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Jordania J. Music as aposematic signal: predator defense strategies in early human evolution. Front Psychol 2024; 14:1271854. [PMID: 38298362 PMCID: PMC10828848 DOI: 10.3389/fpsyg.2023.1271854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 12/18/2023] [Indexed: 02/02/2024] Open
Abstract
The article draws attention to a neglected key element of human evolutionary history-the defense strategies of hominins and early humans against predators. Possible reasons for this neglect are discussed, and the historical development of this field is outlined. Many human morphological and behavioral characteristics-musicality, sense of rhythm, use of dissonances, entrainment, bipedalism, long head hair, long legs, strong body odor, armpit hair, traditions of body painting and cannibalism-are explained as predator avoidance tactics of an aposematic (warning display) defense strategy. The article argues that the origins of human musical faculties should be studied in the wider context of an early, multimodal human defense strategy from predators.
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2
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Lynch LM, Allen KL. Relative Brain Volume of Carnivorans Has Evolved in Correlation with Environmental and Dietary Variables Differentially among Clades. BRAIN, BEHAVIOR AND EVOLUTION 2022; 97:284-297. [PMID: 35235933 DOI: 10.1159/000523787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/16/2022] [Indexed: 12/21/2022]
Abstract
Carnivorans possess relatively large brains compared to most other mammalian clades. Factors like environmental complexity (Cognitive Buffer Hypothesis) and diet quality (Expensive-Tissue Hypothesis) have been proposed as mechanisms for encephalization in other large-brained clades. We examine whether the Cognitive Buffer and Expensive-Tissue Hypotheses account for brain size variation within Carnivora. Under these hypotheses, we predict a positive correlation between brain size and environmental complexity or protein consumption. Relative endocranial volume (phylogenetic generalized least-squares residual from species' mean body mass) and 9 environmental and dietary variables were collected from the literature for 148 species of terrestrial and marine carnivorans. We found that the correlation between relative brain volume and environment and diet differed among clades, a trend consistent with other larger brained vertebrates (i.e., Primates, Aves). Mustelidae and Procyonidae demonstrate larger brains in species with higher-quality diets, consistent with the Expensive-Tissue Hypothesis, while in Herpestidae, correlations between relative brain size and environment are consistent with the Cognitive Buffer Hypothesis. Our results indicate that carnivorans may have evolved relatively larger brains under similar selective pressures as primates despite the considerable differences in life history and behavior between these two clades.
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Affiliation(s)
- Leigha M Lynch
- Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA.,Midwestern University, Glendale, Arizona, USA
| | - Kari L Allen
- Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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3
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Bertola LD, Vermaat M, Lesilau F, Chege M, Tumenta PN, Sogbohossou EA, Schaap OD, Bauer H, Patterson BD, White PA, de Iongh HH, Laros JFJ, Vrieling K. Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo). BMC Genomics 2022; 23:321. [PMID: 35459090 PMCID: PMC9027350 DOI: 10.1186/s12864-022-08510-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/29/2022] [Indexed: 11/23/2022] Open
Abstract
Background Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. Results In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. Conclusions The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08510-y.
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Affiliation(s)
- L D Bertola
- City University of New York, City College of New York, 160 Convent Avenue, New York, NY, 10031, USA. .,Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands. .,Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands.
| | - M Vermaat
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - F Lesilau
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands.,Kenya Wildlife Service, Nairobi, Kenya
| | - M Chege
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands.,Kenya Wildlife Service, Nairobi, Kenya
| | - P N Tumenta
- Centre for Environment and Developmental Studies, Cameroon (CEDC), Yaounde, Cameroon.,Regional Training Centre Specialized in Agriculture, Forest and Wood, University of Dschang, BP 138, Yaounde, Cameroon
| | - E A Sogbohossou
- Laboratoire d'Ecologie Appliquée, Université d'Abomey-Calavi, 03 BP 294, Cotonou, Benin
| | - O D Schaap
- Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
| | - H Bauer
- Wildlife Conservation Research Unit, Zoology, University of Oxford Recanati-Kaplan Centre, Tubney, OX13 5QL, UK
| | - B D Patterson
- Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, 60605, USA
| | - P A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095-1496, USA
| | - H H de Iongh
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, The Netherlands.,Department of Biology, Evolutionary Ecology Group, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - J F J Laros
- Department of Human Genetics, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands.,Leiden Genome Technology Center, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - K Vrieling
- Institute of Biology Leiden (IBL), Leiden University, PO Box 9505, 2300 RA, Leiden, The Netherlands
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4
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Kitchener AC, Hoffmann M, Yamaguchi N, Breitenmoser-Würsten C, Wilting A. A system for designating taxonomic certainty in mammals and other taxa. Mamm Biol 2022. [DOI: 10.1007/s42991-021-00205-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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5
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Bertola LD, Miller SM, Williams VL, Naude VN, Coals P, Dures SG, Henschel P, Chege M, Sogbohossou EA, Ndiaye A, Kiki M, Gaylard A, Ikanda DK, Becker MS, Lindsey P. Genetic guidelines for translocations: Maintaining intraspecific diversity in the lion ( Panthera leo). Evol Appl 2022; 15:22-39. [PMID: 35126646 PMCID: PMC8792481 DOI: 10.1111/eva.13318] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/26/2022] Open
Abstract
Conservation translocations have become an important management tool, particularly for large wildlife species such as the lion (Panthera leo). When planning translocations, the genetic background of populations needs to be taken into account; failure to do so risks disrupting existing patterns of genetic variation, ultimately leading to genetic homogenization, and thereby reducing resilience and adaptability of the species. We urge wildlife managers to include knowledge of the genetic background of source/target populations, as well as species-wide patterns, in any management intervention. We present a hierarchical decision-making tool in which we list 132 lion populations/lion conservation units and provide information on genetic assignment, uncertainty and suitability for translocation for each source/target combination. By including four levels of suitability, from 'first choice' to 'no option', we provide managers with a range of options. To illustrate the extent of international trade of lions, and the potential disruption of natural patterns of intraspecific diversity, we mined the CITES Trade Database for estimated trade quantities of live individuals imported into lion range states during the past 4 decades. We identified 1056 recorded individuals with a potential risk of interbreeding with wild lions, 772 being captive-sourced. Scoring each of the records with our decision-making tool illustrates that only 7% of the translocated individuals were 'first choice' and 73% were 'no option'. We acknowledge that other, nongenetic factors are important in the decision-making process, and hence a pragmatic approach is needed. A framework in which source/target populations are scored based on suitability is not only relevant to lion, but also to other species of wildlife that are frequently translocated. We hope that the presented overview supports managers to include genetics in future management decisions and contributes towards conservation of the lion in its full diversity.
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Affiliation(s)
- Laura D. Bertola
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- City College of New YorkNew YorkNew YorkUSA
| | - Susan M. Miller
- FitzPatrick Institute of African OrnithologyDSI‐NRF Centre of ExcellenceUniversity of Cape TownCape TownSouth Africa
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Vivienne L. Williams
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
| | - Vincent N. Naude
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Peter Coals
- School of Animal, Plant and Environmental SciencesUniversity of the WitwatersrandJohannesburgSouth Africa
- Wildlife Conservation Research UnitUniversity of OxfordOxfordUK
| | | | | | - Monica Chege
- Institute of Environmental Sciences (CML)Leiden UniversityLeidenThe Netherlands
- Kenya Wildlife ServiceNairobiKenya
| | | | | | - Martial Kiki
- Département de Génie de l’EnvironnementUniversité d’Abomey‐CalaviCotonouBenin
| | - Angela Gaylard
- Conservation Development & Assurance DepartmentAfrican Parks NetworkJohannesburgSouth Africa
| | | | | | - Peter Lindsey
- Department of Zoology and EntomologyMammal Research InstituteUniversity of PretoriaPretoriaSouth Africa
- Environmental Futures Research InstituteGriffith UniversityNathanQueenslandAustralia
- Wildlife Conservation NetworkSan FranciscoCaliforniaUSA
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6
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Genetic diversity, viability and conservation value of the global captive population of the Moroccan Royal lions. PLoS One 2021; 16:e0258714. [PMID: 34962925 PMCID: PMC8714086 DOI: 10.1371/journal.pone.0258714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/04/2021] [Indexed: 11/19/2022] Open
Abstract
This study evaluates the diversity of the so-called ‘Moroccan Royal lions’ using genealogical information. Lions are no longer extant in North Africa, but the previous wild population was an important element of the now-recognised northern subspecies (Panthera leo leo) that ranged across West Africa, North Africa and the Middle East into India. The remaining captive population of ‘Moroccan Royal lions’ seems to be significantly endangered by the loss of diversity due to the effective population size decrease. The pedigree file of this captive lion population consisted of 454 individuals, while the reference population included 98 animals (47 males and 51 females). The completeness of the pedigree data significantly decreased with an increasing number of generations. The highest percentage of pedigree completeness (over 70%) was achieved in the first generation of the reference population. Pedigree-based parameters derived from the common ancestor and gene origin were used to estimate the state of diversity. In the reference population, the average inbreeding coefficient was 2.14%, while the individual increase in inbreeding over generations was 2.31%. Overall, the reference population showed lower average inbreeding and average relatedness compared with the pedigree file. The number of founders (47), the effective number of founders (24) and the effective number of ancestors (22) were estimated in the reference population. The effective population size of 14.02 individuals confirms the critically endangered status of the population and rapid loss of diversity in the future. Thus, continuous monitoring of the genetic diversity of the ‘Moroccan Royal lion’ group is required, especially for long-term conservation management purposes, as it would be an important captive group should further DNA studies establish an affinity to P. leo leo.
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7
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Engelbrecht HM, Branch WR, Tolley KA. Snakes on an African plain: the radiation of Crotaphopeltis and Philothamnus into open habitat (Serpentes: Colubridae). PeerJ 2021; 9:e11728. [PMID: 34434643 PMCID: PMC8351568 DOI: 10.7717/peerj.11728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 06/15/2021] [Indexed: 11/20/2022] Open
Abstract
Background The African continent is comprised of several different biomes, although savanna is the most prevalent. The current heterogeneous landscape was formed through long-term vegetation shifts as a result of the global cooling trend since the Oligocene epoch. The overwhelming trend was a shift from primarily forest, to primarily savanna. As such, faunal groups that emerged during the Paleogene/Neogene period and have species distributed in both forest and savanna habitat should show a genetic signature of the possible evolutionary impact of these biome developments. Crotaphopeltis and Philothamnus (Colubridae) are excellent taxa to investigate the evolutionary impact of these biome developments on widespread African colubrid snakes, and whether timing and patterns of radiation are synchronous with biome reorganisation. Methods A phylogenetic framework was used to investigate timing of lineage diversification. Phylogenetic analysis included both genera as well as other Colubridae to construct a temporal framework in order to estimate radiation times for Crotaphopeltis and Philothamnus. Lineage diversification was estimated in Bayesian Evolutionary Analysis Sampling Trees (BEAST), using two mitochondrial markers (cyt–b, ND4), one nuclear marker (c–mos), and incorporating one fossil and two biogeographical calibration points. Vegetation layers were used to classify and confirm species association with broad biome types (‘closed’ = forest, ‘open’ = savanna/other), and the ancestral habitat state for each genus was estimated. Results Philothamnus showed an ancestral state of closed habitat, but the ancestral habitat type for Crotaphopeltis was equivocal. Both genera showed similar timing of lineage diversification diverging from their sister genera during the Oligocene/Miocene transition (ca. 25 Mya), with subsequent species radiation in the Mid-Miocene. Philothamnus appeared to have undergone allopatric speciation during Mid-Miocene forest fragmentation. Habitat generalist and open habitat specialist species emerged as savanna became more prevalent, while at least two forest associated lineages within Crotaphopeltis moved into Afromontane forest habitat secondarily and independently. Discussion With similar diversification times, but contrasting ancestral habitat reconstructions, we show that these genera have responded very differently to the same broad biome shifts. Differences in biogeographical patterns for the two African colubrid genera is likely an effect of distinct life-history traits, such as the arboreous habits of Philothamnus compared to the terrestrial lifestyle of Crotaphopeltis.
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Affiliation(s)
- Hanlie M Engelbrecht
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa.,Kirstenbosch Research Centre, South African National Biodiversity Institute, Cape Town, Western Cape, South Africa.,Department of Botany & Zoology, Stellenbosch University, Cape Town, Western Cape, South Africa
| | - William R Branch
- Herpetology, Port Elizabeth Museum (Bayworld), Port Elizabeth, Eastern Cape, South Africa.,Department of Zoology, Nelson Mandela Metropolitan University, Port Elizabeth, Eastern Cape, South Africa
| | - Krystal A Tolley
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa.,Kirstenbosch Research Centre, South African National Biodiversity Institute, Cape Town, Western Cape, South Africa
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8
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Abstract
In this study, we synthesize terrestrial and marine proxy records, spanning the past 620 ky, to decipher pan-African climate variability and its drivers and potential linkages to hominin evolution. We find a tight correlation between moisture availability across Africa to El Niño Southern Ocean oscillation (ENSO) variability, a manifestation of the Walker Circulation, that was most likely driven by changes in Earth's eccentricity. Our results demonstrate that low-latitude insolation was a prominent driver of pan-African climate change during the Middle to Late Pleistocene. We argue that these low-latitude climate processes governed the dispersion and evolution of vegetation as well as mammals in eastern and western Africa by increasing resource-rich and stable ecotonal settings thought to have been important to early modern humans.
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9
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Pleistocene extinction and geographic singularity explain differences in global felid ensemble structure. Evol Ecol 2021. [DOI: 10.1007/s10682-021-10103-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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10
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Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 2021; 10:e63167. [PMID: 33599612 PMCID: PMC7963486 DOI: 10.7554/elife.63167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Nico L Avenant
- National Museum and Centre for Environmental Management, University of the Free StateBloemfonteinSouth Africa
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums ScotlandEdinburghUnited Kingdom
| | - Erwan Corre
- CNRS, Sorbonne Université, CNRS, ABiMS, Station Biologique de RoscoffRoscoffFrance
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
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11
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Smith BT, Gehara M, Harvey MG. The demography of extinction in eastern North American birds. Proc Biol Sci 2021; 288:20201945. [PMID: 33529556 DOI: 10.1098/rspb.2020.1945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Species are being lost at an unprecedented rate during the Anthropocene. Progress has been made in clarifying how species traits influence their propensity to go extinct, but the role historical demography plays in species loss or persistence is unclear. In eastern North America, five charismatic landbirds went extinct last century, and the causes of their extinctions have been heavily debated. Although these extinctions are most often attributed to post-colonial human activity, other factors such as declining ancestral populations prior to European colonization could have made these species particularly susceptible. We used population genomic data from these extinct birds and compared them with those from four codistributed extant species. We found extinct species harboured lower genetic diversity and effective population sizes than extant species, but both extinct and non-extinct birds had similar demographic histories of population expansion. These demographic patterns are consistent with population size changes associated with glacial-interglacial cycles. The lack of support for overall population declines during the Pleistocene corroborates the view that, although species that went extinct may have been vulnerable due to low diversity or small population size, their disappearance was driven by human activities in the Anthropocene.
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Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Marcelo Gehara
- Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Avenue, Newark, NJ 07102, USA
| | - Michael G Harvey
- Department of Biological Sciences, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
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12
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Curry CJ, Davis BW, Bertola LD, White PA, Murphy WJ, Derr JN. Spatiotemporal Genetic Diversity of Lions Reveals the Influence of Habitat Fragmentation across Africa. Mol Biol Evol 2021; 38:48-57. [PMID: 32667997 PMCID: PMC8480188 DOI: 10.1093/molbev/msaa174] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Direct comparisons between historical and contemporary populations allow for detecting changes in genetic diversity through time and assessment of the impact of habitat fragmentation. Here, we determined the genetic architecture of both historical and modern lions to document changes in genetic diversity over the last century. We surveyed microsatellite and mitochondrial genome variation from 143 high-quality museum specimens of known provenance, allowing us to directly compare this information with data from several recently published nuclear and mitochondrial studies. Our results provide evidence for male-mediated gene flow and recent isolation of local subpopulations, likely due to habitat fragmentation. Nuclear markers showed a significant decrease in genetic diversity from the historical (HE = 0.833) to the modern (HE = 0.796) populations, whereas mitochondrial genetic diversity was maintained (Hd = 0.98 for both). Although the historical population appears to have been panmictic based on nDNA data, hierarchical structure analysis identified four tiers of genetic structure in modern populations and was able to detect most sampling locations. Mitogenome analyses identified four clusters: Southern, Mixed, Eastern, and Western and were consistent between modern and historically sampled haplotypes. Within the last century, habitat fragmentation caused lion subpopulations to become more geographically isolated as human expansion changed the African landscape. This resulted in an increase in fine-scale nuclear genetic structure and loss of genetic diversity as lion subpopulations became more differentiated, whereas mitochondrial structure and diversity were maintained over time.
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Affiliation(s)
- Caitlin J Curry
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - Laura D Bertola
- Department of Biology, City College of New York, New York, NY
| | - Paula A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California Los Angeles, Los Angeles, CA
| | - William J Murphy
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
| | - James N Derr
- Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX
- Department of Veterinary Pathobiology, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX
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13
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de Manuel M, Barnett R, Sandoval-Velasco M, Yamaguchi N, Garrett Vieira F, Zepeda Mendoza ML, Liu S, Martin MD, Sinding MHS, Mak SST, Carøe C, Liu S, Guo C, Zheng J, Zazula G, Baryshnikov G, Eizirik E, Koepfli KP, Johnson WE, Antunes A, Sicheritz-Ponten T, Gopalakrishnan S, Larson G, Yang H, O'Brien SJ, Hansen AJ, Zhang G, Marques-Bonet T, Gilbert MTP. The evolutionary history of extinct and living lions. Proc Natl Acad Sci U S A 2020; 117:10927-10934. [PMID: 32366643 PMCID: PMC7245068 DOI: 10.1073/pnas.1919423117] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Lions are one of the world's most iconic megafauna, yet little is known about their temporal and spatial demographic history and population differentiation. We analyzed a genomic dataset of 20 specimens: two ca. 30,000-y-old cave lions (Panthera leo spelaea), 12 historic lions (Panthera leo leo/Panthera leo melanochaita) that lived between the 15th and 20th centuries outside the current geographic distribution of lions, and 6 present-day lions from Africa and India. We found that cave and modern lions shared an ancestor ca. 500,000 y ago and that the 2 lineages likely did not hybridize following their divergence. Within modern lions, we found 2 main lineages that diverged ca. 70,000 y ago, with clear evidence of subsequent gene flow. Our data also reveal a nearly complete absence of genetic diversity within Indian lions, probably due to well-documented extremely low effective population sizes in the recent past. Our results contribute toward the understanding of the evolutionary history of lions and complement conservation efforts to protect the diversity of this vulnerable species.
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Affiliation(s)
- Marc de Manuel
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - Ross Barnett
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia;
| | - Filipe Garrett Vieira
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - M Lisandra Zepeda Mendoza
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
- School of Medical and Dental Sciences, Institute of Microbiology and Infection, University of Birmingham, B15 2TT Edgbaston, Birmingham, United Kingdom
| | | | - Michael D Martin
- Norwegian University of Science and Technology (NTNU) University Museum, 7012 Trondheim, Norway
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Sarah S T Mak
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Shanlin Liu
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
- BGI-Shenzhen, 518083 Shenzhen, China
| | | | - Jiao Zheng
- BGI-Shenzhen, 518083 Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, 518083 Shenzhen, China
| | - Grant Zazula
- Yukon Palaeontology Program, Department of Tourism and Culture, Government of Yukon, Y1A 2C6 Whitehorse, Yukon, Canada
| | - Gennady Baryshnikov
- Zoological Institute, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Eduardo Eizirik
- Laboratory of Genomics and Molecular Biology, Escola de Ciências da Saúde e da Vida, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS 90619-900, Brazil
- Instituto Nacional de Ciência e Tecnologia - Ecologia Evolução e Conservação da Biodiversidade (INCT-EECBio), Goiânia, GO 74690-900, Brazil
- Instituto Pró-Carnívoros, Atibaia, SP 12945-010, Brazil
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
| | - Warren E Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630
- The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD 20746-2863
- Walter Reed Army Institute of Research, Silver Spring, MD 20910
| | - Agostinho Antunes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, 4450-208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Thomas Sicheritz-Ponten
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, Asian Institute of Medicine, Science and Technology (AIMST), 08100 Bedong, Kedah, Malaysia
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, OX1 3QY Oxford, United Kingdom
| | - Huanming Yang
- BGI-Shenzhen, 518083 Shenzhen, China
- James D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | - Stephen J O'Brien
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO (Information Technologies, Mechanics and Optics) University, 197101 St. Petersburg, Russia;
- Guy Harvey Oceanographic Center Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft. Lauderdale, FL 33004
| | - Anders J Hansen
- Section for GeoGenetics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1350 Copenhagen, Denmark
| | - Guojie Zhang
- BGI-Shenzhen, 518083 Shenzhen, China
- Section for Ecology and Evolution, Department of Biology, Faculty of Science, University of Copenhagen, 2100 Copenhagen, Denmark
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain;
- Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation (CNAG-CRG), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08003 Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark;
- Norwegian University of Science and Technology (NTNU) University Museum, 7012 Trondheim, Norway
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14
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Armstrong EE, Taylor RW, Miller DE, Kaelin CB, Barsh GS, Hadly EA, Petrov D. Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data. BMC Biol 2020; 18:3. [PMID: 31915011 PMCID: PMC6950864 DOI: 10.1186/s12915-019-0734-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The lion (Panthera leo) is one of the most popular and iconic feline species on the planet, yet in spite of its popularity, the last century has seen massive declines for lion populations worldwide. Genomic resources for endangered species represent an important way forward for the field of conservation, enabling high-resolution studies of demography, disease, and population dynamics. Here, we present a chromosome-level assembly from a captive African lion from the Exotic Feline Rescue Center (Center Point, IN) as a resource for current and subsequent genetic work of the sole social species of the Panthera clade. RESULTS Our assembly is composed of 10x Genomics Chromium data, Dovetail Hi-C, and Oxford Nanopore long-read data. Synteny is highly conserved between the lion, other Panthera genomes, and the domestic cat. We find variability in the length of runs of homozygosity across lion genomes, indicating contrasting histories of recent and possibly intense inbreeding and bottleneck events. Demographic analyses reveal similar ancient histories across all individuals during the Pleistocene except the Asiatic lion, which shows a more rapid decline in population size. We show a substantial influence on the reference genome choice in the inference of demographic history and heterozygosity. CONCLUSIONS We demonstrate that the choice of reference genome is important when comparing heterozygosity estimates across species and those inferred from different references should not be compared to each other. In addition, estimates of heterozygosity or the amount or length of runs of homozygosity should not be taken as reflective of a species, as these can differ substantially among individuals. This high-quality genome will greatly aid in the continuing research and conservation efforts for the lion, which is rapidly moving towards becoming a species in danger of extinction.
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Affiliation(s)
| | - Ryan W Taylor
- Department of Biology, Stanford University, Stanford, CA, USA
- End2EndGenomics, LLC, Davis, CA, USA
| | - Danny E Miller
- Department of Pediatrics, Seattle Children's Hospital and The University of Washington, Seattle, WA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | | | - Dmitri Petrov
- Department of Biology, Stanford University, Stanford, CA, USA
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15
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Jhala YV, Banerjee K, Chakrabarti S, Basu P, Singh K, Dave C, Gogoi K. Asiatic Lion: Ecology, Economics, and Politics of Conservation. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00312] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Large-scale mitogenomic analysis of the phylogeography of the Late Pleistocene cave bear. Sci Rep 2019; 9:10700. [PMID: 31417104 PMCID: PMC6695494 DOI: 10.1038/s41598-019-47073-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 07/10/2019] [Indexed: 12/04/2022] Open
Abstract
The cave bear (Ursus spelaeus) is one of the Late Pleistocene megafauna species that faced extinction at the end of the last ice age. Although it is represented by one of the largest fossil records in Europe and has been subject to several interdisciplinary studies including palaeogenetic research, its fate remains highly controversial. Here, we used a combination of hybridisation capture and next generation sequencing to reconstruct 59 new complete cave bear mitochondrial genomes (mtDNA) from 14 sites in Western, Central and Eastern Europe. In a Bayesian phylogenetic analysis, we compared them to 64 published cave bear mtDNA sequences to reconstruct the population dynamics and phylogeography during the Late Pleistocene. We found five major mitochondrial DNA lineages resulting in a noticeably more complex biogeography of the European lineages during the last 50,000 years than previously assumed. Furthermore, our calculated effective female population sizes suggest a drastic cave bear population decline starting around 40,000 years ago at the onset of the Aurignacian, coinciding with the spread of anatomically modern humans in Europe. Thus, our study supports a potential significant human role in the general extinction and local extirpation of the European cave bear and illuminates the fate of this megafauna species.
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17
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Crees JJ, Turvey ST, Freeman R, Carbone C. Mammalian tolerance to humans is predicted by body mass: evidence from long-term archives. Ecology 2019; 100:e02783. [PMID: 31177530 DOI: 10.1002/ecy.2783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 04/04/2019] [Accepted: 05/20/2019] [Indexed: 11/08/2022]
Abstract
Humans are implicated as a major driver of species extinctions from the Late Pleistocene to the present. However, our predictive understanding of human-caused extinction remains poor due to the restricted temporal and spatial scales at which this process is typically assessed, and the risks of bias due to "extinction filters" resulting from a poor understanding of past species declines. We develop a novel continent-wide data set containing country-level last-occurrence records for 31 European terrestrial mammals across the Holocene (c.11,500 yr BP to present), an epoch of relative climatic stability that captures major transitions in human demography. We analyze regional extirpations against a high-resolution database of human population density (HPD) estimates to identify species-specific tolerances to changing HPD through the Holocene. Mammalian thresholds to HPD scale strongly with body mass, with larger-bodied mammals experiencing regional population losses at lower HPDs than smaller-bodied mammals. Our analysis enables us to identify levels of tolerance to HPD for different species, and therefore has wide applicability for determining biotic vulnerability to human impacts. This ecological pattern is confirmed across wide spatiotemporal scales, providing insights into the dynamics of prehistoric extinctions and the modern biodiversity crisis, and emphasizing the role of long-term archives in understanding human-caused biodiversity loss.
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Affiliation(s)
- Jennifer J Crees
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom.,Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Robin Freeman
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Chris Carbone
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
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18
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Smitz N, Jouvenet O, Ambwene Ligate F, Crosmary WG, Ikanda D, Chardonnet P, Fusari A, Meganck K, Gillet F, Melletti M, Michaux JR. A genome-wide data assessment of the African lion (Panthera leo) population genetic structure and diversity in Tanzania. PLoS One 2018; 13:e0205395. [PMID: 30403704 PMCID: PMC6221261 DOI: 10.1371/journal.pone.0205395] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 09/25/2018] [Indexed: 11/29/2022] Open
Abstract
The African lion (Panthera leo), listed as a vulnerable species on the IUCN Red List of Threatened Species (Appendix II of CITES), is mainly impacted by indiscriminate killing and prey base depletion. Additionally, habitat loss by land degradation and conversion has led to the isolation of some subpopulations, potentially decreasing gene flow and increasing inbreeding depression risks. Genetic drift resulting from weakened connectivity between strongholds can affect the genetic health of the species. In the present study, we investigated the evolutionary history of the species at different spatiotemporal scales. Therefore, the mitochondrial cytochrome b gene (N = 128), 11 microsatellites (N = 103) and 9,103 SNPs (N = 66) were investigated in the present study, including a large sampling from Tanzania, which hosts the largest lion population among all African lion range countries. Our results add support that the species is structured into two lineages at the continental scale (West-Central vs East-Southern), underlining the importance of reviewing the taxonomic status of the African lion. Moreover, SNPs led to the identification of three lion clusters in Tanzania, whose geographical distributions are in the northern, southern and western regions. Furthermore, Tanzanian lion populations were shown to display good levels of genetic diversity with limited signs of inbreeding. However, their population sizes seem to have gradually decreased in recent decades. The highlighted Tanzanian African lion population genetic differentiation appears to have resulted from the combined effects of anthropogenic pressure and environmental/climatic factors, as further discussed.
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Affiliation(s)
- Nathalie Smitz
- Barcoding of Organisms and tissues of Policy Concern (BopCo)/Joint Experimental Molecular Unit (JEMU), Royal Museum for Central Africa, Tervuren, Belgium
- Conservation Genetics, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Olivia Jouvenet
- Conservation Genetics, Department of Life Sciences, University of Liège, Liège, Belgium
| | | | | | - Dennis Ikanda
- Tanzania Wildlife Research Institute, Arusha, Tanzania
| | | | - Alessandro Fusari
- Fondation Internationale pour la Gestion de la Faune (IGF), Paris, France
| | - Kenny Meganck
- Barcoding of Organisms and tissues of Policy Concern (BopCo), Royal Museum for Central Africa, Tervuren, Belgium
| | - François Gillet
- Conservation Genetics, Department of Life Sciences, University of Liège, Liège, Belgium
| | - Mario Melletti
- African Buffalo Initiative Group (AfBIG), IUCN/SSC/ASG, Rome, Italy
| | - Johan R. Michaux
- Conservation Genetics, Department of Life Sciences, University of Liège, Liège, Belgium
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UPR AGIRS, Campus International de Baillarguet, Montpellier, France
- * E-mail:
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19
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Barnett R, Sinding MHS, Vieira FG, Mendoza MLZ, Bonnet M, Araldi A, Kienast I, Zambarda A, Yamaguchi N, Henschel P, Gilbert MTP. No longer locally extinct? Tracing the origins of a lion ( Panthera leo) living in Gabon. CONSERV GENET 2018; 19:611-618. [PMID: 31007636 PMCID: PMC6448349 DOI: 10.1007/s10592-017-1039-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/16/2017] [Indexed: 12/22/2022]
Abstract
Lions (Panthera leo) are of particular conservation concern due to evidence of recent, widespread population declines in what has hitherto been seen as a common species, robust to anthropogenic disturbance. Here we use non-invasive methods to recover complete mitochondrial genomes from single hair samples collected in the field in order to explore the identity of the Gabonese Plateaux Batéké lion. Comparison of the mitogenomes against a comprehensive dataset of African lion sequences that includes relevant geographically proximate lion populations from both contemporary and ancient sources, enabled us to identify the Plateaux Batéké lion as a close maternal relative to now extirpated populations found in Gabon and nearby Congo during the twentieth century, and to extant populations of Southern Africa. Our study demonstrates the relevance of ancient DNA methods to field conservation work, and the ability of trace field samples to provide copious genetic information about free-ranging animals.
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Affiliation(s)
- Ross Barnett
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Mikkel-Holder S. Sinding
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- Natural History Museum, University of Oslo, Blindern, P.O. Box 1172, 0318 Oslo, Norway
| | - Filipe G. Vieira
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | | | - Matthieu Bonnet
- The Aspinall Foundation, Port Lympne Wild Animal Park, Hythe, Kent CT21 4PD UK
| | - Alessandro Araldi
- The Aspinall Foundation, Port Lympne Wild Animal Park, Hythe, Kent CT21 4PD UK
| | - Ivonne Kienast
- Congo Program, Wildlife Conservation Society, Brazzaville, Congo
| | - Alice Zambarda
- The Aspinall Foundation, Port Lympne Wild Animal Park, Hythe, Kent CT21 4PD UK
| | - Nobuyuki Yamaguchi
- Department of Biological and Environmental Sciences, Qatar University, Doha, Qatar
| | - Philipp Henschel
- Panthera, 8 West 40th Street, 18th Floor, New York, NY 10018 USA
- Institut de Recherche en Ecologie Tropicale, CENAREST, BP 842 Libreville, Gabon
| | - M. Thomas P. Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
- NTNU University Museum, 7491 Trondheim, Norway
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20
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Atkinson KE, Kitchener AC, Tobe SS, O’Donoghue P. An assessment of the genetic diversity of the founders of the European captive population of Asian lion (Panthera leo leo), using microsatellite markers and studbook analysis. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2017.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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Anco C, Kolokotronis SO, Henschel P, Cunningham SW, Amato G, Hekkala E. Historical mitochondrial diversity in African leopards (Panthera pardus) revealed by archival museum specimens. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:455-473. [PMID: 28423965 DOI: 10.1080/24701394.2017.1307973] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Once found throughout Africa and Eurasia, the leopard (Panthera pardus) was recently uplisted from Near Threatened to Vulnerable by the International Union for the Conservation of Nature (IUCN). Historically, more than 50% of the leopard's global range occurred in continental Africa, yet sampling from this part of the species' distribution is only sparsely represented in prior studies examining patterns of genetic variation at the continental or global level. Broad sampling to determine baseline patterns of genetic variation throughout the leopard's historical distribution is important, as these measures are currently used by the IUCN to direct conservation priorities and management plans. By including data from 182 historical museum specimens, faecal samples from ongoing field surveys, and published sequences representing sub-Saharan Africa, we identify previously unrecognized genetic diversity in African leopards. Our mtDNA data indicates high levels of divergence among regional populations and strongly differentiated lineages in West Africa on par with recent studies of other large vertebrates. We provide a reference benchmark of genetic diversity in African leopards against which future monitoring can be compared. These findings emphasize the utility of historical museum collections in understanding the processes that shape present biodiversity. Additionally, we suggest future research to clarify African leopard taxonomy and to differentiate between delineated units requiring monitoring or conservation action.
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Affiliation(s)
- Corey Anco
- a Department of Biological Sciences , Fordham University , Bronx , USA.,b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
| | - Sergios-Orestis Kolokotronis
- b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA.,c Department of Epidemiology and Biostatistics, School of Public Health , SUNY Downstate Medical Center , Brooklyn , USA
| | | | - Seth W Cunningham
- a Department of Biological Sciences , Fordham University , Bronx , USA
| | - George Amato
- b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
| | - Evon Hekkala
- a Department of Biological Sciences , Fordham University , Bronx , USA.,b Sackler Institute for Comparative Genomics, American Museum of Natural History , New York , USA
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22
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Huntley JW, Voelker G. A tale of the nearly tail-less: the effects of Plio-Pleistocene climate change on the diversification of the African avian genusSylvietta. ZOOL SCR 2017. [DOI: 10.1111/zsc.12240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jerry W. Huntley
- Department of Wildlife and Fisheries Sciences; Texas A&M University; 210 Nagle Hall College Station TX 77843 USA
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences; Texas A&M University; 210 Nagle Hall College Station TX 77843 USA
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23
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The Challenges and Relevance of Exploring the Genetics of North Africa's "Barbary Lion" and the Conservation of Putative Descendants in Captivity. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2016; 2016:6901892. [PMID: 27656310 PMCID: PMC5021484 DOI: 10.1155/2016/6901892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/05/2016] [Accepted: 07/17/2016] [Indexed: 12/03/2022]
Abstract
The lions of North Africa were unique in ecological terms as well as from a human cultural perspective and were the definitive lions of Roman and Medieval Europe. Labelled “Barbary” lions, they were once numerous in North Africa but were exterminated by the mid-20th century. Despite subsequent degeneration of the Atlas Mountain ecosystem through human pressures, the feasibility of lion reintroduction has been debated since the 1970s. Research on the long-established captive lion collection traditionally kept by the sultans and kings of Morocco has enabled selective breeding coordinated across Moroccan and European zoos involving a significant number of animals. Molecular genetic research has recently provided insights into lion phylogeny which, despite previous suggestions that all lions share recent common ancestry, now indicates clear distinctions between lions in North, West, and Central Africa, the Middle East, and India versus those in Southern and Eastern Africa. A review of the evolutionary relevance of North African lions highlights the important challenges and opportunities in understanding relationships between Moroccan lions, extinct North African lions, and extant lion populations in India and West and Central Africa and the potential role for lions in ecosystem recovery in those regions.
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24
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Bertola LD, Jongbloed H, van der Gaag KJ, de Knijff P, Yamaguchi N, Hooghiemstra H, Bauer H, Henschel P, White PA, Driscoll CA, Tende T, Ottosson U, Saidu Y, Vrieling K, de Iongh HH. Phylogeographic Patterns in Africa and High Resolution Delineation of Genetic Clades in the Lion (Panthera leo). Sci Rep 2016; 6:30807. [PMID: 27488946 PMCID: PMC4973251 DOI: 10.1038/srep30807] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 07/08/2016] [Indexed: 11/10/2022] Open
Abstract
Comparative phylogeography of African savannah mammals shows a congruent pattern in which populations in West/Central Africa are distinct from populations in East/Southern Africa. However, for the lion, all African populations are currently classified as a single subspecies (Panthera leo leo), while the only remaining population in Asia is considered to be distinct (Panthera leo persica). This distinction is disputed both by morphological and genetic data. In this study we introduce the lion as a model for African phylogeography. Analyses of mtDNA sequences reveal six supported clades and a strongly supported ancestral dichotomy with northern populations (West Africa, Central Africa, North Africa/Asia) on one branch, and southern populations (North East Africa, East/Southern Africa and South West Africa) on the other. We review taxonomies and phylogenies of other large savannah mammals, illustrating that similar clades are found in other species. The described phylogeographic pattern is considered in relation to large scale environmental changes in Africa over the past 300,000 years, attributable to climate. Refugial areas, predicted by climate envelope models, further confirm the observed pattern. We support the revision of current lion taxonomy, as recognition of a northern and a southern subspecies is more parsimonious with the evolutionary history of the lion.
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Affiliation(s)
- L D Bertola
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - H Jongbloed
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - K J van der Gaag
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - P de Knijff
- Forensic Laboratory for DNA Research, Department of Human Genetics, Leiden University Medical Centre, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - N Yamaguchi
- Qatar University, Department of Biological and Environmental Sciences, College of Arts and Sciences, PO Box 2713, Doha, Qatar
| | - H Hooghiemstra
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1018 XH Amsterdam, The Netherlands
| | - H Bauer
- WildCRU, Recanati-Kaplan Centre, University of Oxford. Tubney House, Abingdon Road, OX13 5QL, UK
| | - P Henschel
- Panthera, 8 West 40th Street, 18th Floor, New York, NY 10018, USA
| | - P A White
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095-1496, USA
| | - C A Driscoll
- Wildlife Institute of India, Dehradun 248001, Uttarakhand, India
| | - T Tende
- A. P. Leventis Ornithological Research Institute, P.O. Box 13404 Jos, Nigeria
| | - U Ottosson
- A. P. Leventis Ornithological Research Institute, P.O. Box 13404 Jos, Nigeria
| | - Y Saidu
- Nigeria National Park Service, PMB 0258 Garki-Abuja, Nigeria
| | - K Vrieling
- Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300 RA Leiden, The Netherlands
| | - H H de Iongh
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300 RA Leiden, The Netherlands.,University of Antwerp, Department Biology, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
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25
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Brito JC, Tarroso P, Vale CG, Martínez-Freiría F, Boratyński Z, Campos JC, Ferreira S, Godinho R, Gonçalves DV, Leite JV, Lima VO, Pereira P, Santos X, da Silva MJF, Silva TL, Velo-Antón G, Veríssimo J, Crochet PA, Pleguezuelos JM, Carvalho SB. Conservation Biogeography of the Sahara-Sahel: additional protected areas are needed to secure unique biodiversity. DIVERS DISTRIB 2016. [DOI: 10.1111/ddi.12416] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- José C. Brito
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua Campo Alegre 4169-007 Porto Portugal
| | - Pedro Tarroso
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Cândida G. Vale
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua Campo Alegre 4169-007 Porto Portugal
| | - Fernando Martínez-Freiría
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Zbyszek Boratyński
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - João C. Campos
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua Campo Alegre 4169-007 Porto Portugal
| | - Sónia Ferreira
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua Campo Alegre 4169-007 Porto Portugal
| | - Raquel Godinho
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua Campo Alegre 4169-007 Porto Portugal
| | - Duarte V. Gonçalves
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua Campo Alegre 4169-007 Porto Portugal
| | - João V. Leite
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Vanessa O. Lima
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Paulo Pereira
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Xavier Santos
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Maria J. Ferreira da Silva
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
- ONE (Organisms and Environment); School of Biosciences; Cardiff University; The Sir Martin Evans Building Museum Avenue Cardiff CF10 3AX UK
- CAPP; School of Social and Political Sciences; Technical University of Lisbon; Rua Almerindo Lessa 1300-663 Lisboa Portugal
| | - Teresa L. Silva
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Universidade do Porto; Rua Campo Alegre 4169-007 Porto Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Joana Veríssimo
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
| | - Pierre-André Crochet
- CNRS-UMR 5175; Centre d'Ecologie Fonctionnelle et Evolutive; 1919 route de Mende F-34293 Montpellier-Cedex 5 France
| | - Juan M. Pleguezuelos
- Departamento de Zoología; Facultad de Ciencias; Universidad de Granada; E-18071 Granada Spain
| | - Sílvia B. Carvalho
- CIBIO/InBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; R. Padre Armando Quintas 4485-661 Vairão Portugal
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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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Bertola LD, Tensen L, van Hooft P, White PA, Driscoll CA, Henschel P, Caragiulo A, Dias-Freedman I, Sogbohossou EA, Tumenta PN, Jirmo TH, de Snoo GR, de Iongh HH, Vrieling K. Autosomal and mtDNA Markers Affirm the Distinctiveness of Lions in West and Central Africa. PLoS One 2015; 10:e0137975. [PMID: 26466139 PMCID: PMC4605676 DOI: 10.1371/journal.pone.0137975] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/25/2015] [Indexed: 12/02/2022] Open
Abstract
The evolutionary history of a species is key for understanding the taxonomy and for the design of effective management strategies for species conservation. The knowledge about the phylogenetic position of the lion (Panthera leo) in West/Central Africa is largely based on mitochondrial markers. Previous studies using mtDNA only have shown this region to hold a distinct evolutionary lineage. In addition, anthropogenic factors have led to a strong decline in West/Central African lion numbers, thus, the conservation value of these populations is particularly high. Here, we investigate whether autosomal markers are concordant with previously described phylogeographic patterns, and confirm the unique position of the West/Central African lion. Analysis of 20 microsatellites and 1,454 bp of the mitochondrial DNA in 16 lion populations representing the entire geographic range of the species found congruence in both types of markers, identifying four clusters: 1) West/Central Africa, 2) East Africa, 3) Southern Africa and 4) India. This is not in line with the current taxonomy, as defined by the IUCN, which only recognizes an African and an Asiatic subspecies. There are no indications that genetic diversity in West/Central Africa lions is lower than in either East or Southern Africa, however, given this genetic distinction and the recent declines of lion numbers in this region, we strongly recommend prioritization of conservation projects in West/Central Africa. As the current taxonomic nomenclature does not reflect the evolutionary history of the lion, we suggest that a taxonomic revision of the lion is warranted.
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Affiliation(s)
- Laura D. Bertola
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300, RA Leiden, The Netherlands
- Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300, RA Leiden, The Netherlands
| | - Laura Tensen
- University of Johannesburg, Department of Zoology, PO Box 524, Johannesburg, Johannesburg, Republic of South Africa
| | - Pim van Hooft
- Wageningen University, Resource Ecology Group, Droevendaalsesteeg 3a, 6708, PB Wageningen, The Netherlands
| | - Paula A. White
- Center for Tropical Research, Institute of the Environment and Sustainability, La Kretz Hall Suite 300, 619 Charles E. Young Dr. East, University of California Los Angeles, Los Angeles, CA, 90095–1496, United States of America
| | | | - Philipp Henschel
- Panthera, 8 West 40th Street, 18th Floor, New York, NY, 10018, United States of America
| | - Anthony Caragiulo
- Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street at Central Park West, New York, NY, 10024, United States of America
| | - Isabela Dias-Freedman
- Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street at Central Park West, New York, NY, 10024, United States of America
| | - Etotépé A. Sogbohossou
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300, RA Leiden, The Netherlands
- Laboratoire d’Ecologie Appliquée, Université d’Abomey-Calavi, Champ de Foire 03 BP 1974, Cotonou, Benin
| | - Pricelia N. Tumenta
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300, RA Leiden, The Netherlands
- Centre for Environment and Development Studies in Cameroon, University of Dschang, BP 410, Maroua, Cameroon
| | - Tuqa H. Jirmo
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300, RA Leiden, The Netherlands
| | - Geert R. de Snoo
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300, RA Leiden, The Netherlands
| | - Hans H. de Iongh
- Leiden University, Institute of Environmental Sciences (CML), PO Box 9518, 2300, RA Leiden, The Netherlands
- University of Antwerp, Department Biology, Evolutionary Ecology Group, Groenenborgerlaan 171, 2020, Antwerpen, Belgium
| | - Klaas Vrieling
- Leiden University, Institute of Biology Leiden (IBL), PO Box 9505, 2300, RA Leiden, The Netherlands
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Stoffel C, Dufresnes C, Okello JBA, Noirard C, Joly P, Nyakaana S, Muwanika VB, Alcala N, Vuilleumier S, Siegismund HR, Fumagalli L. Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene. Mol Ecol 2015; 24:2507-20. [PMID: 25827243 DOI: 10.1111/mec.13179] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/11/2015] [Accepted: 03/18/2015] [Indexed: 11/30/2022]
Abstract
Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial-drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence variation and range-wide sampling. We documented a global demographic and spatial expansion approximately 0.1-0.3 Myr ago, most likely associated with an episode of massive drainage overflow. These events presumably enabled a historical continent-wide gene flow among hippopotamus populations, and hence, no clear continental-scale genetic structuring remains. Nevertheless, present-day hippopotamus populations are genetically disconnected, probably as a result of the mid-Holocene aridification and contemporary anthropogenic pressures. This unique pattern contrasts with the biogeographic paradigms established for savannah-adapted ungulate mammals and should be further investigated in other water-associated taxa. Our study has important consequences for the conservation of the hippo, an emblematic but threatened species that requires specific protection to curtail its long-term decline.
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Affiliation(s)
- Céline Stoffel
- Department of Ecology and Evolution, Laboratory for Conservation Biology, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland
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Alcala N, Vuilleumier S. Turnover and accumulation of genetic diversity across large time-scale cycles of isolation and connection of populations. Proc Biol Sci 2014; 281:20141369. [PMID: 25253456 PMCID: PMC4211446 DOI: 10.1098/rspb.2014.1369] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 08/27/2014] [Indexed: 01/25/2023] Open
Abstract
Major climatic and geological events but also population history (secondary contacts) have generated cycles of population isolation and connection of long and short periods. Recent empirical and theoretical studies suggest that fast evolutionary processes might be triggered by such events, as commonly illustrated in ecology by the adaptive radiation of cichlid fishes (isolation and reconnection of lakes and watersheds) and in epidemiology by the fast adaptation of the influenza virus (isolation and reconnection in hosts). We test whether cyclic population isolation and connection provide the raw material (standing genetic variation) for species evolution and diversification. Our analytical results demonstrate that population isolation and connection can provide, to populations, a high excess of genetic diversity compared with what is expected at equilibrium. This excess is either cyclic (high allele turnover) or cumulates with time depending on the duration of the isolation and the connection periods and the mutation rate. We show that diversification rates of animal clades are associated with specific periods of climatic cycles in the Quaternary. We finally discuss the importance of our results for macroevolutionary patterns and for the inference of population history from genomic data.
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Affiliation(s)
- Nicolas Alcala
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland
| | - Séverine Vuilleumier
- Department of Ecology and Evolution, University of Lausanne, Biophore, 1015 Lausanne, Switzerland Institute of Microbiology, Lausanne University Hospital and University of Lausanne, CH-1011 Lausanne, Switzerland
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Henschel P, Malanda GA, Hunter L. The status of savanna carnivores in the Odzala-Kokoua National Park, northern Republic of Congo. J Mammal 2014. [DOI: 10.1644/13-mamm-a-306] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Tende T, Bensch S, Ottosson U, Hansson B. Dual phylogenetic origins of Nigerian lions (Panthera leo). Ecol Evol 2014; 4:2668-74. [PMID: 25077018 PMCID: PMC4113291 DOI: 10.1002/ece3.1116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 04/16/2014] [Accepted: 04/23/2014] [Indexed: 11/30/2022] Open
Abstract
Lion fecal DNA extracts from four individuals each from Yankari Game Reserve and Kainji-Lake National Park (central northeast and west Nigeria, respectively) were Sanger-sequenced for the mitochondrial cytochrome b gene. The sequences were aligned against 61 lion reference sequences from other parts of Africa and India. The sequence data were analyzed further for the construction of phylogenetic trees using the maximum-likelihood approach to depict phylogenetic patterns of distribution among sequences. Our results show that Nigerian lions grouped together with lions from West and Central Africa. At the smaller geographical scale, lions from Kainji-Lake National Park in western Nigeria grouped with lions from Benin (located west of Nigeria), whereas lions from Yankari Game Reserve in central northeastern Nigeria grouped with the lion populations in Cameroon (located east of Nigeria). The finding that the two remaining lion populations in Nigeria have different phylogenetic origins is an important aspect to consider in future decisions regarding management and conservation of rapidly shrinking lion populations in West Africa.
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Affiliation(s)
- Talatu Tende
- A. P. Leventis Ornithological Research Institute P.O. Box 13404, Jos, Nigeria ; Department of Biology, Lund University Ecology Building, Lund, SE-223 62, Sweden
| | - Staffan Bensch
- Department of Biology, Lund University Ecology Building, Lund, SE-223 62, Sweden
| | - Ulf Ottosson
- A. P. Leventis Ornithological Research Institute P.O. Box 13404, Jos, Nigeria
| | - Bengt Hansson
- Department of Biology, Lund University Ecology Building, Lund, SE-223 62, Sweden
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32
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The potential distribution of the Vulnerable African lion Panthera leo in the face of changing global climate. ORYX 2014. [DOI: 10.1017/s0030605312000919] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractThe objective of this study is to estimate possible impacts of global climate change on the geographical distribution of the African lion Panthera leo in the coming decades. Current lion population occurrence data across Africa and distributions of lions in historical times (6,000–100 years before present) were obtained from the literature and integrated with data on present-day climates to generate ecological niche models. Models based on distributions of African lions were tested for predictive ability based on various subsetting approaches and were projected across Asia, Africa and Europe, to retrodict the distribution of the species for the past 6,000 years. These models were highly accurate, giving confidence in future projections. Future potential distributions were predicted by projecting ecological niche models onto three climate scenarios of future greenhouse gas emissions based on eight climate models for the years 2040–2070. The prediction was of relative range stability into the future: few new areas were identified as becoming suitable for the species but large areas of southern Africa and West Africa are expected to become less suitable. Predictions of effects of climate change on potential distributions of lions may assist conservation efforts by clarifying options for mitigation and response.
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Dupas S, le Ru B, Branca A, Faure N, Gigot G, Campagne P, Sezonlin M, Ndemah R, Ong'amo G, Calatayud PA, Silvain JF. Phylogeography in continuous space: coupling species distribution models and circuit theory to assess the effect of contiguous migration at different climatic periods on genetic differentiation inBusseola fusca(Lepidoptera: Noctuidae). Mol Ecol 2014; 23:2313-25. [DOI: 10.1111/mec.12730] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 03/05/2014] [Accepted: 03/13/2014] [Indexed: 11/27/2022]
Affiliation(s)
- S. Dupas
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
- Université Paris-Sud 11; 91405 Orsay France
| | - B. le Ru
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
- Université Paris-Sud 11; 91405 Orsay France
- Icipe - African Insect Science for Food and Health; PO Box 30772-00100 Nairobi Kenya
| | - A. Branca
- Ecologie, Systématique et Evolution, Bâtiment 360; Université Paris-Sud; F-91405 Orsay France
| | - N. Faure
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
| | - G. Gigot
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
| | - P. Campagne
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
| | - M. Sezonlin
- Département de Zoologie et de Génétique; Faculté des Sciences et Techniques; Université d'Abomey - Calavi; 01 BP 526 Cotonou Bénin
| | - R. Ndemah
- International Institute of Tropical Agriculture; PO Box 2008 Messa Yaoundé Cameroon
| | - G. Ong'amo
- Icipe - African Insect Science for Food and Health; PO Box 30772-00100 Nairobi Kenya
- School of Biological Sciences; University of Nairobi; PO Box 30197 Nairobi Kenya
| | - P.-A. Calatayud
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
- Université Paris-Sud 11; 91405 Orsay France
- Icipe - African Insect Science for Food and Health; PO Box 30772-00100 Nairobi Kenya
| | - J.-F. Silvain
- Laboratoire Evolution, Génomes et Spéciation; UPR 9034; Centre National de la Recherche Scientifique; Institut de Recherche pour le Développement; UR 072; 91198 Gif sur Yvette France
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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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35
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Henschel P, Coad L, Burton C, Chataigner B, Dunn A, MacDonald D, Saidu Y, Hunter LTB. The lion in West Africa is critically endangered. PLoS One 2014; 9:e83500. [PMID: 24421889 PMCID: PMC3885426 DOI: 10.1371/journal.pone.0083500] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/04/2013] [Indexed: 11/19/2022] Open
Abstract
The African lion has declined to <35,000 individuals occupying 25% of its historic range. The situation is most critical for the geographically isolated populations in West Africa, where the species is considered regionally endangered. Elevating their conservation significance, recent molecular studies establish the genetic distinctiveness of West and Central African lions from other extant African populations. Interventions to save West African lions are urgently required. However formulating effective conservation strategies has been hampered by a lack of data on the species' current distribution, status, and potential management deficiencies of protected areas (PAs) harboring lions. Our study synthesized available expert opinion and field data to close this knowledge gap, and formulate recommendations for the conservation of West African lions. We undertook lion surveys in 13 large (>500 km²) PAs and compiled evidence of lion presence/absence for a further eight PAs. All PAs were situated within Lion Conservation Units, geographical units designated as priority lion areas by wildlife experts at a regional lion conservation workshop in 2005. Lions were confirmed in only 4 PAs, and our results suggest that only 406 (273-605) lions remain in West Africa, representing <250 mature individuals. Confirmed lion range is estimated at 49,000 km², or 1.1% of historical range in West Africa. PAs retaining lions were larger than PAs without lions and had significantly higher management budgets. We encourage revision of lion taxonomy, to recognize the genetic distinctiveness of West African lions and highlight their potentially unique conservation value. Further, we call for listing of the lion as critically endangered in West Africa, under criterion C2a(ii) for populations with <250 mature individuals. Finally, considering the relative poverty of lion range states in West Africa, we call for urgent mobilization of investment from the international community to assist range states to increase management effectiveness of PAs retaining lions.
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Affiliation(s)
| | - Lauren Coad
- Environmental Change Institute, University of Oxford, Oxford, United Kingdom
- School of Geography and Environmental Planning, University of Queensland, Brisbane, Australia
| | - Cole Burton
- Alberta Biodiversity Monitoring Institute, University of Alberta, Edmonton, Canada
- Biology Department, University of Victoria, Victoria, British Columbia, Canada
| | | | - Andrew Dunn
- Wildlife Conservation Society, Nigeria Program, Calabar, Nigeria
| | - David MacDonald
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford, The Recanati-Kaplan Centre, Oxford, United Kingdom
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Sheng GL, Soubrier J, Liu JY, Werdelin L, Llamas B, Thomson VA, Tuke J, Wu LJ, Hou XD, Chen QJ, Lai XL, Cooper A. Pleistocene Chinese cave hyenas and the recent Eurasian history of the spotted hyena, Crocuta crocuta. Mol Ecol 2013; 23:522-33. [PMID: 24320717 DOI: 10.1111/mec.12576] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 10/21/2013] [Accepted: 10/22/2013] [Indexed: 11/30/2022]
Abstract
The living hyena species (spotted, brown, striped and aardwolf) are remnants of a formerly diverse group of more than 80 fossil species, which peaked in diversity in the Late Miocene (about 7-8 Ma). The fossil history indicates an African origin, and morphological and ancient DNA data have confirmed that living spotted hyenas (Crocuta crocuta) of Africa were closely related to extinct Late Pleistocene cave hyenas from Europe and Asia. The current model used to explain the origins of Eurasian cave hyena populations invokes multiple migrations out of Africa between 3.5-0.35 Ma. We used mitochondrial DNA sequences from radiocarbon-dated Chinese Pleistocene hyena specimens to examine the origin of Asian populations, and temporally calibrate the evolutionary history of spotted hyenas. Our results support a far more recent evolutionary timescale (430-163 kya) and suggest that extinct and living spotted hyena populations originated from a widespread Eurasian population in the Late Pleistocene, which was only subsequently restricted to Africa. We developed statistical tests of the contrasting population models and their fit to the fossil record. Coalescent simulations and Bayes Factor analysis support the new radiocarbon-calibrated timescale and Eurasian origins model. The new Eurasian biogeographic scenario proposed for the hyena emphasizes the role of the vast steppe grasslands of Eurasia in contrast to models only involving Africa. The new methodology for combining genetic and geological data to test contrasting models of population history will be useful for a wide range of taxa where ancient and historic genetic data are available.
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Affiliation(s)
- Gui-Lian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, 430074, China; Australian Centre for Ancient DNA, School of Earth & Environmental Sciences, University of Adelaide, Adelaide, SA, 5000, Australia
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Dobigny G, Tatard C, Gauthier P, Ba K, Duplantier JM, Granjon L, Kergoat GJ. Mitochondrial and nuclear genes-based phylogeography of Arvicanthis niloticus (Murinae) and sub-Saharan open habitats pleistocene history. PLoS One 2013; 8:e77815. [PMID: 24223730 PMCID: PMC3815218 DOI: 10.1371/journal.pone.0077815] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 09/05/2013] [Indexed: 11/19/2022] Open
Abstract
A phylogeographic study was conducted on the Nile grass rat, Arvicanthis niloticus, a rodent species that is tightly associated with open grasslands from the Sudano-Sahelian regions. Using one mitochondrial (cytochrome b) and one nuclear (intron 7 of Beta Fibrinogen) gene, robust patterns were retrieved that clearly show that (i) the species originated in East Africa concomitantly with expanding grasslands some 2 Ma, and (ii) four parapatric and genetically well-defined lineages differentiated essentially from East to West following Pleistocene bioclimatic cycles. This strongly points towards allopatric genetic divergence within savannah refuges during humid episodes, then dispersal during arid ones; secondary contact zones would have then stabilized around geographic barriers, namely, Niger River and Lake Chad basins. Our results pertinently add to those obtained for several other African rodent as well as non-rodent species that inhabit forests, humid zones, savannahs and deserts, all studies that now allow one to depict a more comprehensive picture of the Pleistocene history of the continent south of the Sahara. In particular, although their precise location remains to be determined, at least three Pleistocene refuges are identified within the West and Central African savannah biome.
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Affiliation(s)
- Gauthier Dobigny
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
- Centre Régional Agrhymet, Rive Droite, Niamey, Niger
| | - Caroline Tatard
- Inra, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
| | - Philippe Gauthier
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
| | - Khalilou Ba
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Dakar, Senegal
| | - Jean-Marc Duplantier
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
| | - Laurent Granjon
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
- IRD, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Dakar, Senegal
| | - Gael J. Kergoat
- Inra, CBGP (IRD, Inra, CIRAD, Montpellier SupAgro), Campus de Baillarguet, Montferrier-sur-Lez, France
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38
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Thomassen HA, Freedman AH, Brown DM, Buermann W, Jacobs DK. Regional differences in seasonal timing of rainfall discriminate between genetically distinct East African giraffe taxa. PLoS One 2013; 8:e77191. [PMID: 24194870 PMCID: PMC3806738 DOI: 10.1371/journal.pone.0077191] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 09/08/2013] [Indexed: 11/18/2022] Open
Abstract
Masai (Giraffa tippelskirchi), Reticulated (G. reticulata) and Rothschild's (G. camelopardalis) giraffe lineages in East Africa are morphologically and genetically distinct, yet in Kenya their ranges abut. This raises the question of how divergence is maintained among populations of a large mammal capable of long-distance travel, and which readily hybridize in zoos. Here we test four hypotheses concerning the maintenance of the phylogeographic boundaries among the three taxa: 1) isolation-by-distance; 2) physical barriers to dispersal; 3) general habitat differences resulting in habitat segregation; or 4) regional differences in the seasonal timing of rainfall, and resultant timing of browse availability. We used satellite remotely sensed and climate data to characterize the environment at the locations of genotyped giraffes. Canonical variate analysis, random forest algorithms, and generalized dissimilarity modelling were employed in a landscape genetics framework to identify the predictor variables that best explained giraffes' genetic divergence. We found that regional differences in the timing of precipitation, and resulting green-up associated with the abundance of browse, effectively discriminate between taxa. Local habitat conditions, topographic and human-induced barriers, and geographic distance did not aid in discriminating among lineages. Our results suggest that selection associated with regional timing of events in the annual climatic cycle may help maintain genetic and phenotypic divergence in giraffes. We discuss potential mechanisms of maintaining divergence, and suggest that synchronization of reproduction with seasonal rainfall cycles that are geographically distinct may contribute to reproductive isolation. Coordination of weaning with green-up cycles could minimize the costs of lactation and predation on the young. Our findings are consistent with theory and empirical results demonstrating the efficacy of seasonal or phenologically dictated selection pressures in contributing to the reproductive isolation of parapatric populations.
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Affiliation(s)
- Henri A. Thomassen
- Center for Tropical Research, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| | - Adam H. Freedman
- Center for Tropical Research, University of California Los Angeles, Los Angeles, California, United States of America
| | - David M. Brown
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Wolfgang Buermann
- Center for Tropical Research, University of California Los Angeles, Los Angeles, California, United States of America
- Department of Atmospheric and Oceanic Sciences, University of California Los Angeles, Los Angeles, California, United States of America
| | - David K. Jacobs
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California, United States of America
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Miller S, Bissett C, Burger A, Courtenay B, Dickerson T, Druce D, Ferreira S, Funston P, Hofmeyr D, Kilian P, Matthews W, Naylor S, Parker D, Slotow R, Toft M, Zimmermann D. Management of Reintroduced Lions in Small, Fenced Reserves in South Africa: An Assessment and Guidelines. ACTA ACUST UNITED AC 2013. [DOI: 10.3957/056.043.0202] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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40
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Brito JC, Godinho R, Martínez-Freiría F, Pleguezuelos JM, Rebelo H, Santos X, Vale CG, Velo-Antón G, Boratyński Z, Carvalho SB, Ferreira S, Gonçalves DV, Silva TL, Tarroso P, Campos JC, Leite JV, Nogueira J, Álvares F, Sillero N, Sow AS, Fahd S, Crochet PA, Carranza S. Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel. Biol Rev Camb Philos Soc 2013; 89:215-31. [DOI: 10.1111/brv.12049] [Citation(s) in RCA: 142] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 05/28/2013] [Accepted: 06/19/2013] [Indexed: 11/28/2022]
Affiliation(s)
- José C. Brito
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
- Departamento de Biologia da; Faculdade de Ciências da Universidade do Porto; Porto 4169-007 Portugal
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
| | - Fernando Martínez-Freiría
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
| | | | - Hugo Rebelo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
- School of Biological Sciences; University of Bristol; Bristol BS8 1UG U.K
| | - Xavier Santos
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
| | - Cândida G. Vale
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
- Departamento de Biologia da; Faculdade de Ciências da Universidade do Porto; Porto 4169-007 Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
| | - Zbyszek Boratyński
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
- Centre of Excellence in Evolutionary Research, Department of Biological and Environmental Science; University of Jyväskylä; Survontie 9 Finland
| | - Sílvia B. Carvalho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
| | - Sónia Ferreira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
- Departamento de Biologia da; Faculdade de Ciências da Universidade do Porto; Porto 4169-007 Portugal
| | - Duarte V. Gonçalves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
- Departamento de Biologia da; Faculdade de Ciências da Universidade do Porto; Porto 4169-007 Portugal
| | - Teresa L. Silva
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
- Departamento de Biologia da; Faculdade de Ciências da Universidade do Porto; Porto 4169-007 Portugal
| | - Pedro Tarroso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
| | - João C. Campos
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
- Departamento de Biologia da; Faculdade de Ciências da Universidade do Porto; Porto 4169-007 Portugal
| | - João V. Leite
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
| | - Joana Nogueira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
- Departamento de Biologia da; Faculdade de Ciências da Universidade do Porto; Porto 4169-007 Portugal
| | - Francisco Álvares
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto; Vairão 4485-661 Portugal
| | - Neftalí Sillero
- Centro de Investigação em Ciências Geo-Espaciais (CICGE) da Universidade do Porto; Porto 4169-007 Portugal
| | - Andack S. Sow
- Département de Biologie; Université Abdelmalek Essaâdi; Tétouan 93002 Morocco
| | - Soumia Fahd
- Département de Biologie; Université Abdelmalek Essaâdi; Tétouan 93002 Morocco
| | - Pierre-André Crochet
- EPHE-UMR 5175; Centre d'Ecologie Fonctionnelle et Evolutive; Montpellier F-34293 France
| | - Salvador Carranza
- Institute of Evolutionary Biology; CSIC-Universitat Pompeu Fabra; Barcelona E-08003 Spain
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Black SA, Fellous A, Yamaguchi N, Roberts DL. Examining the extinction of the Barbary lion and its implications for felid conservation. PLoS One 2013; 8:e60174. [PMID: 23573239 PMCID: PMC3616087 DOI: 10.1371/journal.pone.0060174] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/25/2013] [Indexed: 11/19/2022] Open
Abstract
Estimations of species extinction dates are rarely definitive, yet declarations of extinction or extirpation are important as they define when conservation efforts may cease. Erroneous declarations of extinctions not only destabilize conservation efforts but also corrode local community support. Mismatches in perceptions by the scientific and local communities risk undermining sensitive, but important partnerships. We examine observations relating to the decline and extinction of Barbary lions in North Africa. Whilst the extinction predates the era of the scientific conservation movement, the decline is relatively well documented in historical records. Recently unearthed accounts suggest Barbary lions survived later than previously assumed. We use probabilistic methods to estimate a more recent extinction date for the subspecies. The evidence presented for a much later persistence of lions in North Africa, including generations when sightings were nil, suggests caution when considering felid populations as extinct in the wild. The case raises the possibility that captive animals descended from the Moroccan royal collection are closer contemporaries to wild Barbary lions. Furthermore, our results highlight the vulnerability of very small lion populations and the significance of continued conservation of remnant lion populations in Central and West Africa.
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Affiliation(s)
- Simon A Black
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, United Kingdom.
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42
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Masseti M, Mazza PPA. Western European Quaternary lions: new working hypotheses. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12032] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Marco Masseti
- Department of Evolutionary Biology ‘Leo Pardi’; University of Florence; via del Proconsolo 12; 50122; Florence; Italy
| | - Paul P. A. Mazza
- Department of Earth Sciences; University of Florence; via La Pira 4; 50121; Florence; Italy
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Dubach JM, Briggs MB, White PA, Ament BA, Patterson BD. Genetic perspectives on “Lion Conservation Units” in Eastern and Southern Africa. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0453-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bruche S, Gusset M, Lippold S, Barnett R, Eulenberger K, Junhold J, Driscoll CA, Hofreiter M. A genetically distinct lion (Panthera leo) population from Ethiopia. EUR J WILDLIFE RES 2012. [DOI: 10.1007/s10344-012-0668-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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45
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Abstract
The savannah biome of sub-Saharan Africa harbours the highest diversity of ungulates (hoofed mammals) on Earth. In this review, we compile population genetic data from 19 codistributed ungulate taxa of the savannah biome and find striking concordance in the phylogeographic structuring of species. Data from across taxa reveal distinct regional lineages, which reflect the survival and divergence of populations in isolated savannah refugia during the climatic oscillations of the Pleistocene. Data from taxa across trophic levels suggest distinct savannah refugia were present in West, East, Southern and South-West Africa. Furthermore, differing Pleistocene evolutionary biogeographic scenarios are proposed for East and Southern Africa, supported by palaeoclimatic data and the fossil record. Environmental instability in East Africa facilitated several spatial and temporal refugia and is reflected in the high inter- and intraspecific diversity of the region. In contrast, phylogeographic data suggest a stable, long-standing savannah refuge in the south.
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Affiliation(s)
- E D Lorenzen
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA.
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46
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Lorenzen ED, Nogués-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MTP, Nielsen R, Ho SYW, Goebel T, Graf KE, Byers D, Stenderup JT, Rasmussen M, Campos PF, Leonard JA, Koepfli KP, Froese D, Zazula G, Stafford TW, Aaris-Sørensen K, Batra P, Haywood AM, Singarayer JS, Valdes PJ, Boeskorov G, Burns JA, Davydov SP, Haile J, Jenkins DL, Kosintsev P, Kuznetsova T, Lai X, Martin LD, McDonald HG, Mol D, Meldgaard M, Munch K, Stephan E, Sablin M, Sommer RS, Sipko T, Scott E, Suchard MA, Tikhonov A, Willerslev R, Wayne RK, Cooper A, Hofreiter M, Sher A, Shapiro B, Rahbek C, Willerslev E. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature 2011; 479:359-64. [PMID: 22048313 DOI: 10.1038/nature10574] [Citation(s) in RCA: 310] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 09/16/2011] [Indexed: 11/09/2022]
Abstract
Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.
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Affiliation(s)
- Eline D Lorenzen
- Centre for GeoGenetics, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark
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Molecular biogeography of red deer Cervus elaphus from eastern Europe: insights from mitochondrial DNA sequences. ACTA ACUST UNITED AC 2010; 56:1-12. [PMID: 21350595 PMCID: PMC3026933 DOI: 10.1007/s13364-010-0002-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 10/08/2010] [Indexed: 11/03/2022]
Abstract
European red deer are known to show a conspicuous phylogeographic pattern with three distinct mtDNA lineages (western, eastern and North-African/Sardinian). The western lineage, believed to be indicative of a southwestern glacial refuge in Iberia and southern France, nowadays covers large areas of the continent including the British Isles, Scandinavia and parts of central Europe, while the eastern lineage is primarily found in southeast-central Europe, the Carpathians and the Balkans. However, large parts of central Europe and the whole northeast of the continent were not covered by previous analyses. To close this gap, we produced mtDNA control region sequences from more than 500 red deer from Denmark, Germany, Poland, Lithuania, Belarus, Ukraine and western Russia and combined our data with sequences available from earlier studies to an overall sample size of almost 1,100. Our results show that the western lineage extends far into the European east and is prominent in all eastern countries except for the Polish Carpathians, Ukraine and Russia where only eastern haplotypes occurred. While the latter may actually reflect the natural northward expansion of the eastern lineage after the last ice age, the present distribution of the western lineage in eastern Europe may in large parts be artificial and a result of translocations and reintroduction of red deer into areas where the species became extinct in historical times.
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Miller JM, Hallager S, Monfort SL, Newby J, Bishop K, Tidmus SA, Black P, Houston B, Matthee CA, Fleischer RC. Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus). CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0149-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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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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50
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Meachen‐Samuels JA, Binder WJ. Sexual dimorphism and ontogenetic growth in the American lion and sabertoothed cat from Rancho La Brea. J Zool (1987) 2010. [DOI: 10.1111/j.1469-7998.2009.00659.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. A. Meachen‐Samuels
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles CA, USA
| | - W. J. Binder
- Department of Biology, Loyola Marymount University, Los Angeles, CA, USA
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