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Qi H, Lim QL, Kinoshita K, Nakajima N, Inoue-Murayama M. A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models. Mol Ecol Resour 2024; 24:e13928. [PMID: 38234258 DOI: 10.1111/1755-0998.13928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Individual age can be used to design more efficient and suitable management plans in both in situ and ex situ conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that can accurately estimate age from small amounts of biological material, which can be collected in a minimally invasive manner. In this study, we sequenced five targeted genetic regions and used 8-23 selected CpG sites to build age estimation models using machine learning methods at only about $3-7 per sample. Blood samples of seven Felidae species were used, ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples) and five Panthera species (96 samples). The models achieved satisfactory accuracy, with the mean absolute error of the most accurate models recorded at 1.966, 1.348 and 1.552 years in domestic cats, Tsushima leopard cats and Panthera spp. respectively. We developed the models in domestic cats and Tsushima leopard cats, which were applicable to individuals regardless of health conditions; therefore, these models are applicable to samples collected from individuals with diverse characteristics, which is often the case in conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using only two of the five genetic regions. We do not recommend building a common age estimation model for all the target species using our markers, because of the degraded performance of models that included all species.
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Affiliation(s)
- Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Qi Luan Lim
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | | | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
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Yuan J, Kitchener AC, Lackey LB, Sun T, Jiangzuo Q, Tuohetahong Y, Zhao L, Yang P, Wang G, Huang C, Wang J, Hou W, Liu Y, Chen W, Mi D, Murphy WJ, Li G. The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids. Proc Natl Acad Sci U S A 2024; 121:e2310763120. [PMID: 38165928 PMCID: PMC10786289 DOI: 10.1073/pnas.2310763120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/31/2023] [Indexed: 01/04/2024] Open
Abstract
Habitat degradation and loss of genetic diversity are common threats faced by almost all of today's wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat, Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.
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Affiliation(s)
- Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, EdinburghEH1 1JF, United Kingdom
- School of Geosciences, University of Edinburgh, EdinburghEH9 3PX, United Kingdom
| | | | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Qigao Jiangzuo
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing100044, China
| | | | - Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development Collaborative Innovation Center, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong723099, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Wenhui Hou
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou510070, China
| | - Da Mi
- Xi’an Haorui Genomics Technology Co., Ltd., Xi’an710116, China
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an710049, China
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX77843
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou510070, China
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Lescroart J, Bonilla-Sánchez A, Napolitano C, Buitrago-Torres DL, Ramírez-Chaves HE, Pulido-Santacruz P, Murphy WJ, Svardal H, Eizirik E. Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus. Mol Biol Evol 2023; 40:msad255. [PMID: 37987559 PMCID: PMC10701098 DOI: 10.1093/molbev/msad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023] Open
Abstract
Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for interspecies introgression, and assess patterns of genetic diversity and demographic history. We infer that the Leopardus radiation started in the Early Pliocene as an initial speciation burst, followed by another in its subgenus Oncifelis during the Early Pleistocene. Our findings challenge the long-held notion that ocelot (Leopardus pardalis) and margay (L. wiedii) are sister species and instead indicate that margay is most closely related to the enigmatic Andean cat (L. jacobita), whose whole-genome data are reported here for the first time. In addition, we found that the newly sampled Andean tiger cat (L. tigrinus pardinoides) population from Colombia associates closely with Central American tiger cats (L. tigrinus oncilla). Genealogical discordance was largely attributable to incomplete lineage sorting, yet was augmented by strong gene flow between ocelot and the ancestral branch of Oncifelis, as well as between Geoffroy's cat (L. geoffroyi) and southern tiger cat (L. guttulus). Contrasting demographic trajectories have led to disparate levels of current genomic diversity, with a nearly tenfold difference in heterozygosity between Andean cat and ocelot, spanning the entire range of variability found in extant felids. Our analyses improved our understanding of the speciation history and diversity patterns in this felid radiation, and highlight the benefits to phylogenomic inference of embracing the many heterogeneous signals scattered across the genome.
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Affiliation(s)
- Jonas Lescroart
- Department of Biology, University of Antwerp, Antwerp, Belgium
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Alejandra Bonilla-Sánchez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Faculty of Exact and Natural Sciences, University of Antioquia, Medellín, Colombia
| | - Constanza Napolitano
- Department of Biological Sciences and Biodiversity, University of Los Lagos, Osorno, Chile
- Institute of Ecology and Biodiversity, Concepción, Chile
- Cape Horn International Center, Puerto Williams, Chile
- Andean Cat Alliance, Villa Carlos Paz, Argentina
| | - Diana L Buitrago-Torres
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Héctor E Ramírez-Chaves
- Department of Biological Sciences, University of Caldas, Manizales, Colombia
- Centro de Museos, Museo de Historia Natural, University of Caldas, Manizales, Colombia
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, Brazil
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Macdonald EA, Cushman SA, Landguth EL, Hearn AJ, Malhi Y, Macdonald DW. Simulating impacts of rapid forest loss on population size, connectivity and genetic diversity of Sunda clouded leopards (Neofelis diardi) in Borneo. PLoS One 2018; 13:e0196974. [PMID: 30208031 PMCID: PMC6135353 DOI: 10.1371/journal.pone.0196974] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/18/2018] [Indexed: 11/18/2022] Open
Abstract
Habitat loss is the greatest threat to biodiversity in Borneo, and to anticipate and combat its effects it is important to predict the pattern of loss and its consequences. Borneo is a region of extremely high biodiversity from which forest is being lost faster than in any other. The little-known Sunda clouded leopard (Neofelis diardi) is the top predator in Borneo and is likely to depend critically on habitat connectivity that is currently being rapidly lost to deforestation. We modeled the effects of landscape fragmentation on population size, genetic diversity and population connectivity for the Sunda clouded leopard across the entirety of Borneo. We modelled the impacts of land use change between the years 2000, 2010 and projected forwards to 2020. We found substantial reductions across all metrics between 2000 and 2010: the proportion of landscape connected by dispersal fell by approximately 12.5% and the largest patch size declined by around 15.1%, leading to a predicted 11.4% decline in clouded leopard numbers. We also predict that these trends will accelerate greatly towards 2020, with the percentage of the landscape being connected by dispersal falling by about 57.8%, the largest patch size falling by around 62.8% and the predicted clouded leopard population falling by 62.5% between 2010 and 2020. We predicted that these large declines in clouded leopard population size and connectivity will also substantially reduce the genetic diversity of the remaining clouded leopard population.
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Affiliation(s)
- Ewan A. Macdonald
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
- Wildlife Conservation Research Unit, Zoology Department, University of Oxford, The Recanati-Kaplan Centre, Tubney, Abingdon, United Kingdom
| | - Samuel A. Cushman
- Rocky Mountain Research Station, United States Forest Service, Flagstaff, Arizona, United States of America
| | - Erin L. Landguth
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Andrew J. Hearn
- Wildlife Conservation Research Unit, Zoology Department, University of Oxford, The Recanati-Kaplan Centre, Tubney, Abingdon, United Kingdom
| | - Yadvinder Malhi
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| | - David W. Macdonald
- Wildlife Conservation Research Unit, Zoology Department, University of Oxford, The Recanati-Kaplan Centre, Tubney, Abingdon, United Kingdom
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6
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Ko BJ, An J, Seomun H, Lee MY, Eo SH. Microsatellite DNA analysis reveals lower than expected genetic diversity in the threatened leopard cat (Prionailurus bengalensis) in South Korea. Genes Genomics 2018; 40:521-530. [PMID: 29892957 DOI: 10.1007/s13258-018-0654-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/09/2018] [Indexed: 11/25/2022]
Abstract
To optimize conservation efforts, it is necessary to determine the risk of extinction by collecting reliable population information for a given species. We developed eight novel, polymorphic microsatellite markers and used these markers in conjunction with twelve existing markers to measure genetic diversity of South Korean populations of leopard cat (Prionailurus bengalensis), a species for which population size and habitat area data are unknown in the country, to assess its conservation status. The average number of alleles and the observed heterozygosity of the species were 3.8 and 0.41, respectively, and microsatellite diversity was lower than the average genetic diversity of 57 populations of 12 other felid species, and lower than that of other mammal populations occurring in South Korea, including the raccoon dog (Nyctereutes procyonoides), water deer (Hydropotes inermis), and endangered long-tailed goral (Naemorhedus caudatus). Furthermore, analysis of genetic structure in the national leopard cat population showed no clear genetic differentiation, suggesting that it is not necessary to divide the South Korean leopard cat population into multiple management units for the purposes of conservation. These results indicate that the genetic diversity of the leopard cat in South Korea is unexpectedly low, and that the risk of local extinction is, as a result, substantial. Thus, it is necessary to begin appropriate conservation efforts at a national level to conserve the leopard cat population in South Korea.
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Affiliation(s)
- Byung June Ko
- Department of Forest Resources, Kongju National University, Yesan, Chungnam, South Korea
| | - Junghwa An
- National Institute of Biological Resources (NIBR), Incheon, South Korea
| | - Hong Seomun
- National Institute of Biological Resources (NIBR), Incheon, South Korea
| | - Mu-Yeong Lee
- National Institute of Biological Resources (NIBR), Incheon, South Korea
| | - Soo Hyung Eo
- Department of Forest Resources, Kongju National University, Yesan, Chungnam, South Korea.
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Alberts CC, Saranholi BH, Frei F, Galetti PM. Comparing hair-morphology and molecular methods to identify fecal samples from Neotropical felids. PLoS One 2017; 12:e0184073. [PMID: 28880947 PMCID: PMC5589158 DOI: 10.1371/journal.pone.0184073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/17/2017] [Indexed: 11/19/2022] Open
Abstract
To avoid certain problems encountered with more-traditional and invasive methods in behavioral-ecology studies of mammalian predators, such as felids, molecular approaches have been employed to identify feces found in the field. However, this method requires a complete molecular biology laboratory, and usually also requires very fresh fecal samples to avoid DNA degradation. Both conditions are normally absent in the field. To address these difficulties, identification based on morphological characters (length, color, banding, scales and medullar patterns) of hairs found in feces could be employed as an alternative. In this study we constructed a morphological identification key for guard hairs of eight Neotropical felids (jaguar, oncilla, Geoffroy's cat, margay, ocelot, Pampas cat, puma and jaguarundi) and compared its efficiency to that of a molecular identification method, using the ATP6 region as a marker. For this molecular approach, we simulated some field conditions by postponing sample-conservation procedures. A blind test of the identification key obtained a nearly 70% overall success rate, which we considered equivalent to or better than the results of some molecular methods (probably due to DNA degradation) found in other studies. The jaguar, puma and jaguarundi could be unequivocally discriminated from any other Neotropical felid. On a scale ranging from inadequate to excellent, the key proved poor only for the margay, with only 30% of its hairs successfully identified using this key; and have intermediate success rates for the remaining species, the oncilla, Geoffroy's cat, ocelot and Pampas cat, were intermediate. Complementary information about the known distributions of felid populations may be necessary to substantially improve the results obtained with the key. Our own molecular results were even better, since all blind-tested samples were correctly identified. Part of these identifications were made from samples kept in suboptimal conditions, with some samples remaining outdoors for up to seven days, simulating conditions in the field. It appears that both methods can be used, depending on the available laboratory facilities and on the expected results.
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Affiliation(s)
- Carlos C. Alberts
- LEvEtho (Laboratory of Evolution and Ethology), Faculdade de Ciências e Letras de Assis, Universidade Estadual Paulista, Assis, State of São Paulo, Brazil
| | - Bruno H. Saranholi
- LabBMC (Laboratório de Biodiversidade Molecular e Conservação), Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, State of São Paulo, Brazil
| | - Fernando Frei
- LEA (Laboratório de Estatística Aplicada), Faculdade de Ciências e Letras de Assis, Universidade Estadual Paulista, Assis, State of São Paulo, Brazil
| | - Pedro M. Galetti
- LabBMC (Laboratório de Biodiversidade Molecular e Conservação), Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, State of São Paulo, Brazil
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Amstislavsky SY, Kozhevnikova VV, Muzika VV, Kizilova EA. [Reproductive Biology and a Genome Resource Bank of Felidae]. Ontogenez 2017; 48:93-106. [PMID: 30277358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The main achievements in applying modern reproductive technologies to the banking of the genetic resources of the Felidae family are reviewed. The classification of felids at the level of species and subspecies is revised in the light of recent molecular data. Special emphasis is made on such mainstream technologies as semen collection and cryopreservation followed by artificial insemination, as well as on in vitro maturation and fertilization of oocytes combined with the culture of in vitro-derived felid embryos.
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Metcalf JL, Turney C, Barnett R, Martin F, Bray SC, Vilstrup JT, Orlando L, Salas-Gismondi R, Loponte D, Medina M, De Nigris M, Civalero T, Fernández PM, Gasco A, Duran V, Seymour KL, Otaola C, Gil A, Paunero R, Prevosti FJ, Bradshaw CJA, Wheeler JC, Borrero L, Austin JJ, Cooper A. Synergistic roles of climate warming and human occupation in Patagonian megafaunal extinctions during the Last Deglaciation. Sci Adv 2016; 2:e1501682. [PMID: 27386563 PMCID: PMC4928889 DOI: 10.1126/sciadv.1501682] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 05/27/2016] [Indexed: 06/06/2023]
Abstract
The causes of Late Pleistocene megafaunal extinctions (60,000 to 11,650 years ago, hereafter 60 to 11.65 ka) remain contentious, with major phases coinciding with both human arrival and climate change around the world. The Americas provide a unique opportunity to disentangle these factors as human colonization took place over a narrow time frame (~15 to 14.6 ka) but during contrasting temperature trends across each continent. Unfortunately, limited data sets in South America have so far precluded detailed comparison. We analyze genetic and radiocarbon data from 89 and 71 Patagonian megafaunal bones, respectively, more than doubling the high-quality Pleistocene megafaunal radiocarbon data sets from the region. We identify a narrow megafaunal extinction phase 12,280 ± 110 years ago, some 1 to 3 thousand years after initial human presence in the area. Although humans arrived immediately prior to a cold phase, the Antarctic Cold Reversal stadial, megafaunal extinctions did not occur until the stadial finished and the subsequent warming phase commenced some 1 to 3 thousand years later. The increased resolution provided by the Patagonian material reveals that the sequence of climate and extinction events in North and South America were temporally inverted, but in both cases, megafaunal extinctions did not occur until human presence and climate warming coincided. Overall, metapopulation processes involving subpopulation connectivity on a continental scale appear to have been critical for megafaunal species survival of both climate change and human impacts.
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Affiliation(s)
- Jessica L. Metcalf
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Department of Ecology and Evolutionary Biology, Ramaley Biology, University of Colorado, Boulder, CO 80309–0334, USA
| | - Chris Turney
- Climate Change Research Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Ross Barnett
- Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, DK-1350 Copenhagen, Denmark
| | - Fabiana Martin
- Centro de Estudios del Hombre Austral, Instituto de la Patagonia, UMAG, Avenida Bulnes 01890, Punta Arenas, Chile
| | - Sarah C. Bray
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Acute Leukaemia Laboratory, Centre for Cancer Biology, University of South Australia, Adelaide South Australia 5001, Australia
| | - Julia T. Vilstrup
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, DK-1350 Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5–7, DK-1350 Copenhagen, Denmark
| | - Rodolfo Salas-Gismondi
- Institut des Sciences de l’Evolution, Université de Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
- Departamento de Paleontologia de Vertebrados, Museo de Historia Natural, UNMSM, Avenida Arenales 1256, Lima 14, Peru
| | - Daniel Loponte
- Instituto Nacional de Antropología y Pensamiento Latinoamericano, C1426BJN Ciudad de Buenos Aires, Argentina
| | - Matías Medina
- Área de Arqueología y Etnohistoria, Centro de Estudios Históricos “Prof. Carlos S.A. Segreti,” Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Miguel C. del Corro 308, Córdoba (5000), Argentina
| | - Mariana De Nigris
- Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), CONICET/UBA, 3 de Febrero 1370, C1426BJN Buenos Aires, Argentina
| | - Teresa Civalero
- Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), CONICET/UBA, 3 de Febrero 1370, C1426BJN Buenos Aires, Argentina
| | - Pablo Marcelo Fernández
- Instituto Nacional de Antropología y Pensamiento Latinoamericano (INAPL), CONICET/UBA, 3 de Febrero 1370, C1426BJN Buenos Aires, Argentina
| | - Alejandra Gasco
- CONICET, Laboratorio de Paleoecología Humana, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Victor Duran
- CONICET, Laboratorio de Paleoecología Humana, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina
| | - Kevin L. Seymour
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, Ontario M5S 2C6, Canada
| | - Clara Otaola
- CONICET-IANGLA Grupo Vincualdo San Rafael/ UTN-MHNSR, Parque Mariano Moreno (5600), San Rafael, Mendoza, Argentina
| | - Adolfo Gil
- CONICET-IANGLA Grupo Vincualdo San Rafael/ UTN-MHNSR, Parque Mariano Moreno (5600), San Rafael, Mendoza, Argentina
| | - Rafael Paunero
- Departamento Científico de Arqueología. Facultad de Ciencias Naturales y Museo, UNLP, Avenida Paseo del Bosque s/n (1900), La Plata, Buenos Aires, Argentina
| | - Francisco J. Prevosti
- Centro Regional de Investigaciones Científicas y Transferencia Tecnológica de La Rioja (CRILAR), Provincia de La Rioja, UNLaR, SEGEMAR, UNCa, CONICET, Entre Ríos y Mendoza s/n, (5301), Anillaco, La Rioja, Argentina
| | - Corey J. A. Bradshaw
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jane C. Wheeler
- CONOPA, Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Lima, Peru
| | - Luis Borrero
- CONICET-IMHICIHU, Universidad de Buenos Aires. Saavedra 15, 5 (1083 ACA), Buenos Aires, Argentina
| | - Jeremy J. Austin
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
- Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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10
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Wysocki MA, Feranec RS, Tseng ZJ, Bjornsson CS. Using a Novel Absolute Ontogenetic Age Determination Technique to Calculate the Timing of Tooth Eruption in the Saber-Toothed Cat, Smilodon fatalis. PLoS One 2015; 10:e0129847. [PMID: 26132165 PMCID: PMC4489498 DOI: 10.1371/journal.pone.0129847] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 05/12/2015] [Indexed: 11/19/2022] Open
Abstract
Despite the superb fossil record of the saber-toothed cat, Smilodon fatalis, ontogenetic age determination for this and other ancient species remains a challenge. The present study utilizes a new technique, a combination of data from stable oxygen isotope analyses and micro-computed tomography, to establish the eruption rate for the permanent upper canines in Smilodon fatalis. The results imply an eruption rate of 6.0 millimeters per month, which is similar to a previously published average enamel growth rate of the S. fatalis upper canines (5.8 millimeters per month). Utilizing the upper canine growth rate, the upper canine eruption rate, and a previously published tooth replacement sequence, this study calculates absolute ontogenetic age ranges of tooth development and eruption in S. fatalis. The timing of tooth eruption is compared between S. fatalis and several extant conical-toothed felids, such as the African lion (Panthera leo). Results suggest that the permanent dentition of S. fatalis, except for the upper canines, was fully erupted by 14 to 22 months, and that the upper canines finished erupting at about 34 to 41 months. Based on these developmental age calculations, S. fatalis individuals less than 4 to 7 months of age were not typically preserved at Rancho La Brea. On the whole, S. fatalis appears to have had delayed dental development compared to dental development in similar-sized extant felids. This technique for absolute ontogenetic age determination can be replicated in other ancient species, including non-saber-toothed taxa, as long as the timing of growth initiation and growth rate can be determined for a specific feature, such as a tooth, and that growth period overlaps with the development of the other features under investigation.
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Affiliation(s)
- M. Aleksander Wysocki
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Robert S. Feranec
- Research and Collections Division, New York State Museum, Albany, New York, United States of America
- * E-mail:
| | - Zhijie Jack Tseng
- Division of Paleontology, American Museum of Natural History, New York, New York, United States of America
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11
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Jones KE. Evolutionary allometry of the thoracolumbar centra in felids and bovids. J Morphol 2015; 276:818-31. [PMID: 25773228 DOI: 10.1002/jmor.20382] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 01/29/2015] [Accepted: 02/03/2015] [Indexed: 11/07/2022]
Abstract
Mammals have evolved a remarkable range of body sizes, yet their overall body plan remains unaltered. One challenge of evolutionary biology is to understand the mechanisms by which this size diversity is achieved, and how the mechanical challenges associated with changing body size are overcome. Despite the importance of the axial skeleton in body support and locomotion, and much interest in the allometry of the appendicular skeleton, little is known about vertebral allometry outside primates. This study compares evolutionary allometry of the thoracolumbar centra in two families of quadrupedal running mammals: Felidae and Bovidae. I test the hypothesis that, as size increases, the thoracolumbar region will resist increasing loads by becoming a) craniocaudally shorter, and b) larger in cross-sectional area, particularly in the sagittal plane. Length, width, and height of the thoracolumbar centra of 23 felid and 34 bovid species were taken. Thoracic, prediaphragmatic, lumbar, and postdiaphragmatic lengths were calculated, and diameters were compared at three equivalent positions: the midthoracic, the diaphragmatic and the midlumbar vertebra. Allometric slopes were calculated using a reduced major axis regression, on both raw and independent contrasts data. Slopes and elevations were compared using an ANCOVA. As size increases the thoracolumbar centra become more robust, showing preferential reinforcement in the sagittal plane. There was less allometric shortening of the thoracic than the lumbar region, perhaps reflecting constraints due to its connection with the respiratory apparatus. The thoracic region was more robust in bovids than felids, whereas the lumbar region was longer and more robust in felids than bovids. Elongation of lumbar centra increases the outlever of sagittal bending at intervertebral joints, increasing the total pelvic displacement during dorsomobile running. Both locomotor specializations and functional regionalization of the axial skeleton appear to have influenced its response to increasing size.
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Affiliation(s)
- Katrina E Jones
- Center for Functional Anatomy and Evolution, Johns Hopkins University, 1830 East Monument st., Baltimore, Maryland, USA
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12
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Abstract
The late Pleistocene was a time of environmental change, culminating in an extinction event. Few fossil localities record a temporal series of carnivore fossil populations from this interesting interval as well as Rancho La Brea (RLB). We analysed mandibles of Smilodon fatalis from RLB using 2-D geometric morphometrics to examine whether, and how, mandibular shape changes through time. Smilodon fatalis shows mandibular evolution with oscillations between a small, ancestral-type morph in pits 77 (≈37 Kybp) and 2051 (≈26 Kybp), a larger, more derived morph in pits 91 (≈28 Kybp) and 61-67 (≈13.6 Kybp), and an intermediate morph from pit 13 (≈17.7 Kybp). These oscillations end in pit 61-67, with greatest body size, and are estimated to have its widest gape and lowest bite force. Additionally, variation is lowest in pit 61-67, which was deposited concurrent with the Bølling–Allerød warming event, which may have important implications for the timing or conditions during the extinction event. Contra to a temporal Bergmann's rule, such rapid warming events appear to be correlated with larger, derived, morphologies whereas static, cooler, climates correlate with gracile, ancestral morphologies.
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13
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Trigo TC, Tirelli FP, de Freitas TRO, Eizirik E. Comparative assessment of genetic and morphological variation at an extensive hybrid zone between two wild cats in southern Brazil. PLoS One 2014; 9:e108469. [PMID: 25250657 PMCID: PMC4177223 DOI: 10.1371/journal.pone.0108469] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 08/29/2014] [Indexed: 11/23/2022] Open
Abstract
Increased attention towards the Neotropical cats Leopardus guttulus and L. geoffroyi was prompted after genetic studies identified the occurrence of extensive hybridization between them at their geographic contact zone in southern Brazil. This is a region where two biomes intersect, each of which is associated with one of the hybridizing species (Atlantic Forest with L. guttulus and Pampas with L. geoffroyi). In this study, we conducted in-depth analyses of multiple molecular markers aiming to characterize the magnitude and spatial structure of this hybrid zone. We also performed a morphological assessment of these species, aiming to test their phenotypic differentiation at the contact zone, as well as the correlation between morphological features and the admixture status of the individuals. We found strong evidence for extensive and complex hybridization, with at least 40% of the individuals sampled in Rio Grande do Sul state (southernmost Brazil) identified as hybrids resulting from post-F1 generations. Despite such a high level of hybridization, samples collected in this state still comprised two recognizable clusters (genetically and morphologically). Genetically pure individuals were sampled mainly in regions farther from the contact zone, while hybrids concentrated in a central region (exactly at the interface between the two biomes). The morphological data set also revealed a strong spatial structure, which was correlated with the molecular results but displayed an even more marked separation between the clusters. Hybrids often did not present intermediate body sizes and could not be clearly distinguished morphologically from the parental forms. This observation suggests that some selective pressure may be acting on the hybrids, limiting their dispersal away from the hybrid zone and perhaps favoring genomic combinations that maintain adaptive phenotypic features of one or the other parental species.
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Affiliation(s)
- Tatiane C. Trigo
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
- * E-mail:
| | - Flávia P. Tirelli
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thales R. O. de Freitas
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Faculdade de Biociências, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, Brazil
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14
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Walters-Conte KB, Johnson DLE, Johnson WE, O’Brien SJ, Pecon-Slattery J. The dynamic proliferation of CanSINEs mirrors the complex evolution of Feliforms. BMC Evol Biol 2014; 14:137. [PMID: 24947429 PMCID: PMC4084570 DOI: 10.1186/1471-2148-14-137] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 06/11/2014] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Repetitive short interspersed elements (SINEs) are retrotransposons ubiquitous in mammalian genomes and are highly informative markers to identify species and phylogenetic associations. Of these, SINEs unique to the order Carnivora (CanSINEs) yield novel insights on genome evolution in domestic dogs and cats, but less is known about their role in related carnivores. In particular, genome-wide assessment of CanSINE evolution has yet to be completed across the Feliformia (cat-like) suborder of Carnivora. Within Feliformia, the cat family Felidae is composed of 37 species and numerous subspecies organized into eight monophyletic lineages that likely arose 10 million years ago. Using the Felidae family as a reference phylogeny, along with representative taxa from other families of Feliformia, the origin, proliferation and evolution of CanSINEs within the suborder were assessed. RESULTS We identified 93 novel intergenic CanSINE loci in Feliformia. Sequence analyses separated Feliform CanSINEs into two subfamilies, each characterized by distinct RNA polymerase binding motifs and phylogenetic associations. Subfamily I CanSINEs arose early within Feliformia but are no longer under active proliferation. Subfamily II loci are more recent, exclusive to Felidae and show evidence for adaptation to extant RNA polymerase activity. Further, presence/absence distributions of CanSINE loci are largely congruent with taxonomic expectations within Feliformia and the less resolved nodes in the Felidae reference phylogeny present equally ambiguous CanSINE data. SINEs are thought to be nearly impervious to excision from the genome. However, we observed a nearly complete excision of a CanSINEs locus in puma (Puma concolor). In addition, we found that CanSINE proliferation in Felidae frequently targeted existing CanSINE loci for insertion sites, resulting in tandem arrays. CONCLUSIONS We demonstrate the existence of at least two SINE families within the Feliformia suborder, one of which is actively involved in insertional mutagenesis. We find SINEs are powerful markers of speciation and conclude that the few inconsistencies with expected patterns of speciation likely represent incomplete lineage sorting, species hybridization and SINE-mediated genome rearrangement.
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Affiliation(s)
- Kathryn B Walters-Conte
- Department of Biology, American University, 101 Hurst Hall 4440 Massachusetts Ave, Washington, DC 20016, USA
| | - Diana LE Johnson
- Department of Biological Sciences, The George Washington University, 2036 G St, Washington, DC 20009, USA
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Stephen J O’Brien
- Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, 41 A, Sredniy Avenue St., Petersburg 199034, Russia
| | - Jill Pecon-Slattery
- Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
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15
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Janecka JE, Tewes ME, Laack L, Caso A, Grassman LI, Honeycutt RL. Loss of genetic diversity among ocelots in the United States during the 20th century linked to human induced population reductions. PLoS One 2014; 9:e89384. [PMID: 24586737 PMCID: PMC3935880 DOI: 10.1371/journal.pone.0089384] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 01/20/2014] [Indexed: 11/18/2022] Open
Abstract
Ocelots (Leopardus pardalis) in the United States currently exhibit low levels of genetic diversity. One hypothesis for this observation is that habitat fragmentation, resulting from human induced changes in the landscape during the 20(th) century, created island populations with highly reduced gene flow and increased genetic drift and inbreeding. In an effort to investigate this, we used a portion of the mitochondrial control region and 11 autosomal microsatellite loci to examine historical levels of genetic diversity and infer temporal changes in ocelot populations between 1853 and 2005. Levels of genetic diversity were higher in historical ocelot populations than in extant populations from Texas. The earliest documented loss of mitochondrial haplotype diversity occurred at Laguna Atascosa National Wildlife Refuge. The second extant population inhabiting private lands in Willacy County retained higher levels of genetic diversity through the 1990s, but subsequently lost diversity over the next decade. A similar pattern was observed for autosomal microsatellite loci. This supports the argument that low levels of genetic diversity in Texas are related to human induced population reductions and fragmentation, both of which threaten the remaining ocelots in the United States. At this time, the best means of mitigating the continued erosion of genetic variation are translocation of individuals either from larger populations in Mexico to Texas, or between the Texas populations.
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Affiliation(s)
- Jan E. Janecka
- Caesar Kleberg Wildlife Research Institute, Texas A & M University-Kingsville, Kingsville, Texas, United States of America
| | - Michael E. Tewes
- Caesar Kleberg Wildlife Research Institute, Texas A & M University-Kingsville, Kingsville, Texas, United States of America
| | - Linda Laack
- Laguna Atascosa National Wildlife Refuge, Rio Hondo, Texas, United States of America
| | - Arturo Caso
- Caesar Kleberg Wildlife Research Institute, Texas A & M University-Kingsville, Kingsville, Texas, United States of America
| | - Lon I. Grassman
- Caesar Kleberg Wildlife Research Institute, Texas A & M University-Kingsville, Kingsville, Texas, United States of America
| | - Rodney L. Honeycutt
- Natural Science Division, Pepperdine University, Malibu, California, United States of America
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16
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Abstract
Phylogenetic trees of DNA sequences of a group of specimens may include clades of two kinds: those produced by stochastic processes (random genetic drift) within a species, and clades that represent different species. The ratio of the mean pairwise sequence difference between a pair of clades (K) to the mean pairwise sequence difference within a clade (θ) can be used to determine whether the clades are samples from different species (K/θ ≥ 4) or the same species (K/θ<4) with probability ≥ 0.95. Previously I applied this criterion to delimit species of asexual organisms. Here I use data from the literature to show how it can also be applied to delimit sexual species using four groups of sexual organisms as examples: ravens, spotted leopards, sea butterflies, and liverworts. Mitochondrial or chloroplast genes are used because these segregate earlier during speciation than most nuclear genes and hence detect earlier stages of speciation. In several cases the K/θ ratio was greater than 4, confirming the original authors' intuition that the clades were sufficiently different to be assigned to different species. But the K/θ ratio split each of two liverwort species into two evolutionary species, and showed that support for the distinction between the common and Chihuahuan raven species is weak. I also discuss some possible sources of error in using the K/θ ratio; the most significant one would be cases where males migrate between different populations but females do not, making the use of maternally inherited organelle genes problematic. The K/θ ratio must be used with some caution, like all other methods for species delimitation. Nevertheless, it is a simple theory-based quantitative method for using DNA sequences to make rigorous decisions about species delimitation in sexual as well as asexual eukaryotes.
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Affiliation(s)
- C William Birky
- Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, AZ, USA.
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17
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Sakamoto M, Ruta M. Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity. PLoS One 2012; 7:e39752. [PMID: 22792186 PMCID: PMC3391202 DOI: 10.1371/journal.pone.0039752] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 05/28/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective. Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats. METHODOLOGY/PRINCIPAL FINDINGS A new phylogenetic analysis supports the monophyly of saber-toothed cats (Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various saber-toothed tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae, we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats. CONCLUSIONS/SIGNIFICANCE Ancestors of large cats in the 'Panthera' lineage tend to occupy, at a much later stage, morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional diversity studies, and may reveal novel patterns of morphospace occupation.
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Affiliation(s)
- Manabu Sakamoto
- School of Earth Sciences, University of Bristol, Bristol, United Kingdom.
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18
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Abstract
The complete sequences of the mitochondrial DNA genomes of Panthera tigris, Panthera pardus, and Panthera uncia were determined using the polymerase chain reaction method. The lengths of the complete mitochondrial DNA sequences of the three species were 16990, 16964, and 16773 bp, respectively. Each of the three mitochondrial DNA genomes included 13 protein-coding genes, 22 tRNA, two rRNA, one O(L)R, and one control region. The structures of the genomes were highly similar to those of Felis catus, Acinonyx jubatus, and Neofelis nebulosa. The phylogenies of the genus Panthera were inferred from two combined mitochondrial sequence data sets and the complete mitochondrial genome sequences, by MP (maximum parsimony), ML (maximum likelihood), and Bayesian analysis. The results showed that Panthera was composed of Panthera leo, P. uncia, P. pardus, Panthera onca, P. tigris, and N. nebulosa, which was included as the most basal member. The phylogeny within Panthera genus was N. nebulosa (P. tigris (P. onca (P. pardus, (P. leo, P. uncia)))). The divergence times for Panthera genus were estimated based on the ML branch lengths and four well-established calibration points. The results showed that at about 11.3 MYA, the Panthera genus separated from other felid species and then evolved into the several species of the genus. In detail, N. nebulosa was estimated to be founded about 8.66 MYA, P. tigris about 6.55 MYA, P. uncia about 4.63 MYA, and P. pardus about 4.35 MYA. All these estimated times were older than those estimated from the fossil records. The divergence event, evolutionary process, speciation, and distribution pattern of P. uncia, a species endemic to the central Asia with core habitats on the Qinghai-Tibetan Plateau and surrounding highlands, mostly correlated with the geological tectonic events and intensive climate shifts that happened at 8, 3.6, 2.5, and 1.7 MYA on the plateau during the late Cenozoic period.
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Affiliation(s)
- Lei Wei
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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19
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Allen WL, Cuthill IC, Scott-Samuel NE, Baddeley R. Why the leopard got its spots: relating pattern development to ecology in felids. Proc Biol Sci 2011; 278:1373-80. [PMID: 20961899 PMCID: PMC3061134 DOI: 10.1098/rspb.2010.1734] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 09/20/2010] [Indexed: 11/12/2022] Open
Abstract
A complete explanation of the diversity of animal colour patterns requires an understanding of both the developmental mechanisms generating them and their adaptive value. However, only two previous studies, which involved computer-generated evolving prey, have attempted to make this link. This study examines variation in the camouflage patterns displayed on the flanks of many felids. After controlling for the effects of shared ancestry using a fully resolved molecular phylogeny, this study shows how phenotypes from plausible felid coat pattern generation mechanisms relate to ecology. We found that likelihood of patterning and pattern attributes, such as complexity and irregularity, were related to felids' habitats, arboreality and nocturnality. Our analysis also indicates that disruptive selection is a likely explanation for the prevalence of melanistic forms in Felidae. Furthermore, we show that there is little phylogenetic signal in the visual appearance of felid patterning, indicating that camouflage adapts to ecology over relatively short time scales. Our method could be applied to any taxon with colour patterns that can reasonably be matched to reaction-diffusion and similar models, where the kinetics of the reaction between two or more initially randomly dispersed morphogens determines the outcome of pattern development.
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Affiliation(s)
- William L Allen
- School of Experimental Psychology, University of Bristol, 12a Priory Road, Bristol BS8 1TU, UK.
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20
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Cossíos D, Lucherini M, Ruiz-García M, Angers B. Influence of ancient glacial periods on the Andean fauna: the case of the pampas cat (Leopardus colocolo). BMC Evol Biol 2009; 9:68. [PMID: 19331650 PMCID: PMC2669060 DOI: 10.1186/1471-2148-9-68] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 03/30/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND While numerous studies revealed the major role of environmental changes of the Quaternary on the evolution of biodiversity, research on the influence of that period on current South-American fauna is scarce and have usually focused on lowland regions. In this study, the genetic structure of the pampas cat (Leopardus colocolo), a widely distributed felid, was determined and linked to ancient climate fluctuations on the Andean region. RESULTS Using both mitochondrial sequences and nuclear microsatellites, we inferred the existence of at least four groups of populations in the central Andes, while other three localities, with little sample sizes (n = 3), presented differences in only one of these markers. The distribution of these groups is correlated to latitude, with a central area characterized by admixture of numerous mitochondrial clades. This suggests colonization from at least three glacial refuges and a contact zone between 20 degrees and 23 degrees S following a glaciation event. The similar coalescence times of the mitochondrial haplotypes indicated that the major clades split approximately one million years ago, likely during the Pre-Pastonian glacial period (0.80 - 1.30 MYA), followed by a demographic expansion in every clade during the Aftonian interglacial period (0.45 - 0.62 MYA). Interestingly, this structure roughly corresponds to the current recognised distribution of morphological subspecies. CONCLUSION The four groups of populations identified here must be considered different management units, and we propose the three localities showing differences in only mtDNA or ncDNA as provisional management units. The results revealed the influence of ancient climate fluctuations on the evolutionary history of this species. It is expected that the other species of land vertebrates with a smaller or similar mobility have been affected in the same manner by the glacial and interglacial periods in the central Andes.
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Affiliation(s)
- Daniel Cossíos
- Département de Sciences Biologiques, Université de Montréal, C.P.: 6128, Succ. Centre-Ville, Montréal, H3C 3J7, Canada
| | - Mauro Lucherini
- GECM, Cátedra de Fisiología Animal, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-CONICET, San Juan 670, 8000 Bahía Blanca, Argentina
| | - Manuel Ruiz-García
- Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A No 43-82, Bogotá DC, Colombia
| | - Bernard Angers
- Département de Sciences Biologiques, Université de Montréal, C.P.: 6128, Succ. Centre-Ville, Montréal, H3C 3J7, Canada
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21
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Zamora-Perez A, Gómez-Meda BC, Ramos-Ibarra ML, Batista-González CM, Luna-Aguirre J, González-Rodríguez A, Rodríguez-Avila JL, Zúñiga-González GM. [Felines: an alternative in genetic toxicology studies?]. REV BIOL TROP 2008; 56:969-974. [PMID: 19256458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023] Open
Abstract
The micronuclei (MN) test carry out in peripheral blood is fast, simple, economic and it is used to detect genotoxic environmental agents. MN are fragments of chromosomes or complete chromosomes remaining in the cytoplasm after cell division, which increase when organisms are exposed to genotoxic agents. Therefore, species with the highest values of spontaneous micronucleated erythrocytes (MNE) are the most suitable to be potentials biomonitor of micronucleogenic agents, using a drop of blood. Nine species of Felines that present spontaneous MNE in peripheral blood are shown. From these species, the cat has been previously proven, with positive results and also lion (Panthera leo), yaguaroundi (Felis yagoaroundi), lynx (Lynx ruffus), jaguar (Panthera onca), puma (Puma concolor), tiger (Panthera tigris), ocelote (Felis padalis) and leopard (Panthera pardus) display spontaneous MNE, and with this characteristic this Family can be propose like a potential group to be used in toxicogenetic studies.
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Affiliation(s)
- Ana Zamora-Perez
- Instituto de Investigación en Odontología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, México.
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22
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Luo SJ, Johnson WE, David VA, Menotti-Raymond M, Stanyon R, Cai QX, Beck T, Yuhki N, Pecon-Slattery J, Smith JLD, O'Brien SJ. Development of Y chromosome intraspecific polymorphic markers in the Felidae. ACTA ACUST UNITED AC 2007; 98:400-13. [PMID: 17646273 DOI: 10.1093/jhered/esm063] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Y chromosome haplotyping based on microsatellites and single nucleotide polymorphisms (SNPs) has proved to be a powerful tool for population genetic studies of humans. However, the promise of the approach is hampered in the majority of nonhuman mammals by the lack of Y-specific polymorphic markers. We were able to identify new male-specific polymorphisms in the domestic cat Felis catus and 6 additional Felidae species with a combination of molecular genetic and cytogenetic approaches including 1) identifying domestic cat male-specific microsatellites from markers generated from a male cat microsatellite-enriched genomic library, a flow-sorted Y cosmid library, or a Y-specific cat bacteria artificial chromosome (BAC) clone, (2) constructing microsatellite-enriched libraries from flow-sorted Y chromosomes isolated directly from focal wildcat species, and (3) screening Y chromosome conserved anchored tagged sequences primers in Felidae species. Forty-one male-specific microsatellites were identified, but only 6 were single-copy loci, consistent with the repetitive nature of the Y chromosome. Nucleotide diversity (pi) of Y-linked intron sequences (2.1 kbp) was in the range of 0 (tiger) to 9.95 x 10(-4) (marbled cat), and the number of SNPs ranged from none in the tiger to 7 in the Asian leopard cat. The Y haplotyping system described here, consisting of 4 introns (SMCY3, SMCY7, UTY11, and DBY7) and 1 polymorphic microsatellite (SMCY-STR), represents the first available markers for tracking intraspecific male lineage polymorphisms in Felidae species and promises to provide significant insights to evolutionary and population genetic studies of the species.
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Affiliation(s)
- Shu-Jin Luo
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201, USA.
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23
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Abstract
The trend for elevating known subspecies to the status of species on the basis of inappropriate evidence can potentially divert important conservation funds away from other species.
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Affiliation(s)
- Shai Meiri
- * To whom correspondence should be addressed. E-mail:
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24
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O'Brien SJ, Johnson WE. The evolution of cats. Genomic paw prints in the DNA of the world's wild cats have clarified the cat family tree and uncovered several remarkable migrations in their past. Sci Am 2007; 297:68-75. [PMID: 17695844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
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25
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Grisolia AB, Moreno VR, Campagnari F, Milazzotto MP, Garcia JF, Adania CH, Souza EB. Genetic diversity of microsatellite loci in Leopardus pardalis, Leopardus wiedii and Leopardus tigrinus. Genet Mol Res 2007; 6:382-9. [PMID: 17624861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The microsatellite loci FCA045, FCA077, FCA008, and FCA096 are highly variable molecular markers which were used to determine the genetic diversity in 148 captive Leopardus sp. The PCR-amplified products of microsatellite loci were characterized in ABI Prism 310 Genetic Analyzer. Allele numbers, heterozygosity, polymorphism information content, exclusive allele number, and shared alleles were calculated. Sixty-five alleles were found and their sizes ranged from 116 to 216 bp in four microsatellite loci. The heterozygosity ranged from 0.36 to 0.81 in Leopardus pardalis, 0.57 to 0.67 in L. tigrinus and 0.80 to 0.92 in L. wiedii. The polymorphism information content was from 0.80 to 0.88 in L. pardalis, 0.76 to 0.88 in L. tigrinus and 0.77 to 0.90 in L. wiedii. The margay (L. wiedii) showed the highest index of polymorphism among the three species in this study. These results imply that microsatellite DNA markers can help in the study of the genetic diversity of Leopardus specimens.
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Affiliation(s)
- A B Grisolia
- Departamento de Genética, Instituto de Biociências, UNESP, Botucatu, SP, Brasil.
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26
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King V, Goodfellow PN, Pearks Wilkerson AJ, Johnson WE, O'Brien SJ, Pecon-Slattery J. Evolution of the male-determining gene SRY within the cat family Felidae. Genetics 2007; 175:1855-67. [PMID: 17277366 PMCID: PMC1855139 DOI: 10.1534/genetics.106.066779] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In most placental mammals, SRY is a single-copy gene located on the Y chromosome and is the trigger for male sex determination during embryonic development. Here, we present comparative genomic analyses of SRY (705 bp) along with the adjacent noncoding 5' flank (997 bp) and 3' flank (948 bp) in 36 species of the cat family Felidae. Phylogenetic analyses indicate that the noncoding genomic flanks and SRY closely track species divergence. However, several inconsistencies are observed in SRY. Overall, the gene exhibits purifying selection to maintain function (omega = 0.815) yet SRY is under positive selection in two of the eight felid lineages. SRY has low numbers of nucleotide substitutions, yet most encode amino acid changes between species, and four different species have significantly altered SRY due to insertion/deletions. Moreover, fixation of nonsynonymous substitutions between sister taxa is not consistent and may occur rapidly, as in the case of domestic cat, or not at all over long periods of time, as observed within the Panthera lineage. The former resembles positive selection during speciation, and the latter purifying selection to maintain function. Thus, SRY evolution in cats likely reflects the different phylogeographic histories, selection pressures, and patterns of speciation in modern felids.
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Affiliation(s)
- V King
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom
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28
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Buckley-Beason VA, Johnson WE, Nash WG, Stanyon R, Menninger JC, Driscoll CA, Howard J, Bush M, Page JE, Roelke ME, Stone G, Martelli PP, Wen C, Ling L, Duraisingam RK, Lam PV, O'Brien SJ. Molecular evidence for species-level distinctions in clouded leopards. Curr Biol 2007; 16:2371-6. [PMID: 17141620 PMCID: PMC5618441 DOI: 10.1016/j.cub.2006.08.066] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2006] [Revised: 08/18/2006] [Accepted: 08/21/2006] [Indexed: 11/17/2022]
Abstract
Among the 37 living species of Felidae, the clouded leopard (Neofelis nebulosa) is generally classified as a monotypic genus basal to the Panthera lineage of great cats. This secretive, mid-sized (16-23 kg) carnivore, now severely endangered, is traditionally subdivided into four southeast Asian subspecies (Figure 1A). We used molecular genetic methods to re-evaluate subspecies partitions and to quantify patterns of population genetic variation among 109 clouded leopards of known geographic origin (Figure 1A, Tables S1 ans S2 in the Supplemental Data available online). We found strong phylogeographic monophyly and large genetic distances between N. n. nebulosa (mainland) and N. n. diardi (Borneo; n = 3 individuals) with mtDNA (771 bp), nuclear DNA (3100 bp), and 51 microsatellite loci. Thirty-six fixed mitochondrial and nuclear nucleotide differences and 20 microsatellite loci with nonoverlapping allele-size ranges distinguished N. n. nebulosa from N. n. diardi. Along with fixed subspecies-specific chromosomal differences, this degree of differentiation is equivalent to, or greater than, comparable measures among five recognized Panthera species (lion, tiger, leopard, jaguar, and snow leopard). These distinctions increase the urgency of clouded leopard conservation efforts, and if affirmed by morphological analysis and wider sampling of N. n. diardi in Borneo and Sumatra, would support reclassification of N. n. diardi as a new species (Neofelis diardi).
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Fitzpatrick BM, Turelli M. The geography of mammalian speciation: mixed signals from phylogenies and range maps. Evolution 2006; 60:601-15. [PMID: 16637504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The importance of geographic isolation in speciation has been debated since the 19th century. Since the beginning of the 20th century, the consensus has been that most speciation involves divergence in allopatry. This consensus was based largely on decades of observations by naturalists and verbal arguments against speciation without isolation. Recent attempts to quantify the importance of allopatric versus sympatric speciation using comparative methods called "age-range correlation" (ARC) suggest that allopatric speciation is more common than sympatric speciation. However, very few taxa have been studied and there are concerns about the adequacy of the methods. We propose methodological improvements including changes in the way overlap between clades is quantified and Monte Carlo methods to test the null hypothesis of no relationship between phylogenetic relatedness and geographic range overlap. We analyze 14 clades of mammals, chosen because of the availability of data and the consensus among mammalogists that speciation is routinely allopatric. Although data from a few clades clearly indicate allopatric speciation, divergence with gene flow is plausible in others and many results are inconclusive. The relative rarity of significant correlations between phylogenetic distance and range overlap may have three distinct causes: (1) post-speciation range changes, (2) relative rarity of range overlap, and (3) a mixture of geographic modes of speciation. Our results support skepticism about ARC's power for inferring the biogeography of speciation. Yet, even if few clades provide clear signals, meta-analytic approaches such as ARC may set bounds on the prevalence of alternative modes of speciation.
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Affiliation(s)
- Benjamin M Fitzpatrick
- Section of Evolution and Ecology and Center for Population Biology University of California, Davis 95616, USA.
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Abstract
Assisted reproductive technologies are increasingly applied to support breeding efforts for many endangered felids. To explain the highly variable responses among felids to exogenous gonadotropins (FSH, eCG), we analyzed a 567bp fragment spanning a hyper-variable region of the FSH receptor in the domestic cat (catFSHR) and nine wild felid species/subspecies (felFSHR). Phylogenetic analysis indicated that the newly sequenced felFSHRs, together with the bear FSHR, belong to the carnivore group closely related to the ungulate clade. Within Felidae, genetic distances were 0.0089 +/- 0.0018 for nucleotide and 0.0183 +/- 0.0044 for amino acid (aa) sequences. In pairwise comparisons among catFSHR and all new felFSHRs, similarity ranged from 98.6 to 99.5% for nucleotides and from 97.4 to 98.9% for aa. Besides interspecies variability, intraspecies variation was also detected on both the cDNA and the protein level. There were no indications for an expression of tissue-specific isoforms of FSHR in testis and ovary.
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Affiliation(s)
- Katrin Neubauer
- Leibniz-Institute for Zoo and Wildlife Research, Postfach 601103, D-10252 Berlin, Germany.
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31
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Abstract
Modern felid species descend from relatively recent (<11 million years ago) divergence and speciation events that produced successful predatory carnivores worldwide but that have confounded taxonomic classifications. A highly resolved molecular phylogeny with divergence dates for all living cat species, derived from autosomal, X-linked, Y-linked, and mitochondrial gene segments (22,789 base pairs) and 16 fossil calibrations define eight principal lineages produced through at least 10 intercontinental migrations facilitated by sea-level fluctuations. A ghost lineage analysis indicates that available felid fossils underestimate (i.e., unrepresented basal branch length) first occurrence by an average of 76%, revealing a low representation of felid lineages in paleontological remains. The phylogenetic performance of distinct gene classes showed that Y-chromosome segments are appreciably more informative than mitochondrial DNA, X-linked, or autosomal genes in resolving the rapid Felidae species radiation.
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Affiliation(s)
- Warren E Johnson
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD 21702-1201, USA.
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32
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Barnett R, Barnes I, Phillips MJ, Martin LD, Harington CR, Leonard JA, Cooper A. Evolution of the extinct Sabretooths and the American cheetah-like cat. Curr Biol 2006; 15:R589-90. [PMID: 16085477 DOI: 10.1016/j.cub.2005.07.052] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Abstract
Advances in population and quantitative genomics, aided by the computational algorithms that employ genetic theory and practice, are now being applied to biological questions that surround free-ranging species not traditionally suitable for genetic enquiry. Here we review how applications of molecular genetic tools have been used to describe the natural history, present status, and future disposition of wild cat species. Insight into phylogenetic hierarchy, demographic contractions, geographic population substructure, behavioral ecology, and infectious diseases have revealed strategies for survival and adaptation of these fascinating predators. Conservation, stabilization, and management of the big cats are important areas that derive benefit from the genome resources expanded and applied to highly successful species, imperiled by an expanding human population.
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Affiliation(s)
- Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA.
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Yu L, Zhang YP. Phylogenetic studies of pantherine cats (Felidae) based on multiple genes, with novel application of nuclear beta-fibrinogen intron 7 to carnivores. Mol Phylogenet Evol 2005; 35:483-95. [PMID: 15804417 DOI: 10.1016/j.ympev.2005.01.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Revised: 01/16/2005] [Accepted: 01/26/2005] [Indexed: 11/24/2022]
Abstract
The pantherine lineage of the cat family Felidae (order: Carnivora) includes five big cats of genus Panthera and a great many midsized cats known worldwide. Presumably because of their recent and rapid radiation, the evolutionary relationship among pantherines remains ambiguous. We provide an independent assessment of the evolutionary history of pantherine lineage using two complete mitochondrial (mt) genes (ND2 and ND4) and the nuclear beta-fibrinogen intron 7 gene, whose utility in carnivoran phylogeny was first explored. The available four mt (ND5, cytb, 12S, and 16SrRNA) and two nuclear (IRBP and TTR) sequence loci were also combined to reconstruct phylogeny of 14 closely related cat species. Our analyses of combined mt data (six genes; approximately 3750 bp) and combined mt and nuclear data (nine genes; approximately 6500 bp) obtained identical tree topologies, which were well-resolved and strongly supported for almost all nodes. Monophyly of Panthera genus in pantherine lineage was confirmed and interspecific affinities within this genus revealed a novel branching pattern, with P. tigris diverging first in Panthera genus, followed by P. onca, P. leo, and last two sister species P. pardus and P. uncia. In addition, close association of Neofelis nebulosa to Panthera, the phylogenetic redefinition of Otocolobus manul within the domestic cat group, and the relatedness of Acinonyx jubatus and Puma concolor were all important findings in the resulting phylogenies. The potential utilities of nine different genes for phylogenetic resolution of closely related pantherine species were also evaluated, with special interest in that of the novel nuclear beta-fibrinogen intron 7.
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Affiliation(s)
- Li Yu
- Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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35
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Affiliation(s)
- Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702-1201, USA
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Pecon-Slattery J, Pearks Wilkerson AJ, Murphy WJ, O'Brien SJ. Phylogenetic assessment of introns and SINEs within the Y chromosome using the cat family felidae as a species tree. Mol Biol Evol 2004; 21:2299-309. [PMID: 15329385 DOI: 10.1093/molbev/msh241] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The cat family Felidae was used as a species tree to assess the phylogenetic performance of genes, and their embedded SINE elements, within the nonrecombining region of the Y chromosome (NRY). Genomic segments from single-copy X-Y homologs SMCY, UBE1Y, and ZFY (3,604 bp) were amplified in 36 species of cat. These genes are located within the X-degenerate region of the NRY and are thought to be molecular "fossils" that ceased conventional recombination with the X chromosome early within the placental mammal evolution. The pattern and tempo of evolution at these three genes is significant in light of the recent, rapid evolution of the family over approximately 12 Myr and provides exceptional support for each of the eight recognized felid lineages, as well as clear diagnostic substitutions identifying nearly all species. Bootstrap support and Bayesian posterior probabilities are uniformly high for defining each of the eight monophyletic lineages. Further, the preferential use of specific target-site motifs facilitating SINE insertion is empirically supported by sequence analyses of SINEs embedded within the three genes. Target-site insertion is thought to explain the contradiction between intron phylogeny and results of the SMCY SINE phylogeny that unites distantly related species. Overall, our data suggest X-degenerate genes within the NRY are singularly powerful markers and offer a valuable patrilineal perspective in species evolution.
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