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Bauza Nowotny E, Lyons PJ, Gonzalez-Socoloske D. Identification of the Eastern Massasauga Rattlesnake (Sistrurus catenatus) through genetic analysis of shed skin. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01274-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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2
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Behrooz R, Kaboli M, Arnal V, Nazarizadeh M, Asadi A, Salmanian A, Ahmadi M, Montgelard C. Conservation Below the Species Level: Suitable Evolutionarily Significant Units among Mountain Vipers (the Montivipera raddei complex) in Iran. J Hered 2019; 109:416-425. [PMID: 29401236 DOI: 10.1093/jhered/esy005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/23/2018] [Indexed: 02/05/2023] Open
Abstract
Northern and western mountains of Iran are among the most important biodiversity and endemism hot spots for reptiles in the Middle East. Among herpetofauna, the montivipers represent an emblematic and fragmented endemic group for which estimating their level of genetic differentiation and defining conservation priorities is urgently needed. Here, we present the most comprehensive phylogenetic study on the Montivipera raddei species group comprising all 5 known taxa, among which 3 are endemic to Iran. Based on 2 mitochondrial genes, phylogenetic and phylogeographic analyses revealed 3 major lineages each presenting very contrasting distribution areas. The Iranian montivipers are highly structured in clades showing low genetic diversity and corresponding to high altitude summits. Molecular dating revealed the role of Quaternary paleo-climatic oscillations and altitudinal movements of montivipers in shaping genetic diversity and differentiation of these sky-island taxa. In addition, the best scenario of historical biogeography allowed identifying 3 possible refugial areas in Iran most likely arising by vicariance. Based on our mitochondrial results and pending additional data, we recognize 3 candidate species among the M. raddei complex: M. raddei, Montivipera latifii, and Montivipera kuhrangica that are coherent with their geographical distribution. We propose that the most appropriate evolutionary significant units for conservation of the montivipers are represented by 13 units among which 6 are recognized as high priority. Finally, we suggest some recommendations to the IUCN as well as to the Iranian conservation policies with respect to conservation prioritization.
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Affiliation(s)
- Roozbeh Behrooz
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier, IRD, Montpellier, France
| | - Mohammad Kaboli
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Véronique Arnal
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier, IRD, Montpellier, France
| | - Masoud Nazarizadeh
- Department of Environmental Science, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | - Atefeh Asadi
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier, IRD, Montpellier, France
| | - Amin Salmanian
- Department of Natural Resources Engineering (Habitats and Biodiversity), Faculty of Environment and Energy (FEE), Tehran Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohsen Ahmadi
- Department of Natural Resources, Isfahan University of Technology, Isfahan, Iran
| | - Claudine Montgelard
- CEFE, PSL-EPHE (Biogéographie et Ecologie des Vertébrés), CNRS, Univ. Montpellier, Univ Paul Valéry Montpellier, IRD, Montpellier, France.,Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, Johannesburg, South Africa
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Abstract
Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics.
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Affiliation(s)
- Simon Creer
- School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, United Kingdom
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4
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Malhotra A, Creer S, Harris JB, Thorpe RS. The importance of being genomic: Non-coding and coding sequences suggest different models of toxin multi-gene family evolution. Toxicon 2015; 107:344-58. [DOI: 10.1016/j.toxicon.2015.08.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/31/2015] [Accepted: 08/06/2015] [Indexed: 10/23/2022]
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5
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Genetic Structure is Inconsistent with Subspecies Designations in the Western Massasauga Sistrurus tergeminus. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2015. [DOI: 10.3996/122014-jfwm-093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
The massasauga Sistrurus catenatus was historically divided into three subspecies, but this long-standing taxonomy has recently been called into question. Genetic research now recognizes a split of the species into the eastern massasauga S. catenatus and western massasauga S. tergeminus, with the latter split into two subspecies, the desert massasauga S. t. edwardsii and the prairie massasauga S. t. tergeminus. Although the distinction between geographically isolated populations of S. catenatus and S. tergeminus is well-supported genetically, the geographic relationships among populations of S. t. tergeminus and S. t. edwardsii remain unresolved because of incomplete sampling throughout the species’ range. This poses a difficult challenge for conservation and management of this species. Sistrurus t. tergeminus does not have state or federal conservation status, but S. t. edwardsii has been petitioned for listing under the U.S. Endangered Species Act. In this study, we used nuclear and mitochondrial DNA from 52 individuals from 7 states to explore the taxonomic and geographic relationships between S. t. tergeminus and S. t. edwardsii populations. Maximum likelihood and Bayesian inference frameworks for both nuclear and mtDNA genes indicated that S. t. tergeminus and S. t. edwardsii populations were genetically indistinguishable. However, at the species level, we did find eight well-supported mtDNA clades within S. tergeminus, including individuals from five peripheral populations in 1) Arizona and western New Mexico, 2) Colorado and Kansas, 3) Missouri, 4) Oklahoma, and 5) southern Texas. These peripherally isolated populations surrounded a larger population of individuals from north-central Texas, New Mexico, and Oklahoma that was contiguous with three additional genetically distinct populations. We conclude that the putative subspecies S. t. tergeminus and S. t. edwardsii, as currently defined, most likely represent polytypic phenotypes of S. tergeminus rather than discrete taxonomic entities. Instead, we suggest that S. tergeminus existed historically as a large, contiguous collection of populations that only recently became fragmented into several, as opposed to two, potentially discrete taxonomic entities.
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Rodríguez-Prieto A, Igea J, Castresana J. Development of rapidly evolving intron markers to estimate multilocus species trees of rodents. PLoS One 2014; 9:e96032. [PMID: 24804779 PMCID: PMC4012946 DOI: 10.1371/journal.pone.0096032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 04/03/2014] [Indexed: 11/18/2022] Open
Abstract
One of the major challenges in the analysis of closely related species, speciation and phylogeography is the identification of variable sequence markers that allow the determination of genealogical relationships in multiple genomic regions using coalescent and species tree approaches. Rodent species represent nearly half of the mammalian diversity, but so far no systematic study has been carried out to detect suitable informative markers for this group. Here, we used a bioinformatic pipeline to extract intron sequences from rodent genomes available in databases and applied a series of filters that allowed the identification of 208 introns that adequately fulfilled several criteria for these studies. The main required characteristics of the introns were that they had the maximum possible mutation rates, that they were part of single-copy genes, that they had an appropriate sequence length for amplification, and that they were flanked by exons with suitable regions for primer design. In addition, in order to determine the validity of this approach, we chose ten of these introns for primer design and tested them in a panel of eleven rodent species belonging to different representative families. We show that all these introns can be amplified in the majority of species and that, overall, 79% of the amplifications worked with minimum optimization of the annealing temperature. In addition, we confirmed for a pair of sister species the relatively high level of sequence divergence of these introns. Therefore, we provide here a set of adequate intron markers that can be applied to different species of Rodentia for their use in studies that require significant sequence variability.
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Affiliation(s)
- Ana Rodríguez-Prieto
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Javier Igea
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Imperial College London, Silwood Park Campus, Ascot, Berkshire, United Kingdom
| | - Jose Castresana
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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7
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Yuri T, Kimball RT, Harshman J, Bowie RCK, Braun MJ, Chojnowski JL, Han KL, Hackett SJ, Huddleston CJ, Moore WS, Reddy S, Sheldon FH, Steadman DW, Witt CC, Braun EL. Parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals. BIOLOGY 2013; 2:419-44. [PMID: 24832669 PMCID: PMC4009869 DOI: 10.3390/biology2010419] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/19/2022]
Abstract
Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.
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Affiliation(s)
- Tamaki Yuri
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, Norman, OK 73072, USA
| | - Rebecca T. Kimball
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - John Harshman
- 4869 Pepperwood Way, San Jose, CA 95124, USA; E-Mail:
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA; E-Mail:
| | - Michael J. Braun
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
- Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
| | - Jena L. Chojnowski
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Kin-Lan Han
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
| | - Shannon J. Hackett
- Zoology Department, Field Museum of Natural History, 1400 South Lakeshore Drive, Chicago, IL 60605, USA; E-Mail:
| | - Christopher J. Huddleston
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 4210 Silver Hill Road, Suitland, MD 20746, USA; E-Mails: (M.J.B.); (C.J.H.)
| | - William S. Moore
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI 48202, USA; E-Mail:
| | - Sushma Reddy
- Biology Department, Loyola University Chicago, Chicago, IL 60660, USA; E-Mail:
| | - Frederick H. Sheldon
- Museum of Natural Science, 119 Foster Hall, Louisiana State University, Baton Rouge, LA 70803, USA; E-Mail:
| | - David W. Steadman
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; E-Mail:
| | - Christopher C. Witt
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM 87131, USA; E-Mail:
| | - Edward L. Braun
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; E-Mails: (T.Y.); (R.T.K.); (J.L.C.); (K.-L.H.)
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8
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Anderson CG, Greenbaum E. Phylogeography of Northern Populations of the Black-Tailed Rattlesnake (Crotalus molossus Baird And Girard, 1853), With the Revalidation of C. ornatus Hallowell, 1854. HERPETOLOGICAL MONOGRAPHS 2012. [DOI: 10.1655/herpmonographs-d-11-00012.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Lardeux F, Aliaga C, Tejerina R, Ursic-Bedoya R. Development of Exon-Primed Intron-Crossing (EPIC) PCR primers for the malaria vector Anopheles pseudopunctipennis (Diptera: Culicidae). C R Biol 2012; 335:398-405. [PMID: 22721561 DOI: 10.1016/j.crvi.2012.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 05/14/2012] [Accepted: 05/14/2012] [Indexed: 11/28/2022]
Abstract
Using the Anopheles gambiae Giles genome as a template, we designed, screened and identified 14 novel Exon-Primed Intron-Crossing (EPIC) PCR primer pairs for Anopheles pseudopunctipennis Theobald 1901, a major vector of human Plasmodium sp. in South America. These primers were designed to target the conserved regions flanking consecutive exons of different genes and enabled the amplification of 17 loci of which nine were polymorphic. Polymorphisms at these loci ranged from two to four alleles. Intron length polymorphism analysis is a useful tool, which will allow the study of the population structure of this mosquito species, which remains poorly understood.
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Affiliation(s)
- Frédéric Lardeux
- Institut de recherche pour le développement (IRD), C.P. 9214 La Paz, Bolivia.
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10
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Sanz L, Harrison RA, Calvete JJ. First draft of the genomic organization of a PIII-SVMP gene. Toxicon 2012; 60:455-69. [PMID: 22543188 DOI: 10.1016/j.toxicon.2012.04.331] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 03/27/2012] [Accepted: 04/04/2012] [Indexed: 11/20/2022]
Abstract
The evolutionary pathway of highly toxic proteins expressed in snake venom glands from proteins without toxic function and expressed in non-parotid tissues remains poorly understood. Here we examine gene structure of a representative of a venom protein with an ADAMs metalloproteinase evolutionary origin. The structure of the 15,652 bp Echis ocellatus pre-pro EOC00089-like PIII-SVMP gene was assembled from PCR-amplified sequences of overlapping genomic fragments. The gene comprises 12 exons interrupted by 11 introns. In a homology model of the EOC00089-like protein, the insertion of introns interrupting coding regions lie just after or between secondary structure elements. Long interspersed nuclear retroelements (LINE) L2/CR1 and RTE/Bov-B, short interspersed nuclear retroelements SINE/Sauria, and a hobo-activator DNA (Charlie, hAT) transposon were identified within introns 1, 3, 7 and 8. Pairwise amino acid sequence comparisons between EOC00089-like PIII-SVMP and its closest orthologs, ADAM28, from a mammal, Homo sapiens, and the lizard, Anolis carolinensis, showed that the ORFs of these three proteins share 42%/59%, 49%/69%, and 48%/65% (identity/similarity), respectively. The protein-coding positions interrupted by each of the 11 introns of the Echis PIII-SVMP gene are entirely conserved in the A. carolinensis and human ADAM28 genes. However, the lizard and the human ADAM28 genes contain 5 introns not present in the E. ocellatus gene. Furthermore, Echis and Anolis introns exhibit quantitatively and qualitatively distinctions in their inserted retroelements. These findings identify introns as possible key elements in the recruitment and amplification process of SVMPs into the venom gland of extant snakes. Ongoing reptile genome sequencing projects may shed light on this intriguing aspect of the emergence and evolution of venom toxin genes. Furthermore, the organization of the PIII-SVMP reported here provides a genomic explanation for the emergence of dimeric disintegrin subunits encoded by short messengers.
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Affiliation(s)
- Libia Sanz
- Consejo Superior de Investigaciones Científicas, Valencia, Spain
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11
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Puritz JB, Addison JA, Toonen RJ. Next-generation phylogeography: a targeted approach for multilocus sequencing of non-model organisms. PLoS One 2012; 7:e34241. [PMID: 22470543 PMCID: PMC3314618 DOI: 10.1371/journal.pone.0034241] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 02/24/2012] [Indexed: 11/18/2022] Open
Abstract
The field of phylogeography has long since realized the need and utility of incorporating nuclear DNA (nDNA) sequences into analyses. However, the use of nDNA sequence data, at the population level, has been hindered by technical laboratory difficulty, sequencing costs, and problematic analytical methods dealing with genotypic sequence data, especially in non-model organisms. Here, we present a method utilizing the 454 GS-FLX Titanium pyrosequencing platform with the capacity to simultaneously sequence two species of sea star (Meridiastra calcar and Parvulastra exigua) at five different nDNA loci across 16 different populations of 20 individuals each per species. We compare results from 3 populations with traditional Sanger sequencing based methods, and demonstrate that this next-generation sequencing platform is more time and cost effective and more sensitive to rare variants than Sanger based sequencing. A crucial advantage is that the high coverage of clonally amplified sequences simplifies haplotype determination, even in highly polymorphic species. This targeted next-generation approach can greatly increase the use of nDNA sequence loci in phylogeographic and population genetic studies by mitigating many of the time, cost, and analytical issues associated with highly polymorphic, diploid sequence markers.
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Affiliation(s)
- Jonathan B Puritz
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, Hawai'i, United States of America.
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12
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Flot JF, Blanchot J, Charpy L, Cruaud C, Licuanan WY, Nakano Y, Payri C, Tillier S. Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization? BMC Ecol 2011; 11:22. [PMID: 21970706 PMCID: PMC3269986 DOI: 10.1186/1472-6785-11-22] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 10/04/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Morphological data suggest that, unlike most other groups of marine organisms, scleractinian corals of the genus Stylophora are more diverse in the western Indian Ocean and in the Red Sea than in the central Indo-Pacific. However, the morphology of corals is often a poor predictor of their actual biodiversity: hence, we conducted a genetic survey of Stylophora corals collected in Madagascar, Okinawa, the Philippines and New Caledonia in an attempt to find out the true number of species in these various locations. RESULTS A molecular phylogenetic analysis of the mitochondrial ORF and putative control region concurs with a haploweb analysis of nuclear ITS2 sequences in delimiting three species among our dataset: species A and B are found in Madagascar whereas species C occurs in Okinawa, the Philippines and New Caledonia. Comparison of ITS1 sequences from these three species with data available online suggests that species C is also found on the Great Barrier Reef, in Malaysia, in the South China Sea and in Taiwan, and that a distinct species D occurs in the Red Sea. Shallow-water morphs of species A correspond to the morphological description of Stylophora madagascarensis, species B presents the morphology of Stylophora mordax, whereas species C comprises various morphotypes including Stylophora pistillata and Stylophora mordax. CONCLUSIONS Genetic analysis of the coral genus Stylophora reveals species boundaries that are not congruent with morphological traits. Of the four hypotheses that may explain such discrepancy (phenotypic plasticity, morphological stasis, morphological convergence, and interspecific hybridization), the first two appear likely to play a role but the fourth one is rejected since mitochondrial and nuclear markers yield congruent species delimitations. The position of the root in our molecular phylogenies suggests that the center of origin of Stylophora is located in the western Indian Ocean, which probably explains why this genus presents a higher biodiversity in the westernmost part of its area of distribution than in the "Coral Triangle".
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Affiliation(s)
- Jean-François Flot
- Courant Research Center "Geobiology", University of Göttingen, Goldschmidtstraße 3, 37077 Göttingen, Germany
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
- UMR UPMC-CNRS-MNHN-IRD 7138, Département Systématique et Évolution, Muséum National d'Histoire Naturelle, Case Postale 26, 57 rue Cuvier, 75231 Paris Cedex 05, France
- URBO, Department of Biology, University of Namur, Rue de Bruxelle 61, 5000 Namur, Belgium
| | - Jean Blanchot
- UMR LOBP, Centre d'Océanologie de Marseille, Campus de Luminy, Case 901, 13288 Marseille Cedex 09, France
| | - Loïc Charpy
- UMR LOBP, Centre IRD de Tahiti, BP 529, 98713 Papeete, French Polynesia
| | - Corinne Cruaud
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
| | - Wilfredo Y Licuanan
- Br. Alfred Shields FSC Marine Station and Biology Department, De La Salle University, Manila 1004, Philippines
| | - Yoshikatsu Nakano
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, Okinawa 3422, Japan
| | - Claude Payri
- UR COREUS, IRD, B.P. A5, 98848 Nouméa, New Caledonia
| | - Simon Tillier
- UMR UPMC-CNRS-MNHN-IRD 7138, Département Systématique et Évolution, Muséum National d'Histoire Naturelle, Case Postale 26, 57 rue Cuvier, 75231 Paris Cedex 05, France
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13
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Salicini I, Ibáñez C, Juste J. Multilocus phylogeny and species delimitation within the Natterer's bat species complex in the Western Palearctic. Mol Phylogenet Evol 2011; 61:888-98. [PMID: 21872668 DOI: 10.1016/j.ympev.2011.08.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 06/17/2011] [Accepted: 08/05/2011] [Indexed: 10/17/2022]
Abstract
Delimiting species is a crucial issue for many biological disciplines and is of primary importance for designing effective conservation plans. Traditional taxonomy based on morphological characters can be misled by the presence of phenotypic plesiomorphism or adaptative convergence. The use of multiple locus genetic data appears thus as a powerful tool for recognizing species boundaries. In this study, we used six nuclear introns and two mitochondrial markers to conduct a phylogenetic study of the Myotis nattereri species complex in the Western Palearctic. We combined tree-based and non-tree-based analyses, and also used concatenated phylogenetic methods of the separated nuclear and mitochondrial dataset as well as a recent coalescence-based multilocus approach. The strong concordance between the results of the analyses conducted confirms that M. nattereri is a paraphyletic group that is composed of four well-differentiated lineages in the study area. In the framework of the unified species concept, these four clades can be confidently considered as four valid species. This recognition of new cryptic species in the Western Mediterranean region shows that the biodiversity of this well-studied area is still not fully understood.
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Affiliation(s)
- I Salicini
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Seville, Spain.
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14
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Kubatko LS, Gibbs HL, Bloomquist EW. Inferring Species-Level Phylogenies and Taxonomic Distinctiveness Using Multilocus Data in Sistrurus Rattlesnakes. Syst Biol 2011; 60:393-409. [DOI: 10.1093/sysbio/syr011] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Laura S. Kubatko
- Department of Statistics, The Ohio State University, Columbus, OH 43210, USA
- Departent of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
| | - H. Lisle Gibbs
- Departent of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH 43210, USA
- Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Erik W. Bloomquist
- Mathematical Biosciences Institute, The Ohio State University, Columbus, OH 43210, USA
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15
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Yu L, Luan PT, Jin W, Ryder OA, Chemnick LG, Davis HA, Zhang YP. Phylogenetic Utility of Nuclear Introns in Interfamilial Relationships of Caniformia (Order Carnivora). Syst Biol 2011; 60:175-87. [DOI: 10.1093/sysbio/syq090] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Li Yu
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Peng-Tao Luan
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Wei Jin
- Laboratory for Conservation and Utilization of Bio-Resources and Key Laboratory for Microbial Resources of the Ministry of Education, Yunnan University, Kunming 650091, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
| | - Oliver A. Ryder
- San Diego Zoo Conservation Research, PO Box 120551, San Diego, CA 92112, USA
| | - Leona G. Chemnick
- San Diego Zoo Conservation Research, PO Box 120551, San Diego, CA 92112, USA
| | - Heidi A. Davis
- San Diego Zoo Conservation Research, PO Box 120551, San Diego, CA 92112, USA
| | - Ya-ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming 650223, China
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Igea J, Juste J, Castresana J. Novel intron markers to study the phylogeny of closely related mammalian species. BMC Evol Biol 2010; 10:369. [PMID: 21118501 PMCID: PMC3087552 DOI: 10.1186/1471-2148-10-369] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 11/30/2010] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. RESULTS In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. CONCLUSIONS We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification and enough variability in most species, indicating that this marker set can be very helpful in multilocus phylogenetics of mammals. Due to the lower variability and stronger stochasticity of nuclear markers with respect to mitochondrial genes, studies should be designed to make use of several markers like the ones designed here.
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Affiliation(s)
- Javier Igea
- Institute of Evolutionary Biology (CSIC-UPF), Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Javier Juste
- Estacion Biologica de Donana (CSIC), Avda. Americo Vespucio s/n, 41092 Seville, Spain
| | - Jose Castresana
- Institute of Evolutionary Biology (CSIC-UPF), Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain
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GIBBS HLISLE, DIAZ JOSE. Identification of single copy nuclear DNA markers for North American pit vipers. Mol Ecol Resour 2009; 10:177-80. [DOI: 10.1111/j.1755-0998.2009.02707.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- H. LISLE GIBBS
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH 43210‐1293, USA
| | - JOSE DIAZ
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, OH 43210‐1293, USA
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Luan PT, Lan T, Peng D, Yu L, Zhang YP. [Intra-individual allele heterozygotes in phylogenetic analysis]. YI CHUAN = HEREDITAS 2009; 31:875-81. [PMID: 19819839 DOI: 10.3724/sp.j.1005.2009.00875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The study of evolutionary relationships among organisms is vital in evolutionary biology. To reconstruct a reliable species phylogeny, one of the most important issues is to choose proper molecular markers and take full advantage of phylogenetic information contained in these markers. Intra-individual allele heterozygotes (IIAHs) have been commonly detected in intron phylogenetic studies. How to incorporate IIAHs into phylogenetic framework has been a focus in current studies. In this review, the conception, isolation, and analytic methods of IIAHs in phylogeny were summarized.
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Affiliation(s)
- Peng-Tao Luan
- Laboratory of Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China.
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Flot JF. seqphase: a web tool for interconverting phase input/output files and fasta sequence alignments. Mol Ecol Resour 2009; 10:162-6. [PMID: 21565002 DOI: 10.1111/j.1755-0998.2009.02732.x] [Citation(s) in RCA: 379] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The program phase is widely used for Bayesian inference of haplotypes from diploid genotypes; however, manually creating phase input files from sequence alignments is an error-prone and time-consuming process, especially when dealing with numerous variable sites and/or individuals. Here, a web tool called seqphase is presented that generates phase input files from fasta sequence alignments and converts phase output files back into fasta. During the production of the phase input file, several consistency checks are performed on the dataset and suitable command line options to be used for the actual phase data analysis are suggested. seqphase was written in perl and is freely accessible over the Internet at the address http://www.mnhn.fr/jfflot/seqphase.
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Affiliation(s)
- J-F Flot
- UMR UPMC-CNRS-MNHN-IRD 7138, Département Systématique et Évolution, Muséum National d'Histoire Naturelle, Case Postale 26, 57 rue Cuvier, 75231 Paris Cedex 05, France
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20
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Affiliation(s)
- H. Bradley Shaffer
- Section of Evolution and Ecology, and Center for Population Biology, University of California Davis, CA, 95616, USA E-mail: (H.B.S.) (R.C.T.)
| | - Robert C. Thomson
- Section of Evolution and Ecology, and Center for Population Biology, University of California Davis, CA, 95616, USA E-mail: (H.B.S.) (R.C.T.)
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Foltz DW. An Ancient Repeat Sequence in the ATP Synthase β-Subunit Gene of Forcipulate Sea Stars. J Mol Evol 2007; 65:564-73. [PMID: 17909692 DOI: 10.1007/s00239-007-9036-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Revised: 08/10/2007] [Accepted: 08/17/2007] [Indexed: 10/22/2022]
Abstract
A novel repeat sequence with a conserved secondary structure is described from two nonadjacent introns of the ATP synthase beta-subunit gene in sea stars of the order Forcipulatida (Echinodermata: Asteroidea). The repeat is present in both introns of all forcipulate sea stars examined, which suggests that it is an ancient feature of this gene (with an approximate age of 200 Mya). Both stem and loop regions show high levels of sequence constraint when compared to flanking nonrepetitive intronic regions. The repeat was also detected in (1) the family Pterasteridae, order Velatida and (2) the family Korethrasteridae, order Velatida. The repeat was not detected in (1) the family Echinasteridae, order Spinulosida, (2) the family Astropectinidae, order Paxillosida, (3) the family Solasteridae, order Velatida, or (4) the family Goniasteridae, order Valvatida. The repeat lacks similarity to published sequences in unrestricted GenBank searches, and there are no significant open reading frames in the repeat or in the flanking intron sequences. Comparison via parametric bootstrapping to a published phylogeny based on 4.2 kb of nuclear and mitochondrial sequence for a subset of these species allowed the null hypothesis of a congruent phylogeny to be rejected for each repeat, when compared separately to the published phylogeny. In contrast, the flanking nonrepetitive sequences in each intron yielded separate phylogenies that were each congruent with the published phylogeny. In four species, the repeat in one or both introns has apparently experienced gene conversion. The two introns also show a correlated pattern of nucleotide substitutions, even after excluding the putative cases of gene conversion.
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Affiliation(s)
- David W Foltz
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803-1715, USA.
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