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Sullivan AP, Marciniak S, O'Dea A, Wake TA, Perry GH. Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama. Mol Ecol Resour 2021; 21:1517-1528. [PMID: 33595921 DOI: 10.1111/1755-0998.13361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/26/2021] [Accepted: 02/05/2021] [Indexed: 12/17/2022]
Abstract
Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n = 3), Late Holocene (984-1258 before present [BP]) archaeological midden (n = 5), and mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n = 5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n = 5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7× higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behaviour on mollusc evolutionary biology.
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Affiliation(s)
- Alexis P Sullivan
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, PA, USA
| | - Aaron O'Dea
- Smithsonian Tropical Research Institute, Panama City, Panama.,Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Thomas A Wake
- Smithsonian Tropical Research Institute, Panama City, Panama.,Department of Anthropology and the Costen Institute of Archaeology, University of California, Los Angeles, CA, USA
| | - George H Perry
- Department of Biology, Pennsylvania State University, University Park, PA, USA.,Department of Anthropology, Pennsylvania State University, University Park, PA, USA.,Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
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2
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Fontsere C, Alvarez-Estape M, Lester J, Arandjelovic M, Kuhlwilm M, Dieguez P, Agbor A, Angedakin S, Ayuk Ayimisin E, Bessone M, Brazzola G, Deschner T, Eno-Nku M, Granjon AC, Head J, Kadam P, Kalan AK, Kambi M, Langergraber K, Lapuente J, Maretti G, Jayne Ormsby L, Piel A, Robbins MM, Stewart F, Vergnes V, Wittig RM, Kühl HS, Marques-Bonet T, Hughes DA, Lizano E. Maximizing the acquisition of unique reads in noninvasive capture sequencing experiments. Mol Ecol Resour 2020; 21:745-761. [PMID: 33217149 DOI: 10.1111/1755-0998.13300] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 10/15/2020] [Accepted: 11/13/2020] [Indexed: 11/30/2022]
Abstract
Noninvasive samples as a source of DNA are gaining interest in genomic studies of endangered species. However, their complex nature and low endogenous DNA content hamper the recovery of good quality data. Target capture has become a productive method to enrich the endogenous fraction of noninvasive samples, such as faeces, but its sensitivity has not yet been extensively studied. Coping with faecal samples with an endogenous DNA content below 1% is a common problem when prior selection of samples from a large collection is not possible. However, samples classified as unfavourable for target capture sequencing might be the only representatives of unique specific geographical locations, or to answer the question of interest. To explore how library complexity may be increased without repeating DNA extractions and generating new libraries, in this study we captured the exome of 60 chimpanzees (Pan troglodytes) using faecal samples with very low proportions of endogenous content (<1%). Our results indicate that by performing additional hybridizations of the same libraries, the molecular complexity can be maintained to achieve higher coverage. Also, whenever possible, the starting DNA material for capture should be increased. Finally, we specifically calculated the sequencing effort needed to avoid exhausting the library complexity of enriched faecal samples with low endogenous DNA content. This study provides guidelines, schemes and tools for laboratories facing the challenges of working with noninvasive samples containing extremely low amounts of endogenous DNA.
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Affiliation(s)
- Claudia Fontsere
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Marina Alvarez-Estape
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Jack Lester
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Kuhlwilm
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain
| | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anthony Agbor
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Gregory Brazzola
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tobias Deschner
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Josephine Head
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Parag Kadam
- School of Biological and Environmental Sciences, Liverpool John Moores University, James Parsons Building, Liverpool, UK
| | - Ammie K Kalan
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mohamed Kambi
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kevin Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Juan Lapuente
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Comoé Chimpanzee Conservation Project, Kakpin, Comoé National Park, Ivory Coast, Côte d'Ivoire
| | - Giovanna Maretti
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alex Piel
- Department of Anthropology, University College London, London, UK
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fiona Stewart
- School of Biological and Environmental Sciences, Liverpool John Moores University, James Parsons Building, Liverpool, UK.,Department of Anthropology, University College London, London, UK
| | | | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Côte d'Ivoire
| | - Hjalmar S Kühl
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Esther Lizano
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, PRBB, Barcelona, Catalonia, Spain.,Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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3
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Gutleb DR, Ostner J, Schülke O, Wajjwalku W, Sukmak M, Roos C, Noll A. Non-invasive genotyping with a massively parallel sequencing panel for the detection of SNPs in HPA-axis genes. Sci Rep 2018; 8:15944. [PMID: 30374157 PMCID: PMC6206064 DOI: 10.1038/s41598-018-34223-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 10/08/2018] [Indexed: 11/09/2022] Open
Abstract
We designed a genotyping panel for the investigation of the genetic underpinnings of inter-individual differences in aggression and the physiological stress response. The panel builds on single nucleotide polymorphisms (SNPs) in genes involved in the three subsystems of the hypothalamic-pituitary-adrenal (HPA)-axis: the catecholamine, serotonin and corticoid metabolism. To promote the pipeline for use with wild animal populations, we used non-invasively collected faecal samples from a wild population of Assamese macaques (Macaca assamensis). We targeted loci of 46 previously reported SNPs in 21 candidate genes coding for elements of the HPA-axis and amplified and sequenced them using next-generation Illumina sequencing technology. We compared multiple bioinformatics pipelines for variant calling and variant effect prediction. Based on this strategy and the application of different quality thresholds, we identified up to 159 SNPs with different types of predicted functional effects among our natural study population. This study provides a massively parallel sequencing panel that will facilitate integrating large-scale SNP data into behavioural and physiological studies. Such a multi-faceted approach will promote understanding of flexibility and constraints of animal behaviour and hormone physiology.
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Affiliation(s)
- D R Gutleb
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Goettingen, Göttingen, Germany. .,Research Group Social Evolution in Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany. .,Leibniz Science Campus Primate Cognition, Göttingen, Germany.
| | - J Ostner
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Goettingen, Göttingen, Germany.,Research Group Social Evolution in Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Leibniz Science Campus Primate Cognition, Göttingen, Germany
| | - O Schülke
- Department of Behavioral Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, University of Goettingen, Göttingen, Germany.,Research Group Social Evolution in Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Leibniz Science Campus Primate Cognition, Göttingen, Germany
| | - W Wajjwalku
- Department of Farm Resources and Production Medicine, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom, Thailand
| | - M Sukmak
- Department of Farm Resources and Production Medicine, Faculty of Veterinary Medicine, Kasetsart University, Nakhon Pathom, Thailand
| | - C Roos
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - A Noll
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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Abstract
Conservation genetics is a branch of conservation biology that uses molecular data to assist in the conservation and management of imperiled populations, subspecies, and species. In this review, I examine conservation action plans (CAPs)—instrumental documents designed to influence conservation policy—for selected primate species. I use the information contained in CAPs as a means to guide this review. The primary genetics-based topics that are mentioned in CAPs are genetic connectivity, inbreeding, and subspecies/species delimitation. I discuss these topics as well as historical demographic inference and hybridization using examples from wild primate species to illustrate the myriad ways in which genetics can assist in conservation efforts. I also discuss some recent technological advances such as genomic capture techniques and the potential to do molecular work in remote locations.
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Affiliation(s)
- Richard R. Lawler
- Department of Sociology and Anthropology, James Madison University, Harrisonburg, Virginia 22807, USA
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5
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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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6
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Rich AM, Wasserman MD, Deimel C, Breeden SK, Kaestle F, Hunt KD. Is genetic drift to blame for testicular dysgenesis syndrome in Semliki chimpanzees (Pan troglodytes schweinfurthii)? J Med Primatol 2018; 47:257-269. [PMID: 29799118 DOI: 10.1111/jmp.12352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND We present 3 likely cases of testicular dysgenesis syndrome (TDS) within a community of chimpanzees (Pan troglodytes schweinfurthii). We tested whether genetic drift may be the culprit, as a genetic cause has been suspected to account for TDS among other wildlife. METHODS We successfully sequenced a 367-bp segment spanning the first hypervariable region within the D-loop of the mitochondrial genome for 78 DNA samples. RESULTS We found 24 polymorphic sequence sites consisting of 7 singletons and 17 parsimony informative sites. This sample contained 9 haplotypes with a diversity index of 0.78 (SD = 0.03). All tests against the null hypothesis of neutral polymorphisms were non-significant (P > .10). The mismatch distribution of pairwise differences does not fit a Poisson's curve (raggedness index = 0.166; SSD = 0.12; P = 1). CONCLUSIONS Thus, we found no significant signs of genetic isolation, population expansion, or genetic bottleneck. Alternative causes of TDS and how they might pertain to this population are discussed.
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Affiliation(s)
- Alicia M Rich
- Department of Anthropology, Boston University, Boston, MA, USA
- Department of Anthropology, Indiana University, Bloomington, IN, USA
| | | | - Caroline Deimel
- Department of Anthropology, Indiana University, Bloomington, IN, USA
| | - Scott K Breeden
- Marian University College of Osteopathic Medicine, Indianapolis, IN, USA
| | - Frederika Kaestle
- Department of Anthropology, Indiana University, Bloomington, IN, USA
| | - Kevin D Hunt
- Department of Anthropology, Indiana University, Bloomington, IN, USA
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7
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Detwiler KM. Mitochondrial DNA Analyses of Cercopithecus Monkeys Reveal a Localized Hybrid Origin for C. mitis doggetti in Gombe National Park, Tanzania. INT J PRIMATOL 2018. [DOI: 10.1007/s10764-018-0029-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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8
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Kistler L, Johnson SM, Irwin MT, Louis EE, Ratan A, Perry GH. A massively parallel strategy for STR marker development, capture, and genotyping. Nucleic Acids Res 2017; 45:e142. [PMID: 28666376 PMCID: PMC5587753 DOI: 10.1093/nar/gkx574] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 06/21/2017] [Indexed: 12/11/2022] Open
Abstract
Short tandem repeat (STR) variants are highly polymorphic markers that facilitate powerful population genetic analyses. STRs are especially valuable in conservation and ecological genetic research, yielding detailed information on population structure and short-term demographic fluctuations. Massively parallel sequencing has not previously been leveraged for scalable, efficient STR recovery. Here, we present a pipeline for developing STR markers directly from high-throughput shotgun sequencing data without a reference genome, and an approach for highly parallel target STR recovery. We employed our approach to capture a panel of 5000 STRs from a test group of diademed sifakas (Propithecus diadema, n = 3), endangered Malagasy rainforest lemurs, and we report extremely efficient recovery of targeted loci—97.3–99.6% of STRs characterized with ≥10x non-redundant sequence coverage. We then tested our STR capture strategy on P. diadema fecal DNA, and report robust initial results and suggestions for future implementations. In addition to STR targets, this approach also generates large, genome-wide single nucleotide polymorphism (SNP) panels from flanking regions. Our method provides a cost-effective and scalable solution for rapid recovery of large STR and SNP datasets in any species without needing a reference genome, and can be used even with suboptimal DNA more easily acquired in conservation and ecological studies.
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Affiliation(s)
- Logan Kistler
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.,Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Stephen M Johnson
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Mitchell T Irwin
- Department of Anthropology, Northern Illinois University, DeKalb, IL 60115, USA
| | - Edward E Louis
- Center for Conservation and Research, Omaha's Henry Doorly Zoo and Aquarium, Omaha, NE 68107, USA
| | - Aakrosh Ratan
- Department of Public Health Sciences and Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - George H Perry
- Departments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
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9
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Orkin JD, Yang Y, Yang C, Yu DW, Jiang X. Cost-effective scat-detection dogs: unleashing a powerful new tool for international mammalian conservation biology. Sci Rep 2016; 6:34758. [PMID: 27721442 PMCID: PMC5056371 DOI: 10.1038/srep34758] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/19/2016] [Indexed: 11/30/2022] Open
Abstract
Recently, detection dogs have been utilized to collect fecal samples from cryptic and rare mammals. Despite the great promise of this technique for conservation biology, its broader application has been limited by the high cost (tens to hundreds of thousands of dollars) and logistical challenges of employing a scat-detection dog team while conducting international, collaborative research. Through an international collaboration of primatologists and the Chinese Ministry of Public Security, we trained and used a detection dog to find scat from three species of unhabituated, free-ranging primates, for less than $3,000. We collected 137 non-human primate fecal samples that we confirmed by sequencing taxonomically informative genetic markers. Our detection dog team had a 92% accuracy rate, significantly outperforming our human-only team. Our results demonstrate that detection dogs can locate fecal samples from unhabituated primates with variable diets, locomotion, and grouping patterns, despite challenging field conditions. We provide a model for in-country training, while also building local capacity for conservation and genetic monitoring. Unlike previous efforts, our approach will allow for the wide adoption of scat-detection dogs in international conservation biology.
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Affiliation(s)
- Joseph D. Orkin
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
- Department of Anthropology, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N 1N4, Canada
| | - Yuming Yang
- Kunming Police Dog Training Base, Chinese Ministry of Security, 579 Baiyunlu Kunming, Yunnan, 650204, China
| | - Chunyan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
| | - Douglas W. Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR47TJ, UK
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 32 Jiaochang Donglu, Kunming, Yunnan 650223, China
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10
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Schweizer RM, Robinson J, Harrigan R, Silva P, Galverni M, Musiani M, Green RE, Novembre J, Wayne RK. Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves. Mol Ecol 2015; 25:357-79. [DOI: 10.1111/mec.13467] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Rena M. Schweizer
- Department of Ecology and Evolutionary Biology University of California, Los Angeles 610 Charles E Young Dr East Los Angeles CA 90095 USA
| | - Jacqueline Robinson
- Department of Ecology and Evolutionary Biology University of California, Los Angeles 610 Charles E Young Dr East Los Angeles CA 90095 USA
| | - Ryan Harrigan
- Center for Tropical Research Institute of the Environment and Sustainability University of California 619 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Pedro Silva
- CIBIO/InBio – Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Campus Agrário de Vairão 4485‐661 Vairão Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Rua do Campo Alegre s/n. 4169‐007 Porto Portugal
| | - Marco Galverni
- Laboratory of Genetics ISPRA (Istituto Superiore per la Protezione e Ricerca Ambientale) Via Cà Fornacetta 9 40064 Ozzano dell'Emilia BO Italy
| | - Marco Musiani
- Faculties of Environmental Design and Veterinary Medicine (Joint Appointment) EVDS University of Calgary 2500 University Dr NW Calgary Alberta Canada T2N 1N4
| | - Richard E. Green
- Department of Biomolecular Engineering University of California Santa Cruz CA 95060 USA
| | - John Novembre
- Department of Human Genetics University of Chicago 920 E. 58th Street Chicago IL 60637 USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology University of California, Los Angeles 610 Charles E Young Dr East Los Angeles CA 90095 USA
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11
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Comparative and population mitogenomic analyses of Madagascar's extinct, giant ‘subfossil’ lemurs. J Hum Evol 2015; 79:45-54. [DOI: 10.1016/j.jhevol.2014.06.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 03/25/2014] [Accepted: 06/04/2014] [Indexed: 11/21/2022]
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12
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The Genetic Basis of Primate Behavior: Genetics and Genomics in Field-Based Primatology. INT J PRIMATOL 2013; 35:1-10. [PMID: 25013243 DOI: 10.1007/s10764-013-9732-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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