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Özkan M, Gürün K, Yüncü E, Vural KB, Atağ G, Akbaba A, Fidan FR, Sağlıcan E, Altınışık EN, Koptekin D, Pawłowska K, Hodder I, Adcock SE, Arbuckle BS, Steadman SR, McMahon G, Erdal YS, Bilgin CC, Togan İ, Geigl EM, Götherström A, Grange T, Özer F, Somel M. The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus). Mol Ecol 2024; 33:e17440. [PMID: 38946459 DOI: 10.1111/mec.17440] [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: 07/11/2023] [Revised: 05/17/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024]
Abstract
We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6-6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name 'hydruntine'. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present-day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid-first millennium BCE, a possible sign of its eventual demise.
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Affiliation(s)
- Mustafa Özkan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ali Akbaba
- Department of Anthropology, Ankara University, Ankara, Turkey
- Alparslan University, Muş, Turkey
| | - Fatma Rabia Fidan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Ekin Sağlıcan
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Ezgi N Altınışık
- Department of Anthropology, Human_G Laboratory, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Kamilla Pawłowska
- Department of Palaeoenvironmental Research, Adam Mickiewicz University, Poznań, Poland
| | - Ian Hodder
- Department of Anthropology, Stanford University, Stanford, California, USA
| | - Sarah E Adcock
- Institute for the Study of the Ancient World, New York University, New York, New York, USA
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon R Steadman
- Department of Sociology/Anthropology, SUNY Cortland, Cortland, New York, USA
| | - Gregory McMahon
- Classics, Humanities and Italian Studies Department, University of New Hampshire, Durham, New Hampshire, USA
| | - Yılmaz Selim Erdal
- Department of Anthropology, Human_G Laboratory, Hacettepe University, Ankara, Turkey
| | - C Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, Université de Paris, Paris, France
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Thierry Grange
- Institut Jacques Monod, CNRS, Université de Paris, Paris, France
| | - Füsun Özer
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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2
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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.
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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
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3
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Jevit MJ, Castaneda C, Paria N, Das PJ, Miller D, Antczak DF, Kalbfleisch TS, Davis BW, Raudsepp T. Trio-binning of a hinny refines the comparative organization of the horse and donkey X chromosomes and reveals novel species-specific features. Sci Rep 2023; 13:20180. [PMID: 37978222 PMCID: PMC10656420 DOI: 10.1038/s41598-023-47583-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023] Open
Abstract
We generated single haplotype assemblies from a hinny hybrid which significantly improved the gapless contiguity for horse and donkey autosomal genomes and the X chromosomes. We added over 15 Mb of missing sequence to both X chromosomes, 60 Mb to donkey autosomes and corrected numerous errors in donkey and some in horse reference genomes. We resolved functionally important X-linked repeats: the DXZ4 macrosatellite and ampliconic Equine Testis Specific Transcript Y7 (ETSTY7). We pinpointed the location of the pseudoautosomal boundaries (PAB) and determined the size of the horse (1.8 Mb) and donkey (1.88 Mb) pseudoautosomal regions (PARs). We discovered distinct differences in horse and donkey PABs: a testis-expressed gene, XKR3Y, spans horse PAB with exons1-2 located in Y and exon3 in the X-Y PAR, whereas the donkey XKR3Y is Y-specific. DXZ4 had a similar ~ 8 kb monomer in both species with 10 copies in horse and 20 in donkey. We assigned hundreds of copies of ETSTY7, a sequence horizontally transferred from Parascaris and massively amplified in equids, to horse and donkey X chromosomes and three autosomes. The findings and products contribute to molecular studies of equid biology and advance research on X-linked conditions, sex chromosome regulation and evolution in equids.
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Affiliation(s)
- Matthew J Jevit
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Caitlin Castaneda
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Nandina Paria
- Texas Scottish Rite Hospital for Children, Dallas, TX, 75219, USA
| | - Pranab J Das
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Donald Miller
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, Cornell University, Ithaca, NY, 14853, USA
| | - Theodore S Kalbfleisch
- Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Brian W Davis
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
| | - Terje Raudsepp
- School of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA.
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Kozak S, Merda D, Duquesne F, Breuil MF, Mawhinney I, Petry S. Whole genome sequence analysis of the 2018 Persian onager isolate suggests sublineages within the Taylorella asinigenitalis species. Vet Microbiol 2023; 286:109884. [PMID: 37832214 DOI: 10.1016/j.vetmic.2023.109884] [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: 07/12/2023] [Revised: 09/26/2023] [Accepted: 10/01/2023] [Indexed: 10/15/2023]
Abstract
In 2018, a T. asinigenitalis strain (MCE663) was isolated in a Persian onager tested for contagious equine metritis (CEM) in a United Kingdom (UK) zoo. This bacterium had never been reported in the UK and Multilocus Sequence Typing described a new atypically divergent ST (ST60). Although the causative agent of CEM is the bacterium Taylorella equigenitalis, a first natural outbreak of endometritis caused by T. asinigenitalis ST70 was reported in 2019, putting its pathogenic potential into question. In this context, we aimed to further sequence the T. asinigenitalis MCE663 genome and characterize the strain using phenotypical and genetic approaches. Results showed that it gathered all identification characteristics of T. asinigenitalis with smaller colonies and it was susceptible to all tested antibiotics. Genome-level phylogeny showed that the genome MCE663 formed a distinct phylogroup, and only shared ≈ 96.1% of average nucleotide identity (ANI) with the three published T. asinigenitalis genomes, which together shared ≈ 98.3% ANI. According to current cut-offs consensus for species and subspecies delineation (95% and 98%, respectively), our results support the first insights of a sublineage delineation within the T. asinigenitalis species.
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Affiliation(s)
- Sofia Kozak
- ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Déborah Merda
- ANSES, Paris Est University, SPAAD Unit, Maisons-Alfort, France
| | - Fabien Duquesne
- ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Marie-France Breuil
- ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France
| | - Ian Mawhinney
- APHA Veterinary Investigation Centre, Rougham Hill, Bury St Edmunds, Suffolk, UK
| | - Sandrine Petry
- ANSES, Laboratory for Animal Health, Physiopathology and Epidemiology of Equine Diseases Unit, Goustranville, France.
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5
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Chen J, Zhang S, Liu S, Dong J, Cao Y, Sun Y. Single nucleotide polymorphisms (SNPs) and indels identified from whole-genome re-sequencing of four Chinese donkey breeds. Anim Biotechnol 2023; 34:1828-1839. [PMID: 35382683 DOI: 10.1080/10495398.2022.2053145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
This paper represents the fundamental report of the survey of genome-wide changes of four Chinese indigenous donkey breeds, Dezhou (DZ), Guangling (GL), North China (NC), and Shandong Little donkey (SDL), and the findings will prove usefully for identification of biomarkers that perhaps predict or characterize the growth and coat color patterns. Three genomic regions in CYP3A12, TUBGCP5, and GSTA1 genes, were identified as putative selective sweeps in all researched donkey populations. The loci of candidate genes that may have contributed to the phenotypes in body size (ACSL4, MSI2, ADRA1B, and CDKL5) and coat color patterns (KITLG and TBX3) in donkey populations would be found in underlying strong selection signatures when compared between large and small donkey types, and between different coat colors. The results of the phylogenetic analysis, FST, and principal component analysis (PCA) supported that each population cannot clearly deviate from each other, showing no obvious population structure. We can conclude from the population history that the formation processes between DZS and NC, GL, and SDL are completely different. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Chinese donkey breeding programs.
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Affiliation(s)
- Jianxing Chen
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, China
| | - Shuqin Liu
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Jianbao Dong
- Department of Veterinary Medical Science, Shandong Vocational Animal Science and Veterinary College, Weifang, China
| | - Yanhang Cao
- Modern Animal Husbandry Development Service Center of Dongying, Dongying, China
| | - Yujiang Sun
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
- Vocational College of Dongying, Dongying, China
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6
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Hrabina P, Pernerová L, Suchomel J, Robovský J. Utility of cytochrome c oxidase I for the deciphering of unstable phylogeny and taxonomy of gorals, genus Nemorhaedus Hamilton Smith, 1827 (Bovidae, Ovibovina). Zookeys 2023; 1181:81-110. [PMID: 38313159 PMCID: PMC10838175 DOI: 10.3897/zookeys.1181.108019] [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: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 02/06/2024] Open
Abstract
Gorals represent ungulate mammals of the Palearctic and Indo-Malayan realms that face habitat destruction and intense hunting pressure. Their classification has been the subject of various (mainly genetic) assessments in the last decade, but some results are conflicting, hampering some conservation-based decisions. Genetic sampling of gorals has increased considerably in recent years, at least for mitochondrial (mt) DNA. Results based on two mt genes (cytochrome b and the D-loop) are currently available. Still, the utility of cytochrome oxidase subunit I remains unanalysed, even though it belongs among the gene markers that enable a correct species identification in mammals. This study examines phylogenetic relationships and species delimitation in gorals using all currently available cytochrome oxidase subunit I sequences, including the not yet analysed goral population from Pakistan. Our results of various phylogenetic approaches, such as maximum parsimony, likelihood and Bayesian inference, and exploration of species boundaries via species delimitation support the validity of six species of goral, namely N.baileyi, N.caudatus, N.cranbrooki, N.evansi, N.goral, and N.griseus. This result accords well with results based on other mt genes, especially the cytochrome b from the highly exhaustive data sampling. Our study also summarises common sources of errors in the assessment of goral phylogeny and taxonomy and highlights future priorities in understanding goral diversification.
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Affiliation(s)
- Petr Hrabina
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Ludmila Pernerová
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
| | - Josef Suchomel
- Department of Zoology, Fisheries, Hydrobiology and Apiculture, Mendel University in Brno, Zemědělská 1, Brno, 61300, Czech Republic Mendel University in Brno Brno Czech Republic
| | - Jan Robovský
- Department of Zoology, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, 37005, Czech Republic University of South Bohemia České Budějovice Czech Republic
- Liberec Zoo, Lidové sady 425/1, Liberec, 46001, Czech Republic Liberec Zoo Liberec Czech Republic
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Kavalco KF, Pasa R. Chromosomal Radiation: A model to explain karyotypic diversity in cryptic species. Genet Mol Biol 2023; 46:e20230116. [PMID: 37815421 PMCID: PMC10563172 DOI: 10.1590/1678-4685-gmb-2023-0116] [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: 04/24/2023] [Accepted: 08/22/2023] [Indexed: 10/11/2023] Open
Abstract
We present a concept that explains the pattern of occurrence of widely distributed organisms with large chromosomal diversity, large or small molecular divergence, and the insufficiency or absence of morphological identity. Our model is based on cytogenetic studies associated with molecular and biological data and can be applied to any lineage of sister species, chronospecies, or cryptic species. Through the evaluation of the karyotypic macrostructure, as the physical location of genes e satellites DNAs, in addition to phylogenetic reconstructions from mitochondrial and nuclear genes, per example, we have observed morphologically indistinguishable individuals presenting different locally fixed karyomorphs with phylogeographic discontinuity. The biological process behind this pattern is seen in many groups of cryptic species, in which variation lies mainly in the organization of their genomes but not necessarily in the ecosystems they inhabit or in their external morphology. It's similar to the processes behind other events observed in the distribution of lineages. In this work, we explore the hypothesis of a process analogous to ecological-evolutionary radiation, which we called Chromosomal Radiation. Chromosomal Radiation can be adaptive or non-adaptive and applied to different groups of organisms.
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Affiliation(s)
- Karine Frehner Kavalco
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Genética Ecológica e Evolutiva (LaGEEvo), Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Bioinformática e Genômica, Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
| | - Rubens Pasa
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Genética Ecológica e Evolutiva (LaGEEvo), Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
- Universidade Federal de Viçosa, Instituto de Ciências Biológicas e da Saúde, Laboratório de Bioinformática e Genômica, Campus Rio Paranaíba, Rio Paranaíba, MG, Brazil
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8
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Mármol-Sánchez E, Fromm B, Oskolkov N, Pochon Z, Kalogeropoulos P, Eriksson E, Biryukova I, Sekar V, Ersmark E, Andersson B, Dalén L, Friedländer MR. Historical RNA expression profiles from the extinct Tasmanian tiger. Genome Res 2023; 33:1299-1316. [PMID: 37463752 PMCID: PMC10552650 DOI: 10.1101/gr.277663.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Paleogenomics continues to yield valuable insights into the evolution, population dynamics, and ecology of our ancestors and other extinct species. However, DNA sequencing cannot reveal tissue-specific gene expression, cellular identity, or gene regulation, which are only attainable at the transcriptional level. Pioneering studies have shown that useful RNA can be extracted from ancient specimens preserved in permafrost and historical skins from extant canids, but no attempts have been made so far on extinct species. We extract, sequence, and analyze historical RNA from muscle and skin tissue of a ∼130-year-old Tasmanian tiger (Thylacinus cynocephalus) preserved in desiccation at room temperature in a museum collection. The transcriptional profiles closely resemble those of extant species, revealing specific anatomical features such as slow muscle fibers or blood infiltration. Metatranscriptomic analysis, RNA damage, tissue-specific RNA profiles, and expression hotspots genome-wide further confirm the thylacine origin of the sequences. RNA sequences are used to improve protein-coding and noncoding annotations, evidencing missing exonic loci and the location of ribosomal RNA genes while increasing the number of annotated thylacine microRNAs from 62 to 325. We discover a thylacine-specific microRNA isoform that could not have been confirmed without RNA evidence. Finally, we detect traces of RNA viruses, suggesting the possibility of profiling viral evolution. Our results represent the first successful attempt to obtain transcriptional profiles from an extinct animal species, providing thought-to-be-lost information on gene expression dynamics. These findings hold promising implications for the study of RNA molecules across the vast collections of natural history museums and from well-preserved permafrost remains.
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Affiliation(s)
- Emilio Mármol-Sánchez
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
- The Arctic University Museum of Norway, UiT - The Arctic University of Norway, 9006 Tromsø, Norway
| | - Nikolay Oskolkov
- Department of Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Lund University, 223 62 Lund, Sweden
| | - Zoé Pochon
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Panagiotis Kalogeropoulos
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Eli Eriksson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Inna Biryukova
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Vaishnovi Sekar
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden
| | - Erik Ersmark
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
| | - Björn Andersson
- Department of Cell and Molecular Biology (CMB), Karolinska Institute, 171 77 Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden;
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, 104 05 Stockholm, Sweden
- Department of Zoology, Stockholm University, 106 91 Stockholm, Sweden
| | - Marc R Friedländer
- Department of Molecular Biosciences, The Wenner-Gren Institute, Science for Life Laboratory, Stockholm University, 114 18 Stockholm, Sweden;
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9
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Batcher K, Varney S, Raudsepp T, Jevit M, Dickinson P, Jagannathan V, Leeb T, Bannasch D. Ancient segmentally duplicated LCORL retrocopies in equids. PLoS One 2023; 18:e0286861. [PMID: 37289743 PMCID: PMC10249811 DOI: 10.1371/journal.pone.0286861] [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: 04/17/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
LINE-1 is an active transposable element encoding proteins capable of inserting host gene retrocopies, resulting in retro-copy number variants (retroCNVs) between individuals. Here, we performed retroCNV discovery using 86 equids and identified 437 retrocopy insertions. Only 5 retroCNVs were shared between horses and other equids, indicating that the majority of retroCNVs inserted after the species diverged. A large number (17-35 copies) of segmentally duplicated Ligand Dependent Nuclear Receptor Corepressor Like (LCORL) retrocopies were present in all equids but absent from other extant perissodactyls. The majority of LCORL transcripts in horses and donkeys originate from the retrocopies. The initial LCORL retrotransposition occurred 18 million years ago (17-19 95% CI), which is coincident with the increase in body size, reduction in digit number, and changes in dentition that characterized equid evolution. Evolutionary conservation of the LCORL retrocopy segmental amplification in the Equidae family, high expression levels and the ancient timeline for LCORL retrotransposition support a functional role for this structural variant.
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Affiliation(s)
- Kevin Batcher
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
| | - Scarlett Varney
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
| | - Terje Raudsepp
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Matthew Jevit
- Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Peter Dickinson
- Department of Surgical and Radiological Sciences, University of California Davis, Davis, CA, United States of America
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Danika Bannasch
- Department of Population Health and Reproduction, University of California Davis, Davis, CA, United States of America
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10
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Comaills V, Castellano-Pozo M. Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution. BIOLOGY 2023; 12:biology12050671. [PMID: 37237485 DOI: 10.3390/biology12050671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023]
Abstract
The integrity of the genome is crucial for the survival of all living organisms. However, genomes need to adapt to survive certain pressures, and for this purpose use several mechanisms to diversify. Chromosomal instability (CIN) is one of the main mechanisms leading to the creation of genomic heterogeneity by altering the number of chromosomes and changing their structures. In this review, we will discuss the different chromosomal patterns and changes observed in speciation, in evolutional biology as well as during tumor progression. By nature, the human genome shows an induction of diversity during gametogenesis but as well during tumorigenesis that can conclude in drastic changes such as the whole genome doubling to more discrete changes as the complex chromosomal rearrangement chromothripsis. More importantly, changes observed during speciation are strikingly similar to the genomic evolution observed during tumor progression and resistance to therapy. The different origins of CIN will be treated as the importance of double-strand breaks (DSBs) or the consequences of micronuclei. We will also explain the mechanisms behind the controlled DSBs, and recombination of homologous chromosomes observed during meiosis, to explain how errors lead to similar patterns observed during tumorigenesis. Then, we will also list several diseases associated with CIN, resulting in fertility issues, miscarriage, rare genetic diseases, and cancer. Understanding better chromosomal instability as a whole is primordial for the understanding of mechanisms leading to tumor progression.
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Affiliation(s)
- Valentine Comaills
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
| | - Maikel Castellano-Pozo
- Andalusian Center for Molecular Biology and Regenerative Medicine-CABIMER, University of Pablo de Olavide-University of Seville-CSIC, Junta de Andalucía, 41092 Seville, Spain
- Genetic Department, Faculty of Biology, University of Seville, 41080 Seville, Spain
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11
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A Satellite-Free Centromere in Equus przewalskii Chromosome 10. Int J Mol Sci 2023; 24:ijms24044134. [PMID: 36835543 PMCID: PMC9961726 DOI: 10.3390/ijms24044134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
In mammals, centromeres are epigenetically specified by the histone H3 variant CENP-A and are typically associated with satellite DNA. We previously described the first example of a natural satellite-free centromere on Equus caballus chromosome 11 (ECA11) and, subsequently, on several chromosomes in other species of the genus Equus. We discovered that these satellite-free neocentromeres arose recently during evolution through centromere repositioning and/or chromosomal fusion, after inactivation of the ancestral centromere, where, in many cases, blocks of satellite sequences were maintained. Here, we investigated by FISH the chromosomal distribution of satellite DNA families in Equus przewalskii (EPR), demonstrating a good degree of conservation of the localization of the major horse satellite families 37cen and 2PI with the domestic horse. Moreover, we demonstrated, by ChIP-seq, that 37cen is the satellite bound by CENP-A and that the centromere of EPR10, the ortholog of ECA11, is devoid of satellite sequences. Our results confirm that these two species are closely related and that the event of centromere repositioning which gave rise to EPR10/ECA11 centromeres occurred in the common ancestor, before the separation of the two horse lineages.
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12
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Wong ELY, Nevado B, Hiscock SJ, Filatov DA. Rapid evolution of hybrid breakdown following recent divergence with gene flow in Senecio species on Mount Etna, Sicily. Heredity (Edinb) 2023; 130:40-52. [PMID: 36494489 PMCID: PMC9814926 DOI: 10.1038/s41437-022-00576-4] [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: 06/17/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022] Open
Abstract
How do nascent species evolve reproductive isolation during speciation with on-going gene flow? How do hybrid lineages become stabilised hybrid species? While commonly used genomic approaches provide an indirect way to identify species incompatibility factors, synthetic hybrids generated from interspecific crosses allow direct pinpointing of phenotypic traits involved in incompatibilities and the traits that are potentially adaptive in hybrid species. Here we report the analysis of phenotypic variation and hybrid breakdown in crosses between closely-related Senecio aethnensis and S. chrysanthemifolius, and their homoploid hybrid species, S. squalidus. The two former species represent a likely case of recent (<200 ky) speciation with gene flow driven by adaptation to contrasting conditions of high- and low-elevations on Mount Etna, Sicily. As these species form viable and fertile hybrids, it remains unclear whether they have started to evolve reproductive incompatibility. Our analysis represents the first study of phenotypic variation and hybrid breakdown involving multiple Senecio hybrid families. It revealed wide range of variation in multiple traits, including the traits previously unrecorded in synthetic hybrids. Leaf shape, highly distinct between S. aethnensis and S. chrysanthemifolius, was extremely variable in F2 hybrids, but more consistent in S. squalidus. Our study demonstrates that interspecific incompatibilities can evolve rapidly despite on-going gene flow between the species. Further work is necessary to understand the genetic bases of these incompatibilities and their role in speciation with gene flow.
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Affiliation(s)
- Edgar L. Y. Wong
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK ,grid.507705.0Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Bruno Nevado
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK ,grid.9983.b0000 0001 2181 4263Centre for Ecology, Evolution and Environmental Changes, University of Lisbon, Lisbon, Portugal
| | - Simon J. Hiscock
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK ,Oxford Botanic Garden and Arboretum, Oxford, UK
| | - Dmitry A. Filatov
- grid.4991.50000 0004 1936 8948Department of Biology, University of Oxford, Oxford, UK
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13
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Cardinali I, Giontella A, Tommasi A, Silvestrelli M, Lancioni H. Unlocking Horse Y Chromosome Diversity. Genes (Basel) 2022; 13:genes13122272. [PMID: 36553539 PMCID: PMC9777570 DOI: 10.3390/genes13122272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.
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Affiliation(s)
- Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Andrea Giontella
- Department of Veterinary Medicine, University of Perugia, 06126 Perugia, Italy
- Correspondence: (I.C.); (A.G.)
| | - Anna Tommasi
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
| | | | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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14
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Ren X, Liu Y, Zhao Y, Li B, Bai D, Bou G, Zhang X, Du M, Wang X, Bou T, Shen Y, Dugarjaviin M. Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule. Genes (Basel) 2022; 13:genes13122188. [PMID: 36553455 PMCID: PMC9778318 DOI: 10.3390/genes13122188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/07/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Interspecific hybridization often shows negative effects on hybrids. However, only a few multicellular species, limited to a handful of plants and animals, have shown partial genetic mechanisms by which hybridization leads to low fitness in hybrids. Here, to explore the outcome of combining the two genomes of a horse and donkey, we analyzed the whole-genome sequences from an Equus parent-offspring trio using Illumina platforms. We generated 41.39× and 46.21× coverage sequences for the horse and mule, respectively. For the donkey, a 40.38× coverage sequence was generated and stored in our laboratory. Approximately 24.86 million alleles were discovered that varied from the reference genome. Single nucleotide polymorphisms were used as polymorphic markers for assigning alleles to their parental genomic inheritance. We identified 25,703 Mendelian inheritance error single nucleotide polymorphisms in the mule genome that were not inherited from the parents through Mendelian inheritance. A total of 555 de novo single nucleotide polymorphisms were also identified. The rate of de novo single nucleotide polymorphisms was 2.21 × 10-7 in the mule from the Equus parent-offspring trio. This rate is obviously higher than the natural mutation rate for Equus, which is also consistent with the previous hypothesis that interracial crosses may have a high mutation rate. The genes associated with these single nucleotide polymorphisms are mainly involved in immune processes, DNA repair, and cancer processes. The results of the analysis of three genomes from an Equus parent-offspring trio improved our knowledge of the consequences of the integration of parental genomes in mules.
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15
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Zebras of all stripes repel biting flies at close range. Sci Rep 2022; 12:18617. [PMID: 36329147 PMCID: PMC9633588 DOI: 10.1038/s41598-022-22333-7] [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: 06/03/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022] Open
Abstract
The best-supported hypothesis for why zebras have stripes is that stripes repel biting flies. While this effect is well-established, the mechanism behind it remains elusive. Myriad hypotheses have been suggested, but few experiments have helped narrow the field of possible explanations. In addition, the complex visual features of real zebra pelage and the natural range of stripe widths have been largely left out of experimental designs. In paired-choice field experiments in a Kenyan savannah, we found that hungry Stomoxys flies released in an enclosure strongly preferred to land on uniform tan impala pelts over striped zebra pelts but exhibited no preference between the pelts of the zebra species with the widest stripes and the narrowest stripes. Our findings confirm that zebra stripes repel biting flies under naturalistic conditions and do so at close range (suggesting that several of the mechanisms hypothesized to operate at a distance are unnecessary for the fly-repulsion effect) but indicate that interspecific variation in stripe width is associated with selection pressures other than biting flies.
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16
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Wang Y, Hua X, Shi X, Wang C. Origin, Evolution, and Research Development of Donkeys. Genes (Basel) 2022; 13:1945. [PMID: 36360182 PMCID: PMC9689456 DOI: 10.3390/genes13111945] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 08/11/2023] Open
Abstract
Lack of archaeological and whole-genome diversity data has restricted current knowledge of the evolutionary history of donkeys. With the advancement of science and technology, the discovery of archaeological evidence, the development of molecular genetics, and the improvement of whole-genome sequencing technology, the in-depth understanding of the origin and domestication of donkeys has been enhanced, however. Given the lack of systematic research, the present study carefully screened and collected multiple academic papers and books, journals, and literature on donkeys over the past 15 years. The origin and domestication of donkeys are reviewed in this paper from the aspects of basic information, cultural origin, bioarcheology, mitochondrial and chromosomal microsatellite sequences, and whole-genome sequence comparison. It also highlights and reviews genome assembly technology, by assembling the genome of an individual organism and comparing it with related sample genomes, which can be used to produce more accurate results through big data statistics, analysis, and computational correlation models. Background: The donkey industry in the world and especially in China is developing rapidly, and donkey farming is transforming gradually from the family farming model to large-scale, intensive, and integrated industrial operations, which could ensure the stability of product quality and quantity. However, theoretical research on donkey breeding and its technical development lags far behind that of other livestock, thereby limiting its industrial development. This review provides holistic information for the donkey industry and researchers, that could promote theoretical research, genomic selection (GS), and reproductive management of the donkey population.
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17
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Todd ET, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pérez Pardal L, Patterson Rosa L, Librado P, Ringbauer H, Verdugo M, Southon J, Aury JM, Perdereau A, Vila E, Marzullo M, Prato O, Tecchiati U, Bagnasco Gianni G, Tagliacozzo A, Tinè V, Alhaique F, Cardoso JL, Valente MJ, Telles Antunes M, Frantz L, Shapiro B, Bradley DG, Boulbes N, Gardeisen A, Horwitz LK, Öztan A, Arbuckle BS, Onar V, Clavel B, Lepetz S, Vahdati AA, Davoudi H, Mohaseb A, Mashkour M, Bouchez O, Donnadieu C, Wincker P, Brooks SA, Beja-Pereira A, Wu DD, Orlando L. The genomic history and global expansion of domestic donkeys. Science 2022; 377:1172-1180. [PMID: 36074859 DOI: 10.1126/science.abo3503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.
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Affiliation(s)
- Evelyn T Todd
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Laure Tonasso-Calvière
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Antoine Fages
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Pierre Clavel
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France.,Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Lucía Pérez Pardal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
| | | | - Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Marta Verdugo
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - John Southon
- Earth System Science Department, University of California, Irvine, CA 92697, USA
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Emmanuelle Vila
- Laboratoire Archéorient, Université Lyon 2, Lyon 69007, France
| | - Matilde Marzullo
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Ornella Prato
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Umberto Tecchiati
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Giovanna Bagnasco Gianni
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | | | - Vincenzo Tinè
- Soprintendenza archeologia belle arti e paesaggio per le province di Verona, Rovigo e Vicenza, Verona 37121, Italy
| | | | - João Luís Cardoso
- ICArEHB, Campus de Gambelas, University of Algarve, Faro 8005-139, Portugal.,Universidade Aberta, Lisbon 1269-001, Portugal
| | - Maria João Valente
- Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro 8000-117, Portugal
| | - Miguel Telles Antunes
- Centre for Research on Science and Geological Engineering, Universidade NOVA de Lisboa, Lisbon 1099-085, Portugal
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich 80539, Germany.,School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4DQ, United Kingdom
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Nicolas Boulbes
- Institut de Paléontologie Humaine, Fondation Albert Ier, Paris / UMR 7194 HNHP, MNHN-CNRS-UPVD / EPCC Centre Européen de Recherche Préhistorique, Tautavel 66720, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditéranéennes, Université Paul Valéry - Site Saint-Charles 2, Montpellier 34090, France
| | - Liora Kolska Horwitz
- National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem 9190401, Israel
| | - Aliye Öztan
- Archaeology Department, Ankara University, Ankara 06100, Turkey
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul 34320, Turkey
| | - Benoît Clavel
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Sébastien Lepetz
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord 9416745775, Iran
| | - Hossein Davoudi
- Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Azadeh Mohaseb
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran.,Department of Osteology, National Museum of Iran, Tehran 1136918111, Iran
| | - Olivier Bouchez
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Cécile Donnadieu
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Samantha A Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,DGAOT, Faculty of Sciences, Universidade do Porto, Porto 4169-007, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Universidade do Porto, Vairão 4485-646, Portugal
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
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18
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Bao W, Yu J, He Y, Liu M, Yang X. The diversity analysis and gene function prediction of intestinal bacteria in three equine species. Front Microbiol 2022; 13:973828. [PMID: 36160217 PMCID: PMC9490377 DOI: 10.3389/fmicb.2022.973828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/26/2022] [Indexed: 11/22/2022] Open
Abstract
The intestinal flora has a variety of physiological functions involved in the regulation of host metabolism, immunity and endocrinology, and plays an important role in maintaining the health of the host. In this study, we used high-throughput sequencing technology to analyze the intestinal bacterial diversity and their gene functions in three equine species of the genus Shetland Pony (SP), Mongolian Wild Ass (MA), and Plain Zebra (PZ) in captivity in two wildlife parks in Inner Mongolia Autonomous Region, China. The results showed that only the SP intestinal bacterial abundance index (Chao1) was significantly different (P < 0.05) between the same species in the two wildlife parks, but neither the intestinal bacterial diversity index (Shannon) nor the community composition were significantly different (P > 0.05). The bacterial abundance index (Chao1) was significantly higher in MA than SP (P < 0.05) and highly significantly higher than PZ (P < 0.01); the bacterial diversity index (Shannon) was higher in MA than PZ, but there was no significant difference, but both MA and PZ were significantly higher than SP (P < 0.05). Moreover, the intestinal bacterial community composition was significantly different among the three equine species (P = 0.001). The dominant bacterial phyla for SP, MA, and PZ were Firmicutes and Bacteroidota; among them, the bacterial family with the highest relative abundance was Lachnospiraceae and the bacterial genus was Rikenellaceae_RC9_gut_group. Analysis of the metabolic gene functions of intestinal bacteria revealed that the highest relative abundance at Pathway level 2 was for global and overview maps; at Pathway level 3, the highest relative abundance was for biosynthesis of secondary metabolites. In sum, the intestinal bacterial community composition and diversity of the above three equine species differed significantly, but their metabolic gene functions were similar. Moreover, the results of this manuscript fill the gap in the study of intestinal bacterial diversity in SP, MA, and PZ. It also provides a reference for the study of the dominant bacteria in the intestinal microorganisms of these three equine species and the discovery of novel functional genes.
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19
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Evolution of the Family Equidae, Subfamily Equinae, in North, Central and South America, Eurasia and Africa during the Plio-Pleistocene. BIOLOGY 2022; 11:biology11091258. [PMID: 36138737 PMCID: PMC9495906 DOI: 10.3390/biology11091258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022]
Abstract
Studies of horse evolution arose during the middle of the 19th century, and several hypotheses have been proposed for their taxonomy, paleobiogeography, paleoecology and evolution. The present contribution represents a collaboration of 19 multinational experts with the goal of providing an updated summary of Pliocene and Pleistocene North, Central and South American, Eurasian and African horses. At the present time, we recognize 114 valid species across these continents, plus 4 North African species in need of further investigation. Our biochronology and biogeography sections integrate Equinae taxonomic records with their chronologic and geographic ranges recognizing regional biochronologic frameworks. The paleoecology section provides insights into paleobotany and diet utilizing both the mesowear and light microscopic methods, along with calculation of body masses. We provide a temporal sequence of maps that render paleoclimatic conditions across these continents integrated with Equinae occurrences. These records reveal a succession of extinctions of primitive lineages and the rise and diversification of more modern taxa. Two recent morphological-based cladistic analyses are presented here as competing hypotheses, with reference to molecular-based phylogenies. Our contribution represents a state-of-the art understanding of Plio-Pleistocene Equus evolution, their biochronologic and biogeographic background and paleoecological and paleoclimatic contexts.
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20
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Cappelletti E, Piras FM, Sola L, Santagostino M, Abdelgadir WA, Raimondi E, Lescai F, Nergadze SG, Giulotto E. Robertsonian fusion and centromere repositioning contributed to the formation of satellite-free centromeres during the evolution of zebras. Mol Biol Evol 2022; 39:6650076. [PMID: 35881460 PMCID: PMC9356731 DOI: 10.1093/molbev/msac162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Centromeres are epigenetically specified by the histone H3 variant CENP-A and typically associated to highly repetitive satellite DNA. We previously discovered natural satellite-free neocentromeres in Equus caballus and E. asinus. Here, through ChIP-seq with an anti-CENP-A antibody, we found an extraordinarily high number of centromeres lacking satellite DNA in the zebras E. burchelli (15 of 22) and E. grevyi (13 of 23), demonstrating that the absence of satellite DNA at the majority of centromeres is compatible with genome stability and species survival and challenging the role of satellite DNA in centromere function. Nine satellite-free centromeres are shared between the two species in agreement with their recent separation. We assembled all centromeric regions and improved the reference genome of E. burchelli. Sequence analysis of the CENP-A binding domains revealed that they are LINE-1 and AT-rich with four of them showing DNA amplification. In the two zebras, satellite-free centromeres emerged from centromere repositioning or following Robertsonian fusion. In five chromosomes, the centromeric function arose near the fusion points, which are located within regions marked by traces of ancestral pericentromeric sequences. Therefore, besides centromere repositioning, Robertsonian fusions are an important source of satellite-free centromeres during evolution. Finally, in one case, a satellite-free centromere was seeded on an inversion breakpoint. At eleven chromosomes, whose primary constrictions seemed to be associated to satellite repeats by cytogenetic analysis, satellite-free neocentromeres were instead located near the ancestral inactivated satellite-based centromeres, therefore, the centromeric function has shifted away from a satellite repeat containing locus to a satellite-free new position.
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Affiliation(s)
- Eleonora Cappelletti
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Francesca M Piras
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Lorenzo Sola
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Marco Santagostino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Wasma A Abdelgadir
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Elena Raimondi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Francesco Lescai
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Solomon G Nergadze
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
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21
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Cai D, Zhu S, Gong M, Zhang N, Wen J, Liang Q, Sun W, Shao X, Guo Y, Cai Y, Zheng Z, Zhang W, Hu S, Wang X, Tian H, Li Y, Liu W, Yang M, Yang J, Wu D, Orlando L, Jiang Y. Radiocarbon and genomic evidence for the survival of Equus Sussemionus until the late Holocene. eLife 2022; 11:73346. [PMID: 35543411 PMCID: PMC9142152 DOI: 10.7554/elife.73346] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 05/11/2022] [Indexed: 12/02/2022] Open
Abstract
The exceptionally rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses, and zebras represent three extant subgenera of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in the Pleistocene. We sequenced 26 archaeological specimens from Northern China in the Holocene that could be assigned morphologically and genetically to Equus ovodovi, a species representative of Sussemionus. We present the first high-quality complete genome of the Sussemionus lineage, which was sequenced to 13.4× depth of coverage. Radiocarbon dating demonstrates that this lineage survived until ~3500 years ago, despite continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus phylogenetic tree and found that Sussemionus diverged from the ancestor of non-caballine equids ~2.3–2.7 million years ago and possibly remained affected by secondary gene flow post-divergence. We found that the small genetic diversity, rather than enhanced inbreeding, limited the species’ chances of survival. Our work adds to the growing literature illustrating how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.
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Affiliation(s)
- Dawei Cai
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Siqi Zhu
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Mian Gong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Naifan Zhang
- Bioarchaeology Laboratory, Jilin University, Changchuin, China
| | - Jia Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qiyao Liang
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Weilu Sun
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Xinyue Shao
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yaqi Guo
- Bioarchaeology Laboratory, Jilin University, Changchun, China
| | - Yudong Cai
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhuqing Zheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wei Zhang
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Songmei Hu
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Xiaoyang Wang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - He Tian
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Youqian Li
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Wei Liu
- Heilongjiang Provincial Institute of Cultural Relics and Archaeology, Harbin, China
| | - Miaomiao Yang
- Shaanxi Provincial Institute of Archaeology, Xi'an, China
| | - Jian Yang
- Ningxia Institute of Cultural Relics and Archaeology, Yinchuan, China
| | - Duo Wu
- College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Ludovic Orlando
- 7Centre d'Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, CNRS UMR 5288, Toulouse, France
| | - Yu Jiang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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22
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Liu Y, Li H, Wang M, Zhang X, Yang L, Zhao C, Wu C. Genetic architectures and selection signatures of body height in Chinese indigenous donkeys revealed by next-generation sequencing. Anim Genet 2022; 53:487-497. [PMID: 35535569 DOI: 10.1111/age.13211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/18/2022] [Accepted: 04/13/2022] [Indexed: 01/02/2023]
Abstract
Donkeys are widely distributed labour animals in the world. During the process of the domestication and artificial selection of domestic donkeys, body sizes show significant differences among different breeds of donkeys. Based on the genome resequencing data of 103 Chinese indigenous donkeys from 11 breeds (Biyang, Dezhou, Guangling, Hetian, Jiami, Kulun, Qingyang, Turfan, Tibetan, Xinjiang, and Yunnan), seven Spanish donkeys from two breeds (Zamorano~Leonés and Andalusian), and three wild donkeys, we investigated the population structures of Chinese domestic donkeys with different body sizes. We used FST and XP-EHH analyses to explore the selected regions related to body sizes. The results showed that Chinese indigenous donkeys have a closer relationship with African wild donkeys than with Asian wild donkeys. LCORL/NCAPG, FAM184B, TBX3, and IHH were identified as genes with strong signals in analysis of selection signature (FST and XP-EHH) in large and small donkeys. The seven identified variants can be served as candidate loci affecting the body size of Chinese donkeys. Five of seven loci were located in intron 9 of FAM184B and were in a haplotype block, and one of the identified variants (Chr03:112664848) located in the CDS region of the LCORL gene was found to cause stop-loss. These candidate genes and variants shed new light on the molecular basis of donkey body size and will facilitate the breeding activities of donkeys.
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Affiliation(s)
- Yu Liu
- Equine Center, China Agricultural University, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haijing Li
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd, Liaocheng, China
| | - Min Wang
- Equine Center, China Agricultural University, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xinhao Zhang
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd, Liaocheng, China
| | - Li Yang
- National Engineering Research Center for Gelatin-based Traditional Chinese Medicine, Dong-E-E-Jiao Co. Ltd, Liaocheng, China
| | - Chunjiang Zhao
- Equine Center, China Agricultural University, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China.,National Engineering Laboratory for Animal Breeding, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing, China.,Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China
| | - Changxin Wu
- Equine Center, China Agricultural University, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
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23
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Gömer A, Puff C, Reinecke B, Bracht S, Conze M, Baumgärtner W, Steinmann J, Feige K, Cavalleri JMV, Steinmann E, Todt D. Experimental cross-species infection of donkeys with equine hepacivirus and analysis of host immune signatures. ONE HEALTH OUTLOOK 2022; 4:9. [PMID: 35527255 PMCID: PMC9082851 DOI: 10.1186/s42522-022-00065-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 04/06/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The Equine Hepacivirus (EqHV) is an equine-specific and liver-tropic virus belonging to the diverse genus of Hepaciviruses. It was recently found in a large donkey (Equus asinus) cohort with a similar seroprevalence (30%), but lower rate of RNA-positive animals (0.3%) compared to horses. These rare infection events indicate either a lack of adaptation to the new host or a predominantly acute course of infection. METHODS In order to analyze the susceptibility and the course of EqHV infection in donkeys, we inoculated two adult female donkeys and one control horse intravenously with purified EqHV from a naturally infected horse. Liver biopsies were taken before and after inoculation to study changes in the transcriptome. RESULTS Infection kinetics were similar between the equids. All animals were EqHV PCR-positive from day three. EqHV RNA-levels declined when the animals seroconverted and both donkeys cleared the virus from the blood by week 12. Infection did not have an impact on the clinical findings and no significant histopathological differences were seen. Blood biochemistry revealed a mild increase in GLDH at the time of seroconversion in horses, which was less pronounced in donkeys. Transcriptomic analysis revealed a distinct set of differentially expressed genes, including viral host factors and immune genes. CONCLUSION To summarize, our findings indicate that donkeys are a natural host of EqHV, due to the almost identical infection kinetics. The different immune responses do however suggest different mechanisms in reacting to hepaciviral infections.
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Affiliation(s)
- André Gömer
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- Institute of Virology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Christina Puff
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Birthe Reinecke
- Institute of Experimental Virology, TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany
| | - Stephanie Bracht
- Institute of Experimental Virology, TWINCORE Center for Experimental and Clinical Infection Research, Hannover, Germany
| | - Maria Conze
- Clinic for Horses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Jörg Steinmann
- Institute of Medical Microbiology, University of Hospital Essen, University of Duisburg-Essen, Essen, Germany
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, General Hospital Nürnberg, Paracelsus Medical University, Nürnberg, Germany
| | - Karsten Feige
- Clinic for Horses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Jessika M V Cavalleri
- Clinical Unit of Equine Internal Medicine, Department for Companion Animals and Horses, University of Veterinary Medicine Vienna (Vetmeduni), Vienna, Austria
| | - Eike Steinmann
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Daniel Todt
- Department of Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany.
- European Virus Bioinformatics Center (EVBC), Jena, Germany.
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24
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Molecular Dynamics and Evolution of Centromeres in the Genus Equus. Int J Mol Sci 2022; 23:ijms23084183. [PMID: 35457002 PMCID: PMC9024551 DOI: 10.3390/ijms23084183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 02/01/2023] Open
Abstract
The centromere is the chromosomal locus essential for proper chromosome segregation. While the centromeric function is well conserved and epigenetically specified, centromeric DNA sequences are typically composed of satellite DNA and represent the most rapidly evolving sequences in eukaryotic genomes. The presence of satellite sequences at centromeres hampered the comprehensive molecular analysis of these enigmatic loci. The discovery of functional centromeres completely devoid of satellite repetitions and fixed in some animal and plant species represented a turning point in centromere biology, definitively proving the epigenetic nature of the centromere. The first satellite-free centromere, fixed in a vertebrate species, was discovered in the horse. Later, an extraordinary number of satellite-free neocentromeres had been discovered in other species of the genus Equus, which remains the only mammalian genus with numerous satellite-free centromeres described thus far. These neocentromeres arose recently during evolution and are caught in a stage of incomplete maturation. Their presence made the equids a unique model for investigating, at molecular level, the minimal requirements for centromere seeding and evolution. This model system provided new insights on how centromeres are established and transmitted to the progeny and on the role of satellite DNA in different aspects of centromere biology.
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25
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Bennett EA, Weber J, Bendhafer W, Champlot S, Peters J, Schwartz GM, Grange T, Geigl EM. The genetic identity of the earliest human-made hybrid animals, the kungas of Syro-Mesopotamia. SCIENCE ADVANCES 2022; 8:eabm0218. [PMID: 35030024 PMCID: PMC8759742 DOI: 10.1126/sciadv.abm0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/22/2021] [Indexed: 06/14/2023]
Abstract
Before the introduction of domestic horses in Mesopotamia in the late third millennium BCE, contemporary cuneiform tablets and seals document intentional breeding of highly valued equids called kungas for use in diplomacy, ceremony, and warfare. Their precise zoological classification, however, has never been conclusively determined. Morphometric analysis of equids uncovered in rich Early Bronze Age burials at Umm el-Marra, Syria, placed them beyond the ranges reported for other known equid species. We sequenced the genomes of one of these ~4500-year-old equids, together with an ~11,000-year-old Syrian wild ass (hemippe) from Göbekli Tepe and two of the last surviving hemippes. We conclude that kungas were F1 hybrids between female domestic donkeys and male hemippes, thus documenting the earliest evidence of hybrid animal breeding.
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Affiliation(s)
- E. Andrew Bennett
- Institut Jacques Monod, Université de Paris, CNRS, 75013 Paris, France
| | - Jill Weber
- Near East Section, The University Museum of Archaeology and Anthropology, Philadelphia, PA 19103, USA
| | - Wejden Bendhafer
- Institut Jacques Monod, Université de Paris, CNRS, 75013 Paris, France
| | - Sophie Champlot
- Institut Jacques Monod, Université de Paris, CNRS, 75013 Paris, France
| | - Joris Peters
- ArchaeoBioCenter, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- SNSB, Bavarian State Collection of Palaeoanatomy, 80333 Munich, Germany
| | - Glenn M. Schwartz
- Department of Near Eastern Studies, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Thierry Grange
- Institut Jacques Monod, Université de Paris, CNRS, 75013 Paris, France
| | - Eva-Maria Geigl
- Institut Jacques Monod, Université de Paris, CNRS, 75013 Paris, France
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26
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Singhal S, Derryberry GE, Bravo GA, Derryberry EP, Brumfield RT, Harvey MG. The dynamics of introgression across an avian radiation. Evol Lett 2021; 5:568-581. [PMID: 34917397 PMCID: PMC8645201 DOI: 10.1002/evl3.256] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/11/2021] [Accepted: 08/31/2021] [Indexed: 01/20/2023] Open
Abstract
Hybridization and resulting introgression can play both a destructive and a creative role in the evolution of diversity. Thus, characterizing when and where introgression is most likely to occur can help us understand the causes of diversification dynamics. Here, we examine the prevalence of and variation in introgression using phylogenomic data from a large (1300+ species), geographically widespread avian group, the suboscine birds. We first examine patterns of gene tree discordance across the geographic distribution of the entire clade. We then evaluate the signal of introgression in a subset of 206 species triads using Patterson's D‐statistic and test for associations between introgression signal and evolutionary, geographic, and environmental variables. We find that gene tree discordance varies across lineages and geographic regions. The signal of introgression is highest in cases where species occur in close geographic proximity and in regions with more dynamic climates since the Pleistocene. Our results highlight the potential of phylogenomic datasets for examining broad patterns of hybridization and suggest that the degree of introgression between diverging lineages might be predictable based on the setting in which they occur.
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Affiliation(s)
- Sonal Singhal
- Department of Biology California State University, Dominguez Hills Carson California 90747
| | - Graham E Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Gustavo A Bravo
- Department of Organismic and Evolutionary Biology Harvard University Cambridge Massachusetts 02138.,Museum of Comparative Zoology Harvard University Cambridge Massachusetts 02138
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee 37996
| | - Robb T Brumfield
- Museum of Natural Science Louisiana State University Baton Rouge Louisiana 70803.,Department of Biological Sciences Louisiana State University Baton Rouge Louisiana 70803
| | - Michael G Harvey
- Department of Biological Sciences The University of Texas at El Paso El Paso Texas 79968.,Biodiversity Collections The University of Texas at El Paso El Paso Texas 79968
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27
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Larison B, Pinho GM, Haghani A, Zoller JA, Li CZ, Finno CJ, Farrell C, Kaelin CB, Barsh GS, Wooding B, Robeck TR, Maddox D, Pellegrini M, Horvath S. Epigenetic models developed for plains zebras predict age in domestic horses and endangered equids. Commun Biol 2021; 4:1412. [PMID: 34921240 PMCID: PMC8683477 DOI: 10.1038/s42003-021-02935-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/02/2021] [Indexed: 01/09/2023] Open
Abstract
Effective conservation and management of threatened wildlife populations require an accurate assessment of age structure to estimate demographic trends and population viability. Epigenetic aging models are promising developments because they estimate individual age with high accuracy, accurately predict age in related species, and do not require invasive sampling or intensive long-term studies. Using blood and biopsy samples from known age plains zebras (Equus quagga), we model epigenetic aging using two approaches: the epigenetic clock (EC) and the epigenetic pacemaker (EPM). The plains zebra EC has the potential for broad application within the genus Equus given that five of the seven extant wild species of the genus are threatened. We test the EC's ability to predict age in sister taxa, including two endangered species and the more distantly related domestic horse, demonstrating high accuracy in all cases. By comparing chronological and estimated age in plains zebras, we investigate age acceleration as a proxy of health status. An interaction between chronological age and inbreeding is associated with age acceleration estimated by the EPM, suggesting a cumulative effect of inbreeding on biological aging throughout life.
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Affiliation(s)
- Brenda Larison
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095, USA.
| | - Gabriela M Pinho
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Amin Haghani
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Joseph A Zoller
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Caesar Z Li
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Christopher B Kaelin
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Gregory S Barsh
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - Bernard Wooding
- Quagga Project, Elandsberg Farms, Hermon, 7308, South Africa
| | - Todd R Robeck
- Zoological Operations, SeaWorld Parks and Entertainment, 7007 SeaWorld Drive, Orlando, FL, USA
| | - Dewey Maddox
- White Oak Conservation, 581705 White Oak Road, Yulee, FL, 32097, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego, CA, USA.
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28
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Tombak KJ, Hansen CB, Kinsella JM, Pansu J, Pringle RM, Rubenstein DI. The gastrointestinal nematodes of plains and Grevy's zebras: Phylogenetic relationships and host specificity. Int J Parasitol Parasites Wildl 2021; 16:228-235. [PMID: 34712556 PMCID: PMC8529100 DOI: 10.1016/j.ijppaw.2021.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 01/08/2023]
Abstract
Equids are chronically infected with parasitic strongyle nematodes. There is a rich literature on horse strongyles, but they are difficult to identify morphologically and genetic studies on strongyles infecting other equid species are few, hampering studies of host specificity. We sequenced expelled worms from two sympatric zebra species in central Kenya to expand the strongyle phylogeny and used DNA metabarcoding on faecal samples to genetically characterize zebra nemabiomes for the first time. We generated sequences for several species new to public genetic reference databases, all of which are typical strongyles in wild zebras (i.e., the three species of Cylindropharynx and Cyathostomum montgomeryi), and identified their closest relatives. We also discovered an apparent fungus infecting a quarter of the expelled Crossocephalus viviparus worms, a hyperabundant nematode species in the family Atractidae, hinting at the possibility that zebra host-parasite dynamics may involve a zebra-fungus mutualism. The two zebra species had similar nemabiomes; we found a complete overlap in the list of nematode species they carry and very similar prevalence (i.e., proportion of hosts infected) for the different nematode species. Our study suggests limited host-specificity in zebra strongyles and high potential for transmission between the plains zebra and the endangered Grevy's zebra.
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Affiliation(s)
- Kaia J. Tombak
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ, USA, 08544
- Department of Anthropology, Hunter College of the City University of New York, 695 Park Ave, New York, NY, USA, 10065
- Corresponding author. Department of Anthropology, Hunter College of the City University of New York, 695 Park Ave, New York, NY, 10065, USA.
| | - Christina B. Hansen
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ, USA, 08544
| | | | - Johan Pansu
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ, USA, 08544
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Robert M. Pringle
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ, USA, 08544
| | - Daniel I. Rubenstein
- Department of Ecology and Evolutionary Biology, Princeton University, Guyot Hall, Princeton, NJ, USA, 08544
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29
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Päckert M. No hybrid snowcocks in the Altai-Hyper-variable markers can be problematic for phylogenetic inference. Ecol Evol 2021; 11:16354-16364. [PMID: 34824832 PMCID: PMC8601899 DOI: 10.1002/ece3.8199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/24/2021] [Accepted: 09/10/2021] [Indexed: 11/10/2022] Open
Abstract
A recent article in Ecology and Evolution featured the discovery of hybrid snowcocks (Tetraogallus) and speculated on the hybrid origin of an extant species (T. altaicus). Comprehensive re-analyses of original data from the latter paper reliably refute the phylogenetic hypothesis taken as firm evidence of a past hybridization event in these birds. The new re-analyses showed that there is no evidence of hybridization in these snowcocks from the data available so far.
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Affiliation(s)
- Martin Päckert
- Senckenberg Natural History Collections Museum of Zoology Dresden Germany
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30
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Myers EA, Mulcahy DG, Falk B, Johnson K, Carbi M, de Queiroz K. Interspecific Gene Flow and Mitochondrial Genome Capture During the Radiation of Jamaican Anolis Lizards (Squamata; Iguanidae). Syst Biol 2021; 71:501-511. [PMID: 34735007 DOI: 10.1093/sysbio/syab089] [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: 11/20/2020] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 11/12/2022] Open
Abstract
Gene flow and reticulation are increasingly recognized as important processes in the diversification of many taxonomic groups. With the increasing ease of collecting genomic data and the development of multispecies coalescent network approaches, such reticulations can be accounted for when inferring phylogeny and diversification. Caribbean Anolis lizards are a classic example of an adaptive radiation in which species have independently radiated on the islands of the Greater Antilles into the same ecomorph classes. Within the Jamaican radiation at least one species, A. opalinus, has been documented to be polyphyletic in its mitochondrial DNA, which could be the result of an ancient reticulation event or incomplete lineage sorting. Here we generate mtDNA and genotyping-by-sequencing (GBS) data and implement gene-tree, species-tree, and multispecies coalescent network methods to infer the diversification of this group. Our mtDNA gene-tree recovers the same relationships previously inferred for this group, which is strikingly different from the species-tree inferred from our GBS data. Posterior predictive simulations suggest that our genomic data violate commonly adopted assumptions of the multispecies coalescent model, so we use network approaches to infer phylogenetic relationships. The inferred network topology contains a reticulation event but does not explain the mtDNA polyphyly observed in this group, however coalescent simulations suggest that the observed mtDNA topology is likely the result of past introgression. How common a signature of gene flow and reticulation is across the radiation of Anolis is unknown; however, the reticulation events that we demonstrate here may have allowed for adaptive evolution, as has been suggested in other, more recent adaptive radiations.
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Affiliation(s)
- Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Daniel G Mulcahy
- Global Genome Initiative, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Bryan Falk
- Division of Invertebrate Zoology, Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA
| | - Kiyomi Johnson
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Marina Carbi
- Science Research Mentoring Program, American Museum of Natural History, Central Park West and 79th St., NY, NY 10024, USA
| | - Kevin de Queiroz
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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31
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Myers EA. Genome-wide data reveal extensive gene flow during the diversification of the western rattlesnakes (Viperidae: Crotalinae: Crotalus). Mol Phylogenet Evol 2021; 165:107313. [PMID: 34537323 DOI: 10.1016/j.ympev.2021.107313] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 08/28/2021] [Accepted: 09/14/2021] [Indexed: 11/15/2022]
Abstract
Hybridization and introgression are important, but often overlooked processes when inferring phylogenies. When these processes are not accounted for and a strictly diverging phylogenetic model is applied to groups with a history of hybridization, phylogenetic inference and parameter estimation can be inaccurate. Recent developments in phylogenetic network approaches coupled with the increasing availability of genomic data allow inferences of reticulate evolutionary histories across the tree of life. The western rattlesnake species group (C. viridis species complex, C. mitchellii species complex, C. scutulutas, and C. tigris) is an iconic snake lineage that is widespread across western North America. This group is composed of several species complexes with unclear species limits, likely the result of ongoing gene flow among nascent lineages. Here I generate reduced representation genomic data and test for a history of reticulation within this group. I demonstrate that all species have undergone hybridization with at least one other lineage, suggesting introgression is widespread in this group. Topologies differ between phylogenies estimated under the multispecies coalescent and multispecies network coalescent methods, indicating that gene flow has obscured phylogenetic relationships within this group. These past introgression events are predominantly restricted to species that co-occur geographically. However, within species that have a history of introgression, this signature is detected regardless of specimen sampling across geography. Overall, my results suggest the accumulation of reproductive isolating barriers occurs slowly in rattlesnakes which likely leads to the difficulty in delimiting species, furthermore, the results of this study have implications for trait evolution in this group.
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Affiliation(s)
- Edward A Myers
- Department of Herpetology, American Museum of Natural History, New York, NY, USA; Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.
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Li S, Zhao G, Han H, Li Y, Li J, Wang J, Cao G, Li X. Genome collinearity analysis illuminates the evolution of donkey chromosome 1 and horse chromosome 5 in perissodactyls: A comparative study. BMC Genomics 2021; 22:665. [PMID: 34521340 PMCID: PMC8442440 DOI: 10.1186/s12864-021-07984-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 09/06/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It is important to resolve the evolutionary history of species genomes as it has affected both genome organization and chromosomal architecture. The rapid innovation in sequencing technologies and the improvement in assembly algorithms have enabled the creation of highly contiguous genomes. DNA Zoo, a global organization dedicated to animal conservation, offers more than 150 chromosome-length genome assemblies. This database has great potential in the comparative genomics field. RESULTS Using the donkey (Equus asinus asinus, EAS) genome provided by DNA Zoo as an example, the scaffold N50 length and Benchmarking Universal Single-Copy Ortholog score reached 95.5 Mb and 91.6%, respectively. We identified the cytogenetic nomenclature, corrected the direction of the chromosome-length sequence of the donkey genome, analyzed the genome-wide chromosomal rearrangements between the donkey and horse, and illustrated the evolution of the donkey chromosome 1 and horse chromosome 5 in perissodactyls. CONCLUSIONS The donkey genome provided by DNA Zoo has relatively good continuity and integrity. Sequence-based comparative genomic analyses are useful for chromosome evolution research. Several previously published chromosome painting results can be used to identify the cytogenetic nomenclature and correct the direction of the chromosome-length sequence of new assemblies. Compared with the horse genome, the donkey chromosomes 1, 4, 20, and X have several obvious inversions, consistent with the results of previous studies. A 4.8 Mb inverted structure was first discovered in the donkey chromosome 25 and plains zebra chromosome 11. We speculate that the inverted structure and the tandem fusion of horse chromosome 31 and 4 are common features of non-caballine equids, which supports the correctness of the existing Equus phylogeny to an extent.
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Affiliation(s)
- Shaohua Li
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010110, China
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China
| | - Gaoping Zhao
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China
| | - Hongmei Han
- Department of Physical Education, Hohhot Minzu College, Hohhot, 010051, China
| | - Yunxia Li
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China
| | - Jun Li
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China
| | - Jinfeng Wang
- College of Basic Medicine, Inner Mongolia Medical University, Hohhot, 010110, China
| | - Guifang Cao
- College of Veterinary Science, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Xihe Li
- Research Center for Animal Genetic Resources of Mongolia Plateau, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
- Inner Mongolia Saikexing Institute of Breeding and Reproductive Biotechnology in Domestic Animal, Hohhot, 011517, China.
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33
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Wang Y, Miao X, Zhao Z, Wang Y, Li S, Wang C. Transcriptome Atlas of 16 Donkey Tissues. Front Genet 2021; 12:682734. [PMID: 34434218 PMCID: PMC8381363 DOI: 10.3389/fgene.2021.682734] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022] Open
Abstract
Donkeys (Equus asinus) are important livestock with great economic value in meat, skin, and milk production. However, a lack of knowledge of the transcriptome landscape across a wide range of donkey tissues limits genetic selective breeding and conservation. Here we used transcriptomics to describe the transcriptome landscape, classify the tissue-specific gene expression across all primary donkey tissues, and present supplementary analyses on the protein level of additional donkey milk samples. Overall, 16,013 protein-coding genes and 21,983 transcripts were mapped to the reference genome, including 6,778 ubiquitously expressed genes and 2,601 tissue-enriched genes. Functional analysis revealed that the function of the tissue-enriched genes was highly tissue specific. Tissue-elevated genes that could be associated with unique phenotypes in donkey were analyzed. The results showed that, compared with those in human and other livestock, the lysozyme gene in donkey breast was specifically and highly expressed. The calcium-binding lysozyme, encoded by the lysozyme gene, was also detected in high amounts in donkey milk. Given those intact lysozyme genes that predict potentially functional calcium-binding lysozyme found in only a few species (e.g., donkey and horse), the high expression of the lysozyme gene in donkey breast may contribute to the high lysozyme content in donkey milk. Furthermore, 71% of the proteins in donkey milk overlapped with human milk protein, higher than the overlapping rates of bovine, sheep, and swine with humans. The donkey transcriptomic resource contributes to the available genomic resources to interpret the molecular mechanisms underlying phenotype traits.
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Affiliation(s)
- Yinan Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China.,College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Xinyao Miao
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, China.,Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Zicheng Zhao
- Shenzhen Byoryn Technology Co., Ltd, Shenzhen, China
| | - Yonghui Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
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Zeng L, Liu HQ, Tu XL, Ji CM, Gou X, Esmailizadeh A, Wang S, Wang MS, Wang MC, Li XL, Charati H, Adeola AC, Moshood Adedokun RA, Oladipo O, Olaogun SC, Sanke OJ, Godwin F M, Cecily Ommeh S, Agwanda B, Kasiiti Lichoti J, Han JL, Zheng HK, Wang CF, Zhang YP, Frantz LAF, Wu DD. Genomes reveal selective sweeps in kiang and donkey for high-altitude adaptation. Zool Res 2021; 42:450-460. [PMID: 34156172 PMCID: PMC8317180 DOI: 10.24272/j.issn.2095-8137.2021.095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Over the last several hundred years, donkeys have adapted to high-altitude conditions on the Tibetan Plateau. Interestingly, the kiang, a closely related equid species, also inhabits this region. Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau. Here, we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred. We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys (including 24 from the Tibetan Plateau). Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs. In Tibetan donkeys, however, another gene, i.e., EGLN1, was likely involved in their adaptation to high altitude. In addition, admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys. Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau, as well as the existence of a closely related species already adapted to hypoxia, Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.
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Affiliation(s)
- Lin Zeng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - He-Qun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Xiao-Long Tu
- Annoroad Gene Tech. (Beijing) Co., Ltd., Beijing 100176, China
| | - Chang-Mian Ji
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China.,Biomarker Technologies Corporation, Beijing 101300, China
| | - Xiao Gou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, Yunnan 650201, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | | | - Xiao-Long Li
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hadi Charati
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Adeniyi C Adeola
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Germplasm Bank of Wild Species, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | | | - Olatunbosun Oladipo
- Federal College of Animal Health and Production Technology, Moor-Plantation, Ibadan, Nigeria
| | | | - Oscar J Sanke
- Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660221, Nigeria
| | | | - Sheila Cecily Ommeh
- Institute For Biotechnology Research Jomo Kenyatta University of Agriculture and Technology, Nairobi 62000-00200, Kenya.,Department of Zoology, National Museums of Kenya, Nairobi 40658-00100, Kenya
| | - Bernard Agwanda
- Department of Zoology, National Museums of Kenya, Nairobi 40658-00100, Kenya
| | - Jacqueline Kasiiti Lichoti
- State Department of Livestock, Ministry of Agriculture, Livestock, Fisheries and Irrigation, Nairobi, Kenya
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
| | - Hong-Kun Zheng
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Chang-Fa Wang
- Equus Laboratory, Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Ji'nan, Shandong 250131, China.,Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, Shandong 252059, China. E-mail:
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. E-mail:
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK. E-mail:
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.,Institute of Three-River-Source National Park, Chinese Academy of Sciences, Qinghai 810008, China. E-mail:
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Bamberger S, Xu J, Hausdorf B. Evaluating Species Delimitation Methods in Radiations: The Land Snail Albinaria cretensis Complex on Crete. Syst Biol 2021; 71:439-460. [PMID: 34181027 DOI: 10.1093/sysbio/syab050] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 06/11/2021] [Accepted: 06/26/2021] [Indexed: 01/25/2023] Open
Abstract
Delimiting species in radiations is notoriously difficult because of the small differences between the incipient species, the star-like tree with short branches between species, incomplete lineage sorting, and the possibility of introgression between several of the incipient species. Next generation sequencing data may help to overcome some of these problems. We evaluated methods for species delimitation based on genome-wide markers in a land snail radiation on Crete. Species delimitation in the Albinaria cretensis group was based exclusively on shell characters until now and resulted in classifications distinguishing 3-9 species. We generated sequences of 4270 loci for 140 specimens of the Albinaria cretensis group from 48 populations by double-digest restriction site-associated DNA sequencing. We evaluated three methods for species discovery. The multispecies coalescent approach implemented in the program Bayesian Phylogenetics and Phylogeography resulted in a drastic overestimating of the number of species, whereas Gaussian clustering resulted in an overlumping. Primary species hypotheses based on the maximum percentage of the genome of the individuals derived from ancestral populations as estimated with the program ADMIXTURE moderately overestimated the number of species, but this was the only approach that provided information about gene flow between groups. Two of the methods for species validation that we applied, BFD* and delimitR, resulted in an acceptance of almost all primary species hypotheses, even such based on arbitrary subdivisions of hypotheses based on ADMIXTURE. In contrast, secondary species hypotheses, resulting from an evaluation of primary species hypotheses based on ADMIXTURE with isolation by distance tests, approached the morphological classification, but also uncovered two cryptic species and indicated that some of the previously delimited units should be combined. Thus, we recommend this combination of approaches that provided more detailed insights in the distinctness of barriers between the taxa of a species complex and the spatial distribution of admixture between them than the other methods. The recognition and delimitation of undersampled species remained a major challenge.
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Affiliation(s)
- Sonja Bamberger
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Jie Xu
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
| | - Bernhard Hausdorf
- Center of Natural History, Zoological Museum, University of Hamburg, Martin-Luther-King-Platz 3, 20146 Hamburg, Germany
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36
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Cirilli O, Pandolfi L, Rook L, Bernor RL. Evolution of Old World Equus and origin of the zebra-ass clade. Sci Rep 2021; 11:10156. [PMID: 33980921 PMCID: PMC8114910 DOI: 10.1038/s41598-021-89440-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/21/2021] [Indexed: 11/16/2022] Open
Abstract
Evolution of the genus Equus has been a matter of long debate with a multitude of hypotheses. Currently, there is no consensus on either the taxonomic content nor phylogeny of Equus. Some hypotheses segregate Equus species into three genera, Plesippus, Allohippus and Equus. Also, the evolutionary role of European Pleistocene Equus stenonis in the origin of the zebra-ass clade has been debated. Studies based on skull, mandible and dental morphology suggest an evolutionary relationship between North American Pliocene E. simplicidens and European and African Pleistocene Equus. In this contribution, we assess the validity of the genera Plesippus, Allohippus and Equus by cladistic analysis combined with morphological and morphometrical comparison of cranial anatomy. Our cladistic analysis, based on cranial and postcranial elements (30 taxa, 129 characters), supports the monophyly of Equus, denies the recognition of Plesippus and Allohippus and supports the derivation of Equus grevyi and members of the zebra-ass clade from European stenonine horses. We define the following evolutionary steps directly relevant to the phylogeny of extant zebras and asses: E. simplicidens–E. stenonis–E. koobiforensis–E. grevyi -zebra-ass clade. The North American Pliocene species Equus simplicidens represents the ancestral stock of Old World Pleistocene Equus and the zebra-ass clade. Our phylogenetic results uphold the most recent genomic outputs which indicate an age of 4.0–4.5 Ma for the origin and monophyly of Equus.
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Affiliation(s)
- Omar Cirilli
- Dottorato Regionale Pegaso in Scienze della Terra, Università di Pisa, Via S. Maria 53, 56126, Pisa, Italy. .,Dipartimento di Scienze della Terra, Paleo[Fab]Lab, Università degli Studi di Firenze, Via G. La Pira 4, 50121, Firenze, Italy.
| | - Luca Pandolfi
- Dipartimento di Scienze della Terra, Paleo[Fab]Lab, Università degli Studi di Firenze, Via G. La Pira 4, 50121, Firenze, Italy.
| | - Lorenzo Rook
- Dipartimento di Scienze della Terra, Paleo[Fab]Lab, Università degli Studi di Firenze, Via G. La Pira 4, 50121, Firenze, Italy
| | - Raymond L Bernor
- Laboratory of Evolutionary Biology, Department of Anatomy, College of Medicine, 520 W St. N.W, Washington, DC, 20059, USA.,Department of Anthropology, Human Origins Program, Smithsonian Institution, Washington, DC, 20560, USA
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37
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Wang X, Bou G, Zhang X, Tao L, Shen Y, Na R, Liu G, Ren H, Ren X, Song L, Su S, Bai D, Zhao Y, Li B, Dugarjaviin M. A Fast PCR Test for the Simultaneous Identification of Species and Gender in Horses, Donkeys, Mules and Hinnies. J Equine Vet Sci 2021; 102:103458. [PMID: 34119210 DOI: 10.1016/j.jevs.2021.103458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/21/2021] [Accepted: 03/22/2021] [Indexed: 11/30/2022]
Abstract
Having considered that the current methods are costly and time-consuming, we designed an only 3 pairs primer-based PCR test to accurately identify the species and gender in horses, donkeys, mules and hinnies. Through a thorough sequence comparison between horse and donkey's highly similar genomes, and a vast amount of preliminary confirmation, we found that three fragments, CNGB3 gene on an autosome, displacement loop region on mitochondrial DNA and SRY genes on chromosome Y, within these equine DNA, are enough to enable us achieving our goal. The PCR test described here would be an economical, fast and accurate alternative for the most commonly-used methods, polymerase chain reaction-restriction fragment length polymorphism, microsatellite assay, and sequencing.
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Affiliation(s)
- Xisheng Wang
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Gerelchimeg Bou
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Xinzhuang Zhang
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Li Tao
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Yingchao Shen
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Riga Na
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Guiqin Liu
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China; College of Agronomy, Liaocheng University, Shandong Engineering Technology Research Center for Efficient Breeding and Ecological Feeding of Black Donkey, Shandong Donkey Industry Technology Collaborative Innovation Center, Liaocheng, Shandong Province, China
| | - Hong Ren
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China; Vocational and Technical College, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiujuan Ren
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Lianjie Song
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Shaofeng Su
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Dongyi Bai
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Yiping Zhao
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Bei Li
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China
| | - Manglai Dugarjaviin
- College of animal science, Inner Mongolia Key Laboratory of Equine Genetics, Breeding and Reproduction, Equine Research Center, Inner Mongolia Agricultural University, Hohhot, China.
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38
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Kong S, Kubatko LS. Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data. Syst Biol 2021; 70:891-907. [PMID: 33404632 DOI: 10.1093/sysbio/syaa092] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 11/13/2020] [Indexed: 11/13/2022] Open
Abstract
Interspecific hybridization is an important evolutionary phenomenon that generates genetic variability in a population and fosters species diversity in nature. The availability of large genome scale datasets has revolutionized hybridization studies to shift from the observation of the presence or absence of hybrids to the investigation of the genomic constitution of hybrids and their genome-specific evolutionary dynamics. Although a handful of methods have been proposed in an attempt to identify hybrids, accurate detection of hybridization from genomic data remains a challenging task. In addition to methods that infer phylogenetic networks or that utilize pairwise divergence, site pattern frequency based and population genetic clustering approaches are popularly used in practice, though the performance of these methods under different hybridization scenarios has not been extensively examined. Here, we use simulated data to comparatively evaluate the performance of four tools that are commonly used to infer hybridization events: the site pattern frequency based methods HyDe and the D-statistic (i.e., the ABBA-BABA test) and the population clustering approaches structure and ADMIXTURE. We consider single hybridization scenarios that vary in the time of hybridization and the amount of incomplete lineage sorting (ILS) for different proportions of parental contributions (γ); introgressive hybridization; multiple hybridization scenarios; and a mixture of ancestral and recent hybridization scenarios. We focus on the statistical power to detect hybridization and the false discovery rate (FDR) for comparisons of the D-statistic and HyDe, and the accuracy of the estimates of γ as measured by the mean squared error for HyDe, structure, and ADMIXTURE. Both HyDe and the D-statistic are powerful for detecting hybridization in all scenarios except those with high ILS, although the D-statistic often has an unacceptably high FDR. The estimates of γ in HyDe are impressively robust and accurate whereas structure and ADMIXTURE sometimes fail to identify hybrids, particularly when the proportional parental contributions are asymmetric (i.e., when γ is close to 0). Moreover, the posterior distribution estimated using structure exhibits multimodality in many scenarios, making interpretation difficult. Our results provide guidance in selecting appropriate methods for identifying hybrid populations from genomic data.
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Affiliation(s)
- Sungsik Kong
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - Laura S Kubatko
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.,Department of Statistics, The Ohio State University, Columbus, OH, USA
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Librado P, Khan N, Fages A, Kusliy MA, Suchan T, Tonasso-Calvière L, Schiavinato S, Alioglu D, Fromentier A, Perdereau A, Aury JM, Gaunitz C, Chauvey L, Seguin-Orlando A, Der Sarkissian C, Southon J, Shapiro B, Tishkin AA, Kovalev AA, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Seregély T, Klassen L, Iversen R, Bignon-Lau O, Bodu P, Olive M, Castel JC, Boudadi-Maligne M, Alvarez N, Germonpré M, Moskal-del Hoyo M, Wilczyński J, Pospuła S, Lasota-Kuś A, Tunia K, Nowak M, Rannamäe E, Saarma U, Boeskorov G, Lōugas L, Kyselý R, Peške L, Bălășescu A, Dumitrașcu V, Dobrescu R, Gerber D, Kiss V, Szécsényi-Nagy A, Mende BG, Gallina Z, Somogyi K, Kulcsár G, Gál E, Bendrey R, Allentoft ME, Sirbu G, Dergachev V, Shephard H, Tomadini N, Grouard S, Kasparov A, Basilyan AE, Anisimov MA, Nikolskiy PA, Pavlova EY, Pitulko V, Brem G, Wallner B, Schwall C, Keller M, Kitagawa K, Bessudnov AN, Bessudnov A, Taylor W, Magail J, Gantulga JO, Bayarsaikhan J, Erdenebaatar D, Tabaldiev K, Mijiddorj E, Boldgiv B, Tsagaan T, Pruvost M, Olsen S, Makarewicz CA, Valenzuela Lamas S, Albizuri Canadell S, Nieto Espinet A, Iborra MP, Lira Garrido J, Rodríguez González E, Celestino S, Olària C, Arsuaga JL, Kotova N, Pryor A, Crabtree P, Zhumatayev R, Toleubaev A, Morgunova NL, Kuznetsova T, Lordkipanize D, Marzullo M, Prato O, Bagnasco Gianni G, Tecchiati U, Clavel B, Lepetz S, Davoudi H, Mashkour M, Berezina NY, Stockhammer PW, Krause J, Haak W, Morales-Muñiz A, Benecke N, Hofreiter M, Ludwig A, Graphodatsky AS, Peters J, Kiryushin KY, Iderkhangai TO, Bokovenko NA, Vasiliev SK, Seregin NN, Chugunov KV, Plasteeva NA, Baryshnikov GF, Petrova E, Sablin M, Ananyevskaya E, Logvin A, Shevnina I, Logvin V, Kalieva S, Loman V, Kukushkin I, Merz I, Merz V, Sakenov S, Varfolomeyev V, Usmanova E, Zaibert V, Arbuckle B, Belinskiy AB, Kalmykov A, Reinhold S, Hansen S, Yudin AI, Vybornov AA, Epimakhov A, Berezina NS, Roslyakova N, Kosintsev PA, Kuznetsov PF, Anthony D, Kroonen GJ, Kristiansen K, Wincker P, Outram A, Orlando L. The origins and spread of domestic horses from the Western Eurasian steppes. Nature 2021; 598:634-640. [PMID: 34671162 PMCID: PMC8550961 DOI: 10.1038/s41586-021-04018-9] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/10/2021] [Indexed: 01/13/2023]
Abstract
Domestication of horses fundamentally transformed long-range mobility and warfare1. However, modern domesticated breeds do not descend from the earliest domestic horse lineage associated with archaeological evidence of bridling, milking and corralling2-4 at Botai, Central Asia around 3500 BC3. Other longstanding candidate regions for horse domestication, such as Iberia5 and Anatolia6, have also recently been challenged. Thus, the genetic, geographic and temporal origins of modern domestic horses have remained unknown. Here we pinpoint the Western Eurasian steppes, especially the lower Volga-Don region, as the homeland of modern domestic horses. Furthermore, we map the population changes accompanying domestication from 273 ancient horse genomes. This reveals that modern domestic horses ultimately replaced almost all other local populations as they expanded rapidly across Eurasia from about 2000 BC, synchronously with equestrian material culture, including Sintashta spoke-wheeled chariots. We find that equestrianism involved strong selection for critical locomotor and behavioural adaptations at the GSDMC and ZFPM1 genes. Our results reject the commonly held association7 between horseback riding and the massive expansion of Yamnaya steppe pastoralists into Europe around 3000 BC8,9 driving the spread of Indo-European languages10. This contrasts with the scenario in Asia where Indo-Iranian languages, chariots and horses spread together, following the early second millennium BC Sintashta culture11,12.
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Affiliation(s)
- Pablo Librado
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Naveed Khan
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France ,grid.440522.50000 0004 0478 6450Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Antoine Fages
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Mariya A. Kusliy
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France ,grid.415877.80000 0001 2254 1834Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Tomasz Suchan
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France ,grid.413454.30000 0001 1958 0162W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Laure Tonasso-Calvière
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Stéphanie Schiavinato
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Duha Alioglu
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Aurore Fromentier
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Aude Perdereau
- grid.460789.40000 0004 4910 6535Genoscope, Institut de biologie François-Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay, Evry, France
| | - Charleen Gaunitz
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Lorelei Chauvey
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Clio Der Sarkissian
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - John Southon
- grid.266093.80000 0001 0668 7243Earth System Science Department, University of California, Irvine, Irvine, CA USA
| | - Beth Shapiro
- grid.205975.c0000 0001 0740 6917Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA USA ,grid.205975.c0000 0001 0740 6917Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA USA
| | - Alexey A. Tishkin
- grid.77225.350000000112611077Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Alexey A. Kovalev
- grid.465449.e0000 0001 1214 1108Department of Archaeological Heritage Preservation, Institute of Archaeology of the Russian Academy of Sciences, Moscow, Russia
| | - Saleh Alquraishi
- grid.56302.320000 0004 1773 5396Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed H. Alfarhan
- grid.56302.320000 0004 1773 5396Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Khaled A. S. Al-Rasheid
- grid.56302.320000 0004 1773 5396Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Timo Seregély
- grid.7359.80000 0001 2325 4853Institute for Archaeology, Heritage Conservation Studies and Art History, University of Bamberg, Bamberg, Germany
| | | | - Rune Iversen
- grid.5254.60000 0001 0674 042XSaxo Institute, section of Archaeology, University of Copenhagen, Copenhagen, Denmark
| | - Olivier Bignon-Lau
- grid.4444.00000 0001 2112 9282ArScAn-UMR 7041, Equipe Ethnologie préhistorique, CNRS, MSH-Mondes, Nanterre Cedex, France
| | - Pierre Bodu
- grid.4444.00000 0001 2112 9282ArScAn-UMR 7041, Equipe Ethnologie préhistorique, CNRS, MSH-Mondes, Nanterre Cedex, France
| | - Monique Olive
- grid.4444.00000 0001 2112 9282ArScAn-UMR 7041, Equipe Ethnologie préhistorique, CNRS, MSH-Mondes, Nanterre Cedex, France
| | | | - Myriam Boudadi-Maligne
- grid.412041.20000 0001 2106 639XUMR 5199 De la Préhistoire à l’Actuel : Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cedex, France
| | - Nadir Alvarez
- grid.466902.f0000 0001 2248 6951Geneva Natural History Museum, Geneva, Switzerland ,grid.8591.50000 0001 2322 4988Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Mietje Germonpré
- grid.20478.390000 0001 2171 9581OD Earth & History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Magdalena Moskal-del Hoyo
- grid.413454.30000 0001 1958 0162W. Szafer Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Jarosław Wilczyński
- grid.413454.30000 0001 1958 0162Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Sylwia Pospuła
- grid.413454.30000 0001 1958 0162Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Kraków, Poland
| | - Anna Lasota-Kuś
- grid.413454.30000 0001 1958 0162Institute of Archaeology and Ethnology Polish Academy of Sciences, Kraków, Poland
| | - Krzysztof Tunia
- grid.413454.30000 0001 1958 0162Institute of Archaeology and Ethnology Polish Academy of Sciences, Kraków, Poland
| | - Marek Nowak
- grid.5522.00000 0001 2162 9631Institute of Archaeology, Jagiellonian University, Kraków, Poland
| | - Eve Rannamäe
- Department of Archaeology, Institute of History and Archaeology, Tartu, Estonia
| | - Urmas Saarma
- grid.10939.320000 0001 0943 7661Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
| | - Gennady Boeskorov
- Diamond and Precious Metals Geology Institute, SB RAS, Yakutsk, Russia
| | - Lembi Lōugas
- grid.8207.d0000 0000 9774 6466Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | - René Kyselý
- grid.447879.10000 0001 0792 540XDepartment of Natural Sciences and Archaeometry, Institute of Archaeology of the Czech Academy of Sciences, Prague, Czechia
| | | | - Adrian Bălășescu
- grid.418333.e0000 0004 1937 1389Vasile Pârvan Institute of Archaeology, Department of Bioarchaeology, Romanian Academy, Bucharest, Romania
| | - Valentin Dumitrașcu
- grid.418333.e0000 0004 1937 1389Vasile Pârvan Institute of Archaeology, Department of Bioarchaeology, Romanian Academy, Bucharest, Romania
| | - Roxana Dobrescu
- grid.418333.e0000 0004 1937 1389Vasile Pârvan Institute of Archaeology, Department of Bioarchaeology, Romanian Academy, Bucharest, Romania
| | - Daniel Gerber
- grid.481823.4Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary ,grid.5591.80000 0001 2294 6276Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Viktória Kiss
- grid.481830.60000 0001 2238 5843Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Anna Szécsényi-Nagy
- grid.481823.4Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Balázs G. Mende
- grid.481823.4Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | | | | | - Gabriella Kulcsár
- grid.481830.60000 0001 2238 5843Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Erika Gál
- grid.481830.60000 0001 2238 5843Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest, Hungary
| | - Robin Bendrey
- grid.4305.20000 0004 1936 7988School of History, Classics and Archaeology, University of Edinburgh, Old Medical School, Edinburgh, UK
| | - Morten E. Allentoft
- grid.1032.00000 0004 0375 4078Trace and Environmental DNA (TrEnD) Lab, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia Australia ,grid.5254.60000 0001 0674 042XLundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ghenadie Sirbu
- grid.435140.7Department of Academic Management, Academy of Science of Moldova, Chișinău, Republic of Moldova
| | - Valentin Dergachev
- grid.435140.7Center of Archaeology, Institute of Cultural Heritage, Academy of Science of Moldova, Chișinău, Republic of Moldova
| | - Henry Shephard
- grid.446391.d0000 0001 2190 3450Archaeological Institute of America, Boston, MA USA
| | - Noémie Tomadini
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sandrine Grouard
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Aleksei Kasparov
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | | | - Mikhail A. Anisimov
- grid.424187.c0000 0001 1942 9788Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Pavel A. Nikolskiy
- grid.465388.4Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Elena Y. Pavlova
- grid.424187.c0000 0001 1942 9788Arctic and Antarctic Research Institute, St Petersburg, Russia
| | - Vladimir Pitulko
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | - Gottfried Brem
- grid.6583.80000 0000 9686 6466Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Barbara Wallner
- grid.6583.80000 0000 9686 6466Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Christoph Schwall
- grid.466489.10000 0001 2151 4674Department of Prehistory and Western Asian/Northeast African Archaeology, Austrian Archaeological Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Marcel Keller
- grid.10939.320000 0001 0943 7661Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia ,grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Keiko Kitagawa
- grid.10392.390000 0001 2190 1447SFB 1070 Resource Cultures, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Department of Early Prehistory and Quaternary Ecology, University of Tübingen, Tübingen, Germany ,grid.4444.00000 0001 2112 9282UMR 7194 Muséum National d’Histoire Naturelle, CNRS, UPVD, Paris, France
| | - Alexander N. Bessudnov
- grid.459698.f0000 0000 8989 8101Semenov-Tyan-Shanskii Lipetsk State Pedagogical University, Lipetsk, Russia
| | - Alexander Bessudnov
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | - William Taylor
- grid.266190.a0000000096214564Museum of Natural History, University of Colorado-Boulder, Boulder, CO USA
| | - Jérome Magail
- Musée d’Anthropologie préhistorique de Monaco, Monaco, Monaco
| | - Jamiyan-Ombo Gantulga
- grid.425564.40000 0004 0587 3863Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Jamsranjav Bayarsaikhan
- grid.469873.70000 0004 4914 1197Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany ,Chinggis Khaan Museum, Ulaanbaatar, Mongolia
| | | | - Kubatbeek Tabaldiev
- grid.444269.90000 0004 0387 4627Department of History, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Enkhbayar Mijiddorj
- Department of Archaeology, Ulaanbaatar State University, Ulaanbaatar, Mongolia
| | - Bazartseren Boldgiv
- grid.260731.10000 0001 2324 0259Department of Biology, National University of Mongolia, Ulaanbaatar, Mongolia
| | - Turbat Tsagaan
- grid.425564.40000 0004 0587 3863Institute of Archaeology, Mongolian Academy of Sciences, Ulaanbaatar, Mongolia
| | - Mélanie Pruvost
- grid.412041.20000 0001 2106 639XUMR 5199 De la Préhistoire à l’Actuel : Culture, Environnement et Anthropologie (PACEA), CNRS, Université de Bordeaux, Pessac Cedex, France
| | - Sandra Olsen
- grid.266515.30000 0001 2106 0692Division of Archaeology, Biodiversity Institute, University of Kansas, Lawrence, KS USA
| | - Cheryl A. Makarewicz
- grid.9764.c0000 0001 2153 9986Institute for Prehistoric and Protohistoric Archaeology, Kiel University, Kiel, Germany ,grid.9764.c0000 0001 2153 9986ROOTS Excellence Cluster, Kiel University, Kiel, Germany
| | - Silvia Valenzuela Lamas
- grid.4711.30000 0001 2183 4846Archaeology of Social Dynamics, Institució Milà i Fontanals d’Humanitats, Consejo Superior de Investigaciones Científicas (IMF-CSIC), Barcelona, Spain
| | - Silvia Albizuri Canadell
- grid.5841.80000 0004 1937 0247Departament d’Història i Arqueologia–SERP, Universitat de Barcelona, Barcelona, Spain
| | - Ariadna Nieto Espinet
- grid.15043.330000 0001 2163 1432Grup d’Investigació Prehistòrica, Universitat de Lleida, PID2019-110022GB-I00, Lleida, Spain
| | | | - Jaime Lira Garrido
- grid.8393.10000000119412521Departamento de Medicina Animal, Facultad de Veterinaria, Universidad de Extremadura, Cáceres, Spain ,Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain
| | | | - Sebastián Celestino
- grid.454770.50000 0001 1945 3489Instituto de Arqueología (CSIC–Junta de Extremadura), Mérida, Spain
| | - Carmen Olària
- grid.9612.c0000 0001 1957 9153Laboratori d’Arqueologia Prehistòrica, Universitat Jaume I, Castelló de la Plana, Spain
| | - Juan Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain ,grid.4795.f0000 0001 2157 7667Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Nadiia Kotova
- grid.418751.e0000 0004 0385 8977Department of Eneolithic and Bronze Age, Institute of Archaeology National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alexander Pryor
- grid.8391.30000 0004 1936 8024Department of Archaeology, University of Exeter, Exeter, UK
| | - Pam Crabtree
- grid.137628.90000 0004 1936 8753Center for the Study of Human Origins, Anthropology Department, New York University, New York, NY USA
| | - Rinat Zhumatayev
- grid.77184.3d0000 0000 8887 5266Department of Archaeology, Ethnology and Museology, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Abdesh Toleubaev
- grid.77184.3d0000 0000 8887 5266Department of Archaeology, Ethnology and Museology, Al Farabi Kazakh National University, Almaty, Kazakhstan
| | - Nina L. Morgunova
- grid.445474.20000 0001 1092 7131Scientific Research Department, Orenburg State Pedagogical University, Orenburg, Russia
| | - Tatiana Kuznetsova
- grid.14476.300000 0001 2342 9668Department of paleontology, Faculty of Geology, Moscow State University, Moscow, Russia ,grid.77268.3c0000 0004 0543 9688Institute of Geology and Petroleum Technologies, Kazan Federal University, Kazan, Russia
| | - David Lordkipanize
- grid.452450.20000 0001 0739 408XGeorgian National Museum, Tbilisi, Georgia ,grid.26193.3f0000 0001 2034 6082Tbilisi State University, Tbilisi, Georgia
| | - Matilde Marzullo
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Ornella Prato
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Giovanna Bagnasco Gianni
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Umberto Tecchiati
- grid.4708.b0000 0004 1757 2822Università degli Studi di Milano, Dipartimento di Beni Culturali e Ambientali, Milan, Italy
| | - Benoit Clavel
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Sébastien Lepetz
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France
| | - Hossein Davoudi
- grid.46072.370000 0004 0612 7950University of Tehran, Central Laboratory, Bioarchaeology Laboratory, Archaeozoology Section, Tehran, Iran
| | - Marjan Mashkour
- Centre National de Recherche Scientifique, Muséum national d’Histoire naturelle, Archéozoologie, Archéobotanique (AASPE), CP 56, Paris, France ,grid.46072.370000 0004 0612 7950University of Tehran, Central Laboratory, Bioarchaeology Laboratory, Archaeozoology Section, Tehran, Iran
| | - Natalia Ya. Berezina
- grid.14476.300000 0001 2342 9668Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | - Philipp W. Stockhammer
- grid.419518.00000 0001 2159 1813Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.5252.00000 0004 1936 973XInstitute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich, Munich, Germany
| | - Johannes Krause
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Wolfgang Haak
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany ,grid.1010.00000 0004 1936 7304School of Biological Sciences, The University of Adelaide, Adelaide, South Australia Australia
| | - Arturo Morales-Muñiz
- grid.5515.40000000119578126Department of Biology, Universidad Autónoma de Madrid, Madrid, Spain
| | - Norbert Benecke
- grid.424195.f0000 0001 2106 6832Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Michael Hofreiter
- grid.11348.3f0000 0001 0942 1117Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Mathematics and Science, University of Potsdam, Potsdam, Germany
| | - Arne Ludwig
- grid.418779.40000 0001 0708 0355Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Albrecht Daniel Thaer-Institute, Faculty of Life Sciences, Humboldt University Berlin, Berlin, Germany
| | - Alexander S. Graphodatsky
- grid.415877.80000 0001 2254 1834Department of the Diversity and Evolution of Genomes, Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Joris Peters
- grid.5252.00000 0004 1936 973XArchaeoBioCenter and Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, Munich, Germany ,grid.452781.d0000 0001 2203 6205SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Kirill Yu. Kiryushin
- grid.77225.350000000112611077Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | | | - Nikolay A. Bokovenko
- grid.473277.20000 0001 2291 1890Institute for the History of Material Culture, Russian Academy of Sciences (IHMC RAS), St Petersburg, Russia
| | - Sergey K. Vasiliev
- grid.415877.80000 0001 2254 1834ArchaeoZOOlogy in Siberia and Central Asia—ZooSCAn International Research Laboratory, Institute of Archeology and Ethnography of the Siberian Branch of the RAS, Novosibirsk, Russia
| | - Nikolai N. Seregin
- grid.77225.350000000112611077Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Konstantin V. Chugunov
- grid.426493.e0000 0004 1800 742XDepartment of Eastern European and Siberian Archaeology, State Hermitage Museum, St Petersburg, Russia
| | - Natalya A. Plasteeva
- grid.482778.60000 0001 2197 0186Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Gennady F. Baryshnikov
- grid.439287.30000 0001 2314 7601Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Ekaterina Petrova
- grid.6441.70000 0001 2243 2806Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania
| | - Mikhail Sablin
- grid.439287.30000 0001 2314 7601Zoological Institute, Russian Academy of Sciences, St Petersburg, Russia
| | - Elina Ananyevskaya
- grid.6441.70000 0001 2243 2806Department of Archaeology, History Faculty, Vilnius University, Vilnius, Lithuania
| | - Andrey Logvin
- grid.443586.8Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Irina Shevnina
- grid.443586.8Laboratory for Archaeological Research, Faculty of History and Law, Kostanay State University, Kostanay, Kazakhstan
| | - Victor Logvin
- Department of History and Archaeology, Surgut Governmental University, Surgut, Russia
| | - Saule Kalieva
- Department of History and Archaeology, Surgut Governmental University, Surgut, Russia
| | - Valeriy Loman
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Igor Kukushkin
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Ilya Merz
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
| | - Victor Merz
- Toraighyrov University, Joint Research Center for Archeological Studies, Pavlodar, Kazakhstan
| | - Sergazy Sakenov
- grid.55380.3b0000 0004 0398 5415Faculty of History, L. N. Gumilev Eurasian National University, Nur-Sultan, Kazakhstan
| | - Victor Varfolomeyev
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Emma Usmanova
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
| | - Viktor Zaibert
- grid.77184.3d0000 0000 8887 5266Institute of Archaeology and Steppe Civilizations, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Benjamin Arbuckle
- grid.10698.360000000122483208Department of Anthropology, Alumni Building, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | | | | | - Sabine Reinhold
- grid.424195.f0000 0001 2106 6832Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- grid.424195.f0000 0001 2106 6832Eurasia Department of the German Archaeological Institute, Berlin, Germany
| | - Aleksandr I. Yudin
- Research Center for the Preservation of Cultural Heritage, Saratov, Russia
| | - Alekandr A. Vybornov
- grid.445790.b0000 0001 2218 2982Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Andrey Epimakhov
- grid.440724.10000 0000 9958 5862Russian and Foreign History Department, South Ural State University, Chelyabinsk, Russia ,grid.465317.20000 0001 2224 8785South Ural Department, Institute of History and Archaeology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia
| | - Natalia S. Berezina
- Archaeological School, Chuvash State Institute of Humanities, Cheboksary, Russia
| | - Natalia Roslyakova
- grid.445790.b0000 0001 2218 2982Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - Pavel A. Kosintsev
- grid.482778.60000 0001 2197 0186Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russia ,grid.412761.70000 0004 0645 736XDepartment of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russia
| | - Pavel F. Kuznetsov
- grid.445790.b0000 0001 2218 2982Department of Russian History and Archaeology, Samara State University of Social Sciences and Education, Samara, Russia
| | - David Anthony
- grid.38142.3c000000041936754XDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA USA ,grid.418410.80000 0001 0115 6427Anthropology Faculty, Hartwick College, Oneonta NY, USA
| | - Guus J. Kroonen
- grid.5254.60000 0001 0674 042XDepartment of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen, Denmark ,grid.5132.50000 0001 2312 1970Leiden University Center for Linguistics, Leiden University, Leiden, The Netherlands
| | - Kristian Kristiansen
- grid.8761.80000 0000 9919 9582Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden ,grid.452548.a0000 0000 9817 5300Present Address: Lundbeck Foundation GeoGenetics Centre, Copenhagen, Denmark
| | - Patrick Wincker
- grid.8390.20000 0001 2180 5818Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d’Evry, Université Paris-Saclay, Evry, France
| | - Alan Outram
- grid.8391.30000 0004 1936 8024Department of Archaeology, University of Exeter, Exeter, UK
| | - Ludovic Orlando
- grid.15781.3a0000 0001 0723 035XCentre d’Anthropobiologie et de Génomique de Toulouse, Université Paul Sabatier, Toulouse, France
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Garcia-Erill G, Kjaer MM, Albrechtsen A, Siegismund HR, Heller R. Vicariance followed by secondary gene flow in a young gazelle species complex. Mol Ecol 2020; 30:528-544. [PMID: 33226701 PMCID: PMC7898927 DOI: 10.1111/mec.15738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 01/03/2023]
Abstract
Grant's gazelles have recently been proposed to be a species complex comprising three highly divergent mtDNA lineages (Nanger granti, N. notata and N. petersii). The three lineages have nonoverlapping distributions in East Africa, but without any obvious geographical divisions, making them an interesting model for studying the early‐stage evolutionary dynamics of allopatric speciation in detail. Here, we use genomic data obtained by restriction site‐associated (RAD) sequencing of 106 gazelle individuals to shed light on the evolutionary processes underlying Grant's gazelle divergence, to characterize their genetic structure and to assess the presence of gene flow between the main lineages in the species complex. We date the species divergence to 134,000 years ago, which is recent in evolutionary terms. We find population subdivision within N. granti, which coincides with the previously suggested two subspecies, N. g. granti and N. g. robertsii. Moreover, these two lineages seem to have hybridized in Masai Mara. Perhaps more surprisingly given their extreme genetic differentiation, N. granti and N. petersii also show signs of prolonged admixture in Mkomazi, which we identified as a hybrid population most likely founded by allopatric lineages coming into secondary contact. Despite the admixed composition of this population, elevated X chromosomal differentiation suggests that selection may be shaping the outcome of hybridization in this population. Our results therefore provide detailed insights into the processes of allopatric speciation and secondary contact in a recently radiated species complex.
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Affiliation(s)
- Genís Garcia-Erill
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Michael Munkholm Kjaer
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark.,Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anders Albrechtsen
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Hans Redlef Siegismund
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Rasmus Heller
- Department of Biology, Section for Computational and RNA Biology, University of Copenhagen, Copenhagen N, Denmark
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41
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Donkey genomes provide new insights into domestication and selection for coat color. Nat Commun 2020; 11:6014. [PMID: 33293529 PMCID: PMC7723042 DOI: 10.1038/s41467-020-19813-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 10/29/2020] [Indexed: 11/08/2022] Open
Abstract
Current knowledge about the evolutionary history of donkeys is still incomplete due to the lack of archeological and whole-genome diversity data. To fill this gap, we have de novo assembled a chromosome-level reference genome of one male Dezhou donkey and analyzed the genomes of 126 domestic donkeys and seven wild asses. Population genomics analyses indicate that donkeys were domesticated in Africa and conclusively show reduced levels of Y chromosome variability and discordant paternal and maternal histories, possibly reflecting the consequences of reproductive management. We also investigate the genetic basis of coat color. While wild asses show diluted gray pigmentation (Dun phenotype), domestic donkeys display non-diluted black or chestnut coat colors (non-Dun) that were probably established during domestication. Here, we show that the non-Dun phenotype is caused by a 1 bp deletion downstream of the TBX3 gene, which decreases the expression of this gene and its inhibitory effect on pigment deposition. A new donkey reference genome and comparisons with wild asses yields insights into the evolutionary history of donkey domestication and identifies a genetic variant that results in the non-Dun coat colours of domestic donkeys.
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42
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Blair C, Ané C. Phylogenetic Trees and Networks Can Serve as Powerful and Complementary Approaches for Analysis of Genomic Data. Syst Biol 2020; 69:593-601. [PMID: 31432090 DOI: 10.1093/sysbio/syz056] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 08/15/2019] [Indexed: 11/14/2022] Open
Abstract
Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). However, the MSC assumes no gene flow post divergence, calling for additional methods that can accommodate this limitation. Explicit phylogenetic network methods have emerged, which can simultaneously account for ILS and gene flow by representing evolutionary history as a directed acyclic graph. In this point of view, we highlight some of the strengths and limitations of phylogenetic networks and argue that tree-based inference should not be blindly abandoned in favor of networks simply because they represent more parameter rich models. Attention should be given to model selection of reticulation complexity, and the most robust conclusions regarding evolutionary history are likely obtained when combining tree- and network-based inference.
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Affiliation(s)
- Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA
- Biology PhD Program, CUNY Graduate Center, 365 5th Ave., New York, NY 10016, USA
| | - Cécile Ané
- Department of Botany, University of Wisconsin - Madison, 1300 University Ave, Madison, WI 53706, USA
- Department of Statistics, University of Wisconsin - Madison, 1300 University Ave, Madison, WI 53706, USA
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Câmara RJF, Bueno BL, Resende CF, Balasuriya UBR, Sakamoto SM, dos Reis JKP. Viral Diseases that Affect Donkeys and Mules. Animals (Basel) 2020; 10:ani10122203. [PMID: 33255568 PMCID: PMC7760297 DOI: 10.3390/ani10122203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Donkeys have been neglected and threatened by abandonment, indiscriminate slaughter, and a lack of proper sanitary management. They are often treated as “small horses.” However, donkeys and horses have significant genetic, physiological, and behavioral differences. Specific knowledge about viral infectious diseases that affect donkeys and mules is important to mitigate disease outbreaks. Thus, the purpose of this review is to provide a brief update on viral diseases of donkeys and mules and ways to prevent their spread. Abstract Donkeys (Equus asinus) and mules represent approximately 50% of the entire domestic equine herd in the world and play an essential role in the lives of thousands of people, primarily in developing countries. Despite their importance, donkeys are currently a neglected and threatened species due to abandonment, indiscriminate slaughter, and a lack of proper sanitary management. Specific knowledge about infectious viral diseases that affect this group of Equidae is still limited. In many cases, donkeys and mules are treated like horses, with the physiological differences between these species usually not taken into account. Most infectious diseases that affect the Equidae family are exclusive to the family, and they have a tremendous economic impact on the equine industry. However, some viruses may cross the species barrier and affect humans, representing an imminent risk to public health. Nevertheless, even with such importance, most studies are conducted on horses (Equus caballus), and there is little comparative information on infection in donkeys and mules. Therefore, the objective of this article is to provide a brief update on viruses that affect donkeys and mules, thereby compromising their performance and well-being. These diseases may put them at risk of extinction in some parts of the world due to neglect and the precarious conditions they live in and may ultimately endanger other species’ health and humans.
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Affiliation(s)
- Rebeca Jéssica Falcão Câmara
- Laboratório de Retroviroses, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (R.J.F.C.); (B.L.B.); (C.F.R.)
| | - Bruna Lopes Bueno
- Laboratório de Retroviroses, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (R.J.F.C.); (B.L.B.); (C.F.R.)
| | - Cláudia Fideles Resende
- Laboratório de Retroviroses, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (R.J.F.C.); (B.L.B.); (C.F.R.)
| | - Udeni B. R. Balasuriya
- Louisiana Animal Disease Diagnostic Laboratory and Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, River Rd, Room 1043, Baton Rouge, LA 70803, USA;
| | - Sidnei Miyoshi Sakamoto
- Laboratório Multidisciplinar do Centro de Ciências Biológicas e da Saúde, Departamento de Ciências da Saúde (DCS), Universidade Federal Rural do Semi-Árido, Rio Grande do Norte 59625-900, Brazil;
| | - Jenner Karlisson Pimenta dos Reis
- Laboratório de Retroviroses, Departamento de Medicina Veterinária Preventiva, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (R.J.F.C.); (B.L.B.); (C.F.R.)
- Correspondence: ; Tel.: +55-31-3409-2100
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44
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Orlando L. The Evolutionary and Historical Foundation of the Modern Horse: Lessons from Ancient Genomics. Annu Rev Genet 2020; 54:563-581. [PMID: 32960653 DOI: 10.1146/annurev-genet-021920-011805] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The domestication of the horse some 5,500 years ago followed those of dogs, sheep, goats, cattle, and pigs by ∼2,500-10,000 years. By providing fast transportation and transforming warfare, the horse had an impact on human history with no equivalent in the animal kingdom. Even though the equine sport industry has considerable economic value today, the evolutionary history underlying the emergence of the modern domestic horse remains contentious. In the last decade, novel sequencing technologies have revolutionized our capacity to sequence the complete genome of organisms, including from archaeological remains. Applied to horses, these technologies have provided unprecedented levels of information and have considerably changed models of horse domestication. This review illustrates how ancient DNA, especially ancient genomes, has inspired researchers to rethink the process by which horses were first domesticated and then diversified into a variety of breeds showing a range of traits that are useful to humans.
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Affiliation(s)
- Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse, Faculté de Médecine Purpan, Université Toulouse III-Paul Sabatier, 31000 Toulouse, France;
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Abstract
The equid family contains only one single extant genus, Equus, including seven living species grouped into horses on the one hand and zebras and asses on the other. In contrast, the equine fossil record shows that an extraordinarily richer diversity existed in the past and provides multiple examples of a highly dynamic evolution punctuated by several waves of explosive radiations and extinctions, cross-continental migrations, and local adaptations. In recent years, genomic technologies have provided new analytical solutions that have enhanced our understanding of equine evolution, including the species radiation within Equus; the extinction dynamics of several lineages; and the domestication history of two individual species, the horse and the donkey. Here, we provide an overview of these recent developments and suggest areas for further research.
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Affiliation(s)
- Pablo Librado
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France;
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46
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Phylogenetic Relationships of Turkish Indigenous Donkey Populations Determined by Mitochondrial DNA D-loop Region. Animals (Basel) 2020; 10:ani10111970. [PMID: 33120938 PMCID: PMC7692571 DOI: 10.3390/ani10111970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/18/2020] [Accepted: 10/22/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary This paper represents the first fundamental report of mtDNA diversity in Turkish indigenous donkey breeds and presents findings for the origin and genetic characterization of donkey populations dispersed in seven geographical regions in Turkey, and thus reveals insights into their genetic history. The median-joining network and phylogenetic tree exhibit two different maternal lineages of the 16 Turkish indigenous donkey populations. Abstract In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD) and nucleotide diversity (πD), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions.
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47
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Klumplerova M, Splichalova P, Oppelt J, Futas J, Kohutova A, Musilova P, Kubickova S, Vodicka R, Orlando L, Horin P. Genetic diversity, evolution and selection in the major histocompatibility complex DRB and DQB loci in the family Equidae. BMC Genomics 2020; 21:677. [PMID: 32998693 PMCID: PMC7525986 DOI: 10.1186/s12864-020-07089-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 09/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background The mammalian Major Histocompatibility Complex (MHC) is a genetic region containing highly polymorphic genes with immunological functions. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. The MHC class II sub-region contains genes expressed in antigen presenting cells. The antigen binding site is encoded by the second exon of genes encoding antigen presenting molecules. The exon 2 sequences of these MHC genes have evolved under the selective pressure of pathogens. Interspecific differences can be observed in the class II sub-region. The family Equidae includes a variety of domesticated, and free-ranging species inhabiting a range of habitats exposed to different pathogens and represents a model for studying this important part of the immunogenome. While equine MHC class II DRA and DQA loci have received attention, the genetic diversity and effects of selection on DRB and DQB loci have been largely overlooked. This study aimed to provide the first in-depth analysis of the MHC class II DRB and DQB loci in the Equidae family. Results Three DRB and two DQB genes were identified in the genomes of all equids. The genes DRB2, DRB3 and DQB3 showed high sequence conservation, while polymorphisms were more frequent at DRB1 and DQB1 across all species analyzed. DQB2 was not found in the genome of the Asiatic asses Equus hemionus kulan and E. h. onager. The bioinformatic analysis of non-zero-coverage-bases of DRB and DQB genes in 14 equine individual genomes revealed differences among individual genes. Evidence for recombination was found for DRB1, DRB2, DQB1 and DQB2 genes. Trans-species allele sharing was identified in all genes except DRB1. Site-specific selection analysis predicted genes evolving under positive selection both at DRB and DQB loci. No selected amino acid sites were identified in DQB3. Conclusions The organization of the MHC class II sub-region of equids is similar across all species of the family. Genomic sequences, along with phylogenetic trees suggesting effects of selection as well as trans-species polymorphism support the contention that pathogen-driven positive selection has shaped the MHC class II DRB/DQB sub-regions in the Equidae.
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Affiliation(s)
- Marie Klumplerova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Petra Splichalova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Jan Oppelt
- Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.,Ceitec MU, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic.,National Centre for Biomolecular research, Faculty of Science, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Jan Futas
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic
| | - Aneta Kohutova
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 753/5, 625 00, Brno, Czech Republic
| | - Petra Musilova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Brno, Czech Republic.,Ceitec VRI, RG Animal Cytogenomics, Brno, Czech Republic
| | - Svatava Kubickova
- Department of Genetics and Reproductive Biotechnologies, Veterinary Research Institute, Brno, Czech Republic.,Ceitec VRI, RG Animal Cytogenomics, Brno, Czech Republic
| | - Roman Vodicka
- Zoo Prague, U Trojského zámku 120/3, 171 00, Praha 7, Czech Republic
| | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000, Toulouse, France.,Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K, Copenhagen, Denmark
| | - Petr Horin
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic. .,Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.
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48
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Chan KO, Hutter CR, Wood PL, Grismer LL, Das I, Brown RM. Gene flow creates a mirage of cryptic species in a Southeast Asian spotted stream frog complex. Mol Ecol 2020; 29:3970-3987. [PMID: 32808335 DOI: 10.1111/mec.15603] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 07/29/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Most new cryptic species are described using conventional tree- and distance-based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic inference and species delimitation, the influence of these processes is not frequently evaluated. Using large numbers of exons, introns, and ultraconserved elements obtained using the FrogCap sequence-capture protocol, we compared conventional SDMs with more robust genomic analyses that assess population structure and gene flow to characterize species boundaries in a Southeast Asian frog complex (Pulchrana picturata). Our results showed that gene flow and introgression can produce phylogenetic patterns and levels of divergence that resemble distinct species (up to 10% divergence in mitochondrial DNA). Hybrid populations were inferred as independent (singleton) clades that were highly divergent from adjacent populations (7%-10%) and unusually similar (<3%) to allopatric populations. Such anomalous patterns are not uncommon in Southeast Asian amphibians, which brings into question whether the high levels of cryptic diversity observed in other amphibian groups reflect distinct cryptic species-or, instead, highly admixed and structured metapopulation lineages. Our results also provide an alternative explanation to the conundrum of divergent (sometimes nonsister) sympatric lineages-a pattern that has been celebrated as indicative of true cryptic speciation. Based on these findings, we recommend that species delimitation of continuously distributed "cryptic" groups should not rely solely on conventional SDMs, but should necessarily examine population structure and gene flow to avoid taxonomic inflation.
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Affiliation(s)
- Kin O Chan
- Lee Kong Chian National History Museum, Faculty of Science, National University of Singapore, Singapore
| | - Carl R Hutter
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Museum of Natural Sciences and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Perry L Wood
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA.,Department of Biological Sciences & Museum of Natural History, Auburn University, Auburn, AL, USA
| | - L L Grismer
- Herpetology Laboratory, Department of Biology, La Sierra University, Riverside, CA, USA
| | - Indraneil Das
- Institute of Biodiversity and Environmental Conservation, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, Malaysia
| | - Rafe M Brown
- Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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49
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Mallet J. Alternative views of biological species: reproductively isolated units or genotypic clusters? Natl Sci Rev 2020; 7:1401-1407. [PMID: 34692169 PMCID: PMC8288880 DOI: 10.1093/nsr/nwaa116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, USA
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50
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Marin J, Achaz G, Crombach A, Lambert A. The genomic view of diversification. J Evol Biol 2020; 33:1387-1404. [PMID: 32654283 DOI: 10.1111/jeb.13677] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/11/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022]
Abstract
The process of species diversification is traditionally summarized by a single tree, the species tree, whose reconstruction from molecular data is hindered by frequent conflicts between gene genealogies. Here, we argue that instead of seeing these conflicts as nuisances, we can exploit them to inform the diversification process itself. We adopt a gene-based view of diversification to model the ubiquitous presence of gene flow between diverging lineages, one of the most important processes explaining disagreements among gene trees. We propose a new framework for modelling the joint evolution of gene and species lineages relaxing the hierarchy between the species tree and gene trees inherent to the standard view, as embodied in a popular model known as the multispecies coalescent (MSC). We implement this framework in two alternative models called the gene-based diversification models (GBD): (a) GBD-forward following all evolving genomes through time and (b) GBD-backward based on coalescent theory. They feature four parameters tuning colonization, gene flow, genetic drift and genetic differentiation. We propose an inference method based on differences between gene trees. Applied to two empirical data sets prone to gene flow, we find better support for the GBD-backward model than for the MSC model. Along with the increasing awareness of the extent of gene flow, this work shows the importance of considering the richer signal contained in genomic histories, rather than in the mere species tree, to better apprehend the complex evolutionary history of species.
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Affiliation(s)
- Julie Marin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France
| | - Guillaume Achaz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Institut de Systématique, Évolution, Biodiversité (ISYEB), MNHN, CNRS, EPHE, Sorbonne Université, Paris, France.,UMR 7206 Eco-anthropologie, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique, Université de Paris, Paris, France
| | - Anton Crombach
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Inria, Lyon Antenne La Doua, Villeurbanne, France.,INSA-Lyon, LIRIS, UMR 5205, Université de Lyon, Villeurbanne, France
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, PSL Research University, Paris, France.,Laboratoire de Probabilités, Statistique et Modélisation (LPSM), CNRS UMR 8001, Sorbonne Université, Paris, France
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