1
|
Hartwig Bessa M, Silva Gottschalk M, Jaqueline Robe L. Whole genome phylogenomics helps to resolve the phylogenetic position of the Zygothrica genus group (Diptera, Drosophilidae) and the causes of previous incongruences. Mol Phylogenet Evol 2024:108158. [PMID: 39025321 DOI: 10.1016/j.ympev.2024.108158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/28/2024] [Accepted: 07/14/2024] [Indexed: 07/20/2024]
Abstract
Incomplete Lineage Sorting (ILS) and introgression are among the two main factors causing incongruence between gene and species trees. Advances in phylogenomic studies have allowed us to overcome most of these issues, providing reliable phylogenetic hypotheses while revealing the underlying evolutionary scenario. Across the last century, many incongruent phylogenetic reconstructions were recovered for Drosophilidae, employing a limited sampling of genetic markers or species. In these studies, the monophyly and the phylogenetic positioning of the Zygothrica genus group stood out as one of the most controversial questions. Thus, here, we addressed these issues using a phylogenomic approach, while accessing the influence of ILS and introgressions on the diversification of these species and addressing the spatio-temporal scenario associated with their evolution. For this task, the genomes of nine specimens from six Neotropical species belonging to the Zygothrica genus group were sequenced and evaluated in a phylogenetic framework encompassing other 39 species of Drosophilidae. Nucleotide and amino acid sequences recovered for a set of 2,534 single-copy genes by BUSCO were employed to reconstruct maximum likelihood (ML) concatenated and multi-species coalescent (MSC) trees. Likelihood mapping, quartet sampling, and reticulation tests were employed to infer the level and causes of incongruence. Lastly, a penalized-likelihood molecular clock strategy with fossil calibrations was performed to infer divergence times. Taken together, our results recovered the subdivision of Drosophila into six different lineages, one of which clusters species of the Zygothrica genus group (except for H. duncani). The divergence of this lineage was dated to Oligocene ∼ 31 Mya and seems to have occurred in the same timeframe as other key diversification within Drosophila. According to the concatenated and MSC strategies, this lineage is sister to the clade joining Drosophila (Siphlodora) with the Hawaiian Drosophila and Scaptomyza. Likelihood mapping, quartet sampling, reticulation reconstructions as well as introgression tests revealed that this lineage was the target of several hybridization events involving the ancestors of different Drosophila lineages. Thus, our results generally show introgression as a major source of previous incongruence. Nevertheless, the similar diversification times recovered for several of the Neotropical Drosophila lineages also support the scenario of multiple and simultaneous diversifications taking place at the base of Drosophilidae phylogeny, at least in the Neotropics.
Collapse
Affiliation(s)
- Maiara Hartwig Bessa
- Programa de Pós-Graduação em Biodiversidade Animal (PPGBA), Universidade Federal de Santa Maria (UFSM), Brazil
| | - Marco Silva Gottschalk
- Programa de Pós-Graduação em Biodiversidade Animal (PPGBDiv), Instituto de Biologia, Universidade Federal de Pelotas (UFPel), Brazil
| | - Lizandra Jaqueline Robe
- Programa de Pós-Graduação em Biodiversidade Animal (PPGBA), Universidade Federal de Santa Maria (UFSM), Brazil.
| |
Collapse
|
2
|
Srigyan M, Schubert BW, Bushell M, Santos SHD, Figueiró HV, Sacco S, Eizirik E, Shapiro B. Mitogenomic analysis of a late Pleistocene jaguar from North America. J Hered 2024; 115:424-431. [PMID: 38150503 PMCID: PMC11235123 DOI: 10.1093/jhered/esad082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 12/02/2023] [Accepted: 12/22/2023] [Indexed: 12/29/2023] Open
Abstract
The jaguar (Panthera onca) is the largest living cat species native to the Americas and one of few large American carnivorans to have survived into the Holocene. However, the extent to which jaguar diversity declined during the end-Pleistocene extinction event remains unclear. For example, Pleistocene jaguar fossils from North America are notably larger than the average extant jaguar, leading to hypotheses that jaguars from this continent represent a now-extinct subspecies (Panthera onca augusta) or species (Panthera augusta). Here, we used a hybridization capture approach to recover an ancient mitochondrial genome from a large, late Pleistocene jaguar from Kingston Saltpeter Cave, Georgia, United States, which we sequenced to 26-fold coverage. We then estimated the evolutionary relationship between the ancient jaguar mitogenome and those from other extinct and living large felids, including multiple jaguars sampled across the species' current range. The ancient mitogenome falls within the diversity of living jaguars. All sampled jaguar mitogenomes share a common mitochondrial ancestor ~400 thousand years ago, indicating that the lineage represented by the ancient specimen dispersed into North America from the south at least once during the late Pleistocene. While genomic data from additional and older specimens will continue to improve understanding of Pleistocene jaguar diversity in the Americas, our results suggest that this specimen falls within the variation of extant jaguars despite the relatively larger size and geographic location and does not represent a distinct taxon.
Collapse
Affiliation(s)
- Megha Srigyan
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Blaine W Schubert
- Department of Geosciences, Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States
| | - Matthew Bushell
- Department of Geosciences, Center of Excellence in Paleontology, East Tennessee State University, Johnson City, TN, United States
| | - Sarah H D Santos
- Department of Biology, University of Western Ontario, London, ON, Canada
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Henrique Vieira Figueiró
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
- Environmental Genomics Group, Vale Institute of Technology, Belem, PA, Brazil
| | - Samuel Sacco
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, United States
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, United States
| |
Collapse
|
3
|
Murphy WJ, Harris AJ. Toward telomere-to-telomere cat genomes for precision medicine and conservation biology. Genome Res 2024; 34:655-664. [PMID: 38849156 PMCID: PMC11216403 DOI: 10.1101/gr.278546.123] [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] [Indexed: 06/09/2024]
Abstract
Genomic data from species of the cat family Felidae promise to stimulate veterinary and human medical advances, and clarify the coherence of genome organization. We describe how interspecies hybrids have been instrumental in the genetic analysis of cats, from the first genetic maps to propelling cat genomes toward the T2T standard set by the human genome project. Genotype-to-phenotype mapping in cat models has revealed dozens of health-related genetic variants, the molecular basis for mammalian pigmentation and patterning, and species-specific adaptations. Improved genomic surveillance of natural and captive populations across the cat family tree will increase our understanding of the genetic architecture of traits, population dynamics, and guide a future of genome-enabled biodiversity conservation.
Collapse
Affiliation(s)
- William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA;
- Department of Biology, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
| | - Andrew J Harris
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77843-4458, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, Texas 77843-4458, USA
| |
Collapse
|
4
|
Yuan J, Hu J, Liu W, Chen S, Zhang F, Wang S, Zhang Z, Wang L, Xiao B, Li F, Hofreiter M, Lai X, Westbury MV, Sheng G. Camelus knoblochi genome reveals the complex evolutionary history of Old World camels. Curr Biol 2024; 34:2502-2508.e5. [PMID: 38754423 DOI: 10.1016/j.cub.2024.04.050] [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: 10/17/2023] [Revised: 12/22/2023] [Accepted: 04/22/2024] [Indexed: 05/18/2024]
Abstract
Extant Old World camels (genus Camelus) contributed to the economic and cultural exchanges between the East and West for thousands of years.1,2 Although many remains have been unearthed,3,4,5 we know neither whether the prevalent hybridization observed between extant Camelus species2,6,7 also occurred between extinct lineages and the ancestors of extant Camelus species nor why some populations became extinct while others survived. To investigate these questions, we generated paleogenomic and stable isotope data from an extinct two-humped camel species, Camelus knoblochi. We find that in the mitochondrial phylogeny, all C. knoblochi form a paraphyletic group that nests within the diversity of modern, wild two-humped camels (Camelus ferus). In contrast, they are clearly distinguished from both wild and domesticated (Camelus bactrianus) two-humped camels on the nuclear level. Moreover, the divergence pattern of the three camel species approximates a trifurcation, because the most common topology is only slightly more frequent than the two other possible topologies. This mito-nuclear phylogenetic discordance likely arose due to interspecific gene flow between all three species, suggesting that interspecific hybridization is not exclusive to modern camels but a recurrent phenomenon throughout the evolutionary history of the genus Camelus. These results suggest that the genomic complexity of Old World camels' evolutionary history is underestimated when considering data from only modern species. Finally, we find that C. knoblochi populations began declining prior to the last glacial maximum and, by integrating palaeoecological evidence and stable isotope data, suggest that this was likely due to failure to adapt to a changing environment.
Collapse
Affiliation(s)
- Junxia Yuan
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; Faculty of Materials Science and Chemistry, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China.
| | - Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Earth Sciences, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Wenhui Liu
- Institute of Environmental Archaeology, National Museum of China, East Chang'an Street 16, Beijing 100006, People's Republic of China
| | - Shungang Chen
- Faculty of Materials Science and Chemistry, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China
| | - Fengli Zhang
- Daqing Museum, Wenyuan Street 2, Daqing, Heilongjiang 163711, People's Republic of China
| | - Siren Wang
- Daqing Museum, Wenyuan Street 2, Daqing, Heilongjiang 163711, People's Republic of China
| | - Zhen Zhang
- Zhaoyuan Museum, Zhongyang Street 192, Daqing, Heilongjiang 166599, People's Republic of China
| | - Linying Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Earth Sciences, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Fuqiang Li
- Yifu Museum, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Earth Sciences, China University of Geosciences, Lumo Road 388, Wuhan 430074, People's Republic of China
| | - Michael V Westbury
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, 1353 Copenhagen, Denmark.
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China; School of Environmental Studies, China University of Geosciences, Jincheng Road 68, Wuhan 430078, People's Republic of China.
| |
Collapse
|
5
|
Broggini C, Cavallini M, Vanetti I, Abell J, Binelli G, Lombardo G. From Caves to the Savannah, the Mitogenome History of Modern Lions ( Panthera leo) and Their Ancestors. Int J Mol Sci 2024; 25:5193. [PMID: 38791233 PMCID: PMC11121052 DOI: 10.3390/ijms25105193] [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: 04/16/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Lions (Panthera leo) play a crucial ecological role in shaping and maintaining fragile ecosystems within Africa. Conservation efforts should focus on genetic variability within wild populations when considering reintroduction attempts. We studied two groups of lions from two conservation sites located in Zambia and Zimbabwe to determine their genetic make-up, information that is usually unknown to the sites. In this study, we analysed 17 specimens for cytb and seven microsatellite markers to ascertain family relationships and genetic diversity previously obtained by observational studies. We then produced a standardised haplogroup phylogeny using all available entire mitogenomes, as well as calculating a revised molecular clock. The modern lion lineage diverged ~151 kya and was divided into two subspecies, both containing three distinct haplogroups. We confirm that Panthera leo persica is not a subspecies, but rather a haplogroup of the northern P.l. leo that exited Africa at least ~31 kya. The progenitor to all lions existed ~1.2 Mya, possibly in SE Africa, and later exited Africa and split into the two cave lion lineages ~175 kya. Species demography is correlated to major climactic events. We now have a detailed phylogeny of lion evolution and an idea of their conservation status given the threat of climate change.
Collapse
Affiliation(s)
- Camilla Broggini
- Wildlife Research Unit (UIRCP-UCO), University of Cordoba, 14071 Córdoba, Spain;
| | - Marta Cavallini
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
| | - Isabella Vanetti
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
| | - Jackie Abell
- Centre for Agroecology, Water and Resilience, Coventry University, Coventry CV8 3LG, UK;
| | - Giorgio Binelli
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
| | - Gianluca Lombardo
- Department of Biotechnology and Life Sciences (DBSV), University of Insubria, 21100 Varese, Italy; (M.C.); (I.V.); (G.B.)
| |
Collapse
|
6
|
Kraberger S, Serieys LEK, Leighton GRM, De Koch MD, Munday JS, Bishop JM, Varsani A. Two Lineages of Papillomaviruses Identified from Caracals ( Caracal caracal) in South Africa. Viruses 2024; 16:701. [PMID: 38793583 PMCID: PMC11125996 DOI: 10.3390/v16050701] [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: 04/03/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Papillomaviruses (PV) infect epithelial cells and can cause hyperplastic or neoplastic lesions. In felids, most described PVs are from domestic cats (Felis catus; n = 7 types), with one type identified in each of the five wild felid species studied to date (Panthera uncia, Puma concolor, Leopardus wiedii, Panthera leo persica and Lynx rufus). PVs from domestic cats are highly diverse and are currently classified into three genera (Lambdapapillomavirus, Dyothetapapillomavirus, and Taupapillomavirus), whereas those from wild felids, although diverse, are all classified into the Lambdapapillomavirus genus. In this study, we used a metagenomic approach to identify ten novel PV genomes from rectal swabs of five deceased caracals (Caracal caracal) living in the greater Cape Town area, South Africa. These are the first PVs to be described from caracals, and represent six new PV types, i.e., Caracal caracal papillomavirus (CcarPV) 1-6. These CcarPV fall into two phylogenetically distinct genera: Lambdapapillomavirus, and Treisetapapillomavirus. Two or more PV types were identified in a single individual for three of the five caracals, and four caracals shared at least one of the same PV types with another caracal. This study broadens our understanding of wild felid PVs and provides evidence that there may be several wild felid PV lineages.
Collapse
Affiliation(s)
- Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | | | - Gabriella R M Leighton
- Institute for Communities and Wildlife in Africa (iCWild), Department of Biological Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Matthew D De Koch
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - John S Munday
- School of Veterinary Science, Massey University, Tennant Drive, Palmerston North 4442, New Zealand
| | - Jacqueline M Bishop
- Institute for Communities and Wildlife in Africa (iCWild), Department of Biological Sciences, University of Cape Town, Cape Town 7701, South Africa
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town 7925, South Africa
| |
Collapse
|
7
|
Lawson DJ, Howard-McCombe J, Beaumont M, Senn H. How admixed captive breeding populations could be rescued using local ancestry information. Mol Ecol 2024:e17349. [PMID: 38634332 DOI: 10.1111/mec.17349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/21/2023] [Accepted: 02/26/2024] [Indexed: 04/19/2024]
Abstract
This paper asks the question: can genomic information be used to recover a species that is already on the pathway to extinction due to genetic swamping from a related and more numerous population? We show that a breeding strategy in a captive breeding program can use whole genome sequencing to identify and remove segments of DNA introgressed through hybridisation. The proposed policy uses a generalized measure of kinship or heterozygosity accounting for local ancestry, that is, whether a specific genetic location was inherited from the target of conservation. We then show that optimizing these measures would minimize undesired ancestry while also controlling kinship and/or heterozygosity, in a simulated breeding population. The process is applied to real data representing the hybridized Scottish wildcat breeding population, with the result that it should be possible to breed out domestic cat ancestry. The ability to reverse introgression is a powerful tool brought about through the combination of sequencing with computational advances in ancestry estimation. Since it works best when applied early in the process, important decisions need to be made about which genetically distinct populations should benefit from it and which should be left to reform into a single population.
Collapse
Affiliation(s)
- Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Jo Howard-McCombe
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Helen Senn
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh, UK
| |
Collapse
|
8
|
Carroll RA, Rice ES, Murphy WJ, Lyons LA, Thibaud-Nissen F, Coghill LM, Swanson WF, Terio KA, Boyd T, Warren WC. A chromosome-scale fishing cat reference genome for the evaluation of potential germline risk variants. Sci Rep 2024; 14:8073. [PMID: 38580653 PMCID: PMC10997796 DOI: 10.1038/s41598-024-56003-7] [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: 11/08/2023] [Accepted: 02/29/2024] [Indexed: 04/07/2024] Open
Abstract
The fishing cat, Prionailurus viverrinus, faces a population decline, increasing the importance of maintaining healthy zoo populations. Unfortunately, zoo-managed individuals currently face a high prevalence of transitional cell carcinoma (TCC), a form of bladder cancer. To investigate the genetics of inherited diseases among captive fishing cats, we present a chromosome-scale assembly, generate the pedigree of the zoo-managed population, reaffirm the close genetic relationship with the Asian leopard cat (Prionailurus bengalensis), and identify 7.4 million single nucleotide variants (SNVs) and 23,432 structural variants (SVs) from whole genome sequencing (WGS) data of healthy and TCC cats. Only BRCA2 was found to have a high recurrent number of missense mutations in fishing cats diagnosed with TCC when compared to inherited human cancer risk variants. These new fishing cat genomic resources will aid conservation efforts to improve their genetic fitness and enhance the comparative study of feline genomes.
Collapse
Affiliation(s)
- Rachel A Carroll
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - Edward S Rice
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, Texas A and M University, College Station, TX, 77843-4458, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Lyndon M Coghill
- Bioinformatics and Analytics Core, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA
| | - William F Swanson
- Center for Conservation and Research of Endangered Wildlife, Cincinnati Zoo and Botanical Garden, 3400 Vine St., Cincinnati, OH, 45220, USA
| | - Karen A Terio
- Zoological Pathology Program, University of Illinois, 3300 Golf Rd, Brookfield, IL, 60513, USA
| | - Tyler Boyd
- Oklahoma City Zoo and Botanical Garden, 2000 Remington Pl., Oklahoma, OK, 73111, USA
| | - Wesley C Warren
- Bond Life Sciences Center, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
- Department of Surgery, Bond Life Sciences Center, Institute of Data Science and Informatics, University of Missouri, 1201 Rollins St., Columbia, MO, 65211, USA.
| |
Collapse
|
9
|
Qi H, Lim QL, Kinoshita K, Nakajima N, Inoue-Murayama M. A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models. Mol Ecol Resour 2024; 24:e13928. [PMID: 38234258 DOI: 10.1111/1755-0998.13928] [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: 05/17/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
Individual age can be used to design more efficient and suitable management plans in both in situ and ex situ conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that can accurately estimate age from small amounts of biological material, which can be collected in a minimally invasive manner. In this study, we sequenced five targeted genetic regions and used 8-23 selected CpG sites to build age estimation models using machine learning methods at only about $3-7 per sample. Blood samples of seven Felidae species were used, ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples) and five Panthera species (96 samples). The models achieved satisfactory accuracy, with the mean absolute error of the most accurate models recorded at 1.966, 1.348 and 1.552 years in domestic cats, Tsushima leopard cats and Panthera spp. respectively. We developed the models in domestic cats and Tsushima leopard cats, which were applicable to individuals regardless of health conditions; therefore, these models are applicable to samples collected from individuals with diverse characteristics, which is often the case in conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using only two of the five genetic regions. We do not recommend building a common age estimation model for all the target species using our markers, because of the degraded performance of models that included all species.
Collapse
Affiliation(s)
- Huiyuan Qi
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | - Qi Luan Lim
- Wildlife Research Center, Kyoto University, Kyoto, Japan
| | | | - Nobuyoshi Nakajima
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | | |
Collapse
|
10
|
de Flamingh A, Gnoske TP, Rivera-Colón AG, Simeonovski VA, Kerbis Peterhans JC, Yamaguchi N, Witt KE, Catchen J, Roca AL, Malhi RS. Genomic analysis supports Cape Lion population connectivity prior to colonial eradication and extinction. J Hered 2024; 115:155-165. [PMID: 38150491 DOI: 10.1093/jhered/esad081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/26/2023] [Indexed: 12/29/2023] Open
Abstract
Cape lions (Panthera leo melanochaitus) formerly ranged throughout the grassland plains of the "Cape Flats" in what is today known as the Western Cape Province, South Africa. Cape lions were likely eradicated because of overhunting and habitat loss after European colonization. European naturalists originally described Cape lions as "black-maned lions" and claimed that they were phenotypically distinct. However, other depictions and historical descriptions of lions from the Cape report mixed or light coloration and without black or extensively developed manes. These findings suggest that, rather than forming a distinct population, Cape lions may have had phenotypic and genotypic variation similar to other African lions. Here we investigate Cape lion genome characteristics, population dynamics, and genetic distinctiveness prior to their extinction. We generated genomic data from 2 historic Cape lions to compare to 118 existing high-coverage mitogenomes, and low-coverage nuclear genomes of 53 lions from 13 African countries. We show that, before their eradication, lions from the Cape Flats had diverse mitogenomes and nuclear genomes that clustered with lions from both southern and eastern Africa. Cape lions had high genome-wide heterozygosity and low inbreeding coefficients, indicating that populations in the Cape Flats went extinct so rapidly that genomic effects associated with long-term small population size and isolation were not detectable. Our findings do not support the characterization of Cape lions as phylogeographically distinct, as originally put forth by some European naturalists, and illustrates how alternative knowledge systems, for example, Indigenous perspectives, could potentially further inform interpretations of species histories.
Collapse
Affiliation(s)
- Alida de Flamingh
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
| | - Thomas P Gnoske
- Field Museum of Natural History (FMNH), Chicago, IL, United States
| | | | | | - Julian C Kerbis Peterhans
- Field Museum of Natural History (FMNH), Chicago, IL, United States
- College of Arts & Sciences, Roosevelt University, Chicago, IL, United States
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University of Malaysia Terengganu, Terengganu, Malaysia
| | - Kelsey E Witt
- Department of Genetics & Biochemistry, Center for Human Genetics, Clemson, SC, United States
| | - Julian Catchen
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
- Department of Evolution, Ecology, and Behavior, UIUC, Urbana, IL, United States
| | - Alfred L Roca
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
- Department of Animal Sciences, UIUC, Urbana, IL, United States
| | - Ripan Singh Malhi
- Center for Indigenous Science, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL, United States
- Department of Anthropology, UIUC, Urbana, IL, United States
| |
Collapse
|
11
|
Pisciottano F, Campos MC, Penna C, Bruque CD, Gabaldón T, Saragüeta P. Positive selection in gamete interaction proteins in Carnivora. Mol Ecol 2024; 33:e17263. [PMID: 38318732 DOI: 10.1111/mec.17263] [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: 06/28/2022] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
The absence of robust interspecific isolation barriers among pantherines, including the iconic South American jaguar (Panthera onca), led us to study molecular evolution of typically rapidly evolving reproductive proteins within this subfamily and related groups. In this study, we delved into the evolutionary forces acting on the zona pellucida (ZP) gamete interaction protein family and the sperm-oocyte fusion protein pair IZUMO1-JUNO across the Carnivora order, distinguishing between Caniformia and Feliformia suborders and anticipating few significant diversifying changes in the Pantherinae subfamily. A chromosome-resolved jaguar genome assembly facilitated coding sequences, enabling the reconstruction of protein evolutionary histories. Examining sequence variability across more than 30 Carnivora species revealed that Feliformia exhibited significantly lower diversity compared to its sister taxa, Caniformia. Molecular evolution analyses of ZP2 and ZP3, subunits directly involved in sperm-recognition, unveiled diversifying positive selection in Feliformia, Caniformia and Pantherinae, although no significant changes were linked to sperm binding. Structural cross-linking ZP subunits, ZP4 and ZP1 exhibited lower levels or complete absence of positive selection. Notably, the fusion protein IZUMO1 displayed prominent positive selection signatures and sites in basal lineages of both Caniformia and Feliformia, extending along the Caniformia subtree but absent in Pantherinae. Conversely, JUNO did not exhibit any positive selection signatures across tested lineages and clades. Eight Caniformia-specific positive selected sites in IZUMO1 were detected within two JUNO-interaction clusters. Our findings provide for the first time insights into the evolutionary trajectories of ZP proteins and the IZUMO1-JUNO gamete interaction pair within the Carnivora order.
Collapse
Affiliation(s)
- Francisco Pisciottano
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
| | - María Clara Campos
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
| | - Clementina Penna
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
| | - Carlos David Bruque
- Unidad de Conocimiento Traslacional Hospitalaria Patagónica, Hospital de Alta Complejidad El Calafate SAMIC, El Calafate, Santa Cruz, Argentina
| | - Toni Gabaldón
- Barcelona Supercomputing Center (BSC), Institute for Research in Biomedicine (IRB), and Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Patricia Saragüeta
- Instituto de Biología y Medicina Experimental (IByME-CONICET), Buenos Aires, Argentina
| |
Collapse
|
12
|
Foley NM, Harris AJ, Bredemeyer KR, Ruedi M, Puechmaille SJ, Teeling EC, Criscitiello MF, Murphy WJ. Karyotypic stasis and swarming influenced the evolution of viral tolerance in a species-rich bat radiation. CELL GENOMICS 2024; 4:100482. [PMID: 38237599 PMCID: PMC10879000 DOI: 10.1016/j.xgen.2023.100482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/17/2023] [Accepted: 12/10/2023] [Indexed: 02/17/2024]
Abstract
The emergence of COVID-19 and severe acute respiratory syndrome (SARS) has prioritized understanding bats' viral tolerance. Myotis bats are exceptionally species rich and have evolved viral tolerance. They also exhibit swarming, a cryptic behavior where large, multi-species assemblages gather for mating, which has been hypothesized to promote interspecific hybridization. To resolve the coevolution of genome architecture and their unusual antiviral tolerance, we undertook a phylogenomic analysis of 60 Old World Myotis genomes. We demonstrate an extensive history of introgressive hybridization that has replaced the species phylogeny across 17%-93% of the genome except for pericentromeric regions of macrochromosomes. Introgression tracts were enriched on microchromosome regions containing key antiviral pathway genes overexpressed during viral challenge experiments. Together, these results suggest that the unusual Myotis karyotype may have evolved to selectively position immune-related genes in high recombining genomic regions prone to introgression of divergent alleles, including a diversity of interleukin loci responsible for the release of pro-inflammatory cytokines.
Collapse
Affiliation(s)
- Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Route de Malagnou 1, BP 6434, 1211 Geneva 6, Switzerland
| | - Sebastien J Puechmaille
- Institut des Sciences de l'Évolution, Montpellier (ISEM), Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France; Institut Universitaire de France, Paris, France
| | - Emma C Teeling
- School of Biology and Environmental, Science, Science Centre West, University College Dublin, Belfield, Ireland
| | - Michael F Criscitiello
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA; Department of Veterinary Pathobiology, Texas A&M University, College Station, TX 77843, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA; Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
13
|
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.
Collapse
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.
| |
Collapse
|
14
|
de Oliveira TG, Fox-Rosales LA, Ramírez-Fernández JD, Cepeda-Duque JC, Zug R, Sanchez-Lalinde C, Oliveira MJR, Marinho PHD, Bonilla-Sánchez A, Marques MC, Cassaro K, Moreno R, Rumiz D, Peters FB, Ortega J, Cavalcanti G, Mooring MS, Blankenship SR, Brenes-Mora E, Dias D, Mazim FD, Eizirik E, Diehl JL, Marques RV, Ribeiro ACC, Cruz RA, Pasa E, Meira LPC, Pereira A, Ferreira GB, de Pinho FF, Sena LMM, de Morais VR, Ribeiro Luiz M, Moura VEC, Favarini MO, Leal KPG, Wagner PGC, Dos Santos MC, Sanderson J, Araújo EP, Rodrigues FHG. Ecological modeling, biogeography, and phenotypic analyses setting the tiger cats' hyperdimensional niches reveal a new species. Sci Rep 2024; 14:2395. [PMID: 38287072 PMCID: PMC10825201 DOI: 10.1038/s41598-024-52379-8] [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: 08/15/2023] [Accepted: 01/18/2024] [Indexed: 01/31/2024] Open
Abstract
Recently, the tiger-cat species complex was split into Leopardus tigrinus and Leopardus guttulus, along with other proposed schemes. We performed a detailed analysis integrating ecological modeling, biogeography, and phenotype of the four originally recognized subspecies-tigrinus, oncilla, pardinoides, guttulus-and presented a new multidimensional niche depiction of the species. Species distribution models used > 1400 records from museums and photographs, all checked for species accuracy. Morphological data were obtained from institutional/personal archives. Spotting patterns were established by integrating museum and photographic/camera-trap records. Principal component analysis showed three clearly distinct groups, with the Central American specimens (oncilla) clustering entirely within those of the Andes, namely the pardinoides group of the cloud forests of the southern Central-American and Andean mountain chains (clouded tiger-cat); the tigrinus group of the savannas of the Guiana Shield and central/northeastern Brazil (savanna tiger-cat); and the guttulus group in the lowland forests of the Atlantic Forest domain (Atlantic Forest tiger-cat). This scheme is supported by recent genetic analyses. All species displayed different spotting patterns, with some significant differences in body measurements/proportions. The new distribution presented alarming reductions from the historic range of - 50.4% to - 68.2%. This multidimensional approach revealed a new species of the elusive and threatened tiger-cat complex.
Collapse
Affiliation(s)
- Tadeu G de Oliveira
- Departamento de Biologia, Universidade Estadual do Maranhão (UEMA), Campus Paulo VI, Av. Lourenço Vieira da Silva 1000, Jardim São Cristóvão, São Luís, Maranhão, 65055-310, Brazil.
- Instituto Pro-Carnívoros, Atibaia, SP, Brazil.
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil.
- Programa de Pós-Graduação em Ecologia, Conservação e Manejo da Vida Silvestre -ECMVS, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil.
| | - Lester A Fox-Rosales
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Programa de Pós-Graduação em Ciência Animal, UEMA, São Luís, MA, Brazil
| | - José D Ramírez-Fernández
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Oncilla Conservation, Costa Rica Wildlife Foundation, San José, Costa Rica
| | | | - Rebecca Zug
- Universidad San Francisco de Quito, Quito, Ecuador
| | - Catalina Sanchez-Lalinde
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Onca Fundación para el Estudio de la Diversidad, Bogota, Colombia
| | - Marcelo J R Oliveira
- Programa de Pós-Graduação em Ecologia, Conservação e Manejo da Vida Silvestre -ECMVS, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- Instituto Biotrópicos, Diamantina, MG, Brazil
| | - Paulo H D Marinho
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Universidade Federal do Rio Grande do Norte (UFRN), Natal, RN, Brazil
| | - Alejandra Bonilla-Sánchez
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Mara C Marques
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Zoológico de São Paulo Zoo, São Paulo, SP, Brazil
| | | | - Ricardo Moreno
- Fundación Yaguará Panamá, Ciudad del Saber/Panama City, Panama
| | - Damián Rumiz
- Noel Kempff Mercado Natural History Museum, Santa Cruz de la Sierra, Bolivia
| | - Felipe B Peters
- Instituto Pro-Carnívoros, Atibaia, SP, Brazil
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Josué Ortega
- Fundación Yaguará Panamá, Ciudad del Saber/Panama City, Panama
- Smithsonian Tropical Research Institute, Balboa Ancon, Panama
| | | | - Michael S Mooring
- Point Loma Nazarene University, San Diego, CA, USA
- Quetzal Education & Research Center (QERC), San Gerardo de Dota, Costa Rica
| | | | | | - Douglas Dias
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Programa de Pós-Graduação em Ecologia, Conservação e Manejo da Vida Silvestre -ECMVS, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
- SETEG- Soluções Geológicas e Ambientais, Fortaleza, CE, Brazil
| | - Fábio D Mazim
- Instituto Pro-Carnívoros, Atibaia, SP, Brazil
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Ka'aguy Consultoria Ambiental, Pelotas, RS, Brazil
| | - Eduardo Eizirik
- Instituto Pro-Carnívoros, Atibaia, SP, Brazil
- Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Jaime L Diehl
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
| | | | - Ana Carolina C Ribeiro
- Instituto de Ciências Biológicas, Universidade Federal de Goiás (UFG), Goiânia, GO, Brazil
| | | | - Emanuelle Pasa
- Cruzeiro do Sul Consultoria Ambiental Ltda., Ivoti, RS, Brazil
| | - Lyse P C Meira
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Bioconsultoria Ambiental Ltda., Caetité, BA, Brazil
| | - Alex Pereira
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Bioconsultoria Ambiental Ltda., Caetité, BA, Brazil
| | | | | | - Liana M M Sena
- Programa de Pós-Graduação em Ecologia, Conservação e Manejo da Vida Silvestre -ECMVS, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | | | - Micheli Ribeiro Luiz
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Instituto Felinos do Aguaí, Siderópolis, SC, Brazil
| | - Vitor E C Moura
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Programa de Pós-Graduação em Ecologia e Conservação da Biodiversidade, UEMA, São Luís, MA, Brazil
| | - Marina O Favarini
- Instituto Pro-Carnívoros, Atibaia, SP, Brazil
- Tiger Cats Conservation Initiative (TCCI), São Luís, Brazil
- Programa de Pós-Graduação em Biologia Animal, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Karla P G Leal
- Universidade Federal de Lavras (UFLA), Lavras, MG, Brazil
| | - Paulo G C Wagner
- Centro de Triagem de Animais Silvestres CETAS, IBAMA-RS, Porto Alegre, RS, Brazil
| | | | - James Sanderson
- Re:wild, Austin, TX, USA
- Small Wild Cat Conservation Foundation, Corrales, NM, USA
| | | | | |
Collapse
|
15
|
Yuan J, Kitchener AC, Lackey LB, Sun T, Jiangzuo Q, Tuohetahong Y, Zhao L, Yang P, Wang G, Huang C, Wang J, Hou W, Liu Y, Chen W, Mi D, Murphy WJ, Li G. The genome of the black-footed cat: Revealing a rich natural history and urgent conservation priorities for small felids. Proc Natl Acad Sci U S A 2024; 121:e2310763120. [PMID: 38165928 PMCID: PMC10786289 DOI: 10.1073/pnas.2310763120] [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: 06/27/2023] [Accepted: 10/31/2023] [Indexed: 01/04/2024] Open
Abstract
Habitat degradation and loss of genetic diversity are common threats faced by almost all of today's wild cats. Big cats, such as tigers and lions, are of great concern and have received considerable conservation attention through policies and international actions. However, knowledge of and conservation actions for small wild cats are lagging considerably behind. The black-footed cat, Felis nigripes, one of the smallest felid species, is experiencing increasing threats with a rapid reduction in population size. However, there is a lack of genetic information to assist in developing effective conservation actions. A de novo assembly of a high-quality chromosome-level reference genome of the black-footed cat was made, and comparative genomics and population genomics analyses were carried out. These analyses revealed that the most significant genetic changes in the evolution of the black-footed cat are the rapid evolution of sensory and metabolic-related genes, reflecting genetic adaptations to its characteristic nocturnal hunting and a high metabolic rate. Genomes of the black-footed cat exhibit a high level of inbreeding, especially for signals of recent inbreeding events, which suggest that they may have experienced severe genetic isolation caused by habitat fragmentation. More importantly, inbreeding associated with two deleterious mutated genes may exacerbate the risk of amyloidosis, the dominant disease that causes mortality of about 70% of captive individuals. Our research provides comprehensive documentation of the evolutionary history of the black-footed cat and suggests that there is an urgent need to investigate genomic variations of small felids worldwide to support effective conservation actions.
Collapse
Affiliation(s)
- Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, EdinburghEH1 1JF, United Kingdom
- School of Geosciences, University of Edinburgh, EdinburghEH9 3PX, United Kingdom
| | | | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Qigao Jiangzuo
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing100044, China
| | | | - Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development Collaborative Innovation Center, School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong723099, China
| | - Peng Yang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Wenhui Hou
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Yang Liu
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou510070, China
| | - Da Mi
- Xi’an Haorui Genomics Technology Co., Ltd., Xi’an710116, China
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an710049, China
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX77843
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi’an710119, China
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou510070, China
| |
Collapse
|
16
|
Uvizl M, Puechmaille SJ, Power S, Pippel M, Carthy S, Haerty W, Myers EW, Teeling EC, Huang Z. Comparative Genome Microsynteny Illuminates the Fast Evolution of Nuclear Mitochondrial Segments (NUMTs) in Mammals. Mol Biol Evol 2024; 41:msad278. [PMID: 38124445 PMCID: PMC10764098 DOI: 10.1093/molbev/msad278] [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: 07/18/2023] [Revised: 11/16/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
The escape of DNA from mitochondria into the nuclear genome (nuclear mitochondrial DNA, NUMT) is an ongoing process. Although pervasively observed in eukaryotic genomes, their evolutionary trajectories in a mammal-wide context are poorly understood. The main challenge lies in the orthology assignment of NUMTs across species due to their fast evolution and chromosomal rearrangements over the past 200 million years. To address this issue, we systematically investigated the characteristics of NUMT insertions in 45 mammalian genomes and established a novel, synteny-based method to accurately predict orthologous NUMTs and ascertain their evolution across mammals. With a series of comparative analyses across taxa, we revealed that NUMTs may originate from nonrandom regions in mtDNA, are likely found in transposon-rich and intergenic regions, and unlikely code for functional proteins. Using our synteny-based approach, we leveraged 630 pairwise comparisons of genome-wide microsynteny and predicted the NUMT orthology relationships across 36 mammals. With the phylogenetic patterns of NUMT presence-and-absence across taxa, we constructed the ancestral state of NUMTs given the mammal tree using a coalescent method. We found support on the ancestral node of Fereuungulata within Laurasiatheria, whose subordinal relationships are still controversial. This study broadens our knowledge on NUMT insertion and evolution in mammalian genomes and highlights the merit of NUMTs as alternative genetic markers in phylogenetic inference.
Collapse
Affiliation(s)
- Marek Uvizl
- Department of Zoology, National Museum, 19300 Prague, Czech Republic
- Department of Zoology, Faculty of Science, Charles University, 12844 Prague, Czech Republic
| | - Sebastien J Puechmaille
- Institut des Sciences de l’Evolution de Montpellier (ISEM), University of Montpellier, 34095 Montpellier, France
- Institut Universitaire de France, Paris, France
| | - Sarahjane Power
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- National Bioinformatics Infrastructure Sweden, Uppsala, Sweden
| | - Samuel Carthy
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Colney Ln, NR4 7UZ Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Eugene W Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Zixia Huang
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| |
Collapse
|
17
|
Thawornwattana Y, Seixas F, Yang Z, Mallet J. Major patterns in the introgression history of Heliconius butterflies. eLife 2023; 12:RP90656. [PMID: 38108819 PMCID: PMC10727504 DOI: 10.7554/elife.90656] [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] [Indexed: 12/19/2023] Open
Abstract
Gene flow between species, although usually deleterious, is an important evolutionary process that can facilitate adaptation and lead to species diversification. It also makes estimation of species relationships difficult. Here, we use the full-likelihood multispecies coalescent (MSC) approach to estimate species phylogeny and major introgression events in Heliconius butterflies from whole-genome sequence data. We obtain a robust estimate of species branching order among major clades in the genus, including the 'melpomene-silvaniform' group, which shows extensive historical and ongoing gene flow. We obtain chromosome-level estimates of key parameters in the species phylogeny, including species divergence times, present-day and ancestral population sizes, as well as the direction, timing, and intensity of gene flow. Our analysis leads to a phylogeny with introgression events that differ from those obtained in previous studies. We find that Heliconius aoede most likely represents the earliest-branching lineage of the genus and that 'silvaniform' species are paraphyletic within the melpomene-silvaniform group. Our phylogeny provides new, parsimonious histories for the origins of key traits in Heliconius, including pollen feeding and an inversion involved in wing pattern mimicry. Our results demonstrate the power and feasibility of the full-likelihood MSC approach for estimating species phylogeny and key population parameters despite extensive gene flow. The methods used here should be useful for analysis of other difficult species groups with high rates of introgression.
Collapse
Affiliation(s)
| | - Fernando Seixas
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College LondonLondonUnited Kingdom
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| |
Collapse
|
18
|
Lescroart J, Bonilla-Sánchez A, Napolitano C, Buitrago-Torres DL, Ramírez-Chaves HE, Pulido-Santacruz P, Murphy WJ, Svardal H, Eizirik E. Extensive Phylogenomic Discordance and the Complex Evolutionary History of the Neotropical Cat Genus Leopardus. Mol Biol Evol 2023; 40:msad255. [PMID: 37987559 PMCID: PMC10701098 DOI: 10.1093/molbev/msad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023] Open
Abstract
Even in the genomics era, the phylogeny of Neotropical small felids comprised in the genus Leopardus remains contentious. We used whole-genome resequencing data to construct a time-calibrated consensus phylogeny of this group, quantify phylogenomic discordance, test for interspecies introgression, and assess patterns of genetic diversity and demographic history. We infer that the Leopardus radiation started in the Early Pliocene as an initial speciation burst, followed by another in its subgenus Oncifelis during the Early Pleistocene. Our findings challenge the long-held notion that ocelot (Leopardus pardalis) and margay (L. wiedii) are sister species and instead indicate that margay is most closely related to the enigmatic Andean cat (L. jacobita), whose whole-genome data are reported here for the first time. In addition, we found that the newly sampled Andean tiger cat (L. tigrinus pardinoides) population from Colombia associates closely with Central American tiger cats (L. tigrinus oncilla). Genealogical discordance was largely attributable to incomplete lineage sorting, yet was augmented by strong gene flow between ocelot and the ancestral branch of Oncifelis, as well as between Geoffroy's cat (L. geoffroyi) and southern tiger cat (L. guttulus). Contrasting demographic trajectories have led to disparate levels of current genomic diversity, with a nearly tenfold difference in heterozygosity between Andean cat and ocelot, spanning the entire range of variability found in extant felids. Our analyses improved our understanding of the speciation history and diversity patterns in this felid radiation, and highlight the benefits to phylogenomic inference of embracing the many heterogeneous signals scattered across the genome.
Collapse
Affiliation(s)
- Jonas Lescroart
- Department of Biology, University of Antwerp, Antwerp, Belgium
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Alejandra Bonilla-Sánchez
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Faculty of Exact and Natural Sciences, University of Antioquia, Medellín, Colombia
| | - Constanza Napolitano
- Department of Biological Sciences and Biodiversity, University of Los Lagos, Osorno, Chile
- Institute of Ecology and Biodiversity, Concepción, Chile
- Cape Horn International Center, Puerto Williams, Chile
- Andean Cat Alliance, Villa Carlos Paz, Argentina
| | - Diana L Buitrago-Torres
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
| | - Héctor E Ramírez-Chaves
- Department of Biological Sciences, University of Caldas, Manizales, Colombia
- Centro de Museos, Museo de Historia Natural, University of Caldas, Manizales, Colombia
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, Netherlands
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, Brazil
- Instituto Pró-Carnívoros, Atibaia, Brazil
| |
Collapse
|
19
|
Patterson EC, Lall GM, Neumann R, Ottolini B, Batini C, Sacchini F, Foster AP, Wetton JH, Jobling MA. Mitogenome sequences of domestic cats demonstrate lineage expansions and dynamic mutation processes in a mitochondrial minisatellite. BMC Genomics 2023; 24:690. [PMID: 37978434 PMCID: PMC10655372 DOI: 10.1186/s12864-023-09789-1] [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: 06/23/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND As a population genetic tool, mitochondrial DNA is commonly divided into the ~ 1-kb control region (CR), in which single nucleotide variant (SNV) diversity is relatively high, and the coding region, in which selective constraint is greater and diversity lower, but which provides an informative phylogeny. In some species, the CR contains variable tandemly repeated sequences that are understudied due to heteroplasmy. Domestic cats (Felis catus) have a recent origin and therefore traditional CR-based analysis of populations yields only a small number of haplotypes. RESULTS To increase resolution we used Nanopore sequencing to analyse 119 cat mitogenomes via a long-amplicon approach. This greatly improves discrimination (from 15 to 87 distinct haplotypes in our dataset) and defines a phylogeny showing similar starlike topologies within all major clades (haplogroups), likely reflecting post-domestication expansion. We sequenced RS2, a CR tandem array of 80-bp repeat units, placing RS2 array structures within the phylogeny and increasing overall haplotype diversity. Repeat number varies between 3 and 12 (median: 4) with over 30 different repeat unit types differing largely by SNVs. Five SNVs show evidence of independent recurrence within the phylogeny, and seven are involved in at least 11 instances of rapid spread along repeat arrays within haplogroups. CONCLUSIONS In defining mitogenome variation our study provides key information for the forensic genetic analysis of cat hair evidence, and for the first time a phylogenetically informed picture of tandem repeat variation that reveals remarkably dynamic mutation processes at work in the mitochondrion.
Collapse
Affiliation(s)
- Emily C Patterson
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Gurdeep Matharu Lall
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Rita Neumann
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Barbara Ottolini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Oxford Nanopore Technologies Plc., Oxford Science Park, Edmund Halley Rd, Oxford, OX4 4DQ, UK
| | - Chiara Batini
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
- Present Address: Department of Population Health Sciences, University of Leicester, Leicester, UK
- Biomedical Research Centre, Leicester National Institute for Health and Care Research, Glenfield Hospital, Leicester, UK
| | - Federico Sacchini
- IDEXX Laboratories Italia S.R.L., Via Guglielmo Silva, 36-20149, Milano, MI, Italy
| | - Aiden P Foster
- Bristol Veterinary School, University of Bristol, Langford House, Langford, BS40 5DU, North Somerset, UK
| | - Jon H Wetton
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Mark A Jobling
- Department of Genetics & Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| |
Collapse
|
20
|
Howard-McCombe J, Jamieson A, Carmagnini A, Russo IRM, Ghazali M, Campbell R, Driscoll C, Murphy WJ, Nowak C, O'Connor T, Tomsett L, Lyons LA, Muñoz-Fuentes V, Bruford MW, Kitchener AC, Larson G, Frantz L, Senn H, Lawson DJ, Beaumont MA. Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease. Curr Biol 2023; 33:4761-4769.e5. [PMID: 37935118 DOI: 10.1016/j.cub.2023.10.026] [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: 07/31/2023] [Revised: 09/24/2023] [Accepted: 10/17/2023] [Indexed: 11/09/2023]
Abstract
The European wildcat population in Scotland is considered critically endangered as a result of hybridization with introduced domestic cats,1,2 though the time frame over which this gene flow has taken place is unknown. Here, using genome data from modern, museum, and ancient samples, we reconstructed the trajectory and dated the decline of the local wildcat population from viable to severely hybridized. We demonstrate that although domestic cats have been present in Britain for over 2,000 years,3 the onset of hybridization was only within the last 70 years. Our analyses reveal that the domestic ancestry present in modern wildcats is markedly over-represented in many parts of the genome, including the major histocompatibility complex (MHC). We hypothesize that introgression provides wildcats with protection against diseases harbored and introduced by domestic cats, and that this selection contributes to maladaptive genetic swamping through linkage drag. Using the case of the Scottish wildcat, we demonstrate the importance of local ancestry estimates to both understand the impacts of hybridization in wild populations and support conservation efforts to mitigate the consequences of anthropogenic and environmental change.
Collapse
Affiliation(s)
- Jo Howard-McCombe
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK.
| | - Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK; Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilians University of Munich, Munich, Germany
| | - Alberto Carmagnini
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilians University of Munich, Munich, Germany; School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | - Muhammad Ghazali
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - Ruairidh Campbell
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney OX13 5QL, UK; NatureScot, Great Glen House, Leachkin Road, Inverness IV3 8NW, UK
| | | | - William J Murphy
- Texas A&M University, Veterinary Integrative Biosciences, College Station, TX 77843, USA
| | - Carsten Nowak
- Senckenberg Research Institute and Natural History Museum, Center for Wildlife Genetics, 63571 Weimar, Germany
| | - Terry O'Connor
- BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Louise Tomsett
- Mammal Section, Science Department, Natural History Museum, London SW7 5BD, UK
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK; School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilians University of Munich, Munich, Germany; School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Helen Senn
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK.
| | - Daniel J Lawson
- School of Mathematics, University of Bristol, Bristol BS8 1UG, UK.
| | - Mark A Beaumont
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.
| |
Collapse
|
21
|
Bredemeyer KR, Hillier L, Harris AJ, Hughes GM, Foley NM, Lawless C, Carroll RA, Storer JM, Batzer MA, Rice ES, Davis BW, Raudsepp T, O'Brien SJ, Lyons LA, Warren WC, Murphy WJ. Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution. Nat Genet 2023; 55:1953-1963. [PMID: 37919451 PMCID: PMC10845050 DOI: 10.1038/s41588-023-01548-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/20/2023] [Indexed: 11/04/2023]
Abstract
The role of structurally dynamic genomic regions in speciation is poorly understood due to challenges inherent in diploid genome assembly. Here we reconstructed the evolutionary dynamics of structural variation in five cat species by phasing the genomes of three interspecies F1 hybrids to generate near-gapless single-haplotype assemblies. We discerned that cat genomes have a paucity of segmental duplications relative to great apes, explaining their remarkable karyotypic stability. X chromosomes were hotspots of structural variation, including enrichment with inversions in a large recombination desert with characteristics of a supergene. The X-linked macrosatellite DXZ4 evolves more rapidly than 99.5% of the genome clarifying its role in felid hybrid incompatibility. Resolved sensory gene repertoires revealed functional copy number changes associated with ecomorphological adaptations, sociality and domestication. This study highlights the value of gapless genomes to reveal structural mechanisms underpinning karyotypic evolution, reproductive isolation and ecological niche adaptation.
Collapse
Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - LaDeana Hillier
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Graham M Hughes
- School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Colleen Lawless
- School of Biology & Environmental Sciences, University College Dublin, Dublin, Ireland
| | - Rachel A Carroll
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | | | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Edward S Rice
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Brian W Davis
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Stephen J O'Brien
- Guy Harvey Oceanographic Center, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, University of Missouri, Columbia, MO, USA
| | - Wesley C Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO, USA.
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA.
| |
Collapse
|
22
|
Sun X, Liu YC, Tiunov MP, Gimranov DO, Zhuang Y, Han Y, Driscoll CA, Pang Y, Li C, Pan Y, Velasco MS, Gopalakrishnan S, Yang RZ, Li BG, Jin K, Xu X, Uphyrkina O, Huang Y, Wu XH, Gilbert MTP, O'Brien SJ, Yamaguchi N, Luo SJ. Ancient DNA reveals genetic admixture in China during tiger evolution. Nat Ecol Evol 2023; 7:1914-1929. [PMID: 37652999 DOI: 10.1038/s41559-023-02185-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 08/02/2023] [Indexed: 09/02/2023]
Abstract
The tiger (Panthera tigris) is a charismatic megafauna species that originated and diversified in Asia and probably experienced population contraction and expansion during the Pleistocene, resulting in low genetic diversity of modern tigers. However, little is known about patterns of genomic diversity in ancient populations. Here we generated whole-genome sequences from ancient or historical (100-10,000 yr old) specimens collected across mainland Asia, including a 10,600-yr-old Russian Far East specimen (RUSA21, 8× coverage) plus six ancient mitogenomes, 14 South China tigers (0.1-12×) and three Caspian tigers (4-8×). Admixture analysis showed that RUSA21 clustered within modern Northeast Asian phylogroups and partially derived from an extinct Late Pleistocene lineage. While some of the 8,000-10,000-yr-old Russian Far East mitogenomes are basal to all tigers, one 2,000-yr-old specimen resembles present Amur tigers. Phylogenomic analyses suggested that the Caspian tiger probably dispersed from an ancestral Northeast Asian population and experienced gene flow from southern Bengal tigers. Lastly, genome-wide monophyly supported the South China tiger as a distinct subspecies, albeit with mitochondrial paraphyly, hence resolving its longstanding taxonomic controversy. The distribution of mitochondrial haplogroups corroborated by biogeographical modelling suggested that Southwest China was a Late Pleistocene refugium for a relic basal lineage. As suitable habitat returned, admixture between divergent lineages of South China tigers took place in Eastern China, promoting the evolution of other northern subspecies. Altogether, our analysis of ancient genomes sheds light on the evolutionary history of tigers and supports the existence of nine modern subspecies.
Collapse
Affiliation(s)
- Xin Sun
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Yue-Chen Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Mikhail P Tiunov
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Dmitry O Gimranov
- Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Yekaterinburg, Russia
- Ural Federal University, Yekaterinburg, Russia
| | - Yan Zhuang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yu Han
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Carlos A Driscoll
- Section of Comparative Behavioral Genomics, National Institute on Alcohol Abuse and Alcoholism, NIH, Rockville, MD, USA
| | - Yuhong Pang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Chunmei Li
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Yan Pan
- School of Archaeology and Museology, Peking University, Beijing, China
| | - Marcela Sandoval Velasco
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui-Zheng Yang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi'an, China
| | - Kun Jin
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Xiao Xu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Olga Uphyrkina
- Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far Eastern Branch of the Russian Academy of Sciences, Vladivostok, Russia
| | - Yanyi Huang
- Beijing Advanced Innovation Center for Genomics (ICG), Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Guangdong, China
| | - Xiao-Hong Wu
- School of Archaeology and Museology, Peking University, Beijing, China
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Stephen J O'Brien
- Guy Harvey Oceanographic Center, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA.
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University of Malaysia Terengganu, Kuala Nerus, Terengganu, Malaysia.
| | - Shu-Jin Luo
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
| |
Collapse
|
23
|
Yuan J, Wang G, Zhao L, Kitchener AC, Sun T, Chen W, Huang C, Wang C, Xu X, Wang J, Lu H, Xu L, Jiangzuo Q, Murphy WJ, Wu D, Li G. How genomic insights into the evolutionary history of clouded leopards inform their conservation. SCIENCE ADVANCES 2023; 9:eadh9143. [PMID: 37801506 PMCID: PMC10558132 DOI: 10.1126/sciadv.adh9143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/06/2023] [Indexed: 10/08/2023]
Abstract
Clouded leopards (Neofelis spp.), a morphologically and ecologically distinct lineage of big cats, are severely threatened by habitat loss and fragmentation, targeted hunting, and other human activities. The long-held poor understanding of their genetics and evolution has undermined the effectiveness of conservation actions. Here, we report a comprehensive investigation of the whole genomes, population genetics, and adaptive evolution of Neofelis. Our results indicate the genus Neofelis arose during the Pleistocene, coinciding with glacial-induced climate changes to the distributions of savannas and rainforests, and signatures of natural selection associated with genes functioning in tooth, pigmentation, and tail development, associated with clouded leopards' unique adaptations. Our study highlights high-altitude adaptation as the main factor driving nontaxonomic population differentiation in Neofelis nebulosa. Population declines and inbreeding have led to reduced genetic diversity and the accumulation of deleterious variation that likely affect reproduction of clouded leopards, highlighting the urgent need for effective conservation efforts.
Collapse
Affiliation(s)
- Jiaqing Yuan
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Guiqiang Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Le Zhao
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., School of Bioscience and Engineering, Shaanxi University of Technology, Hanzhong, China
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK
- School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH9 3PX, UK
| | - Ting Sun
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Wu Chen
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Chen Huang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Chen Wang
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| | - Xiao Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Jinhong Wang
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Huimeng Lu
- School of Life Sciences, Northwestern Polytechnical University, Xi’an, China
| | - Lulu Xu
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Qigao Jiangzuo
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - William J. Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Natural History Museum of Zoology Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Gang Li
- College of Life Sciences, Shaanxi Normal University, Xi’an, China
- Guangzhou Zoo, Guangzhou Wildlife Research Center, Guangzhou, China
| |
Collapse
|
24
|
Mochales-Riaño G, Fontsere C, de Manuel M, Talavera A, Burriel-Carranza B, Tejero-Cicuéndez H, AlGethami RHM, Shobrak M, Marques-Bonet T, Carranza S. Genomics reveals introgression and purging of deleterious mutations in the Arabian leopard ( Panthera pardus nimr). iScience 2023; 26:107481. [PMID: 37601769 PMCID: PMC10432787 DOI: 10.1016/j.isci.2023.107481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/21/2023] [Accepted: 07/24/2023] [Indexed: 08/22/2023] Open
Abstract
In endangered species, low-genetic variation and inbreeding result from recent population declines. Genetic screenings in endangered populations help to assess their vulnerability to extinction and to create informed management actions toward their conservation efforts. The leopard, Panthera pardus, is a highly generalist predator with currently eight different subspecies. Yet, genomic data are still lacking for the Critically Endangered Arabian leopard (P. p. nimr). Here, we sequenced the whole genome of two Arabian leopards and assembled the most complete genomic dataset for leopards to date. Our phylogenomic analyses show that leopards are divided into two deeply divergent clades: the African and the Asian. Conservation genomic analyses indicate a prolonged population decline, which has led to an increase in inbreeding and runs of homozygosity, with consequent purging of deleterious mutations in both Arabian individuals. Our study represents the first attempt to genetically inform captive breeding programmes for this Critically Endangered subspecies.
Collapse
Affiliation(s)
| | - Claudia Fontsere
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5A, 1352 Copenhagen, Denmark
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Adrián Talavera
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | | | - Héctor Tejero-Cicuéndez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Department of Biodiversity, Ecology and Evolution, Faculty of Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Raed Hamoud M. AlGethami
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Mohammed Shobrak
- National Center for Wildlife, Prince Saud Al-Faisal for Wildlife Research, P. O Box 1086, Taif, Taif 21944, Saudi Arabia
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Salvador Carranza
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| |
Collapse
|
25
|
Jabin G, Joshi BD, Wang MS, Mukherjee T, Dolker S, Wang S, Chandra K, Chinnadurai V, Sharma LK, Thakur M. Mid-Pleistocene Transitions Forced Himalayan ibex to Evolve Independently after Split into an Allopatric Refugium. BIOLOGY 2023; 12:1097. [PMID: 37626983 PMCID: PMC10451794 DOI: 10.3390/biology12081097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023]
Abstract
Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8-0.5 mya and c. 50-30 kya, with an intermediate large population expansion c. 0.2-0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized as Capra himalayensis for taxonomic revision and conservation planning at a regional and global scale.
Collapse
Affiliation(s)
- Gul Jabin
- Zoological Survey of India, Kolkata 700053, India
- Department of Zoology, University of Calcutta, Kolkata 700019, India
| | | | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Stanzin Dolker
- Zoological Survey of India, Kolkata 700053, India
- Department of Zoology, University of Calcutta, Kolkata 700019, India
| | - Sheng Wang
- Kunming Institute of Zoology, Kunming 650223, China
| | | | | | | | | |
Collapse
|
26
|
Tukhbatullin A, Ermakov O, Kapustina S, Starikov V, Tambovtseva V, Titov S, Brandler O. Surrounded by Kindred: Spermophilus major Hybridization with Other Spermophilus Species in Space and Time. BIOLOGY 2023; 12:880. [PMID: 37372163 DOI: 10.3390/biology12060880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Among the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrel Spermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into the S. major range, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR, cytb) and nuclear (SmcY, BGN, PRKCI, c-myc, i6p53) markers, we determined the contribution of neighboring species to the S. major genome. We showed that 36% of S. major individuals had extraneous alleles. All peripheral species that were in contact with S. major contributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of the S. major genome implications of introgression highlights the importance of implementing conservation measures to protect this species.
Collapse
Affiliation(s)
- Andrey Tukhbatullin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Oleg Ermakov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Svetlana Kapustina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Vladimir Starikov
- Department of Biology and Biotechnology, Institute of Natural and Technical Sciences, Surgut State University, Lenin Avenue 1, Surgut 628412, Russia
| | - Valentina Tambovtseva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Sergey Titov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Oleg Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| |
Collapse
|
27
|
Ruiz-García M, Pinedo-Castro M, Shostell JM. Morphological and Genetics Support for a Hitherto Undescribed Spotted Cat Species (Genus Leopardus; Felidae, Carnivora) from the Southern Colombian Andes. Genes (Basel) 2023; 14:1266. [PMID: 37372446 DOI: 10.3390/genes14061266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
In 1989, a skin of a small spotted cat, from the Galeras Volcano in southern Colombia (Nariño Department), was donated to the Instituto Alexander von Humboldt (identification, ID 5857) at Villa de Leyva (Boyacá Department, Colombia). Although originally classified as Leopardus tigrinus, its distinctiveness merits a new taxonomic designation. The skin is distinct from all known L. tigrinus holotypes as well as from other Leopardus species. Analysis of the complete mitochondrial genomes from 44 felid specimens (including 18 L. tigrinus and all the current known species of the genus Leopardus), the mtND5 gene from 84 felid specimens (including 30 L. tigrinus and all the species of the genus Leopardus), and six nuclear DNA microsatellites (113 felid specimens of all the current known species of the genus Leopardus) indicate that this specimen does not belong to any previously recognized Leopardus taxon. The mtND5 gene suggests this new lineage (the Nariño cat as we name it) is a sister taxon of Leopardus colocola. The mitogenomic and nuclear DNA microsatellite analyses suggest that this new lineage is the sister taxon to a clade formed by Central American and trans-Andean L. tigrinus + (Leopardus geoffroyi + Leopardus guigna). The temporal split between the ancestor of this new possible species and the most recent ancestor within Leopardus was dated to 1.2-1.9 million years ago. We consider that this new unique lineage is a new species, and we propose the scientific name Leopardus narinensis.
Collapse
Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No 43-82, Bogotá 110231, Colombia
| | - Myreya Pinedo-Castro
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No 43-82, Bogotá 110231, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, 2900 University Ave., Crookston, MN 56716, USA
| |
Collapse
|
28
|
Flack N, Drown M, Walls C, Pratte J, McLain A, Faulk C. Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul. NAR Genom Bioinform 2023; 5:lqad033. [PMID: 37025970 PMCID: PMC10071556 DOI: 10.1093/nargab/lqad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/10/2023] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manul's zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for O. manul. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.
Collapse
Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Melissa Drown
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Carrie Walls
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jay Pratte
- Bloomington Parks and Recreation, Miller Park Zoo, Bloomington, IL 61701, USA
| | - Adam McLain
- Department of Biology and Chemistry, SUNY Polytechnic Institute, Utica, NY 13502, USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| |
Collapse
|
29
|
Jones CJP, Aplin JD. Endotheliochorial placental glycosylation reflects evolutionary divergence between Felidae species (Felis catus and Panthera leo) and Canidae (Canisfamiliaris). Placenta 2023; 138:109-112. [PMID: 37262940 DOI: 10.1016/j.placenta.2023.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023]
Abstract
Endotheliochorial cat (Felis catus) and lion (Panthera leo) term placentae and one 6 week placenta (term 60-63 days) from a dog (Canis familiaris) were stained with a panel of 24 lectins to compare glycosylation at the feto-maternal interface. Glycan expression in lion and cat placentae was very similar apart from the occurrence of terminal α-galactose in the lion trophoblast. The dog differed in several respects, particularly in the trophoblast, consistent with species-specific glycotypes differing according to the degree of their evolutionary divergence. The data suggest that evolutionary effects on the glycotype are most readily observed in trophoblast.
Collapse
Affiliation(s)
- Carolyn J P Jones
- Maternal and Fetal Health Research Centre, Division of Developmental Biology & Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Central Manchester University Hospital NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK.
| | - John D Aplin
- Maternal and Fetal Health Research Centre, Division of Developmental Biology & Medicine, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Central Manchester University Hospital NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Oxford Road, Manchester, M13 9WL, UK.
| |
Collapse
|
30
|
Velli E, Caniglia R, Mattucci F. Phylogenetic History and Phylogeographic Patterns of the European Wildcat ( Felis silvestris) Populations. Animals (Basel) 2023; 13:ani13050953. [PMID: 36899811 PMCID: PMC10000227 DOI: 10.3390/ani13050953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/27/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Disentangling phylogenetic and phylogeographic patterns is fundamental to reconstruct the evolutionary histories of taxa and assess their actual conservation status. Therefore, in this study, for the first time, the most exhaustive biogeographic history of European wildcat (Felis silvestris) populations was reconstructed by typing 430 European wildcats, 213 domestic cats, and 72 putative admixed individuals, collected across the entire species' distribution range, at a highly diagnostic portion of the mitochondrial ND5 gene. Phylogenetic and phylogeographic analyses identified two main ND5 lineages (D and W) roughly associated with domestic and wild polymorphisms. Lineage D included all domestic cats, 83.3% of putative admixed individuals, and also 41.4% of wildcats; these latter mostly showed haplotypes belonging to sub-clade Ia, that diverged about 37,700 years ago, long pre-dating any evidence for cat domestication. Lineage W included all the remaining wildcats and putative admixed individuals, spatially clustered into four main geographic groups, which started to diverge about 64,200 years ago, corresponding to (i) the isolated Scottish population, (ii) the Iberian population, (iii) a South-Eastern European cluster, and (iv) a Central European cluster. Our results suggest that the last Pleistocene glacial isolation and subsequent re-expansion from Mediterranean and extra-Mediterranean glacial refugia were pivotal drivers in shaping the extant European wildcat phylogenetic and phylogeographic patterns, which were further modeled by both historical natural gene flow among wild lineages and more recent wild x domestic anthropogenic hybridization, as confirmed by the finding of F. catus/lybica shared haplotypes. The reconstructed evolutionary histories and the wild ancestry contents detected in this study could be used to identify adequate Conservation Units within European wildcat populations and help to design appropriate long-term management actions.
Collapse
|
31
|
Museomics Provides Insights into Conservation and Education: The Instance of an African Lion Specimen from the Museum of Zoology “Pietro Doderlein”. DIVERSITY 2023. [DOI: 10.3390/d15010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Innovative technological approaches are crucial to enhance naturalistic museum collections and develop information repositories of relevant interest to science, such as threatened animal taxa. In this context, museomics is an emerging discipline that provides a novel approach to the enhancement and exploitation of these collections. In the present study, the discovery of a neglected lion skeleton in the Museum of Zoology “Pietro Doderlein” of the University of Palermo (Italy) offered the opportunity to undertake a multidisciplinary project. The aims of the study consisted of the following: (i) adding useful information for museographic strategies, (ii) obtaining a new genetic data repository from a vulnerable species, (iii) strengthening public awareness of wildlife conservation, and (iv) sharing new learning material. The remains of the lion were examined with a preliminary osteological survey, then they were restored by means of 3D printing of missing skeletal fragments. Phylogenetic analyses based on cytochrome b sequence clearly indicate that the specimen belongs to the Central Africa mitochondrial clade. At the end of the study, the complete and restored skeleton was exhibited, along with all of the information and data available from this project. This study shows a useful approach for the restoration and enhancement of a museum specimen, with important opportunities for preserving biodiversity and driving specific conservation policies, but also for providing Life Science learning material.
Collapse
|
32
|
Way to big cats: Directional selection in body size evolution in living felids. J MAMM EVOL 2022. [DOI: 10.1007/s10914-022-09639-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
33
|
Bursell MG, Dikow RB, Figueiró HV, Dudchenko O, Flanagan JP, Aiden EL, Goossens B, Nathan SK, Johnson WE, Koepfli KP, Frandsen PB. Whole genome analysis of clouded leopard species reveals an ancient divergence and distinct demographic histories. iScience 2022; 25:105647. [PMID: 36590460 PMCID: PMC9801239 DOI: 10.1016/j.isci.2022.105647] [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: 05/23/2022] [Revised: 08/08/2022] [Accepted: 11/18/2022] [Indexed: 12/14/2022] Open
Abstract
Similar to other apex predator species, populations of mainland (Neofelis nebulosa) and Sunda (Neofelis diardi) clouded leopards are declining. Understanding their patterns of genetic variation can provide critical insights on past genetic erosion and a baseline for understanding their long-term conservation needs. As a step toward this goal, we present draft genome assemblies for the two clouded leopard species to quantify their phylogenetic divergence, genome-wide diversity, and historical population trends. We estimate that the two species diverged 5.1 Mya, much earlier than previous estimates of 1.41 Mya and 2.86 Mya, suggesting they separated when Sundaland was becoming increasingly isolated from mainland Southeast Asia. The Sunda clouded leopard displays a distinct and reduced effective population size trajectory, consistent with a lower genome-wide heterozygosity and SNP density, relative to the mainland clouded leopard. Our results provide new insights into the evolutionary history and genetic health of this unique lineage of felids.
Collapse
Affiliation(s)
- Madeline G. Bursell
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560, USA
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560, USA
| | - Henrique V. Figueiró
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | | | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA,Center for Theoretical Biological Physics, Rice University, Houston, TX, USA,UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia,Departments of Computer Science and Computational and Applied Mathematics, Rice University,Houston, TX, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Shanghai Institute for Advanced Immunochemical Studies, Shanghai Tech University, Shanghai, China
| | - Benoit Goossens
- Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia,Organisms and Environment Division, Cardiff School of Biosciences, Cardiff, UK,Danau Girang Field Centre, c/o Sabah Wildlife Department, Kota Kinabalu, Sabah, Malaysia
| | | | - Warren E. Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA,The Walter Reed Biosystematics Unit, Museum Support Center MRC-534, Smithsonian Institution, Suitland, MD, USA,Walter Reed Army Institute of Research, Silver Spring, MD, USA,Loyola University Maryland, Baltimore, MD, USA
| | - Klaus-Peter Koepfli
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, VA 22630, USA,Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA,Corresponding author
| | - Paul B. Frandsen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT 84602, USA,Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, DC 20560, USA,Corresponding author
| |
Collapse
|
34
|
Armstrong EE, Campana MG, Solari KA, Morgan SR, Ryder OA, Naude VN, Samelius G, Sharma K, Hadly EA, Petrov DA. Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris). G3 (BETHESDA, MD.) 2022; 12:jkac277. [PMID: 36250809 PMCID: PMC9713438 DOI: 10.1093/g3journal/jkac277] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/14/2022] [Indexed: 04/07/2024]
Abstract
The big cats (genus Panthera) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution genomic studies. We assembled genomes from 3 members of the genus, the tiger (Panthera tigris), the snow leopard (Panthera uncia), and the African leopard (Panthera pardus pardus), at chromosome or near-chromosome level. We used a combination of short- and long-read technologies, as well as proximity ligation data from Hi-C technology, to achieve high continuity and contiguity for each individual. We hope that these genomes will aid in further evolutionary and conservation research of this iconic group of mammals.
Collapse
Affiliation(s)
- Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Department of Biology, Washington State University, Pullman, WA 99164, USA
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian’s National Zoological Park and Conservation Biology Institute, Washington, DC 20008, USA
| | | | - Simon R Morgan
- Department of Biology, Stanford University, Stanford, CA 94305, USA
- Wildlife ACT Fund Trust, Cape Town 8001, South Africa
| | - Oliver A Ryder
- San Diego Zoo Wildlife Alliance, Beckman Center for Conservation Research, San Diego, CA 92027, USA
| | - Vincent N Naude
- Department of Conservation Ecology and Entomology, University of Stellenbosch, Stellenbosch, 7602, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | | | - Koustubh Sharma
- Snow Leopard Trust, Seattle, WA 98103, USA
- Nature Conservation Foundation, Mysore 570 017, India
| | | | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
35
|
Nilson SM, Gandolfi B, Grahn RA, Kurushima JD, Lipinski MJ, Randi E, Waly NE, Driscoll C, Murua Escobar H, Schuster RK, Maruyama S, Labarthe N, Chomel BB, Ghosh SK, Ozpinar H, Rah HC, Millán J, Mendes-de-Almeida F, Levy JK, Heitz E, Scherk MA, Alves PC, Decker JE, Lyons LA. Genetics of randomly bred cats support the cradle of cat domestication being in the Near East. Heredity (Edinb) 2022; 129:346-355. [PMID: 36319737 PMCID: PMC9708682 DOI: 10.1038/s41437-022-00568-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/04/2022] Open
Abstract
Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats' predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor's (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.
Collapse
Affiliation(s)
- Sara M Nilson
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Jennifer D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Monika J Lipinski
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Øst, Denmark
| | - Nashwa E Waly
- Department of Animal Medicine, Faculty of Veterinary Medicine, Assuit University, 71526, Assiut, Egypt
| | | | - Hugo Murua Escobar
- Clinic for Hematology, Oncology and Palliative Care, University Medical Center Rostock, 18055, Rostock, Germany
| | - Rolf K Schuster
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Soichi Maruyama
- Laboratory of Veterinary Public Health, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Norma Labarthe
- Programa de Bioética, Ética Aplicada e Saúde Coletiva, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Bruno B Chomel
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | | | - Haydar Ozpinar
- Graduate School of Health Sciences, Istanbul Gedik University, 34876, İstanbul, Turkey
| | - Hyung-Chul Rah
- Research Institute of Veterinary Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, South Korea
| | - Javier Millán
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Miguel Servet 177, 50013, Zaragoza, Spain
- Fundación ARAID, Avda. de Ranillas, 50018, Zaragoza, Spain
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Flavya Mendes-de-Almeida
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Julie K Levy
- Maddie's Shelter Medicine Program, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32608, USA
| | | | | | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Associate Lab & Faculdade de Ciências, Universidade do Porto, Campus e Vairão, 4485-661, Vila do Conde, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
36
|
Mitochondrial DNA variation of the caracal (Caracal caracal) in Iran and range-wide phylogeographic comparisons. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00328-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
37
|
Eliášová K, Lucas Lledó JI, Grau JH, Loudová M, Bannikova AA, Zolotareva KI, Beneš V, Hulva P, Černá Bolfíková B. Contrasting levels of hybridization across the two contact zones between two hedgehog species revealed by genome-wide SNP data. Heredity (Edinb) 2022; 129:305-315. [PMID: 36229647 PMCID: PMC9613676 DOI: 10.1038/s41437-022-00567-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/29/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022] Open
Abstract
Hybridization and introgression have played important roles in the history of various species, including lineage diversification and the evolution of adaptive traits. Hybridization can accelerate the development of reproductive isolation between diverging species, and thus valuable insight into the evolution of reproductive barrier formation may be gained by studying secondary contact zones. Hedgehogs of the genus Erinaceus, which are insectivores sensitive to changes in climate, are a pioneer model in Pleistocene phylogeography. The present study provides the first genome-wide SNP data regarding the Erinaceus hedgehogs species complex, offering a unique comparison of two secondary contact zones between Erinaceus europaeus and E. roumanicus. Results confirmed diversification of the genus during the Pleistocene period, and detected a new refugial lineage of E. roumanicus outside the Mediterranean basin, most likely in the Ponto-Caspian region. In the Central European zone, the level of hybridization was low, whereas in the Russian-Baltic zone, both species hybridise extensively. Asymmetrical gene flow from E. europaeus to E. roumanicus suggests that reproductive isolation varies according to the direction of the crosses in the hybrid zones. However, no loci with significantly different patterns of introgression were detected. Markedly different pre- and post-zygotic barriers, and thus diverse modes of species boundary maintenance in the two contact zones, likely exist. This pattern is probably a consequence of the different age and thus of the different stage of evolution of reproductive isolating mechanisms in each hybrid zone.
Collapse
Affiliation(s)
- Kristýna Eliášová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic.
| | | | - José Horacio Grau
- Evolutionary Adaptive Genomics, University of Potsdam, Potsdam, Germany
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Miroslava Loudová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | | | | | | | - Pavel Hulva
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| |
Collapse
|
38
|
Ko BJ, An J, Eo SH. Korean Leopard Cat (Prionailurus bengalensis) population with low genetic diversity is distinct from Southeast Asian populations. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
|
39
|
Harvati K, Ackermann RR. Merging morphological and genetic evidence to assess hybridization in Western Eurasian late Pleistocene hominins. Nat Ecol Evol 2022; 6:1573-1585. [PMID: 36064759 DOI: 10.1038/s41559-022-01875-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/08/2022] [Indexed: 11/09/2022]
Abstract
Previous scientific consensus saw human evolution as defined by adaptive differences (behavioural and/or biological) and the emergence of Homo sapiens as the ultimate replacement of non-modern groups by a modern, adaptively more competitive group. However, recent research has shown that the process underlying our origins was considerably more complex. While archaeological and fossil evidence suggests that behavioural complexity may not be confined to the modern human lineage, recent palaeogenomic work shows that gene flow between distinct lineages (for example, Neanderthals, Denisovans, early H. sapiens) occurred repeatedly in the late Pleistocene, probably contributing elements to our genetic make-up that might have been crucial to our success as a diverse, adaptable species. Following these advances, the prevailing human origins model has shifted from one of near-complete replacement to a more nuanced view of partial replacement with considerable reticulation. Here we provide a brief introduction to the current genetic evidence for hybridization among hominins, its prevalence in, and effects on, comparative mammal groups, and especially how it manifests in the skull. We then explore the degree to which cranial variation seen in the fossil record of late Pleistocene hominins from Western Eurasia corresponds with our current genetic and comparative data. We are especially interested in understanding the degree to which skeletal data can reflect admixture. Our findings indicate some correspondence between these different lines of evidence, flag individual fossils as possibly admixed, and suggest that different cranial regions may preserve hybridization signals differentially. We urge further studies of the phenotype to expand our ability to detect the ways in which migration, interaction and genetic exchange have shaped the human past, beyond what is currently visible with the lens of ancient DNA.
Collapse
Affiliation(s)
- K Harvati
- Paleoanthropology section, Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Eberhard Karls Universität Tübingen, Tübingen, Germany.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
| | - R R Ackermann
- Human Evolution Research Institute, University of Cape Town, Cape Town, South Africa.
- Department of Archaeology, University of Cape Town, Cape Town, South Africa.
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', Eberhard Karls Universität Tübingen, Tübingen, Germany.
| |
Collapse
|
40
|
Smith BT, Merwin J, Provost KL, Thom G, Brumfield RT, Ferreira M, Mauck Iii WM, Moyle RG, Wright T, Joseph L. Phylogenomic analysis of the parrots of the world distinguishes artifactual from biological sources of gene tree discordance. Syst Biol 2022; 72:228-241. [PMID: 35916751 DOI: 10.1093/sysbio/syac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 02/22/2022] [Accepted: 07/22/2022] [Indexed: 11/14/2022] Open
Abstract
Gene tree discordance is expected in phylogenomic trees and biological processes are often invoked to explain it. However, heterogeneous levels of phylogenetic signal among individuals within datasets may cause artifactual sources of topological discordance. We examined how the information content in tips and subclades impacts topological discordance in the parrots (Order: Psittaciformes), a diverse and highly threatened clade of nearly 400 species. Using ultraconserved elements from 96% of the clade's species-level diversity, we estimated concatenated and species trees for 382 ingroup taxa. We found that discordance among tree topologies was most common at nodes dating between the late Miocene and Pliocene, and often at the taxonomic level of genus. Accordingly, we used two metrics to characterize information content in tips and assess the degree to which conflict between trees was being driven by lower quality samples. Most instances of topological conflict and non-monophyletic genera in the species tree could be objectively identified using these metrics. For subclades still discordant after tip-based filtering, we used a machine learning approach to determine whether phylogenetic signal or noise was the more important predictor of metrics supporting the alternative topologies. We found that when signal favored one of the topologies, noise was the most important variable in poorly performing models that favored the alternative topology. In sum, we show that artifactual sources of gene tree discordance, which are likely a common phenomenon in many datasets, can be distinguished from biological sources by quantifying the information content in each tip and modeling which factors support each topology.
Collapse
Affiliation(s)
- Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Jon Merwin
- Department of Ornithology, Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA.,Department of Biodiversity, Earth, and Environmental Science, Drexel University, Philadelphia, PA 19103, USA
| | - Kaiya L Provost
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210, USA
| | - Gregory Thom
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Mateus Ferreira
- Centro de Estudos da Biodiversidade, Universidade Federal de Roraima, Av. Cap. Ene Garcez, 2413, Boa Vista, RR, Brazil
| | - William M Mauck Iii
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - Robert G Moyle
- Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, 1345 Jayhawk Blvd., Lawrence, KS 66045, USA
| | - Timothy Wright
- Department of Biology, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Leo Joseph
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| |
Collapse
|
41
|
Hu J, Westbury MV, Yuan J, Wang C, Xiao B, Chen S, Song S, Wang L, Lin H, Lai X, Sheng G. An extinct and deeply divergent tiger lineage from northeastern China recognized through palaeogenomics. Proc Biol Sci 2022; 289:20220617. [PMID: 35892215 PMCID: PMC9326283 DOI: 10.1098/rspb.2022.0617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Tigers (Panthera tigris) are flagship big cats and attract extensive public attention due to their charismatic features and endangered status. Despite this, little is known about their prehistoric lineages and detailed evolutionary histories. Through palaeogenomic analyses, we identified a Pleistocene tiger from northeastern China, dated to beyond the limits of radiocarbon dating (greater than 43 500 years ago). We used a simulated dataset and different reads processing pipelines to test the validity of our results and confirmed that, in both mitochondrial and nuclear phylogenies, this ancient individual belongs to a previously unknown lineage that diverged prior to modern tiger diversification. Based on the mitochondrial genome, the divergence time of this ancient lineage was estimated to be approximately 268 ka (95% CI: 187-353 ka), doubling the known age of tigers' maternal ancestor to around 125 ka (95% CI: 88-168 ka). Furthermore, by combining our findings with putative mechanisms underlying the discordant mito-nuclear phylogenetic placement for the South China tigers, we proposed a more complex scenario of tiger evolution that would otherwise be missed using data from modern tigers only. Our study provides the first glimpses of the genetic antiquity of tigers and demonstrates the utility of aDNA-based investigation for further understanding tiger evolution.
Collapse
Affiliation(s)
- Jiaming Hu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, People's Republic of China,School of Earth Sciences, China University of Geosciences, Wuhan 430074, People's Republic of China
| | - Michael V. Westbury
- Globe Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Junxia Yuan
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Chunxue Wang
- School of Archaeology, Jilin University, Changchun 130012, People's Republic of China
| | - Bo Xiao
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, People's Republic of China,School of Earth Sciences, China University of Geosciences, Wuhan 430074, People's Republic of China
| | - Shungang Chen
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Shiwen Song
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Linying Wang
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Haifeng Lin
- School of Environmental Studies, China University of Geosciences, Wuhan 430078, People's Republic of China
| | - Xulong Lai
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, People's Republic of China,School of Earth Sciences, China University of Geosciences, Wuhan 430074, People's Republic of China
| | - Guilian Sheng
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430078, People's Republic of China,School of Environmental Studies, China University of Geosciences, Wuhan 430078, People's Republic of China
| |
Collapse
|
42
|
de Ferran V, Figueiró HV, de Jesus Trindade F, Smith O, Sinding MHS, Trinca CS, Lazzari GZ, Veron G, Vianna JA, Barbanera F, Kliver S, Serdyukova N, Bulyonkova T, Ryder OA, Gilbert MTP, Koepfli KP, Eizirik E. Phylogenomics of the world's otters. Curr Biol 2022; 32:3650-3658.e4. [PMID: 35779528 DOI: 10.1016/j.cub.2022.06.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
Abstract
Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,1-5 a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.
Collapse
Affiliation(s)
- Vera de Ferran
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Henrique Vieira Figueiró
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Fernanda de Jesus Trindade
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Oliver Smith
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark
| | - Mikkel-Holger S Sinding
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark
| | - Cristine S Trinca
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Gabriele Zenato Lazzari
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Géraldine Veron
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75231 Paris Cedex 5, France
| | - Juliana A Vianna
- Millennium Institute Center for Genome Regulation (CRG), Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuna Mackenna 4860, Santiago 782-0436, Chile
| | - Filippo Barbanera
- Department of Biology, University of Pisa, Via A. Volta 4, 56126 Pisa, Italy
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Natalia Serdyukova
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Tatiana Bulyonkova
- A. P. Ershov Institute of Informatics Systems SB RAS, 6 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA; Department of Evolution, Behavior, and Ecology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA.
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil; Instituto Pró-Carnívoros, Av. Horácio Netto, 1030 - Parque Edmundo Zanoni, Atibaia, São Paulo 12945-010, Brazil.
| |
Collapse
|
43
|
Khandai K, Navarro-Martinez C, Smith B, Buonopane R, Byun SA, Patterson M. Determining Significant Correlation Between Pairs of Extant Characters in a Small Parsimony Framework. J Comput Biol 2022; 29:1132-1154. [PMID: 35723627 DOI: 10.1089/cmb.2022.0141] [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: 11/12/2022] Open
Abstract
When studying the evolutionary relationships among a set of species, the principle of parsimony states that a relationship involving the fewest number of evolutionary events is likely the correct one. Due to its simplicity, this principle was formalized in the context of computational evolutionary biology decades ago by, for example, Fitch and Sankoff. Because the parsimony framework does not require a model of evolution, unlike maximum likelihood or Bayesian approaches, it is often a good starting point when no reasonable estimate of such a model is available. In this work, we devise a method for determining if pairs of discrete characters are significantly correlated across all most parsimonious reconstructions, given a set of species on these characters, and an evolutionary tree. The first step of this method is to use Sankoff's algorithm to compute all most parsimonious assignments of ancestral states (of each character) to the internal nodes of the phylogeny. Correlation between a pair of evolutionary events (e.g., absent to present) for a pair of characters is then determined by the (co-) occurrence patterns between the sets of their respective ancestral assignments. The probability of obtaining a correlation this extreme (or more) under a null hypothesis where the events happen randomly on the evolutionary tree is then used to assess the significance of this correlation. We implement this method: parcours (PARsimonious CO-occURrenceS) and use it to identify significantly correlated evolution among vocalizations and morphological characters in the Felidae family.
Collapse
Affiliation(s)
- Kaustubh Khandai
- Department of Computer Science, Georgia State University, Atlanta, Georgia, USA
| | | | - Brendan Smith
- Department of Biology, Fairfield University, Fairfield, Connecticut, USA
| | - Rebecca Buonopane
- Department of Biology, Fairfield University, Fairfield, Connecticut, USA
| | - Soyong Ashley Byun
- Department of Biology, Fairfield University, Fairfield, Connecticut, USA
| | - Murray Patterson
- Department of Computer Science, Georgia State University, Atlanta, Georgia, USA
| |
Collapse
|
44
|
Harris AJ, Foley NM, Williams TL, Murphy WJ. Tree House Explorer: A Novel Genome Browser for Phylogenomics. Mol Biol Evol 2022; 39:msac130. [PMID: 35700217 PMCID: PMC9246335 DOI: 10.1093/molbev/msac130] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/09/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
Tree House Explorer (THEx) is a genome browser that integrates phylogenomic data and genomic annotations into a single interactive platform for combined analysis. THEx allows users to visualize genome-wide variation in evolutionary histories and genetic divergence on a chromosome-by-chromosome basis, with continuous sliding window comparisons to gene annotations (GFF/GTF), recombination rates, and other user-specified, highly customizable feature annotations. THEx provides a new platform for interactive phylogenomic data visualization to analyze and interpret the diverse evolutionary histories woven throughout genomes. Hosted on Conda, THEx integrates seamlessly into new or pre-existing workflows.
Collapse
Affiliation(s)
- Andrew J Harris
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| | - Nicole M Foley
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
| | - Tiffani L Williams
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics & Genomics, Texas A&M University, College Station, TX, USA
| |
Collapse
|
45
|
Ramirez JL, Lescroart J, Figueiró HV, Torres-Florez JP, Villela PMS, Coutinho LL, Freitas PD, Johnson WE, Antunes A, Galetti PM, Eizirik E. Genomic signatures of divergent ecological strategies in a recent radiation of Neotropical wild cats. Mol Biol Evol 2022; 39:6594307. [PMID: 35639983 PMCID: PMC9189605 DOI: 10.1093/molbev/msac117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Ecological differentiation among diverging species is an important component of the evolutionary process and can be investigated in rapid and recent radiations. Here we use whole genome sequences of five species from the genus Leopardus, a recently diversified Neotropical lineage with species bearing distinctive morphological, ecological and behavioral features, to investigate genome-wide diversity, comparative demographic history and signatures of positive selection. Our results show that divergent ecological strategies are reflected in genomic features, e.g. a generalist species shows historically larger effective population size and higher heterozygosity than habitat specialists. The demographic history of these cats seems to have been jointly driven by climate fluctuations and habitat specialization, with different ecological adaptations leading to distinct trajectories. Finally, a gene involved in vertebrate retinal neurogenesis (POU4F2) was found to be under positive selection in the margay, a cat with notoriously large eyes that are likely associated with its nocturnal and arboreal specializations.
Collapse
Affiliation(s)
- Jorge L Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Peru
| | - Jonas Lescroart
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Department of Biology, University of Antwerp, Antwerp, Belgium
| | - Henrique V Figueiró
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Front Royal, USA
| | - Juan Pablo Torres-Florez
- Instituto Chico Mendes de Conservação da Biodiversidade/Centro Nacional de Pesquisa e Conservação de Mamíferos Aquáticos (ICMBio/CMA), Santos, Brazil
| | | | - Luiz L Coutinho
- Centro de Genômica Funcional, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Patricia D Freitas
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, Washington, DC, USA
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Porto, Portugal.,Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Pedro M Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, Brazil.,Instituto Pró-Carnívoros, Atibaia, SP, Brazil.,INCT-EECBio, Goiânia, GO, Brazil
| |
Collapse
|
46
|
Werhahn G, Senn H, Macdonald DW, Sillero-Zubiri C. The Diversity in the Genus Canis Challenges Conservation Biology: A Review of Available Data on Asian Wolves. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.782528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Taxa belonging to the Genus Canis can challenge taxonomists because species boundaries and distribution ranges are often gradual. Species delineation within Canis is currently not based on consistent criteria, and is hampered by geographical bias and lack of taxonomic research. But a consistent taxonomy is critical, given its importance for assigning legal protection, conservation priorities, and financial resources. We carried out a qualitative review of the major wolf lineages so far identified from Asia from historical to contemporary time and considered relevant morphological, ecological, and genetic evidence. We present full mitochondrial phylogenies and genetic distances between these lineages. This review aims to summarize the available data on contemporary Asian wolf lineages within the context of the larger phylogenetic Canis group and to work toward a taxonomy that is consistent within the Canidae. We found support for the presence and taxon eligibility of Holarctic gray, Himalayan/Tibetan, Indian, and Arabian wolves in Asia and recommend their recognition at the taxonomic levels consistent within the group.
Collapse
|
47
|
Abstract
SignificanceThe dynamics of deleterious variation under contrasting demographic scenarios remain poorly understood in spite of their relevance in evolutionary and conservation terms. Here we apply a genomic approach to study differences in the burden of deleterious alleles between the endangered Iberian lynx (Lynx pardinus) and the widespread Eurasian lynx (Lynx lynx). Our analysis unveils a significantly lower deleterious burden in the former species that should be ascribed to genetic purging, that is, to the increased opportunities of selection against recessive homozygotes due to the inbreeding caused by its smaller population size, as illustrated by our analytical predictions. This research provides theoretical and empirical evidence on the evolutionary relevance of genetic purging under certain demographic conditions.
Collapse
|
48
|
A reduced SNP panel to trace gene flow across southern European wolf populations and detect hybridization with other Canis taxa. Sci Rep 2022; 12:4195. [PMID: 35264717 PMCID: PMC8907317 DOI: 10.1038/s41598-022-08132-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 03/01/2022] [Indexed: 12/18/2022] Open
Abstract
Intra- and inter-specific gene flow are natural evolutionary processes. However, human-induced hybridization is a global conservation concern across taxa, and the development of discriminant genetic markers to differentiate among gene flow processes is essential. Wolves (Canis lupus) are affected by hybridization, particularly in southern Europe, where ongoing recolonization of historic ranges is augmenting gene flow among divergent populations. Our aim was to provide diagnostic canid markers focused on the long-divergent Iberian, Italian and Dinaric wolf populations, based on existing genomic resources. We used 158 canid samples to select a panel of highly informative single nucleotide polymorphisms (SNPs) to (i) distinguish wolves in the three regions from domestic dogs (C. l. familiaris) and golden jackals (C. aureus), and (ii) identify their first two hybrid generations. The resulting 192 SNPs correctly identified the five canid groups, all simulated first-generation (F1) hybrids (0.482 ≤ Qi ≤ 0.512 between their respective parental groups) and all first backcross (BC1) individuals (0.723 ≤ Qi ≤ 0.827 to parental groups). An assay design and test with invasive and non-invasive canid samples performed successfully for 178 SNPs. By separating natural population admixture from inter-specific hybridization, our reduced panel can help advance evolutionary research, monitoring, and timely conservation management.
Collapse
|
49
|
Ruiz-García M, Pinedo-Castro M, Shostell JM. Comparative phylogeography among eight Neotropical wild cat species: no single evolutionary pattern. Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blab170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
The felid species of South America are thought to have arrived on the continent during the Great American Biotic Interchange (GABI) in the Pleistocene. However, molecular and palaeontological data do not agree on how this event affected speciation in felids. Here, we determine both the number of colonization events and the period when felines first migrated from North America to South America. In addition, we evaluate whether similar evolutionary events could have affected the eight Neotropical cat species in their levels of genetic diversity, spatial genetic structure and demographic changes. We analysed four concatenated mitochondrial genes of the jaguar, ocelot, margay, tigrina, pampas cat, Andean cat, puma and jaguarundi. The samples were representative of a wide distribution of these species in Central and South America. Our analysis suggests either three or four colonization events from North America to South America over the past 3 Myr, followed by subsequent speciation events and the attainment of high or very high genetic diversity levels for seven of the species. No unique evolutionary process was detected for any of the current Neotropical cat species.
Collapse
Affiliation(s)
- Manuel Ruiz-García
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No. 43-82, Bogotá DC, Colombia
| | - Myreya Pinedo-Castro
- Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva, Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A, No. 43-82, Bogotá DC, Colombia
| | - Joseph Mark Shostell
- Math, Science and Technology Department, University of Minnesota Crookston, 2900 University Avenue, Crookston, MN 56716, USA
| |
Collapse
|
50
|
Myers AN, Lawhon SD, Diesel AB, Bradley CW, Rodrigues Hoffmann A, Murphy WJ. An ancient haplotype containing antimicrobial peptide gene variants is associated with severe fungal skin disease in Persian cats. PLoS Genet 2022; 18:e1010062. [PMID: 35157719 PMCID: PMC8880935 DOI: 10.1371/journal.pgen.1010062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 02/25/2022] [Accepted: 01/28/2022] [Indexed: 11/19/2022] Open
Abstract
Dermatophytosis, also known as ringworm, is a contagious fungal skin disease affecting humans and animals worldwide. Persian cats exhibit severe forms of the disease more commonly than other breeds of cat, including other long-haired breeds. Certain types of severe dermatophytosis in humans are reportedly caused by monogenic inborn errors of immunity. The goal of this study was to identify genetic variants in Persian cats contributing to the phenotype of severe dermatophytosis. Whole-genome sequencing of case and control Persian cats followed by a genome-wide association study identified a highly divergent, disease-associated haplotype on chromosome F1 containing the S100 family of genes. S100 calcium binding protein A9 (S100A9), which encodes a subunit of the antimicrobial heterodimer known as calprotectin, contained 13 nonsynonymous variants between cases and controls. Evolutionary analysis of S100A9 haplotypes comparing cases, controls, and wild felids suggested the divergent disease-associated haplotype was likely introgressed into the domestic cat lineage and maintained via balancing selection. We demonstrated marked upregulation of calprotectin expression in the feline epidermis during dermatophytosis, suggesting involvement in disease pathogenesis. Given this divergent allele has been maintained in domestic cat and wildcat populations, this haplotype may have beneficial effects against other pathogens. The pathogen specificity of this altered protein should be investigated before attempting to reduce the allele frequency in the Persian cat breed. Further work is needed to clarify if severe Persian dermatophytosis is a monogenic disease or if hidden disease-susceptibility loci remain to be discovered. Consideration should be given to engineering antimicrobial peptides such as calprotectin for topical treatment of dermatophytosis in humans and animals. Fungal skin infections known as ringworm or dermatophytosis affect billions of humans and animals worldwide. Normally the disease is self-limiting in affected individuals. The Persian cat breed is a popular breed known for its long hair coat and short nose as well as its propensity to develop severe, chronic dermatophytosis. By examining the genomes of Persian cats, we discovered that a specific region of DNA is highly altered between cats with and without severe dermatophytosis. The DNA sequence in this region is particularly divergent within a cluster of genes involved in immune defense against pathogens. Notably, alterations to the DNA sequence cause several changes in the antimicrobial protein known as calprotectin, which defends against pathogens in the skin of cats. Persian cats with severe dermatophytosis have a version of calprotectin similar to a version maintained by certain desert-dwelling wild felids such as sand cats and Asiatic wildcats. Therefore, we think this version of the protein is beneficial in some environments or against certain pathogens but not against the fungus that causes ringworm in cats. Our findings suggest changes to calprotectin may affect pathogen specificity and engineered calprotectin could be considered as a novel therapy for dermatophytosis in humans and animals.
Collapse
Affiliation(s)
- Alexandra N. Myers
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, Unites States of America
- * E-mail: (ANM); (WJM)
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, Unites States of America
| | - Alison B. Diesel
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, Unites States of America
| | - Charles W. Bradley
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, Unites States of America
| | - Aline Rodrigues Hoffmann
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, Unites States of America
| | - William J. Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, Unites States of America
- * E-mail: (ANM); (WJM)
| | | |
Collapse
|