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Sitam FT, Salgado‐Lynn M, Denel A, Panjang E, McEwing R, Lightson A, Ogden R, Maruji NA, Yahya NK, Ngau C, Mohd Kulaimi NA, Ithnin H, Rovie‐Ryan J, Abu Bakar MS, Ewart KM. Phylogeography of the Sunda pangolin, Manis javanica: Implications for taxonomy, conservation management and wildlife forensics. Ecol Evol 2023; 13:e10373. [PMID: 37593756 PMCID: PMC10427774 DOI: 10.1002/ece3.10373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 08/19/2023] Open
Abstract
The Sunda pangolin (Manis javanica) is the most widely distributed Asian pangolin species, occurring across much of Southeast Asia and in southern China. It is classified as Critically Endangered and is one of the most trafficked mammals in the world, which not only negatively impacts wild Sunda pangolin populations but also poses a potential disease risk to other species, including humans and livestock. Here, we aimed to investigate the species' phylogeography across its distribution to improve our understanding of the species' evolutionary history, elucidate any taxonomic uncertainties and enhance the species' conservation genetic management and potential wildlife forensics applications. We sequenced mtDNA genomes from 23 wild Sunda pangolins of known provenance originating from Malaysia to fill sampling gaps in previous studies, particularly in Borneo. To conduct phylogenetic and population genetic analyses of Sunda pangolins across their range, we integrated these newly generated mitochondrial genomes with previously generated mtDNA and nuclear DNA data sets (RAD-seq SNP data). We identified an evolutionarily distinct mtDNA lineage in north Borneo, estimated to be ~1.6 million years divergent from lineages in west/south Borneo and the mainland, comparable to the divergence time from the Palawan pangolin. There appeared to be mitonuclear discordance, with no apparent genetic structure across Borneo based on analysis of nuclear SNPs. These findings are consistent with the 'out of Borneo hypothesis', whereby Sunda pangolins diversified in Borneo before subsequently migrating throughout Sundaland, and/or a secondary contact scenario between mainland and Borneo. We have elucidated possible taxonomic issues in the Sunda/Palawan pangolin complex and highlight the critical need for additional georeferenced samples to accurately apportion its range-wide genetic variation into appropriate taxonomic and conservation units. Additionally, these data have improved forensic identification testing involving these species and permit the implementation of geographic provenance testing in some scenarios.
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Affiliation(s)
- Frankie T. Sitam
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Milena Salgado‐Lynn
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
- Organisms and Environment Division, Cardiff School of BiosciencesCardiff UniversityCardiffUK
| | - Azroie Denel
- Sarawak Forestry Corporation (SFC)KuchingMalaysia
| | - Elisa Panjang
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Organisms and Environment Division, Cardiff School of BiosciencesCardiff UniversityCardiffUK
| | | | | | - Rob Ogden
- TRACE Wildlife Forensics NetworkEdinburghUK
- Royal (Dick) School of Veterinary Studies and the Roslin InstituteUniversity of EdinburghEdinburghUK
| | - Nur Alwanie Maruji
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
- Sabah Wildlife Department (SWD)Kota KinabaluMalaysia
| | - Nurhartini Kamalia Yahya
- Danau Girang Field Centre (DGFC)Kota KinabaluMalaysia
- Wildlife Health, Genetic and Forensic Laboratory (WHGFL)Kota KinabaluMalaysia
| | - Cosmas Ngau
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Noor Azleen Mohd Kulaimi
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | - Hartini Ithnin
- Department of Wildlife and National Parks (DWNP/PERHILITAN)National Wildlife Forensic Laboratory (NWFL)Kuala LumpurMalaysia
| | | | | | - Kyle M. Ewart
- TRACE Wildlife Forensics NetworkEdinburghUK
- School of Life and Environmental SciencesUniversity of SydneySydneyNew South WalesAustralia
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Edwards SV, Tonini JFR, Mcinerney N, Welch C, Beerli P. Multilocus phylogeography, population genetics and niche evolution of Australian brown and black-tailed treecreepers (Aves: Climacteris). Biol J Linn Soc Lond 2023. [DOI: 10.1093/biolinnean/blac144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Abstract
The Carpentarian barrier across north-eastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modelling of brown and black-tailed treecreepers (Climacteris picumnus and Climacteris melanurus), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (Fst = 0.91), and revealed a signature of a recent selective sweep in C. picumnus. A variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7–2.8 Mya. Palaeoecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the past ~600 kyr and that the area of interspecific range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.
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Affiliation(s)
- Scott V Edwards
- Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
- Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
| | - João F R Tonini
- Museum of Comparative Zoology, Harvard University , Cambridge, MA 02138 , USA
- Department of Organismic and Evolutionary Biology, Harvard University , Cambridge, MA 02138 , USA
- Department of Biology, University of Richmond , Richmond, VA 23217 , USA
| | - Nancy Mcinerney
- Smithsonian's National Zoo and Conservation Biology Institute , NW, Washington, DC 20008 , USA
| | - Corey Welch
- Department of Biology and Burke Museum, University of Washington , Seattle, WA 98195 , USA
- STEM Scholars Program, Student Innovation Center, Iowa State University , Ames, IA 50011 , USA
| | - Peter Beerli
- Department of Scientific Computing, Florida State University, Florida State University , Tallahassee, FL 32306 , USA
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A forensically validated genetic toolkit for the species and lineage identification of the highly trafficked shingleback lizard (Tiliqua rugosa). Forensic Sci Int Genet 2023; 62:102784. [PMID: 36265334 DOI: 10.1016/j.fsigen.2022.102784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 01/15/2023]
Abstract
Shingleback lizards (Tiliqua rugosa) are among the most trafficked native fauna from Australia in the illegal pet trade. There are four morphologically recognised subspecies of shinglebacks, all with differing overseas market values. Shinglebacks from different geographic locales are often trafficked and housed together, which may complicate identifying the State jurisdiction where the poaching event occurred. Additionally, shinglebacks can be housed and trafficked with other species within the same genus, which may complicate DNA analysis, especially in scenarios where indirect evidence (e.g. swabs, faeces) is taken for analysis. In this study, a forensic genetic toolkit was designed and validated to target shingleback DNA for species identification and geographic origin. To do this, field sampling across Australia was conducted to expand the phylogeographic sampling of shinglebacks across their species range and include populations suspected to be poaching hotspots. A commonly used universal reptile primer set (ND4/LEU) was then validated for use in forensic casework related to the genus Tiliqua. Two additional ND4 primer sets were designed and validated. The first primer set was designed and demonstrated to preferentially amplify an ∼510 bp region of the genus Tiliqua over other reptiles and builds on existing data to expand the available phylogeographic database. The second primer set was designed and demonstrated to solely amplify an ∼220 bp region of T. rugosa ND4 over any other reptile species. Through the validation process, all primers were demonstrated to amplify T. rugosa DNA from a variety of sample types (e.g. degraded, low quality and mixed). Two of the primer sets were able to distinguish the genetic lineage of T. rugosa from the phylogeographic database. This work provides the first forensically validated toolkit and phylogeographic genetic database for Squatmate lizards.
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Ewart KM, Johnson RN, Joseph L, Ogden R, Frankham GJ, Lo N. Phylogeography of the iconic Australian pink cockatoo, Lophochroa leadbeateri. Biol J Linn Soc Lond 2021. [DOI: 10.1093/biolinnean/blaa225] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The pink cockatoo (Lophochroa leadbeateri; or Major Mitchell’s cockatoo) is one of Australia’s most iconic bird species. Two subspecies based on morphology are separated by a biogeographical divide, the Eyrean Barrier. Testing the genetic basis for this subspecies delineation, clarifying barriers to gene flow and identifying any cryptic genetic diversity will likely have important implications for conservation and management. Here, we used genome-wide single nucleotide polymorphisms (SNPs) and mitochondrial DNA data to conduct the first range-wide genetic assessment of the species. The aims were to investigate the phylogeography of the pink cockatoo, to characterize conservation units and to reassess subspecies boundaries. We found consistent but weak genetic structure between the two subspecies based on nuclear SNPs. However, phylogenetic analysis of nuclear SNPs and mitochondrial DNA sequence data did not recover reciprocally monophyletic groups, indicating incomplete evolutionary separation between the subspecies. Consequently, we have proposed that the two currently recognized subspecies be treated as separate management units rather than evolutionarily significant units. Given that poaching is suspected to be a threat to this species, we assessed the utility of our data for wildlife forensic applications. We demonstrated that a subspecies identification test could be designed using as few as 20 SNPs.
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Affiliation(s)
- Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Rebecca N Johnson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, ACT, Australia
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Greta J Frankham
- Australian Centre for Wildlife Genomics, Australian Museum Research Institute, Sydney, NSW, Australia
- Centre for Forensic Science, University of Technology Sydney, Broadway, NSW, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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Hosegood J, Humble E, Ogden R, de Bruyn M, Creer S, Stevens GMW, Abudaya M, Bassos-Hull K, Bonfil R, Fernando D, Foote AD, Hipperson H, Jabado RW, Kaden J, Moazzam M, Peel LR, Pollett S, Ponzo A, Poortvliet M, Salah J, Senn H, Stewart JD, Wintner S, Carvalho G. Phylogenomics and species delimitation for effective conservation of manta and devil rays. Mol Ecol 2020; 29:4783-4796. [PMID: 33164287 DOI: 10.1111/mec.15683] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023]
Abstract
Practical biodiversity conservation relies on delineation of biologically meaningful units. Manta and devil rays (Mobulidae) are threatened worldwide, yet morphological similarities and a succession of recent taxonomic changes impede the development of an effective conservation strategy. Here, we generate genome-wide single nucleotide polymorphism (SNP) data from a geographically and taxonomically representative set of manta and devil ray samples to reconstruct phylogenetic relationships and evaluate species boundaries under the general lineage concept. We show that nominal species units supported by alternative data sources constitute independently evolving lineages, and find robust evidence for a putative new species of manta ray in the Gulf of Mexico. Additionally, we uncover substantial incomplete lineage sorting indicating that rapid speciation together with standing variation in ancestral populations has driven phylogenetic uncertainty within Mobulidae. Finally, we detect cryptic diversity in geographically distinct populations, demonstrating that management below the species level may be warranted in certain species. Overall, our study provides a framework for molecular genetic species delimitation that is relevant to wide-ranging taxa of conservation concern, and highlights the potential for genomic data to support effective management, conservation and law enforcement strategies.
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Affiliation(s)
- Jane Hosegood
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Emily Humble
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Edinburgh, UK.,TRACE Wildlife Forensics Network, Edinburgh, UK
| | - Mark de Bruyn
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Simon Creer
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
| | - Guy M W Stevens
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | | | - Kim Bassos-Hull
- Mote Marine Laboratory, The Center for Shark Research, Sarasota, FL, USA
| | | | - Daniel Fernando
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Blue Resources Trust, Colombo, Sri Lanka
| | - Andrew D Foote
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK.,Department of Natural History, Norwegian University of Science and Technology (NTNU), University Museum, Trondheim, Norway
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | | | - Jennifer Kaden
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | | | - Lauren R Peel
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK.,School of Biological Sciences, University of Western Australia, Crawley, WA, Australia.,The Australian Institute of Marine Science, Crawley, WA, Australia.,Save Our Seas Foundation - D'Arros Research Centre, Geneva, Switzerland
| | - Stephen Pollett
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Alessandro Ponzo
- Large Marine Vertebrates Research Institute Philippines, Jagna, Philippines
| | | | - Jehad Salah
- Ministry of Agriculture Directorate General of Fisheries, Gaza City, Palestine
| | - Helen Senn
- RZSS WildGenes Lab, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Joshua D Stewart
- The Manta Trust, Catemwood House, Norwood Lane, Corscombe, Dorset, DT2 0NT, UK
| | - Sabine Wintner
- KwaZulu-Natal Sharks Board, Umhlanga Rocks, South Africa.,School of Life Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Gary Carvalho
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, UK
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