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Panthum T, Ariyaraphong N, Wongloet W, Wattanadilokchatkun P, Laopichienpong N, Rasoarahona R, Singchat W, Ahmad SF, Kraichak E, Muangmai N, Duengkae P, Fukuda Y, Banks S, Temsiripong Y, Ezaz T, Srikulnath K. Preserving Pure Siamese Crocodile Populations: A Comprehensive Approach Using Multi-Genetic Tools. BIOLOGY 2023; 12:1428. [PMID: 37998027 PMCID: PMC10669835 DOI: 10.3390/biology12111428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/04/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023]
Abstract
Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic SNPs. Different analytical approaches were compared to diagnose the level of hybridization when an admixture was present, wherein three individuals had potential backcrossing. Approximately 17.00-26.00% of loci were conserved between the Siamese and saltwater crocodile genomes. Species-diagnostic SNP loci for Siamese and saltwater crocodiles were identified as 8051 loci and 1288 loci, respectively. To validate the species-diagnostic SNP loci, a PCR-based approach was used by selecting 20 SNP loci for PCR primer design, among which 3 loci were successfully able to differentiate the actual species and different hybridization levels. Mitochondrial and nuclear genetic information, including microsatellite genotyping and species-diagnostic DNA markers, were combined as a novel method that can compensate for the limitations of each method. This method enables conservation prioritization before release into the wild, thereby ensuring sustainable genetic integrity for long-term species survival through reintroduction and management programs.
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Affiliation(s)
- Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nattakan Ariyaraphong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Wongsathit Wongloet
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Pish Wattanadilokchatkun
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Nararat Laopichienpong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
| | - Ryan Rasoarahona
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
| | - Ekaphan Kraichak
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Department of Botany, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
| | - Yusuke Fukuda
- Department of Environment, Parks and Water Security, Northern Territory Government, Darwin, NT 0830, Australia;
| | - Sam Banks
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, NT 0909, Australia;
| | | | - Tariq Ezaz
- Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, Faculty of Science and Technology, University of Canberra, Bruce, ACT 2617, Australia;
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; (T.P.); (N.A.); (W.W.); (P.W.); (N.L.); (R.R.); (W.S.); (S.F.A.); (E.K.); (N.M.); (P.D.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Bangkok 10900, Thailand
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2
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Taylor RS. New tools for the recovery of the kākāpō. Nat Ecol Evol 2023; 7:1589-1590. [PMID: 37640764 DOI: 10.1038/s41559-023-02112-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Affiliation(s)
- Rebecca S Taylor
- Landscape Science and Technology Division, Environment and Climate Change Canada, Ottawa, Ontario, Canada.
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Zhang J, Richards ZT, Adam AAS, Chan CX, Shinzato C, Gilmour J, Thomas L, Strugnell JM, Miller DJ, Cooke I. Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum. Mol Biol Evol 2022; 39:msac201. [PMID: 36219871 PMCID: PMC9578555 DOI: 10.1093/molbev/msac201] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral, Acropora digitifera. We show that three genetically distinct populations are present in northwestern Australia, and that their rapid divergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid divergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.
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Affiliation(s)
- Jia Zhang
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
| | - Zoe T Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
- Collections and Research, Western Australian Museum, 49 Kew Street Welshpool, WA 6106, Australia
| | - Arne A S Adam
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Bentley, WA 6102, Australia
| | - Cheong Xin Chan
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Brisbane, QLD 4072, Australia
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo277-8564, Chiba, Japan
| | - James Gilmour
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
| | - Luke Thomas
- Australia Institute of Marine Science, Indian Oceans Marine Research Centre, Crawley, WA, 6009, Australia
- Oceans Graduate School, The UWA Oceans Institute, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jan M Strugnell
- Department of Marine Biology and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Sustainable Fisheries and Aquaculture, James Cook University, Townsville, QLD, 4811, Australia
| | - David J Miller
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, 4811, Australia
- Marine Climate Change Unit, Okinawa Institute of Science and Technology, Onna-son, Okinawa, Japan 904-0495
| | - Ira Cooke
- Department of Molecular and Cell Biology, James Cook University, Townsville, QLD, 4811, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, QLD, 4811, Australia
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Moreno N, Heaton A, Bruening K, Milligan E, Nelson D, Glaberman S, Chiari Y. Hybridization and low genetic diversity in the endangered Alabama red‐bellied turtle (
Pseudemys alabamensis
). Ecol Evol 2022; 12:e8964. [PMID: 35784082 PMCID: PMC9163798 DOI: 10.1002/ece3.8964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 12/14/2022] Open
Abstract
Pseudemys alabamensis is one of the most endangered freshwater turtle species in the United States due to its restricted geographic distribution in coastal Alabama and Mississippi. Populations of P. alabamensis are geographically isolated from one another by land and saltwater, which could act as barriers to gene flow. It is currently unknown how differentiated these populations are from one another and whether they have experienced reductions in population size. Previous work found morphological differences between Alabama and Mississippi populations, suggesting that they may be evolutionarily distinct. Other Pseudemys turtles such as P. concinna and P. floridana occur naturally within the same geographic area as P. alabamensis and are known to hybridize with each other. These more abundant species could threaten the unique genetic identity of P. alabamensis through introgression. In order to evaluate the endangered status of P. alabamensis and the level of hybridization with other species, we used mitochondrial and nuclear microsatellite markers to assess genetic variation within and among populations of P. alabamensis throughout its range and estimate admixture with co‐occurring Pseudemys species. In P. alabamensis, we found no variation in mitochondrial DNA and an excess of homozygosity in microsatellite data. Our results show genetic differentiation between Alabama and Mississippi populations of P. alabamensis, and low estimated breeding sizes and signs of inbreeding for two populations (Fowl River, Alabama and Biloxi, Mississippi). We also found evidence of admixture between P. alabamensis and P. concinna/P. floridana. Based on our results, P. alabamensis is highly endangered throughout its range and threatened by both low population sizes and hybridization. In order to improve the species’ chances of survival, focus should be placed on habitat preservation, maintenance of genetic diversity within both the Mississippi and Alabama populations, and routine population‐monitoring activities such as nest surveillance and estimates of recruitment.
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Affiliation(s)
- Nickolas Moreno
- Department of Biology University of South Alabama Mobile Alabama USA
- Department of Biology George Mason University Fairfax Virginia USA
| | - Andrew Heaton
- Department of Biology University of South Alabama Mobile Alabama USA
- Grand Bay National Estuarine Research Reserve Mississippi Department of Marine Resources Moss Point Mississippi USA
| | - Kaylin Bruening
- Department of Biology University of South Alabama Mobile Alabama USA
| | - Emma Milligan
- Department of Biology University of South Alabama Mobile Alabama USA
| | - David Nelson
- Department of Biology University of South Alabama Mobile Alabama USA
| | - Scott Glaberman
- Department of Environmental Science and Policy George Mason University Fairfax Virginia USA
| | - Ylenia Chiari
- Department of Biology George Mason University Fairfax Virginia USA
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Teixeira TM, Nazareno AG. One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species. FRONTIERS IN PLANT SCIENCE 2021; 12:730258. [PMID: 34630476 PMCID: PMC8496504 DOI: 10.3389/fpls.2021.730258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Intraspecific genetic variation plays a fundamental role in maintaining the evolutionary potential of wild populations. Hence, the assessment of genetic diversity patterns becomes essential to guide biodiversity conservation policies, particularly for threatened species. To inform management strategies for conservation of Mimosa catharinensis - a narrow endemic, critically endangered plant species - we identified 1,497 unlinked SNP markers derived from a reduced representation sequencing method (i.e., double digest restriction site associated DNA sequencing, or ddRADseq). This set of molecular markers was employed to assess intrapopulation genetic parameters and the demographic history of one extremely small population of M. catharinensis (N=33) located in the Brazilian Atlantic Forest. Contrary to what is expected for narrow endemic and threatened species with small population sizes, we observed a moderate level of genetic diversity for M. catharinensis [uH E(0%missing data)=0.205, 95% CI (0.160, 0.250); uH E(30%missing data)=0.233, 95% CI (0.174, 0.292)]. Interestingly, M. catharinensis, which is a lianescent shrub with no indication of seed production for at least two decades, presented high levels of outcrossing [t (0%missing data)=0.883, SE±0.0483; t (30%missing data)=0.909, SE±0.011] and an apparent absence of inbreeding [F (0%missing data)=-0.145, 95% CI (-0.189, -0.101); F (30%missing data)=-0.105, 95% CI (-0.199, -0.011)]. However, the reconstruction of demographic history of M. catharinensis indicated that the population should be suffered a recent bottleneck. Our population genomic study tackles a central issue in evolution and conservation biology and we expect that it will be useful to help safeguard the remaining genetic diversity reported for this unique genetic resource.
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Affiliation(s)
- Thais M. Teixeira
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alison G. Nazareno
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
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Divergence and introgression in small apes, the genus Hylobates, revealed by reduced representation sequencing. Heredity (Edinb) 2021; 127:312-322. [PMID: 34188193 PMCID: PMC8405704 DOI: 10.1038/s41437-021-00452-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 02/06/2023] Open
Abstract
Gibbons of the genus Hylobates, which inhabit Southeast Asia, show great diversity and comprise seven to nine species. Natural hybridisation has been observed in several species contact zones, but the history and extent of hybridisation and introgression in possibly historical and the current contact zones remain unclear. To uncover Hylobates species phylogeny and the extent of introgression in their evolution, genotyping by random amplicon sequencing-direct (GRAS-Di) was applied to 47 gibbons, representing seven Hylobates species/subspecies and two outgroup gibbon species. Over 200,000 autosomal single-nucleotide variant sites were identified. The autosomal phylogeny supported that divergence from the mainland species began ~3.5 million years ago, and subsequently occurred among the Sundaic island species. Significant introgression signals were detected between H. lar and H. pileatus, H. lar and H. agilis and H. albibarbis and H. muelleri, which all are parapatric and form ongoing hybrid zones. Furthermore, the introgression signals were detected in every analysed individual of these species, indicating a relatively long history of hybridisation, which might have affected the entire gene pool. By contrast, signals of introgression were either not detected or doubtful in other species pairs living on different islands, indicating the rarity of hybridisation and introgression, even though the Sundaic islands were connected during the Pliocene and Pleistocene glacial events.
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7
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Baveja P, Garg KM, Chattopadhyay B, Sadanandan KR, Prawiradilaga DM, Yuda P, Lee JGH, Rheindt FE. Using historical genome-wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild. Evol Appl 2021; 14:698-709. [PMID: 33767745 PMCID: PMC7980273 DOI: 10.1111/eva.13149] [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: 06/05/2020] [Accepted: 10/13/2020] [Indexed: 11/29/2022] Open
Abstract
Urgent conservation action for terminally endangered species is sometimes hampered by taxonomic uncertainty, especially in illegally traded animals that are often cross-bred in captivity. To overcome these problems, we used a genomic approach to analyze historical DNA from museum samples across the Asian Pied Starling (Gracupica contra) complex in tropical Asia, a popular victim of the ongoing songbird crisis whose distinct Javan population ("Javan Pied Starling") is extinct in the wild and subject to admixture in captivity. Comparing genomic profiles across the entire distribution, we detected three deeply diverged lineages at the species level characterized by a lack of genomic intermediacy near areas of contact. Our study demonstrates that the use of historical DNA can be instrumental in delimiting species in situations of taxonomic uncertainty, especially when modern admixture may obfuscate species boundaries. Results of our research will enable conservationists to commence a dedicated ex situ breeding program for the Javan Pied Starling, and serve as a blueprint for similar conservation problems involving terminally endangered species subject to allelic infiltration from close congeners.
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Affiliation(s)
- Pratibha Baveja
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Kritika M. Garg
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Institute of Bioinformatics and Applied BiotechnologyBangaloreIndia
| | - Balaji Chattopadhyay
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Keren R. Sadanandan
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Max Planck Institute for OrnithologySeewiesenGermany
| | | | - Pramana Yuda
- Fakultas TeknobiologiUniversitas Atma Jaya YogyakartaYogyakartaIndonesia
| | - Jessica G. H. Lee
- Department of Conservation and ResearchWildlife Reserves SingaporeSingaporeSingapore
| | - Frank E. Rheindt
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
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Morin PA, Archer FI, Avila CD, Balacco JR, Bukhman YV, Chow W, Fedrigo O, Formenti G, Fronczek JA, Fungtammasan A, Gulland FMD, Haase B, Peter Heide-Jorgensen M, Houck ML, Howe K, Misuraca AC, Mountcastle J, Musser W, Paez S, Pelan S, Phillippy A, Rhie A, Robinson J, Rojas-Bracho L, Rowles TK, Ryder OA, Smith CR, Stevenson S, Taylor BL, Teilmann J, Torrance J, Wells RS, Westgate AJ, Jarvis ED. Reference genome and demographic history of the most endangered marine mammal, the vaquita. Mol Ecol Resour 2020; 21:1008-1020. [PMID: 33089966 PMCID: PMC8247363 DOI: 10.1111/1755-0998.13284] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/08/2020] [Accepted: 10/08/2020] [Indexed: 12/12/2022]
Abstract
The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.
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Affiliation(s)
- Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Frederick I Archer
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Catherine D Avila
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Jennifer R Balacco
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Yury V Bukhman
- Regenerative Biology, Morgridge Institute for Research, Madison, WI, USA
| | | | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Julie A Fronczek
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | | | - Bettina Haase
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | | | - Marlys L Houck
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | - Ann C Misuraca
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | | | - Sadye Paez
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA
| | | | - Adam Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Jacqueline Robinson
- Institute for Human Genetics, University of California, San Francisco, CA, USA
| | | | - Teri K Rowles
- Office of Protected Resources, National Marine Fisheries Service, NOAA, Silver Spring, MD, USA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | | | | | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Jonas Teilmann
- Marine Mammal Research, Department of Bioscience, Aarhus University, Roskilde, Denmark
| | | | - Randall S Wells
- Chicago Zoological Society's Sarasota Dolphin Research Program, c/o Mote Marine Laboratory, Sarasota, FL, USA
| | | | - Erich D Jarvis
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, NY, USA.,Howard Hughes Medical Institute, Chevy Chase, MD, USA
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9
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Wu MY, Low GW, Forcina G, van Grouw H, Lee BPYH, Oh RRY, Rheindt FE. Historic and modern genomes unveil a domestic introgression gradient in a wild red junglefowl population. Evol Appl 2020; 13:2300-2315. [PMID: 33005225 PMCID: PMC7513718 DOI: 10.1111/eva.13023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 01/08/2023] Open
Abstract
The red junglefowl Gallus gallus is the ancestor of the domestic chicken and arguably the most important bird species on Earth. Continual gene flow between domestic and wild populations has compromised its gene pool, especially since the last century when human encroachment and habitat loss would have led to increased contact opportunities. We present the first combined genomic and morphological admixture assessment of a native population of red junglefowl, sampled from recolonized parts of its former range in Singapore, partly using whole genomes resequenced from dozens of individuals. Crucially, this population was genomically anchored to museum samples from adjacent Peninsular Malaysia collected ~110-150 years ago to infer the magnitude of modern domestic introgression across individuals. We detected a strong feral-wild genomic continuum with varying levels of domestic introgression in different subpopulations across Singapore. Using a trait scoring scheme, we determined morphological thresholds that can be used by conservation managers to successfully identify individuals with low levels of domestic introgression, and selected traits that were particularly useful for predicting domesticity in genomic profiles. Our study underscores the utility of combined genomic and morphological approaches in population management and suggests a way forward to safeguard the allelic integrity of wild red junglefowl in perpetuity.
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Affiliation(s)
- Meng Yue Wu
- Department of Biological Sciences National University of Singapore Singapore Singapore
| | - Gabriel Weijie Low
- Department of Biological Sciences National University of Singapore Singapore Singapore
- School of Biological Sciences Monash University Clayton Victoria Australia
| | - Giovanni Forcina
- Department of Biological Sciences National University of Singapore Singapore Singapore
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| | - Hein van Grouw
- Bird Group Department of Life Sciences Natural History Museum Herts UK
| | - Benjamin P Y-H Lee
- Wildlife Management Research Wildlife Management Division National Parks Board Singapore Singapore
| | - Rachel Rui Ying Oh
- Centre of Urban Greenery and Ecology National Parks Board Singapore Singapore
- School of Biological Sciences Centre for Biodiversity and Conservation Sciences University of Queensland Brisbane Queensland Australia
| | - Frank E Rheindt
- Department of Biological Sciences National University of Singapore Singapore Singapore
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10
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Sadanandan KR, Low GW, Sridharan S, Gwee CY, Ng EYX, Yuda P, Prawiradilaga DM, Lee JGH, Tritto A, Rheindt FE. The conservation value of admixed phenotypes in a critically endangered species complex. Sci Rep 2020; 10:15549. [PMID: 32968132 PMCID: PMC7511927 DOI: 10.1038/s41598-020-72428-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/17/2020] [Indexed: 11/19/2022] Open
Abstract
In today's environmental crisis, conservationists are increasingly confronted with terminally endangered species whose last few surviving populations may be affected by allelic introgression from closely related species. Yet there is a worrying lack of evidence-based recommendations and solutions for this emerging problem. We analyzed genome-wide DNA markers and plumage variability in a critically endangered insular songbird, the Black-winged Myna (BWM, Acridotheres melanopterus). This species is highly threatened by the illegal wildlife trade, with its wild population numbering in the low hundreds, and its continued survival urgently depending on ex-situ breeding. Its three subspecies occur along a geographic gradient of melanism and are variably interpreted as three species. However, our integrative approach revealed that melanism poorly reflects the pattern of limited genomic differentiation across BWM subspecies. We also uncovered allelic introgression into the most melanistic subspecies, tertius, from the all-black congeneric Javan Myna (A. javanicus), which is native to the same islands. Based on our results, we recommend the establishment of three separate breeding programs to maintain subspecific traits that may confer local adaptation, but with the option of occasional cross-breeding between insurance populations in order to boost genetic diversity and increase overall viability prospects of each breeding program. Our results underscore the importance of evidence-based integrative approaches when determining appropriate conservation units. Given the rapid increase of terminally endangered organisms in need of ex-situ conservation, this study provides an important blueprint for similar programs dealing with phenotypically variable species.
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Affiliation(s)
- Keren R Sadanandan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- Max Planck Institute for Ornithology, 82319, Seewiesen, Germany
| | - Gabriel W Low
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- School of Biological Sciences, Monash University, Clayton, VIC, 3800, Australia
| | - Sheeraja Sridharan
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
- Department of Biological Sciences, University of Alberta, 116 St & 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Elize Y X Ng
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore
| | - Pramana Yuda
- Universitas Atma Jaya, Jl. Babarsari 44, Janti, Caturtunggal, Kec. Depok, Kabupaten Sleman, Daerah Istimewa Yogyakarta, 55281, Indonesia
| | - Dewi M Prawiradilaga
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Jalan Raya Jakarta Bogor KM 46, Cibinong Science Center, Cibinong, 16911, Indonesia
| | - Jessica G H Lee
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826, Singapore
| | - Anaïs Tritto
- Wildlife Reserves Singapore, 80 Mandai Lake Road, Singapore, 729826, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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11
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Chattopadhyay B, Garg KM, Mendenhall IH, Rheindt FE. Historic reveals Anthropocene threat to a tropical urban fruit bat. Curr Biol 2020; 29:R1299-R1300. [PMID: 31846673 DOI: 10.1016/j.cub.2019.11.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Anthropogenic activities have propelled the Earth into a crisis characterized by unprecedented levels of environmental degradation and habitat loss, generating changes in global climatic regimes and initiating the planet's Sixth Extinction Catastrophe [1]. Loss of population genetic diversity is known to be a harbinger of local and global extinction events [2]. However, there is a lack of direct empirical evidence of historic losses of genetic diversity through periods of anthropogenically linked environmental degradation. We present genomic DNA information from a population of Sunda fruit bats (Cynopterus brachyotis) from Singapore, an exceptionally well-studied tropical rainforest island that has undergone substantial environmental degradation and fragmentation through the Anthropocene of the 1930-1950s [3]. As an effective pollinator and seed disperser, C. brachyotis represents an important keystone species in Singapore's ecosystem [4]. Here we show that comparison of historic DNA from individuals collected in 1931 with modern specimens reveals a nearly 30-fold reduction in effective population size and corresponding levels of decline in genetic diversity estimates. Coalescent population models indicate that Singapore's C. brachyotis bats underwent a continuous decline in genetic diversity followed by a stark bottleneck in approximately the 1940s, consistent with the estimated onset of the Anthropocene [5]. C. brachyotis continues to be considered common across Singapore [4], yet our results reveal large-scale impacts of the Anthropocene on biotic communities, even in those species thought to be tolerant to the effects of environmental degradation.
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Affiliation(s)
- Balaji Chattopadhyay
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.
| | - Kritika M Garg
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.
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