1
|
Abbona CC, Lebrasseur O, Prevosti FJ, Peralta E, González Venanzi L, Frantz L, Larson G, Gil AF, Neme GA. Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities. ROYAL SOCIETY OPEN SCIENCE 2024; 11:231835. [PMID: 38601034 PMCID: PMC11004678 DOI: 10.1098/rsos.231835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 04/12/2024]
Abstract
The southern Mendoza province, located in the northern region of Patagonia, was inhabited by hunter-gatherer groups until historic times. Previous archaeological studies have reported canid remains among faunal assemblages, which were assumed to be part of the human diet. However, the taxonomic identification and significance of these canids within human groups have raised questions. In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (δ13Ccol and δ15N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Cañada Seca. Previous morphological identifications suggested that it belonged to the genus Lycalopex, but our results conclusively demonstrate that the individual belongs to the extinct fox species Dusicyon avus. This finding expands Dusicyon avus' known geographical distribution to Patagonia's northern extremity. Furthermore, statistical predictions based on genetic divergence undermine the hypothesis that hybridization between Canis and Dusicyon, facilitated by the introduction of domestic dogs, played a role in the extinction of Dusicyon species. On the other hand, our findings indicate that a Dusicyon avus individual shared a similar diet and was probably buried alongside humans, suggesting a close relationship between the two species during their lives and deaths.
Collapse
Affiliation(s)
- Cinthia C. Abbona
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Ophélie Lebrasseur
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, OxfordOX1 3TG, UK
| | - Francisco J. Prevosti
- Museo de Ciencias Antropológicas y Naturales, Universidad Nacional de La Rioja (UNLaR), Avenue Luis M. de la Fuente S/N, La Rioja5300, Argentina
| | - Eva Peralta
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Lucio González Venanzi
- Div. Arqueología, Anexo Museo, Laboratory 128 (FCNyM-UNLP), La Plata, Argentina, FHumyAr (UNR), Rosario, Argentina
| | - Laurent Frantz
- Graduate School Life Science Munich, Faculty of Biology/Biocenter, Grosshadernerstr, 2-4, 82152 Planegg-Martinsried, Munich, Germany
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, OxfordOX1 3TG, UK
| | - Adolfo F. Gil
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Gustavo A. Neme
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| |
Collapse
|
2
|
Salazar-Bravo J, Tinoco N, Zeballos H, Brito J, Arenas-Viveros D, Marín-C D, Ramírez-Fernández JD, Percequillo AR, Lee, Jr. TE, Solari S, Colmenares-Pinzon J, Nivelo C, Rodríguez Herrera B, Merino W, Medina CE, Murillo-García O, Pardiñas UF. Systematics and diversification of the Ichthyomyini (Cricetidae, Sigmodontinae) revisited: evidence from molecular, morphological, and combined approaches. PeerJ 2023; 11:e14319. [PMID: 36655048 PMCID: PMC9841913 DOI: 10.7717/peerj.14319] [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: 12/04/2020] [Accepted: 10/09/2022] [Indexed: 01/15/2023] Open
Abstract
Ichthyomyini, a morphologically distinctive group of Neotropical cricetid rodents, lacks an integrative study of its systematics and biogeography. Since this tribe is a crucial element of the Sigmodontinae, the most speciose subfamily of the Cricetidae, we conducted a study that includes most of its recognized diversity (five genera and 19 species distributed from southern Mexico to northern Bolivia). For this report we analyzed a combined matrix composed of four molecular markers (RBP3, GHR, RAG1, Cytb) and 56 morphological traits, the latter including 15 external, 14 cranial, 19 dental, five soft-anatomical and three postcranial features. A variety of results were obtained, some of which are inconsistent with the currently accepted classification and understanding of the tribe. Ichthyomyini is retrieved as monophyletic, and it is divided into two main clades that are here recognized as subtribes: one to contain the genus Anotomys and the other composed by the remaining genera. Neusticomys (as currently recognized) was found to consist of two well supported clades, one of which corresponds to the original concept of Daptomys. Accordingly, we propose the resurrection of the latter as a valid genus to include several species from low to middle elevations and restrict Neusticomys to several highland forms. Numerous other revisions are necessary to reconcile the alpha taxonomy of ichthyomyines with our phylogenetic results, including placement of the Cajas Plateau water rat (formerly Chibchanomys orcesi) in the genus Neusticomys (sensu stricto), and the recognition of at least two new species (one in Neusticomys, one in Daptomys). Additional work is necessary to confirm other unanticipated results, such as the non-monophyletic nature of Rheomys and the presence of a possible new genus and species from Peru. Our results also suggest that ichthyomyines are one of the main Andean radiations of sigmodontine cricetids, with an evolutionary history dating to the Late Miocene and subsequent cladogenesis during the Pleistocene.
Collapse
Affiliation(s)
- Jorge Salazar-Bravo
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States,Instituto de Ecologia, Universidad Mayor de San Andrés, La Paz, Bolivia,Instituto Nacional de Biodiversidad, Quito, Ecuador
| | - Nicolás Tinoco
- Museo de Zoología Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | | | - Jorge Brito
- Instituto Nacional de Biodiversidad, Quito, Ecuador
| | | | - David Marín-C
- Colección Teriológica, Universidad de Antioquia, Medellin, Colombia
| | | | - Alexandre R. Percequillo
- Escola Superior de Agricultura “Luiz de Queiroz”, Departamento de Ciências Biológicas, Universidade de São Paulo, Piracicaba, São Paulo, Brazil
| | - Thomas E. Lee, Jr.
- Department of Biology, Abilene Christian University, Abilene, Texas, United States
| | - Sergio Solari
- Instituto de Biología, Universidad de Antioquia, Medellin, Antioquia, Colombia
| | - Javier Colmenares-Pinzon
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States,Grupo de Estudios en Biodiversidad, Escuela de Biología, Universidad Industrial de Santander, Bucaramanga, Santander, Colombia
| | - Carlos Nivelo
- Museo de Zoologia, Escuela de Biología, Universidad del Azuay, Cuenca, Ecuador,Instituto de Diversidad y Evolución Austral, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Chubut, Argentina
| | | | - William Merino
- Escuela de Biología, Universidad de El Salvador, San Salvador, San Salvador, El Salvador
| | - Cesar E. Medina
- Museo de Historia Natural, Universidad Nacional de San Agustin, Arequipa, Arequipa, Peru
| | - Oscar Murillo-García
- Departamento de Biología, Universidad del Valle, Cali, Valle del Cauca, Colombia
| | - Ulyses F.J. Pardiñas
- Instituto Nacional de Biodiversidad, Quito, Ecuador,Instituto de Diversidad y Evolución Austral, Consejo Nacional de Investigaciones Científicas y Técnicas, Puerto Madryn, Chubut, Argentina
| |
Collapse
|
3
|
Genotyping-by-sequencing (GBS) as a tool for interspecies hybrid detection. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Genotyping-by-sequencing (GBS) is an extremely useful, modern and relatively inexpensive approach to discovering high-quality single-nucleotide polymorphisms (SNPs), which seem to be the most promising markers for identifying hybrid individuals between different species, especially those that can create backcrosses. In addition, GBS could become an invaluable tool in finding backcrosses, even several generations back. Its potential for the use of restriction enzymes and species is almost unlimited. It can also be successfully applied to species for which a reference genome is not established. In this paper, we describe the GBS technique, its main advantages and disadvantages, and the research carried out using this method concerning interspecies hybridisation and the identification of fertile hybrids. We also present future approaches that could be of interest in the context of the GBS method.
Collapse
|
4
|
Rocha S, Trinks A, Harris DJ, Larson G, Cheke AS. The Global and Western Indian Ocean Dispersal of House Geckos From Asia Using Historical and Mitochondrial DNA Perspectives. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.791762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Seven species of house geckos occur across the scattered islands of the Indian Ocean. Two of these, Hemidactylus frenatus and H. parvimaculatus are both widespread and possess distribution profiles that suggest pre-European, or perhaps natural dispersal to some islands. Of these, only H. frenatus currently has sufficient molecular data to begin exploring dispersal patterns. This species is one of the most successful reptile colonists, as demonstrated by its global, pantropical distribution. While in some areas, such as Australia and continental South America, its dispersal patterns are both recent and well-known, early historical records of Hemidactylus in the Indian Ocean islands suggest earlier and/or potentially non-human-mediated dispersals. Here, we reviewed the historical literature and combined those reports with an assessment of mitochondrial DNA diversity of a global sampling of H. frenatus samples that included modern and museum specimens. Our results corroborate previous studies and demonstrate the relatively high diversity within this species’ native range in Southeast Asia. In addition, the phylogenetic analysis suggests both a potential cryptic species complex, as well as global geographic structuring of different H. frenatus mitochondrial lineages. This has important implications for many comparative studies of this complex. Frequent and ongoing dispersals and colonizations complicate the identification of potentially older migration patterns. Further assessments including additional samples and analyses of additional genetic markers are necessary to disentangle older from more recent dispersals within this intriguing species.
Collapse
|
5
|
Bredemeyer KR, Seabury CM, Stickney MJ, McCarrey JR, vonHoldt BM, Murphy WJ. Rapid Macrosatellite Evolution Promotes X-Linked Hybrid Male Sterility in a Feline Interspecies Cross. Mol Biol Evol 2021; 38:5588-5609. [PMID: 34519828 PMCID: PMC8662614 DOI: 10.1093/molbev/msab274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The sterility or inviability of hybrid offspring produced from an interspecific mating result from incompatibilities between parental genotypes that are thought to result from divergence of loci involved in epistatic interactions. However, attributes contributing to the rapid evolution of these regions also complicates their assembly, thus discovery of candidate hybrid sterility loci is difficult and has been restricted to a small number of model systems. Here we reported rapid interspecific divergence at the DXZ4 macrosatellite locus in an interspecific cross between two closely related mammalian species: the domestic cat (Felis silvestris catus) and the Jungle cat (Felis chaus). DXZ4 is an interesting candidate due to its structural complexity, copy number variability, and described role in the critical yet complex biological process of X-chromosome inactivation. However, the full structure of DXZ4 was absent or incomplete in nearly every available mammalian genome assembly given its repetitive complexity. We compared highly continuous genomes for three cat species, each containing a complete DXZ4 locus, and discovered that the felid DXZ4 locus differs substantially from the human ortholog, and that it varies in copy number between cat species. Additionally, we reported expression, methylation, and structural conformation profiles of DXZ4 and the X chromosome during stages of spermatogenesis that have been previously associated with hybrid male sterility. Collectively, these findings suggest a new role for DXZ4 in male meiosis and a mechanism for feline interspecific incompatibility through rapid satellite divergence.
Collapse
Affiliation(s)
- Kevin R Bredemeyer
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| | | | - Mark J Stickney
- Veterinary Medical Teaching Hospital, Texas A&M University, College Station, TX, USA
| | - John R McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | | | - William J Murphy
- Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, USA
| |
Collapse
|
6
|
Baca M, Popović D, Lemanik A, Fewlass H, Talamo S, Zima J, Ridush B, Popov V, Nadachowski A. The Tien Shan vole ( Microtus ilaeus; Rodentia: Cricetidae) as a new species in the Late Pleistocene of Europe. Ecol Evol 2021; 11:16113-16125. [PMID: 34824815 PMCID: PMC8601874 DOI: 10.1002/ece3.8289] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 11/09/2022] Open
Abstract
Grey voles (subgenus Microtus) represent a complex of at least seven closely related and partly cryptic species. The range of these species extends from the Atlantic to the Altai Mountains, but most of them occur east of the Black Sea. Using ancient DNA analyses of the Late Pleistocene specimens, we identified a new mtDNA lineage of grey voles in Europe. Phylogenetic analysis of mitochondrial DNA cytochrome b sequences from 23 voles from three caves, namely, Emine-Bair-Khosar (Crimea, Ukraine), Cave 16 (Bulgaria), and Bacho Kiro (Bulgaria), showed that 14 specimens form a previously unrecognized lineage, sister to the Tien Shan vole. The average sequence divergence of this lineage and the extant Tien Shan vole was 4.8%, which is similar to the divergence of grey vole forms, which are considered distinct species or being on the verge of speciation; M. arvalis and M. obscurus or M. mystacinus and M. rossiaemeridionalis. We estimated the time to the most recent common ancestor of the grey voles to be 0.66 Ma, which is over twice the recent estimates, while the divergence of the extant Tien Shan vole and the new lineage to be 0.29 Ma. Our discovery suggests that grey voles may have been more diversified in the past and that their ranges may have differed substantially from current ones. It also underlines the utility of ancient DNA to decipher the evolutionary history of voles.
Collapse
Affiliation(s)
- Mateusz Baca
- Centre of New TechnologiesUniversity of WarsawWarszawaPoland
| | | | - Anna Lemanik
- Institute of Systematics and Evolution of AnimalsPolish Academy of SciencesKrakówPoland
| | - Helen Fewlass
- Department of Human EvolutionMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
| | - Sahra Talamo
- Department of Human EvolutionMax Planck Institute for Evolutionary AnthropologyLeipzigGermany
- Department of Chemistry G. CiamicianUniversity of BolognaBolognaItaly
| | - Jan Zima
- Institute of Vertebrate BiologyAcademy of Sciences of Czech RepublicBrnoCzech Republic
| | - Bogdan Ridush
- Department of Physical Geography, Geomorphology and PaleogeographyYuriy Fedkovych Chernivtsi National UniversityChernivtsiUkraine
| | - Vasil Popov
- Institute of Biodiversity and Ecosystem ResearchBulgarian Academy of SciencesSophiaBulgaria
| | - Adam Nadachowski
- Institute of Systematics and Evolution of AnimalsPolish Academy of SciencesKrakówPoland
| |
Collapse
|
7
|
Peona V, Palacios-Gimenez OM, Blommaert J, Liu J, Haryoko T, Jønsson KA, Irestedt M, Zhou Q, Jern P, Suh A. The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200186. [PMID: 34304594 PMCID: PMC8310711 DOI: 10.1098/rstb.2020.0186] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 12/17/2022] Open
Abstract
It is a broadly observed pattern that the non-recombining regions of sex-limited chromosomes (Y and W) accumulate more repeats than the rest of the genome, even in species like birds with a low genome-wide repeat content. Here, we show that in birds with highly heteromorphic sex chromosomes, the W chromosome has a transposable element (TE) density of greater than 55% compared to the genome-wide density of less than 10%, and contains over half of all full-length (thus potentially active) endogenous retroviruses (ERVs) of the entire genome. Using RNA-seq and protein mass spectrometry data, we were able to detect signatures of female-specific ERV expression. We hypothesize that the avian W chromosome acts as a refugium for active ERVs, probably leading to female-biased mutational load that may influence female physiology similar to the 'toxic-Y' effect in Drosophila males. Furthermore, Haldane's rule predicts that the heterogametic sex has reduced fertility in hybrids. We propose that the excess of W-linked active ERVs over the rest of the genome may be an additional explanatory variable for Haldane's rule, with consequences for genetic incompatibilities between species through TE/repressor mismatches in hybrids. Together, our results suggest that the sequence content of female-specific W chromosomes can have effects far beyond sex determination and gene dosage. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
Collapse
Affiliation(s)
- Valentina Peona
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Julie Blommaert
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Jing Liu
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
| | - Tri Haryoko
- Museum Zoologicum Bogoriense, Research Centre for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Knud A. Jønsson
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Martin Irestedt
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Qi Zhou
- MOE Laboratory of Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, People's Republic of China
- Department of Neuroscience and Development, University of Vienna, Vienna, Austria
- Center for Reproductive Medicine, The 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, People's Republic of China
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Alexander Suh
- Department of Organismal Biology—Systematic Biology, Uppsala University, Uppsala, Sweden
- School of Biological Sciences—Organisms and the Environment, University of East Anglia, Norwich, UK
| |
Collapse
|
8
|
Buck LT, Katz DC, Ackermann RR, Hlusko LJ, Kanthaswamy S, Weaver TD. Effects of hybridization on pelvic morphology: A macaque model. J Hum Evol 2021; 159:103049. [PMID: 34455262 DOI: 10.1016/j.jhevol.2021.103049] [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: 11/10/2020] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/28/2022]
Abstract
Ancient DNA analyses have shown that interbreeding between hominin taxa occurred multiple times. Although admixture is often reflected in skeletal phenotype, the relationship between the two remains poorly understood, hampering interpretation of the hominin fossil record. Direct study of this relationship is often impossible due to the paucity of hominin fossils and difficulties retrieving ancient genetic material. Here, we use a sample of known ancestry hybrids between two closely related nonhuman primate taxa (Indian and Chinese Macaca mulatta) to investigate the effect of admixture on skeletal morphology. We focus on pelvic shape, which has potential fitness implications in hybrids, as mismatches between maternal pelvic and fetal cranial morphology are often fatal to mother and offspring. As the pelvis is also one of the skeletal regions that differs most between Homo sapiens and Neanderthals, investigating the pelvic consequences of interbreeding could be informative regarding the viability of their hybrids. We find that the effect of admixture in M. mulatta is small and proportional to the relatively small morphological difference between the parent taxa. Sexual dimorphism appears to be the main determinant of pelvic shape in M. mulatta. The lack of difference in pelvic shape between Chinese and Indian M. mulatta is in contrast to that between Neanderthals and H. sapiens, despite a similar split time (in generations) between the hybridizing pairs. Greater phenotypic divergence between hominins may relate to adaptations to disparate environments but may also highlight how the unique degree of cultural buffering in hominins allowed for greater neutral divergence. In contrast to some previous work identifying extreme morphologies in first- and second-generation hybrids, here the relationship between pelvic shape and admixture is linear. This linearity may be because most sampled animals have a multigenerational admixture history or because of relatively high constraints on the pelvis compared with other skeletal regions.
Collapse
Affiliation(s)
- Laura T Buck
- School of Biological and Environmental Sciences, Liverpool John Moores University, UK; Department of Anthropology, University of California Davis, USA.
| | - David C Katz
- Department of Anthropology, University of California Davis, USA; University of Calgary, Cumming School of Medicine, Canada
| | - Rebecca Rogers Ackermann
- Department of Archaeology, University of Cape Town, South Africa; Human Evolution Research Institute, University of Cape Town, South Africa
| | - Leslea J Hlusko
- Department of Integrative Biology, University of California Berkeley, USA; Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Sree Kanthaswamy
- School of Natural and Mathematical Sciences, Arizona State University, USA
| | | |
Collapse
|
9
|
Bikchurina TI, Golenishchev FN, Kizilova EA, Mahmoudi A, Borodin PM. Reproductive Isolation Between Taxonomically Controversial Forms of the Gray Voles ( Microtus, Rodentia; Arvicolinae): Cytological Mechanisms and Taxonomical Implications. Front Genet 2021; 12:653837. [PMID: 34040633 PMCID: PMC8141921 DOI: 10.3389/fgene.2021.653837] [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: 01/15/2021] [Accepted: 03/26/2021] [Indexed: 01/03/2023] Open
Abstract
The formation of hybrid sterility is an important stage of speciation. The voles of the genus Microtus, which is the most speciose genus of rodents, provide a good model for studying the cytological mechanisms of hybrid sterility. The voles of the "mystacinus" group of the subgenus Microtus (2n = 54) comprising several recently diverged forms with unclear taxonomic status are especially interesting. To resolve the taxonomic status of Microtus mystacinus and Microtus kermanensis, we crossed both with Microtus rossiaemeridionalis, and M. kermanensis alone with Microtus arvalis "obscurus" and M. transcaspicus and examined the reproductive performance of their F1 hybrids. All interspecies male hybrids were sterile. Female M. kermanensis × M. arvalis and M. kermanensis × M. transcaspicus hybrids were sterile as well. Therefore, M. mystacinus, M. kermanensis, and M. rossiaemeridionalis could be considered valid species. To gain an insight into the cytological mechanisms of male hybrid sterility, we carried out a histological analysis of spermatogenesis and a cytological analysis of chromosome synapsis, recombination, and epigenetic chromatin modifications in the germ cells of the hybrids using immunolocalization of key meiotic proteins. The hybrids showed wide variation in the onset of spermatogenesis arrest stage, from mature (although abnormal) spermatozoa to spermatogonia only. Chromosome asynapsis was apparently the main cause of meiotic arrest. The degree of asynapsis varied widely across cells, individuals, and the crosses-from partial asynapsis of several small bivalents to complete asynapsis of all chromosomes. The asynapsis was accompanied by a delayed repair of DNA double-strand breaks marked by RAD51 antibodies and silencing of unpaired chromatin marked by γH2A.X antibodies. Overall, the severity of disturbances in spermatogenesis in general and in chromosome synapsis in particular increased in the hybrids with an increase in the phylogenetic distance between their parental species.
Collapse
Affiliation(s)
- Tatiana I Bikchurina
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Laboratory of Structural and Functional Genome Organization, Novosibirsk State University, Novosibirsk, Russia
| | - Fedor N Golenishchev
- Laboratory of Theriology, Zoological Institute, Russian Academy of Sciences, St. Petersburg, Russia
| | - Elena A Kizilova
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Cytology and Genetics, Novosibirsk State University, Novosibirsk, Russia
| | - Ahmad Mahmoudi
- Department of Biology, Faculty of Science, Urmia University, Urmia, Iran
| | - Pavel M Borodin
- Laboratory of Recombination and Segregation Analysis, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Cytology and Genetics, Novosibirsk State University, Novosibirsk, Russia
| |
Collapse
|
10
|
Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 2021; 10:e63167. [PMID: 33599612 PMCID: PMC7963486 DOI: 10.7554/elife.63167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.
Collapse
Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Nico L Avenant
- National Museum and Centre for Environmental Management, University of the Free StateBloemfonteinSouth Africa
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums ScotlandEdinburghUnited Kingdom
| | - Erwan Corre
- CNRS, Sorbonne Université, CNRS, ABiMS, Station Biologique de RoscoffRoscoffFrance
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| |
Collapse
|