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Tian R, Zhang Y, Kang H, Zhang F, Jin Z, Wang J, Zhang P, Zhou X, Lanyon JM, Sneath HL, Woolford L, Fan G, Li S, Seim I. Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder afrotheria. Nat Commun 2024; 15:5568. [PMID: 38956050 PMCID: PMC11219930 DOI: 10.1038/s41467-024-49769-x] [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: 08/23/2023] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Sirenians of the superorder Afrotheria were the first mammals to transition from land to water and are the only herbivorous marine mammals. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly with other afrotherian genomes reveals possible molecular adaptations to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirm that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans. Our analysis also uncovers gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break ~10.7 thousand years ago on the Australian east coast and provide evidence of an associated ecotype, and highlight the need for whole-genome resequencing data from dugong populations worldwide for conservation and genetic management.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Yaolei Zhang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China
| | - Hui Kang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Zhang
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Zhihong Jin
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China
| | - Jiahao Wang
- BGI Research, Qingdao, 266555, China
- BGI Research, Shenzhen, 518083, China
| | - Peijun Zhang
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Janet M Lanyon
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Helen L Sneath
- School of the Environment, The University of Queensland, Lucia, 4072, Australia
| | - Lucy Woolford
- School of Veterinary Sciences, The University of Adelaide, Roseworthy, 5371, Australia
| | - Guangyi Fan
- BGI Research, Qingdao, 266555, China.
- BGI Research, Shenzhen, 518083, China.
- Qingdao Key Laboratory of Marine Genomics BGI Research, Qingdao, 266555, China.
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, 518083, China.
| | - Songhai Li
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
- The Innovation Research Center for Aquatic Mammals, and Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
| | - Inge Seim
- Integrative Biology Laboratory, Nanjing Normal University, Nanjing, 210023, China.
- Marine Mammal and Marine Bioacoustics Laboratory, Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China.
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2
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de Flamingh A, Gnoske TP, Rivera-Colón AG, Simeonovski VA, Kerbis Peterhans JC, Yamaguchi N, Witt KE, Catchen J, Roca AL, Malhi RS. Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction. J Hered 2024; 115:155-165. [PMID: 38150491 DOI: 10.1093/jhered/esad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/26/2023] [Indexed: 12/29/2023] Open
Abstract
Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "black-maned lions" and claimed that they were phenotypically distinct. However, other depictions and historical descriptions of lions from the Cape report mixed or light coloration and without black or extensively developed manes. These findings suggest that, rather than forming a distinct population, Cape lions may have had phenotypic and genotypic variation similar to other African lions. Here we investigate Cape lion genome characteristics, population dynamics, and genetic distinctiveness prior to their extinction. We generated genomic data from 2 historic Cape lions to compare to 118 existing high-coverage mitogenomes, and low-coverage nuclear genomes of 53 lions from 13 African countries. We show that, before their eradication, lions from the Cape Flats had diverse mitogenomes and nuclear genomes that clustered with lions from both southern and eastern Africa. Cape lions had high genome-wide heterozygosity and low inbreeding coefficients, indicating that populations in the Cape Flats went extinct so rapidly that genomic effects associated with long-term small population size and isolation were not detectable. Our findings do not support the characterization of Cape lions as phylogeographically distinct, as originally put forth by some European naturalists, and illustrates how alternative knowledge systems, for example, Indigenous perspectives, could potentially further inform interpretations of species histories.
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Affiliation(s)
- Alida de Flamingh
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
| | - Thomas P Gnoske
- Field Museum of Natural History (FMNH), Chicago, IL, United States
| | | | | | - Julian C Kerbis Peterhans
- Field Museum of Natural History (FMNH), Chicago, IL, United States
- College of Arts & Sciences, Roosevelt University, Chicago, IL, United States
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University of Malaysia Terengganu, Terengganu, Malaysia
| | - Kelsey E Witt
- Department of Genetics & Biochemistry, Center for Human Genetics, Clemson, SC, United States
| | - Julian Catchen
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
- Department of Evolution, Ecology, and Behavior, UIUC, Urbana, IL, United States
| | - Alfred L Roca
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
- Department of Animal Sciences, UIUC, Urbana, IL, United States
| | - Ripan Singh Malhi
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
- Department of Anthropology, UIUC, Urbana, IL, United States
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3
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Prado NA, Armstrong EE, Brown JL, Goldenberg SZ, Leimgruber P, Pearson VR, Maldonado JE, Campana MG. Genomic resources for Asian (Elephas maximus) and African savannah elephant (Loxodonta africana) conservation and health research. J Hered 2023; 114:529-538. [PMID: 37246890 DOI: 10.1093/jhered/esad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023] Open
Abstract
We provide novel genomic resources to help understand the genomic traits involved in elephant health and to aid conservation efforts. We sequence 11 elephant genomes (5 African savannah, 6 Asian) from North American zoos, including 9 de novo assemblies. We estimate elephant germline mutation rates and reconstruct demographic histories. Finally, we provide an in-solution capture assay to genotype Asian elephants. This assay is suitable for analyzing degraded museum and noninvasive samples, such as feces and hair. The elephant genomic resources we present here should allow for more detailed and uniform studies in the future to aid elephant conservation efforts and disease research.
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Affiliation(s)
- Natalia A Prado
- Biology Department, College of Arts and Sciences, Adelphi University, Garden City, NY, United States
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Endocrinology Research Laboratory, Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA, United States
- School of Biological Sciences, Washington State University, Pullman, WA, United States
| | - Janine L Brown
- Endocrinology Research Laboratory, Center for Species Survival, Smithsonian's National Zoo and Conservation Biology Institute, Front Royal, VA, United States
| | - Shifra Z Goldenberg
- Conservation Ecology Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
- Conservation Science and Wildlife Health, San Diego Zoo Wildlife Alliance, Escondido, CA, United States
| | - Peter Leimgruber
- Conservation Ecology Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Virginia R Pearson
- Glenn Rall Laboratory, Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Jesús E Maldonado
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, United States
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de Flamingh A, Ishida Y, Pečnerová P, Vilchis S, Siegismund HR, van Aarde RJ, Malhi RS, Roca AL. Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology. Front Genet 2023; 13:1021004. [PMID: 36712847 PMCID: PMC9876978 DOI: 10.3389/fgene.2022.1021004] [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: 08/16/2022] [Accepted: 12/05/2022] [Indexed: 01/13/2023] Open
Abstract
Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54-21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.
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Affiliation(s)
- Alida de Flamingh
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,*Correspondence: Alida de Flamingh, ; Ripan S. Malhi, ; Alfred L. Roca,
| | - Yasuko Ishida
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Patrícia Pečnerová
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Sahara Vilchis
- Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Hans R. Siegismund
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rudi J. van Aarde
- Department of Zoology and Entomology, Conservation Ecology Research Unit, University of Pretoria, Pretoria, South Africa
| | - Ripan S. Malhi
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,*Correspondence: Alida de Flamingh, ; Ripan S. Malhi, ; Alfred L. Roca,
| | - Alfred L. Roca
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States,Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States,*Correspondence: Alida de Flamingh, ; Ripan S. Malhi, ; Alfred L. Roca,
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Cabrera AA, Rey-Iglesia A, Louis M, Skovrind M, Westbury MV, Lorenzen ED. How low can you go? Introducing SeXY: sex identification from low-quantity sequencing data despite lacking assembled sex chromosomes. Ecol Evol 2022; 12:e9185. [PMID: 36035270 PMCID: PMC9405501 DOI: 10.1002/ece3.9185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/19/2022] [Indexed: 12/01/2022] Open
Abstract
Accurate sex identification is crucial for elucidating the biology of a species. In the absence of directly observable sexual characteristics, sex identification of wild fauna can be challenging, if not impossible. Molecular sexing offers a powerful alternative to morphological sexing approaches. Here, we present SeXY, a novel sex‐identification pipeline, for very low‐coverage shotgun sequencing data from a single individual. SeXY was designed to utilize low‐effort screening data for sex identification and does not require a conspecific sex‐chromosome assembly as reference. We assess the accuracy of our pipeline to data quantity by downsampling sequencing data from 100,000 to 1000 mapped reads and to reference genome selection by mapping to a variety of reference genomes of various qualities and phylogenetic distance. We show that our method is 100% accurate when mapping to a high‐quality (highly contiguous N50 > 30 Mb) conspecific genome, even down to 1000 mapped reads. For lower‐quality reference assemblies (N50 < 30 Mb), our method is 100% accurate with 50,000 mapped reads, regardless of reference assembly quality or phylogenetic distance. The SeXY pipeline provides several advantages over previously implemented methods; SeXY (i) requires sequencing data from only a single individual, (ii) does not require assembled conspecific sex chromosomes, or even a conspecific reference assembly, (iii) takes into account variation in coverage across the genome, and (iv) is accurate with only 1000 mapped reads in many cases.
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Affiliation(s)
| | | | - Marie Louis
- Globe Institute University of Copenhagen Copenhagen K Denmark.,Greenland Institute of Natural Resources Nuuk Greenland
| | - Mikkel Skovrind
- Globe Institute University of Copenhagen Copenhagen K Denmark
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Aznar-Cormano L, Bonnald J, Krief S, Guma N, Debruyne R. Molecular sexing of degraded DNA from elephants and mammoths: a genotyping assay relevant both to conservation biology and to paleogenetics. Sci Rep 2021; 11:7227. [PMID: 33790303 PMCID: PMC8012363 DOI: 10.1038/s41598-021-86010-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 01/29/2021] [Indexed: 11/24/2022] Open
Abstract
It is important to determine the sex of elephants from their samples-faeces from the field or seized ivory-for forensic reasons or to understand population demography and genetic structure. Molecular sexing methods developed in the last two decades have often shown limited efficiency, particularly in terms of sensitivity and specificity, due to the degradation of DNA in these samples. These limitations have also prevented their use with ancient DNA samples of elephants or mammoths. Here we propose a novel TaqMan-MGB qPCR assay to address these difficulties. We designed it specifically to allow the characterization of the genetic sex for highly degraded samples of all elephantine taxa (elephants and mammoths). In vitro experiments demonstrated a high level of sensitivity and low contamination risks. We applied this assay in two actual case studies where it consistently recovered the right genotype for specimens of known sex a priori. In the context of a modern conservation survey of African elephants, it allowed determining the sex for over 99% of fecal samples. In a paleogenetic analysis of woolly mammoths, it produced a robust hypothesis of the sex for over 65% of the specimens out of three PCR replicates. This simple, rapid, and cost-effective procedure makes it readily applicable to large sample sizes.
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Affiliation(s)
- Laetitia Aznar-Cormano
- CNRS, Centre de Recherche en Paléontologie Paris (CR2P), Muséum national d'Histoire naturelle, Sorbonne Université, 57 rue Cuvier, CP 38, 75005, Paris, France
| | - Julie Bonnald
- CNRS, Eco-Anthropologie (EA), Muséum national d'Histoire naturelle, Université Paris Diderot, 17 place du Trocadéro, 75016, Paris, France
- Sebitoli Chimpanzee Project, Sebitoli Research Station, Kibale National Park, Fort Portal, Uganda
| | - Sabrina Krief
- CNRS, Eco-Anthropologie (EA), Muséum national d'Histoire naturelle, Université Paris Diderot, 17 place du Trocadéro, 75016, Paris, France
- Sebitoli Chimpanzee Project, Sebitoli Research Station, Kibale National Park, Fort Portal, Uganda
| | | | - Régis Debruyne
- Direction Générale Déléguée à la Recherche, à l'Expertise, la Valorisation et l'Enseignement (DGD-REVE), Muséum national d'Histoire naturelle, 57 rue Cuvier, CP 17, 75005, Paris, France.
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7
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Sex assignment in a non-model organism in the absence of field records using Diversity Arrays Technology (DArT) data. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01203-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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