1
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Berdan EL, Aubier TG, Cozzolino S, Faria R, Feder JL, Giménez MD, Joron M, Searle JB, Mérot C. Structural Variants and Speciation: Multiple Processes at Play. Cold Spring Harb Perspect Biol 2024; 16:a041446. [PMID: 38052499 PMCID: PMC10910405 DOI: 10.1101/cshperspect.a041446] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Research on the genomic architecture of speciation has increasingly revealed the importance of structural variants (SVs) that affect the presence, abundance, position, and/or direction of a nucleotide sequence. SVs include large chromosomal rearrangements such as fusion/fissions and inversions and translocations, as well as smaller variants such as duplications, insertions, and deletions (CNVs). Although we have ample evidence that SVs play a key role in speciation, the underlying mechanisms differ depending on the type and length of the SV, as well as the ecological, demographic, and historical context. We review predictions and empirical evidence for classic processes such as underdominance due to meiotic aberrations and the coupling effect of recombination suppression before exploring how recent sequencing methodologies illuminate the prevalence and diversity of SVs. We discuss specific properties of SVs and their impact throughout the genome, highlighting that multiple processes are at play, and possibly interacting, in the relationship between SVs and speciation.
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Affiliation(s)
- Emma L Berdan
- Department of Marine Sciences, Gothenburg University, Gothenburg 40530, Sweden
- Bioinformatics Core, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Thomas G Aubier
- Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, UMR 5174, CNRS/IRD, 31077 Toulouse, France
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Complesso Universitario di Monte S. Angelo, 80126 Napoli, Italia
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Laboratório Associado, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, 4485-661 Vairão, Portugal
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Claire Mérot
- CNRS, UMR 6553 Ecobio, OSUR, Université de Rennes, 35000 Rennes, France
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Marková S, Lanier HC, Escalante MA, da Cruz MOR, Horníková M, Konczal M, Weider LJ, Searle JB, Kotlík P. Local adaptation and future climate vulnerability in a wild rodent. Nat Commun 2023; 14:7840. [PMID: 38030627 PMCID: PMC10686993 DOI: 10.1038/s41467-023-43383-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/08/2023] [Indexed: 12/01/2023] Open
Abstract
As climate change continues, species pushed outside their physiological tolerance limits must adapt or face extinction. When change is rapid, adaptation will largely harness ancestral variation, making the availability and characteristics of that variation of critical importance. Here, we used whole-genome sequencing and genetic-environment association analyses to identify adaptive variation and its significance in the context of future climates in a small Palearctic mammal, the bank vole (Clethrionomys glareolus). We found that peripheral populations of bank vole in Britain are already at the extreme bounds of potential genetic adaptation and may require an influx of adaptive variation in order to respond. Analyses of adaptive loci suggest regional differences in climate variables select for variants that influence patterns of population adaptive resilience, including genes associated with antioxidant defense, and support a pattern of thermal/hypoxic cross-adaptation. Our findings indicate that understanding potential shifts in genomic composition in response to climate change may be key to predicting species' fate under future climates.
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Affiliation(s)
- Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Hayley C Lanier
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Marcos O R da Cruz
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
- Sam Noble Museum, University of Oklahoma, 2401 Chautauqua Ave, Norman, OK, 73072, USA
| | - Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic
| | - Mateusz Konczal
- Faculty of Biology, Evolutionary Biology Group, Adam Mickiewicz University, Poznań, Poland
| | - Lawrence J Weider
- School of Biological Sciences, University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21, Liběchov, Czech Republic.
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3
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Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution. Cold Spring Harb Perspect Biol 2023; 15:a041447. [PMID: 37604585 PMCID: PMC10626258 DOI: 10.1101/cshperspect.a041447] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics. While an important role for CRs in speciation has been suggested, evidence primarily stems from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at a macroevolutionary level has been supported by associations between species diversity and rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of CRs and taxa. Now that more broadly applicable and precise CR detection approaches have become available, we address the challenges in filling some of the conceptual and empirical gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.
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Affiliation(s)
- Kay Lucek
- Biodiversity Genomics Laboratory, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - Mabel D Giménez
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Genética Humana de Misiones (IGeHM), Parque de la Salud de la Provincia de Misiones "Dr. Ramón Madariaga," N3300KAZ Posadas, Misiones, Argentina
- Facultad de Ciencias Exactas Químicas y Naturales, Universidad Nacional de Misiones, N3300LQH Posadas, Misiones, Argentina
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, Université de Montpellier, CNRS, EPHE, IRD, 34293 Montpellier, France
| | - Marina Rafajlović
- Department of Marine Sciences, University of Gothenburg, 405 30 Gothenburg, Sweden
- Centre for Marine Evolutionary Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York 14853, USA
| | - Nora Walden
- Centre for Organismal Studies, University of Heidelberg, 69117 Heidelberg, Germany
| | - Anja Marie Westram
- Institute of Science and Technology Austria (ISTA), 3400 Klosterneuburg, Austria
- Faculty of Biosciences and Aquaculture, Nord University, 8026 Bodø, Norway
| | - Rui Faria
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado;
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal
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4
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Thomas GWC, Hughes JJ, Kumon T, Berv JS, Nordgren CE, Lampson M, Levine M, Searle JB, Good JM. The genomic landscape, causes, and consequences of extensive phylogenomic discordance in Old World mice and rats. bioRxiv 2023:2023.08.28.555178. [PMID: 37693498 PMCID: PMC10491188 DOI: 10.1101/2023.08.28.555178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
A species tree is a central concept in evolutionary biology whereby a single branching phylogeny reflects relationships among species. However, the phylogenies of different genomic regions often differ from the species tree. Although tree discordance is often widespread in phylogenomic studies, we still lack a clear understanding of how variation in phylogenetic patterns is shaped by genome biology or the extent to which discordance may compromise comparative studies. We characterized patterns of phylogenomic discordance across the murine rodents (Old World mice and rats) - a large and ecologically diverse group that gave rise to the mouse and rat model systems. Combining new linked-read genome assemblies for seven murine species with eleven published rodent genomes, we first used ultra-conserved elements (UCEs) to infer a robust species tree. We then used whole genomes to examine finer-scale patterns of discordance and found that phylogenies built from proximate chromosomal regions had similar phylogenies. However, there was no relationship between tree similarity and local recombination rates in house mice, suggesting that genetic linkage influences phylogenetic patterns over deeper timescales. This signal may be independent of contemporary recombination landscapes. We also detected a strong influence of linked selection whereby purifying selection at UCEs led to less discordance, while genes experiencing positive selection showed more discordant and variable phylogenetic signals. Finally, we show that assuming a single species tree can result in high error rates when testing for positive selection under different models. Collectively, our results highlight the complex relationship between phylogenetic inference and genome biology and underscore how failure to account for this complexity can mislead comparative genomic studies.
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Affiliation(s)
- Gregg W. C. Thomas
- Division of Biological Sciences, University of Montana, Missoula, MT, 59801
- Informatics Group, Harvard University, Cambridge, MA, 02138
| | - Jonathan J. Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, 92521
| | - Tomohiro Kumon
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Jacob S. Berv
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109
| | - C. Erik Nordgren
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Michael Lampson
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Mia Levine
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853
| | - Jeffrey M. Good
- Division of Biological Sciences, University of Montana, Missoula, MT, 59801
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5
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Sless TJL, Danforth BN, Searle JB. Evolutionary Origins and Patterns of Diversification in Animal Brood Parasitism. Am Nat 2023; 202:107-121. [PMID: 37531277 DOI: 10.1086/724839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
AbstractBrood parasitism involves the exploitation of host parental care rather than the extraction of resources directly from hosts. We identify defining characteristics of this strategy and consider its position along continua with adjacent behaviors but focus on canonical brood parasites, where parasitism is obligate and hosts are noneusocial (thereby distinguishing from social parasitism). A systematic literature survey revealed 59 independently derived brood parasitic lineages with most origins (49) in insects, particularly among bees and wasps, and other origins in birds (seven) and fish (three). Insects account for more than 98% of brood parasitic species, with much of that diversity reflecting ancient (≥100-million-year-old) brood parasitic lineages. Brood parasites usually, but not always, evolve from forms that show parental care. In insects, brood parasitism often first evolves through exploitation of a closely related species, following Emery's rule, but this is less typical in birds, which we discuss. We conducted lineage-level comparisons between brood parasitic clades and their sister groups, finding mixed results but an overall neutral to negative effect of brood parasitism on species richness and diversification. Our review of brood parasites reveals many unanswered questions requiring new research, including further modeling of the coevolutionary dynamics of brood parasites and their hosts.
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6
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Browett SS, Synnott R, O'Meara DB, Antwis RE, Browett SS, Bown KJ, Wangensteen OS, Dawson DA, Searle JB, Yearsley JM, McDevitt AD. Resource competition drives an invasion-replacement event among shrew species on an island. J Anim Ecol 2023; 92:698-709. [PMID: 36617677 DOI: 10.1111/1365-2656.13855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/17/2022] [Indexed: 01/10/2023]
Abstract
Invasive mammals are responsible for the majority of native species extinctions on islands. While most of these extinction events will be due to novel interactions between species (e.g. exotic predators and naive prey), it is more unusual to find incidences where a newly invasive species causes the decline/extinction of a native species on an island when they normally coexist elsewhere in their overlapping mainland ranges. We investigated if resource competition between two insectivorous small mammals was playing a significant role in the rapid replacement of the native pygmy shrew Sorex minutus in the presence of the recently invading greater white-toothed shrew Crocidura russula on the island of Ireland. We used DNA metabarcoding of gut contents from >300 individuals of both species to determine each species' diet and measured the body size (weight and length) during different stages of the invasion in Ireland (before, during and after the species come into contact with one another) and on a French island where both species have long coexisted (acting as a natural 'control' site). Dietary composition, niche width and overlap and body size were compared in these different stages. The body size of the invasive C. russula and composition of its diet changes between when it first invades an area and after it becomes established. During the initial stages of the invasion, individual shrews are larger and consume larger sized invertebrate prey species. During later stages of the invasion, C. russula switches to consuming smaller prey taxa that are more essential for the native species. As a result, the level of interspecific dietary overlap increases from between 11% and 14% when they first come into contact with each other to between 39% and 46% after the invasion. Here we show that an invasive species can quickly alter its dietary niche in a new environment, ultimately causing the replacement of a native species. In addition, the invasive shrew could also be potentially exhausting local resources of larger invertebrate species. These subsequent changes in terrestrial invertebrate communities could have severe impacts further downstream on ecosystem functioning and services.
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Affiliation(s)
- Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland.,NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Rebecca Synnott
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Denise B O'Meara
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Stephen S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Kevin J Bown
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway
| | - Deborah A Dawson
- NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Jeremy B Searle
- Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, New York, USA
| | - Jon M Yearsley
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,Department of Natural Sciences and the Environment, School of Science and Computing, Atlantic Technological University, Galway, Ireland
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7
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Colunga-Salas P, Marines-Macías T, Hernández-Canchola G, Barbosa S, Ramírez C, Searle JB, León-Paniagua L. Population genomics reveals differences in genetic structure between two endemic arboreal rodent species in threatened cloud forest habitat. MAMMAL RES 2023. [DOI: 10.1007/s13364-022-00667-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Abstract
Genomic tools are now commonly used to assess the genetic diversity and genetic structure of species and populations, and they provide the ability to describe and address the negative effects of population declines and fragmentation. However, such studies are lacking for arboreal mammals despite their contribution to various ecosystem services, especially in uncommon and critically endangered ecosystems such as cloud forests. The aim of this work was to evaluate and compare the genetic diversity and population structure of two endemic arboreal mice from Mexican cloud forests that are associated with areas with different levels of impacts from human activities. We performed genotyping-by-sequencing in 47 Habromys schmidlyi and 17 Reithrodontomys wagneri individuals to evaluate genetic diversity and differentiation. In both species, the genetic diversity was low compared to other cricetid species, and we observed different population structure patterns, potentially linked to the different ecological associations. We detected two genetic groups in H. schmidlyi, that is a territorial species present in areas of low incline, while a single genetic group was found in R. wagneri, which forms family groups in areas with steep slopes. Overall, these results highlight how species’ genetic diversity can be differentially impacted depending on differential ecological associations within the same ecosystem. This information is essential for the development of the adequate conservation and management of these species.
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8
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Raspopova AA, Lebedev VS, Searle JB, Bannikova AA. Discordant phylogenies in the
Sorex araneus
group (Soricidae, Mammalia): Footprints of past reticulations? ZOOL SCR 2023. [DOI: 10.1111/zsc.12590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
| | | | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
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9
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Giménez MD, Hughes JJ, Scascitelli M, Gabriel SI, Förster DW, Panithanarak T, Hauffe HC, Searle JB. Tracking Chromosomal Origins in the Northern Italy System of Metacentric Races of the House Mouse. Cytogenet Genome Res 2022; 162:214-230. [DOI: 10.1159/000527106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/15/2022] [Indexed: 12/03/2022] Open
Abstract
The Western European house mouse is chromosomally diverse, with diploid karyotypes ranging from the standard 40 telocentric chromosomes down to 22 chromosomes. Karyotypes are modified through Robertsonian (Rb) fusion of 2 telocentrics into a single metacentric, occurring repeatedly with fixation, and whole-arm reciprocal translocations (WARTs) generating additional novel karyotypes. Over 100 metacentric populations (chromosomal races) have been identified, geographically clustered into “systems.” Chromosomal races within systems often hybridise, and new races may emerge through this hybridisation (“zonal raciation”). We wished to determine the degree to which chromosomal races in a system have evolved independently or share common ancestry. Recombination between chromosomes from hybridising chromosomal races can erase the signals associated with a particular metacentric of interest, making inferences challenging. However, reduced recombination near the centromeres of chromosomal race-specific metacentrics makes centromere-adjacent markers ideal for solving this problem. For the Northern Italy System (NIS), we used microsatellite markers near the centromere to test previous hypotheses about evolutionary relationships of 5 chromosomal races. We chose markers from chromosomes 1, 3, 4, and 6, all of which comprise one arm of a metacentric in at least 2 of these NIS metacentric populations. We used estimates of F<sub>ST</sub> and R<sub>ST</sub>, as well as principal components analyses and neighbour-joining phylogenetic analyses, to infer evolutionary relationships between these 5 chromosomal races and neighbouring mice with the standard karyotype. We showed that the metacentric populations form a single grouping distinct from the standard populations, consistent with their common origin and consistent with a parsimonious sequence of chromosomal rearrangements to explain the relationship of the chromosomal races. That origin and evolution of the chromosomal races in the system would have involved Rb fusions, explaining the occurrence of chromosomal races with diploid numbers as low as 22. However, WARTs and zonal raciation have also been inferred, and the rare occurrence of chromosome 1 in different metacentrics in closely related chromosomal races is almost certainly explained by a WART. Our results with centromeric microsatellites are consistent with the above scenarios, illustrating, once again, the value of markers in the centromeric region to test evolutionary hypotheses in house mouse chromosomal systems.
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10
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Escalante MA, Marková S, Searle JB, Kotlík P. Genic distribution modelling predicts adaptation of the bank vole to climate change. Commun Biol 2022; 5:981. [PMID: 36114276 PMCID: PMC9481625 DOI: 10.1038/s42003-022-03935-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022] Open
Abstract
The most likely pathway for many species to survive future climate change is by pre-existing trait variation providing a fitness advantage under the new climate. Here we evaluate the potential role of haemoglobin (Hb) variation in bank voles under future climate change. We model gene-climate relationships for two functionally distinct Hb types, HbS and HbF, which have a north-south distribution in Britain presenting an unusually tractable system linking genetic variation in physiology to geographical and temporal variation in climate. Projections to future climatic conditions suggest a change in relative climatic suitability that would result in HbS being displaced by HbF in northern Britain. This would facilitate local adaptation to future climate—without Hb displacement, populations in northern Britain would likely be suboptimally adapted because their Hb would not match local climatic conditions. Our study shows how pre-existing physiological differences can influence the adaptive capacity of species to climate change. Haemoglobin variation in British bank voles combined with climate models predict future regional allelic replacement reflecting capacity for adaptation to climate change.
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11
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Morgan AP, Hughes JJ, Didion JP, Jolley WJ, Campbell KJ, Threadgill DW, Bonhomme F, Searle JB, de Villena FPM. Population structure and inbreeding in wild house mice (Mus musculus) at different geographic scales. Heredity (Edinb) 2022; 129:183-194. [PMID: 35764696 PMCID: PMC9411160 DOI: 10.1038/s41437-022-00551-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 11/08/2022] Open
Abstract
House mice (Mus musculus) have spread globally as a result of their commensal relationship with humans. In the form of laboratory strains, both inbred and outbred, they are also among the most widely used model organisms in biomedical research. Although the general outlines of house mouse dispersal and population structure are well known, details have been obscured by either limited sample size or small numbers of markers. Here we examine ancestry, population structure, and inbreeding using SNP microarray genotypes in a cohort of 814 wild mice spanning five continents and all major subspecies of Mus, with a focus on M. m. domesticus. We find that the major axis of genetic variation in M. m. domesticus is a south-to-north gradient within Europe and the Mediterranean. The dominant ancestry component in North America, Australia, New Zealand, and various small offshore islands are of northern European origin. Next we show that inbreeding is surprisingly pervasive and highly variable, even between nearby populations. By inspecting the length distribution of homozygous segments in individual genomes, we find that inbreeding in commensal populations is mostly due to consanguinity. Our results offer new insight into the natural history of an important model organism for medicine and evolutionary biology.
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Affiliation(s)
- Andrew P Morgan
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA.
- Department of Medicine, Duke University Hospital, Durham, NC, USA.
| | - Jonathan J Hughes
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - John P Didion
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Independent Scientist, San Diego, CA, USA
| | | | | | - David W Threadgill
- Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA
| | - Francois Bonhomme
- Institut des Sciences de l'Évolution Montpellier, Université de Montpellier, Montpellier, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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12
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Demirtaş S, Budak M, Korkmaz EM, Searle JB, Bilton DT, Gündüz İ. The complete mitochondrial genome of Talpa martinorum (Mammalia: Talpidae), a mole species endemic to Thrace: genome content and phylogenetic considerations. Genetica 2022; 150:317-325. [PMID: 36029420 DOI: 10.1007/s10709-022-00162-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 08/04/2022] [Indexed: 11/04/2022]
Abstract
The complete mitogenome sequence of Talpa martinorum, a recently described Balkan endemic mole, was assembled from next generation sequence data. The mitogenome is similar to that of the three other Talpa species sequenced to date, being 16,835 bp in length, and containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, an origin of L-strand replication, and a control region or D-loop. Compared to other Talpa mitogenomes sequenced to date, that of T. martinorum differs in the length of D-loop and stop codon usage. TAG and T-- are the stop codons for the ND1 and ATP8 genes, respectively, in T. martinorum, whilst TAA acts as a stop codon for both ND1 and ATP8 in the other three Talpa species sequenced. Phylogeny reconstructions based on Maximum Likelihood and Bayesian inference analyses yielded phylogenies with similar topologies, demonstrating that T. martinorum nests within the western lineage of the genus, being closely related to T. aquitania and T. occidentalis.
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Affiliation(s)
- Sadık Demirtaş
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Mahir Budak
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Ertan M Korkmaz
- Department of Molecular Biology and Genetics, Faculty of Science, Sivas Cumhuriyet University, Sivas, Turkey
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-2701, USA
| | - David T Bilton
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, Devon, PL4 8AA, UK.,Department of Zoology, University of Johannesburg, Auckland Park, PO Box 524, Johannesburg, 2006, South Africa
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey.
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13
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Sless TJL, Searle JB, Danforth BN. Genome of the bee Holcopasites calliopsidis—a species showing the common apid trait of brood parasitism. G3 Genes|Genomes|Genetics 2022; 12:6619165. [PMID: 35762966 PMCID: PMC9339306 DOI: 10.1093/g3journal/jkac160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 05/31/2022] [Indexed: 11/22/2022]
Abstract
Brood parasites represent a substantial but often poorly studied fraction of the wider diversity of bees. Brood parasitic bees complete their life cycles by infiltrating the nests of solitary host bees thereby enabling their offspring to exploit the food provisions intended for the host’s offspring. Here, we present the draft assembly of the bee Holcopasites calliopsidis, the first brood parasitic species to be the subject of detailed genomic analysis. Consistent with previous findings on the genomic signatures of parasitism more broadly, we find that H. calliopsidis has the smallest genome currently known among bees (179 Mb). This small genome does not appear to be the result of purging of repetitive DNA, with some indications of novel repetitive elements which may show signs of recent expansion. Nor does H. calliopsidis demonstrate any apparent net loss of genic content in comparison with nonparasitic species, though many individual gene families do show significant contractions. Although the basis of the small genome size of this species remains unclear, the identification of over 12,000 putative genes—with functional annotation for nearly 10,000 of these—is an important step in investigating the genomic basis of brood parasitism and provides a valuable dataset to be compared against new genomes that remain to be sequenced.
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Affiliation(s)
- Trevor J L Sless
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, NY 14853, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University , Ithaca, NY 14853, USA
| | - Bryan N Danforth
- Department of Entomology, Cornell University , Ithaca, NY 14853, USA
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14
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Kunerth HD, Bogdanowicz SM, Searle JB, Harrison RG, Coates BS, Kozak GM, Dopman EB. Consequences of coupled barriers to gene flow for the build-up of genomic differentiation. Evolution 2022; 76:985-1002. [PMID: 35304922 DOI: 10.1111/evo.14466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 12/09/2021] [Accepted: 12/29/2021] [Indexed: 01/21/2023]
Abstract
Theory predicts that when different barriers to gene flow become coincident, their joint effects enhance reproductive isolation and genomic divergence beyond their individual effects, but empirical tests of this "coupling" hypothesis are rare. Here, we analyze patterns of gene exchange among populations of European corn borer moths that vary in the number of acting barriers, allowing for comparisons of genomic variation when barrier traits or loci are in coincident or independent states. We find that divergence is mainly restricted to barrier loci when populations differ by a single barrier, whereas the coincidence of temporal and behavioral barriers is associated with divergence of two chromosomes harboring barrier loci. Furthermore, differentiation at temporal barrier loci increases in the presence of behavioral divergence and differentiation at behavioral barrier loci increases in the presence of temporal divergence. Our results demonstrate how the joint action of coincident barrier effects leads to levels of genomic differentiation that far exceed those of single barriers acting alone, consistent with theory arguing that coupling allows indirect selection to combine with direct selection and thereby lead to a stronger overall barrier to gene flow. Thus, the state of barriers-independent or coupled-strongly influences the accumulation of genomic differentiation.
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Affiliation(s)
- Henry D Kunerth
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Steven M Bogdanowicz
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Richard G Harrison
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, 14853
| | - Brad S Coates
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, Iowa, 50011
| | - Genevieve M Kozak
- Department of Biology, University of Massachusetts Dartmouth, Dartmouth, Massachusetts, 02747, USA.,Department of Biology, Tufts University, Medford, Massachusetts, 02155
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts, 02155
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15
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Kotlík P, Marková S, Horníková M, Escalante MA, Searle JB. The Bank Vole (Clethrionomys glareolus) as a Model System for Adaptive Phylogeography in the European Theater. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.866605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The legacy of climatic changes during the Pleistocene glaciations allows inferences to be made about the patterns and processes associated with range expansion/colonization, including evolutionary adaptation. With the increasing availability of population genomic data, we have the opportunity to examine these questions in detail and in a variety of non-traditional model species. As an exemplar, here we review more than two decades of work by our group and others that illustrate the potential of a single “non-model model” mammal species - the bank vole (Clethrionomys glareolus), which is particularly well suited to illustrate the complexities that may be associated with range expansion and the power of genomics (and other datasets) to uncover them. We first summarize early phylogeographic work using mitochondrial DNA and then describe new phylogeographic insights gained from population genomic analysis of genome-wide SNP data to highlight the bank vole as one of the most compelling examples of a forest mammal, that survived in cryptic extra-Mediterranean (“northern”) glacial refugia in Europe, and as one of the species in which substantial replacement and mixing of lineages originating from different refugia occurred during end-glacial colonization. Our studies of bank vole hemoglobin structure and function, as well as our recent ecological niche modeling study examining differences among bank vole lineages, led us to develop the idea of “adaptive phylogeography.” This is what we call the study of the role of adaptive differences among populations in shaping phylogeographic patterns. Adaptive phylogeography provides a link between past population history and adaptation that can ultimately help predict the potential of future species responses to climate change. Because the bank vole is part of a community of organisms whose range has repeatedly contracted and then expanded in the past, what we learn from the bank vole will be useful for our understanding of a broad range of species.
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16
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Searle JB, de Villena FPM. The evolutionary significance of meiotic drive. Heredity (Edinb) 2022; 129:44-47. [PMID: 35468941 DOI: 10.1038/s41437-022-00534-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 01/08/2023] Open
Affiliation(s)
- Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA.
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17
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Honka J, Baini S, Searle JB, Kvist L, Aspi J. Genetic assessment reveals inbreeding, possible hybridization, and low levels of genetic structure in a declining goose population. Ecol Evol 2022; 12:e8547. [PMID: 35127046 PMCID: PMC8796947 DOI: 10.1002/ece3.8547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
The population numbers of taiga bean goose (Anser fabalis fabalis) have halved during recent decades. Since this subspecies is hunted throughout most of its range, the decline is of management concern. Knowledge of the genetic population structure and diversity is important for guiding management and conservation efforts. Genetically unique subpopulations might be hunted to extinction if not managed separately, and any inbreeding depression or lack of genetic diversity may affect the ability to adapt to changing environments and increase extinction risk. We used microsatellite and mitochondrial DNA markers to study the genetic population structure and diversity among taiga bean geese breeding within the Central flyway management unit using non-invasively collected feathers. We found some genetic structuring with the maternally inherited mitochondrial DNA between four geographic regions (ɸ ST = 0.11-0.20) but none with the nuclear microsatellite markers (all pairwise F ST-values = 0.002-0.005). These results could be explained by female natal philopatry and male-biased dispersal, which completely homogenizes the nuclear genome. Therefore, the population could be managed as a single unit. Genetic diversity was still at a moderate level (average H E = 0.69) and there were no signs of past population size reductions, although significantly positive inbreeding coefficients in all sampling sites (F IS = 0.05-0.10) and high relatedness values (r = 0.60-0.86) between some individuals could indicate inbreeding. In addition, there was evidence of either incomplete lineage sorting or introgression from the pink-footed goose (Anser brachyrhynchus). The current population is not under threat by genetic impoverishment but monitoring in the future is desirable.
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Affiliation(s)
- Johanna Honka
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Serena Baini
- Department of BiologyUniversity of Rome “Tor Vergata”RomeItaly
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Jouni Aspi
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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18
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Sless TJL, Branstetter MG, Gillung JP, Krichilsky EA, Tobin KB, Straka J, Rozen JG, Freitas FV, Martins AC, Bossert S, Searle JB, Danforth BN. Phylogenetic relationships and the evolution of host preferences in the largest clade of brood parasitic bees (Apidae: Nomadinae). Mol Phylogenet Evol 2021; 166:107326. [PMID: 34666170 DOI: 10.1016/j.ympev.2021.107326] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 10/07/2021] [Accepted: 10/12/2021] [Indexed: 11/27/2022]
Abstract
Brood parasites (also known as cleptoparasites) represent a substantial fraction of global bee diversity. Rather than constructing their own nests, these species instead invade those of host bees to lay their eggs. Larvae then hatch and consume the food provisions intended for the host's offspring. While this life history strategy has evolved numerous times across the phylogeny of bees, the oldest and most speciose parasitic clade is the subfamily Nomadinae (Apidae). However, the phylogenetic relationships among brood parasitic apids both within and outside the Nomadinae have not been fully resolved. Here, we present new findings on the phylogeny of this diverse group of brood parasites based on ultraconserved element (UCE) sequence data and extensive taxon sampling with 114 nomadine species representing all tribes. We suggest a broader definition of the subfamily Nomadinae to describe a clade that includes almost all parasitic members of the family Apidae. The tribe Melectini forms the sister group to all other Nomadinae, while the remainder of the subfamily is composed of two sister clades: a "nomadine line" representing the former Nomadinae sensu stricto, and an "ericrocidine line" that unites several mostly Neotropical lineages. We find the tribe Osirini Handlirsch to be polyphyletic, and divide it into three lineages, including the newly described Parepeolini trib. nov. In addition to our taxonomic findings, we use our phylogeny to explore the evolution of different modes of parasitism, detecting two independent transitions from closed-cell to open-cell parasitism. Finally, we examine how nomadine host-parasite associations have evolved over time. In support of Emery's rule, which suggests close relationships between hosts and parasites, we confirm that the earliest nomadines were parasites of their close free-living relatives within the family Apidae, but that over time their host range broadened to include more distantly related hosts spanning the diversity of bees. This expanded breadth of host taxa may also be associated with the transition to open-cell parasitism.
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Affiliation(s)
- Trevor J L Sless
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Michael G Branstetter
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT 84322, USA
| | - Jessica P Gillung
- Department of Natural Resource Sciences, McGill University, Montreal, QC H9X 3V9, Canada
| | - Erin A Krichilsky
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT 84322, USA; Department of Entomology, Cornell University, Ithaca, NY 14853, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Kerrigan B Tobin
- U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Pollinating Insects Research Unit, Utah State University, Logan, UT 84322, USA
| | - Jakub Straka
- Department of Zoology, Faculty of Science, Charles University, CZ-12844 Prague, Czech Republic
| | - Jerome G Rozen
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Felipe V Freitas
- Departamento de Biologia, Universidade de São Paulo, Ribeirão Preto, SP 14040-900, Brazil
| | - Aline C Martins
- Departamento de Ecologia, Universidade de Brasília, DF 70910-000, Brazil
| | - Silas Bossert
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA; Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA; Department of Entomology, Washington State University, Pullman, WA 99164-6382, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Bryan N Danforth
- Department of Entomology, Cornell University, Ithaca, NY 14853, USA
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19
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Johnson BB, Searle JB, Sparks JP. Novel Allometric Estimators Improve Estimation Accuracy of Body Surface Area, Volume, and Surface Area-to-Volume Ratio in Lungless Salamanders (Urodela: Plethodontidae). HERPETOLOGICA 2021. [DOI: 10.1655/herpetologica-d-21-00013.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Benjamin B. Johnson
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jeremy B. Searle
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Jed P. Sparks
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
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20
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Horníková M, Marková S, Lanier HC, Searle JB, Kotlík P. A dynamic history of admixture from Mediterranean and Carpathian glacial refugia drives genomic diversity in the bank vole. Ecol Evol 2021; 11:8215-8225. [PMID: 34188881 PMCID: PMC8216894 DOI: 10.1002/ece3.7652] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 04/22/2021] [Indexed: 01/26/2023] Open
Abstract
Understanding the historical contributions of differing glacial refugia is key to evaluating the roles of microevolutionary forces, such as isolation, introgression, and selection in shaping genomic diversity in present-day populations. In Europe, where both Mediterranean and extra-Mediterranean (e.g., Carpathian) refugia of the bank vole (Clethrionomys glareolus) have been identified, mtDNA indicates that extra-Mediterranean refugia were the main source of colonization across the species range, while Mediterranean peninsulas harbor isolated, endemic lineages. Here, we critically evaluate this hypothesis using previously generated genomic data (>6,000 SNPs) for over 800 voles, focusing on genomic contributions to bank voles in central Europe, a key geographic area in considering range-wide colonization. The results provide clear evidence that both extra-Mediterranean (Carpathian) and Mediterranean (Spanish, Calabrian, and Balkan) refugia contributed to the ancestry and genomic diversity of bank vole populations across Europe. Few strong barriers to dispersal and frequent admixture events in central Europe have led to a prominent mid-latitude peak in genomic diversity. Although the genomic contribution of the centrally located Carpathian refugium predominates, populations in different parts of Europe have admixed origins from Mediterranean (28%-47%) and the Carpathian (53%-72%) sources. We suggest that the admixture from Mediterranean refugia may have provisioned adaptive southern alleles to more northern populations, facilitating the end-glacial spread of the admixed populations and contributing to increased bank vole diversity in central Europe. This study adds critical details to the complex end-glacial colonization history of this well-studied organism and underscores the importance of genomic data in phylogeographic interpretation.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology Institute of Animal Physiology and Genetics of the Czech Academy of Sciences Liběchov Czech Republic
- Department of Zoology, Faculty of Science Charles University Prague Czech Republic
| | - Silvia Marková
- Laboratory of Molecular Ecology Institute of Animal Physiology and Genetics of the Czech Academy of Sciences Liběchov Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology University of Oklahoma Norman OK USA
- Sam Noble Museum University of Oklahoma Norman OK USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology Institute of Animal Physiology and Genetics of the Czech Academy of Sciences Liběchov Czech Republic
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21
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Johnson BB, Searle JB, Sparks JP. Genome size influences adaptive plasticity of water loss, but not metabolic rates, in lungless salamanders. J Exp Biol 2021; 224:237790. [PMID: 33914029 DOI: 10.1242/jeb.242196] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/09/2021] [Indexed: 12/14/2022]
Abstract
Many expressions of phenotype, such as physiological performance, integrate multiple underlying traits to function. Linking component traits to adaptive physiology thus gives insight into mechanisms of selection acting on performance. Genome size (C-value) is a trait that influences physiology in multiple taxa by exerting a nucleotypic effect, constraining cell size and cellular physiology such that whole-organism mass-specific metabolism is reduced with increasing C-value. We tested for this mechanism of C-value function acting in lungless salamanders, plus an unexplored potential mechanism of C-value effects constraining water transport across the body surface to influence cutaneous water loss rates. We found no evidence for a nucleotypic effect on metabolic rates, but we demonstrate a relationship between C-value and water loss physiology. Under warmer experimental conditions, C-value was inversely correlated with water loss and positively correlated with resistance to water loss, which demonstrated adaptive plasticity at higher temperatures. We hypothesize that this pattern results from differences in cell size constraining diffusion and evaporation of water from the skin under warm conditions when cutaneous perfusion is reduced. Testing this hypothesis may confirm a previously unappreciated adaptive role for C-value variation in this group, and reveals the possibility that genome size influences physiological exchange across transport barriers more broadly.
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Affiliation(s)
- Benjamin B Johnson
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY14853, USA
| | - Jeremy B Searle
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY14853, USA
| | - Jed P Sparks
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY14853, USA
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22
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Cucchi T, Papayianni K, Cersoy S, Aznar-Cormano L, Zazzo A, Debruyne R, Berthon R, Bălășescu A, Simmons A, Valla F, Hamilakis Y, Mavridis F, Mashkour M, Darvish J, Siahsarvi R, Biglari F, Petrie CA, Weeks L, Sardari A, Maziar S, Denys C, Orton D, Jenkins E, Zeder M, Searle JB, Larson G, Bonhomme F, Auffray JC, Vigne JD. Tracking the Near Eastern origins and European dispersal of the western house mouse. Sci Rep 2020; 10:8276. [PMID: 32427845 PMCID: PMC7237409 DOI: 10.1038/s41598-020-64939-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 04/24/2020] [Indexed: 11/13/2022] Open
Abstract
The house mouse (Mus musculus) represents the extreme of globalization of invasive mammals. However, the timing and basis of its origin and early phases of dispersal remain poorly documented. To track its synanthropisation and subsequent invasive spread during the develoment of complex human societies, we analyzed 829 Mus specimens from 43 archaeological contexts in Southwestern Asia and Southeastern Europe, between 40,000 and 3,000 cal. BP, combining geometric morphometrics numerical taxonomy, ancient mitochondrial DNA and direct radiocarbon dating. We found that large late hunter-gatherer sedentary settlements in the Levant, c. 14,500 cal. BP, promoted the commensal behaviour of the house mouse, which probably led the commensal pathway to cat domestication. House mouse invasive spread was then fostered through the emergence of agriculture throughout the Near East 12,000 years ago. Stowaway transport of house mice to Cyprus can be inferred as early as 10,800 years ago. However, the house mouse invasion of Europe did not happen until the development of proto urbanism and exchange networks - 6,500 years ago in Eastern Europe and 4000 years ago in Southern Europe - which in turn may have driven the first human mediated dispersal of cats in Europe.
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Affiliation(s)
- Thomas Cucchi
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France.
| | - Katerina Papayianni
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France
- Malcolm H. Wiener Laboratory for Archaeological Science, American School of Classical Studies, Souidias 54, 10676, Athens, Greece
| | - Sophie Cersoy
- Centre de Recherche sur la Conservation (CRC), Muséum national d'Histoire naturelle, CNRS, Ministère de la Culture, CP 21, 36 rue Geoffroy Saint-Hilaire, 75005, Paris, France
| | - Laetitia Aznar-Cormano
- Centre de recherche en Paléontologie Paris, UMR7207, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, 8 rue Buffon, 75005, Paris, France
| | - Antoine Zazzo
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France
| | - Régis Debruyne
- DGD-REVE, Muséum national d'Histoire naturelle, 17 Place du Trocadéro, bureau E205, 75016, Paris, France
| | - Rémi Berthon
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France
| | - Adrian Bălășescu
- Vasile Pârvan, Institute of Archaeology, Romanian Academy, 11 Henri Coandă Street, Bucarest, Romania
| | - Alan Simmons
- Department of Anthropology, University of Nevada, Las Vegas/Desert Research Institute, Reno, Nevada, USA
| | - François Valla
- Archéologies et Sciences de l'Antiquité (Arscan), UMR 7041 CNRS, Université de Paris Nanterre, Paris I, 92023, Nanterre, France
| | - Yannis Hamilakis
- Joukowsky Institute for Archaeology and the Ancient World, Brown University, Box 1837, 60 George Street, Providence, RI, 02912, USA
| | - Fanis Mavridis
- Ephorate of Palaeoanthropology and Speleology, Hellenic Ministry of Culture and Sports, Ardittou 34B, 11636, Athens, Greece
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France
| | - Jamshid Darvish
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Roohollah Siahsarvi
- Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Cameron A Petrie
- Department of Archaeology and Anthropology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK
| | - Lloyd Weeks
- Archaeology, School of HASS, University of New England, Armidale, NSW, 2351, Australia
| | - Alireza Sardari
- Research Institute of Cultural Heritage and Tourism (RICHT), Iranian Center for Archaeological Research (ICAR), Tehran, Iran
| | - Sepideh Maziar
- Near Eastern Archaeology, Institute für Archäologie Wissenschaften, Johann Wolfgang Goethe Universität, Frankfurt am Main, Germany
| | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité (ISYEB), UMR 7205, Muséum national d'Histoire naturelle, Sorbonne Université, Ecole Pratique des Hautes Etudes, Université des Antilles, CNRS, Paris, France
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Emma Jenkins
- Institute for the Modelling of Socio-Environmental Transitions, Bournemouth University, Talbot Campus, Poole, BH12 5BB, UK
| | - Melinda Zeder
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY, 14853-2701, USA
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, Oxford, OX1 3TG, UK
| | - François Bonhomme
- Institut des Sciences de l'Evolution (ISEM), UMR 4554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Jean-Christophe Auffray
- Institut des Sciences de l'Evolution (ISEM), UMR 4554, CNRS, IRD, EPHE, Université de Montpellier, Montpellier, France
| | - Jean-Denis Vigne
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), UMR 7209, CNRS, Muséum national d'Histoire naturelle, Paris, France
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Marková S, Horníková M, Lanier HC, Henttonen H, Searle JB, Weider LJ, Kotlík P. High genomic diversity in the bank vole at the northern apex of a range expansion: The role of multiple colonizations and end-glacial refugia. Mol Ecol 2020; 29:1730-1744. [PMID: 32248595 DOI: 10.1111/mec.15427] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/10/2020] [Accepted: 03/25/2020] [Indexed: 01/08/2023]
Abstract
The history of repeated northern glacial cycling and southern climatic stability has long dominated explanations for how genetic diversity is distributed within temperate species in Eurasia and North America. However, growing evidence indicates the importance of cryptic refugia for northern colonization dynamics. An important geographic region to assess this is Fennoscandia, where recolonization at the end of the last glaciation was restricted to specific routes and temporal windows. We used genomic data to analyse genetic diversity and colonization history of the bank vole (Myodes glareolus) throughout Europe (>800 samples) with Fennoscandia as the northern apex. We inferred that bank voles colonized Fennoscandia multiple times by two different routes; with three separate colonizations via a southern land-bridge route deriving from a "Carpathian" glacial refugium and one via a north-eastern route from an "Eastern" glacial refugium near the Ural Mountains. Clustering of genome-wide SNPs revealed high diversity in Fennoscandia, with eight genomic clusters: three of Carpathian origin and five Eastern. Time estimates revealed that the first of the Carpathian colonizations occurred before the Younger Dryas (YD), meaning that the first colonists survived the YD in Fennoscandia. Results also indicated that introgression between bank and northern red-backed voles (Myodes rutilus) took place in Fennoscandia just after end-glacial colonization. Therefore, multiple colonizations from the same and different cryptic refugia, temporal and spatial separations and interspecific introgression have shaped bank vole genetic variability in Fennoscandia. Together, these processes drive high genetic diversity at the apex of the northern expansion in this emerging model species.
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Affiliation(s)
- Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.,Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA.,Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | | | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Lawrence J Weider
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
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24
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Vega R, McDevitt AD, Stojak J, Mishta A, Wójcik JM, Kryštufek B, Searle JB. Phylogeographical structure of the pygmy shrew: revisiting the roles of southern and northern refugia in Europe. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz209] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractSouthern and northern glacial refugia are considered paradigms that explain the complex phylogeographical patterns and processes of European biota. Here, we provide a revisited statistical phylogeographical analysis of the pygmy shrew Sorex minutus Linnaeus, 1766 (Eulipotyphla, Soricidae), examining its genetic diversity, genetic differentiation and demographic history in the Mediterranean peninsulas and in Western and Central Europe. The results showed support for genetically distinct and diverse phylogeographical groups consistent with southern and northern glacial refugia, as expected from previous studies. We also identified geographical barriers concordant with glaciated mountain ranges during the Last Glacial Maximum (LGM), early diversification events dated between the Late Pleistocene and Early Holocene for the main phylogeographical groups, and recent (post-LGM) patterns of demographic expansions. This study is the most comprehensive investigation of this species to date, and the results have implications for the conservation of intraspecific diversity and the preservation of the evolutionary potential of S. minutus.
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Affiliation(s)
- Rodrigo Vega
- Ecology Research Group, Section of Natural and Applied Sciences, School of Human and Life Sciences, Canterbury Christ Church University, Becket, Canterbury, Kent, UK
| | - Allan D McDevitt
- Ecosystems and Environment Research Centre, School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Alina Mishta
- Schmalhausen Institute of Zoology, National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Jan M Wójcik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Boris Kryštufek
- Slovenian Museum of Natural History, Prešernova, Ljubljana, Slovenia
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
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25
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Vara C, Capilla L, Ferretti L, Ledda A, Sánchez-Guillén RA, Gabriel SI, Albert-Lizandra G, Florit-Sabater B, Bello-Rodríguez J, Ventura J, Searle JB, Mathias ML, Ruiz-Herrera A. PRDM9 Diversity at Fine Geographical Scale Reveals Contrasting Evolutionary Patterns and Functional Constraints in Natural Populations of House Mice. Mol Biol Evol 2020; 36:1686-1700. [PMID: 31004162 PMCID: PMC6657731 DOI: 10.1093/molbev/msz091] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
One of the major challenges in evolutionary biology is the identification of the genetic basis of postzygotic reproductive isolation. Given its pivotal role in this process, here we explore the drivers that may account for the evolutionary dynamics of the PRDM9 gene between continental and island systems of chromosomal variation in house mice. Using a data set of nearly 400 wild-caught mice of Robertsonian systems, we identify the extent of PRDM9 diversity in natural house mouse populations, determine the phylogeography of PRDM9 at a local and global scale based on a new measure of pairwise genetic divergence, and analyze selective constraints. We find 57 newly described PRDM9 variants, this diversity being especially high on Madeira Island, a result that is contrary to the expectations of reduced variation for island populations. Our analysis suggest that the PRDM9 allelic variability observed in Madeira mice might be influenced by the presence of distinct chromosomal fusions resulting from a complex pattern of introgression or multiple colonization events onto the island. Importantly, we detect a significant reduction in the proportion of PRDM9 heterozygotes in Robertsonian mice, which showed a high degree of similarity in the amino acids responsible for protein–DNA binding. Our results suggest that despite the rapid evolution of PRDM9 and the variability detected in natural populations, functional constraints could facilitate the accumulation of allelic combinations that maintain recombination hotspot symmetry. We anticipate that our study will provide the basis for examining the role of different PRDM9 genetic backgrounds in reproductive isolation in natural populations.
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Affiliation(s)
- Covadonga Vara
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Laia Capilla
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luca Ferretti
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Alice Ledda
- Department for Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Rosa A Sánchez-Guillén
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Instituto de Ecología AC (INECOL), Red de Biología Evolutiva, Xalapa, Veracruz, Mexico
| | - Sofia I Gabriel
- CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Guillermo Albert-Lizandra
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Beatriu Florit-Sabater
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Judith Bello-Rodríguez
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jacint Ventura
- Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY
| | - Maria L Mathias
- CESAM - Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Aurora Ruiz-Herrera
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain.,Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Barcelona, Spain
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26
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Demırtaş S, Silsüpür M, Searle JB, Bilton D, Gündüz İ. What should we call the Levant mole? Unravelling the systematics and demography of Talpa levantis Thomas, 1906 sensu lato (Mammalia: Talpidae). Mamm Biol 2020. [DOI: 10.1007/s42991-020-00010-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Arslan Y, Demi̇rtaş S, Herman JS, Pustilnik JD, Searle JB, Gündüz İ. The Anatolian glacial refugium and human-mediated colonization: a phylogeographical study of the stone marten (Martes foina) in Turkey. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe Anatolian Peninsula, comprising most of modern Turkey, is situated at the junction of Europe, the Middle East and Asia. Together with its complex geomorphological and climatic history, this has given rise to a rich fauna and flora, which exhibits a wide range of historical biogeographical patterns. The stone marten (Martes foina) is a small carnivore that is found across the temperate Palaearctic region including Anatolia, where it is often associated with habitats modified by humans, but few genetic data exist for this species. We sequenced a 1840-bp region of the mitochondrial genome from 97 martens sampled across the peninsula and intron 7 of the nuclear β-fibrinogen gene from 53 of these. Two mitochondrial lineages were recovered, with overlapping eastern and western distributions, but there was no geographical structure for the autosomal marker. Coalescent analyses indicated that both of the lineages originated during the Last Glacial Maximum, one of them within an eastern Anatolian refugium and the other in a western Anatolian or Balkan refugium. The western lineage colonized most of Europe in the Holocene, while the eastern lineage may be endemic to Anatolia, from where it colonized the Iberian Peninsula via human translocation. The presence of at least one refugial stone marten population highlights the importance of Anatolia to the preservation of genetic variation and biodiversity.
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Affiliation(s)
- Yağmur Arslan
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Sadik Demi̇rtaş
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Jeremy S Herman
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Jeremy D Pustilnik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
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28
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Fletcher NK, Acevedo P, Herman JS, Paupério J, Alves PC, Searle JB. Glacial cycles drive rapid divergence of cryptic field vole species. Ecol Evol 2019; 9:14101-14113. [PMID: 31938506 PMCID: PMC6953675 DOI: 10.1002/ece3.5846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 11/07/2022] Open
Abstract
Understanding the factors that contribute to the generation of reproductively isolated forms is a fundamental goal of evolutionary biology. Cryptic species are an especially interesting challenge to study in this context since they lack obvious morphological differentiation that provides clues to adaptive divergence that may drive reproductive isolation. Geographical isolation in refugial areas during glacial cycling is known to be important for generating genetically divergent populations, but its role in the origination of new species is still not fully understood and likely to be situation dependent. We combine analysis of 35,434 single-nucleotide polymorphisms (SNPs) with environmental niche modeling (ENM) to investigate genomic and ecological divergence in three cryptic species formerly classified as the field vole (Microtus agrestis). The SNPs demonstrate high genomic divergence (pairwise F ST values of 0.45-0.72) and little evidence of gene flow among the three field vole cryptic species, and we argue that genetic drift may have been a particularly important mechanism for divergence in the group. The ENM reveals three areas as potential glacial refugia for the cryptic species and differing climatic niches, although with spatial overlap between species pairs. This evidence underscores the role that glacial cycling has in promoting genetic differentiation and reproductive isolation by subdivision into disjunct distributions at glacial maxima in areas relatively close to ice sheets. Future investigation of the intrinsic barriers to gene flow between the field vole cryptic species is required to fully assess the mechanisms that contribute to reproductive isolation. In addition, the Portuguese field vole (M. rozianus) shows a high inbreeding coefficient and a restricted climatic niche, and warrants investigation into its conservation status.
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Affiliation(s)
| | - Pelayo Acevedo
- Instituto de Investigación en Recursos Cinegéticos, IREC (UCLM‐CSIC‐JCCM)Ciudad RealSpain
| | - Jeremy S. Herman
- Department of Natural SciencesNational Museums ScotlandEdinburghUK
| | - Joana Paupério
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto, Campus de VairãoVairãoPortugal
| | - Paulo C. Alves
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto, Campus de VairãoVairãoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoPortoPortugal
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do Porto, Campus de VairãoVairãoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoPortoPortugal
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29
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Campbell P, Arévalo L, Martin H, Chen C, Sun S, Rowe AH, Webster MS, Searle JB, Pasch B. Vocal divergence is concordant with genomic evidence for strong reproductive isolation in grasshopper mice ( Onychomys). Ecol Evol 2019; 9:12886-12896. [PMID: 31788222 PMCID: PMC6875671 DOI: 10.1002/ece3.5770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/13/2022] Open
Abstract
Behavioral barriers to gene flow often evolve faster than intrinsic incompatibilities and can eliminate the opportunity for hybridization between interfertile species. While acoustic signal divergence is a common driver of premating isolation in birds and insects, its contribution to speciation in mammals is less studied. Here we characterize the incidence of, and potential barriers to, hybridization among three closely related species of grasshopper mice (genus Onychomys). All three species use long-distance acoustic signals to attract and localize mates; Onychomys arenicola and Onychomys torridus are acoustically similar and morphologically cryptic whereas Onychomys leucogaster is larger and acoustically distinct. We used genotyping-by-sequencing (GBS) to test for evidence of introgression in 227 mice from allopatric and sympatric localities in the western United States and northern Mexico. We conducted laboratory mating trials for all species pairs to assess reproductive compatibility, and recorded vocalizations from O. arenicola and O. torridus in sympatry and allopatry to test for evidence of acoustic character displacement. Hybridization was rare in nature and, contrary to prior evidence for O. torridus/O. arenicola hybrids, only involved O. leucogaster and O. arenicola. In contrast, laboratory crosses between O. torridus and O. arenicola produced litters whereas O. leucogaster and O. arenicola crosses did not. Call fundamental frequency in O. torridus and O. arenicola was indistinguishable in allopatry but significantly differentiated in sympatry, a pattern consistent with reproductive character displacement. These results suggest that assortative mating based on a long-distance signal is an important isolating mechanism between O. torridus and O. arenicola and highlight the importance of behavioral barriers in determining the permeability of species boundaries.
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Affiliation(s)
- Polly Campbell
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Evolution, Ecology, and Organismal BiologyUniversity of California, RiversideRiversideCAUSA
| | - Lena Arévalo
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Developmental PathologyUniversity of BonnBonnGermany
| | - Heather Martin
- Department of Integrative BiologyOklahoma State UniversityStillwaterOKUSA
| | - Charles Chen
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOKUSA
| | - Shuzhen Sun
- Department of Biochemistry and Molecular BiologyOklahoma State UniversityStillwaterOKUSA
- Department of Forest and Conservation SciencesForest Science CentreThe University of British ColumbiaVancouverBCCanada
| | - Ashlee H. Rowe
- Department of BiologyThe University of OklahomaNormanOKUSA
| | - Michael S. Webster
- Macaulay LibraryCornell Lab of OrnithologyCornell UniversityIthacaNYUSA
- Department of Neurobiology and BehaviorCornell UniversityIthacaNYUSA
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Bret Pasch
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffAZUSA
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30
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Crumsey JM, Searle JB, Sparks JP. Isotope values of California vole (Microtus californicus) hair relate to historical drought and land use patterns in California, USA. Oecologia 2019; 190:769-781. [PMID: 31273518 DOI: 10.1007/s00442-019-04457-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/28/2019] [Indexed: 11/28/2022]
Abstract
Increased drought frequency and intensity and agricultural intensification have been key stressors to ecological systems over the past century. Biological proxies (e.g., pollen, tree rings) have been used to track this environmental change; however, linking these changes to the ecology of organisms remains challenging. Here, we link historical drought records to conditions of high water-stress in grassland habitats through the stable isotope analysis of California vole museum specimens (Microtus californicus). Using museum collections spanning 118-years (1891-2009), isotope values of dated hair tissues were associated with statewide drought metrics on the Palmer Drought Severity Index. We observed a positive correlation between δ15N and δ18O values and drought severity. The range in δ15N values (~ 18‰) is greater than what would be expected as a result of dietary shifts across the landscape (~ 3‰), and is likely attributed to the combined effects of physiological responses of M. californicus and isotopic shifts in plant resources with increased water-stress. Geospatial patterns in δ34S values of hair tissues reflect higher baseline isotope values in coastal habitats. However, comparably high δ34S values in the southern-most inland localities suggest sulfur fertilization of croplands and subsequent transfer to surrounding grassland habitats in 34S enriched forms. A broad δ13C range (- 28.7 to - 14.3‰) further suggests the consumption of C3 and C4 plant-based dietary proteins. As shown here, stable isotope analysis of museum collections can provide a climate and land use record based on the physiological performance and ecology of a study species in a region affected intensely by anthropogenic activities.
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Affiliation(s)
- Jasmine M Crumsey
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-7202, USA. .,Odum School of Ecology, University of Georgia, Athens, GA, 30602-2202, USA.
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-7202, USA
| | - Jed P Sparks
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853-7202, USA
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31
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Herman JS, Stojak J, Paupério J, Jaarola M, Wójcik JM, Searle JB. Genetic variation in field voles ( Microtus agrestis) from the British Isles: selective sweeps or population bottlenecks? Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
| | - Joanna Stojak
- Mammal Research Institute of Polish Academy of Sciences, Białowieża, Poland
| | - Joana Paupério
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairão, Portugal
| | - Maarit Jaarola
- Department of Clinical and Experimental Medicine, Linköping University, Sweden
| | - Jan M Wójcik
- Mammal Research Institute of Polish Academy of Sciences, Białowieża, Poland
| | - Jeremy B Searle
- Department of Ecology and Evolution, Cornell University, Ithaca, NY, USA
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32
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Grize SA, Wilwert E, Searle JB, Lindholm AK. Measurements of hybrid fertility and a test of mate preference for two house mouse races with massive chromosomal divergence. BMC Evol Biol 2019; 19:25. [PMID: 30651079 PMCID: PMC6335807 DOI: 10.1186/s12862-018-1322-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/10/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Western house mice Mus musculus domesticus are among the most important mammalian model species for chromosomal speciation. Hybrids between chromosomal races of M. m. domesticus suffer various degrees of fertility reduction between full fertility and complete sterility, depending on the complexity of the chromosomal differences between the races. This complexity presents itself in hybrids as meiotic configurations of chromosome chains and rings, with longer configurations having a stronger impact on fertility. While hybrids with short configurations have been intensively studied, less work has been done on hybrids with very long configurations. In this study, we investigated laboratory-reared wild mice from two chromosomally very different races in Switzerland found in close proximity. Hybrids between these races form a meiotic chain of fifteen chromosomes. We performed a detailed analysis of male and female hybrid fertility, including three generations of female backcrosses to one of the parental races. We also tested for possible divergence of mate preference in females. RESULTS While all male F1 hybrids were sterile with sperm counts of zero, 48% of female F1 hybrids produced offspring. Their litter sizes ranged from one to three which is significantly lower than the litter size of parental race females. When hybrid females were backcrossed to a parental race, half of the offspring resembled the parental race in karyotype and fertility, while the other half resembled the F1 hybrids. In the preference test, females of both races indicated a lack of a preference for males of their own karyotype. CONCLUSIONS Although the fertility of the F1 hybrids was extremely low because of the complexity of the chromosomal differences between the races, reproductive isolation was not complete. As we did not find assortative female preferences, we expect that contact between these races would lead to the production of hybrids and that gene flow would occur eventually, as fertility can be restored fully after one backcross generation.
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Affiliation(s)
- Sofia A Grize
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Elodie Wilwert
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Anna K Lindholm
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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Queirós J, Acevedo P, Santos JPV, Barasona J, Beltran-Beck B, González-Barrio D, Armenteros JA, Diez-Delgado I, Boadella M, Fernandéz de Mera I, Ruiz-Fons JF, Vicente J, de la Fuente J, Gortázar C, Searle JB, Alves PC. Red deer in Iberia: Molecular ecological studies in a southern refugium and inferences on European postglacial colonization history. PLoS One 2019; 14:e0210282. [PMID: 30620758 PMCID: PMC6324796 DOI: 10.1371/journal.pone.0210282] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 12/19/2018] [Indexed: 01/31/2023] Open
Abstract
The red deer (Cervus elaphus) is a widespread wild ungulate in Europe that has suffered strong anthropogenic impacts over their distribution during the last centuries, but also at the present time, due its economic importance as a game species. Here we focus on the evolutionary history of the red deer in Iberia, one of the three main southern refugial areas for temperate species in Europe, and addressed the hypothesis of a cryptic refugia at higher latitudes during the Last Glacial Maximum (LGM). A total of 911 individuals were sampled, genotyped for 34 microsatellites specifically developed for red deer and sequenced for a fragment of 670 bp of the mitochondrial (mtDNA) D-loop. The results were combined with published mtDNA sequences, and integrated with species distribution models and historical European paleo-distribution data, in order to further examine the alternative glacial refugial models and the influence of cryptic refugia on European postglacial colonization history. Clear genetic differentiation between Iberian and European contemporary populations was observed at nuclear and mtDNA levels, despite the mtDNA haplotypes central to the phylogenetic network are present across western Europe (including Iberia) suggesting a panmictic population in the past. Species distribution models, fossil records and genetic data support a timing of divergence between Iberian and European populations that overlap with the LGM. A notable population structure was also found within the Iberian Peninsula, although several populations displayed high levels of admixture as a consequence of recent red deer translocations. Five D-loop sub-lineages were found in Iberia that belong to the Western European mtDNA lineage, while there were four main clusters based on analysis of nuclear markers. Regarding glacial refugial models, our findings provide detailed support for the hypothesis that red deer may have persisted in cryptic northern refugia in western Europe during the LGM, most likely in southern France, southern Ireland, or in a region between them (continental shelf), and these regions were the source of individuals during the European re-colonization. This evidence heightens the importance of conserving the high mitochondrial and nuclear diversity currently observed in Iberian populations.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- * E-mail:
| | - Pelayo Acevedo
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - João P. V. Santos
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- Departamento de Biologia & CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Jose Barasona
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Beatriz Beltran-Beck
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - David González-Barrio
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose A. Armenteros
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Iratxe Diez-Delgado
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Mariana Boadella
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- SABIOtec. Ed. Polivalente UCLM, Ciudad Real, Spain
| | - Isabel Fernandéz de Mera
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose F. Ruiz-Fons
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Joaquin Vicente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jose de la Fuente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States of America
| | - Christian Gortázar
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, Ciudad Real, Spain
| | - Jeremy B. Searle
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Paulo C. Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, R. Monte-Crasto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Porto, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, United States of America
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Kotlík P, Marková S, Konczal M, Babik W, Searle JB. Genomics of end-Pleistocene population replacement in a small mammal. Proc Biol Sci 2019; 285:rspb.2017.2624. [PMID: 29436497 DOI: 10.1098/rspb.2017.2624] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/17/2018] [Indexed: 12/17/2022] Open
Abstract
Current species distributions at high latitudes are the product of expansion from glacial refugia into previously uninhabitable areas at the end of the last glaciation. The traditional view of postglacial colonization is that southern populations expanded their ranges into unoccupied northern territories. Recent findings on mitochondrial DNA (mtDNA) of British small mammals have challenged this simple colonization scenario by demonstrating a more complex genetic turnover in Britain during the Pleistocene-Holocene transition where one mtDNA clade of each species was replaced by another mtDNA clade of the same species. Here, we provide evidence from one of those small mammals, the bank vole (Clethrionomys glareolus), that the replacement was genome-wide. Using more than 10 000 autosomal SNPs we found that similar to mtDNA, bank vole genomes in Britain form two (north and south) clusters which admix. Therefore, the genome of the original postglacial colonists (the northern cluster) was probably replaced by another wave of migration from a different continental European population (the southern cluster), and we gained support for this by modelling with approximate Bayesian computation. This finding emphasizes the importance of analysis of genome-wide diversity within species under changing climate in creating opportunities for sophisticated testing of population history scenarios.
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Affiliation(s)
- Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Mateusz Konczal
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.,Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland
| | - Wiesław Babik
- Institute of Environmental Sciences, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
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Strážnická M, Marková S, Searle JB, Kotlík P. Playing Hide-and-Seek in Beta-Globin Genes: Gene Conversion Transferring a Beneficial Mutation between Differentially Expressed Gene Duplicates. Genes (Basel) 2018; 9:genes9100492. [PMID: 30321987 PMCID: PMC6209878 DOI: 10.3390/genes9100492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence suggests that adaptation to diverse environments often involves selection on existing variation rather than new mutations. A previous study identified a nonsynonymous single nucleotide polymorphism (SNP) in exon 2 of two paralogous β-globin genes of the bank vole (Clethrionomys glareolus) in Britain in which the ancestral serine (Ser) and the derived cysteine (Cys) allele represent geographically partitioned functional variation affecting the erythrocyte antioxidative capacity. Here we studied the geographical pattern of the two-locus Ser/Cys polymorphism throughout Europe and tested for the geographic correlation between environmental variables and allele frequency, expected if the polymorphism was under spatially heterogeneous environment-related selection. Although bank vole population history clearly is important in shaping the dispersal of the oxidative stress protective Cys allele, analyses correcting for population structure suggest the Europe-wide pattern is affected by geographical variation in environmental conditions. The β-globin phenotype is encoded by the major paralog HBB-T1 but we found evidence of bidirectional gene conversion of exon 2 with the low-expression paralog HBB-T2. Our data support the model where gene conversion reshuffling genotypes between high- and low- expressed paralogs enables tuning of erythrocyte thiol levels, which may help maintain intracellular redox balance under fluctuating environmental conditions. Therefore, our study suggests a possible role for gene conversion between differentially expressed gene duplicates as a mechanism of physiological adaptation of populations to new or changing environments.
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Affiliation(s)
- Michaela Strážnická
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic.
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 12844 Prague 2, Czech Republic.
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6-Suchdol, Czech Republic.
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic.
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 27721 Liběchov, Czech Republic.
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
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Hulme-Beaman A, Cucchi T, Evin A, Searle JB, Dobney K. Exploring Rattus praetor (Rodentia, Muridae) as a possible species complex using geometric morphometrics on dental morphology. Mamm Biol 2018; 92:62-67. [PMID: 30177868 PMCID: PMC6067089 DOI: 10.1016/j.mambio.2018.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Taxonomic uncertainties in the Rattus genus persist due to among-species morphological conservatism coupled with within-species environmental variation in morphology. As a result, this genus contains a number of possible cryptic species. One important example can be found in R. praetor, where morphological studies indicate it is a possible species complex. Genetic studies of R. praetor (limited to analysis of mitochondrial DNA) have been inconclusive, but do indicate such subdivision. Here we use geometric morphometrics to explore this possible species complex by analysing the dental traits of 48 specimens from New Guinea and neighbouring regions. We find separate molar morphologies for Bougainsville Island, central New Guinea and west New Guinea which cannot be easily explained by different environmental factors (climate, precipitation and altitude), strongly suggesting the existence of a number of evolutionarily distinct taxa within what is currently called R. praetor thus supporting previous suggestions that R. praetor is a species complex. Our findings demonstrate the potential of advanced morphological analyses in identifying separate species, contrary to the claims of morphological conservatism. Future analyses should combine geometric morphometrics with genetic analyses over the species range and include sub-fossil specimens from the Bismarck archipelago and Solomon Islands to resolve the evolutionary history of R. praetor.
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Affiliation(s)
- Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK.,Research Centre in Evolutionary Anthropology and Palaeoecology, School of Natural Sciences and Psychology, Liverpool John Moores University, Byrom Street, Liverpool L3 3AF, UK
| | - Thomas Cucchi
- CNRS-Muséum National d'Histoire Naturelle, UMR 7209, Archéozoologie, Archéobotanique Sociétés, Pratiques et Environnement, 55 Rue Buffon, 75005 Paris, France
| | - Allowen Evin
- Institut des Sciences de l'Evolution, Université de Montpellier, UMR CNRS, UM, EPHE, IRD 2 Place Eugène Bataillon, CC065, 34095 Montpellier, Cedex 5, France
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853-2701, USA
| | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK.,Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
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Barbosa S, Mestre F, White TA, Paupério J, Alves PC, Searle JB. Integrative approaches to guide conservation decisions: Using genomics to define conservation units and functional corridors. Mol Ecol 2018; 27:3452-3465. [PMID: 30030869 DOI: 10.1111/mec.14806] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/01/2018] [Accepted: 07/05/2018] [Indexed: 01/13/2023]
Abstract
Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary change for long-term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of evolutionary factors. Existing genetic diversity needs to be thoroughly evaluated and spatially mapped to define conservation units (CUs) in an evolutionary context, and we address that here. We also propose a multidisciplinary approach to determine corridors and functional connectivity between CUs by including genetic diversity in the modelling while controlling for isolation by distance and phylogeographic history. We evaluate our approach on a Near Threatened Iberian endemic rodent by analysing genotyping-by-sequencing (GBS) genomic data from 107 Cabrera voles (Microtus cabrerae), screening the entire species distribution to define categories of CUs and their connectivity: We defined six management units (MUs) which can be grouped into four evolutionarily significant units (ESUs) and three (putatively) adaptive units (AUs). We demonstrate that the three different categories of CU can be objectively defined using genomic data, and their characteristics and connectivity can inform conservation decision-making. In particular, we show that connectivity of the Cabrera vole is very limited in eastern Iberia and that the pre-Pyrenean and part of the Betic geographic nuclei contribute the most to the species genetic diversity. We argue that a multidisciplinary framework for CU definition is essential and that this framework needs a strong evolutionary basis.
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Affiliation(s)
- Soraia Barbosa
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Frederico Mestre
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade de Évora/InBIO Laboratório Associado, Évora, Portugal
| | - Thomas A White
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Joana Paupério
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal
| | - Paulo C Alves
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Jeremy B Searle
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto/InBIO Laboratório Associado, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
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38
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Ferreira CM, Sabino-Marques H, Barbosa S, Costa P, Encarnação C, Alpizar-Jara R, Pita R, Beja P, Mira A, Searle JB, Paupério J, Alves PC. Genetic non-invasive sampling (gNIS) as a cost-effective tool for monitoring elusive small mammals. EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1188-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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39
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Sabino-Marques H, Ferreira CM, Paupério J, Costa P, Barbosa S, Encarnação C, Alpizar-Jara R, Alves PC, Searle JB, Mira A, Beja P, Pita R. Combining genetic non-invasive sampling with spatially explicit capture-recapture models for density estimation of a patchily distributed small mammal. EUR J WILDLIFE RES 2018. [DOI: 10.1007/s10344-018-1206-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Frantz LAF, Rudzinski A, Nugraha AMS, Evin A, Burton J, Hulme-Beaman A, Linderholm A, Barnett R, Vega R, Irving-Pease EK, Haile J, Allen R, Leus K, Shephard J, Hillyer M, Gillemot S, van den Hurk J, Ogle S, Atofanei C, Thomas MG, Johansson F, Mustari AH, Williams J, Mohamad K, Damayanti CS, Wiryadi ID, Obbles D, Mona S, Day H, Yasin M, Meker S, McGuire JA, Evans BJ, von Rintelen T, Ho SYW, Searle JB, Kitchener AC, Macdonald AA, Shaw DJ, Hall R, Galbusera P, Larson G. Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events. Proc Biol Sci 2018; 285:rspb.2017.2566. [PMID: 29643207 PMCID: PMC5904307 DOI: 10.1098/rspb.2017.2566] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 03/16/2018] [Indexed: 11/13/2022] Open
Abstract
The high degree of endemism on Sulawesi has previously been suggested to have vicariant origins, dating back to 40 Ma. Recent studies, however, suggest that much of Sulawesi's fauna assembled over the last 15 Myr. Here, we test the hypothesis that more recent uplift of previously submerged portions of land on Sulawesi promoted diversification and that much of its faunal assemblage is much younger than the island itself. To do so, we combined palaeogeographical reconstructions with genetic and morphometric datasets derived from Sulawesi's three largest mammals: the babirusa, anoa and Sulawesi warty pig. Our results indicate that although these species most likely colonized the area that is now Sulawesi at different times (14 Ma to 2–3 Ma), they experienced an almost synchronous expansion from the central part of the island. Geological reconstructions indicate that this area was above sea level for most of the last 4 Myr, unlike most parts of the island. We conclude that emergence of land on Sulawesi (approx. 1–2 Myr) may have allowed species to expand synchronously. Altogether, our results indicate that the establishment of the highly endemic faunal assemblage on Sulawesi was driven by geological events over the last few million years.
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Affiliation(s)
- Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK .,The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Anna Rudzinski
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Allowen Evin
- Institut des Sciences de l'Evolution, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier, Cedex 05, France.,Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - James Burton
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK.,IUCN SSC Asian Wild Cattle Specialist Group and Chester Zoo, Cedar House, Caughall Road, Upton by Chester, Chester CH2 1LH, UK
| | - Ardern Hulme-Beaman
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - Anna Linderholm
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | - Ross Barnett
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Rodrigo Vega
- Ecology Research Group, Section of Life Sciences, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury CT1 1QU, Kent, UK
| | - Evan K Irving-Pease
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK.,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen K, Denmark
| | - Richard Allen
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Kristin Leus
- Copenhagen Zoo, IUCN SSC Conservation Breeding Specialist Group-Europe, Roskildevej 38, Postboks 7, 2000 Frederiksberg, Denmark.,European Association of Zoos and Aquaria, PO Box 20164, 1000 HD Amsterdam, The Netherlands
| | - Jill Shephard
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium.,Environment and Conservation Sciences, School of Veterinary and Life Sciences, Murdoch University, Perth, Western Australia 6150, Australia
| | - Mia Hillyer
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium.,Molecular Systematics Unit/Terrestrial Zoology, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Sarah Gillemot
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Jeroen van den Hurk
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Sharron Ogle
- Edinburgh Medical School: BMTO, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Cristina Atofanei
- Ecology Research Group, Section of Life Sciences, School of Human and Life Sciences, Canterbury Christ Church University, North Holmes Road, Canterbury CT1 1QU, Kent, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Abdul Haris Mustari
- Department of Forest Resources Conservation and Ecotourism, Faculty of Forestry, Bogor Agricultural University, PO Box 168, Bogor 16001, Indonesia
| | - John Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, Faculty of Sciences, University of Adelaide, Roseworthy, Southern Australia 5371, Australia
| | - Kusdiantoro Mohamad
- Faculty of Veterinary Medicine, Bogor Agricultural University, Jalan Agatis, IPB Campus, Darmaga, Bogor 16680, Indonesia
| | - Chandramaya Siska Damayanti
- Faculty of Veterinary Medicine, Bogor Agricultural University, Jalan Agatis, IPB Campus, Darmaga, Bogor 16680, Indonesia
| | | | - Dagmar Obbles
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, Ch. Deberiotstraat 32, 3000 Leuven, Belgium
| | - Stephano Mona
- Institut de Systématique, Évolution, Biodiversité, ISYEB - UMR 7205 - CNRS, MNHN, UPMC, EPHE, Ecole Pratique des Hautes Etudes, 16 rue Buffon, CP39, 75005 Paris, France.,EPHE, PSL Research University, Paris, France
| | | | | | - Stefan Meker
- Department of Zoology, State Museum of Natural History Stuttgart, Rosenstein 1, 70191 Stuttgart, Germany
| | - Jimmy A McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Thomas von Rintelen
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, Ithaca, NY 14853, USA
| | - Andrew C Kitchener
- Department of Natural Sciences, Chambers Street, National Museums Scotland, Edinburgh EH1 1JF, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Alastair A Macdonald
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK
| | - Darren J Shaw
- Royal (Dick) School of Veterinary Studies & The Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Edinburgh EH25 9RG, UK
| | - Robert Hall
- SE Asia Research Group, Department of Earth Sciences, Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Peter Galbusera
- Centre for Research and Conservation (CRC), Royal Zoological Society of Antwerp, Koningin Astridplein 20-26, 2018 Antwerp, Belgium
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
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Hulme-Beaman A, Searle JB, Stockley P. Sperm competition as an under-appreciated factor in domestication. Biol Lett 2018; 14:rsbl.2018.0043. [PMID: 29563282 DOI: 10.1098/rsbl.2018.0043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 02/27/2018] [Indexed: 02/04/2023] Open
Abstract
Humans created an environment that increased selective pressures on subgroups of those species that became domestic. We propose that the domestication process may in some cases have been facilitated by changes in mating behaviour and resultant sperm competition. By adapting to sperm competition, proto-domestic animals could potentially have outcompeted their wild counterparts in human-constructed niches. This could have contributed to the restriction of gene flow between the proto-domesticates and their wild counterparts, thereby promoting the fixation of other domestication characteristics. Further to this novel perspective for domestication, we emphasize the general potential of postcopulatory sexual selection in the restriction of gene flow between populations, and urge more studies.
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Affiliation(s)
- Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK .,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool L3 3AF, UK
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853-2701, USA
| | - Paula Stockley
- Mammalian Behaviour & Evolution Group, University of Liverpool, Leahurst Campus, Liverpool CH64 7TE, UK
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Matveevsky SN, Pavlova SV, Atsaeva MM, Searle JB, Kolomiets OL. Dual mechanism of chromatin remodeling in the common shrew sex trivalent (XY 1Y 2). Comp Cytogenet 2017; 11:727-745. [PMID: 29114363 PMCID: PMC5672328 DOI: 10.3897/compcytogen.v11i4.13870] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
Here we focus on the XY1Y2 condition in male common shrew Sorex araneus Linnaeus, 1758, applying electron microscopy and immunocytochemistry for a comprehensive analysis of structure, synapsis and behaviour of the sex trivalent in pachytene spermatocytes. The pachytene sex trivalent consists of three distinct parts: short and long synaptic SC fragments (between the X and Y1 and between the X and Y2, respectively) and a long asynaptic region of the X in-between. Chromatin inactivation was revealed in the XY1 synaptic region, the asynaptic region of the X and a very small asynaptic part of the Y2. This inactive part of the sex trivalent, that we named the 'head', forms a typical sex body and is located at the periphery of the meiotic nucleus at mid pachytene. The second part or 'tail', a long region of synapsis between the X and Y2 chromosomes, is directed from the periphery into the nucleus. Based on the distribution patterns of four proteins involved in chromatin inactivation, we propose a model of meiotic silencing in shrew sex chromosomes. Thus, we conclude that pachytene sex chromosomes are structurally and functionally two different chromatin domains with specific nuclear topology: the peripheral inactivated 'true' sex chromosome regions (part of the X and the Y1) and more centrally located transcriptionally active autosomal segments (part of the X and the Y2).
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Affiliation(s)
- Sergey N. Matveevsky
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin str. 3, Moscow 119991, Russia
| | - Svetlana V. Pavlova
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky pr. 33, Moscow 119071, Russia
| | - Maret M. Atsaeva
- Chechen State University, A. Sheripov str. 32, Grozny 364051, Chechen Republic, Russia
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Corson Hall, Cornell University, Ithaca, NY 14853, USA
| | - Oxana L. Kolomiets
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkin str. 3, Moscow 119991, Russia
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Prendergast ME, Buckley M, Crowther A, Frantz L, Eager H, Lebrasseur O, Hutterer R, Hulme-Beaman A, Van Neer W, Douka K, Veall MA, Quintana Morales EM, Schuenemann VJ, Reiter E, Allen R, Dimopoulos EA, Helm RM, Shipton C, Mwebi O, Denys C, Horton M, Wynne-Jones S, Fleisher J, Radimilahy C, Wright H, Searle JB, Krause J, Larson G, Boivin NL. Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets. PLoS One 2017; 12:e0182565. [PMID: 28817590 PMCID: PMC5560628 DOI: 10.1371/journal.pone.0182565] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 07/20/2017] [Indexed: 02/02/2023] Open
Abstract
Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation.
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Affiliation(s)
- Mary E. Prendergast
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA, United States of America
- * E-mail:
| | - Michael Buckley
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Alison Crowther
- School of Social Science, The University of Queensland, Brisbane Queensland, Australia
| | - Laurent Frantz
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, United Kingdom
| | - Heidi Eager
- Dept. Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | - Ophélie Lebrasseur
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
| | - Rainer Hutterer
- Dept. Vertebrates, Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany
| | | | - Wim Van Neer
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Dept. Biology, University of Leuven, Leuven, Belgium
| | - Katerina Douka
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | - Margaret-Ashley Veall
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | | | | | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Richard Allen
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
- Research Laboratory for Archaeology and the History of Art, Oxford University, Oxford, United Kingdom
| | - Evangelos A. Dimopoulos
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
| | | | - Ceri Shipton
- McDonald Institute for Archaeological Research, Cambridge, United Kingdom
- British Institute in Eastern Africa, Nairobi, Kenya
| | - Ogeto Mwebi
- Dept. Zoology, Osteology Section, National Museums of Kenya, Nairobi, Kenya
| | - Christiane Denys
- Dept. Systématique & Evolution, Muséum National d’Histoire Naturelle, Paris, France
| | - Mark Horton
- Dept. Archaeology and Anthropology, University of Bristol, Bristol, United Kingdom
| | | | - Jeffrey Fleisher
- Dept. Anthropology, Rice University, Houston, United States of America
| | - Chantal Radimilahy
- Musée d’Art et d’Archéologie, Université d’Antananarivo, Antananarivo, Madagascar
| | - Henry Wright
- Museum of Anthropology, University of Michigan, Ann Arbor, United States of America
- Santa Fe Institute, Santa Fe NM, United States of America
| | - Jeremy B. Searle
- Dept. Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Greger Larson
- Palaeogenomics & Bio-Archaeology Research Network, Oxford University, Oxford, United Kingdom
| | - Nicole L. Boivin
- Max Planck Institute for the Science of Human History, Jena, Germany
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Hatfield T, Barton N, Searle JB. A MODEL OF A HYBRID ZONE BETWEEN TWO CHROMOSOMAL RACES OF THE COMMON SHREW (SOREX ARANEUS
). Evolution 2017; 46:1129-1145. [DOI: 10.1111/j.1558-5646.1992.tb00624.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/1991] [Accepted: 01/04/1992] [Indexed: 11/28/2022]
Affiliation(s)
- Todd Hatfield
- Department of Zoology; University of Oxford; South Parks Road Oxford OX1 3PS UK
| | - Nick Barton
- Department of Genetics and Biometry; University College London; 4 Stephenson Way London NW1 2HE UK
| | - Jeremy B. Searle
- Department of Zoology; University of Oxford; South Parks Road Oxford OX1 3PS UK
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45
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Hauffe HC, Searle JB. EXTREME KARYOTYPIC VARIATION IN A MUS MUSCULUS DOMESTICUS
HYBRID ZONE: THE TOBACCO MOUSE STORY REVISITED. Evolution 2017; 47:1374-1395. [DOI: 10.1111/j.1558-5646.1993.tb02161.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/1992] [Accepted: 01/22/1993] [Indexed: 11/30/2022]
Affiliation(s)
- Heidi C. Hauffe
- Department of Zoology; University of Oxford; South Parks Road Oxford OX1 3PS UK
| | - Jeremy B. Searle
- Department of Zoology; University of Oxford; South Parks Road Oxford OX1 3PS UK
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46
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Honka J, Kvist L, Heikkinen ME, Helle P, Searle JB, Aspi J. Determining the subspecies composition of bean goose harvests in Finland using genetic methods. EUR J WILDLIFE RES 2017. [DOI: 10.1007/s10344-017-1077-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ballen CJ, Wieman C, Salehi S, Searle JB, Zamudio KR. Enhancing Diversity in Undergraduate Science: Self-Efficacy Drives Performance Gains with Active Learning. CBE Life Sci Educ 2017; 16:16/4/ar56. [PMID: 29054921 PMCID: PMC5749958 DOI: 10.1187/cbe.16-12-0344] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 07/03/2017] [Accepted: 07/11/2017] [Indexed: 05/18/2023]
Abstract
Efforts to retain underrepresented minority (URM) students in science, technology, engineering, and mathematics (STEM) have shown only limited success in higher education, due in part to a persistent achievement gap between students from historically underrepresented and well-represented backgrounds. To test the hypothesis that active learning disproportionately benefits URM students, we quantified the effects of traditional versus active learning on student academic performance, science self-efficacy, and sense of social belonging in a large (more than 250 students) introductory STEM course. A transition to active learning closed the gap in learning gains between non-URM and URM students and led to an increase in science self-efficacy for all students. Sense of social belonging also increased significantly with active learning, but only for non-URM students. Through structural equation modeling, we demonstrate that, for URM students, the increase in self-efficacy mediated the positive effect of active-learning pedagogy on two metrics of student performance. Our results add to a growing body of research that supports varied and inclusive teaching as one pathway to a diversified STEM workforce.
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Affiliation(s)
- Cissy J Ballen
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY 14853
- Department of Biology Teaching and Learning, University of Minnesota, Minneapolis, MN 55455
| | - Carl Wieman
- Graduate School of Education, Stanford University, Stanford, CA 94305
- Department of Physics, Stanford University, Stanford, CA 94305
| | - Shima Salehi
- Graduate School of Education, Stanford University, Stanford, CA 94305
| | - Jeremy B Searle
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY 14853
| | - Kelly R Zamudio
- Department of Ecology & Evolutionary Biology, Cornell University, Ithaca, NY 14853
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48
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Stojak J, McDevitt AD, Herman JS, Kryštufek B, Uhlíková J, Purger JJ, Lavrenchenko LA, Searle JB, Wójcik JM. Between the Balkans and the Baltic: Phylogeography of a Common Vole Mitochondrial DNA Lineage Limited to Central Europe. PLoS One 2016; 11:e0168621. [PMID: 27992546 PMCID: PMC5161492 DOI: 10.1371/journal.pone.0168621] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 12/02/2016] [Indexed: 11/30/2022] Open
Abstract
The common vole (Microtus arvalis) has been a model species of small mammal for studying end-glacial colonization history. In the present study we expanded the sampling from central and eastern Europe, analyzing contemporary genetic structure to identify the role of a potential 'northern glacial refugium', i.e. a refugium at a higher latitude than the traditional Mediterranean refugia. Altogether we analyzed 786 cytochrome b (cytb) sequences (representing mitochondrial DNA; mtDNA) from the whole of Europe, adding 177 new sequences from central and eastern Europe, and we conducted analyses on eight microsatellite loci for 499 individuals (representing nuclear DNA) from central and eastern Europe, adding data on 311 new specimens. Our new data fill gaps in the vicinity of the Carpathian Mountains, the potential northern refugium, such that there is now dense sampling from the Balkans to the Baltic Sea. Here we present evidence that the Eastern mtDNA lineage of the common vole was present in the vicinity of this Carpathian refugium during the Last Glacial Maximum and the Younger Dryas. The Eastern lineage expanded from this refugium to the Baltic and shows low cytb nucleotide diversity in those most northerly parts of the distribution. Analyses of microsatellites revealed a similar pattern but also showed little differentiation between all of the populations sampled in central and eastern Europe.
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Affiliation(s)
- Joanna Stojak
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, United Kingdom
| | - Jeremy S. Herman
- Department of Natural Sciences, National Museums Scotland, Edinburgh, United Kingdom
| | - Boris Kryštufek
- Vertebrate Department, Slovenian Museum of Natural History, Ljubljana, Slovenia
| | - Jitka Uhlíková
- Nature Conservation Agency of the Czech Republic, Prague, Czech Republic
| | - Jenő J. Purger
- Department of Ecology, Institute of Biology, University in Pécs, Pécs, Hungary
| | - Leonid A. Lavrenchenko
- Department of Mammalian Microevolution, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, United States of America
| | - Jan M. Wójcik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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49
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Giménez MD, Förster DW, Jones EP, Jóhannesdóttir F, Gabriel SI, Panithanarak T, Scascitelli M, Merico V, Garagna S, Searle JB, Hauffe HC. A Half-Century of Studies on a Chromosomal Hybrid Zone of the House Mouse. J Hered 2016; 108:25-35. [PMID: 27729448 DOI: 10.1093/jhered/esw061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022] Open
Abstract
The first natural chromosomal variation in the house mouse was described nearly 50 years ago in Val Poschiavo on the Swiss side of the Swiss-Italian border in the Central Eastern Alps. Studies have extended into neighboring Valtellina, and the house mice of the Poschiavo-Valtellina area have been subject to detailed analysis, reviewed here. The maximum extent of this area is 70 km, yet it has 4 metacentric races and the standard 40-chromosome telocentric race distributed in a patchwork fashion. The metacentric races are characterized by highly reduced diploid numbers (2n = 22-26) resulting from Robertsonian fusions, perhaps modified by whole-arm reciprocal translocations. The races hybridize and the whole Poschiavo-Valtellina area can be considered a "hybrid zone." The studies of this area have provided insights into origin of races within hybrid zones, gene flow within hybrid zones and the possibility of speciation in hybrid zones. This provides a case study of how chromosomal rearrangements may impact the genetic structure of populations and their diversification.
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Affiliation(s)
- Mabel D Giménez
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Daniel W Förster
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Eleanor P Jones
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Fríða Jóhannesdóttir
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Sofia I Gabriel
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Thadsin Panithanarak
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Moira Scascitelli
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Valeria Merico
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Silvia Garagna
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Jeremy B Searle
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
| | - Heidi C Hauffe
- From the Department of Biology, University of York, York, UK (Giménez, Förster, Jones, Jóhannesdóttir, Gabriel, Panithanarak, Scascitelli, Searle, and Hauffe); Instituto de Biología Subtropical (UNaM-CONICET), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Misiones, Argentina (Giménez); Department of Evolutionary Genetics, Leibniz-Institute for Zoo and Wildlife Research, Berlin, Germany (Förster); Fera Science, York, UK (Jones); Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, NY 14853-2701 (Jóhannesdóttir and Searle); CESAM-Centre for Environmental and Marine Studies, Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal (Gabriel); Institute of Marine Science, Burapha University, Chonburi, Thailand (Panithanarak); Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", University of Pavia, Pavia, Italy (Merico and Garagna); and Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, S. Michele all'Adige (TN), Italy (Hauffe)
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Shipley JR, Campbell P, Searle JB, Pasch B. Asymmetric energetic costs in reciprocal-cross hybrids between carnivorous mice (Onychomys). ACTA ACUST UNITED AC 2016; 219:3803-3809. [PMID: 27688051 DOI: 10.1242/jeb.148890] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 09/25/2016] [Indexed: 01/07/2023]
Abstract
Aerobic respiration is a fundamental physiological trait dependent on coordinated interactions between gene products of the mitochondrial and nuclear genomes. Mitonuclear mismatch in interspecific hybrids may contribute to reproductive isolation by inducing reduced viability (or even complete inviability) due to increased metabolic costs. However, few studies have tested for effects of mitonuclear mismatch on respiration at the whole-organism level. We explored how hybridization affects metabolic rate in closely related species of grasshopper mice (genus Onychomys) to better understand the role of metabolic costs in reproductive isolation. We measured metabolic rate across a range of temperatures to calculate basal metabolic rate (BMR) and cold-induced metabolic rate (MRc) in O. leucogaster, O. torridus and O. arenicola, and in reciprocal F1 hybrids between the latter two species. Within the genus, we found a negative correlation between mass-specific BMR and body mass. Although O. arenicola was smaller than O. torridus, hybrids from both directions of the cross resembled O. arenicola in body mass. In contrast, hybrid BMR was strongly influenced by the direction of the cross: reciprocal F1 hybrids were different from each other but indistinguishable from the maternal species. In addition, MRc was not significantly different between hybrids and either parental species. These patterns indicate that metabolic costs are not increased in Onychomys F1 hybrids and, while exposure of incompatibilities in F2 hybrids cannot be ruled out, suggest that mitonuclear mismatch does not act as a primary barrier to gene flow. Maternal matching of BMR is suggestive of a strong effect of mitochondrial genotype on metabolism in hybrids. Together, our findings provide insight into the metabolic consequences of hybridization, a topic that is understudied in mammals.
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Affiliation(s)
- J Ryan Shipley
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Polly Campbell
- Department of Integrative Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Bret Pasch
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA .,Bioacoustics Research Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA.,Macaulay Library, Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
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