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Combosch DJ, Burdick D, Primov K, Rios D, Rios K, Fernandez J. Barcoding and mitochondrial phylogenetics of Porites corals. PLoS One 2024; 19:e0290505. [PMID: 38359055 PMCID: PMC10868756 DOI: 10.1371/journal.pone.0290505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/10/2023] [Indexed: 02/17/2024] Open
Abstract
Coral reefs are the most diverse ecosystem on the planet based on the abundance and diversity of phyla and higher taxa. However, it is still difficult to assess the diversity of lower taxa, especially at the species level. One tool for improving the identification of lower taxa are genetic markers that can distinguish cryptic species and assess species boundaries. Here, we present one such approach for an important and challenging group of reef-building corals. Porites corals are the main reef-builders of many coral reefs in the Indo-Pacific, owing to the massive growth forms of some species. The current number of valid Porites species is controversial, inflated with many synonymies, and often based on gross colony morphology although several morphospecies believed to be widespread and common can only be distinguished based on detailed microstructure analyses by taxonomic experts. Here, we test the suitability of multiple regions of mtDNA as genetic barcodes to identify suitable markers for species differentiation and unambiguous identification. Resulting sequencing data was further used for the first phylogenetic analysis of Guam's Porites species. We tested eight different mitochondrial markers and analyzed four in detail for 135 Porites specimens: mtDNA markers were amplified for 67 Porites specimens from Guam, representing 12 nominal Porites species, and combined with 69 mitochondrial genomes, mostly from Hawaii. The combination of all 4 markers distinguished 10 common and 7 uncommon Central-West Pacific Porites species. Most clades separate species along taxonomic boundaries, which is uncommon for Porites corals and testifies to the suitability of our multi-marker approach, and a combination of the two most promising barcodes distinguished 8/10 common species. These barcodes are thus suitable to distinguish virtually cryptic species in one of the most important and challenging coral genera. They offer a cheap, fast and reliable way to identify Porites species for species-level research, monitoring and conservation.
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Affiliation(s)
| | - David Burdick
- Marine Laboratory, University of Guam, Mangilao, Guam
| | - Karim Primov
- Marine Laboratory, University of Guam, Mangilao, Guam
| | - Dareon Rios
- Marine Laboratory, University of Guam, Mangilao, Guam
| | - Kireon Rios
- Marine Laboratory, University of Guam, Mangilao, Guam
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2
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Meißner R, Mokgokong P, Pretorius C, Winter S, Labuschagne K, Kotze A, Prost S, Horin P, Dalton D, Burger PA. Diversity of selected toll-like receptor genes in cheetahs (Acinonyx jubatus) and African leopards (Panthera pardus pardus). Sci Rep 2024; 14:3756. [PMID: 38355905 PMCID: PMC10866938 DOI: 10.1038/s41598-024-54076-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 02/08/2024] [Indexed: 02/16/2024] Open
Abstract
The anthropogenic impact on wildlife is ever increasing. With shrinking habitats, wild populations are being pushed to co-exist in proximity to humans leading to an increased threat of infectious diseases. Therefore, understanding the immune system of a species is key to assess its resilience in a changing environment. The innate immune system (IIS) is the body's first line of defense against pathogens. High variability in IIS genes, like toll-like receptor (TLR) genes, appears to be associated with resistance to infectious diseases. However, few studies have investigated diversity in TLR genes in vulnerable species for conservation. Large predators are threatened globally including leopards and cheetahs, both listed as 'vulnerable' by IUCN. To examine IIS diversity in these sympatric species, we used next-generation-sequencing to compare selected TLR genes in African leopards and cheetahs. Despite differences, both species show some TLR haplotype similarity. Historic cheetahs from all subspecies exhibit greater genetic diversity than modern Southern African cheetahs. The diversity in investigated TLR genes is lower in modern Southern African cheetahs than in African leopards. Compared to historic cheetah data and other subspecies, a more recent population decline might explain the observed genetic impoverishment of TLR genes in modern Southern African cheetahs. However, this may not yet impact the health of this cheetah subspecies.
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Affiliation(s)
- René Meißner
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstraße 1, 1160, Vienna, Austria
| | - Prudent Mokgokong
- South African National Biodiversity Institute, National Zoological Garden, 232 Boom Street, Pretoria, 0002, South Africa
| | - Chantelle Pretorius
- South African National Biodiversity Institute, National Zoological Garden, 232 Boom Street, Pretoria, 0002, South Africa
- WWF South African, Bridge House, Boundary Terraces, Mariendahl Ave, Newlands, 7725, Capetown, South Africa
| | - Sven Winter
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstraße 1, 1160, Vienna, Austria
| | - Kim Labuschagne
- South African National Biodiversity Institute, National Zoological Garden, 232 Boom Street, Pretoria, 0002, South Africa
| | - Antoinette Kotze
- South African National Biodiversity Institute, National Zoological Garden, 232 Boom Street, Pretoria, 0002, South Africa
- University of the Free State, Bloemfontein Campus, Bloemfontein, 9300, South Africa
| | - Stefan Prost
- South African National Biodiversity Institute, National Zoological Garden, 232 Boom Street, Pretoria, 0002, South Africa
- University of Oulu, Pentti Kaiteran Katu 1, 90570, Oulu, Finland
| | - Petr Horin
- Department of Animal Genetics, University of Veterinary Sciences, Brno, Czech Republic
- Central European Institute of Technology, University of Veterinary Sciences Brno (CEITEC Vetuni), Brno, Czech Republic
| | - Desire Dalton
- South African National Biodiversity Institute, National Zoological Garden, 232 Boom Street, Pretoria, 0002, South Africa.
- School of Health and Life Science, Teesside University, Middlesbrough, Tees Valley, TS1 3BX, UK.
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, University of Veterinary Medicine, Savoyenstraße 1, 1160, Vienna, Austria.
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Chakraborty A, Mondal S, Mahajan S, Sharma VK. High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl. Heliyon 2023; 9:e18571. [PMID: 37576271 PMCID: PMC10412995 DOI: 10.1016/j.heliyon.2023.e18571] [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: 01/18/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
An intriguing example of differential adaptability is the case of two Asian peafowl species, Pavo cristatus (blue peafowl) and Pavo muticus (green peafowl), where the former has a "Least Concern" conservation status and the latter is an "Endangered" species. To understand the genetic basis of this differential adaptability of the two peafowl species, a comparative analysis of these species is much needed to gain the genomic and evolutionary insights. Thus, we constructed a high-quality genome assembly of blue peafowl with an N50 value of 84.81 Mb (pseudochromosome-level assembly), and a high-confidence coding gene set to perform the genomic and evolutionary analyses of blue and green peafowls with 49 other avian species. The analyses revealed adaptive evolution of genes related to neuronal development, immunity, and skeletal muscle development in these peafowl species. Major genes related to axon guidance such as NEO1 and UNC5, semaphorin (SEMA), and ephrin receptor showed adaptive evolution in peafowl species. However, blue peafowl showed the presence of 42% more coding genes compared to the green peafowl along with a higher number of species-specific gene clusters, segmental duplicated genes and expanded gene families, and comparatively higher evolution in neuronal and developmental pathways. Blue peafowl also showed longer branch length compared to green peafowl in the species phylogenetic tree. These genomic insights obtained from the high-quality genome assembly of P. cristatus constructed in this study provide new clues on the superior adaptability of the blue peafowl over green peafowl despite having a recent species divergence time.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Samuel Mondal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Vineet K. Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
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Lok S, Lau TNH, Trost B, Tong AHY, Wintle RF, Engstrom MD, Stacy E, Waits LP, Scrafford M, Scherer SW. Chromosomal-level reference genome assembly of the North American wolverine ( Gulo gulo luscus): a resource for conservation genomics. G3 GENES|GENOMES|GENETICS 2022; 12:6604289. [PMID: 35674384 PMCID: PMC9339297 DOI: 10.1093/g3journal/jkac138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/19/2022] [Indexed: 11/21/2022]
Abstract
We report a chromosomal-level genome assembly of a male North American wolverine (Gulo gulo luscus) from the Kugluktuk region of Nunavut, Canada. The genome was assembled directly from long-reads, comprising: 758 contigs with a contig N50 of 36.6 Mb; contig L50 of 20; base count of 2.39 Gb; and a near complete representation (99.98%) of the BUSCO 5.2.2 set of 9,226 genes. A presumptive chromosomal-level assembly was generated by scaffolding against two chromosomal-level Mustelidae reference genomes, the ermine and the Eurasian river otter, to derive a final scaffold N50 of 144.0 Mb and a scaffold L50 of 7. We annotated a comprehensive set of genes that have been associated with models of aggressive behavior, a trait which the wolverine is purported to have in the popular literature. To support an integrated, genomics-based wildlife management strategy at a time of environmental disruption from climate change, we annotated the principal genes of the innate immune system to provide a resource to study the wolverine’s susceptibility to new infectious and parasitic diseases. As a resource, we annotated genes involved in the modality of infection by the coronaviruses, an important class of viral pathogens of growing concern as shown by the recent spillover infections by severe acute respiratory syndrome coronavirus-2 to naïve wildlife. Tabulation of heterozygous single nucleotide variants in our specimen revealed a heterozygosity level of 0.065%, indicating a relatively diverse genetic pool that would serve as a baseline for the genomics-based conservation of the wolverine, a rare cold-adapted carnivore now under threat.
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Affiliation(s)
- Si Lok
- The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Timothy N H Lau
- The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Brett Trost
- The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Amy H Y Tong
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto , ON M5S 3E1, Canada
| | - Richard F Wintle
- The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
| | - Mark D Engstrom
- Department of Natural History, Royal Ontario Museum , Toronto, ON M5S 2C6, Canada
| | - Elise Stacy
- Environmental Science Program, University of Idaho , Moscow, ID 83844, USA
- Wildlife Conservation Society, Arctic Beringia , Fairbanks, AK 99709, USA
| | - Lisette P Waits
- Department of Fish and Wildlife, University of Idaho , Moscow, ID 83844, USA
| | - Matthew Scrafford
- Wildlife Conservation Society Canada , Thunder Bay, ON P7A 4K9, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, ON M5G 0A4, Canada
- McLaughlin Centre, University of Toronto , Toronto, ON M5G 0A4, Canada
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto , ON M5S 1A8, Canada
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5
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Palmqvist P, Rodríguez-Gómez G, Bermúdez de Castro JM, García-Aguilar JM, Espigares MP, Figueirido B, Ros-Montoya S, Granados A, Serrano FJ, Martínez-Navarro B, Guerra-Merchán A. Insights on the Early Pleistocene Hominin Population of the Guadix-Baza Depression (SE Spain) and a Review on the Ecology of the First Peopling of Europe. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.881651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The chronology and environmental context of the first hominin dispersal in Europe have been subject to debate and controversy. The oldest settlements in Eurasia (e.g., Dmanisi, ∼1.8 Ma) suggest a scenario in which the Caucasus and southern Asia were occupied ∼0.4 Ma before the first peopling of Europe. Barranco León (BL) and Fuente Nueva 3 (FN3), two Early Pleistocene archeological localities dated to ∼1.4 Ma in Orce (Guadix-Baza Depression, SE Spain), provide the oldest evidence of hominin presence in Western Europe. At these sites, huge assemblages of large mammals with evidence of butchery and marrow processing have been unearthed associated to abundant Oldowan tools and a deciduous tooth of Homo sp. in the case of BL. Here, we: (i) review the Early Pleistocene archeological sites of Europe; (ii) discuss on the subsistence strategies of these hominins, including new estimates of resource abundance for the populations of Atapuerca and Orce; (iii) use cartographic data of the sedimentary deposits for reconstructing the landscape habitable in Guadix-Baza; and (iv) calculate the size of the hominin population using an estimate of population density based on resource abundance. Our results indicate that Guadix-Baza could be home for a small hominin population of 350–280 individuals. This basin is surrounded by the highest mountainous reliefs of the Alpine-Betic orogen and shows a limited number of connecting corridors with the surrounding areas, which could have limited gene flow with other hominin populations. Isolation would eventually lead to bottlenecks, genetic drift and inbreeding depression, conditions documented in the wild dog population of the basin, which probably compromised the viability of the hominin population in the medium to long term. This explains the discontinuous nature of the archeological record in Guadix-Baza, a situation that can also be extrapolated to the scarcity of hominin settlements for these ancient chronologies in Europe.
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Wemer N, Naude VN, Merwe VC, Smit M, Lange G, Komdeur J. Successful predatory‐avoidance behaviour to lion auditory cues during soft‐release from captivity in cheetah. Ethology 2021. [DOI: 10.1111/eth.13261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nynke Wemer
- Behavioral Physiology and Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen the Netherlands
| | - Vincent N. Naude
- Institute for Communities and Wildlife in Africa University of Cape Town Rondebosch South Africa
| | - Vincent C. Merwe
- Institute for Communities and Wildlife in Africa University of Cape Town Rondebosch South Africa
- Endangered Wildlife Trust Johannesburg South Africa
| | - Marna Smit
- Ashia Cheetah Conservation Paarl South Africa
| | - Gerhard Lange
- Kuzuko Lodge Private Game Reserve Greater Addo Area South Africa
| | - Jan Komdeur
- Behavioral Physiology and Ecology Group Groningen Institute for Evolutionary Life Sciences (GELIFES) University of Groningen Groningen the Netherlands
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Understanding the Role of Semiochemicals on the Reproductive Behaviour of Cheetahs ( Acinonyx jubatus)-A Review. Animals (Basel) 2021; 11:ani11113140. [PMID: 34827872 PMCID: PMC8614540 DOI: 10.3390/ani11113140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/30/2021] [Accepted: 10/31/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary This review aims to provide an in-depth overview of the reproductive physiology and behaviour of cheetahs (Acinonyx jubatus). Specifically, it focuses on the role that pheromones (a class of semiochemicals) play by directly affecting the reproductive (e.g., precopulatory and copulatory) behaviour. Furthermore, it aims to critically analyze current research and provide new insights on study areas needing further investigation. It is clear, for instance, that further research is necessary to investigate the role of semiochemicals in the reproductive behaviour of cheetahs in order to rectify the current behavioural difficulties experienced when breeding younger females. This, in turn, would aid in improving captive breeding and the prevention of asymmetric reproductive aging. Abstract The cheetah species (Acinonyx jubatus) is currently listed as vulnerable according to the International Union for Conservation of Nature (IUCN). Captive breeding has long since been used as a method of conservation of the species, with the aim to produce a healthy, strong population of cheetahs with an increased genetic variety when compared to their wild counterparts. This would then increase the likelihood of survivability once released into protected areas. Unfortunately, breeding females have been reported to be difficult due to the age of these animals. Older females are less fertile, have more difficult parturition, and are susceptible to asymmetric reproductive aging whereas younger females tend to show a significantly lower frequency of mating behaviour than that of older females, which negatively affects breeding introductions, and therefore mating. Nonetheless, the experience from breeding methods used in some breeding centres in South Africa and the Netherlands, which also rely on the role that semiochemicals play in breeding, proves that cheetahs can be bred successfully in captivity. This review aims to give the reader an in-depth overview of cheetahs’ reproductive physiology and behaviour, focusing on the role that pheromones play in this species. Furthermore, it aims to provide new insight into the use of semiochemicals to improve conservation strategies through captive breeding.
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Wiedenfeld DA, Alberts AC, Angulo A, Bennett EL, Byers O, Contreras‐MacBeath T, Drummond G, da Fonseca GAB, Gascon C, Harrison I, Heard N, Hochkirch A, Konstant W, Langhammer PF, Langrand O, Launay F, Lebbin DJ, Lieberman S, Long B, Lu Z, Maunder M, Mittermeier RA, Molur S, Khalifa al Mubarak R, Parr MJ, Ratsimbazafy J, Rhodin AGJ, Rylands AB, Sanderson J, Sechrest W, Soorae P, Supriatna J, Upgren A, Vié J, Zhang L. Conservation resource allocation, small population resiliency, and the fallacy of conservation triage. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:1388-1395. [PMID: 33484006 PMCID: PMC8518633 DOI: 10.1111/cobi.13696] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 01/09/2021] [Accepted: 01/16/2021] [Indexed: 05/30/2023]
Abstract
Some conservation prioritization methods are based on the assumption that conservation needs overwhelm current resources and not all species can be conserved; therefore, a conservation triage scheme (i.e., when the system is overwhelmed, species should be divided into three groups based on likelihood of survival, and efforts should be focused on those species in the group with the best survival prospects and reduced or denied to those in the group with no survival prospects and to those in the group not needing special efforts for their conservation) is necessary to guide resource allocation. We argue that this decision-making strategy is not appropriate because resources are not as limited as often assumed, and it is not evident that there are species that cannot be conserved. Small population size alone, for example, does not doom a species to extinction; plants, reptiles, birds, and mammals offer examples. Although resources dedicated to conserving all threatened species are insufficient at present, the world's economic resources are vast, and greater resources could be dedicated toward species conservation. The political framework for species conservation has improved, with initiatives such as the UN Sustainable Development Goals and other international agreements, funding mechanisms such as The Global Environment Facility, and the rise of many nongovernmental organizations with nimble, rapid-response small grants programs. For a prioritization system to allow no extinctions, zero extinctions must be an explicit goal of the system. Extinction is not inevitable, and should not be acceptable. A goal of no human-induced extinctions is imperative given the irreversibility of species loss.
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Affiliation(s)
| | | | - Ariadne Angulo
- IUCN SSC Amphibian Specialist Group3701 Lake Shore Blvd. W, P.O. Box 48586TorontoONM8W 1P5Canada
| | | | - Onnie Byers
- IUCN SSC Conservation Planning Specialist Group12101 Johnny Cake Ridge RoadApple ValleyMN55124U.S.A.
| | - Topiltzin Contreras‐MacBeath
- Centro de Investigaciones BiológicasUniversidad Autónoma del Estado de MorelosAvenida Universidad 1001, Col. Chamilpa, CP 62209CuernavacaMorelosMexico
| | - Gláucia Drummond
- Fundação BiodiversitasAvenida Celso Porfírio Machado No. 1813, BelvedereBelo HorizonteMG30320–400Brazil
| | | | - Claude Gascon
- The Global Environment Facility1818 H Street NW Rm N8‐800WashingtonDC20433U.S.A.
| | - Ian Harrison
- Conservation InternationalArlingtonVA22202U.S.A.
| | - Nicolas Heard
- Mohamed bin Zayed Species Conservation FundP.O. Box 13112Abu DhabiUAE
| | - Axel Hochkirch
- Department of Biogeography and IUCN SSC Invertebrate Conservation CommitteeTrier UniversityTrier54286Germany
| | - William Konstant
- Margot Marsh Biodiversity Foundation403 Poplar RoadFlourtownPA19031U.S.A.
| | | | | | - Frederic Launay
- Mohamed bin Zayed Species Conservation FundP.O. Box 13112Abu DhabiUAE
- PantheraNew YorkNY10018U.S.A.
| | | | - Susan Lieberman
- Wildlife Conservation Society2300 Southern Blvd.BronxNY10460U.S.A.
| | - Barney Long
- Global Wildlife ConservationAustinTX78704U.S.A.
| | - Zhi Lu
- Center for Nature and Society, School of Life SciencesPeking UniversityBeijing100871China
| | - Michael Maunder
- Center for Ecology and ConservationUniversity of ExeterPenryn CampusCornwallTR10 9FEU.K.
| | | | - Sanjay Molur
- Zoo Outreach Organization12 Thiruvannamalai Nagar, Saravanampatti – Kalapatti Road, SaravanampattiCoimbatoreTamil Nadu641 035India
| | - Razan Khalifa al Mubarak
- Mohamed bin Zayed Species Conservation FundP.O. Box 13112Abu DhabiUAE
- Environment Agency ‐ Abu DhabiP.O. Box 45553Abu DhabiUAE
| | | | - Jonah Ratsimbazafy
- Groupe d'Etude et de Recherche sur les Primates de MadagascarAntananarivoMadagascar
| | | | | | | | | | - Pritpal Soorae
- Environment Agency ‐ Abu DhabiP.O. Box 45553Abu DhabiUAE
| | - Jatna Supriatna
- Department of BiologyFMIPA, University of IndonesiaDepok16421Indonesia
| | - Amy Upgren
- American Bird ConservancyThe PlainsVA20198U.S.A.
| | | | - Li Zhang
- Key Laboratory for Biodiversity Science and Ecological Engineering, Ministry of EducationInstitute of EcologyBeijing Normal UniversityBeijing100875China
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Viitaniemi HM, Leder EH, Suhonen J. Influence of Interspecific Interference Competition on the Genetic Structure of Calopteryx splendens Populations. ANN ZOOL FENN 2021. [DOI: 10.5735/086.059.0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
| | - Erica H. Leder
- Department of Biology, FI-20014 University of Turku, Finland
| | - Jukka Suhonen
- Department of Biology, FI-20014 University of Turku, Finland
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Farquharson KA, Hogg CJ, Grueber CE. Offspring survival changes over generations of captive breeding. Nat Commun 2021; 12:3045. [PMID: 34031378 PMCID: PMC8144597 DOI: 10.1038/s41467-021-22631-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 03/11/2021] [Indexed: 11/28/2022] Open
Abstract
Conservation breeding programs such as zoos play a major role in preventing extinction, but their sustainability may be impeded by neutral and adaptive population genetic change. These changes are difficult to detect for a single species or context, and impact global conservation efforts. We analyse pedigree data from 15 vertebrate species – over 30,000 individuals – to examine offspring survival over generations of captive breeding. Even accounting for inbreeding, we find that the impacts of increasing generations in captivity are highly variable across species, with some showing substantial increases or decreases in offspring survival over generations. We find further differences between dam and sire effects in first- versus multi-generational analysis. Crucially, our multispecies analysis reveals that responses to captivity could not be predicted from species’ evolutionary (phylogenetic) relationships. Even under best-practice captive management, generational fitness changes that cannot be explained by known processes (such as inbreeding depression), are occurring. Captive breeding could prevent species extinctions, but selection for captivity may decrease fitness. Here the authors analyse pedigree data on 15 long-running vertebrate breeding programs and find generational fitness changes that processes such as inbreeding depression cannot explain.
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Affiliation(s)
- Katherine A Farquharson
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW, Australia
| | - Carolyn J Hogg
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW, Australia
| | - Catherine E Grueber
- The University of Sydney, School of Life and Environmental Sciences, Faculty of Science, Sydney, NSW, Australia.
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Siciliano-Martina L, Light JE, Lawing AM. Cranial morphology of captive mammals: a meta-analysis. Front Zool 2021; 18:4. [PMID: 33485360 PMCID: PMC7825229 DOI: 10.1186/s12983-021-00386-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/14/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Captive facilities such as zoos are uniquely instrumental in conservation efforts. To fulfill their potential as bastions for conservation, zoos must preserve captive populations as appropriate proxies for their wild conspecifics; doing so will help to promote successful reintroduction efforts. Morphological changes within captive populations may be detrimental to the fitness of individual animals because these changes can influence functionality; thus, it is imperative to understand the breadth and depth of morphological changes occurring in captive populations. Here, we conduct a meta-analysis of scientific literature reporting comparisons of cranial measures between captive and wild populations of mammals. We investigate the pervasiveness of cranial differences and whether cranial morphological changes are associated with ecological covariates specific to individual species, such as trophic level, dietary breadth, and home range size. RESULTS Cranial measures of skull length, skull width, and the ratio of skull length-to-width differed significantly between many captive and wild populations of mammals reported in the literature. Roughly half of captive populations differed from wild populations in at least one cranial measure, although the degree of changes varied. Carnivorous species with a limited dietary breadth displayed the most consistent changes associated with skull widening. Species with a more generalized diet displayed less morphological changes in captivity. CONCLUSIONS Wild and captive populations of mammals differed in cranial morphology, but the nature and magnitude of their cranial differences varied considerably across taxa. Although changes in cranial morphology occur in captivity, specific changes cannot be generalized for all captive mammal populations. The nature of cranial changes in captivity may be specific to particular taxonomic groups; thus, it may be possible to establish expectations across smaller taxonomic units, or even disparate groups that utilize their cranial morphology in a similar way. Given that morphological changes occurring in captive environments like zoos have the potential to limit reintroduction success, our results call for a critical evaluation of current captive husbandry practices to prevent unnecessary morphological changes.
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Affiliation(s)
- Leila Siciliano-Martina
- Interdisciplinary Program in Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, 77843, USA.
- Department of Biology, Texas State University, San Marcos, TX, 78666, USA.
| | - Jessica E Light
- Interdisciplinary Program in Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, 77843, USA
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, 77843, USA
| | - A Michelle Lawing
- Interdisciplinary Program in Ecology & Evolutionary Biology, Texas A&M University, College Station, TX, 77843, USA
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, 77843, USA
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12
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News Feature: Getting the world's fastest cat to breed with speed. Proc Natl Acad Sci U S A 2020; 116:24911-24915. [PMID: 31822632 DOI: 10.1073/pnas.1918672116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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13
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Schmidt MJ, Steenkamp G, Failing K, Caldwell P, Kirberger RM. A contribution to age determination of cheetahs (Acinonyx jubatus) based on radiographic analysis of the skull and postcranial morphology. PLoS One 2019; 14:e0217999. [PMID: 31185038 PMCID: PMC6559650 DOI: 10.1371/journal.pone.0217999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 05/22/2019] [Indexed: 11/19/2022] Open
Abstract
The aim of this retrospective cross-sectional study was to present comprehensive information about the age-dependent change of skeletal characteristics in captive cheetahs with known age and to assess the benefit of these variables for age estimation in this species. Radiographs of 162 known-age captive and semi-captive cheetahs were retrospectively examined and age-related changes of skull, axial and appendicular skeletal systems were documented. Metric and non-metric variables were used. These parameters were checked for the best correlation with age using a multiple stepwise regression analysis. An overview about the time frames, in which ossification centers appeared and physeal closure occurred is presented. Multiple stepwise regression analysis revealed the status of closure of the coronal suture, the maximum length of the frontal sinus, the condylobasal-, hard palate, and facial length are most significantly correlated with age. Together with the pulp size of the upper canine, these values can be used for an age approximation in cheetahs.
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Affiliation(s)
- Martin J. Schmidt
- Department of Veterinary Clinical Sciences, Small Animal Clinic, Justus-Liebig-University, Frankfurter Strasse, Giessen, Germany
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, Onderstepoort, South Africa
- * E-mail:
| | - Gerhard Steenkamp
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, Onderstepoort, South Africa
| | - Klaus Failing
- Unit for Biomathematics and Data Processing, Faculty of Veterinary Medicine, Justus Liebig-University-Giessen, Giessen, Germany
| | - Peter Caldwell
- Old Chapel Veterinary Clinic, Villeria Pretoria, South Africa
| | - Robert M. Kirberger
- Department of Companion Animal Clinical Studies, Faculty of Veterinary Science, Onderstepoort, South Africa
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14
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Andrews CJ, Thomas DG, Yapura J, Potter MA. Reproductive biology of the 38 extant felid species: a review. Mamm Rev 2018. [DOI: 10.1111/mam.12145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Christopher J. Andrews
- Animal Science Group; School of Agriculture and Environment; Massey University; Private Bag 11-222 Palmerston North 4442 New Zealand
| | - David G. Thomas
- Animal Science Group; School of Agriculture and Environment; Massey University; Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Jimena Yapura
- School of Veterinary Science; Massey University; Private Bag 11-222 Palmerston North 4442 New Zealand
| | - Murray A. Potter
- Wildlife and Ecology Group; School of Agriculture and Environment; Massey University; Private Bag 11-222 Palmerston North 4442 New Zealand
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15
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Schmidt-Küntzel A, Dalton DL, Menotti-Raymond M, Fabiano E, Charruau P, Johnson WE, Sommer S, Marker L, Kotzé A, O’Brien SJ. Conservation Genetics of the Cheetah: Genetic History and Implications for Conservation. CHEETAHS: BIOLOGY AND CONSERVATION 2018. [PMCID: PMC7149701 DOI: 10.1016/b978-0-12-804088-1.00006-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
From allozymes in 1983 to whole genomes in 2015, genetic studies of the cheetah have been extensive. In this chapter we provide an overview of the available literature. Overall, patterns of genetic variation provided evidence of low variability and suggest this loss occurred thousands of years ago. Differences between published subspecies were supported genetically. At a local scale, populations were generally considered panmictic with minor genetic structure. Although cheetahs have persisted despite low genetic variability, important questions arise from these findings: Does the cheetah have the ability to adapt to and evolve with future changes in environmental and infectious pressure? How would cheetahs cope with further loss of genetic diversity? Connectivity in the wild should be maintained via prevention of habitat loss, while management of small isolated populations may require reestablishing gene flow. Genetics could assist captive-breeding decisions and provide forensic evidence as to the geographical origin of illegally traded animals.
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Affiliation(s)
| | - Desiré L. Dalton
- National Zoological Gardens of South Africa, Pretoria, South Africa,University of Venda, Thohoyandou, South Africa
| | | | | | | | - Warren E. Johnson
- Smithsonian Conservation Biology Institute, Front Royal, VA, United States
| | | | | | - Antoinette Kotzé
- National Zoological Gardens of South Africa, Pretoria, South Africa,University of Free State South Africa, Bloemfontein, South Africa
| | - Stephen J. O’Brien
- St. Petersburg State University, St. Petersburg, Russia,Nova Southeastern University, Fort Lauderdale, FL, United States
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O'Brien SJ, Johnson WE, Driscoll CA, Dobrynin P, Marker L. Conservation Genetics of the Cheetah: Lessons Learned and New Opportunities. J Hered 2017; 108:671-677. [PMID: 28821181 PMCID: PMC5892392 DOI: 10.1093/jhered/esx047] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Accepted: 05/02/2017] [Indexed: 01/27/2023] Open
Abstract
The dwindling wildlife species of our planet have become a cause célèbre for conservation groups, governments, and concerned citizens throughout the world. The application of powerful new genetic technologies to surviving populations of threatened mammals has revolutionized our ability to recognize hidden perils that afflict them. We have learned new lessons of survival, adaptation, and evolution from viewing the natural history of genomes in hundreds of detailed studies. A single case history of one species, the African cheetah, Acinonyx jubatus, is here reviewed to reveal a long-term story of conservation challenges and action informed by genetic discoveries and insights. A synthesis of 3 decades of data, interpretation, and controversy, capped by whole genome sequence analysis of cheetahs, provides a compelling tale of conservation relevance and action to protect this species and other threatened wildlife.
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Affiliation(s)
- Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia; Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft Lauderdale, FL; Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA; Laboratory of Neurogenetics, NIAAA, Rockville, MD; and Cheetah Conservation Fund, Otjiwarongo, Namibia
| | - Warren E Johnson
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia; Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft Lauderdale, FL; Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA; Laboratory of Neurogenetics, NIAAA, Rockville, MD; and Cheetah Conservation Fund, Otjiwarongo, Namibia
| | - Carlos A Driscoll
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia; Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft Lauderdale, FL; Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA; Laboratory of Neurogenetics, NIAAA, Rockville, MD; and Cheetah Conservation Fund, Otjiwarongo, Namibia
| | - Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia; Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft Lauderdale, FL; Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA; Laboratory of Neurogenetics, NIAAA, Rockville, MD; and Cheetah Conservation Fund, Otjiwarongo, Namibia
| | - Laurie Marker
- Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia; Guy Harvey Oceanographic Center, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Ft Lauderdale, FL; Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA; Laboratory of Neurogenetics, NIAAA, Rockville, MD; and Cheetah Conservation Fund, Otjiwarongo, Namibia
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17
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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: 13] [Impact Index Per Article: 1.9] [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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18
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Dobrynin P, Liu S, Tamazian G, Xiong Z, Yurchenko AA, Krasheninnikova K, Kliver S, Schmidt-Küntzel A, Koepfli KP, Johnson W, Kuderna LFK, García-Pérez R, Manuel MD, Godinez R, Komissarov A, Makunin A, Brukhin V, Qiu W, Zhou L, Li F, Yi J, Driscoll C, Antunes A, Oleksyk TK, Eizirik E, Perelman P, Roelke M, Wildt D, Diekhans M, Marques-Bonet T, Marker L, Bhak J, Wang J, Zhang G, O'Brien SJ. Genomic legacy of the African cheetah, Acinonyx jubatus. Genome Biol 2015; 16:277. [PMID: 26653294 PMCID: PMC4676127 DOI: 10.1186/s13059-015-0837-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/17/2015] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. RESULTS Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one >100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084-12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p<0.02), a gene mediating spermatozoon development, indicates cheetah fixation of five function-damaging amino acid variants distinct from AKAP4 homologues of other Felidae or mammals; AKAP4 dysfunction may cause the cheetah's extremely high (>80 %) pleiomorphic sperm. CONCLUSIONS The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species' natural history, physiological adaptations and unique reproductive disposition.
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Affiliation(s)
- Pavel Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Shiping Liu
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China. .,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China.
| | - Gaik Tamazian
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Zijun Xiong
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Andrey A Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Ksenia Krasheninnikova
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Sergey Kliver
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Anne Schmidt-Küntzel
- Life Technologies Conservation Genetics Laboratory, Cheetah Conservation Fund, Otjiwarongo, Otjiwarongo, 9000, Namibia.
| | - Klaus-Peter Koepfli
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia. .,National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC, 20007, USA.
| | - Warren Johnson
- National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC, 20007, USA.
| | - Lukas F K Kuderna
- Institut de Biologia Evolutiva (CSIC/UPF), Dr. Aiguader, 88, Barcelona, 08003, Spain.
| | - Raquel García-Pérez
- Institut de Biologia Evolutiva (CSIC/UPF), Dr. Aiguader, 88, Barcelona, 08003, Spain.
| | - Marc de Manuel
- Institut de Biologia Evolutiva (CSIC/UPF), Dr. Aiguader, 88, Barcelona, 08003, Spain.
| | - Ricardo Godinez
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, 02138, Massachusetts, USA.
| | - Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Alexey Makunin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia. .,Institute of Molecular and Cellular Biology of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Vladimir Brukhin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia.
| | - Weilin Qiu
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Long Zhou
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Fang Li
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Jian Yi
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Carlos Driscoll
- Laboratory of Neurogenetics, NIAAA, 5625 Fishers Lane, Rockville, 20852, Maryland, USA.
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas, 177, Porto, 4050-123, Portugal. .,Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, 4169-007, Portugal.
| | - Taras K Oleksyk
- Biology Department, University of Puerto-Rico at Mayaguez, Mayaguez, Puerto Rico.
| | - Eduardo Eizirik
- PUCRS, Faculdade de Biociencias, Laboratorio de Biología Genómica e Molecular, Porto Alegre, 90619-900, Brazil.
| | - Polina Perelman
- Institute of Molecular and Cellular Biology of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
| | - Melody Roelke
- Laboratory of Animal Sciences Progras, Leídos Biomedical Research Inc., Frederick National Laboratory, Frederick, 21702, Maryland, USA.
| | - David Wildt
- National Zoological Park, Smithsonian Conservation Biology Institute, Washington DC, 20007, USA.
| | - Mark Diekhans
- Center for Biomolecular Science and Engineering, University of California, Santa-Cruz, USA.
| | - Tomas Marques-Bonet
- Institut de Biologia Evolutiva (CSIC/UPF), Dr. Aiguader, 88, Barcelona, 08003, Spain. .,Centro Nacional de Analisis Genomics (CNAG), Baldiri Reixach 4, Barcelona, 08013, Spain. .,State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China.
| | - Laurie Marker
- Cheetah Conservation Fund, Otjiwarongo, Otjiwarongo, 9000, Namibia.
| | - Jong Bhak
- Biomedical Engineering Department, UNIST, Ulsan National Institute of Science and Technology, Ulsan, Korea.
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China. .,Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark. .,Princess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah, 21589, Saudi Arabia. .,Macau University of Science and Technology, Taipa, 999078, Macau, China.
| | - Guojie Zhang
- National Genbank, BGI-Shenzhen, Shenzhen, 518083, China. .,Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, Copenhagen, DK-2100, Denmark.
| | - Stephen J O'Brien
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, 41A Sredniy Avenue, St. Petersburg, 199004, Russia. .,Oceanographic Center, Nova Southeastern University Ft Lauderdale, 8000 N. Ocean Drive, Ft Lauderdale, 33004, Florida, USA.
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Toward the genetic origins of a potentially non-native population of threespine stickleback (Gasterosteus aculeatus) in Alberta. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0706-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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Bhattacharya N, Basu N, Banerjee SK, Malakar D. Concern for Pharmacogenomics and Autologous Cell Therapy: Can This Be a Direction Toward Medicine for the Future? Regen Med 2015. [DOI: 10.1007/978-1-4471-6542-2_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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21
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Norman JA, Blackmore CJ, Rourke M, Christidis L. Effects of mitochondrial DNA rate variation on reconstruction of Pleistocene demographic history in a social avian species, Pomatostomus superciliosus. PLoS One 2014; 9:e106267. [PMID: 25181547 PMCID: PMC4152169 DOI: 10.1371/journal.pone.0106267] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 08/04/2014] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial sequence data is often used to reconstruct the demographic history of Pleistocene populations in an effort to understand how species have responded to past climate change events. However, departures from neutral equilibrium conditions can confound evolutionary inference in species with structured populations or those that have experienced periods of population expansion or decline. Selection can affect patterns of mitochondrial DNA variation and variable mutation rates among mitochondrial genes can compromise inferences drawn from single markers. We investigated the contribution of these factors to patterns of mitochondrial variation and estimates of time to most recent common ancestor (TMRCA) for two clades in a co-operatively breeding avian species, the white-browed babbler Pomatostomus superciliosus. Both the protein-coding ND3 gene and hypervariable domain I control region sequences showed departures from neutral expectations within the superciliosus clade, and a two-fold difference in TMRCA estimates. Bayesian phylogenetic analysis provided evidence of departure from a strict clock model of molecular evolution in domain I, leading to an over-estimation of TMRCA for the superciliosus clade at this marker. Our results suggest mitochondrial studies that attempt to reconstruct Pleistocene demographic histories should rigorously evaluate data for departures from neutral equilibrium expectations, including variation in evolutionary rates across multiple markers. Failure to do so can lead to serious errors in the estimation of evolutionary parameters and subsequent demographic inferences concerning the role of climate as a driver of evolutionary change. These effects may be especially pronounced in species with complex social structures occupying heterogeneous environments. We propose that environmentally driven differences in social structure may explain observed differences in evolutionary rate of domain I sequences, resulting from longer than expected retention times for matriarchal lineages in the superciliosus clade.
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Affiliation(s)
- Janette A. Norman
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
- Department of Genetics, University of Melbourne, Parkville, Victoria, Australia
- Museum Victoria, Melbourne, Victoria, Australia
| | - Caroline J. Blackmore
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
| | - Meaghan Rourke
- Museum Victoria, Melbourne, Victoria, Australia
- School of Science and Engineering, Deakin University, Geelong, Victoria, Australia
- New South Wales Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, New South Wales, Australia
| | - Les Christidis
- National Marine Science Centre, Southern Cross University, Coffs Harbour, New South Wales, Australia
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22
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Fast running restricts evolutionary change of the vertebral column in mammals. Proc Natl Acad Sci U S A 2014; 111:11401-6. [PMID: 25024205 DOI: 10.1073/pnas.1401392111] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The mammalian vertebral column is highly variable, reflecting adaptations to a wide range of lifestyles, from burrowing in moles to flying in bats. However, in many taxa, the number of trunk vertebrae is surprisingly constant. We argue that this constancy results from strong selection against initial changes of these numbers in fast running and agile mammals, whereas such selection is weak in slower-running, sturdier mammals. The rationale is that changes of the number of trunk vertebrae require homeotic transformations from trunk into sacral vertebrae, or vice versa, and mutations toward such transformations generally produce transitional lumbosacral vertebrae that are incompletely fused to the sacrum. We hypothesize that such incomplete homeotic transformations impair flexibility of the lumbosacral joint and thereby threaten survival in species that depend on axial mobility for speed and agility. Such transformations will only marginally affect performance in slow, sturdy species, so that sufficient individuals with transitional vertebrae survive to allow eventual evolutionary changes of trunk vertebral numbers. We present data on fast and slow carnivores and artiodactyls and on slow afrotherians and monotremes that strongly support this hypothesis. The conclusion is that the selective constraints on the count of trunk vertebrae stem from a combination of developmental and biomechanical constraints.
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23
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Huang J, Zhao Y, Shiraigol W, Li B, Bai D, Ye W, Daidiikhuu D, Yang L, Jin B, Zhao Q, Gao Y, Wu J, Bao W, Li A, Zhang Y, Han H, Bai H, Bao Y, Zhao L, Zhai Z, Zhao W, Sun Z, Zhang Y, Meng H, Dugarjaviin M. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype. Sci Rep 2014; 4:4958. [PMID: 24828444 PMCID: PMC4021364 DOI: 10.1038/srep04958] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 04/22/2014] [Indexed: 12/22/2022] Open
Abstract
Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsonian translocation event through the wild horse's chromosomes 23 and 24, which contained sequences that were highly homologous with those on the domestic horse's chromosome 5. The four main types of rearrangement, insertion of unknown origin, inserted duplication, inversion, and relocation, are not evenly distributed on all the chromosomes, and some chromosomes, such as the X chromosome, contain more rearrangements than others, and the number of inversions is far less than the number of insertions and relocations in the horse genome. Furthermore, we discovered the percentages of LINE_L1 and LTR_ERV1 are significantly increased in rearrangement regions. The analysis results of the two representative Equus species genomes improved our knowledge of Equus chromosome rearrangement and karyotype evolution.
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Affiliation(s)
- Jinlong Huang
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Yiping Zhao
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Wunierfu Shiraigol
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Bei Li
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Dongyi Bai
- 1] College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China [2]
| | - Weixing Ye
- 1] Shanghai Personal Biotechnology Limited Company, 777 Longwu Road, Shanghai 200236, P.R. China [2]
| | - Dorjsuren Daidiikhuu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Lihua Yang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Burenqiqige Jin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Qinan Zhao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Yahan Gao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Jing Wu
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Wuyundalai Bao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Anaer Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Yuhong Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Haige Han
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Haitang Bai
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Yanqing Bao
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
| | - Lele Zhao
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Zhengxiao Zhai
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Wenjing Zhao
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Zikui Sun
- Shanghai Personal Biotechnology Limited Company, 777 Longwu Road, Shanghai 200236, P.R. China
| | - Yan Zhang
- Virginia Bioinformatics Institute, Virginia Tech, Washington Street, MC0477, Blacksburg, Virginia, 24061, USA
| | - He Meng
- School of Agriculture and Biology, Shanghai Jiaotong University; Shanghai Key Laboratory of Veterinary Biotechnology, 800 Dongchuan Road, Shanghai 200240, P. R. China
| | - Manglai Dugarjaviin
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, P.R. China
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Johnson S, Marker L, Mengersen K, Gordon CH, Melzheimer J, Schmidt-Küntzel A, Nghikembua M, Fabiano E, Henghali J, Wachter B. Modeling the viability of the free-ranging cheetah population in Namibia: an object-oriented Bayesian network approach. Ecosphere 2013. [DOI: 10.1890/es12-00357.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Detection of feline coronavirus in cheetah (Acinonyx jubatus) feces by reverse transcription-nested polymerase chain reaction in cheetahs with variable frequency of viral shedding. J Zoo Wildl Med 2013; 43:776-86. [PMID: 23272344 DOI: 10.1638/2011-0110r1.1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Cheetahs (Acinonyx jubatus) are a highly threatened species because of habitat loss, human conflict, and high prevalence of disease in captivity. An epidemic of feline infectious peritonitis and concern for spread of infectious disease resulted in decreased movement of cheetahs between U.S. zoological facilities for managed captive breeding. Identifying the true feline coronavirus (FCoV) infection status of cheetahs is challenging because of inconsistent correlation between seropositivity and fecal viral shedding. Because the pattern of fecal shedding of FCoV is unknown in cheetahs, this study aimed to assess the frequency of detectable fecal viral shedding in a 30-day period and to determine the most efficient fecal sampling strategy to identify cheetahs shedding FCoV. Fecal samples were collected from 16 cheetahs housed at seven zoological facilities for 30 to 46 consecutive days; the samples were evaluated for the presence of FCoV by reverse transcription-nested polymerase chain reaction (RT-nPCR). Forty-four percent (7/16) of cheetahs had detectable FCoV in feces, and the proportion of positive samples for individual animals ranged from 13 to 93%. Cheetahs shed virus persistently, intermittently, or rarely over 30-46 days. Fecal RT-nPCR results were used to calculate the probability of correctly identifying a cheetah known to shed virus given multiple hypothetical fecal collection schedules. The most efficient hypothetical fecal sample collection schedule was evaluation of five individual consecutive fecal samples, resulting in a 90% probability of identifying a known shedder. Demographic and management risk factors were not significantly associated (P < or = 0.05) with fecal viral shedding. Because some cheetahs shed virus intermittently to rarely, fecal sampling schedules meant to identify all known shedders would be impractical with current tests and eradication of virus from the population unreasonable. Managing the captive population as endemically infected with FCoV may be a more feasible approach.
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Dalton DL, Charruau P, Boast L, Kotzé A. Social and genetic population structure of free-ranging cheetah in Botswana: implications for conservation. EUR J WILDLIFE RES 2013. [DOI: 10.1007/s10344-013-0692-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Muya SM, Bruford MW, Muigai AWT, Osiemo ZB, Mwachiro E, Okita-Ouma B, Goossens B. Substantial molecular variation and low genetic structure in Kenya’s black rhinoceros: implications for conservation. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0256-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Serizawa S, Chambers JK, Une Y. Beta amyloid deposition and neurofibrillary tangles spontaneously occur in the brains of captive cheetahs (Acinonyx jubatus). Vet Pathol 2011; 49:304-12. [PMID: 21712514 DOI: 10.1177/0300985811410719] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Alzheimer disease is a dementing disorder characterized pathologically by Aβ deposition, neurofibrillary tangles, and neuronal loss. Although aged animals of many species spontaneously develop Aβ deposits, only 2 species (chimpanzee and wolverine) have been reported to develop Aβ deposits and neurofibrillary tangles in the same individual. Here, the authors demonstrate the spontaneous occurrence of Aβ deposits and neurofibrillary tangles in captive cheetahs (Acinonyx jubatus). Among 22 cheetahs examined in this study, Aβ deposits were observed in 13. Immunostaining (AT8) revealed abnormal intracellular tau immunoreactivity in 10 of the cheetahs with Aβ deposits, and they were mainly distributed in the parahippocampal cortex and CA1 in a fashion similar to that in human patients with Alzheimer disease. Ultrastructurally, bundles of straight filaments filled the neuronal somata and axons, consistent with tangles. Interestingly, 2 of the cheetahs with the most severe abnormal tau immunoreactivity showed clinical cognitive dysfunction. The authors conclude that cheetahs spontaneously develop age-related neurodegenerative disease with pathologic changes similar to Alzheimer disease.
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Affiliation(s)
- S Serizawa
- Laboratory of Veterinary Pathology, School of Veterinary Medicine, Azabu University, 1-17-71, Fuchinobe, Chuo-ku, Sagamihara, Kanagawa, 252-5201, Japan
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Castro-Prieto A, Wachter B, Sommer S. Cheetah paradigm revisited: MHC diversity in the world's largest free-ranging population. Mol Biol Evol 2011; 28:1455-68. [PMID: 21183613 PMCID: PMC7187558 DOI: 10.1093/molbev/msq330] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
For more than two decades, the cheetah (Acinonyx jubatus) has been considered a paradigm of disease vulnerability associated with low genetic diversity, particularly at the immune genes of the major histocompatibility complex (MHC). Cheetahs have been used as a classic example in numerous conservation genetics textbooks as well as in many related scientific publications. However, earlier studies used methods with low resolution to quantify MHC diversity and/or small sample sizes. Furthermore, high disease susceptibility was reported only for captive cheetahs, whereas free-ranging cheetahs show no signs of infectious diseases and a good general health status. We examined whether the diversity at MHC class I and class II-DRB loci in 149 Namibian cheetahs was higher than previously reported using single-strand conformation polymorphism analysis, cloning, and sequencing. MHC genes were examined at the genomic and transcriptomic levels. We detected ten MHC class I and four class II-DRB alleles, of which nine MHC class I and all class II-DRB alleles were expressed. Phylogenetic analyses and individual genotypes suggested that the alleles belong to four MHC class I and three class II-DRB putative loci. Evidence of positive selection was detected in both MHC loci. Our study indicated that the low number of MHC class I alleles previously observed in cheetahs was due to a smaller sample size examined. On the other hand, the low number of MHC class II-DRB alleles previously observed in cheetahs was further confirmed. Compared with other mammalian species including felids, cheetahs showed low levels of MHC diversity, but this does not seem to influence the immunocompetence of free-ranging cheetahs in Namibia and contradicts the previous conclusion that the cheetah is a paradigm species of disease vulnerability.
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Affiliation(s)
| | - Bettina Wachter
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Simone Sommer
- Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
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30
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TOKARSKA M, PERTOLDI C, KOWALCZYK R, PERZANOWSKI K. Genetic status of the European bison Bison bonasus after extinction in the wild and subsequent recovery. Mamm Rev 2011. [DOI: 10.1111/j.1365-2907.2010.00178.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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31
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Charruau P, Fernandes C, Orozco-Terwengel P, Peters J, Hunter L, Ziaie H, Jourabchian A, Jowkar H, Schaller G, Ostrowski S, Vercammen P, Grange T, Schlötterer C, Kotze A, Geigl EM, Walzer C, Burger PA. Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates. Mol Ecol 2011; 20:706-24. [PMID: 21214655 PMCID: PMC3531615 DOI: 10.1111/j.1365-294x.2010.04986.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.
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Affiliation(s)
- P Charruau
- Department of Biomedical Sciences, Institute of Population Genetics, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
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32
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Affiliation(s)
- Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20851-5635, USA.
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33
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Michalczyk L, Martin OY, Millard AL, Emerson BC, Gage MJG. Inbreeding depresses sperm competitiveness, but not fertilization or mating success in male Tribolium castaneum. Proc Biol Sci 2010; 277:3483-91. [PMID: 20554548 DOI: 10.1098/rspb.2010.0514] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As populations decline to levels where reproduction among close genetic relatives becomes more probable, subsequent increases in homozygous recessive deleterious expression and/or loss of heterozygote advantage can lead to inbreeding depression. Here, we measure how inbreeding across replicate lines of the flour beetle Tribolium castaneum impacts on male reproductive fitness in the absence or presence of male-male competition. Effects on male evolution from mating pattern were removed by enforcing monogamous mating throughout. After inbreeding across eight generations, we found that male fertility in the absence of competition was unaffected. However, we found significant inbreeding depression of sperm competitiveness: non-inbred males won 57 per cent of fertilizations in competition, while inbred equivalents only sired 42 per cent. We also found that the P(2) 'offence' role in sperm competition was significantly more depressed under inbreeding than sperm 'defence' (P(1)). Mating behaviour did not explain these differences, and there was no difference in the viability of offspring sired by inbred or non-inbred males. Sperm length variation was significantly greater in the ejaculates of inbred males. Our results show that male ability to achieve normal fertilization success was not depressed under strong inbreeding, but that inbreeding depression in these traits occurred when conditions of sperm competition were generated.
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Affiliation(s)
- Lukasz Michalczyk
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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34
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Lockyear K, Waddell W, Goodrowe K, MacDonald S. Retrospective investigation of captive red wolf reproductive success in relation to age and inbreeding. Zoo Biol 2009; 28:214-29. [DOI: 10.1002/zoo.20224] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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35
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Kruckenhauser L, Miller WJ, Preleuthner M, Pinsker W. Differentiation of Alpine marmot populations traced by DNA fingerprinting. J ZOOL SYST EVOL RES 2009. [DOI: 10.1111/j.1439-0469.1997.tb00416.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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36
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Preserving genes: a model of the maintenance of genetic variation in a metapopulation under frequency-dependent selection. Genet Res (Camb) 2009. [DOI: 10.1017/s0016672300033267] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SummaryUnderstanding how genetic variability is maintained in natural populations is of both theoretical and practical interest. In particular, the subdivision of populations into demes linked by low levels of migration has been suggested to play an important role. But the maintenance of genetic variation in populations is also often linked to the maintenance of sexual reproduction: any force that acts to maintain sex should also act to maintain variation. One theory for the maintenance of sex, the Red Queen, states that sex and variation are maintained by antagonistic coevolutionary interactions – especially those between hosts and their harmful parasites – that give rise to negative frequency-dependent selection. In this paper I present a model to examine the relationships between population subdivision, negative frequency-dependent selection due to parasites, the maintenance of sex, and the preservation of alleles from fixation. The results show strong interactions between migration rates, negative frequency-dependent selection, and the maintenance of variability for sexual and asexual populations.
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37
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Wójcik JM, Kawałko A, Tokarska M, Jaarola M, Vallenback P, Pertoldi C. Post-bottleneck mtDNA diversity in a free-living population of European bison: implications for conservation. J Zool (1987) 2009. [DOI: 10.1111/j.1469-7998.2008.00515.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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38
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Kotze A, Ehlers K, Cilliers D, Grobler J. The power of resolution of microsatellite markers and assignment tests to determine the geographic origin of cheetah (Acinonyx jubatus) in Southern Africa. Mamm Biol 2008. [DOI: 10.1016/j.mambio.2007.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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39
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Pecon-Slattery J, Troyer JL, Johnson WE, O'Brien SJ. Evolution of feline immunodeficiency virus in Felidae: implications for human health and wildlife ecology. Vet Immunol Immunopathol 2008; 123:32-44. [PMID: 18359092 PMCID: PMC2774529 DOI: 10.1016/j.vetimm.2008.01.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Genetic analyses of feline immunodeficiency viruses provide significant insights on the worldwide distribution and evolutionary history of this emerging pathogen. Large-scale screening of over 3000 samples from all species of Felidae indicates that at least some individuals from most species possess antibodies that cross react to FIV. Phylogenetic analyses of genetic variation in the pol-RT gene demonstrate that FIV lineages are species-specific and suggest that there has been a prolonged period of viral-host co-evolution. The clinical effects of FIV specific to species other than domestic cat are controversial. Comparative genomic analyses of all full-length FIV genomes confirmed that FIV is host specific. Recently sequenced lion subtype E is marginally more similar to Pallas cat FIV though env is more similar to that of domestic cat FIV, indicating a possible recombination between two divergent strains in the wild. Here we review global patterns of FIV seroprevalence and endemnicity, assess genetic differences within and between species-specific FIV strains, and interpret these with patterns of felid speciation to propose an ancestral origin of FIV in Africa followed by interspecies transmission and global dissemination to Eurasia and the Americas. Continued comparative genomic analyses of full-length FIV from all seropositive animals, along with whole genome sequence of host species, will greatly advance our understanding of the role of recombination, selection and adaptation in retroviral emergence.
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Affiliation(s)
- Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute-Frederick, Frederick, MD 21702, United States.
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40
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STACY JOHNERIK, REFSETH UNNHILDE, THORESEN MARIANNE, IMS ROLFANKER, STENSETH NILSCHR, JAKOBSEN KJETILLS. Genetic variability among root voles (Microtus oeconomus) from different geographic regions: populations can be distinguished by DNA fingerprinting. Biol J Linn Soc Lond 2008. [DOI: 10.1111/j.1095-8312.1994.tb00990.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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Marker LL, Pearks Wilkerson AJ, Sarno RJ, Martenson J, Breitenmoser-Würsten C, O'Brien SJ, Johnson WE. Molecular genetic insights on cheetah (Acinonyx jubatus) ecology and conservation in Namibia. ACTA ACUST UNITED AC 2007; 99:2-13. [PMID: 17982159 PMCID: PMC7109834 DOI: 10.1093/jhered/esm081] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The extent and geographic patterns of molecular genetic diversity of the largest remaining free-ranging cheetah population were described in a survey of 313 individuals from throughout Namibia. Levels of relatedness, including paternity/maternity (parentage), were assessed across all individuals using 19 polymorphic microsatellite loci, and unrelated cheetahs (n = 89) from 7 regions were genotyped at 38 loci to document broad geographical patterns. There was limited differentiation among regions, evidence that this is a generally panmictic population. Measures of genetic variation were similar among all regions and were comparable with Eastern African cheetah populations. Parentage analyses confirmed several observations based on field studies, including 21 of 23 previously hypothesized family groups, 40 probable parent/offspring pairs, and 8 sibling groups. These results also verified the successful integration and reproduction of several cheetahs following natural dispersal or translocation. Animals within social groups (family groups, male coalitions, or sibling groups) were generally related. Within the main study area, radio-collared female cheetahs were more closely interrelated than similarly compared males, a pattern consistent with greater male dispersal. The long-term maintenance of current patterns of genetic variation in Namibia depends on retaining habitat characteristics that promote natural dispersal and gene flow of cheetahs.
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Affiliation(s)
- Laurie L Marker
- Cheetah Conservation Fund, PO Box 1755, Otjiwarongo, Namibia
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42
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Milot E, Weimerskirch H, Duchesne P, Bernatchez L. Surviving with low genetic diversity: the case of albatrosses. Proc Biol Sci 2007; 274:779-87. [PMID: 17251114 PMCID: PMC2093973 DOI: 10.1098/rspb.2006.0221] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Low genetic diversity is predicted to negatively impact species viability and has been a central concern for conservation. In contrast, the possibility that some species may thrive in spite of a relatively poor diversity has received little attention. The wandering and Amsterdam albatrosses (Diomedea exulans and Diomedea amsterdamensis) are long-lived seabirds standing at an extreme along the gradient of life strategies, having traits that may favour inbreeding and low genetic diversity. Divergence time of the two species is estimated at 0.84 Myr ago from cytochrome b data. We tested the hypothesis that both albatrosses inherited poor genetic diversity from their common ancestor. Within the wandering albatross, per cent polymorphic loci and expected heterozygosity at amplified fragment length polymorphisms were approximately one-third of the minimal values reported in other vertebrates. Genetic diversity in the Amsterdam albatross, which is recovering from a severe bottleneck, was about twice as low as in the wandering albatross. Simulations supported the hypothesis that genetic diversity in albatrosses was already depleted prior to their divergence. Given the generally high breeding success of these species, it is likely that they are not suffering much from their impoverished diversity. Whether albatrosses are unique in this regard is unknown, but they appear to challenge the classical view about the negative consequences of genetic depletion on species survival.
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Affiliation(s)
- Emmanuel Milot
- Département de biologie, Québec Océan, Université Laval, Québec, Canada G1K 7P4.
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43
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Stow A, Zenger K, Briscoe D, Gillings M, Peddemors V, Otway N, Harcourt R. Isolation and genetic diversity of endangered grey nurse shark (Carcharias taurus) populations. Biol Lett 2007; 2:308-11. [PMID: 17148390 PMCID: PMC1618890 DOI: 10.1098/rsbl.2006.0441] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Anthropogenic impacts are believed to be the primary threats to the eastern Australian population of grey nurse sharks (Carcharias taurus), which is listed as critically endangered, and the most threatened population globally. Analyses of 235 polymorphic amplified fragment length polymorphisms (AFLP) loci and 700 base pairs of mitochondrial DNA control region provide the first account of genetic variation and geographical partitioning (east and west coasts of Australia, South Africa) in C. taurus. Assignment tests, analysis of relatedness and Fst values all indicate that the Australian populations are isolated from South Africa, with negligible migration between the east and west Australian coasts. There are significant differences in levels of genetic variation among regions. Australian C. taurus, particularly the eastern population, has significantly less AFLP variation than the other sampling localities. Further, the eastern Australian sharks possess only a single mitochondrial haplotype, also suggesting a small number of founding individuals. Therefore, historical, rather than anthropogenic processes most likely account for their depauperate genetic variation. These findings have implications for the viability of the eastern Australian population of grey nurse sharks.
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Affiliation(s)
- Adam Stow
- Macquarie University, Department of Biological Sciences, Sydney, NSW 2109, Australia.
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Saarma U, Ho SYW, Pybus OG, Kaljuste M, Tumanov IL, Kojola I, Vorobiev AA, Markov NI, Saveljev AP, Valdmann H, Lyapunova EA, Abramov AV, Männil P, Korsten M, Vulla E, Pazetnov SV, Pazetnov VS, Putchkovskiy SV, Rõkov AM. Mitogenetic structure of brown bears (Ursus arctos L.) in northeastern Europe and a new time frame for the formation of European brown bear lineages. Mol Ecol 2006; 16:401-13. [PMID: 17217353 DOI: 10.1111/j.1365-294x.2006.03130.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We estimated the phylogenetic relationships of brown bear maternal haplotypes from countries of northeastern Europe (Estonia, Finland and European Russia), using sequences of mitochondrial DNA (mtDNA) control region of 231 bears. Twenty-five mtDNA haplotypes were identified. The brown bear population in northeastern Europe can be divided into three haplogroups: one with bears from all three countries, one with bears from Finland and Russia, and the third composed almost exclusively of bears from European Russia. Four haplotypes from Finland and European Russia matched exactly with haplotypes from Slovakia, suggesting the significance of the current territory of Slovakia in ancient demographic processes of brown bears. Based on the results of this study and those from the recent literature, we hypothesize that the West Carpathian Mountains have served either as one of the northernmost refuge areas or as an important movement corridor for brown bears of the Eastern lineage towards northern Europe during or after the last ice age. Bayesian analyses were performed to investigate the temporal framework of brown bear lineages in Europe. The molecular clock was calibrated using Beringian brown bear sequences derived from radiocarbon-dated ancient samples, and the estimated mutation rate was 29.8% (13.3%-47.6%) per million years. The whole European population and Western and Eastern lineages formed about 175,000, 70,000 and 25,000 years before present, respectively. Our approach to estimating the time frame of brown bear evolution demonstrates the importance of using an appropriate mutation rate, and this has implications for other studies of Pleistocene populations.
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Affiliation(s)
- Urmas Saarma
- Department of Integrative Zoology, Institute of Zoology and Hydrobiology, University of Tartu, Vanemuise 46, 51014 Tartu, Estonia.
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Roldan ERS, Gomendio M, Garde JJ, Espeso G, Ledda S, Berlinguer F, del Olmo A, Soler AJ, Arregui L, Crespo C, González R. Inbreeding and Reproduction in Endangered Ungulates: Preservation of Genetic Variation through the Organization of Genetic Resource Banks. Reprod Domest Anim 2006; 41 Suppl 2:82-92. [PMID: 16984472 DOI: 10.1111/j.1439-0531.2006.00772.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is a constant increase in the number of species suffering marked reductions in population size. This reduction in size and the lack of genetic flow may lead to a decrease in genetic variability and to matings between close relatives (i.e. inbreeding) with an ensuing reduction in fitness. It is thus important to understand the mechanism underlying the deleterious effects of inbreeding and to develop reproductive biotechnologies that will allow the reduction of inbreeding depression by facilitating gene exchange between populations. The study of three endangered species of gazelles, Cuvier's gazelle (Gazella cuvieri), Mohor gazelle (Gazella dama mhorr) and dorcas gazelle (Gazella dorcas neglecta) has revealed that inbreeding negatively affects several semen parameters (motility, sperm morphology, acrosome integrity). Semen cryopreservation has been achieved in the three species but success varies depending on the diluent employed and the level of inbreeding. Artificial insemination of Mohor gazelles have led to the birth of the first gazelle born using frozen-thawed semen but improvements are needed before this technology can be applied on a routine basis for the genetic management of the populations. Collection of oocytes after ovarian stimulation, followed by in vitro maturation, fertilization and culture has met with some initial success in the Mohor gazelle. These, together with other reproductive technologies, will offer an invaluable help in preserving the maximum of genetic diversity of these and related endangered ungulate species.
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Affiliation(s)
- E R S Roldan
- Grupo de Ecología y Biología de la Reproducción, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain.
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O’Brien SJ, Troyer JL, Roelke M, Marker L, Pecon-Slattery J. Plagues and adaptation: Lessons from the Felidae models for SARS and AIDS. BIOLOGICAL CONSERVATION 2006; 131:255-267. [PMID: 32226081 PMCID: PMC7096731 DOI: 10.1016/j.biocon.2006.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Research studies of infectious disease outbreaks in wild species of the cat family Felidae have revealed unusual details regarding forces that shape population survival and genetic resistance in these species. A highly virulent feline coronavirus epidemic in African cheetahs, a disease model for human SARS, illustrates the critical role of ancestral population genetic variation. Widespread prevalence of species specific feline immunodeficiency virus (FIV), a relative of HIV-AIDS, occurs with little pathogenesis in felid species, except in domestic cats, suggesting immunological adaptation in species where FIV is endemic. Resolving the interaction of host and pathogen genomes can shed new light on the process of disease outbreak in wildlife and in humankind. The role of disease in endangered populations and species is difficult to access as opportunities to monitor outbreaks in natural populations are limited. Conservation management may benefit greatly from advances in molecular genetic tools developed for human biomedical research to assay the biodiversity of both host species and emerging pathogen. As these examples illustrate, strong parallels exist between disease in human and endangered wildlife and argue for an integration of the research fields of comparative genomics, infectious disease, epidemiology, molecular genetics and population biology for an effective proactive conservation approach.
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Affiliation(s)
- Stephen J. O’Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 21-105, Frederick, MD 21702, USA
| | - Jennifer L. Troyer
- Laboratory of Genomic Diversity, SAIC-Frederick, NCI-Frederick, Frederick MD USA
| | - Melody Roelke
- Laboratory of Genomic Diversity, SAIC-Frederick, NCI-Frederick, Frederick MD USA
| | - Laurie Marker
- Cheetah Conservation Fund, Namibia, Southwest Africa
| | - Jill Pecon-Slattery
- Laboratory of Genomic Diversity, National Cancer Institute, Building 560, Room 21-105, Frederick, MD 21702, USA
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Abstract
Advances in population and quantitative genomics, aided by the computational algorithms that employ genetic theory and practice, are now being applied to biological questions that surround free-ranging species not traditionally suitable for genetic enquiry. Here we review how applications of molecular genetic tools have been used to describe the natural history, present status, and future disposition of wild cat species. Insight into phylogenetic hierarchy, demographic contractions, geographic population substructure, behavioral ecology, and infectious diseases have revealed strategies for survival and adaptation of these fascinating predators. Conservation, stabilization, and management of the big cats are important areas that derive benefit from the genome resources expanded and applied to highly successful species, imperiled by an expanding human population.
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Affiliation(s)
- Stephen J O'Brien
- Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA.
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Laikre L, Prodöhl PA, Jorde PE, Ryman N. Genetic Variability at Minisatellite and Allozyme Loci in Brown Trout (Salmo trutta)-A Comparison. Hereditas 2004. [DOI: 10.1111/j.1601-5223.1995.00191.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Drake GJC, Kennedy LJ, Auty HK, Ryvar R, Ollier WER, Kitchener AC, Freeman AR, Radford AD. The use of reference strand-mediated conformational analysis for the study of cheetah (Acinonyx jubatus) feline leucocyte antigen class II DRB polymorphisms. Mol Ecol 2004; 13:221-9. [PMID: 14653802 DOI: 10.1046/j.1365-294x.2003.02027.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
There is now considerable evidence to suggest the cheetah (Acinonyx jubatus) has limited genetic diversity. However, the extent of this and its significance to the fitness of the cheetah population, both in the wild and captivity, is the subject of some debate. This reflects the difficulty associated with establishing a direct link between low variability at biologically significant loci and deleterious aspects of phenotype in this, and other, species. Attempts to study one such region, the feline leucocyte antigen (FLA), are hampered by a general reliance on cloning and sequencing which is expensive, labour-intensive, subject to PCR artefact and always likely to underestimate true variability. In this study we have applied reference strand-mediated conformational analysis (RSCA) to determine the FLA-DRB phenotypes of 25 cheetahs. This technique was rapid, repeatable and less prone to polymerase chain reaction (PCR)-induced sequence artefacts associated with cloning. Individual cheetahs were shown to have up to three FLA-DRB genes. A total of five alleles were identified (DRB*ha14-17 and DRB*gd01) distributed among four genotypes. Fifteen cheetahs were DRB*ha14/ha15/ha16/ha17, three were DRB*ha15/ha16/ha17, six were DRB*ha14/ha16/ha17 and one was DRB*ha14/ha15/ha16/ha17/gd01. Sequence analysis of DRB*gd01 suggested it was a recombinant of DRB*ha16 and DRB*ha17. Generation of new alleles is difficult to document, and the clear demonstration of such an event is unusual. This study confirms further the limited genetic variability of the cheetah at a biologically significant region. RSCA will facilitate large-scale studies that will be needed to correlate genetic diversity at such loci with population fitness in the cheetah and other species.
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Affiliation(s)
- G J C Drake
- University of Liverpool, Veterinary Teaching Hospital, Leahurst, Chester High Road, Neston, CH64 7TE, UK
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