1
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Lan T, Yang S, Li H, Zhang Y, Li R, Sahu SK, Deng W, Liu B, Shi M, Wang S, Du H, Huang X, Lu H, Liu S, Deng T, Chen J, Wang Q, Han L, Zhou Y, Li Q, Li D, Kristiansen K, Wan QH, Liu H, Fang SG. Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives. Proc Natl Acad Sci U S A 2024; 121:e2406343121. [PMID: 39186654 PMCID: PMC11388402 DOI: 10.1073/pnas.2406343121] [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: 03/28/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
The extinction risk of the giant panda has been demoted from "endangered" to "vulnerable" on the International Union for Conservation of Nature Red List, but its habitat is more fragmented than ever before, resulting in 33 isolated giant panda populations according to the fourth national survey released by the Chinese government. Further comprehensive investigations of the genetic background and in-depth assessments of the conservation status of wild populations are still necessary and urgently needed. Here, we sequenced the genomes of 612 giant pandas with an average depth of ~26× and generated a high-resolution map of genomic variation with more than 20 million variants covering wild individuals from six mountain ranges and captive representatives in China. We identified distinct genetic clusters within the Minshan population by performing a fine-grained genetic structure. The estimation of inbreeding and genetic load associated with historical population dynamics suggested that future conservation efforts should pay special attention to the Qinling and Liangshan populations. Releasing captive individuals with a genetic background similar to the recipient population appears to be an advantageous genetic rescue strategy for recovering the wild giant panda populations, as this approach introduces fewer deleterious mutations into the wild population than mating with differentiated lineages. These findings emphasize the superiority of large-scale population genomics to provide precise guidelines for future conservation of the giant panda.
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Affiliation(s)
- Tianming Lan
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Shangchen Yang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haimeng Li
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
| | - Yi Zhang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- BGI Research, Beijing Genomics Institute, Wuhan 430074, China
| | - Wenwen Deng
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Boyang Liu
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Shiqing Wang
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Hanyu Du
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyu Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Haorong Lu
- China National GeneBank, BGI Research, Beijing Genomics Institute, Shenzhen 518120, China
| | - Shanlin Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Deng
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Jin Chen
- China National GeneBank, BGI Research, Beijing Genomics Institute, Shenzhen 518120, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Lei Han
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yajie Zhou
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Qiye Li
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- BGI Research, Beijing Genomics Institute, Wuhan 430074, China
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Karsten Kristiansen
- Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao 266555, China
| | - Qiu-Hong Wan
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Sheng-Guo Fang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
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2
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Hu Y, Hu Y, Zhou W, Wei F. Conservation Genomics and Metagenomics of Giant and Red Pandas in the Wild. Annu Rev Anim Biosci 2024; 12:69-89. [PMID: 37863091 DOI: 10.1146/annurev-animal-021022-054730] [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: 10/22/2023]
Abstract
Giant pandas and red pandas are endangered species with similar specialized bamboo diet and partial sympatric distribution in China. Over the last two decades, the rapid development of genomics and metagenomics research on these species has enriched our knowledge of their biology, ecology, physiology, genetics, and evolution, which is crucial and useful for their conservation. We describe the evolutionary history, endangerment processes, genetic diversity, and population structure of wild giant pandas and two species of red pandas (Chinese and Himalayan red pandas). In addition, we explore how genomics and metagenomics studies have provided insight into the convergent adaptation of pandas to the specialized bamboo diet. Finally, we discuss how these findings are applied to effective conservation management of giant and red pandas in the wild and in captivity to promote the long-term persistence of these species.
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Affiliation(s)
- Yisi Hu
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fuwen Wei
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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3
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Lucena-Perez M, Paijmans JLA, Nocete F, Nadal J, Detry C, Dalén L, Hofreiter M, Barlow A, Godoy JA. Recent increase in species-wide diversity after interspecies introgression in the highly endangered Iberian lynx. Nat Ecol Evol 2024; 8:282-292. [PMID: 38225424 DOI: 10.1038/s41559-023-02267-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/10/2023] [Indexed: 01/17/2024]
Abstract
Genetic diversity is lost in small and isolated populations, affecting many globally declining species. Interspecific admixture events can increase genetic variation in the recipient species' gene pool, but empirical examples of species-wide restoration of genetic diversity by admixture are lacking. Here we present multi-fold coverage genomic data from three ancient Iberian lynx (Lynx pardinus) approximately 2,000-4,000 years old and show a continuous or recurrent process of interspecies admixture with the Eurasian lynx (Lynx lynx) that increased modern Iberian lynx genetic diversity above that occurring millennia ago despite its recent demographic decline. Our results add to the accumulating evidence for natural admixture and introgression among closely related species and show that this can result in an increase of species-wide genetic diversity in highly genetically eroded species. The strict avoidance of interspecific sources in current genetic restoration measures needs to be carefully reconsidered, particularly in cases where no conspecific source population exists.
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Affiliation(s)
- Maria Lucena-Perez
- Department of Ecology and Evolution, Estación Biológica de Doñana, CSIC, Seville, Spain
| | - Johanna L A Paijmans
- Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Francisco Nocete
- Grupo de Investigación MIDAS, Departamento Historia I (Prehistoria), Universidad de Huelva, Huelva, Spain
| | - Jordi Nadal
- SERP, Departament de Prehistoria, Historia Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Cleia Detry
- UNIARQ - Centro de Arqueologia da Faculdade de Letras da Universidade de Lisboa, Alameda da Universidade, Lisbon, Portugal
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- School of Environmental and Natural Sciences, Bangor University, Bangor, Gwynedd, UK
| | - José A Godoy
- Department of Ecology and Evolution, Estación Biológica de Doñana, CSIC, Seville, Spain.
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4
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Kinneberg VB, Lü DS, Peris D, Ravinet M, Skrede I. Introgression between highly divergent fungal sister species. J Evol Biol 2023; 36:1133-1149. [PMID: 37363874 DOI: 10.1111/jeb.14190] [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: 11/24/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 06/28/2023]
Abstract
To understand how species evolve and adapt to changing environments, it is important to study gene flow and introgression due to their influence on speciation and radiation events. Here, we apply a novel experimental system for investigating these mechanisms using natural populations. The system is based on two fungal sister species with morphological and ecological similarities occurring in overlapping habitats. We examined introgression between these species by conducting whole genome sequencing of individuals from populations in North America and Europe. We assessed genome-wide nucleotide divergence and performed crossing experiments to study reproductive barriers. We further used ABBA-BABA statistics together with a network analysis to investigate introgression, and conducted demographic modelling to gain insight into divergence times and introgression events. The results revealed that the species are highly divergent and incompatible in vitro. Despite this, small regions of introgression were scattered throughout the genomes and one introgression event likely involves a ghost population (extant or extinct). This study demonstrates that introgression can be found among divergent species and that population histories can be studied without collections of all the populations involved. Moreover, the experimental system is shown to be a useful tool for research on reproductive isolation in natural populations.
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Affiliation(s)
- Vilde Bruhn Kinneberg
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Evolution and Paleobiology, Natural History Museum, University of Oslo, Oslo, Norway
| | - Dabao Sun Lü
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - David Peris
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Valencia, Spain
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Inger Skrede
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
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5
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Hou X, Zhao J, Zhang H, Preick M, Hu J, Xiao B, Wang L, Deng M, Liu S, Chang F, Sheng G, Lai X, Hofreiter M, Yuan J. Paleogenomes Reveal a Complex Evolutionary History of Late Pleistocene Bison in Northeastern China. Genes (Basel) 2022; 13:genes13101684. [PMID: 36292570 PMCID: PMC9602171 DOI: 10.3390/genes13101684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/30/2022] Open
Abstract
Steppe bison are a typical representative of the Mid-Late Pleistocene steppes of the northern hemisphere. Despite the abundance of fossil remains, many questions related to their genetic diversity, population structure and dispersal route are still elusive. Here, we present both near-complete and partial mitochondrial genomes, as well as a partial nuclear genome from fossil bison samples excavated from Late Pleistocene strata in northeastern China. Maximum-likelihood and Bayesian trees both suggest the bison clade are divided into three maternal haplogroups (A, B and C), and Chinese individuals fall in two of them. Bayesian analysis shows that the split between haplogroup C and the ancestor of haplogroups A and B dates at 326 ky BP (95% HPD: 397-264 ky BP). In addition, our nuclear phylogenomic tree also supports a basal position for the individual carrying haplogroup C. Admixture analyses suggest that CADG467 (haplogroup C) has a similar genetic structure to steppe bison from Siberia (haplogroup B). Our new findings indicate that the genetic diversity of Pleistocene bison was probably even higher than previously thought and that northeastern Chinese populations of several mammalian species, including Pleistocene bison, were genetically distinct.
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Affiliation(s)
- Xindong Hou
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Jian Zhao
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Michaela Preick
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24–25, 14476 Potsdam, Germany
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Linying Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
| | - Miaoxuan Deng
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Sizhao Liu
- Department of Scientific Research, Dalian Natural History Museum, Dalian 116023, China
| | - Fengqin Chang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, China
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- School of Earth Sciences, China University of Geosciences, Wuhan 430074, China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24–25, 14476 Potsdam, Germany
- Correspondence: (M.H.); (J.Y.); Tel.: +49-331-977-6321 (M.H.); +86-027-6788-3022 (J.Y.)
| | - Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, China
- Correspondence: (M.H.); (J.Y.); Tel.: +49-331-977-6321 (M.H.); +86-027-6788-3022 (J.Y.)
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6
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Guang X, Lan T, Wan QH, Huang Y, Li H, Zhang M, Li R, Zhang Z, Lei Y, Zhang L, Zhang H, Li D, Li X, Li H, Xu Y, Qiao M, Wu D, Tang K, Zhao P, Lin JQ, Kumar Sahu S, Liang Q, Jiang W, Zhang D, Xu X, Liu X, Lisby M, Yang H, Kristiansen K, Liu H, Fang SG. Chromosome-scale genomes provide new insights into subspecies divergence and evolutionary characteristics of the giant panda. Sci Bull (Beijing) 2021; 66:2002-2013. [PMID: 36654170 DOI: 10.1016/j.scib.2021.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/27/2020] [Accepted: 12/25/2020] [Indexed: 02/03/2023]
Abstract
Extant giant pandas are divided into Sichuan and Qinling subspecies. The giant panda has many species-specific characteristics, including comparatively small organs for body size, small genitalia of male individuals, and low reproduction. Here, we report the most contiguous, high-quality chromosome-level genomes of two extant giant panda subspecies to date, with the first genome assembly of the Qinling subspecies. Compared with the previously assembled giant panda genomes based on short reads, our two assembled genomes increased contiguity over 200-fold at the contig level. Additional sequencing of 25 individuals dated the divergence of the Sichuan and Qinling subspecies into two distinct clusters from 10,000 to 12,000 years ago. Comparative genomic analyses identified the loss of regulatory elements in the dachshund family transcription factor 2 (DACH2) gene and specific changes in the synaptotagmin 6 (SYT6) gene, which may be responsible for the reduced fertility of the giant panda. Positive selection analysis between the two subspecies indicated that the reproduction-associated IQ motif containing D (IQCD) gene may at least partly explain the different reproduction rates of the two subspecies. Furthermore, several genes in the Hippo pathway exhibited signs of rapid evolution with giant panda-specific variants and divergent regulatory elements, which may contribute to the reduced inner organ sizes of the giant panda.
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Affiliation(s)
- Xuanmin Guang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Tianming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Hong Li
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Mingchun Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Zhizhong Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Yinghu Lei
- Qinling Research Center of Giant Panda Breeding, Shaanxi Academy of Forestry, Xi'an 710082, China
| | - Ling Zhang
- China Wildlife Conservation Association, Beijing 100714, China
| | - Heming Zhang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Xiaoping Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Haimeng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yan Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Maiju Qiao
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Daifu Wu
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, China
| | - Keyi Tang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pengpeng Zhao
- Qinling Research Center of Giant Panda Breeding, Shaanxi Academy of Forestry, Xi'an 710082, China
| | - Jian-Qing Lin
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qiqi Liang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Danhui Zhang
- Qinling Research Center of Giant Panda Breeding, Shaanxi Academy of Forestry, Xi'an 710082, China
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518120, China
| | - Xin Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Michael Lisby
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Huanming Yang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518120, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark; Qingdao-Europe Advanced Institute for Life Sciences, Qingdao 266555, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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7
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Pérez-Escobar OA, Bellot S, Przelomska NAS, Flowers JM, Nesbitt M, Ryan P, Gutaker RM, Gros-Balthazard M, Wells T, Kuhnhäuser BG, Schley R, Bogarín D, Dodsworth S, Diaz R, Lehmann M, Petoe P, Eiserhardt WL, Preick M, Hofreiter M, Hajdas I, Purugganan M, Antonelli A, Gravendeel B, Leitch IJ, Torres Jimenez MF, Papadopulos AST, Chomicki G, Renner SS, Baker WJ. Molecular clocks and archaeogenomics of a Late Period Egyptian date palm leaf reveal introgression from wild relatives and add timestamps on the domestication. Mol Biol Evol 2021; 38:4475-4492. [PMID: 34191029 PMCID: PMC8476131 DOI: 10.1093/molbev/msab188] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.
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Affiliation(s)
| | - Sidonie Bellot
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Jonathan M Flowers
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Mark Nesbitt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Philippa Ryan
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Muriel Gros-Balthazard
- French National Research Institute for Sustainable Development, Montpellier, BP 64501 - 34394 Cedex 5, France
| | - Tom Wells
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK
| | | | - Rowan Schley
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Diego Bogarín
- Lankester Botanical Garden, University of Costa Rica, San José, 302-7050, Costa Rica
| | - Steven Dodsworth
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Rudy Diaz
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | | | - Peter Petoe
- Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Biology, Aarhus University, 8000 Aarhus C, Denmark
| | - Michaela Preick
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Michael Hofreiter
- Institute of Biochemistry and Biology, University of Potsdam, 14469 Potsdam, Germany
| | - Irka Hajdas
- Department of Earth Sciences, ETH Zurich, 8092, Switzerland
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, United Arab Emirates
| | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK.,Department of Plant Sciences, University of Oxford, Oxford, OX1 3QU, UK.,Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | | | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond TW9 3AE. London, UK
| | - Maria Fernanda Torres Jimenez
- Gothenburg Global Biodiversity Centre and Department of Biological and Environmental Sciences, University of Gothenburg, 413 19, Sweden
| | - Alexander S T Papadopulos
- Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, University of Bangor, Bangor LL57 2UW, UK
| | - Guillaume Chomicki
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO 63130, USA
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8
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Smith AD, Kamiński MJ, Kanda K, Sweet AD, Betancourt JL, Holmgren CA, Hempel E, Alberti F, Hofreiter M. Recovery and analysis of ancient beetle DNA from subfossil packrat middens using high-throughput sequencing. Sci Rep 2021; 11:12635. [PMID: 34135378 PMCID: PMC8209150 DOI: 10.1038/s41598-021-91896-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/26/2021] [Indexed: 11/16/2022] Open
Abstract
The study of ancient DNA is revolutionizing our understanding of paleo-ecology and the evolutionary history of species. Insects are essential components in many ecosystems and constitute the most diverse group of animals. Yet they are largely neglected in ancient DNA studies. We report the results of the first targeted investigation of insect ancient DNA to positively identify subfossil insects to species, which includes the recovery of endogenous content from samples as old as ~ 34,355 ybp. Potential inhibitors currently limiting widespread research on insect ancient DNA are discussed, including the lack of closely related genomic reference sequences (decreased mapping efficiency) and the need for more extensive collaborations with insect taxonomists. The advantages of insect-based studies are also highlighted, especially in the context of understanding past climate change. In this regard, insect remains from ancient packrat middens are a rich and largely uninvestigated resource for exploring paleo-ecology and species dynamics over time.
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Affiliation(s)
- Aaron D Smith
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA.
| | - Marcin J Kamiński
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
- Zoological Museum, Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679, Warszawa, Poland
| | - Kojun Kanda
- USDA Systematic Entomology Laboratory, C/O Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Andrew D Sweet
- Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
- Department of Biological Sciences, Arkansas State University, State University, AR, 72467, USA
| | | | - Camille A Holmgren
- Department of Geography and Planning, SUNY Buffalo State College, Buffalo, NY, USA
| | - Elisabeth Hempel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Museum Für Naturkunde, Berlin, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Federica Alberti
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Reiss-Engelhorn-Museen, Mannheim, Germany
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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9
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Straube N, Lyra ML, Paijmans JLA, Preick M, Basler N, Penner J, Rödel MO, Westbury MV, Haddad CFB, Barlow A, Hofreiter M. Successful application of ancient DNA extraction and library construction protocols to museum wet collection specimens. Mol Ecol Resour 2021; 21:2299-2315. [PMID: 34036732 DOI: 10.1111/1755-0998.13433] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/02/2023]
Abstract
Millions of scientific specimens are housed in museum collections, a large part of which are fluid preserved. The use of formaldehyde as fixative and subsequent storage in ethanol is especially common in ichthyology and herpetology. This type of preservation damages DNA and reduces the chance of successful retrieval of genetic data. We applied ancient DNA extraction and single stranded library construction protocols to a variety of vertebrate samples obtained from wet collections and of different ages. Our results show that almost all samples tested yielded endogenous DNA. Archival DNA extraction was successful across different tissue types as well as using small amounts of tissue. Conversion of archival DNA fragments into single-stranded libraries resulted in usable data even for samples with initially undetectable DNA amounts. Subsequent target capture approaches for mitochondrial DNA using homemade baits on a subset of 30 samples resulted in almost complete mitochondrial genome sequences in several instances. Thus, application of ancient DNA methodology makes wet collection specimens, including type material as well as rare, old or extinct species, accessible for genetic and genomic analyses. Our results, accompanied by detailed step-by-step protocols, are a large step forward to open the DNA archive of museum wet collections for scientific studies.
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Affiliation(s)
- Nicolas Straube
- University Museum of Bergen, Bergen, Norway.,SNSB Bavarian State Collection of Zoology, München, Germany
| | - Mariana L Lyra
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil.,Zoological Institute, Braunschweig University of Technology, Braunschweig, Germany
| | - Johanna L A Paijmans
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michaela Preick
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Nikolas Basler
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Johannes Penner
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany.,Chair of Wildlife Ecology and Management, Albert Ludwigs University Freiburg, Freiburg, Germany
| | - Mark-Oliver Rödel
- Museum für Naturkunde- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Michael V Westbury
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Célio F B Haddad
- Departamento de Biodiversidade, Instituto de Biociências and Centro de Aquicultura (CAUNESP), Laboratório de Herpetologia, Universidade Estadual Paulista - UNESP, Rio Claro, SP, Brazil
| | - Axel Barlow
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michael Hofreiter
- Department of Mathematics and Natural Sciences, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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10
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Barlow A, Paijmans JLA, Alberti F, Gasparyan B, Bar-Oz G, Pinhasi R, Foronova I, Puzachenko AY, Pacher M, Dalén L, Baryshnikov G, Hofreiter M. Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears. Curr Biol 2021; 31:1771-1779.e7. [PMID: 33592193 DOI: 10.1016/j.cub.2021.01.073] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 10/19/2020] [Accepted: 01/21/2021] [Indexed: 11/18/2022]
Abstract
Palaeogenomes provide the potential to study evolutionary processes in real time, but this potential is limited by our ability to recover genetic data over extended timescales.1 As a consequence, most studies so far have focused on samples of Late Pleistocene or Holocene age, which covers only a small part of the history of many clades and species. Here, we report the recovery of a low coverage palaeogenome from the petrous bone of a ∼360,000 year old cave bear from Kudaro 1 cave in the Caucasus Mountains. Analysis of this genome alongside those of several Late Pleistocene cave bears reveals widespread mito-nuclear discordance in this group. Using the time interval between Middle and Late Pleistocene cave bear genomes, we directly estimate ursid nuclear and mitochondrial substitution rates to calibrate their respective phylogenies. This reveals post-divergence mitochondrial transfer as the dominant factor explaining their mito-nuclear discordance. Interestingly, these transfer events were not accompanied by large-scale nuclear introgression. However, we do detect additional instances of nuclear admixture among other cave bear lineages, and between cave bears and brown bears, which are not associated with mitochondrial exchange. Genomic data obtained from the Middle Pleistocene cave bear petrous bone has thus facilitated a revised evolutionary history of this extinct megafaunal group. Moreover, it suggests that petrous bones may provide a means of extending both the magnitude and time depth of palaeogenome retrieval over substantial portions of the evolutionary histories of many mammalian clades.
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Affiliation(s)
- Axel Barlow
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK; Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany.
| | - Johanna L A Paijmans
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Federica Alberti
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, National Academy of Sciences of the Republic of Armenia, 0025, RA, Yerevan, 15 Charents st., Armenia
| | - Guy Bar-Oz
- The Zinman Institute of Archaeology, University of Haifa, 199 Aba-Hushi Avenue, Haifa, Israel 3498838
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Irina Foronova
- V.S. Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, 3, Ac. Koptyuga ave., Novosibirsk, Russia 630090
| | - Andrey Y Puzachenko
- Institute of Geography, Russian Academy of Sciences, Staromonetnyy Pereulok, 29, Moscow, Russia 119017
| | - Martina Pacher
- Naturmuseum St. Gallen, Rorschacher Strasse 263, CH-9016 St. Gallen, Switzerland
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm University, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden; Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Frescativägen 54, 114 18 Stockholm, Sweden
| | - Gennady Baryshnikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034 St. Petersburg, Russia
| | - Michael Hofreiter
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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11
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Paijmans JLA, Barlow A, Becker MS, Cahill JA, Fickel J, Förster DWG, Gries K, Hartmann S, Havmøller RW, Henneberger K, Kern C, Kitchener AC, Lorenzen ED, Mayer F, OBrien SJ, von Seth J, Sinding MHS, Spong G, Uphyrkina O, Wachter B, Westbury MV, Dalén L, Bhak J, Manica A, Hofreiter M. African and Asian leopards are highly differentiated at the genomic level. Curr Biol 2021; 31:1872-1882.e5. [PMID: 33848458 DOI: 10.1016/j.cub.2021.03.084] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 02/05/2021] [Accepted: 03/24/2021] [Indexed: 10/21/2022]
Abstract
Leopards are the only big cats still widely distributed across the continents of Africa and Asia. They occur in a wide range of habitats and are often found in close proximity to humans. But despite their ubiquity, leopard phylogeography and population history have not yet been studied with genomic tools. Here, we present population-genomic data from 26 modern and historical samples encompassing the vast geographical distribution of this species. We find that Asian leopards are broadly monophyletic with respect to African leopards across almost their entire nuclear genomes. This profound genetic pattern persists despite the animals' high potential mobility, and despite evidence of transfer of African alleles into Middle Eastern and Central Asian leopard populations within the last 100,000 years. Our results further suggest that Asian leopards originated from a single out-of-Africa dispersal event 500-600 thousand years ago and are characterized by higher population structuring, stronger isolation by distance, and lower heterozygosity than African leopards. Taxonomic categories do not take into account the variability in depth of divergence among subspecies. The deep divergence between the African subspecies and Asian populations contrasts with the much shallower divergence among putative Asian subspecies. Reconciling genomic variation and taxonomy is likely to be a growing challenge in the genomics era.
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Affiliation(s)
- Johanna L A Paijmans
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; Department of Genetics & Genome Biology, University of Leicester, Leicester LE1 7RH, UK; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Matthew S Becker
- Zambian Carnivore Programme, PO Box 80 Mfuwe, Eastern Province, Zambia
| | - James A Cahill
- Laboratory of Neurogenetics of Language, Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA; Department of Environmental Engineering Sciences, Engineering School of Sustainable Infrastructure and Environment, University of Florida, Gainesville, FL 32611
| | - Joerns Fickel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Daniel W G Förster
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Katrin Gries
- Der Grüne Zoo Wuppertal, Hubertusallee 30, 42117 Wuppertal, Germany
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Rasmus Worsøe Havmøller
- GLOBE institute, University of Copenhagen, Oester Voldgade 5-7, 1350, Copenhagen K, Denmark; Research and Collections, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen OE, Denmark
| | - Kirstin Henneberger
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Christian Kern
- Tierpark Berlin-Friedrichsfelde, Am Tierpark 125, 10319 Berlin, Germany
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK; Institute of Geography, School of Geosciences. Drummond Street, University of Edinburgh EH8 9XP, UK
| | - Eline D Lorenzen
- GLOBE institute, University of Copenhagen, Oester Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Frieder Mayer
- Museum für Naturkunde, Leibniz-Institut für Evolutions und Biodiversitätsforschung, Invalidenstraße 43, 10115 Berlin, Germany
| | - Stephen J OBrien
- Laboratory of Genomics Diversity, Center for Computer Technologies, ITMO University, 49 Kronverkskiy Pr., St. Petersburg, 197101, Russian Federation; Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, 8000 North Ocean Drive, Ft Lauderdale, Florida 33004 USA
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-10691 Stockholm, Sweden
| | | | - Göran Spong
- Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 907 83 UMEA, SWEDEN
| | - Olga Uphyrkina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, 159 Stoletiya Street, Vladivostok, 690022, Russia
| | - Bettina Wachter
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315 Berlin, Germany
| | - Michael V Westbury
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; GLOBE institute, University of Copenhagen, Oester Voldgade 5-7, 1350, Copenhagen K, Denmark
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden; Department of Zoology, Stockholm University, SE-10691 Stockholm, Sweden
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea; Clinomics, UNIST, Ulsan, 44919, Republic of Korea; Personal Genomics Institute, Genome Research Foundation, Cheongju, 28160, Republic of Korea
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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12
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Mitchell KJ, Rawlence NJ. Examining Natural History through the Lens of Palaeogenomics. Trends Ecol Evol 2021; 36:258-267. [PMID: 33455740 DOI: 10.1016/j.tree.2020.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022]
Abstract
The many high-resolution tools that are uniquely applicable to specimens from the Quaternary period (the past ~2.5 Ma) provide an opportunity to cross-validate data and test hypotheses based on the morphology and distribution of fossils. Among these tools is palaeogenomics - the genome-scale sequencing of genetic material from ancient specimens - that can provide direct insight into ecology and evolution, potentially improving the accuracy of inferences about past ecological communities over longer timescales. Palaeogenomics has revealed instances of over- and underestimation of extinct diversity, detected cryptic faunal migration and turnover, allowed quantification of widespread sex biases and sexual dimorphism in the fossil record, revealed past hybridisation events and hybrid individuals, and has highlighted previously unrecognised routes of zoonotic disease transfer.
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Affiliation(s)
- Kieren J Mitchell
- Australian Centre for Ancient DNA (ACAD), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia; Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage (CABAH), School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Nicolas J Rawlence
- Otago Palaeogenetics Laboratory, Department of Zoology, University of Otago, Dunedin, New Zealand
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13
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Dai QL, Li JW, Yang Y, Li M, Zhang K, He LY, Zhang J, Tang B, Liu HP, Li YX, Zhu LF, Yang ZS, Dai Q. Genetic Diversity and Prediction Analysis of Small Isolated Giant Panda Populations After Release of Individuals. Evol Bioinform Online 2020; 16:1176934320939945. [PMID: 32699496 PMCID: PMC7357131 DOI: 10.1177/1176934320939945] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022] Open
Abstract
Release of individuals is an effective conservation approach to protect endangered species. To save this small isolated giant panda population in Liziping Nature Reserve, a few giant pandas have been released to this population. Here we assess genetic diversity and future changes in the population using noninvasive genetic sampling after releasing giant pandas. In this study, a total of 28 giant pandas (including 4 released individuals) were identified in the Liziping, China. Compared with other giant panda populations, this population has medium-level genetic diversity; however, a Bayesian-coalescent method clearly detected, quantified, and dated a recent decrease in population size. The predictions for genetic diversity and survival of the population in the next 100 years indicate that this population has a high risk of extinction. We show that released giant pandas can preserve genetic diversity and improve the probability of survival in this small isolated giant panda population. To promote the recovery of this population, we suggest that panda release should be continued and this population will need to release 10 males and 20 females in the future.
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Affiliation(s)
- Qin-Long Dai
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
- Liziping National Nature Reserve, Shimian, Sichuan, China
- Shimian Research Center of Giant Panda Small Populaion Conservation and Rejuvenation, Shimian, Sichuan, China
| | - Jian-Wei Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
- Liziping National Nature Reserve, Shimian, Sichuan, China
- Shimian Research Center of Giant Panda Small Populaion Conservation and Rejuvenation, Shimian, Sichuan, China
| | - Yi Yang
- Liziping National Nature Reserve, Shimian, Sichuan, China
- Shimian Research Center of Giant Panda Small Populaion Conservation and Rejuvenation, Shimian, Sichuan, China
| | - Min Li
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
- Liziping National Nature Reserve, Shimian, Sichuan, China
- Shimian Research Center of Giant Panda Small Populaion Conservation and Rejuvenation, Shimian, Sichuan, China
| | - Kan Zhang
- Liziping National Nature Reserve, Shimian, Sichuan, China
- Shimian Research Center of Giant Panda Small Populaion Conservation and Rejuvenation, Shimian, Sichuan, China
| | - Liu-Yang He
- Gonggashan National Nature Reserve, Shimian, Sichuan, China
| | - Jun Zhang
- Liziping National Nature Reserve, Shimian, Sichuan, China
- Shimian Research Center of Giant Panda Small Populaion Conservation and Rejuvenation, Shimian, Sichuan, China
| | - Bo Tang
- Liziping National Nature Reserve, Shimian, Sichuan, China
- Shimian Research Center of Giant Panda Small Populaion Conservation and Rejuvenation, Shimian, Sichuan, China
| | - Hui-Ping Liu
- Liziping National Nature Reserve, Shimian, Sichuan, China
- Shimian Research Center of Giant Panda Small Populaion Conservation and Rejuvenation, Shimian, Sichuan, China
| | - Yu-Xia Li
- Shimian Agricultural and Rural Bureau, Shimian, Sichuan, China
| | - Li-Feng Zhu
- Nanjing Normal University, Nanjing, Jiangsu, China
| | - Zhi-Song Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, Sichuan, China
- Sichuan Academy of Giant Panda, Chengdu, Sichuan, China
| | - Qiang Dai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
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14
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Abstract
We present the earliest evidence for domestic cat (Felis catus L., 1758) from Kazakhstan, found as a well preserved skeleton with extensive osteological pathologies dating to 775–940 cal CE from the early medieval city of Dzhankent, Kazakhstan. This urban settlement was located on the intersection of the northern Silk Road route which linked the cities of Khorezm in the south to the trading settlements in the Volga region to the north and was known in the tenth century CE as the capital of the nomad Oghuz. The presence of this domestic cat, presented here as an osteobiography using a combination of zooarchaeological, genetic, and isotopic data, provides proxy evidence for a fundamental shift in the nature of human-animal relationships within a previously pastoral region. This illustrates the broader social, cultural, and economic changes occurring within the context of rapid urbanisation during the early medieval period along the Silk Road.
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15
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Mathieson I, Abascal F, Vinner L, Skoglund P, Pomilla C, Mitchell P, Arthur C, Gurdasani D, Willerslev E, Sandhu MS, Dewar G. An Ancient Baboon Genome Demonstrates Long-Term Population Continuity in Southern Africa. Genome Biol Evol 2020; 12:407-412. [PMID: 32022848 PMCID: PMC7197492 DOI: 10.1093/gbe/evaa019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 12/19/2022] Open
Abstract
Baboons are one of the most abundant large nonhuman primates and are widely studied in biomedical, behavioral, and anthropological research. Despite this, our knowledge of their evolutionary and demographic history remains incomplete. Here, we report a 0.9-fold coverage genome sequence from a 5800-year-old baboon from the site of Ha Makotoko in Lesotho. The ancient baboon is closely related to present-day Papio ursinus individuals from southern Africa-indicating a high degree of continuity in the southern African baboon population. This level of population continuity is rare in recent human populations but may provide a good model for the evolution of Homo and other large primates over similar timespans in structured populations throughout Africa.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania
| | | | - Lasse Vinner
- Centre for GeoGenetics, University of Copenhagen, Denmark
| | | | - Cristina Pomilla
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Omnigen Biodata Ltd., Cambridge, United Kingdom
| | - Peter Mitchell
- School of Archaeology, University of Oxford, United Kingdom
- School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Braamfontein, South Africa
| | - Charles Arthur
- School of Archaeology, University of Oxford, United Kingdom
| | - Deepti Gurdasani
- William Harvey Research Institute, Queen Mary’s University of London, United Kingdom
| | - Eske Willerslev
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Centre for GeoGenetics, University of Copenhagen, Denmark
- Department of Zoology, University of Cambridge, United Kingdom
- The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Manj S Sandhu
- Department of Medicine, University of Cambridge, United Kingdom
| | - Genevieve Dewar
- School of Geography, Archaeology and Environmental Studies, University of the Witwatersrand, Braamfontein, South Africa
- Department of Anthropology, University of Toronto Scarborough, Toronto, Ontario, Canada
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Barlow A, Hartmann S, Gonzalez J, Hofreiter M, Paijmans JLA. Consensify: A Method for Generating Pseudohaploid Genome Sequences from Palaeogenomic Datasets with Reduced Error Rates. Genes (Basel) 2020; 11:E50. [PMID: 31906474 PMCID: PMC7017230 DOI: 10.3390/genes11010050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 11/16/2022] Open
Abstract
A standard practise in palaeogenome analysis is the conversion of mapped short read data into pseudohaploid sequences, frequently by selecting a single high-quality nucleotide at random from the stack of mapped reads. This controls for biases due to differential sequencing coverage, but it does not control for differential rates and types of sequencing error, which are frequently large and variable in datasets obtained from ancient samples. These errors have the potential to distort phylogenetic and population clustering analyses, and to mislead tests of admixture using D statistics. We introduce Consensify, a method for generating pseudohaploid sequences, which controls for biases resulting from differential sequencing coverage while greatly reducing error rates. The error correction is derived directly from the data itself, without the requirement for additional genomic resources or simplifying assumptions such as contemporaneous sampling. For phylogenetic and population clustering analysis, we find that Consensify is less affected by artefacts than methods based on single read sampling. For D statistics, Consensify is more resistant to false positives and appears to be less affected by biases resulting from different laboratory protocols than other frequently used methods. Although Consensify is developed with palaeogenomic data in mind, it is applicable for any low to medium coverage short read datasets. We predict that Consensify will be a useful tool for future studies of palaeogenomes.
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Lan TM, Lin Y, Njaramba-Ngatia J, Guo XS, Li RG, Li HM, Kumar-Sahu S, Wang X, Yang XJ, Guo HB, Xu WH, Kristiansen K, Liu H, Xu YC. Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data. Genes (Basel) 2019; 10:E509. [PMID: 31284503 PMCID: PMC6679096 DOI: 10.3390/genes10070509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 11/16/2022] Open
Abstract
The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.
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Affiliation(s)
- Tian Ming Lan
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yu Lin
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Ren Gui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Hai Meng Li
- BGI-Shenzhen, Shenzhen 518083, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sunil Kumar-Sahu
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xie Wang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
| | - Xiu Juan Yang
- Heilongjiang Provincial Museum, Harbin 150001, China
| | - Hua Bing Guo
- Forest Inventory and Planning Institute of Jilin Province, Changchun 130022, China
| | - Wen Hao Xu
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- BGI-Shenzhen, Shenzhen 518083, China
| | - Huan Liu
- BGI-Shenzhen, Shenzhen 518083, China.
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen 518083, China.
| | - Yan Chun Xu
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China.
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