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Martins AB, Valença-Montenegro MM, Lima MGM, Lynch JW, Svoboda WK, Silva-Júnior JDSE, Röhe F, Boubli JP, Fiore AD. A New Assessment of Robust Capuchin Monkey ( Sapajus) Evolutionary History Using Genome-Wide SNP Marker Data and a Bayesian Approach to Species Delimitation. Genes (Basel) 2023; 14:genes14050970. [PMID: 37239330 DOI: 10.3390/genes14050970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
Robust capuchin monkeys, Sapajus genus, are among the most phenotypically diverse and widespread groups of primates in South America, with one of the most confusing and often shifting taxonomies. We used a ddRADseq approach to generate genome-wide SNP markers for 171 individuals from all putative extant species of Sapajus to access their evolutionary history. Using maximum likelihood, multispecies coalescent phylogenetic inference, and a Bayes Factor method to test for alternative hypotheses of species delimitation, we inferred the phylogenetic history of the Sapajus radiation, evaluating the number of discrete species supported. Our results support the recognition of three species from the Atlantic Forest south of the São Francisco River, with these species being the first splits in the robust capuchin radiation. Our results were congruent in recovering the Pantanal and Amazonian Sapajus as structured into three monophyletic clades, though new morphological assessments are necessary, as the Amazonian clades do not agree with previous morphology-based taxonomic distributions. Phylogenetic reconstructions for Sapajus occurring in the Cerrado, Caatinga, and northeastern Atlantic Forest were less congruent with morphology-based phylogenetic reconstructions, as the bearded capuchin was recovered as a paraphyletic clade, with samples from the Caatinga biome being either a monophyletic clade or nested with the blond capuchin monkey.
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Affiliation(s)
- Amely Branquinho Martins
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, Cabedelo 58310-000, PB, Brazil
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mônica Mafra Valença-Montenegro
- Centro Nacional de Pesquisa e Conservação de Primatas Brasileiros, Instituto Chico Mendes de Conservação da Biodiversidade, Cabedelo 58310-000, PB, Brazil
| | - Marcela Guimarães Moreira Lima
- Laboratório de Biogeografia da Conservação e Macroecologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém 66077-530, PA, Brazil
| | - Jessica W Lynch
- Institute for Society and Genetics, Department of Anthropology, University of California-Los Angeles, Los Angeles, CA 90095, USA
| | - Walfrido Kühl Svoboda
- Instituto Latino-Americano de Ciências da Vida e da Natureza, Centro Interdisciplinar de Ciências da Vida, Universidade Federal da Integração Latino-Americana, Foz do Iguaçu 85870-650, PR, Brazil
| | - José de Sousa E Silva-Júnior
- Museu Paraense Emílio Goeldi, Ministério da Ciência, Tecnologia, Inovações e Comunicações, Coordenação de Zoologia, Campus de Pesquisa, Setor de Mastozoologia, Belém 66077-830, PA, Brazil
| | - Fábio Röhe
- Laboratório de Evolução e Genética Animal, Universidade Federal do Amazonas, Manaus 69067-005, AM, Brazil
| | - Jean Philippe Boubli
- School of Science, Engineering and the Environment, University of Salford, Salford M5 4WT, UK
| | - Anthony Di Fiore
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, The University of Texas at Austin, Austin, TX 78712, USA
- Tiputini Biodiversity Station, Universidad San Francisco de Quito, Quito 170901, Ecuador
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Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing. Heredity (Edinb) 2021; 127:312-322. [PMID: 34188193 PMCID: PMC8405704 DOI: 10.1038/s41437-021-00452-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Gibbons of the genus Hylobates, which inhabit Southeast Asia, show great diversity and comprise seven to nine species. Natural hybridisation has been observed in several species contact zones, but the history and extent of hybridisation and introgression in possibly historical and the current contact zones remain unclear. To uncover Hylobates species phylogeny and the extent of introgression in their evolution, genotyping by random amplicon sequencing-direct (GRAS-Di) was applied to 47 gibbons, representing seven Hylobates species/subspecies and two outgroup gibbon species. Over 200,000 autosomal single-nucleotide variant sites were identified. The autosomal phylogeny supported that divergence from the mainland species began ~3.5 million years ago, and subsequently occurred among the Sundaic island species. Significant introgression signals were detected between H. lar and H. pileatus, H. lar and H. agilis and H. albibarbis and H. muelleri, which all are parapatric and form ongoing hybrid zones. Furthermore, the introgression signals were detected in every analysed individual of these species, indicating a relatively long history of hybridisation, which might have affected the entire gene pool. By contrast, signals of introgression were either not detected or doubtful in other species pairs living on different islands, indicating the rarity of hybridisation and introgression, even though the Sundaic islands were connected during the Pliocene and Pleistocene glacial events.
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Distinct genetic clustering in the weakly differentiated polar cod, Boreogadus saida Lepechin, 1774 from East Siberian Sea to Svalbard. Polar Biol 2021. [DOI: 10.1007/s00300-021-02911-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractThe cold-adapted polar cod Boreogadus saida, a key species in Arctic ecosystems, is vulnerable to global warming and ice retreat. In this study, 1257 individuals sampled in 17 locations within the latitudinal range of 75–81°N from Svalbard to East Siberian Sea were genotyped with a dedicated suite of 116 single-nucleotide polymorphic loci (SNP). The overall pattern of isolation by distance (IBD) found was driven by the two easternmost samples (East Siberian Sea and Laptev Sea), whereas no differentiation was registered in the area between the Kara Sea and Svalbard. Eleven SNP under strong linkage disequilibrium, nine of which could be annotated to chromosome 2 in Atlantic cod, defined two genetic groups of distinct size, with the major cluster containing seven-fold larger number of individuals than the minor. No underlying geographic basis was evident, as both clusters were detected throughout all sampling sites in relatively similar proportions (i.e. individuals in the minor cluster ranging between 4 and 19% on the location basis). Similarly, females and males were also evenly distributed between clusters and age groups. A differentiation was, however, found regarding size at age: individuals belonging to the major cluster were significantly longer in the second year. This study contributes to increasing the population genetic knowledge of this species and suggests that an appropriate management should be ensured to safeguard its diversity.
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Orkin JD, Kuderna LFK, Marques-Bonet T. The Diversity of Primates: From Biomedicine to Conservation Genomics. Annu Rev Anim Biosci 2020; 9:103-124. [PMID: 33197208 DOI: 10.1146/annurev-animal-061220-023138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Until now, the field of primate genomics has focused on two major themes: understanding human evolution and advancing biomedical research. We propose that it is now time for a third theme to receive attention: conservation genomics. As a result of anthropogenic effects, the majority of primate species have become threatened with extinction. A more robust primate conservation genomics will allow for genetically informed population management. Thanks to a steady decline in the cost of sequencing, it has now become feasible to sequence whole primate genomes at the population level. Furthermore, technological advances in noninvasive genomic methods have made it possible to acquire genome-scale data from noninvasive biomaterials. Here, we review recent advances in the analysis of primate diversity, with a focus on genomic data sets across the radiation.
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Affiliation(s)
- Joseph D Orkin
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , ,
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , ,
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, Pompeu Fabra University and Spanish National Research Council, 08003 Barcelona, Spain; , , .,Sequencing Unit, National Genomic Analysis Center, Centre for Genomic Regulation, Barcelona Institute of Science, 08036 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autónoma de Barcelona, 08193 Barcelona, Spain
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Liu W, Xu Y, Li Z, Fan J, Yang Y. Genome-wide mining of microsatellites in king cobra (Ophiophagus hannah) and cross-species development of tetranucleotide SSR markers in Chinese cobra (Naja atra). Mol Biol Rep 2019; 46:6087-6098. [PMID: 31502192 DOI: 10.1007/s11033-019-05044-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/22/2019] [Indexed: 12/13/2022]
Abstract
The complete genome sequence provides the opportunity for genome-wide and coding region analysis of SSRs in the king cobra and for cross-species identification of microsatellite markers in the Chinese cobra. In the Ophiophagus hannah genome, tetranucleotide repeats (38.03%) were the most abundant category, followed by dinucleotides (23.03%), pentanucleotides (13.07%), mononucleotides (11.78%), trinucleotides (11.49%) and hexanucleotides (2.6%). Twenty predominant motifs in the O. hannah genome were (A)n (C)n, (AC)n, (AG)n, (AT)n, (AGG)n, (AAT)n, (AAG)n, (AAC)n, (ATG)n, (ATAG)n, (AAGG)n, (ATCT)n, (CCTT)n, (ATTT)n, (AAAT)n, (AATAG)n, (ATTCT)n, (ATATGT)n, (AGATAT)n. In total, 4344 SSRs were found in coding sequences (CDSs). Tetranucleotides (52.79%) were the most abundant microsatellite type in CDS, followed by trinucleotides (28.50%), dinucleotides (11.02%), pentanucleotides (4.42%), mononucleotides (1.77%), and hexanucleotides (1.50%). A total of 984 CDSs containing microsatellites were assigned 11152 Gene Ontology (GO) functional terms. Gene Ontology (GO) analysis demonstrated that cellular process, cell and binding were the most frequent GO terms in biological process, cellular component and molecular function, respectively. Thirty-two novel highly polymorphic (PIC > 0.5) SSR markers for Naja atra were developed from cross-species amplification based on the tetranucleotide microsatellite sequences in the king cobra genome. The number of alleles (NA) per locus had between 3 and 11 alleles with an average of 6.5, the polymorphism information content (PIC) value ranged from 0.521 to 0.858 (average = 0.707), the observed heterozygosity (Ho) of 32 microsatellite loci ranged from 0.292 to 0.875 (mean = 0.678), the expected heterozygosity (HE) ranged from 0.561 to 0.889 (average = 0.761), and 3 microsatellite loci exhibited statistically significant departure from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction (p < 0.003).
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Affiliation(s)
- Wencong Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China
| | - Yongtao Xu
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zekun Li
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China
| | - Jun Fan
- College of Materials and Chemistry & Chemical Engineering, Chengdu University of Technology, Chengdu, 610059, China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Valencia LM, Martins A, Ortiz EM, Di Fiore A. A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates. PLoS One 2018; 13:e0201254. [PMID: 30118481 PMCID: PMC6097672 DOI: 10.1371/journal.pone.0201254] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 07/11/2018] [Indexed: 01/08/2023] Open
Abstract
Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.
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Affiliation(s)
- Lina M. Valencia
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, University of Texas at Austin, Austin, United States of America
| | - Amely Martins
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, University of Texas at Austin, Austin, United States of America
- Centro Nacional de Pesquisa de Conservação de Primatas Brasileiros, ICMBio/MMA, Brazil, Brazil
| | - Edgardo M. Ortiz
- Department of Integrative Biology, University of Texas at Austin, Austin, United States of America
| | - Anthony Di Fiore
- Primate Molecular Ecology and Evolution Laboratory, Department of Anthropology, University of Texas at Austin, Austin, United States of America
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Tripp EA, Tsai YE, Zhuang Y, Dexter KG. RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra-arid deserts of Namibia. Ecol Evol 2017; 7:7920-7936. [PMID: 29043045 PMCID: PMC5632676 DOI: 10.1002/ece3.3274] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/16/2017] [Accepted: 06/20/2017] [Indexed: 01/04/2023] Open
Abstract
Deserts, even those at tropical latitudes, often have strikingly low levels of plant diversity, particularly within genera. One remarkable exception to this pattern is the genus Petalidium (Acanthaceae), in which 37 of 40 named species occupy one of the driest environments on Earth, the Namib Desert of Namibia and neighboring Angola. To contribute to understanding this enigmatic diversity, we generated RADseq data for 47 accessions of Petalidium representing 22 species. We explored the impacts of 18 different combinations of assembly parameters in de novo assembly of the data across nine levels of missing data plus a best practice assembly using a reference Acanthaceae genome for a total of 171 sequence datasets assembled. RADseq data assembled at several thresholds of missing data, including 90% missing data, yielded phylogenetic hypotheses of Petalidium that were confidently and nearly fully resolved, which is notable given that divergence time analyses suggest a crown age for African species of 3.6-1.4 Ma. De novo assembly of our data yielded the most strongly supported and well-resolved topologies; in contrast, reference-based assembly performed poorly, perhaps due in part to moderate phylogenetic divergence between the reference genome, Ruellia speciosa, and the ingroup. Overall, we found that Petalidium, despite the harshness of the environment in which species occur, shows a net diversification rate (0.8-2.1 species per my) on par with those of diverse genera in tropical, Mediterranean, and alpine environments.
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Affiliation(s)
- Erin A. Tripp
- Department of Ecology & Evolutionary BiologyUCB 334University of ColoradoBoulderCOUSA
- Museum of Natural HistoryUCB 350University of ColoradoBoulderCOUSA
| | - Yi‐Hsin Erica Tsai
- Department of Ecology & Evolutionary BiologyUCB 334University of ColoradoBoulderCOUSA
- Museum of Natural HistoryUCB 350University of ColoradoBoulderCOUSA
| | - Yongbin Zhuang
- Department of Ecology & Evolutionary BiologyUCB 334University of ColoradoBoulderCOUSA
- Museum of Natural HistoryUCB 350University of ColoradoBoulderCOUSA
| | - Kyle G. Dexter
- School of GeoSciencesUniversity of EdinburghEdinburghUK
- Royal Botanic Garden EdinburghEdinburghUK
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Steely CJ, Walker JA, Jordan VE, Beckstrom TO, McDaniel CL, St. Romain CP, Bennett EC, Robichaux A, Clement BN, Raveendran M, Worley KC, Phillips-Conroy J, Jolly CJ, Rogers J, Konkel MK, Batzer MA. Alu Insertion Polymorphisms as Evidence for Population Structure in Baboons. Genome Biol Evol 2017; 9:2418-2427. [PMID: 28957465 PMCID: PMC5622324 DOI: 10.1093/gbe/evx184] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2017] [Indexed: 12/25/2022] Open
Abstract
Male dispersal from the natal group at or near maturity is a feature of most baboon (Papio) species. It potentially has profound effects upon population structure and evolutionary processes, but dispersal, especially for unusually long distances, is not readily documented by direct field observation. In this pilot study, we investigate the possibility of retrieving baboon population structure in yellow (Papio cynocephalus) and kinda (Papio kindae) baboons from the distribution of variation in a genome-wide set of 494 Alu insertion polymorphisms, made available via the recently completed Baboon Genome Analysis Consortium. Alu insertion variation in a mixed population derived from yellow and olive (Papio anubis) baboons identified each individual's proportion of heritage from either parental species. In an unmixed yellow baboon population, our analysis showed greater similarity between neighboring than between more distantly situated groups, suggesting structuring of the population by male dispersal distance. Finally (and very provisionally), an unexpectedly sharp difference in Alu insertion frequencies between members of neighboring social groups of kinda baboons suggests that intergroup migration may be more rare than predicted in this little known species.
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Affiliation(s)
- Cody J. Steely
- Department of Biological Sciences, Louisiana State University
| | | | | | | | | | | | | | - Arianna Robichaux
- Department of Biological Sciences, Louisiana State University
- Department of Biological and Physical Sciences, Northwestern State University of Louisiana
| | - Brooke N. Clement
- Department of Biological Sciences, Louisiana State University
- School of Veterinary Medicine, Louisiana State University
| | | | | | - Kim C. Worley
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | | | - Jeff Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Mark A. Batzer
- Department of Biological Sciences, Louisiana State University
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Abstract
The world of primate genomics is expanding rapidly in new and exciting ways owing to lowered costs and new technologies in molecular methods and bioinformatics. The primate order is composed of 78 genera and 478 species, including human. Taxonomic inferences are complex and likely a consequence of ongoing hybridization, introgression, and reticulate evolution among closely related taxa. Recently, we applied large-scale sequencing methods and extensive taxon sampling to generate a highly resolved phylogeny that affirms, reforms, and extends previous depictions of primate speciation. The next stage of research uses this phylogeny as a foundation for investigating genome content, structure, and evolution across primates. Ongoing and future applications of a robust primate phylogeny are discussed, highlighting advancements in adaptive evolution of genes and genomes, taxonomy and conservation management of endangered species, next-generation genomic technologies, and biomedicine.
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Affiliation(s)
- Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702; Current Affiliation: Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, Virginia 22630;
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Ebel ER, DaCosta JM, Sorenson MD, Hill RI, Briscoe AD, Willmott KR, Mullen SP. Rapid diversification associated with ecological specialization in NeotropicalAdelphabutterflies. Mol Ecol 2015; 24:2392-405. [DOI: 10.1111/mec.13168] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 01/15/2023]
Affiliation(s)
- Emily R. Ebel
- Department of Biology; Boston University; Boston MA 02215 USA
| | | | | | - Ryan I. Hill
- Department of Biological Sciences; University of the Pacific; Stockton CA 95211 USA
| | - Adriana D. Briscoe
- Department of Ecology and Evolutionary Biology; University of California; Irvine CA 92697 USA
| | - Keith R. Willmott
- McGuire Center for Lepidoptera and Biodiversity; Florida Museum of Natural History; University of Florida; Gainesville FL 32611 USA
| | - Sean P. Mullen
- Department of Biology; Boston University; Boston MA 02215 USA
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Burrell AS, Disotell TR, Bergey CM. The use of museum specimens with high-throughput DNA sequencers. J Hum Evol 2015; 79:35-44. [PMID: 25532801 PMCID: PMC4312722 DOI: 10.1016/j.jhevol.2014.10.015] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Revised: 07/08/2014] [Accepted: 10/31/2014] [Indexed: 12/30/2022]
Abstract
Natural history collections have long been used by morphologists, anatomists, and taxonomists to probe the evolutionary process and describe biological diversity. These biological archives also offer great opportunities for genetic research in taxonomy, conservation, systematics, and population biology. They allow assays of past populations, including those of extinct species, giving context to present patterns of genetic variation and direct measures of evolutionary processes. Despite this potential, museum specimens are difficult to work with because natural postmortem processes and preservation methods fragment and damage DNA. These problems have restricted geneticists' ability to use natural history collections primarily by limiting how much of the genome can be surveyed. Recent advances in DNA sequencing technology, however, have radically changed this, making truly genomic studies from museum specimens possible. We review the opportunities and drawbacks of the use of museum specimens, and suggest how to best execute projects when incorporating such samples. Several high-throughput (HT) sequencing methodologies, including whole genome shotgun sequencing, sequence capture, and restriction digests (demonstrated here), can be used with archived biomaterials.
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Affiliation(s)
- Andrew S Burrell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA.
| | - Todd R Disotell
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
| | - Christina M Bergey
- Center for the Study of Human Origins, Department of Anthropology, New York University, 25 Waverly Place, New York, NY 10003, USA; New York Consortium in Evolutionary Primatology, USA
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13
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Viricel A, Pante E, Dabin W, Simon-Bouhet B. Applicability of RAD-tag genotyping for interfamilial comparisons: empirical data from two cetaceans. Mol Ecol Resour 2013; 14:597-605. [DOI: 10.1111/1755-0998.12206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/08/2013] [Accepted: 11/13/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Amélia Viricel
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - Eric Pante
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
| | - Willy Dabin
- Observatoire PELAGIS, UMS 3462 CNRS; Université de La Rochelle; Pôle analytique 5 allées de l'océan La Rochelle 17000 France
| | - Benoit Simon-Bouhet
- Littoral, Environnement et Sociétés (LIENSs) UMR 7266 CNRS; Université de La Rochelle; 2 rue Olympe de Gouges La Rochelle 17000 France
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15
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Perry GH. The Promise and Practicality of Population Genomics Research with Endangered Species. INT J PRIMATOL 2013. [DOI: 10.1007/s10764-013-9702-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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