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Knauf S, Hisgen L, Ågren EO, Barlow AM, Faehndrich M, Voigt U, Fischer L, Grillová L, Hallmaier-Wacker LK, Kik MJL, Klink JC, Křenová J, Lavazza A, Lüert S, Nováková M, Čejková D, Pacioni C, Trogu T, Šmajs D, Roos C. High prevalence and genetic diversity of Treponema paraluisleporidarum isolates in European lagomorphs. Microbiol Spectr 2024; 12:e0177423. [PMID: 38095473 PMCID: PMC10783078 DOI: 10.1128/spectrum.01774-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/17/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Syphilis is an ancient disease of humans and lagomorphs caused by two distinct but genetically closely related bacteria (>98% sequence identity based on the whole genome) of the genus Treponema. While human syphilis is well studied, little is known about the disease in the lagomorph host. Yet, comparative studies are needed to understand mechanisms in host-pathogen coevolution in treponematoses. Importantly, Treponema paraluisleporidarum-infected hare populations provide ample opportunity to study the syphilis-causing pathogen in a naturally infected model population without antibiotic treatment, data that cannot be obtained from syphilis infection in humans. We provide data on genetic diversity and are able to highlight various types of repetitions in one of the two hypervariable regions at the tp0548 locus that have not been described in the human syphilis-causing sister bacterium Treponema pallidum subsp. pallidum.
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Affiliation(s)
- Sascha Knauf
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
- Infection Biology Unit, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
- Professorship for International Animal Health/One Health, Faculty of Veterinary Medicine, Justus Liebig University, Giessen, Germany
| | - Linda Hisgen
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
- Infection Biology Unit, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Erik O. Ågren
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden
| | - Alexander M. Barlow
- Wildlife Network for Disease Surveillance, Bristol Veterinary School, Langford, Somerset, United Kingdom
| | - Marcus Faehndrich
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hanover, Foundation, Hanover, Germany
| | - Ulrich Voigt
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hanover, Foundation, Hanover, Germany
| | - Luisa Fischer
- Wildlife Research Institute, State Agency for Nature, Environment and Consumer Protection North Rhine-Westphalia, Bonn, Germany
| | - Linda Grillová
- Department of Biology, Masaryk University, Brno, Czechia
| | - Luisa K. Hallmaier-Wacker
- Infection Biology Unit, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Marja J. L. Kik
- Pathology Division, Department of Biomedical Health Sciences, Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Jana C. Klink
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hanover, Foundation, Hanover, Germany
| | - Jitka Křenová
- Department of Biology, Masaryk University, Brno, Czechia
| | - Antonio Lavazza
- Department of Animal Health and Welfare – Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - Simone Lüert
- Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald, Germany
- Infection Biology Unit, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
| | | | - Darina Čejková
- Department of Biomedical Engineering, Brno University of Technology, Brno, Czechia
| | - Carlo Pacioni
- Department of Environment, Land, Water and Planning, Arthur Rylah Institute for Environmental Research, Heidelberg, Victoria, Australia
- Environmental and Conservation Sciences, Murdoch University, Murdoch, Australia
| | - Tiziana Trogu
- Department of Animal Health and Welfare – Virology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Brescia, Italy
| | - David Šmajs
- Department of Biology, Masaryk University, Brno, Czechia
| | - Christian Roos
- Primate Genetics Laboratory, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
- Gene Bank of Primates, Deutsches Primatenzentrum GmbH, Leibniz Institute for Primate Research, Göttingen, Germany
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Burbrink FT, Ruane S, Rabibisoa N, Raselimanana AP, Raxworthy CJ, Kuhn A. Speciation rates are unrelated to the formation of population structure in Malagasy gemsnakes. Ecol Evol 2023; 13:e10344. [PMID: 37529593 PMCID: PMC10375368 DOI: 10.1002/ece3.10344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 06/07/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Speciation rates vary substantially across the tree of life. These rates should be linked to the rate at which population structure forms if a continuum between micro and macroevolutionary patterns exists. Previous studies examining the link between speciation rates and the degree of population formation in clades have been shown to be either correlated or uncorrelated depending on the group, but no study has yet examined the relationship between speciation rates and population structure in a young group that is constrained spatially to a single-island system. We examine this correlation in 109 gemsnakes (Pseudoxyrhophiidae) endemic to Madagascar and originating in the early Miocene, which helps control for extinction variation across time and space. We find no relationship between rates of speciation and the formation rates of population structure over space in 33 species of gemsnakes. Rates of speciation show low variation, yet population structure varies widely across species, indicating that speciation rates and population structure are disconnected. We suspect this is largely due to the persistence of some lineages not susceptible to extinction. Importantly, we discuss how delimiting populations versus species may contribute to problems understanding the continuum between shallow and deep evolutionary processes.
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Affiliation(s)
- Frank T. Burbrink
- Department of HerpetologyAmerican Museum of Natural HistoryNew York CityNew YorkUSA
| | - Sara Ruane
- Life Sciences Section, Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Nirhy Rabibisoa
- Sciences de la Vie et de l'Environnement, Faculté des Sciences, de Technologies et de l'EnvironnementUniversité de MahajangaMahajangaMadagascar
| | - Achille P. Raselimanana
- Zoologie et Biodiversité Animale, Faculté des SciencesUniversité d'AntananarivoAntananarivoMadagascar
| | | | - Arianna Kuhn
- Department of HerpetologyAmerican Museum of Natural HistoryNew York CityNew YorkUSA
- Virginia Museum of Natural HistoryMartinsvilleVirginiaUSA
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3
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Tukhbatullin A, Ermakov O, Kapustina S, Starikov V, Tambovtseva V, Titov S, Brandler O. Surrounded by Kindred: Spermophilus major Hybridization with Other Spermophilus Species in Space and Time. BIOLOGY 2023; 12:880. [PMID: 37372163 DOI: 10.3390/biology12060880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Among the numerous described cases of hybridization in mammals, the most intriguing are (a) cases of introgressive hybridization deeply affecting the evolutionary history of species, and (b) models involving not a pair of species but a multi-species complex. Therefore, the hybridization history of the russet ground squirrel Spermophilus major, whose range has repeatedly changed due to climatic fluctuations and now borders the ranges of four related species, is of great interest. The main aims of this study were to determine the direction and intensity of gene introgression, the spatial depth of the infiltration of extraneous genes into the S. major range, and to refine the hypothesis of the hybridogenic replacement of mitochondrial genomes in the studied group. Using phylogenetic analysis of the variability of mitochondrial (CR, cytb) and nuclear (SmcY, BGN, PRKCI, c-myc, i6p53) markers, we determined the contribution of neighboring species to the S. major genome. We showed that 36% of S. major individuals had extraneous alleles. All peripheral species that were in contact with S. major contributed towards its genetic variability. We also proposed a hypothesis for the sequence and localization of serial hybridization events. Our assessment of the S. major genome implications of introgression highlights the importance of implementing conservation measures to protect this species.
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Affiliation(s)
- Andrey Tukhbatullin
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Oleg Ermakov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Svetlana Kapustina
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Vladimir Starikov
- Department of Biology and Biotechnology, Institute of Natural and Technical Sciences, Surgut State University, Lenin Avenue 1, Surgut 628412, Russia
| | - Valentina Tambovtseva
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
| | - Sergey Titov
- Faculty of Physics, Mathematics and Natural Sciences, Belinsky Institute of Teacher Education, Penza State University, Lermontov Str. 37, Penza 440026, Russia
| | - Oleg Brandler
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, Moscow 119334, Russia
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Gaertner K, Michell C, Tapanainen R, Goffart S, Saari S, Soininmäki M, Dufour E, Pohjoismäki JLO. Molecular phenotyping uncovers differences in basic housekeeping functions among closely related species of hares (
Lepus
spp., Lagomorpha: Leporidae). Mol Ecol 2022. [PMID: 36320183 DOI: 10.1111/mec.16755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/16/2022] [Accepted: 10/06/2022] [Indexed: 11/15/2022]
Abstract
Speciation is a fundamental evolutionary process, which results in genetic differentiation of populations and manifests as discrete morphological, physiological and behavioural differences. Each species has travelled its own evolutionary trajectory, influenced by random drift and driven by various types of natural selection, making the association of genetic differences between the species with the phenotypic differences extremely complex to dissect. In the present study, we have used an in vitro model to analyse in depth the genetic and gene regulation differences between fibroblasts of two closely related mammals, the arctic/subarctic mountain hare (Lepus timidus Linnaeus) and the temperate steppe-climate adapted brown hare (Lepus europaeus Pallas). We discovered the existence of a species-specific expression pattern of 1623 genes, manifesting in differences in cell growth, cell cycle control, respiration, and metabolism. Interspecific differences in the housekeeping functions of fibroblast cells suggest that speciation acts on fundamental cellular processes, even in these two interfertile species. Our results help to understand the molecular constituents of a species difference on a cellular level, which could contribute to the maintenance of the species boundary.
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Affiliation(s)
- Kateryna Gaertner
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Craig Michell
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia
| | - Riikka Tapanainen
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Sina Saari
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Manu Soininmäki
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
| | - Eric Dufour
- Mitochondrial Bioenergetics and Metabolism, Faculty of Medicine and Health Technology FI‐33014 Tampere University Tampere Finland
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences FI‐80101 University of Eastern Finland Kuopio Finland
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5
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Reid N, Hughes MF, Hynes RA, Montgomery WI, Prodöhl PA. Bidirectional hybridisation and introgression between introduced European brown hare, Lepus europaeus and the endemic Irish hare, L. timidus hibernicus. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01471-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractIntroduced non-native species can threaten native species through interspecific hybridisation and genetic introgression. We assessed the prevalence of hybridisation and introgression between introduced European brown hare, Lepus europaeus, and the endemic Irish hare, L. timidus hibernicus. Roadkill hares (n = 56) were sequenced for a 379bp section of the mitochondrial DNA D-loop and a 474bp segment of the nuclear transferrin (Tf) gene. A species-specific indel in the transferrin gene was present in L.t. hibernicus and absent in L. europaeus. Excluding three hares from which molecular data could not be recovered, 28 hares (53%) were native L.t. hibernicus, 7 (13%) were non-native L. europaeus and 18 (34%) were hybrids; of which 5 (28%) were first generation (F1) involving bidirectional crosses with mismatched nuclear and mtDNA (3 ♂ europaeus x ♀ hibernicus and 2 ♂ hibernicus x ♀ europaeus). Mixed nuclear transferrin sequences suggested 13 (72%) of hybrids were at least 2nd generation (F2) with 9 (69%) possessing L.t. hibernicus and 4 (31%) L. europaeus mtDNA (the latter indicative of hybrid backcrossing with the non-native). The prevalence of hybridisation at similar mountain-brown hare contact zones throughout Europe is notably lower (4–16%) and typically unidirectional (♂ europaeus x ♀ timidus). A high prevalence of bidirectional hybridisation and introgression (in association with projected climate change) may favour the introduced species over the native. Genetic surveillance and population monitoring are needed to further explore the potential conservation implications of European brown hare in Ireland.
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Dong X, Yi W, Zheng C, Zhu X, Wang S, Xue H, Ye Z, Bu W. Species delimitation of rice seed bugs complex: Insights from mitochondrial genomes and ddRAD‐seq data. ZOOL SCR 2021. [DOI: 10.1111/zsc.12523] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xue Dong
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Wenbo Yi
- Department of Biology Xinzhou Teachers University Xinzhou China
| | - Chenguang Zheng
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Xiuxiu Zhu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Shujing Wang
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Huaijun Xue
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Zhen Ye
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
| | - Wenjun Bu
- Institute of Entomology College of Life Sciences Nankai University Tianjin China
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7
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Hybridization with mountain hares increases the functional allelic repertoire in brown hares. Sci Rep 2021; 11:15771. [PMID: 34349207 PMCID: PMC8338973 DOI: 10.1038/s41598-021-95357-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
Brown hares (Lepus europaeus Pallas) are able to hybridize with mountain hares (L. timidus Linnaeus) and produce fertile offspring, which results in cross-species gene flow. However, not much is known about the functional significance of this genetic introgression. Using targeted sequencing of candidate loci combined with mtDNA genotyping, we found the ancestral genetic diversity in the Finnish brown hare to be small, likely due to founder effect and range expansion, while gene flow from mountain hares constitutes an important source of functional genetic variability. Some of this variability, such as the alleles of the mountain hare thermogenin (uncoupling protein 1, UCP1), might have adaptive advantage for brown hares, whereas immunity-related MHC alleles are reciprocally exchanged and maintained via balancing selection. Our study offers a rare example where an expanding species can increase its allelic variability through hybridization with a congeneric native species, offering a route to shortcut evolutionary adaptation to the local environmental conditions.
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8
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Kraatz B, Belabbas R, Fostowicz-Frelik Ł, Ge DY, Kuznetsov AN, Lang MM, López-Torres S, Mohammadi Z, Racicot RA, Ravosa MJ, Sharp AC, Sherratt E, Silcox MT, Słowiak J, Winkler AJ, Ruf I. Lagomorpha as a Model Morphological System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.636402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Due to their global distribution, invasive history, and unique characteristics, European rabbits are recognizable almost anywhere on our planet. Although they are members of a much larger group of living and extinct mammals [Mammalia, Lagomorpha (rabbits, hares, and pikas)], the group is often characterized by several well-known genera (e.g., Oryctolagus, Sylvilagus, Lepus, and Ochotona). This representation does not capture the extraordinary diversity of behavior and form found throughout the order. Model organisms are commonly used as exemplars for biological research, but there are a limited number of model clades or lineages that have been used to study evolutionary morphology in a more explicitly comparative way. We present this review paper to show that lagomorphs are a strong system in which to study macro- and micro-scale patterns of morphological change within a clade that offers underappreciated levels of diversity. To this end, we offer a summary of the status of relevant aspects of lagomorph biology.
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Brandler OV, Kapustina SY, Nikol’skii AA, Kolesnikov VV, Badmaev BB, Adiya Y. A Study of Hybridization Between Marmota baibacina and M. sibirica in Their Secondary Contact Zone in Mongolian Altai. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.555341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The role of hybridization as one of the factors of speciation in mammals has been underestimated for a long time, but now there is a lot of data on its impact in mammalian evolution. Hybridization of species often occurs in their secondary contact zones, which is a natural model for testing factors that ensure species integrity. Studies of hybrid zones are increasingly revealing the essential role of ecological and behavioral features both in initiating crossbreeding and in maintaining interspecific barriers. We studied the hybridization of two species of marmots Marmota baibacina and M. sibirica in the zone of sympatry in Mongolian Altai Mountains. We used a bioacoustic approach to determine the localization of individuals of different species and their cohabitation sites. Genetic typing with two diploid nuclear markers and one marker each of paternal and maternal lines was used to identify hybrids. Habitat preferences of marmots were studied to understand the conditions for the formation of heterospecific pairs. We found a high proportion of hybrid individuals in boulder screes where conditions for the formation of heterospecific pairs probably exist. Our data indicate the viability and fertility of F1 hybrids and their descendants. We hypothesize that the environmental preferences and behavioral features of both species of marmots are important factors that both create conditions for hybridization and limit hybrid dispersal.
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10
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Sarver BAJ, Herrera ND, Sneddon D, Hunter SS, Settles ML, Kronenberg Z, Demboski JR, Good JM, Sullivan J. Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias). Syst Biol 2021; 70:908-921. [PMID: 33410870 DOI: 10.1093/sysbio/syaa085] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 12/18/2022] Open
Abstract
Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (T. canipes, T. cinereicollis, T. dorsalis, T. quadrivittatus, T. rufus, and T. umbrinus) that show evidence for widespread introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group.
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Affiliation(s)
- Brice A J Sarver
- Department of Biological Sciences, University of Idaho, Moscow, Idaho.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho
| | | | - David Sneddon
- Department of Biological Sciences, University of Idaho, Moscow, Idaho
| | - Samuel S Hunter
- Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho.,UC-Davis Genome Center, Davis, California
| | | | | | - John R Demboski
- Department of Zoology, Denver Museum of Nature & Sciences, Denver, Colorado
| | - Jeffrey M Good
- Division of Biological Sciences, University of Montana, Missoula, Montana.,Wildlife Biology Program, University of Montana, Missoula, Montana
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, Idaho.,Institute for Bioinformatics and Evolutionary Studies (IBEST), University of Idaho, Moscow Idaho
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11
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Quilodrán CS, Tsoupas A, Currat M. The Spatial Signature of Introgression After a Biological Invasion With Hybridization. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.569620] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The accumulation of genome-wide molecular data has emphasized the important role of hybridization in the evolution of many organisms, which may carry introgressed genomic segments resulting from past admixture events with other taxa. Despite a number of examples of hybridization occurring during biological invasions, the resulting spatial patterns of genomic introgression remain poorly understood. Preliminary simulation studies have suggested a heterogeneous spatial level of introgression for invasive taxa after range expansion. We investigated in detail the robustness of this pattern and its persistence over time for both invasive and local organisms. Using spatially explicit simulations, we explored the spatial distribution of introgression across the area of colonization of an invasive taxon hybridizing with a local taxon. The general pattern for neutral loci supported by our results is an increasing introgression of local genes into the invasive taxon with the increase in the distance from the source of the invasion and a decreasing introgression of invasive genes into the local taxon. However, we also show there is some variation in this general trend depending on the scenario investigated. Spatial heterogeneity of introgression within a given taxon is thus an expected neutral pattern in structured populations after a biological invasion with a low to moderate amount of hybridization. We further show that this pattern is consistent with published empirical observations. Using additional simulations, we argue that the spatial pattern of Neanderthal introgression in modern humans, which has been documented to be higher in Asia than in Europe, can be explained by a model of hybridization with Neanderthals in Eurasia during the range expansion of modern humans from Africa. Our results support the view that weak hybridization during range expansion may explain spatially heterogeneous introgression patterns without the need to invoke selection.
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12
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Mao X, Rossiter SJ. Genome-wide data reveal discordant mitonuclear introgression in the intermediate horseshoe bat (Rhinolophus affinis). Mol Phylogenet Evol 2020; 150:106886. [PMID: 32534185 DOI: 10.1016/j.ympev.2020.106886] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 06/01/2020] [Accepted: 06/03/2020] [Indexed: 10/24/2022]
Abstract
Closely related taxa often exhibit mitonuclear discordance attributed to introgression of mitochondrial DNA (mtDNA), yet few studies have considered the underlying causes of mtDNA introgression. Here we test for demographic versus adaptive processes as explanations for mtDNA introgression in three subspecies of the intermediate horseshoe bat (Rhinolophus affinis). We generated sequences of 1692 nuclear genes and 13 mitochondrial protein-coding genes for 48 individuals. Phylogenetic reconstructions based on 320 exon sequences and 2217 single nucleotide polymorphisms (SNPs) both revealed conflicts between the species tree and mtDNA tree. These results, together with geographic patterns of mitonuclear discordance, and shared identical or near-identical mtDNA sequences, suggest extensive introgression of mtDNA between the two parapatric mainland subspecies. Under demographic hypotheses, we would also expect to uncover traces of ncDNA introgression, however, population structure and gene flow analyses revealed little nuclear admixture. Furthermore, we found inconsistent estimates of the timing of population expansion and that of the most recent common ancestor for the clade containing introgressed haplotypes. Without a clear demographic explanation, we also examined whether introgression likely arises from adaptation. We found that five mtDNA genes contained fixed amino acid differences between introgressed and non-introgressed individuals, including putative positive selection found in one codon, although this did not show introgression. While our evidence for rejecting demographic hypotheses is arguably stronger than that for rejecting adaptation, we find no definitive support for either explanation. Future efforts will focus on larger-scale resequencing to decipher the underlying causes of discordant mitonuclear introgression in this system.
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Affiliation(s)
- Xiuguang Mao
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, China; Institute of Eco-Chongming (IEC), East China Normal University, Shanghai 200062, China.
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK.
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13
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Mao X, Tsagkogeorga G, Thong VD, Rossiter SJ. Resolving evolutionary relationships among six closely related taxa of the horseshoe bats (Rhinolophus) with targeted resequencing data. Mol Phylogenet Evol 2019; 139:106551. [DOI: 10.1016/j.ympev.2019.106551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/11/2019] [Accepted: 07/01/2019] [Indexed: 01/04/2023]
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14
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Larsen PA, Matocq MD. Emerging genomic applications in mammalian ecology, evolution, and conservation. J Mammal 2019. [DOI: 10.1093/jmammal/gyy184] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Peter A Larsen
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Marjorie D Matocq
- Department of Natural Resources and Environmental Science; Program in Ecology, Evolution, and Conservation Biology, University of Nevada, Reno, NV, USA
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15
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Kinoshita G, Nunome M, Kryukov AP, Kartavtseva IV, Han SH, Yamada F, Suzuki H. Contrasting phylogeographic histories between the continent and islands of East Asia: Massive mitochondrial introgression and long-term isolation of hares (Lagomorpha: Lepus). Mol Phylogenet Evol 2019; 136:65-75. [PMID: 30951923 DOI: 10.1016/j.ympev.2019.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 03/19/2019] [Accepted: 04/01/2019] [Indexed: 01/16/2023]
Abstract
Hares of the genus Lepus are distributed worldwide, and introgressive hybridization is thought to be pervasive among species, leading to reticulate evolution and taxonomic confusion. Here, we performed phylogeographic analyses of the following species of hare across East Asia: L. timidus, L. mandshuricus, L. coreanus, and L. brachyurus collected from far-eastern Russia, South Korea, and Japan. Nucleotide sequences of one mitochondrial DNA and eight nuclear gene loci were examined, adding sequences of hares in China from databases. All nuclear DNA analyses supported the clear separation of three phylogroups: L. timidus, L. brachyurus, and the L. mandshuricus complex containing L. coreanus. On the other hand, massive mitochondrial introgression from two L. timidus lineages to the L. mandshuricus complex was suggested in continental East Asia. The northern population of the L. mandshuricus complex was mainly associated with introgression from the continental lineage of L. timidus, possibly since the last glacial period, whereas the southern population of the L. mandshuricus complex experienced introgression from another L. timidus lineage related to the Hokkaido population, possibly before the last glacial period. In contrast to continental hares, no evidence of introgression was found in L. brachyurus in the Japanese Archipelago, which showed the oldest divergence amongst East Asian hare lineages. Our findings suggest that glacial-interglacial climate changes in the circum-Japan Sea region promoted distribution shifts and introgressive hybridization among continental hare species, while the geographic structure of the region contributed to long-term isolation of hares on the islands, preventing inter-species gene flow.
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Affiliation(s)
- Gohta Kinoshita
- Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan; Laboratory of Forest Biology Division of Forest & Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake, Sakyoku, Kyoto 606-8502, Japan.
| | - Mitsuo Nunome
- Laboratory of Animal Genetics, Graduate School of Bioagricultural Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Alexey P Kryukov
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - Irina V Kartavtseva
- Laboratory of Evolutionary Zoology and Genetics, Federal Scientific Center of the East Asia Terrestrial Biodiversity, Far East Branch Russian Academy of Sciences, Vladivostok 690022, Russia
| | - San-Hoon Han
- Inter-Korea Wildlife Institute, Namtong-dong, Gumi-si, Kyeongsang-Bukdo 39301, Republic of Korea
| | - Fumio Yamada
- Laboratory of Wildlife Ecology, Forestry and Forest Products Research Institute (FFPRI), Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Hitoshi Suzuki
- Course in Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, N10W5, Kita-ku, Sapporo 060-0810, Japan
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16
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Anderson BM, Thiele KR, Grierson PF, Krauss SL, Nevill PG, Small ID, Zhong X, Barrett MD. Recent range expansion in Australian hummock grasses ( Triodia) inferred using genotyping-by-sequencing. AOB PLANTS 2019; 11:plz017. [PMID: 31037212 PMCID: PMC6481909 DOI: 10.1093/aobpla/plz017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 03/20/2019] [Indexed: 05/30/2023]
Abstract
The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.
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Affiliation(s)
- Benjamin M Anderson
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| | - Kevin R Thiele
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Pauline F Grierson
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Siegfried L Krauss
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
| | - Paul G Nevill
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Australian Research Council Centre for Mine Site Restoration, Curtin University, Bentley, Western Australia, Australia
| | - Ian D Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Xiao Zhong
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, Australia
| | - Matthew D Barrett
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia, Australia
- Kings Park and Botanic Garden, Botanic Gardens and Parks Authority, Kings Park, Western Australia, Australia
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17
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Zinner D, Chuma IS, Knauf S, Roos C. Inverted intergeneric introgression between critically endangered kipunjis and yellow baboons in two disjunct populations. Biol Lett 2018; 14:rsbl.2017.0729. [PMID: 29343565 DOI: 10.1098/rsbl.2017.0729] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/20/2017] [Indexed: 11/12/2022] Open
Abstract
Intergeneric hybridization and introgression was reported from one of two populations of the recently discovered kipunji (Rungwecebus kipunji), a critically endangered African monkey species of southern Tanzania. Kipunjis of the introgressed population (from Mount Rungwe) carry a mitochondrial DNA (mtDNA) haplotype closely related to those of parapatric yellow baboons (Papio cynocephalus), whereas the second kipunji population, in the Udzungwa Mountains, carries the original kipunji mtDNA haplotypes, which diverged from the baboon lineage about 3 million years ago. Interestingly, in our study of yellow baboons in Tanzania, we found that baboons from the southeastern boundary of the Udzungwa Mountains carry mtDNA haplotypes closely related to the original kipunji haplotype, whereas baboons from the northern boundary, as expected, carry mtDNA haplotypes of the northern yellow baboon clade. These findings provide evidence for a case of inverted intergeneric admixture in primates: (i) a baboon mtDNA haplotype introgressed the Mount Rungwe kipunji population by mitochondrial capture and (ii) an Udzungwa Mountains kipunji mtDNA haplotype introgressed a small subpopulation of yellow baboons by either mitochondrial capture or nuclear swamping. The baboon-kipunji example therefore constitutes an interesting system for further studies of the effects of genetic admixture on fitness and speciation.
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Affiliation(s)
- Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Göttingen, Germany
| | - Idrissa S Chuma
- Work Group Neglected Tropical Diseases, German Primate Center, Göttingen, Germany.,Primate Genetics Laboratory, German Primate Center, Göttingen, Germany.,Sokoine University of Agriculture, Morogoro, Tanzania
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, German Primate Center, Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
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18
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Pöschel J, Heltai B, Graciá E, Quintana MF, Velo-Antón G, Arribas O, Valdeón A, Wink M, Fritz U, Vamberger M. Complex hybridization patterns in European pond turtles (Emys orbicularis) in the Pyrenean Region. Sci Rep 2018; 8:15925. [PMID: 30374044 PMCID: PMC6206128 DOI: 10.1038/s41598-018-34178-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 10/06/2018] [Indexed: 11/29/2022] Open
Abstract
Hybrid zones are natural laboratories allowing insights in genetic processes like lineage diversification, speciation and introgression. Using large sampling, 15 microsatellite loci and a mitochondrial marker, we examined the Pyrenean contact zone of three pond turtle taxa (Emys orbicularis orbicularis, E. o. galloitalica, E. o. occidentalis). The Pyrenees are a biogeographically important region separating many lineages endemic to the Iberian Peninsula from their Western European counterparts. We discovered limited admixture, reflecting a complex biogeographic scenario. Simulations using Approximate Bayesian Computing supported that E. o. orbicularis invaded the Iberian Peninsula in the Holocene, circumventing the Pyrenees along the Mediterranean coast, and hybridized in the northern peninsula with the local coastal subspecies galloitalica, and to a lesser extent, with occidentalis. While E. o. occidentalis, and in particular E. o. orbicularis, expanded their ranges considerably during Holocene warming, E. o. galloitalica remained largely confined to its former Iberian refuge. Admixture among the three taxa is surprisingly low, and a future taxonomic investigation that includes the unstudied subspecies of E. orbicularis from North Africa, Eastern Europe and Asia has to determine whether their current status properly reflects their evolutionary divergence or whether certain taxa should be regarded as full species.
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Affiliation(s)
- Julia Pöschel
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Botond Heltai
- Agricultural Biotechnology Institute - National Agricultural Research and Innovation Center, Szent-Györgyi Albert u. 4, 2100, Gödöllő, Hungary
| | - Eva Graciá
- Ecology Area, Department of Applied Biology, Miguel Hernández University, Av. de la Universidad, Torreblanca, 03202, Elche, Spain
| | - Marc Franch Quintana
- CICGE - Centro de Investigação em Ciências Geo-Espaciais, Universidade de Porto, Observatório Astronómico Prof. Manuel de Barros Alameda do Monte da Virgem, 4430-146, Vila Nova de Gaia, Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão, R. Padre Armando Quintas 7, 4485-661, Vairão, Portugal
| | | | - Aitor Valdeón
- Department of Geography and Regional Planning, University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain.,Aranzadi Society of Sciences, Zorroagagaina, 11, 20014, Donostia-San Sebastian, Spain
| | - Michael Wink
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, 69120, Heidelberg, Germany
| | - Uwe Fritz
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany
| | - Melita Vamberger
- Museum of Zoology (Museum für Tierkunde), Senckenberg Dresden, A. B. Meyer Building, 01109, Dresden, Germany.
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19
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Bono JM, Pigage HK, Wettstein PJ, Prosser SA, Pigage JC. Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group. BMC Evol Biol 2018; 18:139. [PMID: 30208839 PMCID: PMC6134581 DOI: 10.1186/s12862-018-1248-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/20/2018] [Indexed: 01/09/2023] Open
Abstract
Background Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert’s squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these studies identified potential areas of secondary contact between divergent lineages, the possibility for introgression has not been tested. Results We used RAD-seq to unravel the complex evolutionary history of the Abert’s squirrel species group. Although some of our findings reinforce inferences based on mitochondrial data, we also find significant areas of discordance. Discordant signals generally arise from previously undetected introgression between divergent populations that differentially affected variation at mitochondrial and nuclear loci. Most notably, our results support earlier claims (disputed by mitochondrial data) that S. aberti kaibabensis, found only on the north rim of the Grand Canyon, is highly divergent from other populations. However, we also detected introgression of S. aberti kaibabensis DNA into other S. aberti populations, which likely accounts for the previously inferred close genetic relationship between this population and those south of the Grand Canyon. Conclusions Overall, the evolutionary history of Abert’s squirrels appears to be shaped largely by divergence during periods of habitat isolation. However, we also found evidence for interbreeding during periods of secondary contact resulting in introgression, with variable effects on mitochondrial and nuclear markers. Our results support the emerging view that populations often diversify under scenarios involving both divergence in isolation and gene flow during secondary contact, and highlight the value of genome-wide datasets for resolving such complex evolutionary histories. Electronic supplementary material The online version of this article (10.1186/s12862-018-1248-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jeremy M Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA.
| | - Helen K Pigage
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Peter J Wettstein
- Department of Surgery, Mayo Clinic, 200 First St. SW, Rochester, MN, 55905, USA
| | - Stephanie A Prosser
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
| | - Jon C Pigage
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, 80918, USA
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20
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Seixas FA, Boursot P, Melo-Ferreira J. The genomic impact of historical hybridization with massive mitochondrial DNA introgression. Genome Biol 2018; 19:91. [PMID: 30056805 PMCID: PMC6065068 DOI: 10.1186/s13059-018-1471-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 06/25/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, Lepus granatensis, displays in its northern range extensive mitochondrial DNA introgression from L. timidus, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA. RESULTS Although the average nuclear and mtDNA introgression patterns contrast strongly, they fit a single demographic model of post-glacial invasive replacement of timidus by granatensis. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X chromosome and in low recombining regions. CONCLUSIONS General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.
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Affiliation(s)
- Fernando A Seixas
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France
| | - Pierre Boursot
- Institut des Sciences de l'Évolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095, Montpellier, France.
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal.
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua Campo Alegre s/n, 4169-007, Porto, Portugal.
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21
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Levänen R, Kunnasranta M, Pohjoismäki J. Mitochondrial DNA Introgression at the Northern Edge of the Brown Hare (Lepus europaeus) Range. ANN ZOOL FENN 2018. [DOI: 10.5735/086.055.0103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Riikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Natural Resources Institute Finland (Luke), Yliopistokatu 6, FI-80100, Joensuu, Finland
| | - Jaakko Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
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22
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Levänen R, Thulin CG, Spong G, Pohjoismäki JLO. Widespread introgression of mountain hare genes into Fennoscandian brown hare populations. PLoS One 2018; 13:e0191790. [PMID: 29370301 PMCID: PMC5784980 DOI: 10.1371/journal.pone.0191790] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/11/2018] [Indexed: 11/29/2022] Open
Abstract
In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.
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Affiliation(s)
- Riikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Carl-Gustaf Thulin
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Spong
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
- * E-mail:
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23
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Marques JP, Ferreira MS, Farelo L, Callahan CM, Hackländer K, Jenny H, Montgomery WI, Reid N, Good JM, Alves PC, Melo-Ferreira J. Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares. Sci Data 2017; 4:170178. [PMID: 29206218 PMCID: PMC5716010 DOI: 10.1038/sdata.2017.178] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 10/13/2017] [Indexed: 11/14/2022] Open
Abstract
We report the first mountain hare (Lepus timidus) transcriptome, produced by de novo assembly of RNA-sequencing reads. Data were obtained from eight specimens sampled in two localities, Alps and Ireland. The mountain hare tends to be replaced by the invading European hare (Lepus europaeus) in their numerous contact zones where the species hybridize, which affects their gene pool to a yet unquantified degree. We characterize and annotate the mountain hare transcriptome, detect polymorphism in the two analysed populations and use previously published data on the European hare (three specimens, representing the European lineage of the species) to identify 4 672 putative diagnostic sites between the species. A subset of 85 random independent SNPs was successfully validated using PCR and Sanger sequencing. These valuable genomic resources can be used to design tools to assess population status and monitor hybridization between species.
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Affiliation(s)
- João P. Marques
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências do Porto, Porto 4169-007, Portugal
| | - Mafalda S. Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências do Porto, Porto 4169-007, Portugal
| | - Liliana Farelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal
| | - Colin M. Callahan
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Klaus Hackländer
- Institute of Wildlife Biology and Game Management, BOKU-University of Natural Resources and Life Sciences, Vienna 1180, Austria
| | - Hannes Jenny
- Amt für Jagd und Fischerei Graubünden, Chur 7001, Switzerland
| | - W. Ian Montgomery
- Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5BN, UK
- School of Biological Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Neil Reid
- Institute of Global Food Security, School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5BN, UK
- School of Biological Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, 32 Campus Drive, Missoula, MT 59812, USA
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências do Porto, Porto 4169-007, Portugal
| | - José Melo-Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal
- Departamento de Biologia, Faculdade de Ciências do Porto, Porto 4169-007, Portugal
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