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Jabin G, Joshi BD, Wang MS, Mukherjee T, Dolker S, Wang S, Chandra K, Chinnadurai V, Sharma LK, Thakur M. Mid-Pleistocene Transitions Forced Himalayan ibex to Evolve Independently after Split into an Allopatric Refugium. BIOLOGY 2023; 12:1097. [PMID: 37626983 PMCID: PMC10451794 DOI: 10.3390/biology12081097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023]
Abstract
Pleistocene glaciations had profound impact on the spatial distribution and genetic makeup of species in temperate ecosystems. While the glacial period trapped several species into glacial refugia and caused abrupt decline in large populations, the interglacial period facilitated population growth and range expansion leading to allopatric speciation. Here, we analyzed 40 genomes of four species of ibex and found that Himalayan ibex in the Pamir Mountains evolved independently after splitting from its main range about 0.1 mya following the Pleistocene species pump concept. Demographic trajectories showed Himalayan ibex experienced two historic bottlenecks, one each c. 0.8-0.5 mya and c. 50-30 kya, with an intermediate large population expansion c. 0.2-0.16 mya coinciding with Mid-Pleistocene Transitions. We substantiate with multi-dimensional evidence that Himalayan ibex is an evolutionary distinct phylogenetic species of Siberian ibex which need to be prioritized as Capra himalayensis for taxonomic revision and conservation planning at a regional and global scale.
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Affiliation(s)
- Gul Jabin
- Zoological Survey of India, Kolkata 700053, India
- Department of Zoology, University of Calcutta, Kolkata 700019, India
| | | | - Ming-Shan Wang
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | | | - Stanzin Dolker
- Zoological Survey of India, Kolkata 700053, India
- Department of Zoology, University of Calcutta, Kolkata 700019, India
| | - Sheng Wang
- Kunming Institute of Zoology, Kunming 650223, China
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Genomic heterozygosity is associated with parasite abundance, but the effects are not mediated by host condition. Evol Ecol 2023; 37:75-96. [PMID: 36568713 PMCID: PMC9666582 DOI: 10.1007/s10682-022-10175-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/17/2022] [Indexed: 12/27/2022]
Abstract
Whether, when, and how genetic diversity buffers individuals and populations against infectious disease risk is a critical and open question for understanding wildlife disease and zoonotic disease risk. Several, but not all, studies have found negative relationships between infection and heterozygosity in wildlife. Since they can host multiple zoonotic infections, we sampled a population of wild deer mice (Peromyscus maniculatus), sequenced their genomes, and examined their fecal samples for coccidia and nematode eggs. We analyzed coccidia infection status, abundance, and coinfection status in relation to per-locus and per-individual measures of heterozygosity, as well as identified SNPs associated with infection status. Since heterozygosity might affect host condition, and condition is known to affect immunity, it was included as a co-variate in the per-individual analyses and as response variable in relation to heterozygosity. Not only did coccidia-infected individuals have lower levels of genome-wide per-locus diversity across all metrics, but we found an inverse relationship between genomic diversity and severity of coccidia infection. We also found weaker evidence that coinfected individuals had lower levels of private allelic variation than all other groups. In the per-individual analyses, relationships between heterozygosity and infection were marginal but followed the same negative trends. Condition was negatively correlated with infection, but was not associated with heterozygosity, suggesting that effects of heterozygosity on infection were not mediated by host condition in this system. Association tests identified multiple loci involved in the inflammatory response, with a particular role for NF-κB signaling, supporting previous work on the genetic basis of coccidia resistance. Taken together, we find that increased genome-wide neutral diversity, the presence of specific genetic variants, and improved condition positively impact infection status. Our results underscore the importance of considering host genomic variation as a buffer against infection, especially in systems that can harbor zoonotic diseases. Supplementary Information The online version contains supplementary material available at 10.1007/s10682-022-10175-8.
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Brambilla A, von Hardenberg A, Canedoli C, Brivio F, Sueur C, Stanley CR. Long term analysis of social structure: evidence of age‐based consistent associations in male Alpine ibex. OIKOS 2022. [DOI: 10.1111/oik.09511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Alice Brambilla
- Dept of Evolutionary Biology and Environmental Studies, Univ. of Zurich Zurich Switzerland
- Alpine Wildlife Research Center, Gran Paradiso National Park Torino Italy
| | - Achaz von Hardenberg
- Conservation Biology Research Group, Dept of Biological Sciences, Univ. of Chester Chester UK
| | - Claudia Canedoli
- Dept of Earth and Environmental Sciences, Univ. of Milano Bicocca Milano Italy
| | | | - Cédric Sueur
- Univ. de Strasbourg, CNRS, IPHC UMR 7178 Strasbourg France
- Inst. Universitaire de France, Saint‐Michel 103 Paris France
| | - Christina R. Stanley
- Conservation Biology Research Group, Dept of Biological Sciences, Univ. of Chester Chester UK
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Moroni B, Brambilla A, Rossi L, Meneguz PG, Bassano B, Tizzani P. Hybridization between Alpine Ibex and Domestic Goat in the Alps: A Sporadic and Localized Phenomenon? Animals (Basel) 2022; 12:ani12060751. [PMID: 35327148 PMCID: PMC8944563 DOI: 10.3390/ani12060751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary The Alpine ibex (Capra ibex) is a protected wild ungulate. The species is known to have a low genetic variability and to occasionally suffer from local population decline as a consequence of epidemic diseases. Another, less investigated, threat for the species’ long-term conservation is represented by the hybridization with feral domestic goats that may breed with ibex if abandoned in the mountain at the end of the summer pasture. Further reproduction and the spread of hybrids may jeopardize the genetic integrity of wild Alpine ibex. By means of an online survey and using a network of experts, we mapped unpublished evidence on observed hybridization events between Alpine ibex and feral domestic goats. The results of this study suggested that hybrids are currently distributed in several countries, and their presence is not a rare event, with some clusters including 4–20 probable hybrids. This calls for more studies clearly quantifying hybrids in Alpine ibex colonies, but also highlights the need for conservation actions aimed at controlling this phenomenon, such as the effective management of domestic herds grazing in Alpine ibex core areas and clear guidelines on hybrid management. Abstract The Alpine ibex (Capra ibex) is a mountain ungulate living in the European Alps. Although being currently classified as a species of Least Concern (LC) by the IUCN, a potential threat for its long-term conservation is introgression following hybridization with domestic goats (Capra hircus). Hybridization has been documented in Switzerland in captive and free ranging animals, although accurate data to assess the extent of this phenomenon in natural conditions in the Alps are lacking. Using an online survey and a network of experts, we collected and mapped unpublished evidence of hybridization events that occurred between Alpine ibex and feral domestic goats from 2000 to 2021. The results of this study showed that hybrids are distributed in most of the Alpine countries, and their presence is not a sporadic event, with some clusters including 4–20 probable hybrids. Our results illustrated the need for establishing a standardized and effective protocol to identify hybrids in the field (such as a formal description of the morphological traits characterizing hybrids), as well as clear guidelines for hybrid management. Even more importantly, this study also highlighted the need for actions aimed at avoiding hybridization, such as the effective management of domestic herds grazing in Alpine ibex core areas.
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Affiliation(s)
- Barbara Moroni
- Department of Veterinary Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Italy; (L.R.); (P.G.M.); (P.T.)
- Correspondence:
| | - Alice Brambilla
- Alpine Wildlife Research Centre, Gran Paradiso National Park, 10080 Noasca, Italy; (A.B.); (B.B.)
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| | - Luca Rossi
- Department of Veterinary Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Italy; (L.R.); (P.G.M.); (P.T.)
| | - Pier Giuseppe Meneguz
- Department of Veterinary Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Italy; (L.R.); (P.G.M.); (P.T.)
| | - Bruno Bassano
- Alpine Wildlife Research Centre, Gran Paradiso National Park, 10080 Noasca, Italy; (A.B.); (B.B.)
| | - Paolo Tizzani
- Department of Veterinary Sciences, University of Turin, Largo Braccini 2, 10095 Grugliasco, Italy; (L.R.); (P.G.M.); (P.T.)
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Willisch CS, Neuhaus P. Reproductive effort affects subsequent horn growth in sexually dimorphic male ungulates. Evol Ecol 2021. [DOI: 10.1007/s10682-021-10128-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AbstractTrade-offs between reproductive effort and subsequent growth in males are not well explored, despite their relevance in questions of individual energy allocation. Regarding the growth of sexual secondary characters in polygynous breeding male mammals, indeed, no conclusive studies exist. We investigated in male Alpine ibex (Capra ibex) the relationship between their behavioral reproductive effort, current horn size, and subsequent horn growth. While controlling for age, no evidence was found for male behavioral reproductive effort during the rut being affected by their horn size. On the other hand, reproductive effort significantly decreased age-specific horn growth during the following summer. Our study provides evidence that growth of secondary sexual characters is traded against behavioral investments in reproduction in a male mammal. It bears important implications for the understanding of energy allocation between various life-history components and the evolutionary ecology of secondary sexual characters.
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Kessler C, Brambilla A, Waldvogel D, Camenisch G, Biebach I, Leigh DM, Grossen C, Croll D. A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics. Mol Ecol Resour 2021; 22:66-85. [PMID: 34152681 PMCID: PMC9292246 DOI: 10.1111/1755-0998.13452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Polymorphism for immune functions can explain significant variation in health and reproductive success within species. Drastic loss in genetic diversity at such loci constitutes an extinction risk and should be monitored in species of conservation concern. However, effective implementations of genome‐wide immune polymorphism sets into high‐throughput genotyping assays are scarce. Here, we report the design and validation of a microfluidics‐based amplicon sequencing assay to comprehensively capture genetic variation in Alpine ibex (Capra ibex). This species represents one of the most successful large mammal restorations recovering from a severely depressed census size and a massive loss in diversity at the major histocompatibility complex (MHC). We analysed 65 whole‐genome sequencing sets of the Alpine ibex and related species to select the most representative markers and to prevent primer binding failures. In total, we designed ~1,000 amplicons densely covering the MHC, further immunity‐related genes as well as randomly selected genome‐wide markers for the assessment of neutral population structure. Our analysis of 158 individuals shows that the genome‐wide markers perform equally well at resolving population structure as RAD‐sequencing or low‐coverage genome sequencing data sets. Immunity‐related loci show unexpectedly high degrees of genetic differentiation within the species. Such information can now be used to define highly targeted individual translocations. Our design strategy can be realistically implemented into genetic surveys of a large range of species. In conclusion, leveraging whole‐genome sequencing data sets to design targeted amplicon assays allows the simultaneous monitoring of multiple genetic risk factors and can be translated into species conservation recommendations.
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Affiliation(s)
- Camille Kessler
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Alice Brambilla
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Alpine Wildlife Research Center, Gran Paradiso National Park, Italy
| | - Dominique Waldvogel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Iris Biebach
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Deborah M Leigh
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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Pérez-González J, Carranza J, Martínez R, Benítez-Medina JM. Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis. Animals (Basel) 2021; 11:1630. [PMID: 34072907 PMCID: PMC8229303 DOI: 10.3390/ani11061630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Host genetic diversity tends to limit disease spread in nature and buffers populations against epidemics. Genetic diversity in wildlife is expected to receive increasing attention in contexts related to disease transmission and human health. Ungulates such as wild boar (Sus scrofa) and red deer (Cervus elaphus) are important zoonotic hosts that can be precursors to disease emergence and spread in humans. Tuberculosis is a zoonotic disease with relevant consequences and can present high prevalence in wild boar and red deer populations. Here, we review studies on the genetic diversity of ungulates and determine to what extent these studies consider its importance on the spread of disease. This assessment also focused on wild boar, red deer, and tuberculosis. We found a disconnection between studies treating genetic diversity and those dealing with infectious diseases. Contrarily, genetic diversity studies in ungulates are mainly concerned with conservation. Despite the existing disconnection between studies on genetic diversity and studies on disease emergence and spread, the knowledge gathered in each discipline can be applied to the other. The bidirectional applications are illustrated in wild boar and red deer populations from Spain, where TB is an important threat for wildlife, livestock, and humans.
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Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Córdoba, Spain;
| | - Remigio Martínez
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
| | - José Manuel Benítez-Medina
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
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Zanet S, Ferroglio E, Orlandini F, Bassano B, Battisti E, Brambilla A. Bronchopulmonary Nematodes in Alpine Ibex: Shedding of First Stage Larvae Analyzed at the Individual Host Level. Front Vet Sci 2021; 8:663268. [PMID: 33996985 PMCID: PMC8116586 DOI: 10.3389/fvets.2021.663268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/06/2021] [Indexed: 12/03/2022] Open
Abstract
Pneumonia is the most frequent cause of death for Alpine ibex (Capra ibex) in Gran Paradiso National Park, (Italy). The etiology of this form of pneumonia is currently unknown and the identification of the primary etiological agent remains difficult due to biological and logistic constraints. Uncovering individual differences in Protostrongylid prevalence and intensity is important to further investigate the epidemiology of respiratory diseases and their relationship to heterozygosity and inbreeding in a once almost extinct population like C. ibex. In a group of 21 individually recognizable adult male we monitored monthly prevalence and intensity of Protostrongylid first-stage larvae using Baerman's technique from June to September 2019. First-stage larvae of 5 genera were detected. Muellerius (P = 100%, CI95% = 84–100) and Protostrongylus (P = 86%, CI95%:71–100) were two dominant genera according to Bush's importance index. Neostrongylus (P = 38%,CI95%: 17–59), Cystocaulus (P = 33%,CI95% = 13–53) were classified as co-dominant genera while Dictyocaulus filaria (P = 0.05%, CI95% = 0.04–0.13) was detected, for the first time in Alpine ibex, in one subject. Protostrongylidae larval excretion varied significantly over time, with minimum L1 excretion in July. Individual median larval intensity ranged from 4.4 lpg to 82.2 lpg with Poulin's discrepancy index showing highly aggregated distribution patterns for Muellerius spp. (D = 0.283, CI95% = 0.760–0.895) and Protostrongylus spp. (D = 0.635, CI95% = 0.580–0.705). Presented data provide the necessary base point to further investigate how lungworm infection account for the different rates of progression of pneumonia in C. ibex. Individual aggregation of larval intensity must be further evaluated to determine whether these differences mirror different levels of parasitic infection related to individual differences in immune response, hormonal-states or genetic fitness.
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Affiliation(s)
- Stefania Zanet
- Department Veterinary Sciences, University of Turin, Turin, Italy
| | - Ezio Ferroglio
- Department Veterinary Sciences, University of Turin, Turin, Italy
| | | | - Bruno Bassano
- Gran Paradiso National Park, Alpine Wildlife Research Center, Noasca, Italy
| | - Elena Battisti
- Department Veterinary Sciences, University of Turin, Turin, Italy
| | - Alice Brambilla
- Gran Paradiso National Park, Alpine Wildlife Research Center, Noasca, Italy.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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Ivy-Israel NMD, Moore CE, Schwartz TS, Steury TD, Zohdy S, Newbolt CH, Ditchkoff SS. Association between sexually selected traits and allelic distance in two unlinked MHC II loci in white-tailed deer (Odocoileus virginianus). Evol Ecol 2021. [DOI: 10.1007/s10682-021-10108-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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10
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Albery GF, Morris A, Morris S, Kenyon F, Nussey DH, Pemberton JM. Fitness Costs of Parasites Explain Multiple Life-History Trade-Offs in a Wild Mammal. Am Nat 2021; 197:324-335. [PMID: 33625970 DOI: 10.1086/712633] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractReproduction in wild animals can divert limited resources away from immune defense, resulting in increased parasite burdens. A long-standing prediction of life-history theory states that these parasites can harm the reproductive individual, reducing its subsequent survival and fecundity, producing reproduction-fitness trade-offs. Here, we examined associations among reproductive allocation, immunity, parasitism, and subsequent survival and fecundity in a wild population of individually identified red deer (Cervus elaphus). Using path analysis, we investigated whether costs of lactation in terms of downstream survival and fecundity were mediated by changes in strongyle nematode count and mucosal antibody levels. Lactating females exhibited increased parasite counts, which were in turn associated with substantially decreased fitness in the following year in terms of overwinter survival, fecundity, subsequent calf weight, and parturition date. This study offers observational evidence for parasite regulation of multiple life-history trade-offs, supporting the role of parasites as an important mediating factor in wild mammal populations.
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Buzan E, Gerič U, Potušek S, Flajšman K, Pokorny B. First Insights into the Population Genetic Structure and Heterozygosity-Fitness Relationship in Roe Deer Inhabiting the Area between the Alps and Dinaric Mountains. Animals (Basel) 2020; 10:ani10122276. [PMID: 33276566 PMCID: PMC7761463 DOI: 10.3390/ani10122276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 11/21/2022] Open
Abstract
Simple Summary We determined the genetic variability, population structure, and influence of genetic factors on two parameters of fitness (body mass and reproductive ability) in roe deer females in the contact zone between the Alps and the Dinaric Mountains by utilizing microsatellite variations in 214 individuals collected throughout Slovenia, Central Europe. Spatial differences in the genetic diversity of the species can be explained by population history, different approaches to population management and/or different connectivity among subpopulations. The population genetic structure confirms the high side fidelity of roe deer, but also shows the existence of admixtures of genes among different areas. We found evidence that genetic factors, including individual heterozygosity, influence body mass, confirming that heterozygosity positively affects fitness in wild populations. However, as the effect of genetic factors is usually masked or overruled by the influence of environmental factors, i.e., availability of resources, data on the joint influence of external and intrinsic factors on fitness and other life-history traits are needed to better predict the population dynamics of targeted species, which would enable sustainable, science-based population management. Abstract Across its pan-European distribution, the European roe deer (Capreolus capreolus) faces a wide diversity of environmental and climatic conditions; therefore, several factors, including intrinsic ones, shape life-history traits and cause significant variability in parameters of fitness. By utilizing microsatellite variations in 214 roe deer females collected throughout Slovenia, Central Europe, we determined the genetic variability and population structure of this species in the contact zone between the Alps and the Dinaric Mountains, i.e., over a wider area where data on the genetic outlook for this—the most common and widespread European wild ungulate—have been completely lacking so far. Throughout the country, we found moderate microsatellite diversity (Ho = 0.57–0.65) in relation to the observed heterozygosity reported for other roe deer populations in Europe. Spatial differences in genetic diversity of the species in Slovenia can be explained by population history linked to varying approaches to population management and/or different connectivity among subpopulations in topographically differentiated habitats. A country-wide pattern of genetic structure is clearly defined by separation of the populations into three groups present in the following regions: (i) Southern sub-Mediterranean and Karst regions, (ii) Central Slovenia, and (iii) the Sub-Pannonian Region in the north-east. This is also confirmed by evidencing a moderate isolation by distance, especially by separating southern samples (coastal Slovenia) from others. Levels of genetic differentiation vary among populations, which can be explained by the effect of natural geographical barriers or the presence of anthropogenic barriers such as urban areas and highways. In the subset of 172 yearling females, we analyzed the influence of genetic advantage (individual heterozygosity) and other genetic data (reflected in the structuring of the population) on body mass and reproductive ability. We found evidence that genetic factors influence the body mass of roe deer yearling females (explaining altogether 18.8% of body mass variance), and the level of individual heterozygosity alone also positively affected body mass, which is in accordance with the theory that heterozygosity is commonly positively correlated with fitness in wild populations. However, we did not uncover any effect of heterozygosity on two parameters of reproductive ability (fertility and potential reproductive outcome), indicating that several other factors, especially environmental ones, have a predominant effect on the parameters of fitness in roe deer.
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Affiliation(s)
- Elena Buzan
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (E.B.); (U.G.); (S.P.)
- Environmental Protection College, Trg mladosti 7, 3320 Velenje, Slovenia
| | - Urška Gerič
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (E.B.); (U.G.); (S.P.)
| | - Sandra Potušek
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000 Koper, Slovenia; (E.B.); (U.G.); (S.P.)
| | - Katarina Flajšman
- Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia;
| | - Boštjan Pokorny
- Environmental Protection College, Trg mladosti 7, 3320 Velenje, Slovenia
- Slovenian Forestry Institute, Večna pot 2, 1000 Ljubljana, Slovenia;
- Correspondence:
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12
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Piza-Roca C, Schoeman D, Frere C. Fitness benefits of male dominance behaviours depend on the degree of individual inbreeding in a polyandrous lizard. Proc Biol Sci 2020; 287:20200097. [PMID: 32429806 PMCID: PMC7287366 DOI: 10.1098/rspb.2020.0097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/21/2020] [Indexed: 01/21/2023] Open
Abstract
In polyandrous species, sexual selection extends beyond mating competition to selection for egg fertilization. As a result, the degree to which factors influencing mating success impact overall reproductive success becomes variable. Here, we used a longitudinal behavioural and genetic dataset for a population of eastern water dragons (Intellagama lesueurii) to investigate the degree to which male dominance, a pre-mating selection trait, influences overall reproductive success, measured as the number of surviving offspring. Moreover, we examine the interactive effects with a genetic trait, individual inbreeding, known to influence the reproductive success of males in this species. We found fitness benefits of male dominance, measured as body size and frequency of dominance behaviours displayed. However, individuals' propensity to display dominance behaviours had mixed effects, depending on the degree of inbreeding. While inbred males benefited from frequent displays, highly outbred males exhibited better reproductive outputs when displaying to a lesser extent. Given that outbred males have enhanced reproductive success in this species, the costs of displaying dominance behaviours may outweigh the benefits. Overall, our results demonstrate the fitness benefits of dominance in a polyandrous lizard, and suggest that these are modulated by an independent genetic trait. Our results may contribute to explaining the presence of alternative mating tactics in this species, owing to the variability in net fitness benefits of dominance. Our findings also reveal the challenges associated with investigating fitness traits in isolation, which may undermine the validity of results when important interactions are ignored.
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Affiliation(s)
- Carmen Piza-Roca
- Global-Change Ecology Research Group, University of the Sunshine Coast, Queensland, Australia
| | - David Schoeman
- Global-Change Ecology Research Group, University of the Sunshine Coast, Queensland, Australia
- Centre for African Conservation Ecology, Department of Zoology, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa
| | - Celine Frere
- Global-Change Ecology Research Group, University of the Sunshine Coast, Queensland, Australia
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Brambilla A, Von Hardenberg A, Nelli L, Bassano B. Distribution, status, and recent population dynamics of Alpine ibexCapra ibexin Europe. Mamm Rev 2020. [DOI: 10.1111/mam.12194] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Alice Brambilla
- Department of Evolutionary Biology and Environmental Studies University of Zurich Winterthurerstrasse 1908057Zurich ZH Switzerland
- Alpine Wildlife Research Centre Gran Paradiso National Park Frazione Jamonin 510080Noasca TO Italy
| | - Achaz Von Hardenberg
- Conservation Biology Research Group Department of Biological Sciences University of Chester Parkgate RoadCH2 4BJChester UK
| | - Luca Nelli
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Graham Kerr BuildingG12 8QQGlasgow UK
| | - Bruno Bassano
- Alpine Wildlife Research Centre Gran Paradiso National Park Frazione Jamonin 510080Noasca TO Italy
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Quéméré E, Rossi S, Petit E, Marchand P, Merlet J, Game Y, Galan M, Gilot-Fromont E. Genetic epidemiology of the Alpine ibex reservoir of persistent and virulent brucellosis outbreak. Sci Rep 2020; 10:4400. [PMID: 32157133 PMCID: PMC7064506 DOI: 10.1038/s41598-020-61299-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 02/25/2020] [Indexed: 01/23/2023] Open
Abstract
While it is now broadly accepted that inter-individual variation in the outcomes of host-pathogen interactions is at least partially genetically controlled, host immunogenetic characteristics are rarely investigated in wildlife epidemiological studies. Furthermore, most immunogenetic studies in the wild focused solely on the major histocompatibility complex (MHC) diversity despite it accounts for only a fraction of the genetic variation in pathogen resistance. Here, we investigated immunogenetic diversity of the Alpine ibex (Capra ibex) population of the Bargy massif, reservoir of a virulent outbreak of brucellosis. We analysed the polymorphism and associations with disease resistance of the MHC Class II Drb gene and several non-MHC genes (Toll-like receptor genes, Slc11A1) involved in the innate immune response to Brucella in domestic ungulates. We found a very low neutral genetic diversity and a unique MHC Drb haplotype in this population founded few decades ago from a small number of individuals. By contrast, other immunity-related genes have maintained polymorphism and some showed significant associations with the brucellosis infection status hence suggesting a predominant role of pathogen-mediated selection in their recent evolutionary trajectory. Our results highlight the need to monitor immunogenetic variation in wildlife epidemiological studies and to look beyond the MHC.
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Affiliation(s)
- Erwan Quéméré
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.
- ESE, Ecology and Ecosystems Health, Agrocampus Ouest, INRAE, 35042 Rennes, France.
| | - Sophie Rossi
- Office Français de la Biodiversité, Unité Sanitaire de la Faune, Gap, France
| | - Elodie Petit
- Office Français de la Biodiversité, Unité Ongulés sauvages, Gières, France
| | - Pascal Marchand
- Office Français de la Biodiversité, Unité Ongulés sauvages, Gières, France
| | - Joël Merlet
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France
| | - Yvette Game
- Laboratoire Départemental d'Analyses Vétérinaires de Savoie, Chambéry, France
| | - Maxime Galan
- CBGP, INRAE, CIRAD, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Emmanuelle Gilot-Fromont
- Université de Lyon, VetAgro Sup - Campus vétérinaire de Lyon, Marcy l'Étoile, France
- Université de Lyon 1, UMR CNRS 5558 Laboratoire de Biométrie et Biologie Evolutive (LBBE), Villeurbanne, France
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15
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Fuller J, Ferchaud A, Laporte M, Le Luyer J, Davis TB, Côté SD, Bernatchez L. Absence of founder effect and evidence for adaptive divergence in a recently introduced insular population of white‐tailed deer (
Odocoileus virginianus
). Mol Ecol 2019; 29:86-104. [DOI: 10.1111/mec.15317] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/16/2022]
Affiliation(s)
- Jérémie Fuller
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Jérémy Le Luyer
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | | | - Steeve D. Côté
- Département de Biologie Université Laval Québec QC Canada
- Natural Sciences and Engineering Research Council of Canada (NSERC) Research Chair in Integrated Management of the Resources of Anticosti Island and Centre d'Études Nordiques (CEN) Québec QC Canada
| | - Louis Bernatchez
- Département de Biologie Université Laval Québec QC Canada
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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16
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Moss JB, Gerber GP, Welch ME. Heterozygosity-Fitness Correlations Reveal Inbreeding Depression in Neonatal Body Size in a Critically Endangered Rock Iguana. J Hered 2019; 110:818-829. [PMID: 31617903 DOI: 10.1093/jhered/esz060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 10/09/2019] [Indexed: 01/16/2023] Open
Abstract
Inbreeding depression, though challenging to identify in nature, may play an important role in regulating the dynamics of small and isolated populations. Conversely, greater expression of genetic load can enhance opportunities for natural selection. Conditional expression concentrates these opportunities for selection and may lead to failure of detection. This study investigates the possibility for age-dependent expression of inbreeding depression in a critically endangered population of rock iguanas, Cyclura nubila caymanensis. We employ heterozygote-fitness correlations to examine the contributions of individual genetic factors to body size, a fitness-related trait. Nonsignificant reductions in homozygosity (up to 7%) were detected between neonates and individuals surviving past their first year, which may reflect natural absorption of inbreeding effects by this small, fecund population. The majority of variation in neonate body size was attributed to maternal or environmental effects (i.e., clutch identity and incubation length); however, heterozygosity across 22 microsatellite loci also contributed significantly and positively to model predictions. Conversely, effects of heterozygosity on fitness were not detectable when adults were examined, suggesting that inbreeding depression in body size may be age dependent in this taxon. Overall, these findings emphasize the importance of taking holistic, cross-generational approaches to genetic monitoring of endangered populations.
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Affiliation(s)
- Jeanette B Moss
- Biological Sciences Department, Mississippi State University, Mississippi State, MS
| | - Glenn P Gerber
- Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Mark E Welch
- Biological Sciences Department, Mississippi State University, Mississippi State, MS
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17
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Gagnon M, Yannic G, Perrier C, Côté SD. No evidence of inbreeding depression in fast declining herds of migratory caribou. J Evol Biol 2019; 32:1368-1381. [PMID: 31514251 DOI: 10.1111/jeb.13533] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 08/19/2019] [Accepted: 08/26/2019] [Indexed: 12/28/2022]
Abstract
Identifying inbreeding depression early in small and declining populations is essential for management and conservation decisions. Correlations between heterozygosity and fitness (HFCs) provide a way to identify inbreeding depression without prior knowledge of kinship among individuals. In Northern Quebec and Labrador, the size of two herds of migratory caribou (Rivière-George, RG and Rivière-aux-Feuilles, RAF) has declined by one to two orders of magnitude in the last three decades. This raises the question of a possible increase in inbreeding depression originating from, and possibly contributing to, the demographic decline in those populations. Here, we tested for the association of genomic inbreeding indices (estimated with 22,073 SNPs) with body mass and survival in 400 caribou sampled in RG and RAF herds between 1996 and 2016. We found no association of individual heterozygosity or inbreeding coefficient with body mass or annual survival. Furthermore, those genomic inbreeding indices remained stable over the period monitored. These results suggest that the rapid and intense demographic decline of the herds did not cause inbreeding depression in those populations. Although we found no evidence for HFCs, if demographic decline continues, it is possible that such inbreeding depression would be triggered.
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Affiliation(s)
- Marianne Gagnon
- Département de Biologie, Caribou Ungava and Centre d'Études Nordiques, Université Laval, Quebec, QC, Canada
| | - Glenn Yannic
- CNRS, LECA, Université Grenoble Alpes, University Savoie Mont Blanc, Grenoble, France
| | - Charles Perrier
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul Valery Montpellier, Montpellier, France
| | - Steeve D Côté
- Département de Biologie, Caribou Ungava and Centre d'Études Nordiques, Université Laval, Quebec, QC, Canada
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18
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Fu CZ, Guang XM, Wan QH, Fang SG. Genome Resequencing Reveals Congenital Causes of Embryo and Nestling Death in Crested Ibis (Nipponia nippon). Genome Biol Evol 2019; 11:2125-2135. [PMID: 31298688 PMCID: PMC6685491 DOI: 10.1093/gbe/evz149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2019] [Indexed: 12/18/2022] Open
Abstract
The crested ibis (Nipponia nippon) is endangered worldwide. Although a series of conservation measures have markedly increased the population size and distribution area of these birds, the high mortality of embryos and nestlings considerably decreases the survival potential of this bird species. High-throughput sequencing technology was utilized to compare whole genomes between ten samples from dead crested ibises (including six dead embryos and four dead nestlings aged 0-45 days) and 32 samples from living birds. The results indicated that the dead samples all shared the genetic background of a specific ancestral subpopulation. Furthermore, the dead individuals were less genetically diverse and suffered higher degrees of inbreeding compared with these measures in live birds. Several candidate genes (KLHL3, SETDB2, TNNT2, PKP1, AK1, and EXOSC3) associated with detrimental diseases were identified in the genomic regions that differed between the alive and dead samples, which are likely responsible for the death of embryos and nestlings. In addition, in these regions, we also found several genes involved in the protein catabolic process (UBE4A and LONP1), lipid metabolism (ACOT1), glycan biosynthesis and metabolism (HYAL1 and HYAL4), and the immune system (JAM2) that are likely to promote the normal development of embryos and nestlings. The aberrant conditions of these genes and biological processes may contribute to the death of embryos and nestlings. Our data identify congenital factors underlying the death of embryos and nestlings at the whole genome level, which may be useful toward informing more effective conservation efforts for this bird species.
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Affiliation(s)
- Chun-Zheng Fu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
| | - Xuan-Min Guang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
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19
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Portanier E, Garel M, Devillard S, Maillard D, Poissant J, Galan M, Benabed S, Poirel MT, Duhayer J, Itty C, Bourgoin G. Both candidate gene and neutral genetic diversity correlate with parasite resistance in female Mediterranean mouflon. BMC Ecol 2019; 19:12. [PMID: 30836982 PMCID: PMC6402107 DOI: 10.1186/s12898-019-0228-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Parasite infections can have substantial impacts on population dynamics and are accordingly a key challenge for wild population management. Here we studied genetic mechanisms driving parasite resistance in a large herbivore through a comprehensive approach combining measurements of neutral (16 microsatellites) and adaptive (MHC DRB1 exon 2) genetic diversity and two types of gastrointestinal parasites (nematodes and coccidia). RESULTS While accounting for other extrinsic and intrinsic predictors known to impact parasite load, we show that both neutral genetic diversity and DRB1 are associated with resistance to gastrointestinal nematodes. Intermediate levels of multi-locus heterozygosity maximized nematodes resistance, suggesting that both in- and outbreeding depression might occur in the population. DRB1 heterozygosity and specific alleles effects were detected, suggesting the occurrence of heterozygote advantage, rare-allele effects and/or fluctuating selection. On the contrary, no association was detected between genetic diversity and resistance to coccidia, indicating that different parasite classes are impacted by different genetic drivers. CONCLUSIONS This study provides important insights for large herbivores and wild sheep pathogen management, and in particular suggests that factors likely to impact genetic diversity and allelic frequencies, including global changes, are also expected to impact parasite resistance.
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Affiliation(s)
- Elodie Portanier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive, 69100 Villeurbanne, France
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
- Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l’Etoile, France
| | - Mathieu Garel
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Sébastien Devillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive, 69100 Villeurbanne, France
| | - Daniel Maillard
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Jocelyn Poissant
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Canada
| | - Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 34980 Montferrier Sur Lez, France
| | - Slimania Benabed
- Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l’Etoile, France
| | - Marie-Thérèse Poirel
- Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l’Etoile, France
| | - Jeanne Duhayer
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Christian Itty
- Office National de la Chasse et de la Faune Sauvage, Unité Ongulés Sauvages, 5 allée de Bethléem, Z.I. Mayencin, 38610 Gières, France
| | - Gilles Bourgoin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive, 69100 Villeurbanne, France
- Université de Lyon, VetAgro Sup, Campus Vétérinaire de Lyon, 1 Avenue Bourgelat, BP 83, 69280 Marcy l’Etoile, France
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20
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Morris MRJ, Kaufman R, Rogers SM. Heterozygosity and asymmetry:
Ectodysplasin
as a form of genetic stress in marine threespine stickleback. Evolution 2019; 73:378-389. [DOI: 10.1111/evo.13678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 11/16/2018] [Accepted: 12/14/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Matthew R. J. Morris
- Biological SciencesUniversity of Calgary 2500 University Dr NW Calgary AB T2N 1N4 Canada
- Current Address: Biological SciencesAmbrose University 150 Ambrose Cir SW Calgary AB T3H 0L5 Canada
| | - Rebecca Kaufman
- Biological SciencesUniversity of Calgary 2500 University Dr NW Calgary AB T2N 1N4 Canada
| | - Sean M. Rogers
- Biological SciencesUniversity of Calgary 2500 University Dr NW Calgary AB T2N 1N4 Canada
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21
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Brambilla A, Keller L, Bassano B, Grossen C. Heterozygosity-fitness correlation at the major histocompatibility complex despite low variation in Alpine ibex ( Capra ibex). Evol Appl 2018; 11:631-644. [PMID: 29875807 PMCID: PMC5979623 DOI: 10.1111/eva.12575] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/30/2017] [Indexed: 01/06/2023] Open
Abstract
Crucial for the long-term survival of wild populations is their ability to fight diseases. Disease outbreaks can lead to severe population size reductions, which makes endangered and reintroduced species especially vulnerable. In vertebrates, the major histocompatibility complex (MHC) plays an important role in determining the immune response. Species that went through severe bottlenecks often show very low levels of genetic diversity at the MHC. Due to the known link between the MHC and immune response, such species are expected to be at particular risk in case of disease outbreaks. However, so far, only few studies have shown that low MHC diversity is correlated with increased disease susceptibility in species after severe bottlenecks. We investigated genetic variation at the MHC and its correlations with disease resistance and other fitness-related traits in Alpine ibex (Capra ibex), a wild goat species that underwent a strong bottleneck in the last century and that is known to have extremely low genetic variability, both genome-wide and at the MHC. We studied MHC variation in male ibex of Gran Paradiso National Park, the population used as a source for all postbottleneck reintroductions. We found that individual MHC heterozygosity (based on six microsatellites) was not correlated with genome-wide neutral heterozygosity. MHC heterozygosity, but not genome-wide heterozygosity, was positively correlated with resistance to infectious keratoconjunctivitis and with body mass. Our results show that genetic variation at the MHC plays an important role in disease resistance and, hence, should be taken into account for successfully managing species conservation.
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Affiliation(s)
- Alice Brambilla
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich (ZH)Switzerland
- Alpine Wildlife Research CentreGran Paradiso National ParkNoasca (TO)Italy
| | - Lukas Keller
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich (ZH)Switzerland
| | - Bruno Bassano
- Alpine Wildlife Research CentreGran Paradiso National ParkNoasca (TO)Italy
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurich (ZH)Switzerland
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22
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Heterozygosity–behavior and heterozygosity–fitness correlations in a salamander with limited dispersal. POPUL ECOL 2018. [DOI: 10.1007/s10144-017-0604-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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23
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Grossen C, Biebach I, Angelone-Alasaad S, Keller LF, Croll D. Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations. Evol Appl 2017; 11:123-139. [PMID: 29387150 PMCID: PMC5775499 DOI: 10.1111/eva.12490] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 04/04/2017] [Indexed: 12/30/2022] Open
Abstract
Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long‐term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101,822 genomewide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive breeding and secondary reintroductions from established populations. This stepwise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genomewide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding.
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Affiliation(s)
- Christine Grossen
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Iris Biebach
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Samer Angelone-Alasaad
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies University of Zürich Zürich Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel Neuchâtel Switzerland
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24
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Corlatti L, Storch I, Filli F, Anderwald P. Does selection on horn length of males and females differ in protected and hunted populations of a weakly dimorphic ungulate? Ecol Evol 2017; 7:3713-3723. [PMID: 28616168 PMCID: PMC5468124 DOI: 10.1002/ece3.2963] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 03/02/2017] [Accepted: 03/07/2017] [Indexed: 11/25/2022] Open
Abstract
Weaponry in ungulates may be costly to grow and maintain, and different selective pressures in males and females may lead to sex‐biased natural survival. Sexual differences in the relationship between weapon growth and survival may increase under anthropogenic selection through culling, for example because of trophy hunting. Selection on weaponry growth under different scenarios has been largely investigated in males of highly dimorphic ungulates, for which survival costs (either natural or hunting related) are thought to be greatest. Little is known, however, about the survival costs of weaponry in males and females of weakly dimorphic species. We collected information on horn length and age at death/shooting of 407 chamois Rupicapra rupicapra in a protected population and in two hunted populations with different hunting regimes, to explore sexual differences in the selection on early horn growth under contrasting selective pressures. We also investigated the variation of horn growth and body mass in yearling males (n = 688) and females (n = 539) culled in one of the hunted populations over 14 years. The relationship between horn growth and survival showed remarkable sexual differences under different evolutionary scenarios. Within the protected population, under natural selection, we found no significant trade‐off in either males or females. Under anthropogenic pressure, selection on early horn growth of culled individuals showed diametrically opposed sex‐biased patterns, depending on the culling regime and hunters’ preferences. Despite the selective bias between males and females in one of the hunted populations, we did not detect significant sex‐specific differences in the long‐term pattern of early growth. The relationship between early horn growth and natural survival in either sex might suggest stabilizing selection on horn size in chamois. Selection through culling can be strongly sex‐biased also in weakly dimorphic species, depending on hunters’ preferences and hunting regulations, and long‐term data are needed to reveal potential undesirable evolutionary consequences.
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Affiliation(s)
- Luca Corlatti
- Freiburg Institute for Advanced Studies University of Freiburg Freiburg Germany.,Chair of Wildlife Ecology and Management University of Freiburg Freiburg Germany.,Institute of Wildlife Biology and Game Management University of Natural Resources and Life Sciences Vienna Vienna Austria
| | - Ilse Storch
- Chair of Wildlife Ecology and Management University of Freiburg Freiburg Germany
| | - Flurin Filli
- Swiss National Park Chastè Planta-Wildenberg Zernez Switzerland
| | - Pia Anderwald
- Swiss National Park Chastè Planta-Wildenberg Zernez Switzerland
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25
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DeMay SM, Becker PA, Rachlow JL, Waits LP. Genetic monitoring of an endangered species recovery: demographic and genetic trends for reintroduced pygmy rabbits (Brachylagus idahoensis). J Mammal 2017. [DOI: 10.1093/jmammal/gyw197] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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26
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Frasier TR. A note on the use of multiple linear regression in molecular ecology. Mol Ecol Resour 2015; 16:382-7. [PMID: 26650184 DOI: 10.1111/1755-0998.12499] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/20/2015] [Accepted: 11/26/2015] [Indexed: 11/29/2022]
Abstract
Multiple linear regression analyses (also often referred to as generalized linear models--GLMs, or generalized linear mixed models--GLMMs) are widely used in the analysis of data in molecular ecology, often to assess the relative effects of genetic characteristics on individual fitness or traits, or how environmental characteristics influence patterns of genetic differentiation. However, the coefficients resulting from multiple regression analyses are sometimes misinterpreted, which can lead to incorrect interpretations and conclusions within individual studies, and can propagate to wider-spread errors in the general understanding of a topic. The primary issue revolves around the interpretation of coefficients for independent variables when interaction terms are also included in the analyses. In this scenario, the coefficients associated with each independent variable are often interpreted as the independent effect of each predictor variable on the predicted variable. However, this interpretation is incorrect. The correct interpretation is that these coefficients represent the effect of each predictor variable on the predicted variable when all other predictor variables are zero. This difference may sound subtle, but the ramifications cannot be overstated. Here, my goals are to raise awareness of this issue, to demonstrate and emphasize the problems that can result and to provide alternative approaches for obtaining the desired information.
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Affiliation(s)
- Timothy R Frasier
- Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, Nova Scotia, Canada, B3H 3C3
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