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Wilder AP, Steiner CC, Hendricks S, Haller BC, Kim C, Korody ML, Ryder OA. Genetic load and viability of a future restored northern white rhino population. Evol Appl 2024; 17:e13683. [PMID: 38617823 PMCID: PMC11009427 DOI: 10.1111/eva.13683] [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: 11/28/2023] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 04/16/2024] Open
Abstract
As biodiversity loss outpaces recovery, conservationists are increasingly turning to novel tools for preventing extinction, including cloning and in vitro gametogenesis of biobanked cells. However, restoration of populations can be hindered by low genetic diversity and deleterious genetic load. The persistence of the northern white rhino (Ceratotherium simum cottoni) now depends on the cryopreserved cells of 12 individuals. These banked genomes have higher genetic diversity than southern white rhinos (C. s. simum), a sister subspecies that successfully recovered from a severe bottleneck, but the potential impact of genetic load is unknown. We estimated how demographic history has shaped genome-wide genetic load in nine northern and 13 southern white rhinos. The bottleneck left southern white rhinos with more fixed and homozygous deleterious alleles and longer runs of homozygosity, whereas northern white rhinos retained more deleterious alleles masked in heterozygosity. To gauge the impact of genetic load on the fitness of a northern white rhino population restored from biobanked cells, we simulated recovery using fitness of southern white rhinos as a benchmark for a viable population. Unlike traditional restoration, cell-derived founders can be reintroduced in subsequent generations to boost lost genetic diversity and relieve inbreeding. In simulations with repeated reintroduction of founders into a restored population, the fitness cost of genetic load remained lower than that borne by southern white rhinos. Without reintroductions, rapid growth of the restored population (>20-30% per generation) would be needed to maintain comparable fitness. Our results suggest that inbreeding depression from genetic load is not necessarily a barrier to recovery of the northern white rhino and demonstrate how restoration from biobanked cells relieves some constraints of conventional restoration from a limited founder pool. Established conservation methods that protect healthy populations will remain paramount, but emerging technologies hold promise to bolster these tools to combat the extinction crisis.
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Affiliation(s)
- Aryn P. Wilder
- Conservation GeneticsSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
| | - Cynthia C. Steiner
- Conservation GeneticsSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
| | - Sarah Hendricks
- Conservation GeneticsSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
- Institute for Interdisciplinary Data SciencesUniversity of IdahoMoscowIdahoUSA
| | | | - Chang Kim
- University of CaliforniaSanta Cruz Genomics InstituteSanta CruzCaliforniaUSA
- Department of Neurological SurgeryUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Marisa L. Korody
- Conservation GeneticsSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
| | - Oliver A. Ryder
- Conservation GeneticsSan Diego Zoo Wildlife AllianceEscondidoCaliforniaUSA
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2
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Campos Cassavia Cintra de Oliveira L, Queiroz Vacari G, Maurício Barbanti Duarte J. A Method to Freeze Skin Samples for Cryobanks: A Test of Some Cryoprotectants for an Endangered Deer. Biopreserv Biobank 2023. [PMID: 37944047 DOI: 10.1089/bio.2023.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023] Open
Abstract
The genetic diversity of endangered deer species, such as Mazama jucunda, can be preserved with the help of somatic cell cryopreservation. This procedure allows obtaining several cells from the individual even after its death, which is very important for applications in reproductive biotechnologies. This study's objective was to test cryopreservation protocols of skin fragments of M. jucunda, using different cryoprotectants in slow freezing. We evaluated four treatments, composed of three cryoprotectants, dimethyl sulfoxide (DMSO), polyvinylpyrrolidone (PVP), and ethylene glycol (EG), used alone and in combination. There was also a control group where the tissue did not undergo cryopreservation. Skin fragments were collected from the medial region of the pelvic limbs of three individuals. Each fragment was divided into 10 equal parts, standardized by weight, making two pieces for each treatment and control from each animal. The collected fragments were evaluated in culture, based on the speed of occupation of the free spaces of the cell culture flask. Cell viability was also evaluated using Trypan Blue dye and the mitotic index to understand the effect of toxicity and freezing on cell membrane integrity and cell division capacity, respectively. The treatments that used association with PVP proved to be more damaging to the cells, taking longer to reach confluence. EG alone showed better results than DMSO in the slow-freezing protocol. Clinical Trial Registration Number is 1390/21.
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Affiliation(s)
- Laura Campos Cassavia Cintra de Oliveira
- Departamento de Zootecnia, Deer Conservation and Research Center (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias, São Paulo State University, Jaboticabal, Brazil
| | - Gabrielle Queiroz Vacari
- Departamento de Zootecnia, Deer Conservation and Research Center (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias, São Paulo State University, Jaboticabal, Brazil
| | - José Maurício Barbanti Duarte
- Departamento de Zootecnia, Deer Conservation and Research Center (NUPECCE), Faculdade de Ciências Agrárias e Veterinárias, São Paulo State University, Jaboticabal, Brazil
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3
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Nguyen TD, Li H, Zhuang Y, Chen B, Kinoshita K, Jamal MA, Xu K, Guo J, Jiao D, Tanabe K, Wei Y, Li Z, Cheng W, Qing Y, Zhao HY, Wei HJ. In vitro and in vivo development of interspecies Asian elephant embryos reconstructed with pig enucleated oocytes. Anim Biotechnol 2023; 34:1909-1918. [PMID: 35404767 DOI: 10.1080/10495398.2022.2058005] [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] [Indexed: 11/01/2022]
Abstract
Interspecies somatic cell nuclear transfer (iSCNT) has an immense potential to rescue endangered animals and extinct species like mammoths. In this study, we successfully established an Asian elephant's fibroblast cell lines from ear tissues, performed iSCNT with porcine oocytes and evaluated the in vitro and in vivo development of reconstructed embryos. A total of 7780 elephant-pig iSCNT embryos were successfully reconstructed and showed in vitro development with cleavage rate, 4-cell, 8-cell and blastocyst rate of 73.01, 30.48, 5.64, and 4.73%, respectively. The total number of elephant-pig blastocyte cells and diameter of hatched blastocyte was 38.67 and 252.75 μm, respectively. Next, we designed species-specific markers targeting EDNRB, AGRP and TYR genes to verify the genome of reconstructed embryos with donor nucleus/species. The results indicated that 53.2, 60.8, and 60.8% of reconstructed embryos (n = 235) contained elephant genome at 1-cell, 2-cell and 4-cell stages, respectively. However, the percentages decreased to 32.3 and 32.7% at 8-cell and blastocyst stages, respectively. Furthermore, we also evaluated the in vivo development of elephant-pig iSCNT cloned embryos and transferred 2260 reconstructed embryos into two surrogate gilts that successfully became pregnant and a total of 11 (1 and 10) fetuses were surgically recovered after 17 and 19 days of gestation, respectively. The crown-rump length and width of elephant-pig cloned fetuses were smaller than the control group. Unfortunately, none of these fetuses contained elephant genomes, which suggested that elephant embryos failed to develop in vivo. In conclusion, we successfully obtained elephant-pig reconstructed embryos for the first time and these embryos are able to develop to blastocyst, but the in vivo developmental failure needs further investigated.
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Affiliation(s)
- Tien Dat Nguyen
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Honghui Li
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yiquan Zhuang
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Bowei Chen
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Keiji Kinoshita
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
| | - Muhammad Ameen Jamal
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Kaixiang Xu
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jianxiong Guo
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
| | - Deling Jiao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Kumiko Tanabe
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
| | - Yunfang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhuo Li
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Wenming Cheng
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yubo Qing
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Hong-Ye Zhao
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Hong-Jiang Wei
- Yunnan Province Key Laboratory for Porcine Gene Editing and Xenotransplantation, Kunming, China
- Xenotransplantation Engineering Research Center in Yunnan Province, Kunming, China
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
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Mooney A, Ryder OA, Houck ML, Staerk J, Conde DA, Buckley YM. Maximizing the potential for living cell banks to contribute to global conservation priorities. Zoo Biol 2023; 42:697-708. [PMID: 37283210 DOI: 10.1002/zoo.21787] [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: 02/05/2023] [Revised: 04/30/2023] [Accepted: 05/24/2023] [Indexed: 06/08/2023]
Abstract
Although cryobanking represents a powerful conservation tool, a lack of standardized information on the species represented in global cryobanks, and inconsistent prioritization of species for future sampling, hinder the conservation potential of cryobanking, resulting in missed conservation opportunities. We analyze the representation of amphibian, bird, mammal, and reptile species within the San Diego Zoo Wildlife Alliance Frozen Zoo® living cell collection (as of April 2019) and implement a qualitative framework for the prioritization of species for future sampling. We use global conservation assessment schemes (including the International Union for Conservation of Nature (IUCN) Red List of Threatened Species™, the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES), the Alliance for Zero Extinction, the EDGE of Existence, and Climate Change Vulnerability), and opportunities for sample acquisition from the global zoo and aquarium community, to identify priority species for cryobanking. We show that 965 species, including 5% of all IUCN Red List "Threatened" amphibians, birds, mammals, and reptiles, were represented in the collection and that sampling from within existing zoo and aquarium collections could increase representation to 16.6% (by sampling an additional 707 "Threatened" species). High-priority species for future cryobanking efforts include the whooping crane (Grus americana), crested ibis (Nipponia nippon), and Siberian crane (Leucogeranus leucogeranus). Each of these species are listed under every conservation assessment scheme and have ex situ populations available for sampling. We also provide species prioritizations based on subsets of these assessment schemes together with sampling opportunities from the global zoo and aquarium community. We highlight the difficulties in obtaining in situ samples, and encourage the formation of a global cryobanking database together with the establishment of new cryobanks in biodiversity-rich regions.
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Affiliation(s)
- Andrew Mooney
- Dublin Zoo, Phoenix Park, Dublin, Ireland
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland
- Species360 Conservation Science Alliance, Bloomington, Minnesota, USA
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, California, USA
| | - Marlys L Houck
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, Escondido, California, USA
| | - Johanna Staerk
- Species360 Conservation Science Alliance, Bloomington, Minnesota, USA
- Interdisciplinary Centre on Population Dynamics, University of Southern Denmark, Odense M, Denmark
- Department of Biology, University of Southern Denmark, Odense M, Denmark
| | - Dalia A Conde
- Species360 Conservation Science Alliance, Bloomington, Minnesota, USA
- Interdisciplinary Centre on Population Dynamics, University of Southern Denmark, Odense M, Denmark
- Department of Biology, University of Southern Denmark, Odense M, Denmark
| | - Yvonne M Buckley
- School of Natural Sciences, Zoology, Trinity College Dublin, Dublin, Ireland
- School of Biological Sciences, University of Queensland, St Lucia, Australia
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5
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Meek MH, Beever EA, Barbosa S, Fitzpatrick SW, Fletcher NK, Mittan-Moreau CS, Reid BN, Campbell-Staton SC, Green NF, Hellmann JJ. Understanding Local Adaptation to Prepare Populations for Climate Change. Bioscience 2022. [DOI: 10.1093/biosci/biac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Abstract
Adaptation within species to local environments is widespread in nature. Better understanding this local adaptation is critical to conserving biodiversity. However, conservation practices can rely on species’ trait averages or can broadly assume homogeneity across the range to inform management. Recent methodological advances for studying local adaptation provide the opportunity to fine-tune efforts for managing and conserving species. The implementation of these advances will allow us to better identify populations at greatest risk of decline because of climate change, as well as highlighting possible strategies for improving the likelihood of population persistence amid climate change. In the present article, we review recent advances in the study of local adaptation and highlight ways these tools can be applied in conservation efforts. Cutting-edge tools are available to help better identify and characterize local adaptation. Indeed, increased incorporation of local adaptation in management decisions may help meet the imminent demands of managing species amid a rapidly changing world.
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Affiliation(s)
- Mariah H Meek
- Department of Integrative Biology, AgBio Research, and the Ecology, Evolution, and Behavior Program Michigan State University , East Lansing, Michigan, United States
| | - Erik A Beever
- Department of Ecology, Montana State University , Bozeman, Montana, United States
| | - Soraia Barbosa
- Department of Fish and Wildlife Sciences, University of Idaho , Moscow, Idaho, United States
| | - Sarah W Fitzpatrick
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
| | - Nicholas K Fletcher
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, New York, United States
- Department of Biology, University of Maryland , College Park, Maryland, United States
| | - Cinnamon S Mittan-Moreau
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, New York, United States
| | - Brendan N Reid
- Department of Integrative Biology, Michigan State University , Hickory Corners, Michigan, United States
- Department of Ecology, Evolution, and Natural Resources, Rutgers University , New Brunswick, New Jersey, United States
| | - Shane C Campbell-Staton
- Department of Ecology and Evolutionary Biology, Princeton University , Princeton, New Jersey, United States
| | - Nancy F Green
- US Fish and Wildlife Service, Falls Church , Virginia, United States
| | - Jessica J Hellmann
- Institute of the Environment and Department of Ecology, Evolution, and Behavior, University of Minnesota , Saint Paul, Minnesota, United States
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6
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Knockdown of YY1 Inhibits XIST Expression and Enhances Cloned Pig Embryo Development. Int J Mol Sci 2022; 23:ijms232314572. [PMID: 36498896 PMCID: PMC9739934 DOI: 10.3390/ijms232314572] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
The technique of cloning has wide applications in animal husbandry and human biomedicine. However, the very low developmental efficiency of cloned embryos limits the application of cloning. Ectopic XIST-expression-induced abnormal X chromosome inactivation (XCI) is a primary cause of the low developmental competence of cloned mouse and pig embryos. Knockout or knockdown of XIST improves cloning efficiency in both pigs and mice. The transcription factor Yin yang 1(YY1) plays a critical role in XCI by triggering the transcription of X-inactive specific transcript (XIST) and facilitating the localization of XIST RNA on the X chromosome. This study aimed to investigate whether RNA interference to suppress the expression of YY1 can inhibit erroneous XIST expression, rescue abnormal XCI, and improve the developmental ability of cloned pig embryos. The results showed that YY1 binds to the 5' regulatory region of the porcine XIST gene in pig cells. The microinjection of YY1 siRNA into cloned pig embryos reduced the transcript abundance of XIST and upregulated the mRNA level of X-linked genes at the 4-cell and blastocyst stages. The siRNA-mediated knockdown of YY1 altered the transcriptome and enhanced the in vitro and in vivo developmental efficiency of cloned porcine embryos. These results suggested that YY1 participates in regulating XIST expression and XCI in cloned pig embryos and that the suppression of YY1 expression can increase the developmental rate of cloned pig embryos. The present study established a new method for improving the efficiency of pig cloning.
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7
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Scott SE, Cain B, de Kort SR, Johnson B, Khayale C, Versteege L, Bettridge CM. Group composition impacts reproductive output and population viability in captive white rhinoceros. Anim Conserv 2022. [DOI: 10.1111/acv.12833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- S. E. Scott
- Department of Natural Sciences, Ecology and Environment Research Centre Manchester Metropolitan University Manchester UK
- Joint Nature Conservation Committee Aberdeen UK
| | - B. Cain
- Department of Natural Sciences, Ecology and Environment Research Centre Manchester Metropolitan University Manchester UK
| | - S. R. de Kort
- Department of Natural Sciences, Ecology and Environment Research Centre Manchester Metropolitan University Manchester UK
| | | | | | - L. Versteege
- Safaripark Beekse Bergen Hilvarenbeek The Netherlands
| | - C. M. Bettridge
- Department of Natural Sciences, Ecology and Environment Research Centre Manchester Metropolitan University Manchester UK
- School of Natural Sciences Bangor University Bangor UK
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8
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Rodger JC, Clulow J. Resetting the paradigm of reproductive science and conservation. Anim Reprod Sci 2022; 246:106911. [PMID: 34955327 DOI: 10.1016/j.anireprosci.2021.106911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/14/2022]
Abstract
In the application of reproductive science to conservation breeding, it has long been assumed that artificial insemination using frozen thawed sperm would be the default technology. This has always been problematic considering the wide range of tolerance to freeze thawing among vertebrate sperm. Furthermore, those providing leadership for genome banking should be proactive to preserve maximum genetic diversity, however, for many species there is little or no sperm motility after thawing of cryopreserved sperm. In this review article, there is the contention that a much wider range of tissues should be banked, and the range of evolving advanced reproductive and developmental technologies should be considered for conservation breeding programs, to realize the maximum opportunities of genome banking to contribute to conservation of animal species.
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Affiliation(s)
- John C Rodger
- FAUNA Research Alliance, PO Box 5092, Kahibah, NSW, Australia; Conservation Science Research Group, The University of Newcastle, Callaghan, NSW, Australia.
| | - John Clulow
- FAUNA Research Alliance, PO Box 5092, Kahibah, NSW, Australia; Conservation Science Research Group, The University of Newcastle, Callaghan, NSW, Australia
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9
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Whole-genome resequencing of Chinese pangolins reveals a population structure and provides insights into their conservation. Commun Biol 2022; 5:821. [PMID: 36008681 PMCID: PMC9411537 DOI: 10.1038/s42003-022-03757-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 07/22/2022] [Indexed: 11/18/2022] Open
Abstract
Poaching and trafficking have a substantial negative impact on the population growth and range expansion of the Chinese pangolin (Manis pentadactyla). However, recently reported activities of Chinese pangolins in several sites of Guangdong province in China indicate a promising sign for the recovery of this threatened species. Here, we re-sequence genomes of 15 individuals and perform comprehensive population genomics analyses with previously published 22 individuals. These Chinese pangolins are found to be divided into three distinct populations. Multiple lines of evidence indicate the existence of a newly discovered population (CPA) comprises entirely of individuals from Guangdong province. The other two populations (CPB and CPC) have previously been documented. The genetic differentiation of the CPA and CPC is extremely large (FST = 0.541), which is larger than many subspecies-level differentiations. Even for the closer CPA and CPB, their differentiation (FST = 0.101) is still comparable with the population-level differentiation of many endangered species. Further analysis reveals that the CPA and CPB populations separate 2.5–4.0 thousand years ago (kya), and on the other hand, CPA and CPC diverge around 25–40 kya. The CPA population harbors more runs of homozygosity (ROHs) than the CPB and CPC populations, indicating that inbreeding is more prevalent in the CPA population. Although the CPC population has less mutational load than CPA and CPB populations, we predict that several Loss of Function (LoF) mutations will be translocated into the CPA or CPB populations by using the CPC as a donor population for genetic rescue. Our findings imply that the conservation of Chinese pangolins is challenging, and implementing genetic rescue among the three groups should be done with extreme caution. Whole-genome resequencing of Chinese pangolins reveals a new population CPA that is genetically distinct from and harbor more homozygosity than CPB and CPC populations, indicating prevalence in inbreeding and implying challenges in conservation.
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10
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Zywitza V, Rusha E, Shaposhnikov D, Ruiz-Orera J, Telugu N, Rishko V, Hayashi M, Michel G, Wittler L, Stejskal J, Holtze S, Göritz F, Hermes R, Wang J, Izsvák Z, Colleoni S, Lazzari G, Galli C, Hildebrandt TB, Hayashi K, Diecke S, Drukker M. Naïve-like pluripotency to pave the way for saving the northern white rhinoceros from extinction. Sci Rep 2022; 12:3100. [PMID: 35260583 PMCID: PMC8904600 DOI: 10.1038/s41598-022-07059-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 02/09/2022] [Indexed: 11/09/2022] Open
Abstract
The northern white rhinoceros (NWR) is probably the earth’s most endangered mammal. To rescue the functionally extinct species, we aim to employ induced pluripotent stem cells (iPSCs) to generate gametes and subsequently embryos in vitro. To elucidate the regulation of pluripotency and differentiation of NWR PSCs, we generated iPSCs from a deceased NWR female using episomal reprogramming, and observed surprising similarities to human PSCs. NWR iPSCs exhibit a broad differentiation potency into the three germ layers and trophoblast, and acquire a naïve-like state of pluripotency, which is pivotal to differentiate PSCs into primordial germ cells (PGCs). Naïve culturing conditions induced a similar expression profile of pluripotency related genes in NWR iPSCs and human ESCs. Furthermore, naïve-like NWR iPSCs displayed increased expression of naïve and PGC marker genes, and a higher integration propensity into developing mouse embryos. As the conversion process was aided by ectopic BCL2 expression, and we observed integration of reprogramming factors, the NWR iPSCs presented here are unsuitable for gamete production. However, the gained insights into the developmental potential of both primed and naïve-like NWR iPSCs are fundamental for in future PGC-specification in order to rescue the species from extinction using cryopreserved somatic cells.
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Affiliation(s)
- Vera Zywitza
- Technology Platform Pluripotent Stem Cells, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Ejona Rusha
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Dmitry Shaposhnikov
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Narasimha Telugu
- Technology Platform Pluripotent Stem Cells, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Valentyna Rishko
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, 85764, Neuherberg, Germany
| | - Masafumi Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Geert Michel
- FEMTransgenic Technologies, Charité, 13125, Berlin, Germany
| | - Lars Wittler
- Department of Developmental Genetics, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Jan Stejskal
- ZOO Dvůr Králové, Štefánikova 1029, 544 01, Dvůr Králové nad Labem, Czech Republic
| | - Susanne Holtze
- Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany
| | - Frank Göritz
- Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany
| | - Robert Hermes
- Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany
| | - Jichang Wang
- Mobile DNA, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Zsuzsanna Izsvák
- Mobile DNA, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Silvia Colleoni
- Laboratory of Reproductive Technologies, Avantea, 26100, Cremona, Italy
| | - Giovanna Lazzari
- Laboratory of Reproductive Technologies, Avantea, 26100, Cremona, Italy.,Fondazione Avantea, 26100, Cremona, Italy
| | - Cesare Galli
- Laboratory of Reproductive Technologies, Avantea, 26100, Cremona, Italy.,Fondazione Avantea, 26100, Cremona, Italy
| | - Thomas B Hildebrandt
- Leibniz Institute for Zoo and Wildlife Research, 10315, Berlin, Germany.,Faculty of Veterinary Medicine, Freie Universität Berlin, 14163, Berlin, Germany
| | - Katsuhiko Hayashi
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Sebastian Diecke
- Technology Platform Pluripotent Stem Cells, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
| | - Micha Drukker
- Induced Pluripotent Stem Cell Core Facility, Helmholtz Zentrum München, 85764, Neuherberg, Germany. .,Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, 2300 RA, Leiden, The Netherlands.
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11
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Ex Situ Conservation and Genetic Rescue of Endangered Polish Cattle and Pig Breeds with the Aid of Modern Reproductive Biotechnology – A Review. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2021-0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The development and optimization of reproductive biotechnology – specifically semen cryopreservation, spermatological diagnostics, and intraspecies cloning by somatic cell nuclear transfer (SCNT) – have become essential techniques to conserve the genetic resources and establish genetic reserves of endangered or vanishing native Polish livestock breeds. Moreover, this biotechnology is necessary for perpetuating biological diversity and enhancing genetic variability as well as for restoring and reintroducing breeds into anthropogenic agricultural ecosystems. On the one hand, the purpose of our paper is to interpret recent efforts aimed at the ex situ conservation of native cattle and pig breeds. On the other, it emphasizes the prominent role played by the National Research Institute of Animal Production (NRIAP) in maintaining biodiversity in agricultural environmental niches. Furthermore, our paper provides an overview of the conventional and modern strategies of the banking and cryopreservation of germplasm-carrier biological materials and somatic cell lines, spermatological diagnostics, and semen-based and SCNT-mediated assisted reproductive technologies (ART s). These are the most reliable and powerful tools for ex situ protection of the genetic resources of endangered breeds of livestock, especially cattle and pigs.
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12
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Liu S, Westbury MV, Dussex N, Mitchell KJ, Sinding MHS, Heintzman PD, Duchêne DA, Kapp JD, von Seth J, Heiniger H, Sánchez-Barreiro F, Margaryan A, André-Olsen R, De Cahsan B, Meng G, Yang C, Chen L, van der Valk T, Moodley Y, Rookmaaker K, Bruford MW, Ryder O, Steiner C, Bruins-van Sonsbeek LGR, Vartanyan S, Guo C, Cooper A, Kosintsev P, Kirillova I, Lister AM, Marques-Bonet T, Gopalakrishnan S, Dunn RR, Lorenzen ED, Shapiro B, Zhang G, Antoine PO, Dalén L, Gilbert MTP. Ancient and modern genomes unravel the evolutionary history of the rhinoceros family. Cell 2021; 184:4874-4885.e16. [PMID: 34433011 DOI: 10.1016/j.cell.2021.07.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 12/27/2022]
Abstract
Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.
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Affiliation(s)
- Shanlin Liu
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing 100193, China; The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark.
| | - Michael V Westbury
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Nicolas Dussex
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Mikkel-Holger S Sinding
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Peter D Heintzman
- The Arctic University Museum of Norway, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - David A Duchêne
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Joshua D Kapp
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Johanna von Seth
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia
| | - Fátima Sánchez-Barreiro
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Ashot Margaryan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Remi André-Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
| | - Binia De Cahsan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Guanliang Meng
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Chentao Yang
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Lei Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Tom van der Valk
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou 0950, Republic of South Africa
| | - Kees Rookmaaker
- Editor of the Rhino Resource Center, Utrecht, the Netherlands
| | - Michael W Bruford
- School of Biosciences, Sir Martin Evans Building, Cardiff University, Cardiff CF10 3AX, UK; Sustainable Places Research Institute, Cardiff University, Cardiff CF10 3BA, UK
| | - Oliver Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Cynthia Steiner
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | | | - Sergey Vartanyan
- N.A. Shilo North-East Interdisciplinary Scientific Research Institute, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan 685000, Russia
| | - Chunxue Guo
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China
| | - Alan Cooper
- South Australian Museum, Adelaide, SA 5000, Australia
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia; Ural Federal University, Yekaterinburg, Russia
| | - Irina Kirillova
- Institute of Geography, Russian Academy of Sciences, Moscow 119017, Russia
| | - Adrian M Lister
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain; Centre Nacional d'Anàlisi Genòmica, Centre for Genomic Regulation (CNAG-CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain; Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Shyam Gopalakrishnan
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Robert R Dunn
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Eline D Lorenzen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA; Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 96050, USA
| | - Guojie Zhang
- China National Genebank, BGI Shenzhen, Shenzhen 518083, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Pierre-Olivier Antoine
- Institut des Sciences de l'Évolution, Université Montpellier, CNRS, IRD, EPHE, Montpellier 34095, France
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius vag 20C, Stockholm 10691, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm 10405, Sweden; Department of Zoology, Stockholm University, Stockholm 10691, Sweden.
| | - M Thomas P Gilbert
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, 1353 Copenhagen, Denmark; Norwegian University of Science and Technology (NTNU) University Museum, Trondheim 7012, Norway.
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13
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Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, Westbury MV, de Manuel M, Margaryan A, Ciucani MM, Vieira FG, Patramanis Y, Kalthoff DC, Timmons Z, Sicheritz-Pontén T, Dalén L, Ryder OA, Zhang G, Marquès-Bonet T, Moodley Y, Gilbert MTP. Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum). Mol Ecol 2021; 30:6355-6369. [PMID: 34176179 PMCID: PMC9291831 DOI: 10.1111/mec.16043] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 01/08/2023]
Abstract
Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a remarkable decline in the last 150 years due to human activities. Its subspecies, the northern (NWR) and the southern white rhinoceros (SWR), however, underwent opposite fates: the NWR vanished quickly, while the SWR recovered after the severe decline. Such demographic events are predicted to have an erosive effect at the genomic level, linked to the extirpation of diversity, and increased genetic drift and inbreeding. However, there is little empirical data available to directly reconstruct the subtleties of such processes in light of distinct demographic histories. Therefore, we generated a whole-genome, temporal data set consisting of 52 resequenced white rhinoceros genomes, representing both subspecies at two time windows: before and during/after the bottleneck. Our data reveal previously unknown population structure within both subspecies, as well as quantifiable genomic erosion. Genome-wide heterozygosity decreased significantly by 10% in the NWR and 36% in the SWR, and inbreeding coefficients rose significantly by 11% and 39%, respectively. Despite the remarkable loss of genomic diversity and recent inbreeding it suffered, the only surviving subspecies, the SWR, does not show a significant accumulation of genetic load compared to its historical counterpart. Our data provide empirical support for predictions about the genomic consequences of shrinking populations, and our findings have the potential to inform the conservation efforts of the remaining white rhinoceroses.
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Affiliation(s)
| | - Shyam Gopalakrishnan
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,DTU Bioinformatics, Kongens Lyngby, Hovedstaden, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Marc de Manuel
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain
| | - Ashot Margaryan
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Marta M Ciucani
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Filipe G Vieira
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Daniela C Kalthoff
- Department of Zoology, Swedish Museum of Natural History, Stockholm, Sweden
| | - Zena Timmons
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Thomas Sicheritz-Pontén
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA, USA
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.,BGI-Shenzhen, Shenzhen, China
| | - Tomás Marquès-Bonet
- Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Barcelona, Spain.,National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, South Africa
| | - M Thomas P Gilbert
- GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
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14
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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.
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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.
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15
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The ART of bringing extinction to a freeze - History and future of species conservation, exemplified by rhinos. Theriogenology 2021; 169:76-88. [PMID: 33940218 DOI: 10.1016/j.theriogenology.2021.04.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/18/2022]
Abstract
The ongoing mass extinction of animal species at an unprecedented rate is largely caused by human activities. Progressive habitat destruction and fragmentation is resulting in accelerated loss of biodiversity on a global scale. Over decades, captive breeding programs of non-domestic species were characterized by efforts to optimize species-specific husbandry, to increase studbook-based animal exchange, and to improve enclosure designs. To counter the ongoing dramatic loss of biodiversity, new approaches are warranted. Recently, new ideas, particularly the application of assisted reproduction technologies (ART), have been incorporated into classical zoo breeding programs. These technologies include semen and oocyte collection, artificial insemination, and in-vitro embryo generation. More futuristic ideas of advanced ART (aART) implement recent advances in biotechnology and stem-cell related approaches such as cloning, inner cell mass transfer (ICM), and the stem-cell-associated techniques (SCAT) for the generation of gametes and ultimately embryos of highly endangered species, such as the northern white rhinoceros (Ceratotherium simum cottoni) of which only two female individuals are left. Both, ART and aART greatly depend on and benefit from the rapidly evolving cryopreservation techniques and biobanking not only of genetic, but also of viable cellular materials suitable for the generation of induced pluripotent stem cells (iPSC). The availability of cryopreserved materials bridges gaps in time and space, thereby optimizing the available genetic variability and enhancing the chance to restore viable populations.
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16
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Moodley Y, Westbury MV, Russo IRM, Gopalakrishnan S, Rakotoarivelo A, Olsen RA, Prost S, Tunstall T, Ryder OA, Dalén L, Bruford MW. Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros. Mol Biol Evol 2021; 37:3105-3117. [PMID: 32585004 DOI: 10.1093/molbev/msaa148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Africa's black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. Although their precursor species Diceros praecox and Ceratotherium mauritanicum appear in the fossil record ∼5.2 Ma, by 4 Ma both were still mixed feeders, and were even spatiotemporally sympatric at several Pliocene sites in what is today Africa's Rift Valley. Here, we ask whether or not D. praecox and C. mauritanicum were reproductively isolated when they came into Pliocene secondary contact. We sequenced and de novo assembled the first annotated black rhinoceros reference genome and compared it with available genomes of other black and white rhinoceros. We show that ancestral gene flow between D. praecox and C. mauritanicum ceased sometime between 3.3 and 4.1 Ma, despite conventional methods for the detection of gene flow from whole genome data returning false positive signatures of recent interspecific migration due to incomplete lineage sorting. We propose that ongoing Pliocene genetic exchange, for up to 2 My after initial divergence, could have potentially hindered the development of obligate feeding strategies until both species were fully reproductively isolated, but that the more severe and shifting paleoclimate of the early Pleistocene was likely the ultimate driver of ecological specialization in African rhinoceros.
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Affiliation(s)
- Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
| | - Michael V Westbury
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Isa-Rita M Russo
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrinajoro Rakotoarivelo
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa.,Natiora Ahy Madagasikara, Ampahibe, Antananarivo, Madagascar
| | - Remi-Andre Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, Germany.,South African National Biodiversity Institute, National Zoological Gardens, Pretoria, Republic of South Africa
| | - Tate Tunstall
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cardiff, United Kingdom.,Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
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17
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Korody ML, Ford SM, Nguyen TD, Pivaroff CG, Valiente-Alandi I, Peterson SE, Ryder OA, Loring JF. Rewinding Extinction in the Northern White Rhinoceros: Genetically Diverse Induced Pluripotent Stem Cell Bank for Genetic Rescue. Stem Cells Dev 2021; 30:177-189. [PMID: 33406994 PMCID: PMC7891310 DOI: 10.1089/scd.2021.0001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Extinction rates are rising, and current conservation technologies may not be adequate for reducing species losses. Future conservation efforts may be aided by the generation of induced pluripotent stem cells (iPSCs) from highly endangered species. Generation of a set of iPSCs from multiple members of a species can capture some of the dwindling genetic diversity of a disappearing species. We generated iPSCs from fibroblasts cryopreserved in the Frozen Zoo®: nine genetically diverse individuals of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni) and two from the closely related southern white rhinoceros (Ceratotherium simum simum). We used a nonintegrating Sendai virus reprogramming method and developed analyses to confirm the cells' pluripotency and differentiation potential. This work is the first step of a long-term interdisciplinary plan to apply assisted reproduction techniques to the conservation of this highly endangered species. Advances in iPSC differentiation may enable generation of gametes in vitro from deceased and nonreproductive individuals that could be used to repopulate the species.
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Affiliation(s)
- Marisa L Korody
- San Diego Zoo Global, Beckman Center for Conservation Research, Escondido, California, USA.,Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Sarah M Ford
- San Diego Zoo Global, Beckman Center for Conservation Research, Escondido, California, USA
| | - Thomas D Nguyen
- San Diego Zoo Global, Beckman Center for Conservation Research, Escondido, California, USA.,Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Cullen G Pivaroff
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Iñigo Valiente-Alandi
- San Diego Zoo Global, Beckman Center for Conservation Research, Escondido, California, USA
| | - Suzanne E Peterson
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
| | - Oliver A Ryder
- San Diego Zoo Global, Beckman Center for Conservation Research, Escondido, California, USA
| | - Jeanne F Loring
- Department of Molecular Medicine, Scripps Research, La Jolla, California, USA
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18
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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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Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros. Curr Biol 2020; 30:3871-3879.e7. [PMID: 32795436 DOI: 10.1016/j.cub.2020.07.046] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/18/2020] [Accepted: 07/14/2020] [Indexed: 02/01/2023]
Abstract
Ancient DNA has significantly improved our understanding of the evolution and population history of extinct megafauna. However, few studies have used complete ancient genomes to examine species responses to climate change prior to extinction. The woolly rhinoceros (Coelodonta antiquitatis) was a cold-adapted megaherbivore widely distributed across northern Eurasia during the Late Pleistocene and became extinct approximately 14 thousand years before present (ka BP). While humans and climate change have been proposed as potential causes of extinction [1-3], knowledge is limited on how the woolly rhinoceros was impacted by human arrival and climatic fluctuations [2]. Here, we use one complete nuclear genome and 14 mitogenomes to investigate the demographic history of woolly rhinoceros leading up to its extinction. Unlike other northern megafauna, the effective population size of woolly rhinoceros likely increased at 29.7 ka BP and subsequently remained stable until close to the species' extinction. Analysis of the nuclear genome from a ∼18.5-ka-old specimen did not indicate any increased inbreeding or reduced genetic diversity, suggesting that the population size remained steady for more than 13 ka following the arrival of humans [4]. The population contraction leading to extinction of the woolly rhinoceros may have thus been sudden and mostly driven by rapid warming in the Bølling-Allerød interstadial. Furthermore, we identify woolly rhinoceros-specific adaptations to arctic climate, similar to those of the woolly mammoth. This study highlights how species respond differently to climatic fluctuations and further illustrates the potential of palaeogenomics to study the evolutionary history of extinct species.
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20
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Ryder OA, Friese C, Greely HT, Sandler R, Saragusty J, Durrant BS, Redford KH. Exploring the limits of saving a subspecies: The ethics and social dynamics of restoring northern white rhinos (
Ceratotherium simum cottoni
). CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.241] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Affiliation(s)
- Oliver A. Ryder
- San Diego Zoo Institute for Conservation Research Escondido California USA
| | - Carrie Friese
- Sociology DepartmentLondon School of Economics and Political Science London UK
| | | | - Ronald Sandler
- Department of Philosophy and ReligionNortheastern University Boston Massachusetts USA
| | - Joseph Saragusty
- Laboratory of Embryology. Faculty of Veterinary Medicine, Campus Coste San AgostinoUniversity of Teramo Teramo Italy
| | - Barbara S. Durrant
- San Diego Zoo Institute for Conservation Research Escondido California USA
| | - Kent H. Redford
- Archipelago Consulting Portland Maine USA
- Department of Environmental StudiesUniversity of New England Biddeford Maine USA
- Environmental Futures Research Institute, Griffith University Brisbane Queensland Australia
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21
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Lindblad-Toh K. What animals can teach us about evolution, the human genome, and human disease. Ups J Med Sci 2020; 125:1-9. [PMID: 32054372 PMCID: PMC7054949 DOI: 10.1080/03009734.2020.1722298] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
During the past 20 years, since I started as a postdoc, the world of genetics and genomics has changed dramatically. My main research goal throughout my career has been to understand human disease genetics, and I have developed comparative genomics and comparative genetics to generate resources and tools for understanding human disease. Through comparative genomics I have worked to sequence enough mammals to understand the functional potential of each base in the human genome as well as chosen vertebrates to study the evolutionary changes that have given many species their key traits. Through comparative genetics, I have developed the dog as a model for human disease, characterising the genome itself and determining a list of germ-line loci and somatic mutations causing complex diseases and cancer in the dog. Pulling all these findings and resources together opens new doors for understanding genome evolution, the genetics of complex traits and cancer in man and his best friend.
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Affiliation(s)
- Kerstin Lindblad-Toh
- Department for Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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22
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Praxedes ÉA, Queiroz Neta LB, Borges AA, Silva MB, Santos MVO, Ribeiro LR, Silva HVR, Pereira AF. Quantitative and descriptive histological aspects of jaguar (
Panthera onca
Linnaeus, 1758) ear skin as a step towards formation of biobanks. Anat Histol Embryol 2019; 49:121-129. [DOI: 10.1111/ahe.12500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 07/11/2019] [Accepted: 09/03/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Érika A. Praxedes
- Laboratory of Animal Biotechnology Federal Rural University of Semi‐Arid Mossoro Brazil
| | - Luiza B. Queiroz Neta
- Laboratory of Animal Biotechnology Federal Rural University of Semi‐Arid Mossoro Brazil
| | - Alana A. Borges
- Laboratory of Animal Biotechnology Federal Rural University of Semi‐Arid Mossoro Brazil
| | - Maria B. Silva
- Laboratory of Animal Biotechnology Federal Rural University of Semi‐Arid Mossoro Brazil
| | - Maria V. O. Santos
- Laboratory of Animal Biotechnology Federal Rural University of Semi‐Arid Mossoro Brazil
| | - Leandro R. Ribeiro
- Aba‐Yby Conservation Institute Environmental Park and Zoo Ecopoint Fortaleza Brazil
| | - Herlon V. R. Silva
- Laboratory of Reproduction of Carnivorous Ceara State University Fortaleza Brazil
| | - Alexsandra F. Pereira
- Laboratory of Animal Biotechnology Federal Rural University of Semi‐Arid Mossoro Brazil
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23
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Praxedes ÉA, Oliveira LRMD, Silva MB, Borges AA, Santos MVDO, Silva HVR, Oliveira MFD, Silva AR, Pereira AF. Effects of cryopreservation techniques on the preservation of ear skin – An alternative approach to conservation of jaguar, Panthera onca (Linnaeus, 1758). Cryobiology 2019; 88:15-22. [DOI: 10.1016/j.cryobiol.2019.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Revised: 03/13/2019] [Accepted: 04/24/2019] [Indexed: 11/26/2022]
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24
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Dental microwear textures and dietary preferences of extant rhinoceroses (Perissodactyla, Mammalia). MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00427-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Abstract
De-extinction projects for species such as the woolly mammoth and passenger pigeon have greatly stimulated public and scientific interest, producing a large body of literature and much debate. To date, there has been little consistency in descriptions of de-extinction technologies and purposes. In 2016, a special committee of the International Union for the Conservation of Nature (IUCN) published a set of guidelines for de-extinction practice, establishing the first detailed description of de-extinction; yet incoherencies in published literature persist. There are even several problems with the IUCN definition. Here I present a comprehensive definition of de-extinction practice and rationale that expounds and reconciles the biological and ecological inconsistencies in the IUCN definition. This new definition brings together the practices of reintroduction and ecological replacement with de-extinction efforts that employ breeding strategies to recover unique extinct phenotypes into a single “de-extinction” discipline. An accurate understanding of de-extinction and biotechnology segregates the restoration of certain species into a new classification of endangerment, removing them from the purview of de-extinction and into the arena of species’ recovery. I term these species as “evolutionarily torpid species”; a term to apply to species falsely considered extinct, which in fact persist in the form of cryopreserved tissues and cultured cells. For the first time in published literature, all currently active de-extinction breeding programs are reviewed and their progress presented. Lastly, I review and scrutinize various topics pertaining to de-extinction in light of the growing body of peer-reviewed literature published since de-extinction breeding programs gained public attention in 2013.
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26
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Hybrid white-rhino embryos created in last-ditch effort to stop extinction. Nature 2018. [DOI: 10.1038/d41586-018-05636-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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