1
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Heterozygous Trees Rebound the Fastest after Felling by Beavers to Positively Affect Arthropod Community Diversity. FORESTS 2021. [DOI: 10.3390/f12060694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Although genetic diversity within stands of trees is known to have community-level consequences, whether such effects are present at an even finer genetic scale is unknown. We examined the hypothesis that genetic variability (heterozygosity) within an individual plant would affect its dependent community, which adds a new dimension to the importance of genetic diversity. Our study contrasted foliar arthropod community diversity and microsatellite marker-derived measures of genetic diversity of cottonwood (Populus fremontii) trees that had been felled by beavers (Castor canadensis) and were resprouting, relative to adjacent standing, unfelled trees. Three patterns emerged: 1. Productivity (specific leaf area), phytochemical defenses (salicortin), and arthropod community richness, abundance, and diversity were positively correlated with the heterozygosity of individual felled trees, but not with that of unfelled trees; 2. These relationships were not explained by population substructure, genetic relatedness of the trees, or hybridization; 3. The underlying mechanism appears to be that beaver herbivory stimulates increased productivity (i.e., 2× increase from the most homozygous to the most heterozygous tree) that is the greatest in more heterozygous trees. Salicortin defenses in twigs were also expressed at higher concentrations in more heterozygous trees (i.e., 3× increase from the most homozygous to the most heterozygous tree), which suggests that this compound may dissuade further herbivory by beavers, as has been found for other mammalian herbivores. We suggest that high stress to trees as a consequence of felling reveals a heterozygosity–productivity linkage, which in turn is attractive to arthropods. Although experiments are required to demonstrate causality, these results link the genetic diversity of individual trees to community diversity, supporting the hypothesis that interactions among foundation species (beavers and trees) have community-level effects, and underscores the importance of genetic diversity for biodiversity, conservation, and restoration.
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2
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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.
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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
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3
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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.
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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
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4
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Litzke V, Ottensmann M, Forcada J, Heitzmann L, Ivan Hoffman J. Heterozygosity at neutral and immune loci is not associated with neonatal mortality due to microbial infection in Antarctic fur seals. Ecol Evol 2019; 9:7985-7996. [PMID: 31380066 PMCID: PMC6662382 DOI: 10.1002/ece3.5317] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/02/2019] [Accepted: 05/08/2019] [Indexed: 11/08/2022] Open
Abstract
Numerous studies have reported correlations between the heterozygosity of genetic markers and fitness. These heterozygosity-fitness correlations (HFCs) play a central role in evolutionary and conservation biology, yet their mechanistic basis remains open to debate. For example, fitness associations have been widely reported at both neutral and functional loci, yet few studies have directly compared the two, making it difficult to gauge the relative contributions of genome-wide inbreeding and specific functional genes to fitness. Here, we compared the effects of neutral and immune gene heterozygosity on death from bacterial infection in Antarctic fur seal (Arctocephalus gazella) pups. We specifically developed a panel of 13 microsatellites from expressed immune genes and genotyped these together with 48 neutral loci in 234 individuals, comprising 39 pups that were classified at necropsy as having most likely died of bacterial infection together with a five times larger matched sample of healthy surviving pups. Identity disequilibrium quantified from the neutral markers was positive and significant, indicative of variance in inbreeding within the study population. However, multilocus heterozygosity did not differ significantly between healthy and infected pups at either class of marker, and little evidence was found for fitness associations at individual loci. These results support a previous study of Antarctic fur seals that found no effects of heterozygosity at nine neutral microsatellites on neonatal survival and thereby help to refine our understanding of how HFCs vary across the life cycle. Given that nonsignificant HFCs are underreported in the literature, we also hope that our study will contribute toward a more balanced understanding of the wider importance of this phenomenon.
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Affiliation(s)
- Vivienne Litzke
- Department of Animal BehaviourBielefeld UniversityBielefeldGermany
| | | | | | | | - Joseph Ivan Hoffman
- Department of Animal BehaviourBielefeld UniversityBielefeldGermany
- British Antarctic Survey, High CrossCambridgeUK
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5
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Bichet C, Vedder O, Sauer‐Gürth H, Becker PH, Wink M, Bouwhuis S. Contrasting heterozygosity‐fitness correlations across life in a long‐lived seabird. Mol Ecol 2019; 28:671-685. [DOI: 10.1111/mec.14979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/09/2018] [Accepted: 12/10/2018] [Indexed: 01/14/2023]
Affiliation(s)
| | - Oscar Vedder
- Institute of Avian Research Wilhelmshaven Germany
- Groningen Institute for Evolutionary Life Sciences University of Groningen Groningen The Netherlands
| | - Hedwig Sauer‐Gürth
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Heidelberg Germany
| | | | - Michael Wink
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Heidelberg Germany
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6
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Eberhart-Phillips LJ, Küpper C, Carmona-Isunza MC, Vincze O, Zefania S, Cruz-López M, Kosztolányi A, Miller TEX, Barta Z, Cuthill IC, Burke T, Székely T, Hoffman JI, Krüger O. Demographic causes of adult sex ratio variation and their consequences for parental cooperation. Nat Commun 2018; 9:1651. [PMID: 29695803 PMCID: PMC5917032 DOI: 10.1038/s41467-018-03833-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 03/15/2018] [Indexed: 11/09/2022] Open
Abstract
The adult sex ratio (ASR) is a fundamental concept in population biology, sexual selection, and social evolution. However, it remains unclear which demographic processes generate ASR variation and how biases in ASR in turn affect social behaviour. Here, we evaluate the demographic mechanisms shaping ASR and their potential consequences for parental cooperation using detailed survival, fecundity, and behavioural data on 6119 individuals from six wild shorebird populations exhibiting flexible parental strategies. We show that these closely related populations express strikingly different ASRs, despite having similar ecologies and life histories, and that ASR variation is largely driven by sex differences in the apparent survival of juveniles. Furthermore, families in populations with biased ASRs were predominantly tended by a single parent, suggesting that parental cooperation breaks down with unbalanced sex ratios. Taken together, our results indicate that sex biases emerging during early life have profound consequences for social behaviour.
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Affiliation(s)
- Luke J Eberhart-Phillips
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615, Bielefeld, Germany. .,Research Group Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str. 5, 82319, Seewiesen, Germany.
| | - Clemens Küpper
- Research Group Behavioural Genetics and Evolutionary Ecology, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str. 5, 82319, Seewiesen, Germany
| | - María Cristina Carmona-Isunza
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Orsolya Vincze
- Hungarian Department of Biology and Ecology, Babeş-Bolyai University, RO-400006, Cluj Napoca, Romania.,MTA-DE Behavioural Ecology Research Group, Department of Evolutionary Zoology, University of Debrecen, Debrecen, 4032, Hungary
| | - Sama Zefania
- Department of Animal Biology, Faculty of Sciences, University of Toliara, PO Box 185, Toliara, Madagascar
| | - Medardo Cruz-López
- Posgrado de Ciencias del Mar y Limnología, Unidad Académica Mazatlán, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, México D.F., Mexico
| | - András Kosztolányi
- Department of Ecology, University of Veterinary Medicine Budapest, Budapest, 1078, Hungary
| | - Tom E X Miller
- Department of BioSciences, Program in Ecology and Evolutionary Biology, Rice University, MS-170, Houston, TX, 77005, USA
| | - Zoltán Barta
- MTA-DE Behavioural Ecology Research Group, Department of Evolutionary Zoology, University of Debrecen, Debrecen, 4032, Hungary
| | - Innes C Cuthill
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Tamás Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.,MTA-DE Behavioural Ecology Research Group, Department of Evolutionary Zoology, University of Debrecen, Debrecen, 4032, Hungary
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615, Bielefeld, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Morgenbreede 45, 33615, Bielefeld, Germany
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7
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Phillips KP, Jorgensen TH, Jolliffe KG, Richardson DS. Evidence of opposing fitness effects of parental heterozygosity and relatedness in a critically endangered marine turtle? J Evol Biol 2017; 30:1953-1965. [PMID: 28787533 DOI: 10.1111/jeb.13152] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/27/2017] [Accepted: 07/31/2017] [Indexed: 01/13/2023]
Abstract
How individual genetic variability relates to fitness is important in understanding evolution and the processes affecting populations of conservation concern. Heterozygosity-fitness correlations (HFCs) have been widely used to study this link in wild populations, where key parameters that affect both variability and fitness, such as inbreeding, can be difficult to measure. We used estimates of parental heterozygosity and genetic similarity ('relatedness') derived from 32 microsatellite markers to explore the relationship between genetic variability and fitness in a population of the critically endangered hawksbill turtle, Eretmochelys imbricata. We found no effect of maternal MLH (multilocus heterozygosity) on clutch size or egg success rate, and no single-locus effects. However, we found effects of paternal MLH and parental relatedness on egg success rate that interacted in a way that may result in both positive and negative effects of genetic variability. Multicollinearity in these tests was within safe limits, and null simulations suggested that the effect was not an artefact of using paternal genotypes reconstructed from large samples of offspring. Our results could imply a tension between inbreeding and outbreeding depression in this system, which is biologically feasible in turtles: female-biased natal philopatry may elevate inbreeding risk and local adaptation, and both processes may be disrupted by male-biased dispersal. Although this conclusion should be treated with caution due to a lack of significant identity disequilibrium, our study shows the importance of considering both positive and negative effects when assessing how variation in genetic variability affects fitness in wild systems.
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Affiliation(s)
- K P Phillips
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK.,NERC Biomolecular Analysis Facility (NBAF), Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.,Evolutionary Biology Group, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - T H Jorgensen
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK.,Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - K G Jolliffe
- Victoria, Mahé, Republic of Seychelles.,Drie Kuilen Private Nature Reserve, Breede River District, South Africa
| | - D S Richardson
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich, UK
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8
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Sex-specific early survival drives adult sex ratio bias in snowy plovers and impacts mating system and population growth. Proc Natl Acad Sci U S A 2017. [PMID: 28634289 DOI: 10.1073/pnas.1620043114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Adult sex ratio (ASR) is a central concept in population biology and a key factor in sexual selection, but why do most demographic models ignore sex biases? Vital rates often vary between the sexes and across life history, but their relative contributions to ASR variation remain poorly understood-an essential step to evaluate sex ratio theories in the wild and inform conservation. Here, we combine structured two-sex population models with individual-based mark-recapture data from an intensively monitored polygamous population of snowy plovers. We show that a strongly male-biased ASR (0.63) is primarily driven by sex-specific survival of juveniles rather than adults or dependent offspring. This finding provides empirical support for theories of unbiased sex allocation when sex differences in survival arise after the period of parental investment. Importantly, a conventional model ignoring sex biases significantly overestimated population viability. We suggest that sex-specific population models are essential to understand the population dynamics of sexual organisms: reproduction and population growth are most sensitive to perturbations in survival of the limiting sex. Overall, our study suggests that sex-biased early survival may contribute toward mating system evolution and population persistence, with implications for both sexual selection theory and biodiversity conservation.
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9
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Ferrer ES, García-Navas V, Bueno-Enciso J, Sanz JJ, Ortego J. Multiple sexual ornaments signal heterozygosity in male blue tits. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12513] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Esperanza S. Ferrer
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Avda. Carlos III s/n 45071 Toledo Spain
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM); Ronda de Toledo s/n 13071 Ciudad Real Spain
| | - Vicente García-Navas
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Avda. Carlos III s/n 45071 Toledo Spain
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM); Ronda de Toledo s/n 13071 Ciudad Real Spain
- Evolution and Genetics of Love, Life and Death Group; Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Javier Bueno-Enciso
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Avda. Carlos III s/n 45071 Toledo Spain
| | - Juan José Sanz
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales (CSIC); C/ José Gutiérrez Abascal 2 28006 Madrid Spain
| | - Joaquín Ortego
- Conservation and Evolutionary Genetics Group; Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Avda. Américo Vespucio s/n 41092 Seville Spain
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10
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García-Navas V, Cáliz-Campal C, Ferrer ES, Sanz JJ, Ortego J. Heterozygosity at a single locus explains a large proportion of variation in two fitness-related traits in great tits: a general or a local effect? J Evol Biol 2014; 27:2807-19. [DOI: 10.1111/jeb.12539] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 12/14/2022]
Affiliation(s)
- V. García-Navas
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - C. Cáliz-Campal
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - E. S. Ferrer
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - J. J. Sanz
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - J. Ortego
- Conservation and Evolutionary Genetics Group; Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
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11
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Ferrer ES, García-Navas V, Sanz JJ, Ortego J. Individual genetic diversity and probability of infection by avian malaria parasites in blue tits (Cyanistes caeruleus). J Evol Biol 2014; 27:2468-82. [PMID: 25264126 DOI: 10.1111/jeb.12489] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/01/2014] [Indexed: 11/30/2022]
Abstract
Understanding the importance of host genetic diversity for coping with parasites and infectious diseases is a long-standing goal in evolutionary biology. Here, we study the association between probability of infection by avian malaria (Plasmodium relictum) and individual genetic diversity in three blue tit (Cyanistes caeruleus) populations that strongly differ in prevalence of this parasite. For this purpose, we screened avian malaria infections and genotyped 789 blue tits across 26 microsatellite markers. We used two different arrays of markers: 14 loci classified as neutral and 12 loci classified as putatively functional. We found a significant relationship between probability of infection and host genetic diversity estimated at the subset of neutral markers that was not explained by strong local effects and did not differ among the studied populations. This relationship was not linear, and probability of infection increased up to values of homozygosity by locus (HL) around 0.15, reached a plateau at values of HL from 0.15 to 0.40 and finally declined among a small proportion of highly homozygous individuals (HL > 0.4). We did not find evidence for significant identity disequilibrium, which may have resulted from a low variance of inbreeding in the study populations and/or the small power of our set of markers to detect it. A combination of subtle positive and negative local effects and/or a saturation threshold in the association between probability of infection and host genetic diversity in combination with increased resistance to parasites in highly homozygous individuals may explain the observed negative quadratic relationship. Overall, our study highlights that parasites play an important role in shaping host genetic variation and suggests that the use of large sets of neutral markers may be more appropriate for the study of heterozygosity-fitness correlations.
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Affiliation(s)
- E S Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ciudad Real, Spain; Departamento de Ciencias Ambientales, Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
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12
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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.
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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
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13
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Miller JM, Coltman DW. Assessment of identity disequilibrium and its relation to empirical heterozygosity fitness correlations: a meta-analysis. Mol Ecol 2014; 23:1899-909. [DOI: 10.1111/mec.12707] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 01/31/2023]
Affiliation(s)
- Joshua M. Miller
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
| | - David W. Coltman
- Department of Biological Sciences; University of Alberta; Edmonton Alberta T6G 2E9 Canada
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14
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Estimating genome-wide heterozygosity: effects of demographic history and marker type. Heredity (Edinb) 2013; 112:240-7. [PMID: 24149650 DOI: 10.1038/hdy.2013.99] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Revised: 09/04/2013] [Accepted: 09/16/2013] [Indexed: 01/03/2023] Open
Abstract
Heterozygosity-fitness correlations (HFCs) are often used to link individual genetic variation to differences in fitness. However, most studies examining HFCs find weak or no correlations. Here, we derive broad theoretical predictions about how many loci are needed to adequately measure genomic heterozygosity assuming different levels of identity disequilibrium (ID), a proxy for inbreeding. We then evaluate the expected ability to detect HFCs using an empirical data set of 200 microsatellites and 412 single nucleotide polymorphisms (SNPs) genotyped in two populations of bighorn sheep (Ovis canadensis), with different demographic histories. In both populations, heterozygosity was significantly correlated across marker types, although the strength of the correlation was weaker in a native population compared with one founded via translocation and later supplemented with additional individuals. Despite being bi-allelic, SNPs had similar correlations to genome-wide heterozygosity as microsatellites in both populations. For both marker types, this association became stronger and less variable as more markers were considered. Both populations had significant levels of ID; however, estimates were an order of magnitude lower in the native population. As with heterozygosity, SNPs performed similarly to microsatellites, and precision and accuracy of the estimates of ID increased as more loci were considered. Although dependent on the demographic history of the population considered, these results illustrate that genome-wide heterozygosity, and therefore HFCs, are best measured by a large number of markers, a feat now more realistically accomplished with SNPs than microsatellites.
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Investigation of individual heterozygosity correlated to growth traits in Tongshan Black-boned goat. Mol Biol Rep 2013; 40:6075-9. [DOI: 10.1007/s11033-013-2717-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
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Boerner M, Hoffman JI, Amos W, Chakarov N, Kruger O. No correlation between multi-locus heterozygosity and fitness in the common buzzard despite heterozygote advantage for plumage colour. J Evol Biol 2013; 26:2233-43. [PMID: 23980596 DOI: 10.1111/jeb.12221] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 06/18/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
Abstract
Correlations between heterozygosity and fitness are frequently found but rarely well understood. Fitness can be affected by single loci of large effect which correlate with neutral markers via linkage disequilibrium, or as a result of variation in genome-wide heterozygosity following inbreeding. We explored these alternatives in the common buzzard, a raptor species in which three colour morphs differ in their lifetime reproductive success. Using 18 polymorphic microsatellite loci, we evaluated potential genetic differences among the morphs which may lead to subpopulation structuring and tested for correlations between three fitness-related traits and heterozygosity, both genome wide and at each locus separately. Despite their assortative mating pattern, the buzzard morphs were found to be genetically undifferentiated. Multilocus heterozygosity was only found to be correlated with a single fitness-related trait, infection with the blood parasite, Leucocytozoon buteonis, and this was via interactions with vole abundance and age. One locus also showed a significant relationship with blood parasite infection and ectoparasite infestation. The vicinity of this locus contains two genes, one of which is potentially implicated in the immune system of birds. We conclude that genome-wide heterozygosity is unlikely to be a major determinant of parasite burden and body condition in the polymorphic common buzzard.
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Affiliation(s)
- M Boerner
- Department of Animal Behaviour, Bielefeld University, Bielefeld, Germany
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Laine VN, Herczeg G, Shikano T, Primmer CR. Heterozygosity-behaviour correlations in nine-spined stickleback (Pungitius pungitius) populations: contrasting effects at random and functional loci. Mol Ecol 2012; 21:4872-84. [DOI: 10.1111/j.1365-294x.2012.05741.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 06/18/2012] [Accepted: 06/20/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Veronika N. Laine
- Division of Genetics and Physiology, Department of Biology; University of Turku; Turku; FI-20014; Finland
| | - Gábor Herczeg
- Ecological Genetics Research Unit, Department of Biosciences; University of Helsinki; PO Box 65; Helsinki; FI-00014; Finland
| | - Takahito Shikano
- Ecological Genetics Research Unit, Department of Biosciences; University of Helsinki; PO Box 65; Helsinki; FI-00014; Finland
| | - Craig R. Primmer
- Division of Genetics and Physiology, Department of Biology; University of Turku; Turku; FI-20014; Finland
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Szulkin M, David P. Negative heterozygosity-fitness correlations observed with microsatellites located in functional areas of the genome. Mol Ecol 2012; 20:3949-52. [PMID: 21951418 DOI: 10.1111/j.1365-294x.2011.05277.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Genome-wide heterozygosity inferred from neutral markers such as microsatellites is often expected to (i) reflect individual inbreeding and (ii) covary positively with fitness, generating positive heterozygosity-fitness correlations (HFCs). The often forgotten other end of the inbreeding-outbreeding continuum is outbreeding depression: past a certain degree of heterozygosity, heterozygotes tend to have lower fitness than homozygotes. Outbreeding depression arises from the breakup of co-adapted gene complexes and/or the introgression of nonlocally adapted genes. Provided that a correlation in heterozygosity exists across loci, outbreeding depression will be reflected in negative HFCs. In this issue, Olano-Marin et al. (2011a) describe negative heterozygosity-fitness correlations (HFCs) in blue tits Cyanistes caeruleus (Fig. 1), whereby heterozygosity has a significant, negative effect on female hatching success and recruitment. This study, together with a similar study by the same authors published in Evolution (Olano-Marin et al. 2011b), forms an original contribution in two respects. First, in the same population, positive and negative HFCs were recorded, revealing both inbreeding and outbreeding depression depending on the trait studied (whereby both processes were reliant on unknown, and possibly different, sets of coding loci). Second, a large number of microsatellite markers were split into two functional groups: microsatellite markers were either designed using zebra finch expressed sequence tags (ESTs) or derived using traditional cloning methods and presumed to be neutral. Contrasting large classes of loci and their varying levels of polymorphism, rather than looking for one locus that would stand out among tens of randomly selected markers, pave the way for a more elegant and powerful approach to explore how HFCs vary across traits and among regions of the genome. [Figure: see text].
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Affiliation(s)
- Marta Szulkin
- Edward Grey Institute, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
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Yang X, Qian L, Wu H, Fan Z, Wang C. Population differentiation, bottleneck and selection of Eurasian perch (Perca fluviatilis L.) at the Asian edge of its natural range. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2011.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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WETZEL DANIELP, STEWART IANRK, WESTNEAT DAVIDF. Heterozygosity predicts clutch and egg size but not plasticity in a house sparrow population with no evidence of inbreeding. Mol Ecol 2011; 21:406-20. [DOI: 10.1111/j.1365-294x.2011.05380.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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21
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Rheindt FE, Székely T, Edwards SV, Lee PLM, Burke T, Kennerley PR, Bakewell DN, Alrashidi M, Kosztolányi A, Weston MA, Liu WT, Lei WP, Shigeta Y, Javed S, Zefania S, Küpper C. Conflict between genetic and phenotypic differentiation: the evolutionary history of a 'lost and rediscovered' shorebird. PLoS One 2011; 6:e26995. [PMID: 22096515 PMCID: PMC3212520 DOI: 10.1371/journal.pone.0026995] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 10/07/2011] [Indexed: 12/03/2022] Open
Abstract
Understanding and resolving conflicts between phenotypic and genetic differentiation is central to evolutionary research. While phenotypically monomorphic species may exhibit deep genetic divergences, some morphologically distinct taxa lack notable genetic differentiation. Here we conduct a molecular investigation of an enigmatic shorebird with a convoluted taxonomic history, the White-faced Plover (Charadrius alexandrinus dealbatus), widely regarded as a subspecies of the Kentish Plover (C. alexandrinus). Described as distinct in 1863, its name was consistently misapplied in subsequent decades until taxonomic clarification ensued in 2008. Using a recently proposed test of species delimitation, we reconfirm the phenotypic distinctness of dealbatus. We then compare three mitochondrial and seven nuclear DNA markers among 278 samples of dealbatus and alexandrinus from across their breeding range and four other closely related plovers. We fail to find any population genetic differentiation between dealbatus and alexandrinus, whereas the other species are deeply diverged at the study loci. Kentish Plovers join a small but growing list of species for which low levels of genetic differentiation are accompanied by the presence of strong phenotypic divergence, suggesting that diagnostic phenotypic characters may be encoded by few genes that are difficult to detect. Alternatively, gene expression differences may be crucial in producing different phenotypes whereas neutral differentiation may be lagging behind.
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Affiliation(s)
- Frank E Rheindt
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
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Harrison XA, Bearhop S, Inger R, Colhoun K, Gudmundsson GA, Hodgson D, McElwaine G, Tregenza T. Heterozygosity-fitness correlations in a migratory bird: an analysis of inbreeding and single-locus effects. Mol Ecol 2011; 20:4786-95. [PMID: 21973192 DOI: 10.1111/j.1365-294x.2011.05283.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Studies in a multitude of taxa have described a correlation between heterozygosity and fitness and usually conclude that this is evidence for inbreeding depression. Here, we have used multilocus heterozygosity (MLH) estimates from 15 microsatellite markers to show evidence of heterozygosity-fitness correlations (HFCs) in a long-distance migratory bird, the light-bellied Brent goose. We found significant, positive heterozygosity-heterozygosity correlations between random subsets of the markers we employed, and no evidence that a model containing all loci as individual predictors in a multiple regression explained significantly more variation than a model with MLH as a single predictor. Collectively, these results lend support to the hypothesis that the HFCs we have observed are a function of inbreeding depression. However, we do find that fitness correlations are only detectable in years where population-level productivity is high enough for the reproductive asymmetry between high and low heterozygosity individuals to become apparent. We suggest that lack of evidence of heterozygosity-fitness correlations in animal systems may be because heterozygosity is a poor proxy measure of inbreeding, especially when employing low numbers of markers, but alternatively because the asymmetries between individuals of different heterozygosities may only be apparent when environmental effects on fitness are less pronounced.
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Affiliation(s)
- Xavier A Harrison
- Centre for Ecology and Conservation, University of Exeter, Tremough Campus, Penryn, Cornwall TR10 9EZ, UK.
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OLANO-MARIN JUANITA, MUELLER JAKOBC, KEMPENAERS BART. Heterozygosity and survival in blue tits (Cyanistes caeruleus): contrasting effects of presumably functional and neutral loci. Mol Ecol 2011; 20:4028-41. [DOI: 10.1111/j.1365-294x.2011.05177.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Kirk H, Freeland JR. Applications and implications of neutral versus non-neutral markers in molecular ecology. Int J Mol Sci 2011; 12:3966-88. [PMID: 21747718 PMCID: PMC3131602 DOI: 10.3390/ijms12063966] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/06/2011] [Accepted: 06/07/2011] [Indexed: 11/17/2022] Open
Abstract
The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection.
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Affiliation(s)
- Heather Kirk
- Department of Biology, Trent University, Peterborough, Ontario K9J 7B8, Canada; E-Mail:
| | - Joanna R. Freeland
- Department of Biology, Trent University, Peterborough, Ontario K9J 7B8, Canada; E-Mail:
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