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Musiani M, Randi E. Conservation genomics of wolves: The global impact of RK Wayne's research. J Hered 2024; 115:458-469. [PMID: 38381553 DOI: 10.1093/jhered/esae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/31/2024] [Accepted: 02/20/2024] [Indexed: 02/23/2024] Open
Abstract
RK Wayne has arguably been the most influential geneticist of canids, famously promoting the conservation of wolves in his homeland, the United States. His influence has been felt in other countries and regions outside the contiguous United States, where he inspired others, also including former graduate students and research fellows of his, to use modern molecular techniques to examine the evolutionary biology of canids to inform the conservation and management of wolves. In this review, we focus on the implications of Wayne's work on wolves outside the United States. He envisioned a clear future for wolf conservation research, involving the study of wolves' ecological and genetic diversity, and the description of ecotypes requiring conservation. He also documented widespread hybridization among canids and introgression of DNA from domestic dogs to wolves, a process that started dozens of thousands of years ago. His work therefore calls for innovative studies, such as examining the potential fitness benefits of introgression. Inspired by his results, for example, on the purging of deleterious alleles in small populations, wolf researchers should use novel molecular tools to challenge other conservation genetics paradigms. Overall, RK Wayne's work constitutes a call for answers, which as scientists or citizens concerned with conservation matters, we are obliged to address, as we contribute to monitoring and maintaining biodiversity during our period of dramatic transformations of the biosphere.
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Affiliation(s)
- Marco Musiani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali (BiGeA), University of Bologna, Bologna, Italy
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Aalborg Øst, Denmark
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2
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Lowe WH, Addis BR, Cochrane MM. Outbreeding reduces survival during metamorphosis in a headwater stream salamander. Mol Ecol 2024; 33:e17375. [PMID: 38699973 DOI: 10.1111/mec.17375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 05/05/2024]
Abstract
Assessing direct fitness effects of individual genetic diversity is challenging due to the intensive and long-term data needed to quantify survival and reproduction in the wild. But resolving these effects is necessary to determine how inbreeding and outbreeding influence eco-evolutionary processes. We used 8 years of capture-recapture data and single nucleotide polymorphism genotypes for 1906 individuals to test for effects of individual heterozygosity on stage-specific survival probabilities in the salamander Gyrinophilus porphyriticus. The life cycle of G. porphyriticus includes an aquatic larval stage followed by metamorphosis into a semi-aquatic adult stage. In our study populations, the larval stage lasts 6-10 years, metamorphosis takes several months, and lifespan can reach 20 years. Previous studies showed that metamorphosis is a sensitive life stage, leading us to predict that fitness effects of individual heterozygosity would occur during metamorphosis. Consistent with this prediction, monthly probability of survival during metamorphosis declined with multi-locus heterozygosity (MLH), from 0.38 at the lowest MLH (0.10) to 0.06 at the highest MLH (0.38), a reduction of 84%. Body condition of larvae also declined significantly with increasing MLH. These relationships were consistent in the three study streams. With evidence of localised inbreeding within streams, these results suggest that outbreeding disrupts adaptations in pre-metamorphic and metamorphic individuals to environmental gradients along streams, adding to evidence that headwater streams are hotspots of microgeographic adaptation. Our results also underscore the importance of incorporating life history in analyses of the fitness effects of individual genetic diversity and suggest that metamorphosis and similar discrete life stage transitions may be critical periods of viability selection.
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Affiliation(s)
- Winsor H Lowe
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brett R Addis
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Madaline M Cochrane
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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3
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Huvier N, Moyne G, Kaerle C, Mouzon-Moyne L. Time is running out: Microsatellite data predict the imminent extinction of the boreal lynx (Lynx lynx) in France. FRONTIERS IN CONSERVATION SCIENCE 2023. [DOI: 10.3389/fcosc.2023.1080561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
The Eurasian lynx reappeared in the French Jura Mountains, in the late 1970s, as the result of the dispersion of lynxes from the Carpathian region reintroduced in Switzerland in the early 1970s. Since then, the state of this population has remained poorly known. One estimate gives the number of individuals between 120 and 150. Opportunistic observation and monitoring suggest poor connectivity with the populations in Germany or in other parts of Switzerland. Forty years after its comeback in France, we could expect a higher number of individuals, but possible inbreeding depression as well as threats such as poaching and collisions with cars may explain the limitation of number of individuals observed and may lead to a new extinction of the specie in this region. We used 23 microsatellite markers and 78 DNA samples, collected between 2008 and 2020, to establish the genetic state of the French Jura Mountain lynx population. Our results show extremely low genetic diversity with an observed heterozygosity (Ho) of 0.36 and an effective population size (Ne) of 38.2. When comparing the source population (Carpathian), the inbreeding level is very worrying (Fe = 0.41). These results are among the lowest recorded for the Eurasian lynx. To avoid extinction, which we estimate will occur in approximately 30 years, we recommend the introduction of new genetic material. Although reintroduction is controversial, solutions such as the replacement of poached lynxes and the exchange of orphan lynxes between care centers are good initial actions for population strengthening. This offers a rapid intervention while studying solutions for more sustainable conservation
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Snead AA, Alda F. Time-Series Sequences for Evolutionary Inferences. Integr Comp Biol 2022; 62:1771-1783. [PMID: 36104153 DOI: 10.1093/icb/icac146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 01/05/2023] Open
Affiliation(s)
- Anthony A Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Fernando Alda
- Department of Biology, Geology and Environmental Science, University of Tennessee at Chattanooga, 615 McCallie Ave, Chattanooga, TN 37403, USA
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Smeds L, Ellegren H. From high masked to high realized genetic load in inbred Scandinavian wolves. Mol Ecol 2022; 32:1567-1580. [PMID: 36458895 DOI: 10.1111/mec.16802] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
When new mutations arise at functional sites they are more likely to impair than improve fitness. If not removed by purifying selection, such deleterious mutations will generate a genetic load that can have negative fitness effects in small populations and increase the risk of extinction. This is relevant for the highly inbred Scandinavian wolf (Canis lupus) population, founded by only three wolves in the 1980s and suffering from inbreeding depression. We used functional annotation and evolutionary conservation scores to study deleterious variation in a total of 209 genomes from both the Scandinavian and neighbouring wolf populations in northern Europe. The masked load (deleterious mutations in heterozygote state) was highest in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles, fixation of deleterious variants and a significant increase in the per-individual realized load (deleterious mutations in homozygote state; an increase by 45% in protein-coding genes) over five generations of inbreeding. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and thereby shifting deleterious alleles from homozygous into heterozygote genotypes. However, in the absence of permanent connectivity to Finnish and Russian populations, inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the magnitude of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Hans Ellegren
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
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Nabutanyi P, Wittmann MJ. Modeling minimum viable population size with multiple genetic problems of small populations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2022; 36:e13940. [PMID: 35674090 DOI: 10.1111/cobi.13940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 02/14/2022] [Accepted: 02/18/2022] [Indexed: 06/15/2023]
Abstract
An important goal for conservation is to define minimum viable population (MVP) sizes for long-term persistence of a species. There is increasing evidence of the role of genetics in population extinction; thus, conservation practitioners are starting to consider the effects of deleterious mutations (DM), in particular the effects of inbreeding depression on fitness. We sought to develop methods to account for genetic problems other than inbreeding depression in MVP estimates, quantify the effect of the interaction of multiple genetic problems on MVP sizes, and find ways to reduce the arbitrariness of time and persistence probability thresholds in MVP analyses. To do so, we developed ecoevolutionary quantitative models to track population size and levels of genetic diversity. We assumed a biallelic multilocus genome with loci under single or multiple, interacting genetic forces. We included mutation-selection-drift balance (for loci with DM) and 3 forms of balancing selection for loci for which variation is lost through genetic drift. We defined MVP size as the lowest population size that avoids an ecoevolutionary extinction vortex. For populations affected by only balancing selection, MVP size decreased rapidly as mutation rates increased. For populations affected by mutation-selection-drift balance, the MVP size increased rapidly. In addition, MVP sizes increased rapidly as the number of loci increased under the same or different selection mechanisms until even arbitrarily large populations could not survive. In the case of fixed number of loci under selection, interaction of genetic problems did not always increase MVP sizes. To further enhance understanding about interaction of genetic problems, there is need for more empirical studies to reveal how different genetic processes interact in the genome.
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Affiliation(s)
- Peter Nabutanyi
- Department of Theoretical Biology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Meike J Wittmann
- Department of Theoretical Biology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
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Ellwanger C, Steger L, Pollack C, Wells R, Benjamin Fant J. Anthropogenic fragmentation increases risk of genetic decline in the threatened orchid Platanthera leucophaea. Ecol Evol 2022; 12:e8578. [PMID: 35222956 PMCID: PMC8855017 DOI: 10.1002/ece3.8578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 12/24/2021] [Accepted: 01/05/2022] [Indexed: 11/06/2022] Open
Abstract
Protecting biodiversity requires an understanding of how anthropogenic changes impact the genetic processes associated with extinction risk. Studies of the genetic changes due to anthropogenic fragmentation have revealed conflicting results. This is likely due to the difficulty in isolating habitat loss and fragmentation, which can have opposing impacts on genetic parameters. The well-studied orchid, Platanthera leucophaea, provides a rich dataset to address this issue, allowing us to examine range-wide genetic changes. Midwestern and Northeastern United States. We sampled 35 populations of P. leucophaea that spanned the species' range and varied in patch composition, degree of patch isolation, and population size. From these populations we measured genetic parameters associated with increased extinction risk. Using this combined dataset, we modeled landscape variables and population metrics against genetic parameters to determine the best predictors of increased extinction risk. All genetic parameters were strongly associated with population size, while development and patch isolation showed an association with genetic diversity and genetic structure. Genetic diversity was lowest in populations with small census sizes, greater urbanization pressures (habitat loss), and small patch area. All populations showed moderate levels of inbreeding, regardless of size. Contrary to expectation, we found that critically small populations had negative inbreeding values, indicating non-random mating not typically observed in wild populations, which we attribute to selection for less inbred individuals. The once widespread orchid, Platanthera leucophaea, has suffered drastic declines and extant populations show changes in the genetic parameters associated with increased extinction risk, especially smaller populations. Due to the important correlation with risk and habitat loss, we advocate continued monitoring of population sizes by resource managers, while the critically small populations may need additional management to reverse genetic declines.
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Affiliation(s)
- Claire Ellwanger
- Plant Biology and ConservationChicago Botanic GardenGlencoeIllinoisUSA
- Plant Biology and ConservationNorthwestern University, O.T. Hogan HallEvanstonIllinoisUSA
- U.S. Forest ServiceOkanogan‐Wenatchee National ForestWenatcheeWashingtonUSA
| | - Laura Steger
- Plant Biology and ConservationChicago Botanic GardenGlencoeIllinoisUSA
- School of Life SciencesArizona State UniversityTempeArizonaUSA
| | - Cathy Pollack
- U.S. Fish and Wildlife ServiceChicago Field OfficeChicagoIllinoisUSA
| | - Rachel Wells
- Plant Biology and ConservationChicago Botanic GardenGlencoeIllinoisUSA
- Department of BiologyUniversity of LouisvilleLouisvilleKentuckyUSA
| | - Jeremie Benjamin Fant
- Plant Biology and ConservationChicago Botanic GardenGlencoeIllinoisUSA
- Plant Biology and ConservationNorthwestern University, O.T. Hogan HallEvanstonIllinoisUSA
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8
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Åkesson M, Flagstad Ø, Aspi J, Kojola I, Liberg O, Wabakken P, Sand H. Genetic signature of immigrants and their effect on genetic diversity in the recently established Scandinavian wolf population. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01423-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractTransboundary connectivity is a key component when conserving and managing animal species that require large areas to maintain viable population sizes. Wolves Canis lupus recolonized the Scandinavian Peninsula in the early 1980s. The population is geographically isolated and relies on immigration to not lose genetic diversity and to maintain long term viability. In this study we address (1) to what extent the genetic diversity among Scandinavian wolves has recovered during 30 years since its foundation in relation to the source populations in Finland and Russia, (2) if immigration has occurred from both Finland and Russia, two countries with very different wolf management and legislative obligations to ensure long term viability of wolves, and (3) if immigrants can be assumed to be unrelated. Using 26 microsatellite loci we found that although the genetic diversity increased among Scandinavian wolves (n = 143), it has not reached the same levels found in Finland (n = 25) or in Russia (n = 19). Low genetic differentiation between Finnish and Russian wolves, complicated our ability to determine the origin of immigrant wolves (n = 20) with respect to nationality. Nevertheless, based on differences in allelic richness and private allelic richness between the two countries, results supported the occurrence of immigration from both countries. A priori assumptions that immigrants are unrelated is non-advisable, since 5.8% of the pair-wise analyzed immigrants were closely related. To maintain long term viability of wolves in Northern Europe, this study highlights the potential and need for management actions that facilitate transboundary dispersal.
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Wikenros C, Gicquel M, Zimmermann B, Flagstad Ø, Åkesson M. Age at first reproduction in wolves: different patterns of density dependence for females and males. Proc Biol Sci 2021; 288:20210207. [PMID: 33823674 PMCID: PMC8059544 DOI: 10.1098/rspb.2021.0207] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/09/2021] [Indexed: 01/14/2023] Open
Abstract
Age at first reproduction constitutes a key life-history trait in animals and is evolutionarily shaped by fitness benefits and costs of delayed versus early reproduction. The understanding of how intrinsic and extrinsic changes affects age at first reproduction is crucial for conservation and management of threatened species because of its demographic effects on population growth and generation time. For a period of 40 years in the Scandinavian wolf (Canis lupus) population, including the recolonization phase, we estimated age at first successful reproduction (pup survival to at least three weeks of age) and examined how the variation among individuals was explained by sex, population size (from 1 to 74 packs), primiparous or multiparous origin, reproductive experience of the partner and inbreeding. Median age at first reproduction was 3 years for females (n = 60) and 2 years for males (n = 74), and ranged between 1 and 8-10 years of age (n = 297). Female age at first reproduction decreased with increasing population size, and increased with higher levels of inbreeding. The probability for males to reproduce later first decreased, reaching its minimum when the number of territories approached 40-60, and then increased with increasing population size. Inbreeding for males and reproductive experience of parents and partners for both sexes had overall weak effects on age at first reproduction. These results allow for more accurate parameter estimates when modelling population dynamics for management and conservation of small and vulnerable wolf populations, and show how humans through legal harvest and illegal hunting influence an important life-history trait like age at first reproduction.
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Affiliation(s)
- Camilla Wikenros
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, 73993 Riddarhyttan, Sweden
| | - Morgane Gicquel
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, 73993 Riddarhyttan, Sweden
| | - Barbara Zimmermann
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Campus Evenstad, Inland Norway University of Applied Sciences, 2480 Koppang, Norway
| | - Øystein Flagstad
- Norwegian Institute for Nature Research, PO Box 5685 Torgard, 7485 Trondheim, Norway
| | - Mikael Åkesson
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, 73993 Riddarhyttan, Sweden
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10
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Nabutanyi P, Wittmann MJ. Models for Eco-Evolutionary Extinction Vortices under Balancing Selection. Am Nat 2021; 197:336-350. [PMID: 33625964 DOI: 10.1086/712805] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractThe smaller a population is, the faster it loses genetic diversity as a result of genetic drift. Loss of genetic diversity can reduce population growth rate, making populations even smaller and more vulnerable to loss of genetic diversity. Ultimately, the population can be driven to extinction by this "eco-evolutionary extinction vortex." While there are already quantitative models for extinction vortices resulting from inbreeding depression and mutation accumulation, to date extinction vortices resulting from loss of genetic diversity at loci under various forms of balancing selection have been mainly described verbally. To understand better when such extinction vortices arise and to develop methods for detecting them, we propose quantitative eco-evolutionary models, both stochastic individual-based simulations and deterministic approximations, linking loss of genetic diversity and population decline. Using mathematical analysis and simulations, we identify parameter combinations that exhibit strong interactions between population size and genetic diversity and match our definition of an eco-evolutionary vortex (i.e., per capita population decline rates and per-locus fixation rates increase with decreasing population size and number of polymorphic loci). We further highlight cues that may be exhibited by such populations but find that classical early-warning signals are of limited use in detecting populations undergoing an eco-evolutionary extinction vortex.
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11
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Yang H, You CJ, Tsui CKM, Tembrock LR, Wu ZQ, Yang DP. Phylogeny and biogeography of the Japanese rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae) based on SNP markers. Ecol Evol 2021; 11:153-173. [PMID: 33437420 PMCID: PMC7790660 DOI: 10.1002/ece3.6982] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/23/2020] [Accepted: 10/16/2020] [Indexed: 12/05/2022] Open
Abstract
The Japanese rhinoceros beetle Trypoxylus dichotomus is one of the largest beetle species in the world and is commonly used in traditional Chinese medicine. Ten subspecies of T. dichotomus and a related Trypoxylus species (T. kanamorii) have been described throughout Asia, but their taxonomic delimitations remain problematic. To clarify issues such as taxonomy, and the degree of genetic differentiation of Trypoxylus populations, we investigated the genetic structure, genetic variability, and phylogeography of 53 specimens of Trypoxylus species from 44 locations in five Asian countries (China, Japan, Korea, Thailand, and Myanmar). Using specific-locus amplified fragment sequencing (SLAF-seq) techniques, we developed 330,799 SLAFs over 114.16M reads, in turn yielding 46,939 high-resolution single nucleotide polymorphisms (SNPs) for genotyping. Phylogenetic analysis of SNPs indicated the presence of three distinct genetic groups, suggesting that the various subspecies could be treated as three groups of populations. PCA and ADMIXTURE analysis also identified three genetic clusters (North, South, West), which corresponded to their locations, suggesting that geographic factors were important in maintaining within population homogeneity and between population divergence. Analyses of SNP data confirmed the monophyly of certain subspecies on islands, while other subspecies (e.g., T. d. septentrionalis) were found to be polyphyletic and nested in more than one lineage. AMOVA demonstrated high level of differentiation among populations/groups. Also, pairwise F ST values revealed high differentiation, particularly between South and West, as well as between North and South. Despite the differentiation, measurable gene flow was inferred between genetic clusters but at varying rates and directions. Our study demonstrated that SLAF-seq derived markers outperformed 16S and COII sequences and provided improved resolution of the genetic differentiation of rhinoceros beetle populations from a large part of the species' range.
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Affiliation(s)
- Huan Yang
- School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
| | - Chong Juan You
- Beijing Key Laboratory for Forest Pest ControlBeijing Forestry UniversityBeijingChina
| | - Clement K. M. Tsui
- Department of PathologySidra MedicineDohaQatar
- Department of Pathology and Laboratory MedicineWeill Cornell Medicine‐QatarAr‐RayyanQatar
- Division of Infectious DiseasesFaculty of MedicineUniversity of British ColumbiaVancouverBCCanada
| | - Luke R. Tembrock
- Department of Agricultural BiologyColorado State UniversityFort CollinsCOUSA
| | - Zhi Qiang Wu
- Shenzhen BranchGuangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - De Po Yang
- School of Pharmaceutical SciencesSun Yat‐Sen UniversityGuangzhouChina
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12
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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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13
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Szewczyk M, Nowak S, Niedźwiecka N, Hulva P, Špinkytė-Bačkaitienė R, Demjanovičová K, Bolfíková BČ, Antal V, Fenchuk V, Figura M, Tomczak P, Stachyra P, Stępniak KM, Zwijacz-Kozica T, Mysłajek RW. Dynamic range expansion leads to establishment of a new, genetically distinct wolf population in Central Europe. Sci Rep 2019; 9:19003. [PMID: 31831858 PMCID: PMC6908625 DOI: 10.1038/s41598-019-55273-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/06/2019] [Indexed: 11/12/2022] Open
Abstract
Local extinction and recolonization events can shape genetic structure of subdivided animal populations. The gray wolf (Canis lupus) was extirpated from most of Europe, but recently recolonized big part of its historical range. An exceptionally dynamic expansion of wolf population is observed in the western part of the Great European Plain. Nonetheless, genetic consequences of this process have not yet been fully understood. We aimed to assess genetic diversity of this recently established wolf population in Western Poland (WPL), determine its origin and provide novel data regarding the population genetic structure of the grey wolf in Central Europe. We utilized both spatially explicit and non-explicit Bayesian clustering approaches, as well as a model-independent, multivariate method DAPC, to infer genetic structure in large dataset (881 identified individuals) of wolf microsatellite genotypes. To put the patterns observed in studied population into a broader biogeographic context we also analyzed a mtDNA control region fragment widely used in previous studies. In comparison to a source population, we found slightly reduced allelic richness and heterozygosity in the newly recolonized areas west of the Vistula river. We discovered relatively strong west-east structuring in lowland wolves, probably reflecting founder-flush and allele surfing during range expansion, resulting in clear distinction of WPL, eastern lowland and Carpathian genetic groups. Interestingly, wolves from recently recolonized mountainous areas (Sudetes Mts, SW Poland) clustered together with lowland, but not Carpathian wolf populations. We also identified an area in Central Poland that seems to be a melting pot of western, lowland eastern and Carpathian wolves. We conclude that the process of dynamic recolonization of Central European lowlands lead to the formation of a new, genetically distinct wolf population. Together with the settlement and establishment of packs in mountains by lowland wolves and vice versa, it suggests that demographic dynamics and possibly anthropogenic barriers rather than ecological factors (e.g. natal habitat-biased dispersal patterns) shape the current wolf genetic structure in Central Europe.
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Affiliation(s)
- Maciej Szewczyk
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.,Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland.,Department of Vertebrate Ecology and Zoology, Faculty of Biology, University of Gdańsk, Wita Stwosza 59, 80-308, Gdańsk, Poland
| | - Sabina Nowak
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | - Natalia Niedźwiecka
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | - Pavel Hulva
- Faculty of Science, Charles University in Prague, Viničná 7, 128 43, Prague, Czech Republic.,Faculty of Science, University of Ostrava, Chittussiho 10, 170 00, Ostrava, Czech Republic
| | | | - Klára Demjanovičová
- Faculty of Science, University of Ostrava, Chittussiho 10, 170 00, Ostrava, Czech Republic
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Prague 6, 165 00, Czech Republic
| | - Vladimír Antal
- State Nature Conservancy of Slovak Republic, Tajovského 28B, 974 01, Banská Bystrica, Slovakia
| | - Viktar Fenchuk
- APB-BirdLife Belarus, Engelsa 34A - 1, 220030, Minsk, Belarus
| | - Michał Figura
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | - Patrycja Tomczak
- Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland.,Institute of Romance Studies, Faculty of Modern Languages and Literature, Adam Mickiewicz University in Poznań, Al. Niepodległości 4, 61-874, Poznań, Poland
| | | | - Kinga M Stępniak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.,Association for Nature "Wolf", Twardorzeczka, Cynkowa 4, 34-324, Lipowa, Poland
| | | | - Robert W Mysłajek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawińskiego 5a, 02-106, Warsaw, Poland.
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14
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Yates MC, Bowles E, Fraser DJ. Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish. Proc Biol Sci 2019; 286:20191989. [PMID: 31771476 DOI: 10.1098/rspb.2019.1989] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size (Ne), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had no effect on either fitness correlate, which was determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low Ne, and long-term isolation can represent important sources of variation and are capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.
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Affiliation(s)
- M C Yates
- Department of Biology, UQAM, Montreal, QC, Canada H3C 3P8.,Group for Interuniversity Research in Limnology and Aquatic Environment (GRIL), Montreal, QC, Canada H3C 3J7
| | - E Bowles
- Department of Biology, Concordia University, Montreal, QC, Canada H4B 1R6
| | - D J Fraser
- Department of Biology, Concordia University, Montreal, QC, Canada H4B 1R6.,Group for Interuniversity Research in Limnology and Aquatic Environment (GRIL), Montreal, QC, Canada H3C 3J7
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15
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Ramírez‐Barrera SM, Velasco JA, Orozco‐Téllez TM, Vázquez‐López AM, Hernández‐Baños BE. What drives genetic and phenotypic divergence in the Red-crowned Ant tanager ( Habia rubica, Aves: Cardinalidae), a polytypic species? Ecol Evol 2019; 9:12339-12352. [PMID: 31832165 PMCID: PMC6854386 DOI: 10.1002/ece3.5742] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/07/2019] [Accepted: 09/15/2019] [Indexed: 01/28/2023] Open
Abstract
AIM The effects of geographic and environmental variables on patterns of genetic and phenotypic differentiation have been thoroughly studied. Ecological speciation involves reproductive isolation due to divergent natural selection that can result in a positive correlation between genetic divergence and adaptive phenotypic divergence (isolation by adaptation, IBA). If the phenotypic target of selection is unknown or not easily measured, environmental variation can be used as a proxy, expecting positive correlation between genetic and environmental distances, independent of geographic distances (isolation by environment, IBE). The null model is that the amount of gene flow between populations decreases as the geographic distance between them increases, and genetic divergence is due simply to the neutral effects of genetic drift (isolation by distance, IBD). However, since phenotypic differentiation in natural populations may be autocorrelated with geographic distance, it is often difficult to distinguish IBA from the neutral expectation of IBD. In this work, we test hypotheses of IBA, IBE, and IBD in the Red-crowned Ant tanager (Habia rubica). LOCATION Mesoamerica (Mexico-Central America) and South America. TAXON Habia rubica (Aves: Cardinalidae). METHODS We compiled genetic data, coloration, and morphometric data from specimens from collections in Mexico and the United States. We used the Multiple Matrix Regression with Randomization (MMRR) approach to evaluate the influence of geographic and environmental distances on genetic and phenotypic differentiation of H. rubica at both phylogroup and population levels. RESULTS Our results provide strong evidence that geographic distance is the main driver of genetic variation in H. rubica. We did not find evidence that climate variation is driving population differentiation in this species across a widespread geographic region. MAIN CONCLUSIONS Our data point to geographic isolation as the main factor structuring genetic variation within populations of H. rubica and suggest that climate is not playing a major role in genetic differentiation within this species.
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Affiliation(s)
- Sandra M. Ramírez‐Barrera
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Departamento de Biología EvolutivaFacultad de CienciasMuseo de ZoologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Julián A. Velasco
- Centro de Ciencias de la AtmósferaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Tania M. Orozco‐Téllez
- Departamento de Biología EvolutivaFacultad de CienciasMuseo de ZoologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Alma M. Vázquez‐López
- Posgrado en Ciencias BiológicasUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
- Departamento de Biología EvolutivaFacultad de CienciasMuseo de ZoologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
| | - Blanca E. Hernández‐Baños
- Departamento de Biología EvolutivaFacultad de CienciasMuseo de ZoologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
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16
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Smeds L, Kojola I, Ellegren H. The evolutionary history of grey wolf Y chromosomes. Mol Ecol 2019; 28:2173-2191. [PMID: 30788868 PMCID: PMC6850511 DOI: 10.1111/mec.15054] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 12/30/2022]
Abstract
Analyses of Y chromosome haplotypes uniquely provide a paternal picture of evolutionary histories and offer a very useful contrast to studies based on maternally inherited mitochondrial DNA (mtDNA). Here we used a bioinformatic approach based on comparison of male and female sequence coverage to identify 4.7 Mb from the grey wolf (Canis lupis) Y chromosome, probably representing most of the male-specific, nonampliconic sequence from the euchromatic part of the chromosome. We characterized this sequence and then identified ≈1,500 Y-linked single nucleotide polymorphisms in a sample of 145 resequenced male wolves, including 75 Finnish wolf genomes newly sequenced in this study, and in 24 dogs and eight other canids. We found 53 Y chromosome haplotypes, of which 26 were seen in grey wolves, that clustered in four major haplogroups. All four haplogroups were represented in samples of Finnish wolves, showing that haplogroup lineages were not partitioned on a continental scale. However, regional population structure was indicated because individual haplotypes were never shared between geographically distant areas, and genetically similar haplotypes were only found within the same geographical region. The deepest split between grey wolf haplogroups was estimated to have occurred 125,000 years ago, which is considerably older than recent estimates of the time of divergence of wolf populations. The distribution of dogs in a phylogenetic tree of Y chromosome haplotypes supports multiple domestication events, or wolf paternal introgression, starting 29,000 years ago. We also addressed the disputed origin of a recently founded population of Scandinavian wolves and observed that founding as well as most recent immigrant haplotypes were present in the neighbouring Finnish population, but not in sequenced wolves from elsewhere in the world, or in dogs.
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Affiliation(s)
- Linnéa Smeds
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke), Rovaniemi, Finland
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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17
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Pilot M, Greco C, vonHoldt BM, Randi E, Jędrzejewski W, Sidorovich VE, Konopiński MK, Ostrander EA, Wayne RK. Widespread, long-term admixture between grey wolves and domestic dogs across Eurasia and its implications for the conservation status of hybrids. Evol Appl 2018; 11:662-680. [PMID: 29875809 PMCID: PMC5978975 DOI: 10.1111/eva.12595] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/03/2018] [Indexed: 01/05/2023] Open
Abstract
Hybridisation between a domesticated species and its wild ancestor is an important conservation problem, especially if it results in the introgression of domestic gene variants into wild species. Nevertheless, the legal status of hybrids remains unregulated, partially because of the limited understanding of the hybridisation process and its consequences. The occurrence of hybridisation between grey wolves and domestic dogs is well documented from different parts of the wolf geographic range, but little is known about the frequency of hybridisation events, their causes and the genetic impact on wolf populations. We analysed 61K SNPs spanning the canid genome in wolves from across Eurasia and North America and compared that data to similar data from dogs to identify signatures of admixture. The haplotype block analysis, which included 38 autosomes and the X chromosome, indicated the presence of individuals of mixed wolf-dog ancestry in most Eurasian wolf populations, but less admixture was present in North American populations. We found evidence for male-biased introgression of dog alleles into wolf populations, but also identified a first-generation hybrid resulting from mating between a female dog and a male wolf. We found small blocks of dog ancestry in the genomes of 62% Eurasian wolves studied and melanistic individuals with no signs of recent admixed ancestry, but with a dog-derived allele at a locus linked to melanism. Consequently, these results suggest that hybridisation has been occurring in different parts of Eurasia on multiple timescales and is not solely a recent phenomenon. Nevertheless, wolf populations have maintained genetic differentiation from dogs, suggesting that hybridisation at a low frequency does not diminish distinctiveness of the wolf gene pool. However, increased hybridisation frequency may be detrimental for wolf populations, stressing the need for genetic monitoring to assess the frequency and distribution of individuals resulting from recent admixture.
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Affiliation(s)
| | - Claudia Greco
- Department of Environmental Monitoring and Biodiversity ConservationItalian National Institute for Environmental Protection and ResearchBolognaItaly
| | - Bridgett M. vonHoldt
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
| | - Ettore Randi
- Department of Environmental Monitoring and Biodiversity ConservationItalian National Institute for Environmental Protection and ResearchBolognaItaly
- Department 18/Section of Environmental EngineeringAalborg UniversityAalborgDenmark
| | - Włodzimierz Jędrzejewski
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
- Present address:
Instituto Venezolano de Investigaciones Cientificas (IVIC)Centro de EcologiaCaracasVenezuela
| | | | | | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCAUSA
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18
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Wells DA, Cant MA, Nichols HJ, Hoffman JI. A high-quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal. Mol Ecol 2018; 27:2271-2288. [PMID: 29603504 DOI: 10.1111/mec.14570] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 03/05/2018] [Accepted: 03/12/2018] [Indexed: 01/07/2023]
Abstract
Inbreeding depression, the reduced fitness of offspring of closely related parents, is commonplace in both captive and wild populations and has important consequences for conservation and mating system evolution. However, because of the difficulty of collecting pedigree and life-history data from wild populations, relatively few studies have been able to compare inbreeding depression for traits at different points in the life cycle. Moreover, pedigrees give the expected proportion of the genome that is identical by descent (IBDg ) whereas in theory with enough molecular markers realized IBDg can be quantified directly. We therefore investigated inbreeding depression for multiple life-history traits in a wild population of banded mongooses using pedigree-based inbreeding coefficients (fped ) and standardized multilocus heterozygosity (sMLH) measured at 35-43 microsatellites. Within an information theoretic framework, we evaluated support for either fped or sMLH as inbreeding terms and used sequential regression to determine whether the residuals of sMLH on fped explain fitness variation above and beyond fped . We found no evidence of inbreeding depression for survival, either before or after nutritional independence. By contrast, inbreeding was negatively associated with two quality-related traits, yearling body mass and annual male reproductive success. Yearling body mass was associated with fped but not sMLH, while male annual reproductive success was best explained by both fped and residual sMLH. Thus, our study not only uncovers variation in the extent to which different traits show inbreeding depression, but also reveals trait-specific differences in the ability of pedigrees and molecular markers to explain fitness variation and suggests that for certain traits, genetic markers may capture variation in realized IBDg above and beyond the pedigree expectation.
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Affiliation(s)
- David A Wells
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany.,School of Natural Science and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Michael A Cant
- College of Life and Environmental Sciences, University of Exeter, Penryn, UK
| | - Hazel J Nichols
- School of Natural Science and Psychology, Liverpool John Moores University, Liverpool, UK
| | - Joseph I Hoffman
- Department of Animal Behaviour, University of Bielefeld, Bielefeld, Germany
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19
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Kardos M, Åkesson M, Fountain T, Flagstad Ø, Liberg O, Olason P, Sand H, Wabakken P, Wikenros C, Ellegren H. Genomic consequences of intensive inbreeding in an isolated wolf population. Nat Ecol Evol 2017; 2:124-131. [PMID: 29158554 DOI: 10.1038/s41559-017-0375-4] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/19/2017] [Indexed: 12/26/2022]
Abstract
Inbreeding (mating between relatives) is a major concern for conservation as it decreases individual fitness and can increase the risk of population extinction. We used whole-genome resequencing of 97 grey wolves (Canis lupus) from the highly inbred Scandinavian wolf population to identify 'identical-by-descent' (IBD) chromosome segments as runs of homozygosity (ROH). This gave the high resolution required to precisely measure realized inbreeding as the IBD fraction of the genome in ROH (F ROH). We found a striking pattern of complete or near-complete homozygosity of entire chromosomes in many individuals. The majority of individual inbreeding was due to long IBD segments (>5 cM) originating from ancestors ≤10 generations ago, with 10 genomic regions showing very few ROH and forming candidate regions for containing loci contributing strongly to inbreeding depression. Inbreeding estimated with an extensive pedigree (F P) was strongly correlated with realized inbreeding measured with the entire genome (r 2 = 0.86). However, inbreeding measured with the whole genome was more strongly correlated with multi-locus heterozygosity estimated with as few as 500 single nucleotide polymorphisms, and with F ROH estimated with as few as 10,000 single nucleotide polymorphisms, than with F P. These results document in fine detail the genomic consequences of intensive inbreeding in a population of conservation concern.
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Affiliation(s)
- Marty Kardos
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.,Flathead Lake Biological Station, University of Montana, Polson, MA, 59860, USA
| | - Mikael Åkesson
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | - Toby Fountain
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Øystein Flagstad
- Norwegian Institute for Nature Research, PO Box 5685, Sluppen, NO-7485, Trondheim, Norway
| | - Olof Liberg
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | - Pall Olason
- Wallenberg Advanced Bioinformatics Infrastructure, Science for Life Laboratory, Uppsala University, 75123, Uppsala, Sweden
| | - Håkan Sand
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | - Petter Wabakken
- Faculty of Applied Ecology and Agricultural Sciences, Campus Evenstad, Inland Norway University of Applied Sciences, NO-2480, Elverum, Norway
| | - Camilla Wikenros
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.
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20
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Linnell JDC, Trouwborst A, Fleurke FM. When is it acceptable to kill a strictly protected carnivore? Exploring the legal constraints on wildlife management within Europe’s Bern Convention. NATURE CONSERVATION 2017. [DOI: 10.3897/natureconservation.21.12836] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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21
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Springate L, Frasier TR. Gamete compatibility genes in mammals: candidates, applications and a potential path forward. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170577. [PMID: 28878999 PMCID: PMC5579115 DOI: 10.1098/rsos.170577] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/31/2017] [Indexed: 06/01/2023]
Abstract
Fertilization represents a critical stage in biology, where successful alleles of a previous generation are shuffled into new arrangements and subjected to the forces of selection in the next generation. Although much research has been conducted on how variation in morphological and behavioural traits lead to variation in fertilization patterns, surprisingly little is known about fertilization at a molecular level, and specifically about how genes expressed on the sperm and egg themselves influence fertilization patterns. In mammals, several genes have been identified whose products are expressed on either the sperm or the egg, and which influence the fertilization process, but the specific mechanisms are not yet known. Additionally, in 2014 an interacting pair of proteins was identified: 'Izumo' on the sperm, and 'Juno' on the egg. With the identification of these genes comes the first opportunity to understand the molecular aspects of fertilization in mammals, and to identify how the genetic characteristics of these genes influence fertilization patterns. Here, we review recent progress in our understanding of fertilization and gamete compatibility in mammals, which should provide a helpful guide to researchers interested in untangling the molecular mechanisms of fertilization and the resulting impacts on population biology and evolutionary processes.
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22
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Population Genetics and Demography Unite Ecology and Evolution. Trends Ecol Evol 2017; 32:141-152. [DOI: 10.1016/j.tree.2016.12.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 12/08/2016] [Accepted: 12/10/2016] [Indexed: 12/31/2022]
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23
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Rochus CM, Johansson AM. Estimation of genetic diversity in Gute sheep: pedigree and microsatellite analyses of an ancient Swedish breed. Hereditas 2017; 154:4. [PMID: 28163665 PMCID: PMC5282709 DOI: 10.1186/s41065-017-0026-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 01/20/2017] [Indexed: 12/03/2022] Open
Abstract
Background Breeds with small population size are in danger of an increased inbreeding rate and loss of genetic diversity, which puts them at risk for extinction. In Sweden there are a number of local breeds, native breeds which have adapted to specific areas in Sweden, for which efforts are being made to keep them pure and healthy over time. One example of such a breed is the Swedish Gute sheep. The objective of this study was to estimate inbreeding and genetic diversity of Swedish Gute sheep. Results Three datasets were analysed: pedigree information of the whole population, pedigree information for 100 animals of the population, and microsatellite genotypes for 94 of the 100 animals. The average inbreeding coefficient for lambs born during a six year time period (2007–2012) did not increase during that time period. The inbreeding calculated from the entire pedigree (0.038) and for a sample of the population (0.018) was very low. Sheep were more heterozygous at the microsatellite markers than expected (average multilocus heterozygosity and Ritland inbreeding estimates 1.01845 and -0.03931) and five of seven microsatellite markers were not in Hardy Weinberg equilibrium due to heterozygosity excess. The total effective population size estimated from the pedigree information was 155.4 and the average harmonic mean effective population size estimated from microsatellites was 88.3. Pedigree and microsatellite genotype estimations of inbreeding were consistent with a breeding program with the purpose of reducing inbreeding. Conclusion Our results showed that current breeding programs of the Swedish Gute sheep are consistent with efforts of keeping this breed viable and these breeding programs are an example for other small local breeds in conserving breeds for the future. Electronic supplementary material The online version of this article (doi:10.1186/s41065-017-0026-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christina M Rochus
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7023, Uppsala, SE-75007 Sweden.,UFR Génétique, Élevage et Reproduction; Sciences de la Vie et Santé, AgroParisTech, Université Paris-Saclay, Paris, France.,Génétique Physiologie Systèmes d'Elevage (GenPhySE), Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7023, Uppsala, SE-75007 Sweden
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24
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Widdig A, Muniz L, Minkner M, Barth Y, Bley S, Ruiz-Lambides A, Junge O, Mundry R, Kulik L. Low incidence of inbreeding in a long-lived primate population isolated for 75 years. Behav Ecol Sociobiol 2016; 71:18. [PMID: 28018027 PMCID: PMC5145906 DOI: 10.1007/s00265-016-2236-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 11/13/2022]
Abstract
ABSTRACT When close relatives mate, offspring are expected to suffer fitness consequences due to inbreeding depression. Inbreeding has previously been quantified in two ways: using a sufficiently large panel of markers or deep and complete pedigrees over several generations. However, the application of both approaches is still limited by the challenge of compiling such data for species with long generation times, such as primates. Here, we assess inbreeding in rhesus macaques living on Cayo Santiago (Puerto Rico), a population genetically isolated since 1938, but descendant of a large set of presumably unrelated founders. Using comprehensive genetic data, we calculated inbreeding coefficients (F) for 2669 individuals with complete three generation pedigrees and 609 individuals with complete four generation pedigrees. We found that 0.79 and 7.39% of individuals had an F > 0 when using data from three and four generation pedigrees, respectively. No evidence of an increase in inbreeding over the study period (up to 23 years) was found. Furthermore, the observed mean relatedness of breeding pairs differed significantly from the distribution of parental relatedness expected as simulated based on previous reproductive data, suggesting that kin generally avoid breeding with each other. Finally, inbreeding was not a predictor of early mortality measured as survival until weaning and sexual maturation, respectively. Our results remain consistent with three estimators of inbreeding (standardized heterozygosity, internal relatedness, and homozygosity by loci) using up to 42 highly polymorphic microsatellites for the same set of individuals. Together, our results demonstrate that close inbreeding may not be prevalent even in populations isolated over long periods when mechanisms of inbreeding avoidance can operate. SIGNIFICANCE STATEMENT When close relatives mate, offspring may suffer from such inbreeding, e.g., via lower survival and/or fertility. Using (i) a large panel of genetic markers and (ii) complete three or four generation pedigrees, respectively, we show that incidences of inbreeding in a long-lived primate population are rare, even after genetic isolation for 75 years. Moreover, our simulations suggest that kin in our population generally avoid breeding with each other. Finally, the few inbred individuals detected in our large sample did not suffer from lower survival. Given that many animal species face dramatic habitat loss combined with critical population declines, our study provides important implications for conservation biology in general and for population management in particular.
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Affiliation(s)
- Anja Widdig
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- German Center for Integrative Biodiversity Research (iDiv), Deutscher Platz 5E, 04103 Leipzig, Germany
| | - Laura Muniz
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Mirjam Minkner
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Yvonne Barth
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Stefanie Bley
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
| | - Angelina Ruiz-Lambides
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
- Caribbean Primate Research Center, University of Puerto Rico, Medical Sciences Campus, Punta Santiago, PO Box 906, San Juan, PR 00741 USA
| | - Olaf Junge
- Institute of Medical Informatics and Statistics, University Medical Center Schleswig-Holstein, Campus Kiel, Brunswiker Straße 10, 24105 Kiel, Germany
| | - Roger Mundry
- Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Lars Kulik
- Junior Research Group of Primate Kin Selection, Department of Primatology, Max-Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Research Group of Behavioural Ecology, Institute of Biology, University of Leipzig, Talstraße 33, 04103 Leipzig, Germany
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25
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Ferrer ES, García-Navas V, Sanz JJ, Ortego J. The strength of the association between heterozygosity and probability of interannual local recruitment increases with environmental harshness in blue tits. Ecol Evol 2016; 6:8857-8869. [PMID: 28035274 PMCID: PMC5192745 DOI: 10.1002/ece3.2591] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/10/2016] [Accepted: 10/17/2016] [Indexed: 02/02/2023] Open
Abstract
The extent of inbreeding depression and the magnitude of heterozygosity–fitness correlations (HFC) have been suggested to depend on the environmental context in which they are assayed, but little evidence is available for wild populations. We combine extensive molecular and capture–mark–recapture data from a blue tit (Cyanistes caeruleus) population to (1) analyze the relationship between heterozygosity and probability of interannual adult local recruitment and (2) test whether environmental stress imposed by physiologically suboptimal temperatures and rainfall influence the magnitude of HFC. To address these questions, we used two different arrays of microsatellite markers: 14 loci classified as neutral and 12 loci classified as putatively functional. We found significant relationships between heterozygosity and probability of interannual local recruitment that were most likely explained by variation in genomewide heterozygosity. The strength of the association between heterozygosity and probability of interannual local recruitment was positively associated with annual accumulated precipitation. Annual mean heterozygosity increased over time, which may have resulted from an overall positive selection on heterozygosity over the course of the study period. Finally, neutral and putatively functional loci showed similar trends, but the former had stronger effect sizes and seemed to better reflect genomewide heterozygosity. Overall, our results show that HFC can be context dependent, emphasizing the need to consider the role of environmental heterogeneity as a key factor when exploring the consequences of individual genetic diversity on fitness in natural populations.
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Affiliation(s)
- Esperanza S Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM) Ciudad Real Spain; Departamento de Ciencias Ambientales Facultad de Ciencias Ambientales y Bioquímica Universidad de Castilla-La Mancha Toledo Spain
| | - Vicente García-Navas
- Grupo de Investigación de la Biodiversidad Genética y Cultural Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM) Ciudad Real Spain; Departamento de Ciencias Ambientales Facultad de Ciencias Ambientales y Bioquímica Universidad de Castilla-La Mancha Toledo Spain; Institute of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland; Department of Integrative Ecology Estación Biológica de Doñana (EBD-CSIC) Seville Spain
| | - Juan José Sanz
- Departamento de Ecología Evolutiva Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD-CSIC) Seville Spain
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Dutoit L, Burri R, Nater A, Mugal CF, Ellegren H. Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome. Mol Ecol Resour 2016; 17:586-597. [DOI: 10.1111/1755-0998.12602] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 09/02/2016] [Accepted: 09/19/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Ludovic Dutoit
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Reto Burri
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Alexander Nater
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Carina F. Mugal
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology; Evolutionary Biology Centre; Uppsala University; Norbyvägen 18D SE-752 36 Uppsala Sweden
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First genealogy for a wild marine fish population reveals multigenerational philopatry. Proc Natl Acad Sci U S A 2016; 113:13245-13250. [PMID: 27799530 DOI: 10.1073/pnas.1611797113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Natal philopatry, the return of individuals to their natal area for reproduction, has advantages and disadvantages for animal populations. Natal philopatry may generate local genetic adaptation, but it may also increase the probability of inbreeding that can compromise persistence. Although natal philopatry is well documented in anadromous fishes, marine fish may also return to their birth site to spawn. How philopatry shapes wild fish populations is, however, unclear because it requires constructing multigenerational pedigrees that are currently lacking for marine fishes. Here we present the first multigenerational pedigree for a marine fish population by repeatedly genotyping all individuals in a population of the orange clownfish (Amphiprion percula) at Kimbe Island (Papua New Guinea) during a 10-y period. Based on 2927 individuals, our pedigree analysis revealed that longitudinal philopatry was recurrent over five generations. Progeny tended to settle close to their parents, with related individuals often sharing the same colony. However, successful inbreeding was rare, and genetic diversity remained high, suggesting occasional inbreeding does not impair local population persistence. Local reproductive success was dependent on the habitat larvae settled into, rather than the habitat they came from. Our study suggests that longitudinal philopatry can influence both population replenishment and local adaptation of marine fishes. Resolving multigenerational pedigrees during a relatively short period, as we present here, provides a framework for assessing the ability of marine populations to persist and adapt to accelerating climate change.
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Milleret C, Wabakken P, Liberg O, Åkesson M, Flagstad Ø, Andreassen HP, Sand H. Let's stay together? Intrinsic and extrinsic factors involved in pair bond dissolution in a recolonizing wolf population. J Anim Ecol 2016; 86:43-54. [PMID: 27559712 PMCID: PMC5215671 DOI: 10.1111/1365-2656.12587] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 08/18/2016] [Indexed: 11/30/2022]
Abstract
For socially monogamous species, breeder bond dissolution has important consequences for population dynamics, but the extent to which extrinsic or intrinsic population factors causes pair dissolution remain poorly understood, especially among carnivores. Using an extensive life‐history data set, a survival analysis and competing risks framework, we examined the fate of 153 different wolf (Canis lupus) pairs in the recolonizing Scandinavian wolf population, during 14 winters of snow tracking and DNA monitoring. Wolf pair dissolution was generally linked to a mortality event and was strongly affected by extrinsic (i.e. anthropogenic) causes. No divorce was observed, and among the pair dissolution where causes have been identified, death of one or both wolves was always involved. Median time from pair formation to pair dissolution was three consecutive winters (i.e. approximately 2 years). Pair dissolution was mostly human‐related, primarily caused by legal control actions (36·7%), verified poaching (9·2%) and traffic‐related causes (2·1%). Intrinsic factors, such as disease and age, accounted for only 7·7% of pair dissolutions. The remaining 44·3% of dissolution events were from unknown causes, but we argue that a large portion could be explained by an additional source of human‐caused mortality, cryptic poaching. Extrinsic population factors, such as variables describing the geographical location of the pair, had a stronger effect on risk of pair dissolution compared to anthropogenic landscape characteristics. Population intrinsic factors, such as the inbreeding coefficient of the male pair member, had a negative effect on pair bond duration. The mechanism behind this result remains unknown, but might be explained by lower survival of inbred males or more complex inbreeding effects mediated by behaviour. Our study provides quantitative estimates of breeder bond duration in a social carnivore and highlights the effect of extrinsic (i.e. anthropogenic) and intrinsic factors (i.e. inbreeding) involved in wolf pair bond duration. Unlike the effects of intrinsic and extrinsic factors that are commonly reported on individual survival or population growth, here we provide quantitative estimates of their potential effect on the social unit of the population, the wolf pair.
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Affiliation(s)
- Cyril Milleret
- Faculty of Applied Ecology and Agricultural Sciences, Hedmark University of Applied Sciences, Evenstad, N-2480, Koppang, Norway
| | - Petter Wabakken
- Faculty of Applied Ecology and Agricultural Sciences, Hedmark University of Applied Sciences, Evenstad, N-2480, Koppang, Norway
| | - Olof Liberg
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | - Mikael Åkesson
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | - Øystein Flagstad
- Norwegian Institute for Nature Research, Tungasletta 2, 7485, Trondheim, Norway
| | - Harry Peter Andreassen
- Faculty of Applied Ecology and Agricultural Sciences, Hedmark University of Applied Sciences, Evenstad, N-2480, Koppang, Norway
| | - Håkan Sand
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
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Hindrikson M, Remm J, Pilot M, Godinho R, Stronen AV, Baltrūnaité L, Czarnomska SD, Leonard JA, Randi E, Nowak C, Åkesson M, López-Bao JV, Álvares F, Llaneza L, Echegaray J, Vilà C, Ozolins J, Rungis D, Aspi J, Paule L, Skrbinšek T, Saarma U. Wolf population genetics in Europe: a systematic review, meta-analysis and suggestions for conservation and management. Biol Rev Camb Philos Soc 2016; 92:1601-1629. [PMID: 27682639 DOI: 10.1111/brv.12298] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 08/01/2016] [Accepted: 08/26/2016] [Indexed: 01/04/2023]
Abstract
The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human-carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the 'pre-genomic era' and the first insights of the 'genomics era'. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south-west (lowest genetic diversity) to north-east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650-850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science-based wolf conservation and management at regional and Europe-wide scales.
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Affiliation(s)
- Maris Hindrikson
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Jaanus Remm
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
| | - Malgorzata Pilot
- School of Life Sciences, University of Lincoln, Green Lane, LN6 7DL, Lincoln, UK
| | - Raquel Godinho
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - Astrid Vik Stronen
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
| | - Laima Baltrūnaité
- Laboratory of Mammalian Biology, Nature Research Centre, Akademijos 2, 08412, Vilnius, Lithuania
| | - Sylwia D Czarnomska
- Mammal Research Institute Polish Academy of Sciences, Waszkiewicza 1, 17-230, Białowieża, Poland
| | - Jennifer A Leonard
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Ettore Randi
- Department of Chemistry and Bioscience, Section of Biology and Environmental Science, Aalborg University, Fredrik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), 40064, Ozzano dell'Emilia, Bologna, Italy
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - Mikael Åkesson
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Sciences, SE-730 91, Riddarhyttan, Sweden
| | | | - Francisco Álvares
- CIBIO/InBio - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - Luis Llaneza
- ARENA Asesores en Recursos Naturales S.L. c/Perpetuo Socorro, n° 12 Entlo 2B, 27003, Lugo, Spain
| | - Jorge Echegaray
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Carles Vilà
- Department of Integrative Ecology, Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Avd. Americo Vespucio s/n, 41092, Seville, Spain
| | - Janis Ozolins
- Latvian State Forest Research Institute "Silava", Rigas iela 111, LV-2169, Salaspils, Latvia
| | - Dainis Rungis
- Latvian State Forest Research Institute "Silava", Rigas iela 111, LV-2169, Salaspils, Latvia
| | - Jouni Aspi
- Department of Genetics and Physiology, University of Oulu, 90014, Oulu, Finland
| | - Ladislav Paule
- Department of Phytology, Faculty of Forestry, Technical University, T.G. Masaryk str. 24, SK-96053, Zvolen, Slovakia
| | - Tomaž Skrbinšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Vecna pot 111, 1000, Ljubljana, Slovenia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51014, Tartu, Estonia
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Åkesson M, Liberg O, Sand H, Wabakken P, Bensch S, Flagstad Ø. Genetic rescue in a severely inbred wolf population. Mol Ecol 2016; 25:4745-56. [PMID: 27497431 PMCID: PMC5054837 DOI: 10.1111/mec.13797] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/14/2016] [Accepted: 07/29/2016] [Indexed: 11/29/2022]
Abstract
Natural populations are becoming increasingly fragmented which is expected to affect their viability due to inbreeding depression, reduced genetic diversity and increased sensitivity to demographic and environmental stochasticity. In small and highly inbred populations, the introduction of only a few immigrants may increase vital rates significantly. However, very few studies have quantified the long-term success of immigrants and inbred individuals in natural populations. Following an episode of natural immigration to the isolated, severely inbred Scandinavian wolf (Canis lupus) population, we demonstrate significantly higher pairing and breeding success for offspring to immigrants compared to offspring from native, inbred pairs. We argue that inbreeding depression is the underlying mechanism for the profound difference in breeding success. Highly inbred wolves may have lower survival during natal dispersal as well as competitive disadvantage to find a partner. Our study is one of the first to quantify and compare the reproductive success of first-generation offspring from migrants vs. native, inbred individuals in a natural population. Indeed, our data demonstrate the profound impact single immigrants can have in small, inbred populations, and represent one of very few documented cases of genetic rescue in a population of large carnivores.
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Affiliation(s)
- Mikael Åkesson
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, Riddarhyttan, SE-730 91, Sweden.
| | - Olof Liberg
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, Riddarhyttan, SE-730 91, Sweden
| | - Håkan Sand
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, Riddarhyttan, SE-730 91, Sweden
| | - Petter Wabakken
- Department of Applied Ecology and Agricultural Sciences, Hedmark University College, Evenstad, NO-2480, Norway
| | - Staffan Bensch
- Department of Biology, Lund University, Box 118, Lund, SE-221 00, Sweden
| | - Øystein Flagstad
- Norwegian Institute for Nature Research, P.O. Box 5685 Sluppen, Trondheim, NO-7485, Norway
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31
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Ordiz A, Milleret C, Kindberg J, Månsson J, Wabakken P, Swenson JE, Sand H. Wolves, people, and brown bears influence the expansion of the recolonizing wolf population in Scandinavia. Ecosphere 2015. [DOI: 10.1890/es15-00243.1] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Galaverni M, Caniglia R, Milanesi P, Lapalombella S, Fabbri E, Randi E. Choosy Wolves? Heterozygote Advantage But No Evidence of MHC-Based Disassortative Mating. J Hered 2015; 107:134-42. [PMID: 26610365 DOI: 10.1093/jhered/esv090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/27/2015] [Indexed: 11/13/2022] Open
Abstract
A variety of nonrandom mate choice strategies, including disassortative mating, are used by vertebrate species to avoid inbreeding, maintain heterozygosity and increase fitness. Disassortative mating may be mediated by the major histocompatibility complex (MHC), an important gene cluster controlling immune responses to pathogens. We investigated the patterns of mate choice in 26 wild-living breeding pairs of gray wolf (Canis lupus) that were identified through noninvasive genetic methods and genotyped at 3 MHC class II and 12 autosomal microsatellite (STR) loci. We tested for deviations from random mating and evaluated the covariance of genetic variables at functional and STR markers with fitness proxies deduced from pedigree reconstructions. Results did not show evidences of MHC-based disassortative mating. Rather we found a higher peptide similarity between mates at MHC loci as compared with random expectations. Fitness values were positively correlated with heterozygosity of the breeders at both MHC and STR loci, whereas they decreased with relatedness at STRs. These findings may indicate fitness advantages for breeders that, while avoiding highly related mates, are more similar at the MHC and have high levels of heterozygosity overall. Such a pattern of MHC-assortative mating may reflect local coadaptation of the breeders, while a reduction in genetic diversity may be balanced by heterozygote advantages.
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Affiliation(s)
- Marco Galaverni
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi).
| | - Romolo Caniglia
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi)
| | - Pietro Milanesi
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi)
| | - Silvana Lapalombella
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi)
| | - Elena Fabbri
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi)
| | - Ettore Randi
- From the Laboratorio di genetica, ISPRA, via Cà Fornacetta 9, 40064 Ozzano dell'Emilia (Bologna), Italy (Galaverni, Caniglia, Milanesi, Fabbri, and Randi); Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Via Selmi 3, 40126 Bologna, Italy (Lapalombella); and Department 18/Section of Environmental Engineering, Aalborg University, 9220 Aalborg, Denmark (Randi)
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Uzans AJ, Lucas Z, McLeod BA, Frasier TR. Small Ne of the Isolated and Unmanaged Horse Population on Sable Island. J Hered 2015; 106:660-5. [PMID: 26170253 DOI: 10.1093/jhered/esv051] [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: 03/05/2015] [Accepted: 06/24/2015] [Indexed: 11/12/2022] Open
Abstract
For small, isolated populations 2 common conservation concerns relate to genetic threats: inbreeding and negative consequences associated with loss of genetic diversity due to drift. Mitigating these threats often involves conservation actions that can be controversial, such as translocations or captive breeding programs. Although such actions have been successful in some situations, in others they have had undesirable outcomes. Here, we estimated the effective population size (N e ) of the Sable Island horses to assess the risk to this population of these genetic threats. We found surprising consistency of N e estimates across the 5 different methods used, with a mean of 48 effective individuals. This estimate falls below the 50 criterion of the "50/500 rule," below which inbreeding depression is a concern for population viability. However, simulations and knowledge of population history indicate that this population is still in its early stages of approaching equilibrium between mutation, drift, and genetic diversity; and no negative consequences have been identified that could be associated with inbreeding depression. Therefore, we do not recommend taking management action (such as translocations) at this stage. Rather, we propose continued monitoring of genetic diversity and fitness over time so that trends and any substantial changes can be detected. This represents one of the few unmanaged horse populations in the world, and therefore these data will not only alert us to serious concerns regarding their conservation status, but will also provide a wealth of information about how natural processes drive patterns of reproduction, mortality, and population growth over time.
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Affiliation(s)
- Andrea J Uzans
- From the Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, Nova Scotia B3H 3C3, Canada (Uzans, McLeod, and Frasier); PO Box 64, Halifax CRO, Halifax, Nova Scotia B3J 2L4, Canada (Lucas); and Nova Scotia Museum of Natural History, Halifax, Nova Scotia B3H 3A6, Canada (Lucas and McLeod)
| | - Zoe Lucas
- From the Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, Nova Scotia B3H 3C3, Canada (Uzans, McLeod, and Frasier); PO Box 64, Halifax CRO, Halifax, Nova Scotia B3J 2L4, Canada (Lucas); and Nova Scotia Museum of Natural History, Halifax, Nova Scotia B3H 3A6, Canada (Lucas and McLeod)
| | - Brenna A McLeod
- From the Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, Nova Scotia B3H 3C3, Canada (Uzans, McLeod, and Frasier); PO Box 64, Halifax CRO, Halifax, Nova Scotia B3J 2L4, Canada (Lucas); and Nova Scotia Museum of Natural History, Halifax, Nova Scotia B3H 3A6, Canada (Lucas and McLeod)
| | - Timothy R Frasier
- From the Department of Biology, Saint Mary's University, 923 Robie Street, Halifax, Nova Scotia B3H 3C3, Canada (Uzans, McLeod, and Frasier); PO Box 64, Halifax CRO, Halifax, Nova Scotia B3J 2L4, Canada (Lucas); and Nova Scotia Museum of Natural History, Halifax, Nova Scotia B3H 3A6, Canada (Lucas and McLeod).
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Ortego J, Bonal R, Muñoz A, Espelta JM. Living on the edge: the role of geography and environment in structuring genetic variation in the southernmost populations of a tropical oak. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:676-683. [PMID: 25284378 DOI: 10.1111/plb.12272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/26/2014] [Indexed: 06/03/2023]
Abstract
Understanding the factors determining genetic diversity and structure in peripheral populations is a long-standing goal of evolutionary biogeography, yet little empirical information is available for tropical species. In this study, we combine information from nuclear microsatellite markers and niche modelling to analyse the factors structuring genetic variation across the southernmost populations of the tropical oak Quercus segoviensis. First, we tested the hypothesis that genetic variability decreases with population isolation and increases with local habitat suitability and stability since the Last Glacial Maximum (LGM). Second, we employed a recently developed multiple matrix regression with randomisation (MMRR) approach to study the factors associated with genetic divergence among the studied populations and test the relative contribution of environmental and geographic isolation to contemporary patterns of genetic differentiation. We found that genetic diversity was negatively correlated with average genetic differentiation with other populations, indicating that isolation and limited gene flow have contributed to erode genetic variability in some populations. Considering the relatively small size of the study area (<120 km), analyses of genetic structure indicate a remarkable inter-population genetic differentiation. Environmental dissimilarity and differences in current and past climate niche suitability and their additive effects were not associated with genetic differentiation after controlling for geographic distance, indicating that local climate does not contribute to explain spatial patterns of genetic structure. Overall, our data indicate that geographic isolation, but not current or past climate, is the main factor determining contemporary patterns of genetic diversity and structure within the southernmost peripheral populations of this tropical oak.
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Affiliation(s)
- J Ortego
- Conservation and Evolutionary Genetics Group, Department of Integrative Ecology, Estación Biológica de Doñana, Seville, Spain; Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos, Ciudad Real, Spain
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Minias P, Minias A, Dziadek J. Heterozygosity correlates with body size, nest site quality and productivity in a colonial waterbird, the whiskered tern ( Chlidonias hybrida, Aves: Sternidae). J ZOOL SYST EVOL RES 2014. [DOI: 10.1111/jzs.12084] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Piotr Minias
- Department of Teacher Training and Biodiversity Studies; University of Łódź; Łódź Poland
| | - Alina Minias
- Institute of Medical Biology of the Polish Academy of Sciences; Łódź Poland
| | - Jarosław Dziadek
- Institute of Medical Biology of the Polish Academy of Sciences; Łódź Poland
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Zimmermann B, Nelson L, Wabakken P, Sand H, Liberg O. Behavioral responses of wolves to roads: scale-dependent ambivalence. ACTA ACUST UNITED AC 2014; 25:1353-1364. [PMID: 25419085 PMCID: PMC4235582 DOI: 10.1093/beheco/aru134] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 06/30/2014] [Accepted: 07/07/2014] [Indexed: 11/14/2022]
Abstract
Throughout their recent recovery in several industrialized countries, large carnivores have had to cope with a changed landscape dominated by human infrastructure. Population growth depends on the ability of individuals to adapt to these changes by making use of new habitat features and at the same time to avoid increased risks of mortality associated with human infrastructure. We analyzed the summer movements of 19 GPS-collared resident wolves (Canis lupus L.) from 14 territories in Scandinavia in relation to roads. We used resource and step selection functions, including >12000 field-checked GPS-positions and 315 kill sites. Wolves displayed ambivalent responses to roads depending on the spatial scale, road type, time of day, behavioral state, and reproductive status. At the site scale (approximately 0.1 km2), they selected for roads when traveling, nearly doubling their travel speed. Breeding wolves moved the fastest. At the patch scale (10 km2), house density rather than road density was a significant negative predictor of wolf patch selection. At the home range scale (approximately 1000 km2), breeding wolves increased gravel road use with increasing road availability, although at a lower rate than expected. Wolves have adapted to use roads for ease of travel, but at the same time developed a cryptic behavior to avoid human encounters. This behavioral plasticity may have been important in allowing the successful recovery of wolf populations in industrialized countries. However, we emphasize the role of roads as a potential cause of increased human-caused mortality. We studied how wolves in Scandinavia respond to roads built to ease human travel but degrading habitat quality for many wildlife species. Wolves responded with ambivalence: They both selected and avoided roads, all depending on the spatial and temporal scale and their behavioral status. To understand the multi-scale effects of human infrastructure on animal behavior is important with regard to the recent come-back of many wildlife species to now industrialized countries.
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Affiliation(s)
- Barbara Zimmermann
- Faculty of Applied Ecology and Agricultural Sciences, Hedmark University College, Evenstad , N-2480 Koppang , Norway and
| | - Lindsey Nelson
- Faculty of Applied Ecology and Agricultural Sciences, Hedmark University College, Evenstad , N-2480 Koppang , Norway and
| | - Petter Wabakken
- Faculty of Applied Ecology and Agricultural Sciences, Hedmark University College, Evenstad , N-2480 Koppang , Norway and
| | - Håkan Sand
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Science , SE-73091 Riddarhyttan , Sweden
| | - Olof Liberg
- Department of Ecology, Grimsö Wildlife Research Station, Swedish University of Agricultural Science , SE-73091 Riddarhyttan , Sweden
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Senn H, Ogden R, Frosch C, Syrůčková A, Campbell-Palmer R, Munclinger P, Durka W, Kraus RHS, Saveljev AP, Nowak C, Stubbe A, Stubbe M, Michaux J, Lavrov V, Samiya R, Ulevicius A, Rosell F. Nuclear and mitochondrial genetic structure in the Eurasian beaver (Castor fiber) - implications for future reintroductions. Evol Appl 2014; 7:645-62. [PMID: 25067948 PMCID: PMC4105916 DOI: 10.1111/eva.12162] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 04/01/2014] [Indexed: 12/24/2022] Open
Abstract
Many reintroduction projects for conservation fail, and there are a large number of factors that may contribute to failure. Genetic analysis can be used to help stack the odds of a reintroduction in favour of success, by conducting assessment of source populations to evaluate the possibility of inbreeding and outbreeding depression and by conducting postrelease monitoring. In this study, we use a panel of 306 SNP (single nucleotide polymorphism) markers and 487-489 base pairs of mitochondrial DNA control region sequence data to examine 321 individuals from possible source populations of the Eurasian beaver for a reintroduction to Scotland. We use this information to reassess the phylogenetic history of the Eurasian beavers, to examine the genetic legacy of past reintroductions on the Eurasian landmass and to assess the future power of the genetic markers to conduct ongoing monitoring via parentage analysis and individual identification. We demonstrate the capacity of medium density genetic data (hundreds of SNPs) to provide information suitable for applied conservation and discuss the difficulty of balancing the need for high genetic diversity against phylogenetic best fit when choosing source population(s) for reintroduction.
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Affiliation(s)
- Helen Senn
- WildGenes Laboratory, Royal Zoological Society of Scotland Edinburgh, UK
| | - Rob Ogden
- WildGenes Laboratory, Royal Zoological Society of Scotland Edinburgh, UK
| | - Christiane Frosch
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt Gelnhausen, Germany
| | - Alena Syrůčková
- Department of Zoology, Faculty of Science, Charles University in Prague Prague, Czech Republic
| | | | - Pavel Munclinger
- Department of Zoology, Faculty of Science, Charles University in Prague Prague, Czech Republic
| | - Walter Durka
- Department of Community Ecology, Helmholtz Centre for Environmental Research - UFZ Halle, Germany
| | - Robert H S Kraus
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt Gelnhausen, Germany
| | - Alexander P Saveljev
- Russian Research Institute of Game Management and Fur Farming, Russian Academy of Sciences Kirov, Russia
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt Gelnhausen, Germany
| | - Annegret Stubbe
- Martin-Luther-Universität Halle-Wittenberg Institut für Biologie Bereich Zoologie/Molekulare Ökologie Hoher Weg 4 Halle/Saale, Germany
| | - Michael Stubbe
- Martin-Luther-Universität Halle-Wittenberg Institut für Biologie Domplatz 4 Halle/Saale, Germany
| | - Johan Michaux
- Conservation Genetics Unit, Institute of Botany (Bat. 22), University of Liège (Sart Tilman) Liège, Belgium
| | | | - Ravchig Samiya
- Department of Zoology, School of Biology and Biotechnology, National University of Mongolia Ulaanbaatar, Mongolia
| | - Alius Ulevicius
- Faculty of Natural Sciences, Vilnius University Vilnius, Lithuania
| | - Frank Rosell
- Telemark University College, Department of Environmental Sciences Telemark, Norway
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García-Navas V, Ferrer ES, Sanz JJ, Ortego J. The role of immigration and local adaptation on fine-scale genotypic and phenotypic population divergence in a less mobile passerine. J Evol Biol 2014; 27:1590-603. [DOI: 10.1111/jeb.12412] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/18/2014] [Accepted: 04/11/2014] [Indexed: 11/28/2022]
Affiliation(s)
- V. García-Navas
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - E. S. Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - J. J. Sanz
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - J. Ortego
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Conservation and Evolutionary Genetics Group; Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
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Cain B, Wandera AB, Shawcross SG, Edwin Harris W, Stevens-Wood B, Kemp SJ, Okita-Ouma B, Watts PC. Sex-biased inbreeding effects on reproductive success and home range size of the critically endangered black rhinoceros. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2014; 28:594-603. [PMID: 24641512 DOI: 10.1111/cobi.12175] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Accepted: 07/02/2013] [Indexed: 06/03/2023]
Abstract
A central premise of conservation biology is that small populations suffer reduced viability through loss of genetic diversity and inbreeding. However, there is little evidence that variation in inbreeding impacts individual reproductive success within remnant populations of threatened taxa, largely due to problems associated with obtaining comprehensive pedigree information to estimate inbreeding. In the critically endangered black rhinoceros, a species that experienced severe demographic reductions, we used model selection to identify factors associated with variation in reproductive success (number of offspring). Factors examined as predictors of reproductive success were age, home range size, number of nearby mates, reserve location, and multilocus heterozygosity (a proxy for inbreeding). Multilocus heterozygosity predicted male reproductive success (p< 0.001, explained deviance >58%) and correlated with male home range size (p < 0.01, r(2) > 44%). Such effects were not apparent in females, where reproductive success was determined by age (p < 0.01, explained deviance 34%) as females raise calves alone and choose between, rather than compete for, mates. This first report of a 3-way association between an individual male's heterozygosity, reproductive output, and territory size in a large vertebrate is consistent with an asymmetry in the level of intrasexual competition and highlights the relevance of sex-biased inbreeding for the management of many conservation-priority species. Our results contrast with the idea that wild populations of threatened taxa may possess some inherent difference from most nonthreatened populations that necessitates the use of detailed pedigrees to study inbreeding effects. Despite substantial variance in male reproductive success, the increased fitness of more heterozygous males limits the loss of heterozygosity. Understanding how individual differences in genetic diversity mediate the outcome of intrasexual competition will be essential for effective management, particularly in enclosed populations, where individuals have restricted choice about home range location and where the reproductive impact of translocated animals will depend upon the background distribution in individual heterozygosity.
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Affiliation(s)
- Bradley Cain
- Division of Biology and Conservation Ecology, Manchester Metropolitan University, Manchester, M1 5GD, United Kingdom
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41
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Miller JM, Coltman DW. Assessment of identity disequilibrium and its relation to empirical heterozygosity fitness correlations: a meta-analysis. Mol Ecol 2014; 23:1899-909. [DOI: 10.1111/mec.12707] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 01/31/2023]
Affiliation(s)
- Joshua M. Miller
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - David W. Coltman
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
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Caniglia R, Fabbri E, Galaverni M, Milanesi P, Randi E. Noninvasive sampling and genetic variability, pack structure, and dynamics in an expanding wolf population. J Mammal 2014. [DOI: 10.1644/13-mamm-a-039] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Tende T, Hansson B, Ottosson U, Åkesson M, Bensch S. Individual identification and genetic variation of lions (Panthera leo) from two protected areas in Nigeria. PLoS One 2014; 9:e84288. [PMID: 24427283 PMCID: PMC3888380 DOI: 10.1371/journal.pone.0084288] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 11/15/2013] [Indexed: 11/23/2022] Open
Abstract
This survey was conducted in two protected areas in Nigeria to genetically identify individual lions and to determine the genetic variation within and between the populations. We used faecal sample DNA, a non-invasive alternative to the risky and laborious task of taking samples directly from the animals, often preceded by catching and immobilization. Data collection in Yankari Game Reserve (YGR) spanned through a period of five years (2008 -2012), whereas data in Kainji Lake National Park (KLNP) was gathered for a period of three years (2009, 2010 and 2012). We identified a minimum of eight individuals (2 males, 3 females, 3 unknown) from YGR and a minimum of ten individuals (7 males, 3 females) from KLNP. The two populations were found to be genetically distinct as shown by the relatively high fixation index (FST = 0.17) with each population exhibiting signs of inbreeding (YGR FIS = 0.49, KLNP FIS = 0.38). The genetic differentiation between the Yankari and Kainji lions is assumed to result from large spatial geographic distance and physical barriers reducing gene flow between these two remaining wild lion populations in Nigeria. To mitigate the probable inbreeding depression in the lion populations within Nigeria it might be important to transfer lions between parks or reserves or to reintroduce lions from the zoos back to the wild.
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Affiliation(s)
- Talatu Tende
- A.P. Leventis Ornithological Research Institute, Department of Zoology, University of Jos, Plateau State, Nigeria
- Department of Biology, Lund University, Lund, Sweden
| | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
| | - Ulf Ottosson
- A.P. Leventis Ornithological Research Institute, Department of Zoology, University of Jos, Plateau State, Nigeria
| | - Mikael Åkesson
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, Riddarhyttan, Sweden
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Thonhauser KE, Thoß M, Musolf K, Klaus T, Penn DJ. Multiple paternity in wild house mice (Mus musculus musculus): effects on offspring genetic diversity and body mass. Ecol Evol 2013; 4:200-9. [PMID: 24558575 PMCID: PMC3925383 DOI: 10.1002/ece3.920] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 11/12/2013] [Accepted: 11/14/2013] [Indexed: 11/18/2022] Open
Abstract
Multiple mating is common in many species, but it is unclear whether multiple paternity enhances offspring genetic diversity or fitness. We conducted a survey on wild house mice (Mus musculus musculus), and we found that in 73 pregnant females, 29% of litters had multiple sires, which is remarkably similar to the 23–26% found in feral populations of Mus musculus domesticus in the USA and Australia, respectively. The question is: How has selection maintained multiple mating in these subspecies since the evolutionary divergence, ca. 2800–6000 years ago? We found no evidence that multiple paternity enhanced females’ litter size, contrary to the fertility assurance or genetic benefits hypotheses. Multiple paternity was associated with reduced mean and variance in offspring body mass, which suggests that females allocate fewer resources or that there is increased intrauterine conflict in multiple-versus single-sired litters. We found increased allelic diversity (though not heterozygosity) in multiple-sired litters, as predicted by the genetic diversity hypothesis. Finally, we found that the dams’ heterozygosity was correlated with the mean heterozygosity of their offspring in single-and multiple-sired litters, suggesting that outbred, heterozygous females were more likely to avoid inbreeding than inbred, homozygous females. Future studies are needed to examine how increased genetic diversity of litters and smaller mean (and variance) offspring body mass associated with multiple paternity affect offspring fitness.
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Affiliation(s)
- Kerstin E Thonhauser
- Konrad Lorenz Institute of Ethology Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Austria
| | - Michaela Thoß
- Konrad Lorenz Institute of Ethology Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Austria
| | - Kerstin Musolf
- Konrad Lorenz Institute of Ethology Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Austria ; Department of Biology, Brooklyn College Brooklyn, New York, USA
| | - Teresa Klaus
- Konrad Lorenz Institute of Ethology Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Austria
| | - Dustin J Penn
- Konrad Lorenz Institute of Ethology Department of Integrative Biology and Evolution, University of Veterinary Medicine Vienna, Austria
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45
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The effect of multiple paternity on genetic diversity of small populations during and after colonisation. PLoS One 2013; 8:e75587. [PMID: 24204577 PMCID: PMC3810386 DOI: 10.1371/journal.pone.0075587] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 08/15/2013] [Indexed: 11/19/2022] Open
Abstract
Genetic variation within and among populations is influenced by the genetic content of the founders and the migrants following establishment. This is particularly true if populations are small, migration rate low and habitats arranged in a stepping-stone fashion. Under these circumstances the level of multiple paternity is critical since multiply mated females bring more genetic variation into founder groups than single mated females. One such example is the marine snail Littorina saxatilis that during postglacial times has invaded mainland refuge areas and thereafter small islands emerging due to isostatic uplift by occasional rafting of multiply mated females. We modelled effects of varying degrees of multiple paternity on the genetic variation of island populations colonised by the founders spreading from the mainland, by quantifying the population heterozygosity during both the transient colonisation process, and after a steady state (with migration) has been reached. During colonisation, multiple mating by males increased the heterozygosity by in comparison with single paternity, while in the steady state the increase was compared with single paternity. In the steady state the increase of heterozygosity due to multiple paternity is determined by a corresponding increase in effective population size. During colonisation, by contrast, the increase in heterozygosity is larger and it cannot be explained in terms of the effective population size alone. During the steady-state phase bursts of high genetic variation spread through the system, and far from the mainland this led to short periods of high diversity separated by long periods of low diversity. The size of these fluctuations was boosted by multiple paternity. We conclude that following glacial periods of extirpation, recolonization of isolated habitats by this species has been supported by its high level of multiple paternity.
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Frasier TR, Gillett RM, Hamilton PK, Brown MW, Kraus SD, White BN. Postcopulatory selection for dissimilar gametes maintains heterozygosity in the endangered North Atlantic right whale. Ecol Evol 2013; 3:3483-94. [PMID: 24223284 PMCID: PMC3797493 DOI: 10.1002/ece3.738] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 07/23/2013] [Accepted: 07/24/2013] [Indexed: 11/09/2022] Open
Abstract
Although small populations are expected to lose genetic diversity through genetic drift and inbreeding, a number of mechanisms exist that could minimize this genetic decline. Examples include mate choice for unrelated mates and fertilization patterns biased toward genetically dissimilar gametes. Both processes have been widely documented, but the long-term implications have received little attention. Here, we combined over 25 years of field data with high-resolution genetic data to assess the long-term impacts of biased fertilization patterns in the endangered North Atlantic right whale. Offspring have higher levels of microsatellite heterozygosity than expected from this gene pool (effect size = 0.326, P < 0.011). This pattern is not due to precopulatory mate choice for genetically dissimilar mates (P < 0.600), but instead results from postcopulatory selection for gametes that are genetically dissimilar (effect size = 0.37, P < 0.003). The long-term implication is that heterozygosity has slowly increased in calves born throughout the study period, as opposed to the slight decline that was expected. Therefore, this mechanism represents a natural means through which small populations can mitigate the loss of genetic diversity over time.
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Affiliation(s)
- T R Frasier
- Department of Biology and Forensic Sciences Program, Saint Mary's University 923 Robie Street, Halifax, Nova Scotia, B3H 3C3, Canada
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Grueber CE, Wallis GP, Jamieson IG. Genetic drift outweighs natural selection at toll-like receptor (TLR) immunity loci in a re-introduced population of a threatened species. Mol Ecol 2013; 22:4470-82. [DOI: 10.1111/mec.12404] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Revised: 05/14/2013] [Accepted: 05/23/2013] [Indexed: 01/22/2023]
Affiliation(s)
| | - Graham P. Wallis
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
| | - Ian G. Jamieson
- Department of Zoology; University of Otago; PO Box 56 Dunedin 9054 New Zealand
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Sindičić M, Polanc P, Gomerčić T, Jelenčič M, Huber Đ, Trontelj P, Skrbinšek T. Genetic data confirm critical status of the reintroduced Dinaric population of Eurasian lynx. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0491-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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49
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Liu D, Ma Y, Li H, Xu Y, Zhang Y, Dahmer T, Bai S, Wang J. Simultaneous polyandry and heteropaternity in tiger (Panthera tigris altaica): Implications for conservation of genetic diversity in captive populations of felids. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s11434-013-5722-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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50
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Silió L, Rodríguez MC, Fernández A, Barragán C, Benítez R, Óvilo C, Fernández AI. Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics. J Anim Breed Genet 2013; 130:349-60. [PMID: 24074172 DOI: 10.1111/jbg.12031] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 12/20/2012] [Indexed: 12/22/2022]
Abstract
Multilocus homozygosity, measured as the proportion of the autosomal genome in homozygous genotypes or in runs of homozygosity, was compared with the respective pedigree inbreeding coefficients in 64 Iberian pigs genotyped using the Porcine SNP60 Beadchip. Pigs were sampled from a set of experimental animals with a large inbreeding variation born in a closed strain with a completely recorded multi-generation genealogy. Individual inbreeding coefficients calculated from pedigree were strongly correlated with the different SNP-derived metrics of homozygosity (r = 0.814-0.919). However, unequal correlations between molecular and pedigree inbreeding were observed at chromosomal level being mainly dependent on the number of SNPs and on the correlation between heterozygosities measured across different loci. A panel of 192 SNPs of intermediate frequencies was selected for genotyping 322 piglets to test inbreeding depression on postweaning growth performance (daily gain and weight at 90 days). The negative effects on these traits of homozygosities calculated from the genotypes of 168 quality-checked SNPs were similar to those of inbreeding coefficients. The results support that few hundreds of SNPs may be useful for measuring inbreeding and inbreeding depression, when the population structure or the mating system causes a large variance of inbreeding.
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Affiliation(s)
- L Silió
- Departamento de Mejora Genética Animal, INIA, Madrid, Spain
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