1
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Srigyan M, Schubert BW, Bushell M, Santos SHD, Figueiró HV, Sacco S, Eizirik E, Shapiro B. Mitogenomic analysis of a late Pleistocene jaguar from North America. J Hered 2024; 115:424-431. [PMID: 38150503 PMCID: PMC11235123 DOI: 10.1093/jhered/esad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023] Open
Abstract
The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.
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Affiliation(s)
- Megha Srigyan
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Blaine W Schubert
- Department of Geosciences, Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States
| | - Matthew Bushell
- Department of Geosciences, Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States
| | - Sarah H D Santos
- Department of Biology, University of Western Ontario, London, ON, Canada
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Henrique Vieira Figueiró
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Environmental Genomics Group, Vale Institute of Technology, Belem, PA, Brazil
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, United States
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Broggini C, Cavallini M, Vanetti I, Abell J, Binelli G, Lombardo G. From Caves to the Savannah, the Mitogenome History of Modern Lions ( Panthera leo) and Their Ancestors. Int J Mol Sci 2024; 25:5193. [PMID: 38791233 PMCID: PMC11121052 DOI: 10.3390/ijms25105193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Lions (Panthera leo) play a crucial ecological role in shaping and maintaining fragile ecosystems within Africa. Conservation efforts should focus on genetic variability within wild populations when considering reintroduction attempts. We studied two groups of lions from two conservation sites located in Zambia and Zimbabwe to determine their genetic make-up, information that is usually unknown to the sites. In this study, we analysed 17 specimens for cytb and seven microsatellite markers to ascertain family relationships and genetic diversity previously obtained by observational studies. We then produced a standardised haplogroup phylogeny using all available entire mitogenomes, as well as calculating a revised molecular clock. The modern lion lineage diverged ~151 kya and was divided into two subspecies, both containing three distinct haplogroups. We confirm that Panthera leo persica is not a subspecies, but rather a haplogroup of the northern P.l. leo that exited Africa at least ~31 kya. The progenitor to all lions existed ~1.2 Mya, possibly in SE Africa, and later exited Africa and split into the two cave lion lineages ~175 kya. Species demography is correlated to major climactic events. We now have a detailed phylogeny of lion evolution and an idea of their conservation status given the threat of climate change.
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Affiliation(s)
- Camilla Broggini
- Wildlife Research Unit (UIRCP-UCO), University of Cordoba, 14071 Córdoba, Spain;
| | - Marta Cavallini
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
| | - Isabella Vanetti
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
| | - Jackie Abell
- Centre for Agroecology, Water and Resilience, Coventry University, Coventry CV8 3LG, UK;
| | - Giorgio Binelli
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
| | - Gianluca Lombardo
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
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3
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Patterson EC, Lall GM, Neumann R, Ottolini B, Sacchini F, Foster AP, Jobling MA, Wetton JH. Defining cat mitogenome variation and accounting for numts via multiplex amplification and Nanopore sequencing. Forensic Sci Int Genet 2023; 67:102944. [PMID: 37820546 DOI: 10.1016/j.fsigen.2023.102944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 09/14/2023] [Accepted: 10/04/2023] [Indexed: 10/13/2023]
Abstract
Hair shed by domestic cats is a potentially useful source of forensic evidence. Analysable hair DNA is predominantly mitochondrial, but the recent domestication history of cats means that mtDNA diversity is low. A 402-bp control region segment is usually sequenced, defining only a small number of distinct haplotypes in populations. Previously, we used a long-amplicon approach to sequence whole mitogenomes in a sample of blood DNAs from 119 UK cats, greatly increasing observed diversity and reducing random match probabilities. To exploit this variation for forensic analysis, we here describe a multiplex system that amplifies the cat mitogenome in 60 overlapping amplicons of mean length 360 bp, followed by Nanopore sequencing. Variants detected in multiplex sequence data from unrooted hair completely mirror those from long-amplicon data from blood from the same individuals. However, applying the multiplex to matched blood DNA reveals additional sequence variants which derive from the major feline nuclear mitochondrial insertion sequence (numt), which covers 7.9 kb of the 17-kb mitogenome and exists in multiple tandem copies. We use long-amplicon Nanopore sequencing to investigate numt variation in a set of cats, together with an analysis of published genome sequences, and show that numt arrays are variable in both structure and sequence, thus providing a potential source of uncertainty when nuclear DNA predominates in a sample. Forensic application of the multiplex was demonstrated by matching hairs from a cat with skeletal remains from its putative mother, both of which shared a globally common haplotype at the control region. The random match probability in this case with the CR 402-bp segment was 0.21 and this decreased to 0.03 when considering the whole mitogenome. The developed multiplex and sequencing approach, when applied to cat hair where nuclear DNA is scarce, can provide a reliable and highly discriminating source of forensic genetic evidence from a single hair. The confounding effect of numt co-amplification in degraded samples where mixed sequences are observed can be mitigated by variant phasing, and by comparison with numt sequence diversity data, such as those presented here.
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Affiliation(s)
- Emily C Patterson
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Gurdeep Matharu Lall
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Barbara Ottolini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK
| | - Federico Sacchini
- IDEXX Laboratories Italia S.r.l., Via Guglielmo Silva, 36-20149 Milano (MI), Italy
| | - Aiden P Foster
- Bristol Veterinary School, University of Bristol, Langford House, Langford, North Somerset BS40 5DU, UK
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester LE1 7RH UK.
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4
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Sun X, Liu YC, Tiunov MP, Gimranov DO, Zhuang Y, Han Y, Driscoll CA, Pang Y, Li C, Pan Y, Velasco MS, Gopalakrishnan S, Yang RZ, Li BG, Jin K, Xu X, Uphyrkina O, Huang Y, Wu XH, Gilbert MTP, O'Brien SJ, Yamaguchi N, Luo SJ. Ancient DNA reveals genetic admixture in China during tiger evolution. Nat Ecol Evol 2023; 7:1914-1929. [PMID: 37652999 DOI: 10.1038/s41559-023-02185-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.
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Affiliation(s)
- Xin Sun
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Yue-Chen Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mikhail P Tiunov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Dmitry O Gimranov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Ural Federal University, Yekaterinburg, Russia
| | - Yan Zhuang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yu Han
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Carlos A Driscoll
- Section of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, MD, USA
| | - Yuhong Pang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Chunmei Li
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Yan Pan
- School of Archaeology and Museology, Peking University, Beijing, China
| | - Marcela Sandoval Velasco
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui-Zheng Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Kun Jin
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Olga Uphyrkina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Guangdong, China
| | - Xiao-Hong Wu
- School of Archaeology and Museology, Peking University, Beijing, China
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Stephen J O'Brien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA.
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University of Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia.
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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5
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Liu H, Wang D, Zhang C, Pu T, Xiong L, Wei F, Hu Y. Development of short-target primers for species identification in biological studies of Carnivora. Ecol Evol 2023; 13:e10135. [PMID: 37250442 PMCID: PMC10212699 DOI: 10.1002/ece3.10135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/27/2023] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Noninvasive genetic sampling greatly facilitates studies on the genetics, ecology, and conservation of threatened species. Species identification is often a prerequisite for noninvasive sampling-based biological studies. Due to the low quantity and quality of genomic DNA from noninvasive samples, high-performance short-target PCR primers are necessary for DNA barcoding applications. The order Carnivora is characterized by an elusive habit and threatened status. In this study, we developed three pairs of short-target primers for identifying Carnivora species. The COI279 primer pair was suitable for samples with better DNA quality. The COI157a and COI157b primer pairs performed well for noninvasive samples and reduced the interference of nuclear mitochondrial pseudogenes (numts). COI157a could effectively identify samples from Felidae, Canidae, Viverridae, and Hyaenidae, while COI157b could be applied to samples from Ursidae, Ailuridae, Mustelidae, Procyonidae, and Herpestidae. These short-target primers will facilitate noninvasive biological studies and efforts to conserve Carnivora species.
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Affiliation(s)
- Huiwen Liu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dan Wang
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | | | | | - Lijuan Xiong
- School of Life SciencesGuizhou Normal UniversityGuiyangChina
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation BiologyInstitute of Zoology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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6
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Salis AT, Bray SCE, Lee MSY, Heiniger H, Barnett R, Burns JA, Doronichev V, Fedje D, Golovanova L, Harington CR, Hockett B, Kosintsev P, Lai X, Mackie Q, Vasiliev S, Weinstock J, Yamaguchi N, Meachen JA, Cooper A, Mitchell KJ. Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge. Mol Ecol 2022; 31:6407-6421. [PMID: 34748674 DOI: 10.1111/mec.16267] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023]
Abstract
The Bering Land Bridge connecting North America and Eurasia was periodically exposed and inundated by oscillating sea levels during the Pleistocene glacial cycles. This land connection allowed the intermittent dispersal of animals, including humans, between Western Beringia (far northeast Asia) and Eastern Beringia (northwest North America), changing the faunal community composition of both continents. The Pleistocene glacial cycles also had profound impacts on temperature, precipitation and vegetation, impacting faunal community structure and demography. While these palaeoenvironmental impacts have been studied in many large herbivores from Beringia (e.g., bison, mammoths, horses), the Pleistocene population dynamics of the diverse guild of carnivorans present in the region are less well understood, due to their lower abundances. In this study, we analyse mitochondrial genome data from ancient brown bears (Ursus arctos; n = 103) and lions (Panthera spp.; n = 39), two megafaunal carnivorans that dispersed into North America during the Pleistocene. Our results reveal striking synchronicity in the population dynamics of Beringian lions and brown bears, with multiple waves of dispersal across the Bering Land Bridge coinciding with glacial periods of low sea levels, as well as synchronous local extinctions in Eastern Beringia during Marine Isotope Stage 3. The evolutionary histories of these two taxa underline the crucial biogeographical role of the Bering Land Bridge in the distribution, turnover and maintenance of megafaunal populations in North America.
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Affiliation(s)
- Alexander T Salis
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Division of Vertebrate Zoology, American Museum of Natural History, New York, New York, USA
| | - Sarah C E Bray
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Registry of Senior Australians (ROSA), South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
| | - Michael S Y Lee
- College of Science and Engineering, Flinders University, Bedford Park, South Australia, Australia.,South Australian Museum, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Ross Barnett
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - James A Burns
- Curator Emeritus, Royal Alberta Museum, Edmonton, Alberta, Canada
| | | | - Daryl Fedje
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | | | - C Richard Harington
- Curator Emeritus and Research Associate, Research Division (Paleobiology), Canadian Museum of Nature, Ottawa, Canada
| | - Bryan Hockett
- US Department of Interior, Bureau of Land Management, Nevada State Office, Reno, Nevada, USA
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Department of History, Ural Federal University, Yekaterinburg, Russia
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Quentin Mackie
- Department of Anthropology, University of Victoria, Victoria, B.C, Canada
| | - Sergei Vasiliev
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Russia
| | - Jacobo Weinstock
- Faculty of Humanities (Archaeology), University of Southampton, UK
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Malaysia
| | - Julie A Meachen
- Anatomy Department, Des Moines University, Des Moines, Iowa, USA
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.,Department of Zoology, Otago Palaeogenetics Laboratory, University of Otago, Dunedin, New Zealand
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7
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Triant DA, Pearson WR. Comparison of detection methods and genome quality when quantifying nuclear mitochondrial insertions in vertebrate genomes. Front Genet 2022; 13:984513. [PMID: 36482890 PMCID: PMC9723244 DOI: 10.3389/fgene.2022.984513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 11/03/2022] [Indexed: 01/27/2024] Open
Abstract
The integration of mitochondrial genome fragments into the nuclear genome is well documented, and the transfer of these mitochondrial nuclear pseudogenes (numts) is thought to be an ongoing evolutionary process. With the increasing number of eukaryotic genomes available, genome-wide distributions of numts are often surveyed. However, inconsistencies in genome quality can reduce the accuracy of numt estimates, and methods used for identification can be complicated by the diverse sizes and ages of numts. Numts have been previously characterized in rodent genomes and it was postulated that they might be more prevalent in a group of voles with rapidly evolving karyotypes. Here, we examine 37 rodent genomes, and an additional 26 vertebrate genomes, while also considering numt detection methods. We identify numts using DNA:DNA and protein:translated-DNA similarity searches and compare numt distributions among rodent and vertebrate taxa to assess whether some groups are more susceptible to transfer. A combination of protein sequence comparisons (protein:translated-DNA) and BLASTN genomic DNA searches detect 50% more numts than genomic DNA:DNA searches alone. In addition, higher-quality RefSeq genomes produce lower estimates of numts than GenBank genomes, suggesting that lower quality genome assemblies can overestimate numts abundance. Phylogenetic analysis shows that mitochondrial transfers are not associated with karyotypic diversity among rodents. Surprisingly, we did not find a strong correlation between numt counts and genome size. Estimates using DNA: DNA analyses can underestimate the amount of mitochondrial DNA that is transferred to the nucleus.
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Affiliation(s)
- Deborah A. Triant
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
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8
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Bredemeyer KR, Seabury CM, Stickney MJ, McCarrey JR, vonHoldt BM, Murphy WJ. Rapid Macrosatellite Evolution Promotes X-Linked Hybrid Male Sterility in a Feline Interspecies Cross. Mol Biol Evol 2021; 38:5588-5609. [PMID: 34519828 PMCID: PMC8662614 DOI: 10.1093/molbev/msab274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The sterility or inviability of hybrid offspring produced from an interspecific mating result from incompatibilities between parental genotypes that are thought to result from divergence of loci involved in epistatic interactions. However, attributes contributing to the rapid evolution of these regions also complicates their assembly, thus discovery of candidate hybrid sterility loci is difficult and has been restricted to a small number of model systems. Here we reported rapid interspecific divergence at the DXZ4 macrosatellite locus in an interspecific cross between two closely related mammalian species: the domestic cat (Felis silvestris catus) and the Jungle cat (Felis chaus). DXZ4 is an interesting candidate due to its structural complexity, copy number variability, and described role in the critical yet complex biological process of X-chromosome inactivation. However, the full structure of DXZ4 was absent or incomplete in nearly every available mammalian genome assembly given its repetitive complexity. We compared highly continuous genomes for three cat species, each containing a complete DXZ4 locus, and discovered that the felid DXZ4 locus differs substantially from the human ortholog, and that it varies in copy number between cat species. Additionally, we reported expression, methylation, and structural conformation profiles of DXZ4 and the X chromosome during stages of spermatogenesis that have been previously associated with hybrid male sterility. Collectively, these findings suggest a new role for DXZ4 in male meiosis and a mechanism for feline interspecific incompatibility through rapid satellite divergence.
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Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | | | - Mark J Stickney
- Veterinary Medical Teaching Hospital, Texas A&M University, College Station, TX, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
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9
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Avoiding common numts to provide reliable species identification for tiger parts. FORENSIC SCIENCE INTERNATIONAL: REPORTS 2021. [DOI: 10.1016/j.fsir.2020.100166] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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10
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Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion. Sci Rep 2020; 10:12621. [PMID: 32724178 PMCID: PMC7387438 DOI: 10.1038/s41598-020-69474-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/08/2020] [Indexed: 11/08/2022] Open
Abstract
The cave lion is an extinct felid that was widespread across the Holarctic throughout the Late Pleistocene. Its closest extant relative is the lion (Panthera leo), but the timing of the divergence between these two taxa, as well as their taxonomic ranking are contentious. In this study we analyse 31 mitochondrial genome sequences from cave lion individuals that, through a combination of 14C and genetic tip dating, are estimated to be from dates extending well into the mid-Pleistocene. We identified two deeply diverged and well-supported reciprocally monophyletic mitogenome clades in the cave lion, and an additional third distinct lineage represented by a single individual. One of these clades was restricted to Beringia while the other was prevalent across western Eurasia. These observed clade distributions are in line with previous observations that Beringian and European cave lions were morphologically distinct. The divergence dates for these lineages are estimated to be far older than those between extant lions subspecies. By combining our radiocarbon tip-dates with a split time prior that takes into account the most up-to-date fossil stem calibrations, we estimated the mitochondrial DNA divergence between cave lions and lions to be 1.85 Million ya (95% 0.52- 2.91 Mya). Taken together, these results support previous hypotheses that cave lions existed as at least two subspecies during the Pleistocene, and that lions and cave lions were distinct species.
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11
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Pfau RS, Goetze JR, Martin RE, Matocha KG, Nelson AD. Spatial and temporal genetic diversity of the Texas kangaroo rat, Dipodomys elator (Rodentia: Heteromyidae). J Mammal 2019. [DOI: 10.1093/jmammal/gyz090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractThe Texas kangaroo rat (Dipodomys elator) is listed as a threatened species in Texas because of its scarcity and small geographic range. We assessed patterns of genetic diversity in D. elator that could affect extinction risk or influence management decisions. Specific objectives included: 1) document levels of genetic diversity, 2) document the degree and patterns of genetic divergence among localities, and 3) compare levels of genetic diversity between different time periods at the same locality. Portions of the mitochondrial genome (mtDNA; control region, cytochrome c oxidase subunit I, and cytochrome b) were sequenced and nuclear microsatellites were examined. Low mtDNA diversity was observed, which could be explained by an historical, species-wide genetic bottleneck. In contrast, microsatellites exhibited ample variation, and analyses were conducted using data from 11 loci and four populations (designated Quanah, Iowa Park, Vernon, and Harrold). Allelic diversity and heterozygosity were similar between populations and temporal samples. Estimates of effective population size (Ne) ranged from 5 to 856, depending on method and population, with Iowa Park showing consistently lower values than Quanah. All methods addressing population structure indicated that the Iowa Park population was divergent from the others, with Vernon and Harrold showing a somewhat intermediate relationship but with a closer affiliation with Quanah than Iowa Park, despite their closer proximity to Iowa Park. This pattern did not conform to isolation by distance, thus genetic drift appears to have played a greater role than gene flow in establishing genetic structure. There was much less difference between temporal samples compared to geographic samples, indicating that genetic drift has had only minimal impacts in shifting allelic frequencies over the time periods examined (17–36 years).
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Affiliation(s)
- Russell S Pfau
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Jim R Goetze
- Natural Sciences Department, Laredo Community College, Laredo, TX, USA
| | | | - Kenneth G Matocha
- Department of Biology, South Arkansas Community College, El Dorado, AR, USA
| | - Allan D Nelson
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
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12
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Curry CJ, White PA, Derr JN. Genetic analysis of African lions (Panthera leo) in Zambia support movement across anthropogenic and geographical barriers. PLoS One 2019; 14:e0217179. [PMID: 31150429 PMCID: PMC6544237 DOI: 10.1371/journal.pone.0217179] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/06/2019] [Indexed: 11/18/2022] Open
Abstract
The Luangwa Valley in eastern Zambia is a transverse offshoot of the Great Rift Valley system. This region appears to have an isolating effect as evidenced by suspected endemic subspecies, such as the Cookson's wildebeest and Thornicroft's giraffe. Recent mitochondrial DNA studies demonstrated that African lions in Zambia consist of two highly diverse eastern and western sub-populations. Herein, we report nuclear and mitochondrial DNA results from 409 lions that support this population substructure across Zambia but proposes only partial isolation of the Luangwa Valley with more movement between the populations than previously thought. Population assignment analysis identifies two populations with little evidence of admixture assigning lions to either the eastern or western sub-populations. A high occurrence of private alleles and clear evidence for a Wahlund effect further justify the presence of a highly structured population. But, while mitochondrial DNA analysis still shows little to no matrilineal gene flow (FST = 0.53) between sub-populations, microsatellite analysis suggests there is gene flow (FST = 0.04) with low but significant isolation-by-distance and an average of 6 migrants per generation. Evidence of isolation-by-distance is also found in factorial correspondence analysis with the Lower Zambezi National Park and eastern corridor clusters overlapping isolated clusters of the Luangwa Valley and western sub-population. From this evidence, the Luangwa Valley appears separated from the western sub-population with some dispersal through the southern regions of the eastern sub-population. Both the eastern and western sub-populations have high heterozygosity (0.68 and 0.69, respectively) and genetic diversity (0.47 and 0.50, respectively) values, indicative of genetically healthy populations.
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Affiliation(s)
- Caitlin J. Curry
- Interdisciplinary Program of Genetics, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Paula A. White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, United States of America
| | - James N. Derr
- Interdisciplinary Program of Genetics, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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13
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Benedict BD, Castellanos AA, Light JE. Phylogeographic assessment of the Heermann’s kangaroo rat (Dipodomys heermanni). J Mammal 2018. [DOI: 10.1093/jmammal/gyy166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Bridgett D Benedict
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Adrian A Castellanos
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX 77843, USA
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14
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Monterroso P, Godinho R, Oliveira T, Ferreras P, Kelly MJ, Morin DJ, Waits LP, Alves PC, Mills LS. Feeding ecological knowledge: the underutilised power of faecal
DNA
approaches for carnivore diet analysis. Mamm Rev 2018. [DOI: 10.1111/mam.12144] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pedro Monterroso
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
| | - Raquel Godinho
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Teresa Oliveira
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM) Ronda de Toledo 12 Ciudad Real 13071 Spain
| | - Marcella J. Kelly
- Department of Fish and Wildlife ConservationVirginia Tech 146 Cheatham Hall Blacksburg VA 24061‐0321 USA
| | - Dana J. Morin
- Cooperative Wildlife Research LaboratorySouthern Illinois University 251 Lincoln Drive Carbondale IL 62901 USA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of Idaho 875 Perimeter Drive MS 1136 Moscow ID 83844‐1136 USA
| | - Paulo C. Alves
- CIBIO/InBIOCentro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto. Campus de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do Porto R. Campo Alegre s/n Porto 4169‐007 Portugal
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
| | - L. Scott Mills
- Wildlife Biology ProgramUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
- Office of Research and Creative ScholarshipUniversity of Montana 32 Campus Drive Missoula MT 59812 USA
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15
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Kaya S, Çıplak B. Possibility of numt co-amplification from gigantic genome of Orthoptera: testing efficiency of standard PCR protocol in producing orthologous COI sequences. Heliyon 2018; 4:e00929. [PMID: 30519651 PMCID: PMC6260432 DOI: 10.1016/j.heliyon.2018.e00929] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/06/2018] [Accepted: 11/08/2018] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial DNA has been the preferential genome biodiversity studies. However, several factors contribute to its inadequacy. Numts constitute one of the main complications that prevent obtaining orthologous mitochondrial sequences. Orthoptera have been a model group in numt studies because of their huge genome size. In this study we aimed to; (i) test efficiency of standard PCR protocol in producing orthologous sequences of cytochrome C oxidase, (ii) study presence/absence of numts in several unstudied Orthoptera species, (iii) test if there is a threshold between the length of mtDNA targeted for amplification and possibility of encountering numts, and (iv) estimate reliability of the sequences in databases in light of these findings. For these aims we studied 38 species of Orthoptera representing different sublineages and genome sizes. DNA extracted from each sample was used to amplify five different fragments of COI region by standard PCR protocol. Sequenced PCR amplicons were checked for numt possibility by several different numt criteria. No sequences without numt signs were obtained for the first fragment. The number of samples with numt signs for the other four fragments differed between the suborders Ensifera and Caelifera. The percentage of samples with numt signs was higher in Caelifera than Ensifera for all fragments. The numt percentage considerably decreased for the longest two fragments. Numts are more prevalent in families with larger genome size. We arrived at the following conclusions: (i) numts are common in all members of Orthoptera, but, their prevalence differs among intra-lineages, especially more prevalent in Caelifera, (ii) there seems a correlation between numt rate and genome size, (iii) there is no threshold to avoid numt co-amplification, but, a 1,000 bp length may be a threshold for Ensifera, (iv) Folmer region of COI doesn't seem an appropriate marker for animal barcoding. Additionally, a phylogenetic tree produced from the numt sequences of fragment four detected in genus Anterastes suggested a paleonumt gained in generic ancestor a 3.5-4 times slower divergence rate for numt sequences.
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Affiliation(s)
- Sarp Kaya
- Mehmet Akif Ersoy Üniversitesi, Burdur Vocational School of Healt Services, Burdur, Turkey
| | - Battal Çıplak
- Department of Biology, Faculty of Science, Akdeniz University, 07058, Antalya, Turkey
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16
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Strange RM, Delaney KJ. First Report of a Mitochondrial Pseudogene in Agnathan Vertebrates (Cyclostomata: Petromyzontidae). J Mol Evol 2018; 86:187-189. [PMID: 29564489 DOI: 10.1007/s00239-018-9835-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 03/15/2018] [Indexed: 11/28/2022]
Abstract
We report herein the characterization of a nuclear paralog of a fragment of the mitochondrial genome (a numt) in two closely related species of lampreys (Ichthyomyzon spp.). Although numts have been characterized in several vertebrate taxa, numts have yet to be reported for fishes in general. Given the phylogenetic position of lampreys relative to other vertebrates, the presence of numts within the lamprey genome is either evidence of an ancestral trait lost in other fishes but uniquely retained in agnathans and amniotes, or (more intriguingly) a product of the genome rearrangements these animals undergo during development.
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Affiliation(s)
- Rex Meade Strange
- Department of Biology, University of Southern Indiana, 8600 University Blvd., Evansville, IN, 47712, USA.
| | - Kimberly J Delaney
- Department of Biology, University of Southern Indiana, 8600 University Blvd., Evansville, IN, 47712, USA
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17
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Ancient mitochondrial pseudogenes reveal hybridization between distant lineages in the evolution of the Rupicapra genus. Gene 2017; 628:63-71. [DOI: 10.1016/j.gene.2017.07.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 07/07/2017] [Accepted: 07/11/2017] [Indexed: 11/23/2022]
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18
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Machida RJ, Lin YY. Occurrence of mitochondrial CO1 pseudogenes in Neocalanus plumchrus (Crustacea: Copepoda): Hybridization indicated by recombined nuclear mitochondrial pseudogenes. PLoS One 2017; 12:e0172710. [PMID: 28231343 PMCID: PMC5322918 DOI: 10.1371/journal.pone.0172710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 02/08/2017] [Indexed: 11/18/2022] Open
Abstract
A portion of the mitochondrial cytochrome c oxidase I gene was sequenced using both genomic DNA and complement DNA from three planktonic copepod Neocalanus species (N. cristatus, N. plumchrus, and N. flemingeri). Small but critical sequence differences in CO1 were observed between gDNA and cDNA from N. plumchrus. Furthermore, careful observation revealed the presence of recombination between sequences in gDNA from N. plumchrus. Moreover, a chimera of the N. cristatus and N. plumchrus sequences was obtained from N. plumchrus gDNA. The observed phenomena can be best explained by the preferential amplification of the nuclear mitochondrial pseudogenes from gDNA of N. plumchrus. Two conclusions can be drawn from the observations. First, nuclear mitochondrial pseudogenes are pervasive in N. plumchrus. Second, a mating between a female N. cristatus and a male N. plumchrus produced viable offspring, which further backcrossed to a N. plumchrus individual. These observations not only demonstrate intriguing mating behavior in these species, but also emphasize the importance of careful interpretation of species marker sequences amplified from gDNA.
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Affiliation(s)
- Ryuji J. Machida
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
- * E-mail:
| | - Ya-Ying Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
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19
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Buddhakosai W, Klinsawat W, Smith O, Sukmak M, Kaolim N, Duangchantrasiri S, Simcharoen A, Siriaroonrat B, Wajjwalku W. Mitogenome analysis reveals a complex phylogeographic relationship within the wild tiger population of Thailand. ENDANGER SPECIES RES 2016. [DOI: 10.3354/esr00729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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20
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Curry CJ, White PA, Derr JN. Mitochondrial Haplotype Diversity in Zambian Lions: Bridging a Gap in the Biogeography of an Iconic Species. PLoS One 2015; 10:e0143827. [PMID: 26674533 PMCID: PMC4686026 DOI: 10.1371/journal.pone.0143827] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 11/10/2015] [Indexed: 11/18/2022] Open
Abstract
Analysis of DNA sequence diversity at the 12S to 16S mitochondrial genes of 165 African lions (Panthera leo) from five main areas in Zambia has uncovered haplotypes which link Southern Africa with East Africa. Phylogenetic analysis suggests Zambia may serve as a bridge connecting the lion populations in southern Africa to eastern Africa, supporting earlier hypotheses that eastern-southern Africa may represent the evolutionary cradle for the species. Overall gene diversity throughout the Zambian lion population was 0.7319 +/- 0.0174 with eight haplotypes found; three haplotypes previously described and the remaining five novel. The addition of these five novel haplotypes, so far only found within Zambia, nearly doubles the number of haplotypes previously reported for any given geographic location of wild lions. However, based on an AMOVA analysis of these haplotypes, there is little to no matrilineal gene flow (Fst = 0.47) when the eastern and western regions of Zambia are considered as two regional sub-populations. Crossover haplotypes (H9, H11, and Z1) appear in both populations as rare in one but common in the other. This pattern is a possible result of the lion mating system in which predominately males disperse, as all individuals with crossover haplotypes were male. The determination and characterization of lion sub-populations, such as done in this study for Zambia, represent a higher-resolution of knowledge regarding both the genetic health and connectivity of lion populations, which can serve to inform conservation and management of this iconic species.
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Affiliation(s)
- Caitlin J. Curry
- Interdisciplinary Program of Genetics, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States of America
| | - Paula A. White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA, United States of America
| | - James N. Derr
- Interdisciplinary Program of Genetics, Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States of America
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21
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Ko YJ, Yang EC, Lee JH, Lee KW, Jeong JY, Park K, Chung O, Bhak J, Lee JH, Yim HS. Characterization of cetacean Numt and its application into cetacean phylogeny. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0353-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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22
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Raupach MJ, Radulovici AE. Looking back on a decade of barcoding crustaceans. Zookeys 2015; 539:53-81. [PMID: 26798245 PMCID: PMC4714055 DOI: 10.3897/zookeys.539.6530] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/20/2015] [Indexed: 02/07/2023] Open
Abstract
Species identification represents a pivotal component for large-scale biodiversity studies and conservation planning but represents a challenge for many taxa when using morphological traits only. Consequently, alternative identification methods based on molecular markers have been proposed. In this context, DNA barcoding has become a popular and accepted method for the identification of unknown animals across all life stages by comparison to a reference library. In this review we examine the progress of barcoding studies for the Crustacea using the Web of Science data base from 2003 to 2014. All references were classified in terms of taxonomy covered, subject area (identification/library, genetic variability, species descriptions, phylogenetics, methods, pseudogenes/numts), habitat, geographical area, authors, journals, citations, and the use of the Barcode of Life Data Systems (BOLD). Our analysis revealed a total number of 164 barcoding studies for crustaceans with a preference for malacostracan crustaceans, in particular Decapoda, and for building reference libraries in order to identify organisms. So far, BOLD did not establish itself as a popular informatics platform among carcinologists although it offers many advantages for standardized data storage, analyses and publication.
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Affiliation(s)
- Michael J. Raupach
- Molecular Taxonomy of Marine Organisms, German Centre of Marine Biodiversity Research (DZMB), Senckenberg am Meer, Südstrand 44, 26382 Wilhelmshaven, Germany
| | - Adriana E. Radulovici
- Biodiversity Institute of Ontario (BIO), University of Guelph, 50 Stone Road E, Guelph (ON) N1G 2W1, Ontario, Canada
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23
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Samaniego Castruita JA, Zepeda Mendoza ML, Barnett R, Wales N, Gilbert MTP. Odintifier--A computational method for identifying insertions of organellar origin from modern and ancient high-throughput sequencing data based on haplotype phasing. BMC Bioinformatics 2015. [PMID: 26216337 PMCID: PMC4517485 DOI: 10.1186/s12859-015-0682-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Cellular organelles with genomes of their own (e.g. plastids and mitochondria) can pass genetic sequences to other organellar genomes within the cell in many species across the eukaryote phylogeny. The extent of the occurrence of these organellar-derived inserted sequences (odins) is still unknown, but if not accounted for in genomic and phylogenetic studies, they can be a source of error. However, if correctly identified, these inserted sequences can be used for evolutionary and comparative genomic studies. Although such insertions can be detected using various laboratory and bioinformatic strategies, there is currently no straightforward way to apply them as a standard organellar genome assembly on next-generation sequencing data. Furthermore, most current methods for identification of such insertions are unsuitable for use on non-model organisms or ancient DNA datasets. Results We present a bioinformatic method that uses phasing algorithms to reconstruct both source and inserted organelle sequences. The method was tested in different shotgun and organellar-enriched DNA high-throughput sequencing (HTS) datasets from ancient and modern samples. Specifically, we used datasets from lions (Panthera leo ssp. and Panthera leo leo) to characterize insertions from mitochondrial origin, and from common grapevine (Vitis vinifera) and bugle (Ajuga reptans) to characterize insertions derived from plastid genomes. Comparison of the results against other available organelle genome assembly methods demonstrated that our new method provides an improvement in the sequence assembly. Conclusion Using datasets from a wide range of species and different levels of complexity we showed that our novel bioinformatic method based on phasing algorithms can be used to achieve the next two goals: i) reference-guided assembly of chloroplast/mitochondrial genomes from HTS data and ii) identification and simultaneous assembly of odins. This method represents the first application of haplotype phasing for automatic detection of odins and reference-based organellar genome assembly. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0682-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jose Alfredo Samaniego Castruita
- Centre for GeoGenetics, The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark.
| | - Marie Lisandra Zepeda Mendoza
- Centre for GeoGenetics, The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark.
| | - Ross Barnett
- Centre for GeoGenetics, The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark.
| | - Nathan Wales
- Centre for GeoGenetics, The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark.
| | - M Thomas P Gilbert
- Centre for GeoGenetics, The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, DK-1350, Denmark.
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24
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Ning Y, Liu H, Jiang G, Ma J. Phylogenetic relationship of Eurasian lynx (Lynx lynx) revealed by complete mitochondrial genome. Mitochondrial DNA A DNA Mapp Seq Anal 2015. [PMID: 26195214 DOI: 10.3109/19401736.2015.1066356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The Eurasian lynx (Lynx lynx) is an Endangered species in northeast China. We first obtained muscle sample, extracted the sample DNA and sequenced the whole mtDNA genome of lynx from northeast China. We reconstructed the phylogenetic tree of Eurasian lynx and 10 other most closely related Felidae species. This lynx's complete mitogenome is 17 054bp in length, includes 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and one control region. The phylogenetic tree confirmed previous research results.
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Affiliation(s)
- Yao Ning
- a Feline Research Center of Chinese State Forestry Administration, College of Wildlife Resources, Northeast Forestry University , Harbin , P.R. China
| | - Hui Liu
- a Feline Research Center of Chinese State Forestry Administration, College of Wildlife Resources, Northeast Forestry University , Harbin , P.R. China
| | - Guangshun Jiang
- a Feline Research Center of Chinese State Forestry Administration, College of Wildlife Resources, Northeast Forestry University , Harbin , P.R. China
| | - Jianzhang Ma
- a Feline Research Center of Chinese State Forestry Administration, College of Wildlife Resources, Northeast Forestry University , Harbin , P.R. China
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25
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Xue HR, Yamaguchi N, Driscoll CA, Han Y, Bar-Gal GK, Zhuang Y, Mazak JH, Macdonald DW, O'Brien SJ, Luo SJ. Genetic ancestry of the extinct Javan and Bali tigers. J Hered 2015; 106:247-57. [PMID: 25754539 DOI: 10.1093/jhered/esv002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 01/26/2015] [Indexed: 11/12/2022] Open
Abstract
The Bali (Panthera tigris balica) and Javan (P. t. sondaica) tigers are recognized as distinct tiger subspecies that went extinct in the 1940s and 1980s, respectively. Yet their genetic ancestry and taxonomic status remain controversial. Following ancient DNA procedures, we generated concatenated 1750bp mtDNA sequences from 23 museum samples including 11 voucher specimens from Java and Bali and compared these to diagnostic mtDNA sequences from 122 specimens of living tiger subspecies and the extinct Caspian tiger. The results revealed a close genetic affinity of the 3 groups from the Sunda Islands (Bali, Javan, and Sumatran tigers P. t. sumatrae). Bali and Javan mtDNA haplotypes differ from Sumatran haplotypes by 1-2 nucleotides, and the 3 island populations define a monophyletic assemblage distinctive and equidistant from other mainland subspecies. Despite this close phylogenetic relationship, no mtDNA haplotype was shared between Sumatran and Javan/Bali tigers, indicating little or no matrilineal gene flow among the islands after they were colonized. The close phylogenetic relationship among Sunda tiger subspecies suggests either recent colonization across the islands, or else a once continuous tiger population that had subsequently isolated into different island subspecies. This supports the hypothesis that the Sumatran tiger is the closest living relative to the extinct Javan and Bali tigers.
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Affiliation(s)
- Hao-Ran Xue
- From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India
| | - Nobuyuki Yamaguchi
- From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India
| | - Carlos A Driscoll
- From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India
| | - Yu Han
- From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India
| | - Gila Kahila Bar-Gal
- From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India
| | - Yan Zhuang
- From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India
| | - Ji H Mazak
- From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India
| | - David W Macdonald
- From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India
| | - Stephen J O'Brien
- From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India
| | - Shu-Jin Luo
- From the College of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China (Xue, Han, Zhuang, and Luo); the Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney, Abingdon OX13 5QL, UK (Yamaguchi, Driscoll, and Macdonald); the School of Life Sciences, Beijing Normal University, Beijing 100875, China (Han); the Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel (Bar-Gal); the Shanghai Science and Technology Museum, Shanghai 200127, China (Mazak); the Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St Petersburg 199004, Russia (O'Brien); and the Oceanographic Center, Nova Southeastern University, Ft Lauderdale, FL 33004, USA (O'Brien). Nobuyuki Yamaguchi is now at Department of Biological and Environmental Sciences, University of Qatar, PO Box 2713, Doha, Qatar. Carlos A. Driscoll is now at WWF-India at Wildlife Institute of India, Chandrabani, Dehadun, Uttarakhand 248001, India.
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Mondol S, Kumar NS, Gopalaswamy A, Sunagar K, Karanth KU, Ramakrishnan U. Identifying species, sex and individual tigers and leopards in the Malenad-Mysore Tiger Landscape, Western Ghats, India. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0371-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Discrimination of tiger using a novel high resolution melting (HRM) and multiplex SNP-specific HRM (MSS-HRM) technique. Forensic Sci Int Genet 2014; 13:30-3. [PMID: 25064274 DOI: 10.1016/j.fsigen.2014.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 06/26/2014] [Accepted: 07/01/2014] [Indexed: 11/22/2022]
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28
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Barnett R, Yamaguchi N, Shapiro B, Ho SYW, Barnes I, Sabin R, Werdelin L, Cuisin J, Larson G. Revealing the maternal demographic history of Panthera leo using ancient DNA and a spatially explicit genealogical analysis. BMC Evol Biol 2014; 14:70. [PMID: 24690312 PMCID: PMC3997813 DOI: 10.1186/1471-2148-14-70] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/13/2014] [Indexed: 11/15/2022] Open
Abstract
Background Understanding the demographic history of a population is critical to conservation and to our broader understanding of evolutionary processes. For many tropical large mammals, however, this aim is confounded by the absence of fossil material and by the misleading signal obtained from genetic data of recently fragmented and isolated populations. This is particularly true for the lion which as a consequence of millennia of human persecution, has large gaps in its natural distribution and several recently extinct populations. Results We sequenced mitochondrial DNA from museum-preserved individuals, including the extinct Barbary lion (Panthera leo leo) and Iranian lion (P. l. persica), as well as lions from West and Central Africa. We added these to a broader sample of lion sequences, resulting in a data set spanning the historical range of lions. Our Bayesian phylogeographical analyses provide evidence for highly supported, reciprocally monophyletic lion clades. Using a molecular clock, we estimated that recent lion lineages began to diverge in the Late Pleistocene. Expanding equatorial rainforest probably separated lions in South and East Africa from other populations. West African lions then expanded into Central Africa during periods of rainforest contraction. Lastly, we found evidence of two separate incursions into Asia from North Africa, first into India and later into the Middle East. Conclusions We have identified deep, well-supported splits within the mitochondrial phylogeny of African lions, arguing for recognition of some regional populations as worthy of independent conservation. More morphological and nuclear DNA data are now needed to test these subdivisions.
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Affiliation(s)
- Ross Barnett
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, UK.
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29
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Baeza JA, Fuentes MS. Exploring phylogenetic informativeness and nuclear copies of mitochondrial DNA (numts) in three commonly used mitochondrial genes: mitochondrial phylogeny of peppermint, cleaner, and semi-terrestrial shrimps (Caridea:Lysmata,Exhippolysmata, andMerguia). Zool J Linn Soc 2013. [DOI: 10.1111/zoj.12044] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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30
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Morgan JAT, Macbeth M, Broderick D, Whatmore P, Street R, Welch DJ, Ovenden JR. Hybridisation, paternal leakage and mitochondrial DNA linearization in three anomalous fish (Scombridae). Mitochondrion 2013; 13:852-61. [PMID: 23774068 DOI: 10.1016/j.mito.2013.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Revised: 06/04/2013] [Accepted: 06/07/2013] [Indexed: 11/16/2022]
Abstract
Using mitochondrial DNA for species identification and population studies assumes that the genome is maternally inherited, circular, located in the cytoplasm and lacks recombination. This study explores the mitochondrial genomes of three anomalous mackerel. Complete mitochondrial genome sequencing plus nuclear microsatellite genotyping of these fish identified them as Scomberomorus munroi (spotted mackerel). Unlike normal S. munroi, these three fish also contained different linear, mitochondrial genomes of Scomberomorus semifasciatus (grey mackerel). The results are best explained by hybridisation, paternal leakage and mitochondrial DNA linearization. This unusual observation may provide an explanation for mtDNA outliers in animal population studies.
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Affiliation(s)
- Jess A T Morgan
- Molecular Fisheries Laboratory, University of Queensland, PO Box 6097, St Lucia, Queensland 4072, Australia; Queensland Alliance for Agriculture and Food Innovation, University of Queensland, 306 Carmody Rd, St Lucia, Queensland 4072, Australia.
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31
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Kim SJ, Lee KY, Ju SJ. Nuclear mitochondrial pseudogenes in Austinograea alayseae hydrothermal vent crabs (Crustacea: Bythograeidae): effects on DNA barcoding. Mol Ecol Resour 2013; 13:781-7. [PMID: 23663201 DOI: 10.1111/1755-0998.12119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 04/09/2013] [Accepted: 04/11/2013] [Indexed: 11/30/2022]
Abstract
Members of the brachyuran crab family, Bythograeidae, are among the most abundant and common crabs in vent fields. However, their identification based on morphological characteristics often leads to incorrect species recognition due to a lack of taxonomic factors and the existence of sibling (or cryptic) species. For these reasons, we used DNA barcoding for vent crabs using mitochondrial cytochrome c oxidase subunit 1 (CO1). However, several nuclear mitochondrial pseudogenes (Numts) were amplified from Austinograea alayseae Guinot, 1990, using universal primers (Folmer primers). The Numts were characterized in six haplotypes, with 13.58-14.11% sequence divergence from A. alayseae, a higher nonsynonymous substitution ratio than true CO1, and the formation of an independent clade in bythograeids. In a neighbour-joining tree, the origin of the Numts would be expected to incorporate into the nucleus at an ancestral node of Austinograea, and they mutated more slowly in the nucleus than CO1 in the mitochondria. This evolutionary process may have resulted in the higher binding affinity of Numts for the Folmer primers than CO1. In the present study, we performed long PCR for the amplification of CO1 in A. alayseae. We also present evidence that Numts can introduce serious ambiguity into DNA barcoding, including overestimating the number of species in bythograeids. These results may help in conducting taxonomic studies using mitochondrial genes from organisms living in hydrothermal vent fields.
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Affiliation(s)
- Se-Joo Kim
- Deep-sea and Seabed Resources Research Division, Korea Institute of Ocean Science & Technology, Gyeonggi-do, 426-744, Korea
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32
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Wang JF, Zhang YP, Yu L. [Summary of phylogeny in family Felidae of Carnivora]. YI CHUAN = HEREDITAS 2012. [PMID: 23208134 DOI: 10.3724/sp.j.1005.2012.01365] [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
Felidae (cats) is one of the strict carnivorous groups in the order Carnivora, many of which are most familiar and spectacular to us. They are the top predators in the world. Thirty-six of 37 living cat species are considered as either "endangered" or "threatened". The relationships among species of the family Felidae, which evolved recently and rapidly, are difficult to resolve, and have been the subject of debate. Construction of a reliable Felidae phylogeny will be of evolutionarily significance and conservation value. In this paper, we summarized phylogeny of Felidae, including cytological, morphological and molecular evidence, and pointed out the existing phylogenetic problems. This review is expected to guide future researches of Felidae phylogeny, and to lay a theoretic foundation for the protection of this animal group.
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Affiliation(s)
- Jin-Feng Wang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, China.
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33
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Macholán M, Vyskočilová MM, Bejček V, Šťastný K. Mitochondrial DNA sequence variation and evolution of Old World house mice (Mus musculus). FOLIA ZOOLOGICA 2012. [DOI: 10.25225/fozo.v61.i3.a12.2012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Miloš Macholán
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, v.v.i., Veveří 97, 602 00 Brno, Czech Republic
| | - Martina Mrkvicová Vyskočilová
- Laboratory of Mammalian Evolutionary Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, v.v.i., Veveří 97, 602 00 Brno, Czech Republic
| | - Vladimír Bejček
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences, Kamýcká 129, 165 21 Prague, Czech Republic
| | - Karel Šťastný
- Department of Ecology, Faculty of Environmental Sciences, Czech University of Life Sciences, Kamýcká 129, 165 21 Prague, Czech Republic
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34
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Kitpipit T, Tobe SS, Linacre A. The complete mitochondrial genome analysis of the tiger (Panthera tigris). Mol Biol Rep 2011; 39:5745-54. [PMID: 22207170 DOI: 10.1007/s11033-011-1384-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 12/14/2011] [Indexed: 12/14/2022]
Abstract
The complete mitochondrial genomes of five tiger samples from three subspecies (P. t. sumatrae, P. t. altica, and P. t. tigris) were successfully obtained by using 26 specifically designed Panthera-specific primer sets. The genome organization and gene arrangement of the five tiger samples were similar to each other; however polymorphic tandem repeat sequences were observed in the control region (CR). This led to a difference in the genome lengths obtained from these five samples with an average size of 16,994 bp for the five tiger mitochondrial genomes. The nucleotide base composition was on average as follows: A, 31.8%; T, 27.0%; C, 26.6%; G, 14.6% and exhibited compositional asymmetry. Most of tiger mitochondrial genome characteristics are similar to those of other common vertebrate species; however, some distinctive features were observed in the CR. First, the repetitive sequence 2 (RS 2) contained two repeat units of 80 bp and the first 15 bp of what would be the third repeat motif. The repetitive sequence 3 (RS 3) contained 47-50 repeat motifs of a shorter 8 bp (ACGTAYAC)(n). Second, length heteroplasmy polycystosine (poly-C) stretches was observed at the end of the HV I locus in all tiger samples.
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Affiliation(s)
- Thitika Kitpipit
- School of Biological Sciences, Flinders University, Adelaide, 5001, Australia
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35
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Behura SK, Lobo NF, Haas B, deBruyn B, Lovin DD, Shumway MF, Puiu D, Romero-Severson J, Nene V, Severson DW. Complete sequences of mitochondria genomes of Aedes aegypti and Culex quinquefasciatus and comparative analysis of mitochondrial DNA fragments inserted in the nuclear genomes. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2011; 41:770-7. [PMID: 21640823 PMCID: PMC3162086 DOI: 10.1016/j.ibmb.2011.05.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 05/18/2011] [Accepted: 05/19/2011] [Indexed: 05/15/2023]
Abstract
We present complete sequences of the mitochondrial genomes for two important mosquitoes, Aedes aegypti and Culex quinquefasciatus, that are major vectors of dengue virus and lymphatic filariasis, respectively. The A. aegypti mitochondrial genome is 16,655 bp in length and that of C. quinquefasciatus is 15,587 bp, yet both contain 13 protein coding genes, 22 transfer RNA (tRNA) genes, one 12S ribosomal RNA (rRNA) gene, one 16S rRNA gene and a control region (CR) in the same order. The difference in the genome size is due to the difference in the length of the control region. We also analyzed insertions of nuclear copies of mtDNA-like sequences (NUMTs) in a comparative manner between the two mosquitoes. The NUMT sequences occupy ~0.008% of the A. aegypti genome and ~0.001% of the C. quinquefasciatus genome. Several NUMTs were found localized in the introns of predicted protein coding genes in both genomes (32 genes in A. aegypti but only four in C. quinquefasciatus). None of these NUMT-containing genes had an ortholog between the two species or had paralogous copies within a genome that was also NUMT-containing. It was further observed that the NUMT-containing genes were relatively longer but had lower GC content compared to the NUMT-less paralogous copies. Moreover, stretches of homologies are present among the genic and non-genic NUMTs that may play important roles in genomic rearrangement of NUMTs in these genomes. Our study provides new insights on understanding the roles of nuclear mtDNA sequences in genome complexities of these mosquitoes.
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Affiliation(s)
- Susanta K Behura
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Neil F Lobo
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Brian Haas
- J. Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, MD 20850
| | - Becky deBruyn
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Diane D Lovin
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Martin F Shumway
- J. Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, MD 20850
| | - Daniela Puiu
- J. Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, MD 20850
| | - Jeanne Romero-Severson
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
| | - Vishvanath Nene
- J. Craig Venter Institute (JCVI), 9704 Medical Center Drive, Rockville, MD 20850
| | - David W Severson
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556
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Chaves PB, Graeff VG, Lion MB, Oliveira LR, Eizirik E. DNA barcoding meets molecular scatology: short mtDNA sequences for standardized species assignment of carnivore noninvasive samples. Mol Ecol Resour 2011; 12:18-35. [PMID: 21883979 DOI: 10.1111/j.1755-0998.2011.03056.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although species assignment of scats is important to study carnivore biology, there is still no standardized assay for the identification of carnivores worldwide, which would allow large-scale routine assessments and reliable cross-comparison of results. Here, we evaluate the potential of two short mtDNA fragments [ATP6 (126 bp) and cytochrome oxidase I gene (COI) (187 bp)] to serve as standard markers for the Carnivora. Samples of 66 species were sequenced for one or both of these segments. Alignments were complemented with archival sequences and analysed with three approaches (tree-based, distance-based and character-based). Intraspecific genetic distances were generally lower than between-species distances, resulting in diagnosable clusters for 86% (ATP6) and 85% (COI) of the species. Notable exceptions were recently diverged species, most of which could still be identified using diagnostic characters and uniqueness of haplotypes or by reducing the geographic scope of the comparison. In silico analyses were also performed for a 110-bp cytochrome b (cytb) segment, whose identification success was lower (70%), possibly due to the smaller number of informative sites and/or the influence of misidentified sequences obtained from GenBank. Finally, we performed case studies with faecal samples, which supported the suitability of our two focal markers for poor-quality DNA and allowed an assessment of prey DNA co-amplification. No evidence of prey DNA contamination was found for ATP6, while some cases were observed for COI and subsequently eliminated by the design of more specific primers. Overall, our results indicate that these segments hold good potential as standard markers for accurate species-level identification in the Carnivora.
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Affiliation(s)
- Paulo B Chaves
- Programa de Pós-Graduação em Zoologia, Pontifícia Universidade Católica do Rio Grande do Sul, Faculdade de Biociências, Av. Ipiranga, 6681, 90619-900 Porto Alegre, RS, Brazil
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Abstract
The utility of molecular genetic approaches in conservation of endangered taxa is now commonly recognized. Over the past decade, conservation genetic analyses based on mitochondrial DNA sequencing and microsatellite genotyping have provided powerful tools to resolve taxonomy uncertainty of tiger subspecies, to define conservation units, to reconstruct phylogeography and demographic history, to examine the genetic ancestry of extinct subspecies, to assess population genetic status non-invasively, and to verify genetic background of captive tigers worldwide. The genetic status of tiger subspecies and populations and implications for developing strategies for the survival of this charismatic species both in situ and ex situ are discussed.
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Affiliation(s)
- Shu-Jin Luo
- School of Life Sciences, Peking University, Beijing, ChinaLaboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, USA
| | - Warren E Johnson
- School of Life Sciences, Peking University, Beijing, ChinaLaboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, USA
| | - Stephen J O'Brien
- School of Life Sciences, Peking University, Beijing, ChinaLaboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, USA
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Cho SJ, Lee YS, Lee JI, Bang JI, Yang J, Klassen H, Kong IK. Confirmation of germ-line transmission in the red fluorescence protein (RFP) transgenic cloned male cat. Cell Reprogram 2010; 12:739-47. [PMID: 20818992 DOI: 10.1089/cell.2010.0009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The production of transgenic animals is highly desirable for biotechnology and basic research. We investigated the reproductive ability of a red fluorescence protein (RFP) transgenic cloned male cat (RFP TG cat) by natural mating with a domestic female cat. The RFP expression levels were examined in early embryogenesis, tissues from 45-day-old two fetuses, and four RFP TG cat offspring. The RFP gene was detected in tissue samples from one dead kitten, including several organs and the skin. Also, under a fluorescent light source, we were able to directly detect the RFP expression of in in vitro-produced blastocysts derived with sperm from the RFP TG cat. These results indicate that the RFP TG cat exhibits normal reproductive fertility, stable germ-line transmission of the RFP transgene, and characteristic RFP expression in its offspring. We isolated feline neural progenitor cells from a 45-day-old fetus derived from the natural mating of the RFP TG cat with a domestic female cat. Isolated brain and retinal progenitor cells were successfully passaged at least four times post isolation (day 23), and showed a high RFP expression level. This method of producing genetically modified cloned cats will be important for generating biomedical models of human diseases.
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Affiliation(s)
- Su-Jin Cho
- Division of Applied Life Science (BK21), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
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Zhang W, Yue B, Wang X, Zhang X, Xie Z, Liu N, Fu W, Yuan Y, Chen D, Fu D, Zhao B, Yin Y, Yan X, Wang X, Zhang R, Liu J, Li M, Tang Y, Hou R, Zhang Z. Analysis of variable sites between two complete South China tiger (Panthera tigris amoyensis) mitochondrial genomes. Mol Biol Rep 2010; 38:4257-64. [DOI: 10.1007/s11033-010-0548-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 11/17/2010] [Indexed: 11/29/2022]
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Shao R, Barker SC. Chimeric mitochondrial minichromosomes of the human body louse, Pediculus humanus: evidence for homologous and non-homologous recombination. Gene 2010; 473:36-43. [PMID: 21092752 DOI: 10.1016/j.gene.2010.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Revised: 10/15/2010] [Accepted: 11/04/2010] [Indexed: 10/18/2022]
Abstract
The mitochondrial (mt) genome of the human body louse, Pediculus humanus, consists of 18 minichromosomes. Each minichromosome is 3 to 4 kb long and has 1 to 3 genes. There is unequivocal evidence for recombination between different mt minichromosomes in P. humanus. It is not known, however, how these minichromosomes recombine. Here, we report the discovery of eight chimeric mt minichromosomes in P. humanus. We classify these chimeric mt minichromosomes into two groups: Group I and Group II. Group I chimeric minichromosomes contain parts of two different protein-coding genes that are from different minichromosomes. The two parts of protein-coding genes in each Group I chimeric minichromosome are joined at a microhomologous nucleotide sequence; microhomologous nucleotide sequences are hallmarks of non-homologous recombination. Group II chimeric minichromosomes contain all of the genes and the non-coding regions of two different minichromosomes. The conserved sequence blocks in the non-coding regions of Group II chimeric minichromosomes resemble the "recombination repeats" in the non-coding regions of the mt genomes of higher plants. These repeats are essential to homologous recombination in higher plants. Our analyses of the nucleotide sequences of chimeric mt minichromosomes indicate both homologous and non-homologous recombination between minichromosomes in the mitochondria of the human body louse.
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Affiliation(s)
- Renfu Shao
- The University of Queensland, School of Chemistry and Molecular Biosciences, Queensland 4072, Australia.
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41
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den Tex RJ, Maldonado JE, Thorington R, Leonard JA. Nuclear copies of mitochondrial genes: another problem for ancient DNA. Genetica 2010; 138:979-84. [PMID: 20700629 DOI: 10.1007/s10709-010-9481-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 07/30/2010] [Indexed: 11/28/2022]
Abstract
The application of ancient DNA techniques is subject to many problems caused primarily by low quality and by low quantity of DNA. For these reasons most studies employing ancient DNA rely on the characterization of mitochondrial DNA, which is present in many more copies per cell than nuclear DNA and hence more copies are likely to survive. We used universal and taxon specific mitochondrial primers to amplify DNA from museum specimens, and found many instances where the amplification of nuclear copies of the mitochondrial gene (numts) instead of the targeted mitochondrial fragment had occurred. Furthermore, the likelihood of amplifying numts increased dramatically when universal primers were utilized. Here we suggest that ancient DNA practitioners must consider the possibility that numts can be amplified at higher rates than previously thought. This is another complication for ancient DNA studies, but it also suggests that more extensive inclusion of nuclear markers in ancient DNA studies should be feasible.
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Affiliation(s)
- Robert-Jan den Tex
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
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42
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Davis BW, Li G, Murphy WJ. Supermatrix and species tree methods resolve phylogenetic relationships within the big cats, Panthera (Carnivora: Felidae). Mol Phylogenet Evol 2010; 56:64-76. [DOI: 10.1016/j.ympev.2010.01.036] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2009] [Revised: 01/28/2010] [Accepted: 01/29/2010] [Indexed: 11/17/2022]
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Lachish-Zalait A, Lau CK, Fichtman B, Zimmerman E, Harel A, Gaylord MR, Forbes DJ, Elbaum M. Transportin mediates nuclear entry of DNA in vertebrate systems. Traffic 2010; 10:1414-28. [PMID: 19761539 DOI: 10.1111/j.1600-0854.2009.00968.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Delivery of DNA to the cell nucleus is an essential step in many types of viral infection, transfection, gene transfer by the plant pathogen Agrobacterium tumefaciens and in strategies for gene therapy. Thus, the mechanism by which DNA crosses the nuclear pore complex (NPC) is of great interest. Using nuclei reconstituted in vitro in Xenopus egg extracts, we previously studied DNA passage through the nuclear pores using a single-molecule approach based on optical tweezers. Fluorescently labeled DNA molecules were also seen to accumulate within nuclei. Here we find that this import of DNA relies on a soluble protein receptor of the importin family. To identify this receptor, we used different pathway-specific cargoes in competition studies as well as pathway-specific dominant negative inhibitors derived from the nucleoporin Nup153. We found that inhibition of the receptor transportin suppresses DNA import. In contrast, inhibition of importin beta has little effect on the nuclear accumulation of DNA. The dependence on transportin was fully confirmed in assays using permeabilized HeLa cells and a mammalian cell extract. We conclude that the nuclear import of DNA observed in these different vertebrate systems is largely mediated by the receptor transportin. We further report that histones, a known cargo of transportin, can act as an adaptor for the binding of transportin to DNA.
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Affiliation(s)
- Aurelie Lachish-Zalait
- Department of Materials and Interfaces, Weizmann Institute of Science, Rehovot 76100, Israel
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Oliveira R, Castro D, Godinho R, Luikart G, Alves PC. Species identification using a small nuclear gene fragment: application to sympatric wild carnivores from South-western Europe. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9947-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Henry P, Miquelle D, Sugimoto T, McCullough DR, Caccone A, Russello MA. In situ population structure and ex situ representation of the endangered Amur tiger. Mol Ecol 2009; 18:3173-84. [PMID: 19555412 DOI: 10.1111/j.1365-294x.2009.04266.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The Amur tiger (Panthera tigris altaica) is a critically endangered felid that suffered a severe demographic contraction in the 1940s. In this study, we sampled 95 individuals collected throughout their native range to investigate questions relative to population genetic structure and demographic history. Additionally, we sampled targeted individuals from the North American ex situ population to assess the genetic representation found in captivity. Population genetic and Bayesian structure analyses clearly identified two populations separated by a development corridor in Russia. Despite their well-documented 20th century decline, we failed to find evidence of a recent population bottleneck, although genetic signatures of a historical contraction were detected. This disparity in signal may be due to several reasons, including historical paucity in population genetic variation associated with postglacial colonization and potential gene flow from a now extirpated Chinese population. Despite conflicting signatures of a bottleneck, our estimates of effective population size (N(e) = 27-35) and N(e)/N ratio (0.07-0.054) were substantially lower than the only other values reported for a wild tiger population. Lastly, the extent and distribution of genetic variation in captive and wild populations were similar, yet gene variants persisted ex situ that were lost in situ. Overall, our results indicate the need to secure ecological connectivity between the two Russian populations to minimize loss of genetic diversity and overall susceptibility to stochastic events, and support a previous study suggesting that the captive population may be a reservoir of gene variants lost in situ.
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Affiliation(s)
- P Henry
- Department of Biology, Centre for Species at Risk and Habitat Studies, University of British Columbia Okanagan, Kelowna, BC, Canada
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BARNETT ROSS, SHAPIRO BETH, BARNES IAN, HO SIMONYW, BURGER JOACHIM, YAMAGUCHI NOBUYUKI, HIGHAM THOMASFG, WHEELER HTODD, ROSENDAHL WILFRIED, SHER ANDREIV, SOTNIKOVA MARINA, KUZNETSOVA TATIANA, BARYSHNIKOV GENNADYF, MARTIN LARRYD, HARINGTON CRICHARD, BURNS JAMESA, COOPER ALAN. Phylogeography of lions (Panthera leossp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity. Mol Ecol 2009; 18:1668-77. [DOI: 10.1111/j.1365-294x.2009.04134.x] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Mitochondrial phylogeography illuminates the origin of the extinct caspian tiger and its relationship to the amur tiger. PLoS One 2009; 4:e4125. [PMID: 19142238 PMCID: PMC2624500 DOI: 10.1371/journal.pone.0004125] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 11/23/2008] [Indexed: 11/19/2022] Open
Abstract
The Caspian tiger (Panthera tigris virgata) flourished in Central Asian riverine forest systems in a range disjunct from that of other tigers, but was driven to extinction in 1970 prior to a modern molecular evaluation. For over a century naturalists puzzled over the taxonomic validity, placement, and biogeographic origin of this enigmatic animal. Using ancient-DNA (aDNA) methodology, we generated composite mtDNA haplotypes from twenty wild Caspian tigers from throughout their historic range sampled from museum collections. We found that Caspian tigers carry a major mtDNA haplotype differing by only a single nucleotide from the monomorphic haplotype found across all contemporary Amur tigers (P. t. altaica). Phylogeographic analysis with extant tiger subspecies suggests that less than 10,000 years ago the Caspian/Amur tiger ancestor colonized Central Asia via the Gansu Corridor (Silk Road) from eastern China then subsequently traversed Siberia eastward to establish the Amur tiger in the Russian Far East. The conservation implications of these findings are far reaching, as the observed genetic depletion characteristic of modern Amur tigers likely reflects these founder migrations and therefore predates human influence. Also, due to their evolutionary propinquity, living Amur tigers offer an appropriate genetic source should reintroductions to the former range of the Caspian tiger be implemented.
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Haag T, Santos AS, De Angelo C, Srbek-Araujo AC, Sana DA, Morato RG, Salzano FM, Eizirik E. Development and testing of an optimized method for DNA-based identification of jaguar (Panthera onca) and puma (Puma concolor) faecal samples for use in ecological and genetic studies. Genetica 2009; 136:505-12. [PMID: 19137401 DOI: 10.1007/s10709-008-9347-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Accepted: 12/11/2008] [Indexed: 11/26/2022]
Abstract
The elusive nature and endangered status of most carnivore species imply that efficient approaches for their non-invasive sampling are required to allow for genetic and ecological studies. Faecal samples are a major potential source of information, and reliable approaches are needed to foster their application in this field, particularly in areas where few studies have been conducted. A major obstacle to the reliable use of faecal samples is their uncertain species-level identification in the field, an issue that can be addressed with DNA-based assays. In this study we describe a sequence-based approach that efficiently distinguishes jaguar versus puma scats, and that presents several desirable properties: (1) considerably high amplification and sequencing rates; (2) multiple diagnostic sites reliably differentiating the two focal species; (3) high information content that allows for future application in other carnivores; (4) no evidence of amplification of prey DNA; and (5) no evidence of amplification of a nuclear mitochondrial DNA insertion known to occur in the jaguar. We demonstrate the reliability and usefulness of this approach by evaluating 55 field-collected samples from four locations in the highly fragmented Atlantic Forest biome of Brazil and Argentina, and document the presence of one or both of these endangered felids in each of these areas.
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Affiliation(s)
- Taiana Haag
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
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Christiansen P. Phylogeny of the great cats (Felidae: Pantherinae), and the influence of fossil taxa and missing characters. Cladistics 2008; 24:977-992. [DOI: 10.1111/j.1096-0031.2008.00226.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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