1
|
Kunde MN, Barlow A, Klittich AM, Yakupova A, Patel RP, Fickel J, Förster DW. First mitogenome phylogeny of the sun bear Helarctos malayanus reveals a deep split between Indochinese and Sundaic lineages. Ecol Evol 2023; 13:e9969. [PMID: 37082317 PMCID: PMC10111171 DOI: 10.1002/ece3.9969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 03/04/2023] [Accepted: 03/14/2023] [Indexed: 04/22/2023] Open
Abstract
The sun bear Helarctos malayanus is one of the most endangered ursids, and to date classification of sun bear populations has been based almost exclusively on geographic distribution and morphology. The very few molecular studies focussing on this species were limited in geographic scope. Using archival and non-invasively collected sample material, we have added a substantial number of complete or near-complete mitochondrial genome sequences from sun bears of several range countries of the species' distribution. We here report 32 new mitogenome sequences representing sun bears from Cambodia, Thailand, Peninsular Malaysia, Sumatra, and Borneo. Reconstruction of phylogenetic relationships revealed two matrilines that diverged ~295 thousand years ago: one restricted to portions of mainland Indochina (China, Cambodia, Thailand; "Mainland clade"), and one comprising bears from Borneo, Sumatra, Peninsular Malaysia but also Thailand ("Sunda clade"). Generally recent coalescence times in the mitochondrial phylogeny suggest that recent or historical demographic processes have resulted in a loss of mtDNA variation. Additionally, analysis of our data in conjunction with shorter mtDNA sequences revealed that the Bornean sun bear, classified as a distinct subspecies (H. m. euryspilus), does not harbor a distinctive matriline. Further molecular studies of H. malayanus are needed, which should ideally include data from nuclear loci.
Collapse
Affiliation(s)
- Miriam N. Kunde
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
- School of EnvironmentGriffith UniversityNathan Campus, 170 Kessels Road, NathanBrisbaneQueensland4111Australia
| | - Axel Barlow
- School of Natural SciencesBangor UniversityBangorGwyneddLL57 2DGUK
| | - Achim M. Klittich
- Institute for Biochemistry and BiologyUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476PotsdamGermany
| | - Aliya Yakupova
- Computer Technologies LaboratoryITMO University197101Saint PetersburgRussia
| | - Riddhi P. Patel
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
- Institute for Biochemistry and BiologyUniversity of PotsdamKarl‐Liebknecht‐Str. 24–2514476PotsdamGermany
| | - Daniel W. Förster
- Leibniz Institute for Zoo and Wildlife ResearchAlfred‐Kowalke‐Str. 1710315BerlinGermany
| |
Collapse
|
2
|
von Seth J, Dussex N, Díez-Del-Molino D, van der Valk T, Kutschera VE, Kierczak M, Steiner CC, Liu S, Gilbert MTP, Sinding MHS, Prost S, Guschanski K, Nathan SKSS, Brace S, Chan YL, Wheat CW, Skoglund P, Ryder OA, Goossens B, Götherström A, Dalén L. Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations. Nat Commun 2021; 12:2393. [PMID: 33896938 PMCID: PMC8071806 DOI: 10.1038/s41467-021-22386-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/01/2021] [Indexed: 02/02/2023] Open
Abstract
Small populations are often exposed to high inbreeding and mutational load that can increase the risk of extinction. The Sumatran rhinoceros was widespread in Southeast Asia, but is now restricted to small and isolated populations on Sumatra and Borneo, and most likely extinct on the Malay Peninsula. Here, we analyse 5 historical and 16 modern genomes from these populations to investigate the genomic consequences of the recent decline, such as increased inbreeding and mutational load. We find that the Malay Peninsula population experienced increased inbreeding shortly before extirpation, which possibly was accompanied by purging. The populations on Sumatra and Borneo instead show low inbreeding, but high mutational load. The currently small population sizes may thus in the near future lead to inbreeding depression. Moreover, we find little evidence for differences in local adaptation among populations, suggesting that future inbreeding depression could potentially be mitigated by assisted gene flow among populations.
Collapse
Affiliation(s)
- Johanna von Seth
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - Nicolas Dussex
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| | - David Díez-Del-Molino
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
| | - Verena E Kutschera
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Marcin Kierczak
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Cynthia C Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Shanlin Liu
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - M Thomas P Gilbert
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg, Frankfurt, Germany
- South African National Biodiversity Institute, National Zoological Garden, Pretoria, South Africa
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala, Sweden
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yvonne L Chan
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | | | | | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, CA, USA
| | - Benoit Goossens
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
- Organisms and Environment Division, Cardiff School of Biosciences, Cardiff, UK
- Sustainable Places Research Institute, Cardiff University, Cardiff, UK
- Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
| |
Collapse
|
3
|
Abstract
AbstractConservation genetics can provide data needed by conservation practitioners for their decisions regarding the management of vulnerable or endangered species, such as the sun bear Helarctos malayanus. Throughout its range, the sun bear is threatened by loss and fragmentation of its habitat and the illegal trade of both live bears and bear parts. Sharply declining population numbers and population sizes, and a lack of natural dispersal between populations all threaten the genetic diversity of the remaining populations of this species. In this first population genetics study of sun bears using microsatellite markers, we analyzed 68 sun bear samples from Cambodia to investigate population structure and genetic diversity. We found evidence for two genetically distinct populations in the West and East of Cambodia. Ongoing or recent gene flow between these populations does not appear sufficient to alleviate loss of diversity in these populations, one of which (West Cambodia) is characterized by significant inbreeding. We were able to assign 85% of sun bears of unknown origin to one of the two populations with high confidence (assignment probability ≥ 85%), providing valuable information for future bear reintroduction programs. Further, our results suggest that developed land (mostly agricultural mosaics) acts as a barrier to gene flow for sun bears in Cambodia. We highlight that regional sun bear conservation action plans should consider promoting population connectivity and enforcing wildlife protection of this threatened species.
Collapse
|
4
|
|
5
|
Genetic variation of complete mitochondrial genome sequences of the Sumatran rhinoceros (Dicerorhinus sumatrensis). CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1011-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
6
|
Gippoliti S, Cotterill FPD, Zinner D, Groves CP. Impacts of taxonomic inertia for the conservation of African ungulate diversity: an overview. Biol Rev Camb Philos Soc 2017; 93:115-130. [PMID: 28429851 DOI: 10.1111/brv.12335] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 01/27/2023]
Abstract
We review the state of African ungulate taxonomy over the last 120 years, with an emphasis on the introduction of the polytypic species concept and the discipline's general neglect since the middle of the 20th century. We single out negative consequences of 'orthodox' taxonomy, highlighting numerous cases of neglect of threatened lineages, unsound translocations that led to lineage introgression, and cases of maladaptation to local conditions including parasitic infections. Additionally, several captive breeding programmes have been hampered by chromosome rearrangements caused by involuntary lineage mixing. We advocate that specimen-based taxonomy should regain its keystone role in mammal research and conservation biology, with its scientific values augmented with genomic evidence. While integration with molecular biology, ecology and behaviour is needed for a full understanding of ungulate alpha diversity, we stress that morphological diversity has been neglected despite its tremendous practical importance for some groups of 'utilizers' such as trophy hunters, wildlife tourists and conservationists. We conclude that there is no evidence that purported 'taxonomic inflation' has adverse effects on ungulate conservation: rather, it is taxonomic inertia that has such adverse effects. We stress that sound science, founded on robust taxonomy, should underpin effective sustainable management (hunting, ranching, captive breeding and reintroduction programmes) of this unique African natural resource.
Collapse
Affiliation(s)
- Spartaco Gippoliti
- Società Italiana di Storia della Fauna 'G. Altobello' Viale Liegi 48, 00198, Roma, Italy
| | - Fenton P D Cotterill
- Geoecodynamics Research Hub, Department of Earth Sciences, University of Stellenbosch, Stellenbosch, 7602, South Africa
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, 37077, Göttingen, Germany
| | - Colin P Groves
- School of Archaeology & Anthropology, Australian National University, Canberra, Australia
| |
Collapse
|
7
|
Moodley Y, Russo IRM, Dalton DL, Kotzé A, Muya S, Haubensak P, Bálint B, Munimanda GK, Deimel C, Setzer A, Dicks K, Herzig-Straschil B, Kalthoff DC, Siegismund HR, Robovský J, O’Donoghue P, Bruford MW. Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis). Sci Rep 2017; 7:41417. [PMID: 28176810 PMCID: PMC5296875 DOI: 10.1038/srep41417] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 12/09/2016] [Indexed: 11/09/2022] Open
Abstract
The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species' once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide genetic structure of historic and modern populations using the largest and most geographically representative sample of black rhinoceroses ever assembled. Using both mitochondrial and nuclear datasets, we described a staggering loss of 69% of the species' mitochondrial genetic variation, including the most ancestral lineages that are now absent from modern populations. Genetically unique populations in countries such as Nigeria, Cameroon, Chad, Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer exist. We found that the historic range of the West African subspecies (D. b. longipes), declared extinct in 2011, extends into southern Kenya, where a handful of individuals survive in the Masai Mara. We also identify conservation units that will help maintain evolutionary potential. Our results suggest a complete re-evaluation of current conservation management paradigms for the black rhinoceros.
Collapse
Affiliation(s)
- Yoshan Moodley
- Department of Zoology, University of Venda, Private Bag X5050, Thohoyandou 0950, Republic of South Africa
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Isa-Rita M. Russo
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - Desiré L. Dalton
- National Zoological Gardens of South Africa, 232 Boom Street, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, 205 Nelson Mandela Drive, West Park, Bloemfontein, 9300 South Africa
| | - Antoinette Kotzé
- National Zoological Gardens of South Africa, 232 Boom Street, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, 205 Nelson Mandela Drive, West Park, Bloemfontein, 9300 South Africa
| | - Shadrack Muya
- Department of Zoology, Jomo Kenyatta University of Agriculture and Technology, Kenyatta Avenue, Nairobi, 00200, Kenya
| | - Patricia Haubensak
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Boglárka Bálint
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Gopi K. Munimanda
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Caroline Deimel
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Andrea Setzer
- Konrad Lorenz Institute of Ethology, Department of Integrative Biology and Evolution, University of Veterinary Medicine, Vienna, Austria, Savoyenstr. 1A, 1160 Austria
| | - Kara Dicks
- Department of Biological Sciences, Thomas Building, University of Chester, Chester, CH1 4BJ, United Kingdom
| | | | - Daniela C. Kalthoff
- Swedish Museum of Natural History, Frescativägen 40, Stockholm, 10405, Sweden
| | - Hans R. Siegismund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, DK-2200, Denmark
| | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic
| | - Paul O’Donoghue
- Department of Biological Sciences, Thomas Building, University of Chester, Chester, CH1 4BJ, United Kingdom
| | - Michael W. Bruford
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| |
Collapse
|
8
|
Will current conservation responses save the Critically Endangered Sumatran rhinoceros Dicerorhinus sumatrensis? ORYX 2015. [DOI: 10.1017/s0030605315000472] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractThe Critically Endangered Sumatran rhinoceros Dicerorhinus sumatrensis formerly ranged across South-east Asia. Hunting and habitat loss have made it one of the rarest large mammals and the species faces extinction despite decades of conservation efforts. The number of individuals remaining is unknown as a consequence of inadequate methods and lack of funds for the intensive field work required to estimate the population size of this rare and solitary species. However, all information indicates that numbers are low and declining. A few individuals persist in Borneo, and three tiny populations remain on the Indonesian island of Sumatra and show evidence of breeding. Rhino Protection Units are deployed at all known breeding sites but poaching and a presumed low breeding rate remain major threats. Protected areas have been created for the rhinoceros and other in situ conservation efforts have increased but the species has continued to go locally extinct across its range. Conventional captive breeding has also proven difficult; from a total of 45 Sumatran rhinoceros taken from the wild since 1984 there were no captive births until 2001. Since then only two pairs have been actively bred in captivity, resulting in four births, three by the same pair at the Cincinnati Zoo and one at the Sumatran Rhino Sanctuary in Sumatra, with the sex ratio skewed towards males. To avoid extinction it will be necessary to implement intensive management zones, manage the metapopulation as a single unit, and develop advanced reproductive techniques as a matter of urgency. Intensive census efforts are ongoing in Bukit Barisan Selatan but elsewhere similar efforts remain at the planning stage.
Collapse
|
9
|
Jachowski DS, Kesler DC, Steen DA, Walters JR. Redefining baselines in endangered species recovery. J Wildl Manage 2014. [DOI: 10.1002/jwmg.800] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- David S. Jachowski
- School of Agricultural, Forest, and Environmental Sciences; Clemson University; 258 Lehotsky Hall Clemson SC 29634 USA
| | - Dylan C. Kesler
- Department of Fisheries and Wildlife Sciences; University of Missouri; 302 Natural Resources Building Columbia MO 65211 USA
| | - David A. Steen
- Alabama Natural Heritage Program; Department of Biological Sciences; Auburn University; 1090 South Donahue Drive Auburn AL 36849 USA
| | - Jeffrey R. Walters
- Department of Biological Sciences; Virginia Tech, Blacksburg; 1405 Perry Street VA 24061 USA
| |
Collapse
|
10
|
|