities of the host animals from which blood meals are derived. Modern blood meal analyses rely on polymerase chain reaction (PCR), DNA sequencing, and bioinformatic comparisons of blood meal DNA sequences to reference databases. Ideally, primers used in blood meal analysis PCRs amplify templates from a taxonomically diverse range of vertebrates, produce a short amplicon, and avoid co-amplification of non-target templates. Few primer sets that fit these requirements are available for the cytochrome c oxidase subunit I (COI) gene, the species identification marker with the highest taxonomic coverage in reference databases. Here, we present new primer sets designed to amplify fragments of the DNA barcoding region of the vertebrate COI gene, while avoiding co-amplification of mosquito templates, without multiplexed or nested PCR. Primers were validated using host vertebrate DNA templates from mosquito blood meals of known origin, representing all terrestrial vertebrate classes, and field-collected mosquito blood meals of unknown origin. We found that the primers were generally effective in amplifying vertebrate host, but not mosquito DNA templates. Applied to the sample of unknown mosquito blood meals, > 98% (60/61) of blood meals samples were reliably identified, demonstrating the feasibility of identifying mosquito hosts with the new primers. These primers are beneficial in that they can be used to amplify COI templates from a diverse range of vertebrate hosts using standard PCR, thereby streamlining the process of identifying the hosts of mosquitoes, and could be applied to next generation DNA sequencing and metabarcoding approaches.
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Affiliation(s)
- Lawrence E. Reeves
- Entomology and Nematology Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Jennifer L. Gillett-Kaufman
- Entomology and Nematology Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Akito Y. Kawahara
- McGuire Center for Lepidoptera and Biodiversity, Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Phillip E. Kaufman
- Entomology and Nematology Department, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, United States of America
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14
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Michaelides SN, Goodman RM, Crombie RI, Kolbe JJ. Independent introductions and sequential founder events shape genetic differentiation and diversity of the invasive green anole (Anolis carolinensis) on Pacific Islands. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12704] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
| | - Rachel M. Goodman
- Department of Biology; Hampden-Sydney College; Hampden Sydney VA USA
| | | | - Jason J. Kolbe
- Department of Biological Sciences; University of Rhode Island; Kingston RI USA
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15
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Inferring responses to climate dynamics from historical demography in neotropical forest lizards. Proc Natl Acad Sci U S A 2017; 113:7978-85. [PMID: 27432951 DOI: 10.1073/pnas.1601063113] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future.
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16
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Suzuki-Ohno Y, Morita K, Nagata N, Mori H, Abe S, Makino T, Kawata M. Factors restricting the range expansion of the invasive green anole Anolis carolinensis on Okinawa Island, Japan. Ecol Evol 2017. [PMID: 28649347 PMCID: PMC5478079 DOI: 10.1002/ece3.3002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The green anole Anolis carolinensis invaded the Ogasawara Islands in Japan, drove various native species to extinction, and its distribution expanded 14 years after initial establishment. A. carolinensis invaded Okinawa Island, but it has not expanded its distribution in more than 25 years, although its density is extremely high in the southern region. To determine whether A. carolinensis has the potential to expand its distribution on Okinawa Island, we performed phylogenetic analysis of mitochondrial ND2 DNA sequences to study the origin of A. carolinensis that invaded Okinawa Island. We further used a species distribution model (MaxEnt) based on the distribution of native populations in North America to identify ecologically suitable areas on Okinawa Island. Nucleotide sequence analysis shows that the invader A. carolinensis originated in the western part of the Gulf Coast and inland areas of the United States and that a portion of the anoles on Okinawa was not introduced via the Ogasawara Islands. The MaxEnt predictions indicate that most areas in Okinawa Island are suitable for A. carolinensis. Therefore, A. carolinensis may have the potential to expand its distribution in Okinawa Island. The predictions indicate that habitat suitability is high in areas of high annual mean temperature and urbanized areas. The values of precipitation in summer in the northern region of Okinawa Island were higher compared with those of North America, which reduced the habitat suitability in Okinawa Island. Adaptation to low temperatures, an increase in the mean temperature through global warming, and an increase in open environments through land development will likely expand the distribution of A. carolinensis in Okinawa Island. Therefore, we must continue to monitor the introduced populations and be alert to the possibility that city planning that increases open environments may cause their range to expand.
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Affiliation(s)
- Yukari Suzuki-Ohno
- Department of Ecology and Evolutionary Biology Graduate School of Life Sciences Tohoku University Sendai Miyagi Japan
| | - Kenjiro Morita
- Department of Ecology and Evolutionary Biology Graduate School of Life Sciences Tohoku University Sendai Miyagi Japan
| | - Nobuaki Nagata
- Department of Ecology and Evolutionary Biology Graduate School of Life Sciences Tohoku University Sendai Miyagi Japan
| | - Hideaki Mori
- Ogasawara Division Japan Wildlife Research Center Tokyo Japan
| | - Shintaro Abe
- Naha Nature Conservation Office Ministry of the Environment Naha Okinawa Japan
| | - Takashi Makino
- Department of Ecology and Evolutionary Biology Graduate School of Life Sciences Tohoku University Sendai Miyagi Japan
| | - Masakado Kawata
- Department of Ecology and Evolutionary Biology Graduate School of Life Sciences Tohoku University Sendai Miyagi Japan
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17
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Ruggiero RP, Bourgeois Y, Boissinot S. LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis. Front Genet 2017; 8:44. [PMID: 28450881 PMCID: PMC5389967 DOI: 10.3389/fgene.2017.00044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 03/29/2017] [Indexed: 12/30/2022] Open
Abstract
Vertebrate genomes differ considerably in size and structure. Among the features that show the most variation is the abundance of Long Interspersed Nuclear Elements (LINEs). Mammalian genomes contain 100,000s LINEs that belong to a single clade, L1, and in most species a single family is usually active at a time. In contrast, non-mammalian vertebrates (fish, amphibians and reptiles) contain multiple active families, belonging to several clades, but each of them is represented by a small number of recently inserted copies. It is unclear why vertebrate genomes harbor such drastic differences in LINE composition. To address this issue, we conducted whole genome resequencing to investigate the population genomics of LINEs across 13 genomes of the lizard Anolis carolinensis sampled from two geographically and genetically distinct populations in the Eastern Florida and the Gulf Atlantic regions of the United States. We used the Mobile Element Locator Tool to identify and genotype polymorphic insertions from five major clades of LINEs (CR1, L1, L2, RTE and R4) and the 41 subfamilies that constitute them. Across these groups we found large variation in the frequency of polymorphic insertions and the observed length distributions of these insertions, suggesting these groups vary in their activity and how frequently they successfully generate full-length, potentially active copies. Though we found an abundance of polymorphic insertions (over 45,000) most of these were observed at low frequencies and typically appeared as singletons. Site frequency spectra for most LINEs showed a significant shift toward low frequency alleles compared to the spectra observed for total genomic single nucleotide polymorphisms. Using Tajima's D, FST and the mean number of pairwise differences in LINE insertion polymorphisms, we found evidence that negative selection is acting on LINE families in a length-dependent manner, its effects being stronger in the larger Eastern Florida population. Our results suggest that a large effective population size and negative selection limit the expansion of polymorphic LINE insertions across these populations and that the probability of LINE polymorphisms reaching fixation is extremely low.
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18
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Burbrink FT, Chan YL, Myers EA, Ruane S, Smith BT, Hickerson MJ. Asynchronous demographic responses to Pleistocene climate change in Eastern Nearctic vertebrates. Ecol Lett 2016; 19:1457-1467. [DOI: 10.1111/ele.12695] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/27/2016] [Accepted: 09/15/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Frank T. Burbrink
- Department of Herpetology The American Museum of Natural History Central Park West and 79th Street New York NY10024 USA
| | - Yvonne L. Chan
- iDepartment ’Iolani School 563 Kamoku Street Honolulu HI96826 USA
| | - Edward A. Myers
- Department of Biology 6S‐143 College of Staten Island 2800 Victory Boulevard Staten Island NY10314 USA
- Department of Biology The Graduate School and University Center The City University of New York 365 Fifth Ave. NY10016 USA
| | - Sara Ruane
- Museum of Natural Science Louisiana State University 119 Foster Hall Baton Rouge LA70803 USA
| | - Brian Tilston Smith
- Department of Ornithology The American Museum of Natural History Central Park West and 79th Street New York NY10024 USA
| | - Michael J. Hickerson
- Department of Biology The Graduate School and University Center The City University of New York 365 Fifth Ave. NY10016 USA
- Biology Department City College of New York New York NY10016 USA
- Division of Invertebrate Zoology The American Museum of Natural History Central Park West and 79th Street New York NY10024 USA
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19
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Manthey JD, Tollis M, Lemmon AR, Moriarty Lemmon E, Boissinot S. Diversification in wild populations of the model organism Anolis carolinensis: A genome-wide phylogeographic investigation. Ecol Evol 2016; 6:8115-8125. [PMID: 27891220 PMCID: PMC5108263 DOI: 10.1002/ece3.2547] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 09/14/2016] [Accepted: 09/19/2016] [Indexed: 01/14/2023] Open
Abstract
The green anole (Anolis carolinensis) is a lizard widespread throughout the southeastern United States and is a model organism for the study of reproductive behavior, physiology, neural biology, and genomics. Previous phylogeographic studies of A. carolinensis using mitochondrial DNA and small numbers of nuclear loci identified conflicting and poorly supported relationships among geographically structured clades; these inconsistencies preclude confident use of A. carolinensis evolutionary history in association with morphological, physiological, or reproductive biology studies among sampling localities and necessitate increased effort to resolve evolutionary relationships among natural populations. Here, we used anchored hybrid enrichment of hundreds of genetic markers across the genome of A. carolinensis and identified five strongly supported phylogeographic groups. Using multiple analyses, we produced a fully resolved species tree, investigated relative support for each lineage across all gene trees, and identified mito‐nuclear discordance when comparing our results to previous studies. We found fixed differences in only one clade—southern Florida restricted to the Everglades region—while most polymorphisms were shared between lineages. The southern Florida group likely diverged from other populations during the Pliocene, with all other diversification during the Pleistocene. Multiple lines of support, including phylogenetic relationships, a latitudinal gradient in genetic diversity, and relatively more stable long‐term population sizes in southern phylogeographic groups, indicate that diversification in A. carolinensis occurred northward from southern Florida.
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Affiliation(s)
| | - Marc Tollis
- Biodesign Institute Arizona State University Tempe AZ USA
| | - Alan R Lemmon
- Department of Scientific Computing Florida State University Tallahassee FL USA
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20
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Prates I, Rivera D, Rodrigues MT, Carnaval AC. A mid‐
P
leistocene rainforest corridor enabled synchronous invasions of the
A
tlantic
F
orest by
A
mazonian anole lizards. Mol Ecol 2016; 25:5174-5186. [DOI: 10.1111/mec.13821] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 08/10/2016] [Accepted: 08/22/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Ivan Prates
- Department of Biology City College of New York 160 Convent Avenue Marshak Science Building, Room J‐526 New York NY 10031 USA
- Department of Biology Graduate Center City University of New York 365 Fifth Avenue, Room 4315 New York NY 10016 USA
| | - Danielle Rivera
- Department of Biology City College of New York 160 Convent Avenue Marshak Science Building, Room J‐526 New York NY 10031 USA
- Department of Biology University of Texas at Arlington 501 S. Nedderman Drive Arlington TX 76019 USA
| | - Miguel T. Rodrigues
- Departamento de Zoologia Instituto de Biociências Universidade de São Paulo Rua do Matão Travessa 14, n. 321 São Paulo SP 05508‐090 Brazil
| | - Ana C. Carnaval
- Department of Biology City College of New York 160 Convent Avenue Marshak Science Building, Room J‐526 New York NY 10031 USA
- Department of Biology Graduate Center City University of New York 365 Fifth Avenue, Room 4315 New York NY 10016 USA
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21
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Campbell‐Staton SC, Edwards SV, Losos JB. Climate‐mediated adaptation after mainland colonization of an ancestrally subtropical island lizard,
A
nolis carolinensis. J Evol Biol 2016; 29:2168-2180. [DOI: 10.1111/jeb.12935] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 06/07/2016] [Accepted: 06/24/2016] [Indexed: 01/08/2023]
Affiliation(s)
| | - S. V. Edwards
- Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
- Museum of Comparative Zoology Harvard University Cambridge MA USA
| | - J. B. Losos
- Department of Organismic and Evolutionary Biology Harvard University Cambridge MA USA
- Museum of Comparative Zoology Harvard University Cambridge MA USA
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22
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Guarnizo CE, Werneck FP, Giugliano LG, Santos MG, Fenker J, Sousa L, D’Angiolella AB, dos Santos AR, Strüssmann C, Rodrigues MT, Dorado-Rodrigues TF, Gamble T, Colli GR. Cryptic lineages and diversification of an endemic anole lizard (Squamata, Dactyloidae) of the Cerrado hotspot. Mol Phylogenet Evol 2016; 94:279-89. [DOI: 10.1016/j.ympev.2015.09.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/06/2015] [Accepted: 09/08/2015] [Indexed: 01/17/2023]
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23
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Jaffe AL, Campbell-Staton SC, Losos JB. Geographical variation in morphology and its environmental correlates in a widespread North American lizard,Anolis carolinensis(Squamata: Dactyloidae). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12711] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander L. Jaffe
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
| | | | - Jonathan B. Losos
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
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24
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Fedrizzi N, Stiassny MLJ, Boehm JT, Dougherty ER, Amato G, Mendez M. Population Genetic Structure of the Dwarf Seahorse (Hippocampus zosterae) in Florida. PLoS One 2015. [PMID: 26200110 PMCID: PMC4511636 DOI: 10.1371/journal.pone.0132308] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The dwarf seahorse (Hippocampus zosterae) is widely distributed throughout near-shore habitats of the Gulf of Mexico and is of commercial significance in Florida, where it is harvested for the aquarium and curio trades. Despite its regional importance, the genetic structure of dwarf seahorse populations remains largely unknown. As an aid to ongoing conservation efforts, we employed three commonly applied mtDNA markers (ND4, DLoop and CO1) to investigate the genetic structuring of H. zosterae in Florida using samples collected throughout its range in the state. A total of 1450 bp provided sufficient resolution to delineate four populations of dwarf seahorses, as indicated by significant fixation indices. Despite an overall significant population structure, we observed evidence of interbreeding between individuals from geographically distant sites, supporting the hypothesis that rafting serves to maintain a degree of population connectivity. All individuals collected from Pensacola belong to a single distinct subpopulation, which is highly differentiated from the rest of Floridian dwarf seahorses sampled. Our findings highlight the utility of mtDNA markers in evaluating barriers to gene flow and identifying genetically distinct populations, which are vital to the development of comprehensive conservation strategies for exploited taxa.
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Affiliation(s)
- Nathan Fedrizzi
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, United States of America
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- * E-mail:
| | - Melanie L. J. Stiassny
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Department of Ichthyology, Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
| | - J. T. Boehm
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Department of Ecology, Evolution and Behavior, CUNY Graduate Center, New York, New York, United States of America
| | - Eric R. Dougherty
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
| | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
| | - Martin Mendez
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, United States of America
- Latin America and Caribbean Program, Wildlife Conservation Society, Bronx, New York, United States of America
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25
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Macedonia JM, Clark DL, Cherry LE, Mohamed NE, Bartel BW. Comparison of Headbob Displays in Gray-Dewlapped and Red-Dewlapped Populations of Green Anoles (Anolis carolinensis). HERPETOLOGICA 2015. [DOI: 10.1655/herpetologica-d-14-00045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Geneva AJ, Hilton J, Noll S, Glor RE. Multilocus phylogenetic analyses of Hispaniolan and Bahamian trunk anoles (distichus species group). Mol Phylogenet Evol 2015; 87:105-17. [PMID: 25772800 DOI: 10.1016/j.ympev.2015.02.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 01/14/2015] [Accepted: 02/16/2015] [Indexed: 01/31/2023]
Abstract
The distichus species group includes six species and 21 subspecies of trunk ecomorph anoles distributed across Hispaniola and its satellite islands as well as the northern Bahamas. Although this group has long served as a model system for studies of reproductive character displacement, adaptation, behavior and speciation, it has never been the subject of a comprehensive phylogenetic analysis. Our goal here is to generate a multilocus phylogenetic dataset (one mitochondrial and seven nuclear loci) and to use this dataset to infer phylogenetic relationships among the majority of the taxa assigned to the distichus species group. We use these phylogenetic trees to address three topics about the group's evolution. First, we consider longstanding taxonomic controversies about the status of several species and subspecies assigned to the distichus species group. Second, we investigate the biogeographic history of the group and specifically test the hypotheses that historical division of Hispaniola into two paleo-islands contributed to the group's diversification and that Bahamian and Hispaniolan satellite island populations are derived from colonists from the main Hispaniolan landmass. Finally, third, we use comparative phylogenetic analyses to test the hypothesis that divergence between pale yellow and darkly pigmented orange or red dewlap coloration has occurred repeatedly across the distichus species group.
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Affiliation(s)
- Anthony J Geneva
- Department of Biology, University of Rochester, Rochester, NY 14627, United States.
| | - Jared Hilton
- Department of Biology, University of Rochester, Rochester, NY 14627, United States.
| | - Sabina Noll
- Department of Biology, University of Rochester, Rochester, NY 14627, United States.
| | - Richard E Glor
- Herpetology Division, Biodiversity Institute, University of Kansas, Lawrence, KS 66045, United States; Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, United States.
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27
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Seal JN, Brown L, Ontiveros C, Thiebaud J, Mueller UG. Gone to Texas: phylogeography of twoTrachymyrmex(Hymenoptera: Formicidae) species along the southeastern coastal plain of North America. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12426] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jon N. Seal
- Integrative Biology; University of Texas at Austin; 1 University Station #C0930 Austin TX 78712 USA
- Department of Biology; University of Texas at Tyler; 3900 University Blvd Tyler TX 75799 USA
| | - Larrimy Brown
- Department of Biology; University of Texas at Tyler; 3900 University Blvd Tyler TX 75799 USA
| | - Cynthia Ontiveros
- Department of Biology; University of Texas at Tyler; 3900 University Blvd Tyler TX 75799 USA
| | - Jeffrey Thiebaud
- Integrative Biology; University of Texas at Austin; 1 University Station #C0930 Austin TX 78712 USA
| | - Ulrich G. Mueller
- Integrative Biology; University of Texas at Austin; 1 University Station #C0930 Austin TX 78712 USA
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28
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Sugawara H, Takahashi H, Hayashi F. Microsatellite Analysis of the Population Genetic Structure ofAnolis carolinensisIntroduced to the Ogasawara Islands. Zoolog Sci 2015; 32:47-52. [DOI: 10.2108/zs140041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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29
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Fahey AL, Ricklefs RE, Dewoody JA. DNA-based approaches for evaluating historical demography in terrestrial vertebrates. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12259] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Anna L. Fahey
- Departments of Forestry and Natural Resource; Purdue University; West Lafayette Indiana 47907 USA
| | - Robert E. Ricklefs
- Department of Biology; University of Missouri at St Louis; St Louis MO 63121 USA
| | - J. Andrew Dewoody
- Departments of Forestry and Natural Resource; Purdue University; West Lafayette Indiana 47907 USA
- Biological Sciences; Purdue University; West Lafayette Indiana 47907 USA
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30
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Tollis M, Boissinot S. Lizards and LINEs: selection and demography affect the fate of L1 retrotransposons in the genome of the green anole (Anolis carolinensis). Genome Biol Evol 2014; 5:1754-68. [PMID: 24013105 PMCID: PMC3787681 DOI: 10.1093/gbe/evt133] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Autonomous retrotransposons lacking long terminal repeats (LTR) account for much of the variation in genome size and structure among vertebrates. Mammalian genomes contain hundreds of thousands of non-LTR retrotransposon copies, mostly resulting from the amplification of a single clade known as L1. The genomes of teleost fish and squamate reptiles contain a much more diverse array of non-LTR retrotransposon families, whereas copy number is relatively low. The majority of non-LTR retrotransposon insertions in nonmammalian vertebrates also appear to be very recent, suggesting strong purifying selection limits the accumulation of non-LTR retrotransposon copies. It is however unclear whether this turnover model, originally proposed in Drosophila, applies to nonmammalian vertebrates. Here, we studied the population dynamics of L1 in the green anole lizard (Anolis carolinensis). We found that although most L1 elements are recent in this genome, truncated insertions accumulate readily, and many are fixed at both the population and species level. In contrast, full-length L1 insertions are found at lower population frequencies, suggesting that the turnover model only applies to longer L1 elements in Anolis. We also found that full-length L1 inserts are more likely to be fixed in populations of small effective size, suggesting that the strength of purifying selection against deleterious alleles is highly dependent on host demographic history. Similar mechanisms seem to be controlling the fate of non-LTR retrotransposons in both Anolis and teleostean fish, which suggests that mammals have considerably diverged from the ancestral vertebrate in terms of how they interact with their intragenomic parasites.
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Affiliation(s)
- Marc Tollis
- Biology Department, Queens College, City University of New York, Flushing
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31
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Gamble T, Zarkower D. Identification of sex-specific molecular markers using restriction site-associated DNA sequencing. Mol Ecol Resour 2014; 14:902-13. [DOI: 10.1111/1755-0998.12237] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Revised: 01/24/2014] [Accepted: 01/28/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Tony Gamble
- Department of Genetics, Cell Biology, and Development; University of Minnesota; Minneapolis MN USA
- Bell Museum of Natural History; University of Minnesota; Minneapolis MN USA
| | - David Zarkower
- Department of Genetics, Cell Biology, and Development; University of Minnesota; Minneapolis MN USA
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Tollis M, Boissinot S. Genetic variation in the green anole lizard (Anolis carolinensis) reveals island refugia and a fragmented Florida during the quaternary. Genetica 2013; 142:59-72. [PMID: 24379168 DOI: 10.1007/s10709-013-9754-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 12/23/2013] [Indexed: 11/27/2022]
Abstract
The green anole lizard (Anolis carolinensis) is a model organism for behavior and genomics that is native to the southeastern United States. It is currently thought that the ancestors of modern green anoles dispersed to peninsular Florida from Cuba. However, the climatic changes and geological features responsible for the early diversification of A. carolinensis in North America have remained largely unexplored. This is because previous studies (1) differ in their estimates of the divergence times of populations, (2) are based on a single genetic locus or (3) did not test specific hypotheses regarding the geologic and topographic history of Florida. Here we provide a multi-locus study of green anole genetic diversity and find that the Florida peninsula contains a larger number of genetically distinct populations that are more diverse than those on the continental mainland. As a test of the island refugia hypothesis in Pleistocene Florida, we use a coalescent approach to estimate the divergence times of modern green anole lineages. We find that all demographic events occurred during or after the Upper Pliocene and suggest that green anole diversification was driven by population divergence on interglacial island refugia in Florida during the Lower Pleistocene, while the region was often separated from continental North America. When Florida reconnected to the mainland, two separate dispersal events led to the expansion of green anole populations across the Atlantic Seaboard and Gulf Coastal Plain.
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Affiliation(s)
- Marc Tollis
- Biology Department, Queens College, City University of New York (CUNY), 65-30 Kissena Boulevard, Flushing, New York, NY, USA,
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Kosushkin SA, Grechko VV. Molecular genetic relationships and some issues of systematics of rock lizards of the genus Darevskia (Squamata: Lacertidae) based on locus analysis of SINE-type repeats (Squam1). RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413070089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gartner GEA, Gamble T, Jaffe AL, Harrison A, Losos JB. Left-right dewlap asymmetry and phylogeography ofAnolis lineatuson Aruba and Curaçao. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12131] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Classification and evolutionary analysis of the basic helix-loop-helix gene family in the green anole lizard, Anolis carolinensis. Mol Genet Genomics 2013; 288:365-80. [PMID: 23756994 DOI: 10.1007/s00438-013-0755-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/25/2013] [Indexed: 12/15/2022]
Abstract
Helix-loop-helix (bHLH) proteins play essential regulatory roles in a variety of biological processes. These highly conserved proteins form a large transcription factor superfamily, and are commonly identified in large numbers within animal, plant, and fungal genomes. The bHLH domain has been well studied in many animal species, but has not yet been characterized in non-avian reptiles. In this study, we identified 102 putative bHLH genes in the genome of the green anole lizard, Anolis carolinensis. Based on phylogenetic analysis, these genes were classified into 43 families, with 43, 24, 16, 3, 10, and 3 members assigned into groups A, B, C, D, E, and F, respectively, and 3 members categorized as "orphans". Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with highly conserved patterns observed for introns and additional domains. Results from phylogenetic analysis of the H/E(spl) family suggest that genome and tandem gene duplications have contributed to this family's expansion. Our classification and evolutionary analysis has provided insights into the evolutionary diversification of animal bHLH genes, and should aid future studies on bHLH protein regulation of key growth and developmental processes.
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GOODMAN RM, ECHTERNACHT AC, HALL JC, DENG LD, WELCH JN. Influence of geography and climate on patterns of cell size and body size in the lizardAnolis carolinensis. Integr Zool 2013; 8:184-96. [DOI: 10.1111/1749-4877.12041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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