1
|
Hewett AM, Johnston SE, Morris A, Morris S, Pemberton JM. Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer. Mol Ecol 2024; 33:e17335. [PMID: 38549143 DOI: 10.1111/mec.17335] [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: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/20/2024] [Indexed: 04/23/2024]
Abstract
Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.
Collapse
Affiliation(s)
- Anna M Hewett
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Department of Ecology and Evolution, University of Lausanne (UNIL), Lausanne, Switzerland
| | - Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alison Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Sean Morris
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Josephine M Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
2
|
Ishibashi Y. Preservation of genetic diversity in a highly fragmented population of the gray-sided vole Myodes rufocanus in an intensive farming region. Ecol Evol 2023; 13:e10472. [PMID: 37736279 PMCID: PMC10509600 DOI: 10.1002/ece3.10472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 08/11/2023] [Accepted: 08/18/2023] [Indexed: 09/23/2023] Open
Abstract
Individual dispersal plays an important role in preserving genetic diversity in density-fluctuating populations of arvicoline rodents. When habitats are fragmented and dispersal between habitats is severely constrained, genetic diversity can be lost. Here, I investigated whether genetic diversity in the gray-sided vole Myodes rufocanus was preserved in an intensive farming region in Japan, where voles inhabited isolated windbreak forests along the borders of plowed lands. Genetic structure was examined in 673 vole samples (330 in spring and 343 in fall) collected at 34 windbreak forests located 0.35-20 km apart. A part of the control region (425 bp) of mitochondrial DNA (mtDNA) was sequenced in 673 voles, yielding 76 haplotypes. Genetic differentiation of maternally inherited mtDNA among trapping sites was markedly lower in males than in females in both seasons, indicating strong male-biased dispersal. Genotypes at six microsatellite DNA loci were determined in 494 voles (245 in spring and 249 in fall) from 18 trapping sites, and loci harbored 16-24 alleles. The mean number of alleles per locus (allelic diversity) at trapping sites was positively correlated with the number of examined individuals (density) in both seasons, and the relationship was very similar to that of a previous study performed in much less fragmented populations. The genetic differentiation of microsatellite DNA among trapping sites decreased considerably from spring to fall. In a STRUCTURE analysis with a most probable cluster number of two, closer trapping sites showed more similar mean values of cluster admixture proportions. The present findings indicate that gene flow among isolated windbreak forests, which occurred mainly by dispersal of males, was not restrained in this intensive farming region. Furthermore, the results suggest that genetic diversity in the study population was preserved as well as in less fragmented populations.
Collapse
Affiliation(s)
- Yasuyuki Ishibashi
- Hokkaido Research CenterForestry and Forest Products Research InstituteSapporoJapan
| |
Collapse
|
3
|
Pemberton JM, Kruuk LE, Clutton-Brock T. The Unusual Value of Long-Term Studies of Individuals: The Example of the Isle of Rum Red Deer Project. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2022. [DOI: 10.1146/annurev-ecolsys-012722-024041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Long-term studies of individuals enable incisive investigations of questions across ecology and evolution. Here, we illustrate this claim by reference to our long-term study of red deer on the Isle of Rum, Scotland. This project has established many of the characteristics of social organization, selection, and population ecology typical of large, polygynous, seasonally breeding mammals, with wider implications for our understanding of sexual selection and the evolution of sex differences, as well as for their population dynamics and population management. As molecular genetic techniques have developed, the project has pivoted to investigate evolutionary genetic questions, also breaking new ground in this field. With ongoing advances in genomics and statistical approaches and the development of increasingly sophisticated ways to assay new phenotypic traits, the questions that long-term studies such as the red deer study can answer become both broader and ever more sophisticated. They also offer powerful means of understanding the effects of ongoing climate change on wild populations.
Collapse
Affiliation(s)
- Josephine M. Pemberton
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Loeske E.B. Kruuk
- Institute of Ecology and Evolution, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Clutton-Brock
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
4
|
Hierlmeier VR, Struck N, Krapf P, Kopf T, Hofinger AM, Leitner V, Stromberger PJE, Freier KP, Steiner FM, Schlick‐Steiner BC. Persistent, Bioaccumulative, and Toxic Chemicals in Wild Alpine Insects: A Methodological Case Study. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2022; 41:1215-1227. [PMID: 35088916 PMCID: PMC9311829 DOI: 10.1002/etc.5303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/29/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
With their high persistence in the environment and their potential for long-range atmospheric transport, persistent, bioaccumulative, and toxic chemicals (PBTs) may be among the numerous anthropogenic threats to insect populations worldwide. The effects of PBTs on insects have been investigated in the laboratory, but topical field studies are scarce. A reason might be the multiple challenges faced by PBT-related field studies on wild insects. We studied two species of bumblebees (Bombus spp.) and of ants (Formica spp.) in two high-elevation locations in the Austrian and German Alps to tackle two of these challenges. First, PBTs occur in minuscule concentrations compared with other substances in the environment. Therefore, the practicability of body burden data from pooled individuals was tested. Second, fitness proxies like fecundity, which typically are endpoints for chemical toxicity, are difficult to quantify in the field. Hence, fluctuating asymmetry of bumblebee wings and ant heads was tested as an alternative endpoint. To exclude the possibility that fluctuating asymmetry was caused by genetic stressors, inbreeding levels were estimated using population-genetic markers, and their relationships to fluctuating asymmetry in the same individuals were assessed. We successfully quantified polychlorinated biphenyls and Hg as PBTs using the pooled samples and found PBT data from pooled individuals useful, in that significant correlations to fluctuating asymmetry were identified in bumblebees and ants. This finding confirmed the potential of fluctuating asymmetry to indicate PBT effects in wild insects. Inbreeding did not interfere with PBT links to fluctuating asymmetry in any instance. Our findings contribute to the development of a quantitative methodological framework for investigating the effects of persistent environmental chemicals on wild insects. Environ Toxicol Chem 2022;41:1215-1227. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Collapse
Affiliation(s)
- Veronika Rosa Hierlmeier
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
- Bavarian Environment AgencyGarmisch‐PartenkirchenGermany
| | - Nils Struck
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Patrick Krapf
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | - Timotheus Kopf
- Department of EcologyUniversity of InnsbruckInnsbruckAustria
| | | | | | | | | | | | | |
Collapse
|
5
|
Flucher SM, Krapf P, Arthofer W, Suarez AV, Crozier RH, Steiner FM, Schlick-Steiner BC. Effect of social structure and introduction history on genetic diversity and differentiation. Mol Ecol 2021; 30:2511-2527. [PMID: 33811410 DOI: 10.1111/mec.15911] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 03/03/2021] [Accepted: 03/19/2021] [Indexed: 12/31/2022]
Abstract
Invasive species are a global threat to biodiversity, and understanding their history and biology is a major goal of invasion biology. Population-genetic approaches allow insights into these features, as population structure is shaped by factors such as invasion history (number, origin and age of introductions) and life-history traits (e.g., mating system, dispersal capability). We compared the relative importance of these factors by investigating two closely related ants, Tetramorium immigrans and Tetramorium tsushimae, that differ in their social structure and invasion history in North America. We used mitochondrial DNA sequences and microsatellite alleles to estimate the source and number of introduction events of the two species, and compared genetic structure among native and introduced populations. Genetic diversity of both species was strongly reduced in introduced populations, which also differed genetically from native populations. Genetic differentiation between ranges and the reduction in microsatellite diversity were more severe in the more recently introduced and supercolonial T. tsushimae. However, the loss of mitochondrial haplotype diversity was more pronounced in T. immigrans, which has single-queen colonies and was introduced earlier. Tetramorium immigrans was introduced at least twice from Western Europe to North America and once independently to South America. Its monogyny might have limited genetic diversity per introduction, but new mutations and successive introductions over a long time may have added to the gene pool in the introduced range. Polygyny in T. tsushimae probably facilitated the simultaneous introduction of several queens from a Japanese population to St. Louis, USA. In addition to identifying introduction pathways, our results reveal how social structure can influence the population-genetic consequences of founder events.
Collapse
Affiliation(s)
- Sylvia M Flucher
- Molecular Ecology Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Patrick Krapf
- Molecular Ecology Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Wolfgang Arthofer
- Molecular Ecology Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Andrew V Suarez
- Department of Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ross H Crozier
- School of Marine and Tropical Biology, James Cook University, Townsville, QLD, Australia
| | - Florian M Steiner
- Molecular Ecology Group, Department of Ecology, University of Innsbruck, Innsbruck, Austria
| | | |
Collapse
|
6
|
Botero-Delgadillo E, Quirici V, Vásquez RA, Kempenaers B. Heterozygosity-Fitness Correlations in a Continental Island Population of Thorn-Tailed Rayadito. J Hered 2020; 111:628-639. [PMID: 33277658 DOI: 10.1093/jhered/esaa056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/04/2020] [Indexed: 11/15/2022] Open
Abstract
Heterozygosity-fitness correlations (HFCs) have been used to monitor the effects of inbreeding in threatened populations. HFCs can also be useful to investigate the potential effects of inbreeding in isolated relict populations of long-term persistence and to better understand the role of inbreeding and outbreeding as drivers of changes in genetic diversity. We studied a continental island population of thorn-tailed rayadito (Aphrastura spinicauda) inhabiting the relict forest of Fray Jorge National Park, north-central Chile. This population has experienced a long-term, gradual process of isolation since the end of the Tertiary. Using 10 years of field data in combination with molecular techniques, we tested for HFCs to assess the importance of inbreeding depression. If inbreeding depression is important, we predict a positive relationship between individual heterozygosity and fitness-related traits. We genotyped 183 individuals at 12 polymorphic microsatellite loci and used 7 measures of reproductive success and estimates of apparent survival to calculate HFCs. We found weak to moderate statistical support (P-values between 0.05 and 0.01) for a linear effect of female multi-locus heterozygosity (MLH) on clutch size and nonlinear effects on laying date and fledging success. While more heterozygous females laid smaller clutches, nonlinear effects indicated that females with intermediate values of MLH started laying earlier and had higher fledging success. We found no evidence for effects of MLH on annual fecundity or on apparent survival. Our results along with the long-term demographic stability of the study population contradict the hypothesis that inbreeding depression occurs in this population.
Collapse
Affiliation(s)
- Esteban Botero-Delgadillo
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Verónica Quirici
- Departamento de Ecología y Biodiversidad, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Santiago, Chile.,Centro de investigación para la sustentabilidad, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo A Vásquez
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| |
Collapse
|
7
|
Alemu SW, Kadri NK, Harland C, Faux P, Charlier C, Caballero A, Druet T. An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree. Heredity (Edinb) 2020; 126:410-423. [PMID: 33159183 PMCID: PMC8027009 DOI: 10.1038/s41437-020-00383-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 11/13/2022] Open
Abstract
The estimation of the inbreeding coefficient (F) is essential for the study of inbreeding depression (ID) or for the management of populations under conservation. Several methods have been proposed to estimate the realized F using genetic markers, but it remains unclear which one should be used. Here we used whole-genome sequence data for 245 individuals from a Holstein cattle pedigree to empirically evaluate which estimators best capture homozygosity at variants causing ID, such as rare deleterious alleles or loci presenting heterozygote advantage and segregating at intermediate frequency. Estimators relying on the correlation between uniting gametes (FUNI) or on the genomic relationships (FGRM) presented the highest correlations with these variants. However, homozygosity at rare alleles remained poorly captured. A second group of estimators relying on excess homozygosity (FHOM), homozygous-by-descent segments (FHBD), runs-of-homozygosity (FROH) or on the known genealogy (FPED) was better at capturing whole-genome homozygosity, reflecting the consequences of inbreeding on all variants, and for young alleles with low to moderate frequencies (0.10 < . < 0.25). The results indicate that FUNI and FGRM might present a stronger association with ID. However, the situation might be different when recessive deleterious alleles reach higher frequencies, such as in populations with a small effective population size. For locus-specific inbreeding measures or at low marker density, the ranking of the methods can also change as FHBD makes better use of the information from neighboring markers. Finally, we confirmed that genomic measures are in general superior to pedigree-based estimates. In particular, FPED was uncorrelated with locus-specific homozygosity.
Collapse
Affiliation(s)
- Setegn Worku Alemu
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Naveen Kumar Kadri
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Chad Harland
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Pierre Faux
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Carole Charlier
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Armando Caballero
- Centro de Investigación Mariña, Departamento de Bioquímica, Genética e Inmunología, Edificio CC Experimentais, Universidade de Vigo, Campus de Vigo, As Lagoas, Marcosende, 36310, Vigo, Spain
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R & Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| |
Collapse
|
8
|
de Jong JF, van Hooft P, Megens HJ, Crooijmans RPMA, de Groot GA, Pemberton JM, Huisman J, Bartoš L, Iacolina L, van Wieren SE, Ydenberg RC, Prins HHT. Fragmentation and Translocation Distort the Genetic Landscape of Ungulates: Red Deer in the Netherlands. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.535715] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
9
|
Botero-Delgadillo E, Gilsenan C, Mueller JC, Kempenaers B. Negative effects of individual heterozygosity on reproductive success in a wild bird population. Mol Ecol 2020; 29:3196-3216. [PMID: 32668071 DOI: 10.1111/mec.15553] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 07/03/2020] [Indexed: 01/01/2023]
Abstract
The evolutionary consequences of individual genetic diversity are frequently studied by assessing heterozygosity-fitness correlations (HFCs). The prevalence of positive and negative HFCs and the predominance of general versus local effects in wild populations are far from understood, partly because comprehensive studies testing for both inbreeding and outbreeding depression are lacking. We studied a genetically diverse population of blue tits in southern Germany using a genome-wide set of 87 microsatellites to investigate the relationship between proxies of reproductive success and measures of multilocus and single-locus individual heterozygosity (MLH and SLH). We used complimentary measures of MLH and partitioned markers into functional categories according to their position in the blue tit genome. HFCs based on MLH were consistently negative for functional loci, whereas correlations were rather inconsistent for loci found in nonfunctional areas of the genome. Clutch size was the only reproductive variable showing a general effect. We found evidence for local effects for three measures of reproductive success: arrival date at the breeding site, the probability of breeding at the study site and male reproductive success. For these, we observed consistent, and relatively strong, negative effects at one functional locus. Remarkably, this marker had a similar effect in another blue tit population from Austria (~400 km to the east). We suggest that a genetic local effect on timing of arrival might be responsible for most negative HFCs detected, with carry-over effects on other reproductive traits. This effect could reflect individual differences in the distance between overwintering areas and breeding sites.
Collapse
Affiliation(s)
- Esteban Botero-Delgadillo
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Carol Gilsenan
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| |
Collapse
|
10
|
Yorisue T, Iguchi A, Yasuda N, Yoshioka Y, Sato T, Fujita Y. Evaluating the effect of overharvesting on genetic diversity and genetic population structure of the coconut crab. Sci Rep 2020; 10:10026. [PMID: 32572270 PMCID: PMC7308380 DOI: 10.1038/s41598-020-66712-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 02/20/2020] [Indexed: 11/19/2022] Open
Abstract
Birgus latro (coconut crab) is an edible crustacean that has experienced serious overharvesting throughout its whole habitat range; however, the negative effects of overharvesting on the genetic diversity within B. latro populations have not been elucidated. Here, we report sex ratio, body size, and genetic diversity in populations of B. latro in the Ryukyu Islands where large-male-biased overharvesting of B. latro has continued. In 2 of the study populations, the sex ratio was significantly skewed toward females, and in all of the study populations large males were rare, which we attributed to sex- and size-biased overharvesting. We found no differences in genetic diversity between small and large individuals, suggesting that genetic diversity, even among the large (i.e., old) individuals, may have had already been negatively affected by overharvesting. Continued monitoring of sex ratio, body size and genetic diversity are needed for effective management of the study populations.
Collapse
Affiliation(s)
- Takefumi Yorisue
- Integrative Aquatic Biology, Onagawa Field Center, Graduate School of Agricultural Science, Tohoku University, 3-1 Mukai, Konori-hama, Onagawa, Oshika, Miyagi, 986-2242, Japan.
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan, AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
| | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan, AIST Tsukuba Central 7, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8567, Japan.
| | - Nina Yasuda
- Department of Marine Biology and Environmental Science, Faculty of Agriculture, University of Miyazaki, Gakuenkibana-dai Nishi 1-1, Miyazaki, 889-2192, Japan
| | - Yuki Yoshioka
- Department of Bioresources Engineering, National Institute of Technology, Okinawa College, 905, Henoko, Nago, Okinawa, 905-2192, Japan
| | - Taku Sato
- Research Center for Marine Invertebrates, National Research Institute of Fisheries and Environment of Inland Sea, Japan Fisheries Research and Education Agency, Momoshima, Onomichi, Hiroshima, 722-0061, Japan
| | - Yoshihisa Fujita
- Okinawa Prefectural University of Arts, 1-4, Shuri Tonokura-cho, Naha-shi, Okinawa, 903-8602, Japan
| |
Collapse
|
11
|
Mitrus C, Mitrus J, Rutkowski R. Individual Heterozygosity Influences Arrival Times and Mating Success of Male Red-Breasted Flycatchers Ficedula parva. Zool Stud 2020; 59:e12. [PMID: 32760458 PMCID: PMC7396921 DOI: 10.6620/zs.2020.59-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 02/22/2020] [Indexed: 11/18/2022]
Abstract
We examined the relationship between individual heterozygosity of male Red-breasted Flycatchers (Ficedula parva; a small long-distance migratory, socially monogamous bird species) and their mating success, arrival time and age. Using eight polymorphic microsatellite loci, we found that male heterozygosity is related to both mating success and arrival time, but not to age. Mated and earlier arriving males had higher heterozygosity than later arrivals and bachelors, but we did not find a relationship between age and individual heterozygosity of males. To our knowledge, this is the first study to provide evidence about the relationship between individual genetic diversity and arrival time, thus arrival time could be used as a signal of individual heterozygosity and quality.
Collapse
Affiliation(s)
- Cezary Mitrus
- Department of Vertebrate Ecology and Paleontology, Institute of Biology, Wrocław University of Environmental and Life Sciences, Chełmońskiego 38c, 51-631 Wrocław, Poland. E-mail: (C. Mitrus)
| | - Joanna Mitrus
- Department of Plant Physiology and Genetics, Siedlce University of Natural Sciences and Humanities, Prusa 12, 08-110 Siedlce, Poland. E-mail: (J. Mitrus)
| | - Robert Rutkowski
- Museum and Institute of Zoology, Polish Academy of Sciences, Wilcza 64, 00-679 Warsaw, Poland. E-mail: (Rutkowski)
| |
Collapse
|
12
|
Angom S, Tuboi C, Ghazi MGU, Badola R, Hussain SA. Demographic and genetic structure of a severely fragmented population of the endangered hog deer (Axis porcinus) in the Indo-Burma biodiversity hotspot. PLoS One 2020; 15:e0210382. [PMID: 32027650 PMCID: PMC7004368 DOI: 10.1371/journal.pone.0210382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 12/17/2019] [Indexed: 11/29/2022] Open
Abstract
The population of the globally endangered hog deer (Axis porcinus) has declined severely across its geographic range. Intensive monitoring of its demographic and genetic status is necessary. We examined the demographic and genetic structure of a small hog deer population in Keibul Lamjao National Park (KLNP), located on the western fringe of the Indo-Burma biodiversity hotspot for conservation planning. The distribution pattern of hog deer in the Park was derived based on the presence/absence of faecal pellets in 1 km × 1 km grids. We used double-observer distance sampling method to derive the hog deer abundance and population structure and compared with previous data to derive the population trend. We determined the genetic diversity of the population through microsatellite screening and bottleneck detection. The overall pellet density was 0.34 ± 0.02 pellets km-2 restricted to only 22.34 ± 0.20 km2 area of the park. The estimated density of the deer in the park was 1.82–4.32 individuals km-2. The population showed a declining trend from 2006–08 (p < 0.05, R2 = 0.916) with 8% annum-1 and an increasing trend from 2003–2018 (p < 0.05, R2 = 0.9304) with 10% annum-1. The adult male-to-female ratio and fawn-to-doe ratio were 36.2 ± 1.9 males per 100 females and 16.5 ± 0.4 fawns per 100 females, respectively. The molecular examination suggested that the mean number of alleles at 23 loci was 2.70 ± 0.18, the observed heterozygosity (Ho) ranged from 0.26 to 0.63 (mean 0.42 ± 0.02), the expected heterozygosity (He) ranged from 0.23 to 0.73 (χ = 0.51 ± 0.03), and the polymorphic information content (PIC) ranged from 0.2 to 0.67 (χ = 0.43 ± 0.03) indicating a moderate level of genetic diversity. Although no bottleneck in the population was observed, the loss of genetic diversity may affect the evolutionary potential of the species at the site by limiting the selection flexibility. Conservation planning coupled with scientific management regime will help in the long term persistence of the population in the region.
Collapse
Affiliation(s)
- Sangeeta Angom
- Wildlife Institute of India, Dehra Dun, Uttarakhand, India
| | - Chongpi Tuboi
- Wildlife Institute of India, Dehra Dun, Uttarakhand, India
| | | | - Ruchi Badola
- Wildlife Institute of India, Dehra Dun, Uttarakhand, India
| | | |
Collapse
|
13
|
McFarlane SE, Hunter DC, Senn HV, Smith SL, Holland R, Huisman J, Pemberton JM. Increased genetic marker density reveals high levels of admixture between red deer and introduced Japanese sika in Kintyre, Scotland. Evol Appl 2020; 13:432-441. [PMID: 31993087 PMCID: PMC6976951 DOI: 10.1111/eva.12880] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 09/01/2019] [Accepted: 10/10/2019] [Indexed: 12/14/2022] Open
Abstract
Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date, many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here, we use 44,999 single nucleotide polymorphisms (SNPs) and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre, we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.
Collapse
Affiliation(s)
- S. Eryn McFarlane
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of BiologyLund UniversityLundSweden
| | - Darren C. Hunter
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Helen V. Senn
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- WildGenes LaboratoryRoyal Zoological Society of ScotlandEdinburghUK
| | - Stephanie L. Smith
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
- The Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEaster Bush CampusMidlothian, EdinburghUK
| | - Rebecca Holland
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Jisca Huisman
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| | - Josephine M. Pemberton
- Institute of Evolutionary BiologySchool of Biological ScienceUniversity of EdinburghEdinburghUK
| |
Collapse
|
14
|
Gélin U, Keller M, de Beaupuis V, Nowak R, Lévy F, Locatelli Y. Impact of hybridization between sika and red deer on phenotypic traits of the newborn and mother–young relationships. Anim Behav 2019. [DOI: 10.1016/j.anbehav.2019.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
15
|
Kerk M, Onorato DP, Hostetler JA, Bolker BM, Oli MK. Dynamics, Persistence, and Genetic Management of the Endangered Florida Panther Population. WILDLIFE MONOGRAPHS 2019. [DOI: 10.1002/wmon.1041] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Madelon Kerk
- Department of Wildlife Ecology and Conservation University of Florida 110 Newins‐Ziegler Hall Gainesville FL 32611‐0430 USA
| | - David P. Onorato
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 298 Sabal Palm Road Naples FL 34114 USA
| | - Jeffrey A. Hostetler
- Fish and Wildlife Research Institute Florida Fish and Wildlife Conservation Commission 100 8th Avenue SE St. Petersburg FL 33701 USA
| | - Benjamin M. Bolker
- Departments of Mathematics and Statistics and Biology McMaster University 314 Hamilton Hall Hamilton ON L8S 4K1 Canada
| | - Madan K. Oli
- Department of Wildlife Ecology and Conservation University of Florida 110 Newins‐Ziegler Hall Gainesville FL 32611‐0430 USA
| |
Collapse
|
16
|
Fine-Scale Resolution of Runs of Homozygosity Reveal Patterns of Inbreeding and Substantial Overlap with Recessive Disease Genotypes in Domestic Dogs. G3-GENES GENOMES GENETICS 2019; 9:117-123. [PMID: 30429214 PMCID: PMC6325901 DOI: 10.1534/g3.118.200836] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Inbreeding leaves distinct genomic traces, most notably long genomic tracts that are identical by descent and completely homozygous. These runs of homozygosity (ROH) can contribute to inbreeding depression if they contain deleterious variants that are fully or partially recessive. Several lines of evidence have been used to show that long (> 5 megabase) ROH are disproportionately likely to harbor deleterious variation, but the extent to which long vs. short tracts contribute to autozygosity at loci known to be deleterious and recessive has not been studied. In domestic dogs, nearly 200 mutations are known to cause recessive diseases, most of which can be efficiently assayed using SNP arrays. By examining genome-wide data from over 200,000 markers, including 150 recessive disease variants, we built high-resolution ROH density maps for nearly 2,500 dogs, recording ROH down to 500 kilobases. We observed over 678 homozygous deleterious recessive genotypes in the panel across 29 loci, 90% of which overlapped with ROH inferred by GERMLINE. Although most of these genotypes were contained in ROH over 5 Mb in length, 14% were contained in short (0.5 - 2.5 megabase) tracts, a significant enrichment compared to the genetic background, suggesting that even short tracts are useful for computing inbreeding metrics like the coefficient of inbreeding estimated from ROH (FROH ). In our dataset, FROH differed significantly both within and among dog breeds. All breeds harbored some regions of reduced genetic diversity due to drift or selective sweeps, but the degree of inbreeding and the proportion of inbreeding caused by short vs. long tracts differed between breeds, reflecting their different population histories. Although only available for a few species, large genome-wide datasets including recessive disease variants hold particular promise not only for disentangling the genetic architecture of inbreeding depression, but also evaluating and improving upon current approaches for detecting ROH.
Collapse
|
17
|
Carella M, Agell G, Uriz MJ. Asexual reproduction and heterozygote selection in an Antarctic demosponge (Stylocordyla chupachus, Suberitida). Polar Biol 2018. [DOI: 10.1007/s00300-018-2436-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
18
|
Muller LI, Murrow JL, Lupardus JL, Clark JD, Yarkovich JG, Stiver WH, Delozier EK, Slabach BL, Cox JJ, Miller BF. Genetic structure in Elk persists after translocation. J Wildl Manage 2018. [DOI: 10.1002/jwmg.21482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lisa I. Muller
- University of Tennessee, Department of Forestry; Wildlife and Fisheries; 274 Ellington Hall Knoxville TN 37996 USA
| | - Jennifer L. Murrow
- University of Maryland; Environmental Science and Policy Program; 0214 Symons Hall College Park MD 20742 USA
| | - Jason L. Lupardus
- University of Tennessee, Department of Forestry; Wildlife and Fisheries; 274 Ellington Hall Knoxville TN 37996 USA
| | - Joseph D. Clark
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Southern Appalachian Research Branch; University of Tennessee; 274 Ellington Hall Knoxville TN 37996 USA
| | - Joseph G. Yarkovich
- National Park Service; Great Smoky Mountains National Park; 107 Park Headquarters Road Gatlinburg TN 37738 USA
| | - William H. Stiver
- National Park Service; Great Smoky Mountains National Park; 107 Park Headquarters Road Gatlinburg TN 37738 USA
| | - E. Kim Delozier
- National Park Service; Great Smoky Mountains National Park; 107 Park Headquarters Road Gatlinburg TN 37738 USA
| | - Brittany L. Slabach
- University of Kentucky; Department of Biology; 101 T.H. Morgan Building Lexington KY 40546 USA
| | - John. J. Cox
- University of Kentucky; Department of Forestry; 102 T.P. Copper Building Lexington KY 40546 USA
| | - Bradley F. Miller
- Tennessee Wildlife Resources Agency; 3030 Wildlife Way Morristown TN 37814 USA
| |
Collapse
|
19
|
Freitas FC, Morales-Corrêa E Castro AC, Barbosa NCCP, Fernandes OA. Characterization and Comparison of Genetic Variation in Cotesia flavipes (Hymenoptera: Braconidae) Mass Reared for Biological Pest Control Using Microsatellite Markers. NEOTROPICAL ENTOMOLOGY 2018; 47:433-439. [PMID: 28600642 DOI: 10.1007/s13744-017-0531-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 04/25/2017] [Indexed: 06/07/2023]
Abstract
The larval parasitoid Cotesia flavipes (Cameron) (Hymenoptera: Braconidae) is an important biological control agent of the sugarcane borer, Diatraea saccharalis (Fabricius) (Lepidoptera: Crambidae). This exotic parasitoid has been mass reared for field release since its introduction in the 1970s. Insects are exchanged between labs or introduced from the field, but without basic studies or criteria. Thus, the objective of this study was to evaluate the genetic variability of insects from six Brazilian States (São Paulo, Minas Gerais, Paraná, Goiás, Maranhão, and Alagoas) using microsatellites. Analysis of five loci using at least 22 females from each location was performed. The molecular analysis made possible to verify that four out of the five loci analyzed were polymorphic. The allele frequencies of three loci were in agreement with the Hardy-Weinberg Equilibrium for all insects of all regions. It was also observed that five alleles were exclusively presented in only two loci. The variation among and within populations was 24.65 and 75.34%, respectively. The estimated shared genotypes between the C. flavipes individuals showed that K = 2 was the most likely number of genetic groups causing the current variation, as well as high shared genotypes from these groups of the individuals. Considering all the analyzed loci, the genetic differentiation was at a moderate level. We suggest a possible mixture of biological materials based on genetic distances and the degree of structuring displayed.
Collapse
Affiliation(s)
- F C Freitas
- Faculdade de Ciências Agrárias e Veterinárias, Univ Estadual Paulista (Unesp), Jaboticabal, SP, 14884-900, Brasil
| | - A C Morales-Corrêa E Castro
- Faculdade de Ciências Agrárias e Veterinárias, Univ Estadual Paulista (Unesp), Jaboticabal, SP, 14884-900, Brasil
| | - N C C P Barbosa
- Faculdade de Ciências Agrárias e Veterinárias, Univ Estadual Paulista (Unesp), Jaboticabal, SP, 14884-900, Brasil
| | - O A Fernandes
- Faculdade de Ciências Agrárias e Veterinárias, Univ Estadual Paulista (Unesp), Jaboticabal, SP, 14884-900, Brasil.
- São Paulo State Univ, Rod. Prof. Paulo Donato Castellane km 5, Jaboticabal, SP, 14884-000, Brasil.
| |
Collapse
|
20
|
Ramadan S, Dawod A, El-Garhy O, Nowier AM, Eltanany M, Inoue-Murayama M. Genetic characterization of 11 microsatellite loci in Egyptian pigeons ( Columba livia domestica) and their cross-species amplification in other Columbidae populations. Vet World 2018; 11:497-505. [PMID: 29805216 PMCID: PMC5960790 DOI: 10.14202/vetworld.2018.497-505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 03/19/2018] [Indexed: 02/04/2023] Open
Abstract
Aim This study aimed to analyze the genetic diversity and relationships of 10 Egyptian pigeon populations belonging to Columba livia domestica speciesusing 11 microsatellite markers and to investigate the success of these markers amplification across another eight pigeon species. Methods Genomic DNA was isolated from feather samples of179 pigeon samples from 10 Egyptian breeds: Asfer Weraq (n=14), Austoraly (n=20), Reehani (n=21), Messawed (n=17), Nemssawy (n=27), Otatti (n=12), Morasla (n=17), Tumbler (n=22), Halaby Asfer (n=10), and Karakandy (n=19) in addition to Japanese feral pigeons (n=30). Genotyping was done using 11 specific polymorphic microsatellite makers. Moreover, 37 samples not belonging to C. livia domestica but belonging to another eight pigeon species were genotyped. The polymerase chain reaction (PCR) products were electrophoresed on an ABI 3130xl DNA Sequencer. The basic measures of genetic diversity and phylogenetic trees were computed using bioinformatics software. Results Across the 10 studied Egyptian populations, the number of alleles per locus ranged from 3 to 19 and the average number of alleles observed was 9.091. The lowest value of expected heterozygosity (0.373) was obtained for the Reehani breed, and the highest value (0.706) was found for Morasla breed. The overall expected heterozygosity of Egyptian pigeons was 0.548. The FST coefficient which indicates fixation coefficients of subpopulations within the total population for the 11 loci varied from 0.318 to 0.114 with a relatively high mean (0.226). In our study, the FIS showed a relatively high average(0.037). The pairwise Reynolds's genetic distance between the11 studied pigeon populations recorded lower values between Otatti and Austoraly (0.025) and between Morasla and Japanese feral pigeons (0.054). These results are supported by clustering pattern either by the neighbor-joining phylogenetic tree or by a Bayesian clustering of STRUCTURE with the admixture method. Conclusions We confirm the applicability of the CliµD17, CliµT17, CliµD16, CliµD32, CliµT13, CliµD01, PG1, PG2, PG4, PG6, and PG7 microsatellite markers among Egyptian domestic pigeons and across other pigeon species using cross-species amplification method. The information from this study should be useful for genetic characterization and for developing conservation programs of this important species.
Collapse
Affiliation(s)
- Sherif Ramadan
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,Department of Animal Wealth Development, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Ahmed Dawod
- Department of Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Sadat City University, Egypt
| | - Osama El-Garhy
- Animal Production Department, Faculty of Agriculture, Benha University, Toukh, Egypt
| | - Amira M Nowier
- Department of Biotechnology Research, Animal Production Research Institute, ARC, Dokki, Egypt
| | - Marwa Eltanany
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Kyoto, Japan.,Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba, Japan
| |
Collapse
|
21
|
Indykiewicz P, Podlaszczuk P, Surmacki A, Kudelska K, Kosicki J, Kamiński M, Minias P. Scale-of-choice effect in the assortative mating by multiple ornamental and non-ornamental characters in the black-headed gull. Behav Ecol Sociobiol 2017. [DOI: 10.1007/s00265-017-2411-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
22
|
Smouse PE, Banks SC, Peakall R. Converting quadratic entropy to diversity: Both animals and alleles are diverse, but some are more diverse than others. PLoS One 2017; 12:e0185499. [PMID: 29088229 PMCID: PMC5663342 DOI: 10.1371/journal.pone.0185499] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 09/13/2017] [Indexed: 12/14/2022] Open
Abstract
The use of diversity metrics has a long history in population ecology, while population genetic work has been dominated by variance-derived metrics instead, a technical gap that has slowed cross-communication between the fields. Interestingly, Rao’s Quadratic Entropy (RQE), comparing elements for ‘degrees of divergence’, was originally developed for population ecology, but has recently been deployed for evolutionary studies. We here translate RQE into a continuous diversity analogue, and then construct a multiply nested diversity partition for alleles, individuals, populations, and species, each component of which exhibits the behavior of proper diversity metrics, and then translate these components into [0,1]—scaled form. We also deploy non-parametric statistical tests of the among-stratum components and novel tests of the homogeneity of within-stratum diversity components at any hierarchical level. We then illustrate this new analysis with eight nSSR loci and a pair of close Australian marsupial (Antechinus) congeners, using both ‘different is different’ and ‘degree of difference’ distance metrics. The total diversity in the collection is larger than that within either species, but most of the within-species diversity is resident within single populations. The combined A. agilis collection exhibits more diversity than does the combined A. stuartii collection, possibly attributable to localized differences in either local ecological disturbance regimes or differential levels of population isolation. Beyond exhibiting different allelic compositions, the two congeners are becoming more divergent for the arrays of allele sizes they possess.
Collapse
Affiliation(s)
- Peter E. Smouse
- Department of Ecology, Evolution & Natural Resources, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Sam C. Banks
- The Fenner School of Environment and Society, The Australian National University, Acton, ACT, Australia
- * E-mail:
| | - Rod Peakall
- Research School of Biology, The Australian National University, Acton, ACT, Australia
| |
Collapse
|
23
|
Heterozygosity–fitness correlations in blue tit nestlings (Cyanistis caeruleus) under contrasting rearing conditions. Evol Ecol 2017. [DOI: 10.1007/s10682-017-9911-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
24
|
Coulson T, Albon S, Slate J, Pemberton J. MICROSATELLITE LOCI REVEAL SEX-DEPENDENT RESPONSES TO INBREEDING AND OUTBREEDING IN RED DEER CALVES. Evolution 2017; 53:1951-1960. [PMID: 28565463 DOI: 10.1111/j.1558-5646.1999.tb04575.x] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/1998] [Accepted: 06/22/1999] [Indexed: 11/29/2022]
Abstract
Mean d2 is a recently devised microsatellite-based measure that is hypothesised to allow the detection of inbreeding depression and heterosis in free-living populations. Two studies that have investigated the measure have both demonstrated an association between mean d2 and traits related to fitness. Here we present an association between mean d1 and an important component of fitness, first-year overwinter survival, in a population of red deer on the Isle of Rum, Scotland. The association between survival and mean d2 differed between males and females. As predicted, outbred female calves (high mean d2 ) survived better than those that were inbred (low mean d2 ). However, the association was in the opposite direction in male calves. We suggest that this difference is due to different early growth strategies between the sexes. The association between mean d2 and survival was not significantly influenced by any single locus. Decomposition of mean d2 into a recent inbreeding component and an outbreeding component showed that it was the degree of outbreeding that influenced survival in males and both the degree of outbreeding and recent inbreeding that influenced survival in females. Our analyses suggest that mean d2 is an easy-to-calculate measure of inbreeding and degree of outbreeding that can reveal interesting interactions between genetics and ecology.
Collapse
Affiliation(s)
- Tim Coulson
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, United Kingdom
| | - Steve Albon
- Institute of Terrestrial Ecology, Hill of Brathens, Glassel, Banchory, AB31 4BY, Scotland
| | - Jon Slate
- Institute of Cell, Animal and Population Biology, University of Edinburgh West Mains Road, Edinburgh, EH9 3JT, Scotland
| | - Josephine Pemberton
- Institute of Cell, Animal and Population Biology, University of Edinburgh West Mains Road, Edinburgh, EH9 3JT, Scotland
| |
Collapse
|
25
|
Wells SJ, Ji W, Gleeson D, Jones B, Dale J. Population Social Structure Facilitates Indirect Fitness Benefits from Extra-Pair Mating. Front Ecol Evol 2017. [DOI: 10.3389/fevo.2017.00018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
26
|
González AV, Santelices B. Frequency of chimerism in populations of the kelp Lessonia spicata in central Chile. PLoS One 2017; 12:e0169182. [PMID: 28234957 PMCID: PMC5325190 DOI: 10.1371/journal.pone.0169182] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 12/13/2016] [Indexed: 11/23/2022] Open
Abstract
Chimerism occurs when two genetically distinct conspecific individuals fuse together generating a single entity. Coalescence and chimerism in red seaweeds has been positively related to an increase in body size, and the consequent reduction in susceptibility to mortality factors, thus increasing survival, reproductive potential and tolerance to stress in contrast to genetically homogeneous organisms. In addition, they showed that a particular pattern of post-fusion growth maintains higher genetic diversity and chimerism in the holdfast but homogenous axes. In Chilean kelps (brown seaweeds), intraorganismal genetic heterogeneity (IGH) and holdfast coalescence has been described in previous research, but the extent of chimerism in wild populations and the patterns of distribution of the genetically heterogeneous thallus zone have scarcely been studied. Since kelps are under continuous harvesting, with enormous social, ecological and economic importance, natural chimerism can be considered a priceless in-situ reservoir of natural genetic resources and variability. In this study, we therefore examined the frequency of IGH and chimerism in three harvested populations of Lessonia spicata. We then evaluated whether chimeric wild-type holdfasts show higher genetic diversity than erect axes (stipe and lamina) and explored the impact of this on the traditional estimation of genetic diversity at the population level. We found a high frequency of IGH (60-100%) and chimerism (33.3-86.7%), varying according to the studied population. We evidenced that chimerism occurs mostly in holdfasts, exhibiting heterogeneous tissues, whereas stipes and lamina were more homogeneous, generating a vertical gradient of allele and genotype abundance as well as divergence, constituting the first time "within- plant" genetic patterns have been reported in kelps. This is very different from the chimeric patterns described in land plants and animals. Finally, we evidenced that IGH affected genetic differentiation among populations, showed lower levels of FST index when we compared holdfast than lamina samples. In the light of this, future studies should evaluate the significance of chimeric holdfasts in their ability to increase kelps resilience, improve restoration and ecosystem service.
Collapse
Affiliation(s)
- Alejandra V. González
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Bernabé Santelices
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile. Santiago, Chile
| |
Collapse
|
27
|
Pérez‐González J, Costa V, Santos P, Carranza J, Zsolnai A, Fernández‐Llario P, Monteiro NM, Anton I, Beja‐Pereira A. Heterozygosity decrease in wild boar mating system ‐ a case of outbreeding avoidance? J Zool (1987) 2016. [DOI: 10.1111/jzo.12426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. Pérez‐González
- Ungulate Research Unit Cátedra de Recursos Cinegéticos y Piscícolas (CRCP) University of Córdoba Córdoba Spain
| | - V. Costa
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto (CIBIO‐UP) Vairão Portugal
| | - P. Santos
- Departamento de Paisagem, Ambiente e Ordenamento Escola de Ciências e Tecnologia Instituto de Ciências Agrárias e Ambientais Mediterrânicas Instituto de Investigaçao e Formaçao Avançada Universidade de Évora Évora Portugal
| | - J. Carranza
- Ungulate Research Unit Cátedra de Recursos Cinegéticos y Piscícolas (CRCP) University of Córdoba Córdoba Spain
| | - A. Zsolnai
- NARIC ‐ Research Institute for Animal Breeding Nutrition and Food Science Herceghalom Hungary
- University of Kaposvár Kaposvár Hungary
| | - P. Fernández‐Llario
- Biology and Ethology Unit University of Extremadura Cáceres Spain
- Innovación en Gestión y Conservación de Ungulados S.L. Cáceres Spain
| | - N. M. Monteiro
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto (CIBIO‐UP) Vairão Portugal
- Centro de Investigação em Biomedicina (CEBIMED) Faculty of Health Sciences University Fernando Pessoa Porto Portugal
| | - I. Anton
- NARIC ‐ Research Institute for Animal Breeding Nutrition and Food Science Herceghalom Hungary
| | - A. Beja‐Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto (CIBIO‐UP) Vairão Portugal
| |
Collapse
|
28
|
Kardos M, Taylor HR, Ellegren H, Luikart G, Allendorf FW. Genomics advances the study of inbreeding depression in the wild. Evol Appl 2016; 9:1205-1218. [PMID: 27877200 PMCID: PMC5108213 DOI: 10.1111/eva.12414] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 08/05/2016] [Indexed: 12/12/2022] Open
Abstract
Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high-throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability.
Collapse
Affiliation(s)
- Marty Kardos
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | | | - Hans Ellegren
- Department of Evolutionary BiologyEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Gordon Luikart
- Division of Biological SciencesUniversity of MontanaMissoulaMTUSA
- Flathead Lake Biological StationDivision of Biological SciencesUniversity of MontanaPolsonMTUSA
| | | |
Collapse
|
29
|
Huchard E, Schliehe-Diecks S, Kappeler PM, Kraus C. The inbreeding strategy of a solitary primate,Microcebus murinus. J Evol Biol 2016; 30:128-140. [DOI: 10.1111/jeb.12992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/10/2016] [Accepted: 10/12/2016] [Indexed: 11/30/2022]
Affiliation(s)
- E. Huchard
- ISEM UMR 5554; CNRS; Université de Montpellier; Montpellier France
| | - S. Schliehe-Diecks
- Behavioral Ecology Sociobiology Unit; German Primate Center; Göttingen Germany
- Department of Sociobiology/Anthropology; Georg-August-University of Göttingen; Göttingen Germany
| | - P. M. Kappeler
- Behavioral Ecology Sociobiology Unit; German Primate Center; Göttingen Germany
- Department of Sociobiology/Anthropology; Georg-August-University of Göttingen; Göttingen Germany
| | - C. Kraus
- Behavioral Ecology Sociobiology Unit; German Primate Center; Göttingen Germany
- Department of Sociobiology/Anthropology; Georg-August-University of Göttingen; Göttingen Germany
| |
Collapse
|
30
|
Queirós J, Vicente J, Alves PC, de la Fuente J, Gortazar C. Tuberculosis, genetic diversity and fitness in the red deer, Cervus elaphus. INFECTION GENETICS AND EVOLUTION 2016; 43:203-12. [PMID: 27245150 DOI: 10.1016/j.meegid.2016.05.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 05/20/2016] [Accepted: 05/22/2016] [Indexed: 12/16/2022]
Abstract
Understanding how genetic diversity, infections and fitness interact in wild populations is a major challenge in ecology and management. These interactions were addressed through heterozygosity-fitness correlation analyses, by assessing the genetic diversity, tuberculosis (TB) and body size in adult red deer. Heterozygosity-fitness correlation models provided a better understanding of the link between genetic diversity and TB at individual and population levels. A single local effect was found for Ceh45 locus at individual level, enhancing the importance of its close functional genes in determining TB presence. At population level, the ability of the red deer to control TB progression correlated positively with population genetic diversity, indicating that inbred populations might represent more risk of deer TB severity. Statistical models also gained insights into the dynamics of multi-host interaction in natural environments. TB prevalence in neighbouring wild boar populations was positively associated with deer TB at both individual and population levels. Additionally, TB presence correlated positively with red deer body size, for which "general and local effect" hypotheses were found. Although body size might be correlated with age, an indirect genetic effect on TB presence could be implied. This study provides new insights towards understanding host-pathogen interactions in wild populations and their relation to fitness traits.
Collapse
Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, R. Monte-Crasto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s⁄n, 4169-007 Porto, Portugal; SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain.
| | - Joaquín Vicente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain
| | - Paulo C Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, R. Monte-Crasto, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s⁄n, 4169-007 Porto, Portugal; Wildlife Biology Program, University of Montana, Missoula, MT 59812, USA
| | - José de la Fuente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain; Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Christian Gortazar
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071 Ciudad Real, Spain
| |
Collapse
|
31
|
Hoffmann GS, Johannesen J, Griebeler EM. Population dynamics of a natural red deer population over 200 years detected via substantial changes of genetic variation. Ecol Evol 2016; 6:3146-53. [PMID: 27096075 PMCID: PMC4828584 DOI: 10.1002/ece3.2063] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 02/01/2016] [Accepted: 02/09/2016] [Indexed: 11/23/2022] Open
Abstract
Most large mammals have constantly been exposed to anthropogenic influence over decades or even centuries. Because of their long generation times and lack of sampling material, inferences of past population genetic dynamics, including anthropogenic impacts, have only relied on the analysis of the structure of extant populations. Here, we investigate for the first time the change in the genetic constitution of a natural red deer population over two centuries, using up to 200‐year‐old antlers (30 generations) stored in trophy collections. To the best of our knowledge, this is the oldest DNA source ever used for microsatellite population genetic analyses. We demonstrate that government policy and hunting laws may have strong impacts on populations that can lead to unexpectedly rapid changes in the genetic constitution of a large mammal population. A high ancestral individual polymorphism seen in an outbreeding population (1813–1861) was strongly reduced in descendants (1923–1940) during the mid‐19th and early 20th century by genetic bottlenecks. Today (2011), individual polymorphism and variance among individuals is increasing in a constant‐sized (managed) population. Differentiation was high among periods (FST > ***); consequently, assignment tests assigned individuals to their own period with >85% probability. In contrast to the high variance observed at nuclear microsatellite loci, mtDNA (D‐loop) was monomorphic through time, suggesting that male immigration dominates the genetic evolution in this population.
Collapse
Affiliation(s)
| | - Jes Johannesen
- Department of Ecology Institute of Zoology Johannes Gutenberg-University of Mainz D-55099 Mainz Germany
| | - Eva Maria Griebeler
- Department of Ecology Institute of Zoology Johannes Gutenberg-University of Mainz D-55099 Mainz Germany
| |
Collapse
|
32
|
Carranza J, Salinas M, de Andrés D, Pérez‐González J. Iberian red deer: paraphyletic nature at mtDNA but nuclear markers support its genetic identity. Ecol Evol 2016; 6:905-22. [PMID: 26843924 PMCID: PMC4729781 DOI: 10.1002/ece3.1836] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 10/07/2015] [Accepted: 10/21/2015] [Indexed: 01/15/2023] Open
Abstract
Red deer populations in the Iberian glacial refugium were the main source for postglacial recolonization and subspecific radiation in north-western Europe. However, the phylogenetic history of Iberian red deer (Cervus elaphus hispanicus) and its relationships with northern European populations remain uncertain. Here, we study DNA sequences at the mitochondrial control region along with STR markers for over 680 specimens from all the main red deer populations in Spain and other west European areas. Our results from mitochondrial and genomic DNA show contrasting patterns, likely related to the nature of these types of DNA markers and their specific processes of change over time. The results, taken together, bring support to two distinct, cryptic maternal lineages for Iberian red deer that predated the last glacial maximum and that have maintained geographically well differentiated until present. Haplotype relationships show that only one of them contributed to the northern postglacial recolonization. However, allele frequencies of nuclear markers evidenced one main differentiation between Iberian and northern European subspecies although also supported the structure of both matrilines within Iberia. Thus, our findings reveal a paraphyletic nature for Iberian red deer but also its genetic identity and differentiation with respect to northern subspecies. Finally, we suggest that maintaining the singularity of Iberian red deer requires preventing not only restocking practices with red deer specimens belonging to other European populations but also translocations between both Iberian lineages.
Collapse
Affiliation(s)
- Juan Carranza
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
| | - María Salinas
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
| | - Damián de Andrés
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
- Instituto de AgrobiotecnologíaCSIC‐UPNA‐Gobierno de Navarra31192MutilvaNavarraSpain
| | - Javier Pérez‐González
- Ungulate Research UnitCátedra de Recursos Cinegéticos y Piscícolas (CRCP)Universidad de Córdoba14071CórdobaSpain
| |
Collapse
|
33
|
Saeed AF, Wang R, Wang S. Microsatellites in Pursuit of Microbial Genome Evolution. Front Microbiol 2016; 6:1462. [PMID: 26779133 PMCID: PMC4700210 DOI: 10.3389/fmicb.2015.01462] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 12/07/2015] [Indexed: 12/27/2022] Open
Abstract
Microsatellites or short sequence repeats are widespread genetic markers which are hypermutable 1-6 bp long short nucleotide motifs. Significantly, their applications in genetics are extensive due to their ceaseless mutational degree, widespread length variations and hypermutability skills. These features make them useful in determining the driving forces of evolution by using powerful molecular techniques. Consequently, revealing important questions, for example, what is the significance of these abundant sequences in DNA, what are their roles in genomic evolution? The answers of these important questions are hidden in the ways these short motifs contributed in altering the microbial genomes since the origin of life. Even though their size ranges from 1 -to- 6 bases, these repeats are becoming one of the most popular genetic probes in determining their associations and phylogenetic relationships in closely related genomes. Currently, they have been widely used in molecular genetics, biotechnology and evolutionary biology. However, due to limited knowledge; there is a significant gap in research and lack of information concerning hypermutational mechanisms. These mechanisms play a key role in microsatellite loci point mutations and phase variations. This review will extend the understandings of impacts and contributions of microsatellite in genomic evolution and their universal applications in microbiology.
Collapse
Affiliation(s)
- Abdullah F. Saeed
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, School of Life Sciences, Fujian Agriculture and Forestry UniversityFuzhou, China
| | | | | |
Collapse
|
34
|
Moreno E, Pérez-González J, Carranza J, Moya-Laraño J. Better Fitness in Captive Cuvier's Gazelle despite Inbreeding Increase: Evidence of Purging? PLoS One 2015; 10:e0145111. [PMID: 26679703 PMCID: PMC4682998 DOI: 10.1371/journal.pone.0145111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 11/27/2015] [Indexed: 11/19/2022] Open
Abstract
Captive breeding of endangered species often aims at preserving genetic diversity and to avoid the harmful effects of inbreeding. However, deleterious alleles causing inbreeding depression can be purged when inbreeding persists over several generations. Despite its great importance both for evolutionary biology and for captive breeding programmes, few studies have addressed whether and to which extent purging may occur. Here we undertake a longitudinal study with the largest captive population of Cuvier's gazelle managed under a European Endangered Species Programme since 1975. Previous results in this population have shown that highly inbred mothers tend to produce more daughters, and this fact was used in 2006 to reach a more appropriate sex-ratio in this polygynous species by changing the pairing strategy (i.e., pairing some inbred females instead of keeping them as surplus individuals in the population). Here, by using studbook data we explore whether purging has occurred in the population by investigating whether after the change in pairing strategy a) inbreeding and homozygosity increased at the population level, b) fitness (survival) increased, and c) the relationship between inbreeding and juvenile survival, was positive. Consistent with the existence of purging, we found an increase in inbreeding coefficients, homozygosity and juvenile survival. In addition, we showed that in the course of the breeding programme the relationship between inbreeding and juvenile survival was not uniform but rather changed over time: it was negative in the early years, flat in the middle years and positive after the change in pairing strategy. We highlight that by allowing inbred individuals to mate in captive stocks we may favour sex-ratio bias towards females, a desirable managing strategy to reduce the surplus of males that force most zoos to use ethical culling and euthanizing management tools. We discuss these possibilities but also acknowledge that many other effects should be considered before implementing inbreeding and purging as elements in management decisions.
Collapse
Affiliation(s)
- Eulalia Moreno
- Estación Experimental de Zonas Áridas (CSIC), Dept. Ecología Funcional y Evolutiva, Ctra. de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
- * E-mail:
| | - Javier Pérez-González
- Ungulate Research Unit, Cátedra de Recursos Cinegéticos y Piscícolas, Universidad de Córdoba, E-14071, Córdoba, Spain
- Guardería Rural, Mancomunidad Integral de Municipios Centro, E-06810, Calamonte, Badajoz, Spain
| | - Juan Carranza
- Ungulate Research Unit, Cátedra de Recursos Cinegéticos y Piscícolas, Universidad de Córdoba, E-14071, Córdoba, Spain
| | - Jordi Moya-Laraño
- Estación Experimental de Zonas Áridas (CSIC), Dept. Ecología Funcional y Evolutiva, Ctra. de Sacramento s/n, E-04120, La Cañada de San Urbano, Almería, Spain
| |
Collapse
|
35
|
Minias P, Wojczulanis-Jakubas K, Rutkowski R, Kaczmarek K. Local Heterozygosity Effects on Nestling Growth and Condition in the Great Cormorant. Evol Biol 2015; 42:452-460. [PMID: 26586922 PMCID: PMC4642584 DOI: 10.1007/s11692-015-9339-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 07/08/2015] [Indexed: 11/25/2022]
Abstract
Under inbreeding, heterozygosity at neutral genetic markers is likely to reflect genome-wide heterozygosity and, thus, is expected to correlate with fitness. There is, however, growing evidence that some of heterozygosity-fitness correlations (HFCs) can be explained by ‘local effects’, where noncoding loci are at linkage disequilibrium with functional genes. The aim of this study was to investigate correlations between heterozygosity at seven microsatellite loci and two fitness-related traits, nestling growth rate and nutritional condition, in a recently bottlenecked population of great cormorant Phalacrocorax carbo sinensis. We found that heterozygosity was positively associated with both nestling traits at the between-brood level, but the individual (within-brood) effects of heterozygosity were non-significant. We also found that only one locus per trait was primarily responsible for the significant multi-locus HFCs, suggesting a linkage disequilibrium with non-identified functional loci. The results give support for ‘local effect’ hypothesis, confirming that HFCs may not only be interpreted as evidence of inbreeding and that genetic associations between functional and selectively neutral markers could be much more common in natural populations than previously thought.
Collapse
Affiliation(s)
- Piotr Minias
- />Department of Teacher Training and Biodiversity Studies, University of Łódź, Banacha 1/3, 90-237 Łódź, Poland
- />Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53201 USA
| | | | - Robert Rutkowski
- />Department of Molecular and Biometrical Techniques, Museum and Institute of Zoology PAS, 00-679 Warsaw, Poland
| | | |
Collapse
|
36
|
González‐Ittig RE, Polop FJ, Andreo VC, Chiappero MB, Levis S, Calderón G, Provensal MC, Polop JJ, Gardenal CN. Temporal fine‐scale genetic variation in the zoonosis‐carrying long‐tailed pygmy rice rat in
P
atagonia,
A
rgentina. J Zool (1987) 2015. [DOI: 10.1111/jzo.12238] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- R. E. González‐Ittig
- Instituto de Diversidad y Ecología Animal CONICET‐Facultad de Ciencias Exactas Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | - F. J. Polop
- Departamento de Ciencias Naturales Universidad Nacional de Río Cuarto Córdoba Argentina
| | - V. C. Andreo
- Departamento de Ciencias Naturales Universidad Nacional de Río Cuarto Córdoba Argentina
| | - M. B. Chiappero
- Instituto de Diversidad y Ecología Animal CONICET‐Facultad de Ciencias Exactas Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| | - S. Levis
- Instituto Nacional de Enfermedades Virales Humanas (INEVH) ‘Dr. J. Maiztegui’ Pergamino Argentina
| | - G. Calderón
- Instituto Nacional de Enfermedades Virales Humanas (INEVH) ‘Dr. J. Maiztegui’ Pergamino Argentina
| | - M. C. Provensal
- Departamento de Ciencias Naturales Universidad Nacional de Río Cuarto Córdoba Argentina
| | - J. J. Polop
- Departamento de Ciencias Naturales Universidad Nacional de Río Cuarto Córdoba Argentina
| | - C. N. Gardenal
- Instituto de Diversidad y Ecología Animal CONICET‐Facultad de Ciencias Exactas Físicas y Naturales Universidad Nacional de Córdoba Córdoba Argentina
| |
Collapse
|
37
|
Velando A, Barros Á, Moran P. Heterozygosity-fitness correlations in a declining seabird population. Mol Ecol 2015; 24:1007-18. [PMID: 25626726 DOI: 10.1111/mec.13092] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 01/12/2023]
Abstract
Loss of genetic diversity is thought to lead to increased risk of extinction in endangered populations due to decreasing fitness of homozygous individuals. Here, we evaluated the presence of inbreeding depression in a long-lived seabird, the European shag (Phalacrocorax aristotelis), after a severe decline in population size by nearly 70%. During three reproductive seasons, 85 breeders were captured and genotyped at seven microsatellite loci. Nest sites were monitored during the breeding season to estimate reproductive success as the number of chicks surviving to full-size-grown per nest. Captured birds were tagged with a ring with an individual code, and resighting data were collected during 7-year period. We found a strong effect of multilocus heterozygosity on female reproductive performance, and a significant, although weaker, effect on breeder survival. However, our matrix population model suggests that this relatively small effect of genetic diversity on breeder survival may have a profound effect on fitness. This highlights the importance of integrating life history consequences in HFC studies. Importantly, heterozygosity was correlated across loci, suggesting that genomewide effects, rather than single loci, are responsible for the observed HFCs. Overall, the HFCs are a worrying symptom of genetic erosion in this declining population. Many long-lived species are prone to extinction, and future studies should evaluate the magnitude of fitness impact of genetic deterioration on key population parameters, such as survival of breeders.
Collapse
Affiliation(s)
- Alberto Velando
- Departamento de Ecoloxía e Bioloxía Animal, Universidade de Vigo, Campus As Lagoas, 36310, Vigo, Spain
| | | | | |
Collapse
|
38
|
Queirós J, Godinho R, Lopes S, Gortazar C, de la Fuente J, Alves PC. Effect of microsatellite selection on individual and population genetic inferences: an empirical study using cross-specific and species-specific amplifications. Mol Ecol Resour 2014; 15:747-60. [PMID: 25403329 DOI: 10.1111/1755-0998.12349] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 11/27/2022]
Abstract
Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations.
Collapse
Affiliation(s)
- J Queirós
- 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 da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - R 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 da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal
| | - S Lopes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661, Vairão, Portugal
| | - C Gortazar
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - J de la Fuente
- SaBio Research Group, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - P C Alves
- 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 da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
| |
Collapse
|
39
|
Mijangos JL, Pacioni C, Spencer PBS, Craig MD. Contribution of genetics to ecological restoration. Mol Ecol 2014; 24:22-37. [DOI: 10.1111/mec.12995] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Revised: 10/17/2014] [Accepted: 11/01/2014] [Indexed: 12/17/2022]
Affiliation(s)
- Jose Luis Mijangos
- School of Veterinary and Life Sciences; Murdoch University; Murdoch WA 6150 Australia
| | - Carlo Pacioni
- School of Veterinary and Life Sciences; Murdoch University; Murdoch WA 6150 Australia
| | - Peter B. S. Spencer
- School of Veterinary and Life Sciences; Murdoch University; Murdoch WA 6150 Australia
| | - Michael D. Craig
- School of Veterinary and Life Sciences; Murdoch University; Murdoch WA 6150 Australia
- School of Plant Biology; University of Western Australia; Crawley WA 6009 Australia
| |
Collapse
|
40
|
Hama-Ali EO, Alwee SSRS, Tan SG, Panandam JM, Ling HC, Namasivayam P, Peng HB. Illegitimacy and sibship assignments in oil palm (Elaeis guineensis Jacq.) half-sib families using single locus DNA microsatellite markers. Mol Biol Rep 2014; 42:917-25. [PMID: 25399079 DOI: 10.1007/s11033-014-3829-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Accepted: 11/10/2014] [Indexed: 12/01/2022]
Abstract
Oil palm breeding has been progressing very well in Southeast Asia, especially in Malaysia and Indonesia. Despite this progress, there are still problems due to the difficulty of controlled crossing in oil palm. Contaminated/illegitimate progeny has appeared in some breeding programs; late and failure of detection by the traditional method causes a waste of time and labor. The use of molecular markers improves the integrity of breeding programs in perennial crops such as oil palm. Four half-sib families with a total of 200 progeny were used in this study. Thirty polymorphic single locus DNA microsatellites markers were typed to identify the illegitimate individuals and to obtain the correct parental and progeny assignments by using the CERVUS and COLONY programs. Three illegitimate palms (1.5%) were found, and 16 loci proved to be sufficient for sibship assignments without parental genotypes by using the COLONY program. The pairwise-likelihood score (PLS) method was better for half-sib family assignments than the full likelihood (FL) method.
Collapse
Affiliation(s)
- Emad Omer Hama-Ali
- Department of Field Crops, Faculty of Agricultural Sciences, University of Sulaimani, Sulaimani, Iraqi Kurdistan Region,
| | | | | | | | | | | | | |
Collapse
|
41
|
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
| |
Collapse
|
42
|
Northrup JM, Shafer ABA, Anderson CR, Coltman DW, Wittemyer G. Fine-scale genetic correlates to condition and migration in a wild cervid. Evol Appl 2014; 7:937-48. [PMID: 25469172 PMCID: PMC4211723 DOI: 10.1111/eva.12189] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/30/2014] [Indexed: 12/18/2022] Open
Abstract
The relationship between genetic variation and phenotypic traits is fundamental to the study and management of natural populations. Such relationships often are investigated by assessing correlations between phenotypic traits and heterozygosity or genetic differentiation. Using an extensive data set compiled from free-ranging mule deer (Odocoileus hemionus), we combined genetic and ecological data to (i) examine correlations between genetic differentiation and migration timing, (ii) screen for mitochondrial haplotypes associated with migration timing, and (iii) test whether nuclear heterozygosity was associated with condition. Migration was related to genetic differentiation (more closely related individuals migrated closer in time) and mitochondrial haplogroup. Body fat was related to heterozygosity at two nuclear loci (with antagonistic patterns), one of which is situated near a known fat metabolism gene in mammals. Despite being focused on a widespread panmictic species, these findings revealed a link between genetic variation and important phenotypes at a fine scale. We hypothesize that these correlations are either the result of mixing refugial lineages or differential mitochondrial haplotypes influencing energetics. The maintenance of phenotypic diversity will be critical to enable the potential tracking of changing climatic conditions, and these correlates highlight the need to consider evolutionary mechanisms in management, even in widely distributed panmictic species.
Collapse
Affiliation(s)
- Joseph M Northrup
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University Fort Collins, CO, USA
| | - Aaron B A Shafer
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University Uppsala, Sweden
| | - Charles R Anderson
- Mammals Research Section, Colorado Parks and Wildlife Grand Junction, CO, USA
| | - David W Coltman
- Department of Biological Sciences, University of Alberta Edmonton, AB, Canada
| | - George Wittemyer
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University Fort Collins, CO, USA
| |
Collapse
|
43
|
Canal D, Serrano D, Potti J. Exploring heterozygosity-survival correlations in a wild songbird population: contrasting effects between juvenile and adult stages. PLoS One 2014; 9:e105020. [PMID: 25122217 PMCID: PMC4133379 DOI: 10.1371/journal.pone.0105020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/03/2014] [Indexed: 11/22/2022] Open
Abstract
The relationship between genetic diversity and fitness, a major issue in evolutionary and conservation biology, is expected to be stronger in traits affected by many loci and those directly influencing fitness. Here we explore the influence of heterozygosity measured at 15 neutral markers on individual survival, one of the most important parameters determining individual fitness. We followed individual survival up to recruitment and during subsequent adult life of 863 fledgling pied flycatchers born in two consecutive breeding seasons. Mark-recapture analyses showed that individual heterozygosity did not influence juvenile or adult survival. In contrast, the genetic relatedness of parents was negatively associated with the offspring’s survival during the adult life, but this effect was not apparent in the juvenile (from fledgling to recruitment) stage. Stochastic factors experienced during the first year of life in this long-distance migratory species may have swamped a relationship between heterozygosity and survival up to recruitment.
Collapse
Affiliation(s)
- David Canal
- Doñana Biological Station – CSIC, Department of Evolutionary Ecology, Sevilla, Spain
- * E-mail:
| | - David Serrano
- Doñana Biological Station – CSIC, Department of Conservation Biology, Sevilla, Spain
| | - Jaime Potti
- Doñana Biological Station – CSIC, Department of Evolutionary Ecology, Sevilla, Spain
| |
Collapse
|
44
|
|
45
|
Fordham DA, Brook BW, Moritz C, Nogués-Bravo D. Better forecasts of range dynamics using genetic data. Trends Ecol Evol 2014; 29:436-43. [DOI: 10.1016/j.tree.2014.05.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 05/17/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
|
46
|
Pemberton TJ, Rosenberg NA. Population-genetic influences on genomic estimates of the inbreeding coefficient: a global perspective. Hum Hered 2014; 77:37-48. [PMID: 25060268 DOI: 10.1159/000362878] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND/AIMS Culturally driven marital practices provide a key instance of an interaction between social and genetic processes in shaping patterns of human genetic variation, producing, for example, increased identity by descent through consanguineous marriage. A commonly used measure to quantify identity by descent in an individual is the inbreeding coefficient, a quantity that reflects not only consanguinity, but also other aspects of kinship in the population to which the individual belongs. Here, in populations worldwide, we examine the relationship between genomic estimates of the inbreeding coefficient and population patterns in genetic variation. METHODS Using genotypes at 645 microsatellites, we compare inbreeding coefficients from 5,043 individuals representing 237 populations worldwide to demographic consanguinity frequency estimates available for 26 populations as well as to other quantities that can illuminate population-genetic influences on inbreeding coefficients. RESULTS We observe higher inbreeding coefficient estimates in populations and geographic regions with known high levels of consanguinity or genetic isolation and in populations with an increased effect of genetic drift and decreased genetic diversity with increasing distance from Africa. For the small number of populations with specific consanguinity estimates, we find a correlation between inbreeding coefficients and consanguinity frequency (r = 0.349, p = 0.040). CONCLUSIONS The results emphasize the importance of both consanguinity and population-genetic factors in influencing variation in inbreeding coefficients, and they provide insight into factors useful for assessing the effect of consanguinity on genomic patterns in different populations.
Collapse
Affiliation(s)
- Trevor J Pemberton
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Man., Canada
| | | |
Collapse
|
47
|
Variation at genes influencing facial morphology are not associated with developmental imprecision in human faces. PLoS One 2014; 9:e99009. [PMID: 24914781 PMCID: PMC4051657 DOI: 10.1371/journal.pone.0099009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 05/09/2014] [Indexed: 12/05/2022] Open
Abstract
Facial asymmetries are commonly used as a proxy for human developmental imprecision resulting from inbreeding, and thus reduced genetic heterozygosity. Several environmental factors influence human facial asymmetry (e.g., health care, parasites), but the generalizability of findings on genetic stressors has been limited in humans by sample characteristics (island populations, endogamy) and indirect genetic assessment (inference from pedigrees). In a sample of 3215 adult humans from the Rotterdam Study, we therefore studied the relationship of facial asymmetry, estimated from nine mid-facial landmarks, with genetic variation at 102 single nucleotide polymorphism (SNP) loci recently associated with facial shape variation. We further tested whether the degree of individual heterozygosity is negatively correlated with facial asymmetry. An ANOVA tree regression did not identify any SNP relating to either fluctuating asymmetry or total asymmetry. In a general linear model, only age and sex—but neither heterozygosity nor any SNP previously reported to covary with facial shape—was significantly related to total or fluctuating asymmetry of the midface. Our study does not corroborate the common assumption in evolutionary and behavioral biology that morphological asymmetries reflect heterozygosity. Our results, however, may be affected by a relatively small degree of inbreeding, a relatively stable environment, and an advanced age in the Rotterdam sample. Further large-scale genetic studies, including gene expression studies, are necessary to validate the genetic and developmental origin of morphological asymmetries.
Collapse
|
48
|
Annavi G, Newman C, Buesching CD, Macdonald DW, Burke T, Dugdale HL. Heterozygosity-fitness correlations in a wild mammal population: accounting for parental and environmental effects. Ecol Evol 2014; 4:2594-609. [PMID: 25360289 PMCID: PMC4203301 DOI: 10.1002/ece3.1112] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 04/24/2014] [Indexed: 02/02/2023] Open
Abstract
HFCs (heterozygosity–fitness correlations) measure the direct relationship between an individual's genetic diversity and fitness. The effects of parental heterozygosity and the environment on HFCs are currently under-researched. We investigated these in a high-density U.K. population of European badgers (Meles meles), using a multimodel capture–mark–recapture framework and 35 microsatellite loci. We detected interannual variation in first-year, but not adult, survival probability. Adult females had higher annual survival probabilities than adult males. Cubs with more heterozygous fathers had higher first-year survival, but only in wetter summers; there was no relationship with individual or maternal heterozygosity. Moist soil conditions enhance badger food supply (earthworms), improving survival. In dryer years, higher indiscriminate mortality rates appear to mask differential heterozygosity-related survival effects. This paternal interaction was significant in the most supported model; however, the model-averaged estimate had a relative importance of 0.50 and overlapped zero slightly. First-year survival probabilities were not correlated with the inbreeding coefficient (f); however, small sample sizes limited the power to detect inbreeding depression. Correlations between individual heterozygosity and inbreeding were weak, in line with published meta-analyses showing that HFCs tend to be weak. We found support for general rather than local heterozygosity effects on first-year survival probability, and g2 indicated that our markers had power to detect inbreeding. We emphasize the importance of assessing how environmental stressors can influence the magnitude and direction of HFCs and of considering how parental genetic diversity can affect fitness-related traits, which could play an important role in the evolution of mate choice.
Collapse
Affiliation(s)
- Geetha Annavi
- Wildlife Conservation Research Unit, Department of Zoology, Recanati-Kaplan Centre, University of Oxford Tubney House, Abingdon Road, Tubney, Abingdon, Oxfordshire, OX13 5QL, U.K ; NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, S10 2TN, U.K ; Faculty of Science, Department of Biology, University of Putra Malaysia UPM 43400, Serdang, Selangor, Malaysia
| | - Christopher Newman
- Wildlife Conservation Research Unit, Department of Zoology, Recanati-Kaplan Centre, University of Oxford Tubney House, Abingdon Road, Tubney, Abingdon, Oxfordshire, OX13 5QL, U.K
| | - Christina D Buesching
- Wildlife Conservation Research Unit, Department of Zoology, Recanati-Kaplan Centre, University of Oxford Tubney House, Abingdon Road, Tubney, Abingdon, Oxfordshire, OX13 5QL, U.K
| | - David W Macdonald
- Wildlife Conservation Research Unit, Department of Zoology, Recanati-Kaplan Centre, University of Oxford Tubney House, Abingdon Road, Tubney, Abingdon, Oxfordshire, OX13 5QL, U.K
| | - Terry Burke
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, S10 2TN, U.K
| | - Hannah L Dugdale
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield Sheffield, S10 2TN, U.K ; Theoretical Biology, Centre for Ecological and Evolutionary Studies, University of Groningen PO Box 11103, 9700 CC, Groningen, The Netherlands ; Behavioural Ecology and Self-Organization, Centre for Ecological and Evolutionary Studies, University of Groningen PO Box 11103, 9700 CC, Groningen, The Netherlands
| |
Collapse
|
49
|
Vranckx G, Jacquemyn H, Mergeay J, Cox K, Janssens P, Gielen BAS, Muys B, Honnay O. The effect of drought stress on heterozygosity-fitness correlations in pedunculate oak (Quercus robur). ANNALS OF BOTANY 2014; 113:1057-69. [PMID: 24638819 PMCID: PMC3997642 DOI: 10.1093/aob/mcu025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 02/07/2014] [Indexed: 05/15/2023]
Abstract
BACKGROUND AND AIMS The interaction between forest fragmentation and predicted climate change may pose a serious threat to tree populations. In small and spatially isolated forest fragments, increased homozygosity may directly affect individual tree fitness through the expression of deleterious alleles. Climate change-induced drought stress may exacerbate these detrimental genetic consequences of forest fragmentation, as the fitness response to low levels of individual heterozygosity is generally thought to be stronger under environmental stress than under optimal conditions. METHODS To test this hypothesis, a greenhouse experiment was performed in which various transpiration and growth traits of 6-month-old seedlings of Quercus robur differing in multilocus heterozygosity (MLH) were recorded for 3 months under a well-watered and a drought stress treatment. Heterozygosity-fitness correlations (HFC) were examined by correlating the recorded traits of individual seedlings to their MLH and by studying their response to drought stress. KEY RESULTS Weak, but significant, effects of MLH on several fitness traits were obtained, which were stronger for transpiration variables than for the recorded growth traits. High atmospheric stress (measured as vapour pressure deficit) influenced the strength of the HFCs of the transpiration variables, whereas only a limited effect of the irrigation treatment on the HFCs was observed. CONCLUSIONS Under ongoing climate change, increased atmospheric stress in the future may strengthen the negative fitness responses of trees to low MLH. This indicates the necessity to maximize individual multilocus heterozygosity in forest tree breeding programmes.
Collapse
Affiliation(s)
- Guy Vranckx
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, Box 2435, 3001 Leuven, Belgium
| | - Hans Jacquemyn
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, Box 2435, 3001 Leuven, Belgium
| | - Joachim Mergeay
- Research Institute for Nature and Forest (INBO), Flemish Government, Gaverstraat 4, 9500 Geraardsbergen, Belgium
| | - Karen Cox
- Research Institute for Nature and Forest (INBO), Flemish Government, Gaverstraat 4, 9500 Geraardsbergen, Belgium
| | - Pieter Janssens
- Soil Service of Belgium, Willem de Croylaan 48, 3001 Leuven, Belgium
| | - Bie An Sofie Gielen
- Division of Forest, Nature and Landscape, University of Leuven, Celestijnenlaan 200E, Box 2411, 3001 Leuven, Belgium
| | - Bart Muys
- Division of Forest, Nature and Landscape, University of Leuven, Celestijnenlaan 200E, Box 2411, 3001 Leuven, Belgium
| | - Olivier Honnay
- Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, Box 2435, 3001 Leuven, Belgium
| |
Collapse
|
50
|
Winternitz JC, Wares JP, Yabsley MJ, Altizer S. Wild cyclic voles maintain high neutral and MHC diversity without strong evidence for parasite-mediated selection. Evol Ecol 2014. [DOI: 10.1007/s10682-014-9709-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
|