201
|
Phillips P, Livieri TM, Swanson BJ. Genetic signature of disease epizootic and reintroduction history in an endangered carnivore. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
AbstractEmerging infectious diseases have recently increased in wildlife and can result in population declines and the loss of genetic diversity in susceptible populations. As populations of impacted species decline, genetic diversity can be lost, with ramifications including reduced effective population size and increased population structuring. For species of conservation concern, which may already have low genetic diversity, the loss of genetic diversity can be especially important. To investigate the impacts of a novel pathogen on genetic diversity in a genetically depauperate endangered species, we assessed the ramifications of a sylvatic plague-induced bottleneck in black-footed ferrets (Mustela nigripes). Following a plague epizootic, we genotyped 184 ferrets from Conata Basin and Badlands National Park, South Dakota, at seven microsatellite loci. We compared our results to pre-plague studies in the same population. We observed population substructuring into three genetic clusters. These clusters reflect founder effects from ferret reintroduction events followed by genetic drift. Compared to the pre-plague population, we observed losses of allelic diversity in all clusters, as well as significantly reduced heterozygosity in one cluster. These results indicate that disease epizootics may reduce population size and also genetic diversity. Our results suggest the importance of early and sustained management in mitigating disease epizootics in naïve populations for the maintenance of genetic diversity.
Collapse
Affiliation(s)
- Payton Phillips
- Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
- Department of Biology, Temple University, Philadelphia, PA, USA
| | | | - Bradley J Swanson
- Department of Biology, Central Michigan University, Mount Pleasant, MI, USA
| |
Collapse
|
202
|
Consistent scaling of inbreeding depression in space and time in a house sparrow metapopulation. Proc Natl Acad Sci U S A 2020; 117:14584-14592. [PMID: 32513746 DOI: 10.1073/pnas.1909599117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Inbreeding may increase the extinction risk of small populations. Yet, studies using modern genomic tools to investigate inbreeding depression in nature have been limited to single populations, and little is known about the dynamics of inbreeding depression in subdivided populations over time. Natural populations often experience different environmental conditions and differ in demographic history and genetic composition, characteristics that can affect the severity of inbreeding depression. We utilized extensive long-term data on more than 3,100 individuals from eight islands in an insular house sparrow metapopulation to examine the generality of inbreeding effects. Using genomic estimates of realized inbreeding, we discovered that inbred individuals had lower survival probabilities and produced fewer recruiting offspring than noninbred individuals. Inbreeding depression, measured as the decline in fitness-related traits per unit inbreeding, did not vary appreciably among populations or with time. As a consequence, populations with more resident inbreeding (due to their demographic history) paid a higher total fitness cost, evidenced by a larger variance in fitness explained by inbreeding within these populations. Our results are in contrast to the idea that effects of inbreeding generally depend on ecological factors and genetic differences among populations, and expand the understanding of inbreeding depression in natural subdivided populations.
Collapse
|
203
|
|
204
|
Hedrick PW. Galapagos Islands Endemic Vertebrates: A Population Genetics Perspective. J Hered 2020; 110:137-157. [PMID: 30541084 DOI: 10.1093/jhered/esy066] [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] [Accepted: 12/10/2018] [Indexed: 11/12/2022] Open
Abstract
The organisms of the Galapagos Islands played a central role in the development of the theory of evolution by Charles Darwin. Examination of the population genetics factors of many of these organisms with modern molecular methods has expanded our understanding of their evolution. Here, I provide a perspective on how selection, gene flow, genetic drift, mutation, and inbreeding have contributed to the evolution of 6 iconic Galapagos species: flightless cormorant, pink iguana, marine iguana, Galapagos hawk, giant tortoises, and Darwin's finches. Because of the inherent biological differences among these species that have colonized the Galapagos, different population genetic factors appear to be more or less important in these different species. For example, the Galapagos provided novel environments in which strong selection took place and the Darwin's finches diversified to produce new species and the cormorant adapted to the nutrient-rich western shores of the Galapagos by losing its ability to fly and genomic data have now identified candidate genes. In both the pink iguana, which exists in one small population, and the Galapagos hawk, which has small population sizes, genetic drift has been potentially quite important. There appears to be very limited interisland gene flow in the flightless cormorant and the Galapagos hawk. On the other hand, both the marine iguana and some of the Darwin's finches appear to have significant interisland gene flow. Hybridization between species and subspecies has also introduced new adaptive variation, and in some cases, hybridization might have resulted in despeciation. Overall, new population genetics and genomics research has provided additional insight into the evolution of vertebrate species in the Galapagos.
Collapse
|
205
|
Revised Calculation of Kalinowski’s Ancestral and New Inbreeding Coefficients. DIVERSITY 2020. [DOI: 10.3390/d12040155] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
To test for the presence of purging in populations, the classical pedigree-based inbreeding coefficient (F) can be decomposed into Kalinowski’s ancestral (FANC) and new (FNEW) inbreeding coefficients. The FANC and FNEW can be calculated by a stochastic approach known as gene dropping. However, the only publicly available algorithm for the calculation of FANC and FNEW, implemented in GRain v 2.1 (and also incorporated in the PEDIG software package), has produced biased estimates. The FANC was systematically underestimated and consequently, FNEW was overestimated. To illustrate this bias, we calculated FANC and FNEW by hand for simple example pedigrees. We revised the GRain program so that it now provides unbiased estimates. Correlations between the biased and unbiased estimates of FANC and FNEW, obtained for example data sets of Hungarian Pannon White rabbits (22,781 individuals) and Dutch Holstein Friesian cattle (37,061 individuals), were high, i.e., >0.96. Although the magnitude of bias appeared to be small, results from studies based on biased estimates should be interpreted with caution. The revised GRain program (v 2.2) is now available online and can be used to calculate unbiased estimates of FANC and FNEW.
Collapse
|
206
|
Wilder AP, Navarro AY, King SND, Miller WB, Thomas SM, Steiner CC, Ryder OA, Shier DM. Fitness costs associated with ancestry to isolated populations of an endangered species. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01272-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
207
|
Yoshida K, Ravinet M, Makino T, Toyoda A, Kokita T, Mori S, Kitano J. Accumulation of Deleterious Mutations in Landlocked Threespine Stickleback Populations. Genome Biol Evol 2020; 12:479-492. [PMID: 32232440 PMCID: PMC7197494 DOI: 10.1093/gbe/evaa065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2020] [Indexed: 02/06/2023] Open
Abstract
Colonization of new habitats often reduces population sizes and may result in the accumulation of deleterious mutations by genetic drift. Compared with the genomic basis for adaptation to new environments, genome-wide analysis of deleterious mutations in isolated populations remains limited. In the present study, we investigated the accumulation of deleterious mutations in five endangered freshwater populations of threespine stickleback (Gasterosteus aculeatus) in the central part of the mainland of Japan. Using whole-genome resequencing data, we first conducted phylogenomic analysis and confirmed at least two independent freshwater colonization events in the central mainland from ancestral marine ecotypes. Next, analyses of single nucleotide polymorphisms showed a substantial reduction of heterozygosity in freshwater populations compared with marine populations. Reduction in heterozygosity was more apparent at the center of each chromosome than the peripheries and on X chromosomes compared with autosomes. Third, bioinformatic analysis of deleterious mutations showed increased accumulation of putatively deleterious mutations in the landlocked freshwater populations compared with marine populations. For the majority of populations examined, the frequencies of putatively deleterious mutations were higher on X chromosomes than on autosomes. The interpopulation comparison indicated that the majority of putatively deleterious mutations may have accumulated independently. Thus, whole-genome resequencing of endangered populations can help to estimate the accumulation of deleterious mutations and inform us of which populations are the most severely endangered. Furthermore, analysis of variation among chromosomes can give insights into whether any particular chromosomes are likely to accumulate deleterious mutations.
Collapse
Affiliation(s)
- Kohta Yoshida
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Mark Ravinet
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.,Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway.,School of Life Sciences, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Takashi Makino
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Tomoyuki Kokita
- Department of Marine Bioscience, Fukui Prefectural University, Obama, Fukui, Japan
| | - Seiichi Mori
- Biological Laboratories, Gifu-kyoritsu University, Ogaki, Gifu, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| |
Collapse
|
208
|
Cayuela H, Besnard A, Cote J, Laporte M, Bonnaire E, Pichenot J, Schtickzelle N, Bellec A, Joly P, Léna J. Anthropogenic disturbance drives dispersal syndromes, demography, and gene flow in amphibian populations. ECOL MONOGR 2020. [DOI: 10.1002/ecm.1406] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Hugo Cayuela
- Univ. Lyon Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA F‐69622 Villeurbanne France
- EPHE, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, CNRS PSL Research University Montpellier F‐34293 France
| | - Aurélien Besnard
- EPHE, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, CNRS PSL Research University Montpellier F‐34293 France
| | - Julien Cote
- CNRS, Université Toulouse III Paul Sabatier, ENFA UMR5174EDB (Laboratoire Évolution & Diversité Biologique) 118 route de Narbonne F‐31062 Toulouse France
| | - Martin Laporte
- EPHE, UM, SupAgro, IRD, INRA, UMR 5175 CEFE, CNRS PSL Research University Montpellier F‐34293 France
| | - Eric Bonnaire
- Office National des Forêts Agence de Verdun 55100 Verdun France
| | - Julian Pichenot
- Centre de Recherche et Formation en Eco‐éthologie (CERFE) CERFE 08240 Boult‐aux‐Bois France
| | - Nicolas Schtickzelle
- Earth and Life Institute Biodiversity Research Centre Université Catholique de Louvain 1348 Louvain‐la‐Neuve Belgium
| | - Arnaud Bellec
- Univ. Lyon Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA F‐69622 Villeurbanne France
| | - Pierre Joly
- Univ. Lyon Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA F‐69622 Villeurbanne France
| | - Jean‐Paul Léna
- Univ. Lyon Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR5023 LEHNA F‐69622 Villeurbanne France
| |
Collapse
|
209
|
Tremmel M, Steinitz H, Kliot A, Harari A, Lubin Y. Dispersal, endosymbiont abundance and fitness-related consequences of inbreeding and outbreeding in a social beetle. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Most social species outbreed. However, some have persistent inbreeding with occasional outbreeding, and the decision of the individual regarding whether to stay in the natal group and inbreed or to disperse, with the potential to outbreed, is flexible and may depend on social, genetic and ecological benefits and costs. Few of these factors have been investigated experimentally in these systems. The beetle Coccotrypes dactyliperda Fabricius, 1801 (Scolytidae: Xyloborinae) lives in extended family colonies inside date seeds. The beetles inbreed, but some individuals disperse away from the natal seed and may outbreed. We investigated dispersal behaviour and assessed fitness-related measures in inbred and outbred offspring, in addition to the relative abundance of two endosymbionts. We predicted inbred offspring to have higher fitness-related measures and a reduced tendency to disperse than outbred offspring, owing to fitness benefits of cooperation within the colony, whereas increased endosymbiont abundance will promote dispersal of their hosts, thus enhancing their own spread in the population. Dispersing beetles were more active than ones that remained in the natal seed. As predicted, fewer inbred offspring dispersed than outbred offspring, but they matured and dispersed earlier. Fitness-related measures of inbred mothers were either lower (number of offspring) or not different (body mass) from those of outbred mothers. Inbred dispersers had greater amounts of Wolbachia, suggesting a role in dispersal. The results support the hypothesis that inbred females reduce dispersal and that early maturation and dispersal are likely to be benefits of increased cooperation in brood care.
Collapse
Affiliation(s)
- Martin Tremmel
- Department of Entomology, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Hadas Steinitz
- Department of Entomology, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Adi Kliot
- Department of Entomology, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
- Earlham Institute, Norwich, UK
| | - Ally Harari
- Department of Entomology, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Yael Lubin
- Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| |
Collapse
|
210
|
Purging of highly deleterious mutations through severe bottlenecks in Alpine ibex. Nat Commun 2020; 11:1001. [PMID: 32081890 PMCID: PMC7035315 DOI: 10.1038/s41467-020-14803-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/05/2020] [Indexed: 12/14/2022] Open
Abstract
Human activity has caused dramatic population declines in many wild species. The resulting bottlenecks have a profound impact on the genetic makeup of a species with unknown consequences for health. A key genetic factor for species survival is the evolution of deleterious mutation load, but how bottleneck strength and mutation load interact lacks empirical evidence. We analyze 60 complete genomes of six ibex species and the domestic goat. We show that historic bottlenecks rather than the current conservation status predict levels of genome-wide variation. By analyzing the exceptionally well-characterized population bottlenecks of the once nearly extinct Alpine ibex, we find genomic evidence of concurrent purging of highly deleterious mutations but accumulation of mildly deleterious mutations. This suggests that recolonization bottlenecks induced both relaxed selection and purging, thus reshaping the landscape of deleterious mutation load. Our findings highlight that even populations of ~1000 individuals can accumulate mildly deleterious mutations. Conservation efforts should focus on preventing population declines below such levels to ensure long-term survival of species. Although there is extensive theory predicting the effects of population bottlenecks on mutation load, there is little empirical evidence from recent bottlenecks. Here, Grossen et al. compare the consequences of population bottlenecks in six ibex species for genome-wide variation and mutation load.
Collapse
|
211
|
Li YL, Wang L, Wu JW, Ye XP, Garber PA, Yan Y, Liu JH, Li BG, Qi XG. Bachelor groups in primate multilevel society facilitate gene flow across fragmented habitats. Curr Zool 2020; 66:113-122. [PMID: 32211037 PMCID: PMC7083096 DOI: 10.1093/cz/zoaa006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/10/2020] [Indexed: 11/25/2022] Open
Abstract
In the face of ongoing habitat fragmentation, many primate species have experienced reduced gene flow resulting in a reduction of genetic diversity, population bottlenecks, and inbreeding depression, including golden snub-nosed monkeys Rhinopithecus roxellana. Golden snub-nosed monkeys live in a multilevel society composed of several 1 male harem units that aggregate to form a cohesive breeding band, which is followed by one or more bachelor groups composed of juvenile, subadult, and adult male members. In this research, we examine the continuous landscape resistance surface, the genetic diversity and patterns of gene flow among 4 isolated breeding bands and 1 all-male band in the Qinling Mountains, China. Landscape surface modeling suggested that human activities and ecological factors severely limit the movement of individuals among breeding bands. Although these conditions are expected to result in reduced gene flow, reduced genetic diversity, and an increased opportunity for a genetic bottleneck, based on population genetic analyses of 13 microsatellite loci from 188 individuals inhabiting 4 isolated breeding bands and 1 all-male band, we found high levels of genetic diversity but low levels of genetic divergence, as well as high rates of gene flow between males residing in the all-male band and each of the 4 breeding bands. Our results indicate that the movement of bachelor males across the landscape, along with their association with several different breeding bands, appears to provide a mechanism for promoting gene flows and maintaining genetic diversity that may counteract the otherwise isolating effects of habitat fragmentation.
Collapse
Affiliation(s)
- Yu-Li Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Lu Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Jin-Wei Wu
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Xin-Ping Ye
- College of Life Science, Shaanxi Normal University, Xi'an, 710119, China
| | - Paul A Garber
- Anthropology Department, University of Illinois, Urbana, IL, 61801, USA
| | - Ying Yan
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Jia-Hui Liu
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Science, Kumming, 650223, China
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Science, Northwest University, Xi'an, 710069, China
| |
Collapse
|
212
|
Robertson DN, Sullivan TJ, Westerman EL. Lack of sibling avoidance during mate selection in the butterfly Bicyclus anynana. Behav Processes 2020; 173:104062. [PMID: 31981681 DOI: 10.1016/j.beproc.2020.104062] [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: 08/26/2019] [Revised: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 11/29/2022]
Abstract
Species susceptible to inbreeding depression are hypothesized to combat this problem through a number of different mechanisms, including kin recognition. For species with kin recognition, it is unknown if filial recognition is innate or due to prior juvenile experience with siblings. Here, we first test for the presence of kin recognition, and then test these two hypotheses for the development of filial recognition, in the butterfly Bicyclus anynana, a species that suffers from inbreeding depression when forcibly inbred but recovers within a few generations when allowed to breed freely. We evaluate whether the rapid recovery from inbreeding depression is associated with either innate or learned filial recognition. First, we determined whether females innately prefer unrelated males over sibling males using females reared in isolation and then given a choice between an unrelated and a sibling male. Then, we determined if females raised with siblings learned to detect and avoid mating with siblings as adults when provided a choice between an unrelated male and a sibling male. Finally, we determined if females raised with siblings could learn to detect and avoid mating with familiar siblings when given a choice between familiar and unfamiliar siblings. We found that females mated randomly in all three choice combinations. Observed male behavior also did not influence female mating outcome. Our results suggest that adult females do not innately avoid or learn to avoid siblings during mate selection, and that filial detection may not be as critical to reproductive fitness in B. anynana as previously thought.
Collapse
Affiliation(s)
- Deonna N Robertson
- University of Arkansas, Fayetteville 850 W. Dickson St. Fayetteville 72701 USA
| | - Timothy J Sullivan
- University of Arkansas, Fayetteville 850 W. Dickson St. Fayetteville 72701 USA; Gloucester Marine Genomics Institute, 417 Main Street, Gloucester, MA 01930 USA
| | - Erica L Westerman
- University of Arkansas, Fayetteville 850 W. Dickson St. Fayetteville 72701 USA.
| |
Collapse
|
213
|
Waters CD, Hard JJ, Fast DE, Knudsen CM, Bosch WJ, Naish KA. Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon. Mol Ecol 2020; 29:658-672. [PMID: 31957935 DOI: 10.1111/mec.15356] [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: 07/22/2019] [Revised: 12/09/2019] [Accepted: 01/13/2020] [Indexed: 01/14/2023]
Abstract
Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by comparing observed and expected homozygosity, across four generations in two hatchery lines of Chinook salmon that were derived from the same source. The lines are managed as "integrated" with the founding wild stock, with ongoing gene flow, and as "segregated" with no gene flow. While relatedness and inbreeding increased in the first generation of both lines, possibly due to population subdivision caused by hatchery initiation, the integrated line had significantly lower levels in some subsequent generations (relatedness: F2 -F4 ; inbreeding F2 ). Generally, inbreeding was similar between the lines despite large differences in effective numbers of breeders. Inbreeding did not affect fecundity, reproductive effort, return timing, fork length, weight, condition factor, and daily growth coefficient. However, it delayed spawn timing by 1.75 days per one standard deviation increase in F (~0.16). The results indicate that integrated management may reduce inbreeding but also suggest that it is relatively low in a small, segregated hatchery population that maximized number of breeders. Our findings demonstrate the utility of genomics to monitor inbreeding under alternative management strategies in captive breeding programs.
Collapse
Affiliation(s)
- Charles D Waters
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Jeffrey J Hard
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | | | | | | | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| |
Collapse
|
214
|
Varona L, Altarriba J, Moreno C, Martínez-Castillero M, Casellas J. A multivariate analysis with direct additive and inbreeding depression load effects. Genet Sel Evol 2019; 51:78. [PMID: 31878872 PMCID: PMC6933709 DOI: 10.1186/s12711-019-0521-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
Background Inbreeding is caused by mating between related individuals and its most common consequence is inbreeding depression. Several studies have detected heterogeneity in inbreeding depression among founder individuals, and recently a procedure for predicting hidden inbreeding depression loads associated with founders and the Mendelian sampling of non-founders has been developed. The objectives of our study were to expand this model to predict the inbreeding loads for all individuals in the pedigree and to estimate the covariance between the inbreeding loads and the additive genetic effects for the trait of interest. We tested the proposed approach with simulated data and with two datasets of records on weaning weight from the Spanish Pirenaica and Rubia Gallega beef cattle breeds. Results The posterior estimates of the variance components with the simulated datasets did not differ significantly from the simulation parameters. In addition, the correlation between the predicted and simulated inbreeding loads were always positive and ranged from 0.27 to 0.82. The beef cattle datasets comprised 35,126 and 75,194 records on weights between 170 and 250 days of age, and pedigrees of 308,836 and 384,434 individual-sire-dam entries for the Pirenaica and Rubia Gallega breeds, respectively. The posterior mean estimates of the variance of inbreeding depression loads were 29,967.8 and 28,222.4 for the Pirenaica and Rubia Gallega breeds, respectively. They were larger than those of the additive variance (695.0 and 439.8 for Pirenaica and Rubia Gallega, respectively), because they should be understood as the variance of the inbreeding depression achieved by a fully inbred (100%) descendant. Therefore, the inbreeding loads have to be rescaled for smaller inbreeding coefficients. In addition, a strong negative correlation (− 0.43 ± 0.10) between additive effects and inbreeding loads was detected in the Pirenaica, but not in the Rubia Gallega breed. Conclusions The results of the simulation study confirmed the ability of the proposed procedure to predict inbreeding depression loads for all individuals in the populations. Furthermore, the results obtained from the two real datasets confirmed the variability in the inbreeding depression loads in both breeds and suggested a negative correlation of the inbreeding loads with the additive genetic effects in the Pirenaica breed.
Collapse
Affiliation(s)
- Luis Varona
- Departamento de Anatomía Embriología y Genética Animal, Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013, Saragossa, Spain.
| | - Juan Altarriba
- Departamento de Anatomía Embriología y Genética Animal, Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013, Saragossa, Spain
| | - Carlos Moreno
- Departamento de Anatomía Embriología y Genética Animal, Instituto Agroalimentario de Aragón (IA2), Universidad de Zaragoza, 50013, Saragossa, Spain
| | - María Martínez-Castillero
- Dipartimento di Agronomia Animali, Alimenti Risorce Naturali e Ambiente, Università degli Studi di Padova, 35122, Padua, Italy
| | - Joaquim Casellas
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| |
Collapse
|
215
|
Yates MC, Bowles E, Fraser DJ. Small population size and low genomic diversity have no effect on fitness in experimental translocations of a wild fish. Proc Biol Sci 2019; 286:20191989. [PMID: 31771476 DOI: 10.1098/rspb.2019.1989] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Little empirical work in nature has quantified how wild populations with varying effective population sizes and genetic diversity perform when exposed to a gradient of ecologically important environmental conditions. To achieve this, juvenile brook trout from 12 isolated populations or closed metapopulations that differ substantially in population size and genetic diversity were transplanted to previously fishless ponds spanning a wide gradient of ecologically important variables. We evaluated the effect of genome-wide variation, effective population size (Ne), pond habitat, and initial body size on two fitness correlates (survival and growth). Genetic variables had no effect on either fitness correlate, which was determined primarily by habitat (pond temperature, depth, and pH) and initial body size. These results suggest that some vertebrate populations with low genomic diversity, low Ne, and long-term isolation can represent important sources of variation and are capable of maintaining fitness in, and ultimately persisting and adapting to, changing environments. Our results also reinforce the paramount importance of improving available habitat and slowing habitat degradation for species conservation.
Collapse
Affiliation(s)
- M C Yates
- Department of Biology, UQAM, Montreal, QC, Canada H3C 3P8.,Group for Interuniversity Research in Limnology and Aquatic Environment (GRIL), Montreal, QC, Canada H3C 3J7
| | - E Bowles
- Department of Biology, Concordia University, Montreal, QC, Canada H4B 1R6
| | - D J Fraser
- Department of Biology, Concordia University, Montreal, QC, Canada H4B 1R6.,Group for Interuniversity Research in Limnology and Aquatic Environment (GRIL), Montreal, QC, Canada H3C 3J7
| |
Collapse
|
216
|
Buckley J, Daly R, Cobbold CA, Burgess K, Mable BK. Changing environments and genetic variation: natural variation in inbreeding does not compromise short-term physiological responses. Proc Biol Sci 2019; 286:20192109. [PMID: 31744436 DOI: 10.1098/rspb.2019.2109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Selfing plant lineages are surprisingly widespread and successful in a broad range of environments, despite showing reduced genetic diversity, which is predicted to reduce their long-term evolutionary potential. However, appropriate short-term plastic responses to new environmental conditions might not require high levels of standing genetic variation. In this study, we tested whether mating system variation among populations, and associated changes in genetic variability, affected short-term responses to environmental challenges. We compared relative fitness and metabolome profiles of naturally outbreeding (genetically diverse) and inbreeding (genetically depauperate) populations of a perennial plant, Arabidopsis lyrata, under constant growth chamber conditions and an outdoor common garden environment outside its native range. We found no effect of inbreeding on survival, flowering phenology or short-term physiological responses. Specifically, naturally occurring inbreeding had no significant effects on the plasticity of metabolome profiles, using either multivariate approaches or analysis of variation in individual metabolites, with inbreeding populations showing similar physiological responses to outbreeding populations over time in both growing environments. We conclude that low genetic diversity in naturally inbred populations may not always compromise fitness or short-term physiological capacity to respond to environmental change, which could help to explain the global success of selfing mating strategies.
Collapse
Affiliation(s)
- James Buckley
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Rónán Daly
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Karl Burgess
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Barbara K Mable
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| |
Collapse
|
217
|
Lindsay WR, Andersson S, Bererhi B, Höglund J, Johnsen A, Kvarnemo C, Leder EH, Lifjeld JT, Ninnes CE, Olsson M, Parker GA, Pizzari T, Qvarnström A, Safran RJ, Svensson O, Edwards SV. Endless forms of sexual selection. PeerJ 2019; 7:e7988. [PMID: 31720113 PMCID: PMC6839514 DOI: 10.7717/peerj.7988] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 10/04/2019] [Indexed: 12/11/2022] Open
Abstract
In recent years, the field of sexual selection has exploded, with advances in theoretical and empirical research complementing each other in exciting ways. This perspective piece is the product of a "stock-taking" workshop on sexual selection and sexual conflict. Our aim is to identify and deliberate on outstanding questions and to stimulate discussion rather than provide a comprehensive overview of the entire field. These questions are organized into four thematic sections we deem essential to the field. First we focus on the evolution of mate choice and mating systems. Variation in mate quality can generate both competition and choice in the opposite sex, with implications for the evolution of mating systems. Limitations on mate choice may dictate the importance of direct vs. indirect benefits in mating decisions and consequently, mating systems, especially with regard to polyandry. Second, we focus on how sender and receiver mechanisms shape signal design. Mediation of honest signal content likely depends on integration of temporally variable social and physiological costs that are challenging to measure. We view the neuroethology of sensory and cognitive receiver biases as the main key to signal form and the 'aesthetic sense' proposed by Darwin. Since a receiver bias is sufficient to both initiate and drive ornament or armament exaggeration, without a genetically correlated or even coevolving receiver, this may be the appropriate 'null model' of sexual selection. Thirdly, we focus on the genetic architecture of sexually selected traits. Despite advances in modern molecular techniques, the number and identity of genes underlying performance, display and secondary sexual traits remains largely unknown. In-depth investigations into the genetic basis of sexual dimorphism in the context of long-term field studies will reveal constraints and trajectories of sexually selected trait evolution. Finally, we focus on sexual selection and conflict as drivers of speciation. Population divergence and speciation are often influenced by an interplay between sexual and natural selection. The extent to which sexual selection promotes or counteracts population divergence may vary depending on the genetic architecture of traits as well as the covariance between mating competition and local adaptation. Additionally, post-copulatory processes, such as selection against heterospecific sperm, may influence the importance of sexual selection in speciation. We propose that efforts to resolve these four themes can catalyze conceptual progress in the field of sexual selection, and we offer potential avenues of research to advance this progress.
Collapse
Affiliation(s)
- Willow R. Lindsay
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Staffan Andersson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Badreddine Bererhi
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Arild Johnsen
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Charlotta Kvarnemo
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Erica H. Leder
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Jan T. Lifjeld
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Calum E. Ninnes
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States of America
| | - Mats Olsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
| | - Geoff A. Parker
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Tommaso Pizzari
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, United Kingdom
| | - Anna Qvarnström
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Rebecca J. Safran
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States of America
| | - Ola Svensson
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, Huddinge, Sweden
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States of America
- Gothenburg Centre for Advanced Studies in Science and Technology, Chalmers University of Technology, Göteborg, Sweden
| |
Collapse
|
218
|
Cabalzar AP, Fields PD, Kato Y, Watanabe H, Ebert D. Parasite-mediated selection in a natural metapopulation of Daphnia magna. Mol Ecol 2019; 28:4770-4785. [PMID: 31591747 DOI: 10.1111/mec.15260] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 09/17/2019] [Accepted: 09/27/2019] [Indexed: 01/03/2023]
Abstract
Parasite-mediated selection varying across time and space in metapopulations is expected to result in host local adaptation and the maintenance of genetic diversity in disease-related traits. However, nonadaptive processes like migration and extinction-(re)colonization dynamics might interfere with adaptive evolution. Understanding how adaptive and nonadaptive processes interact to shape genetic variability in life-history and disease-related traits can provide important insights into their evolution in subdivided populations. Here we investigate signatures of spatially fluctuating, parasite-mediated selection in a natural metapopulation of Daphnia magna. Host genotypes from infected and uninfected populations were genotyped at microsatellite markers, and phenotyped for life-history and disease traits in common garden experiments. Combining phenotypic and genotypic data a QST -FST -like analysis was conducted to test for signatures of parasite mediated selection. We observed high variation within and among populations for phenotypic traits, but neither an indication of host local adaptation nor a cost of resistance. Infected populations have a higher gene diversity (Hs) than uninfected populations and Hs is strongly positively correlated with fitness. These results suggest a strong parasite effect on reducing population level inbreeding. We discuss how stochastic processes related to frequent extinction-(re)colonization dynamics as well as host and parasite migration impede the evolution of resistance in the infected populations. We suggest that the genetic and phenotypic patterns of variation are a product of dynamic changes in the host gene pool caused by the interaction of colonization bottlenecks, inbreeding, immigration, hybrid vigor, rare host genotype advantage and parasitism. Our study highlights the effect of the parasite in ameliorating the negative fitness consequences caused by the high drift load in this metapopulation.
Collapse
Affiliation(s)
- Andrea P Cabalzar
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | - Yasuhiko Kato
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Hajime Watanabe
- Department of Biotechnology, Division of Advance Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland.,Tvärminne Zoological Station, Tvärminne, Finland
| |
Collapse
|
219
|
|
220
|
Pérez-Tris J, Llanos-Garrido A, Bloor P, Carbonell R, Tellería JL, Santos T, Díaz JA. Increased individual homozygosity is correlated with low fitness in a fragmented lizard population. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
AbstractIsolation owing to anthropogenic habitat fragmentation is expected to increase the homozygosity of individuals, which might reduce their fitness as a result of inbreeding depression. Using samples from a fragmented population of the lizard Psammodromus algirus, for which we had data about two correlates of fitness, we genotyped individuals for six microsatellite loci that correctly capture genome-wide individual homozygosity of these lizards (as validated with an independent sample of lizards genotyped for both these microsatellites and > 70 000 single nucleotide polymorphisms). Our data revealed genetic structure at a very small geographical scale, which was compatible with restricted gene flow among populations disconnected in a matrix of inhospitable habitat. Lizards from the same fragment were genetically more related to one another than expected by chance, and individual homozygosity was greater in small than in large fragments. Within fragments, individual homozygosity was negatively associated with adult body size and clutch mass, revealing a link among reduced gene flow, increased homozygosity and lowered fitness that might reduce population viability deterministically. Our results contribute to mounting evidence of the impact of the loss of genetic diversity on fragmented wild populations.
Collapse
Affiliation(s)
- Javier Pérez-Tris
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| | - Alejandro Llanos-Garrido
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| | - Paul Bloor
- Instituto de Genética, Universidad Nacional de Colombia, Bogotá D.C., Colombia
| | - Roberto Carbonell
- Consejería de Medio Ambiente, Servicio Espacios Naturales, Valladolid, Spain
| | - José Luis Tellería
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| | - Tomás Santos
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| | - José A Díaz
- Departamento de Biodiversidad, Ecología y Evolución, Universidad Complutense de Madrid, Madrid, Spain
| |
Collapse
|
221
|
Zhao L, Li Y, Lou J, Yang Z, Liao H, Fu Q, Guo Z, Lian S, Hu X, Bao Z. Transcriptomic Profiling Provides Insights into Inbreeding Depression in Yesso Scallop Patinopecten yessoensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:623-633. [PMID: 31300903 DOI: 10.1007/s10126-019-09907-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 05/30/2019] [Indexed: 06/10/2023]
Abstract
Inbreeding often causes a decline in biological fitness, known as inbreeding depression. In genetics study, inbreeding coefficient f gives the proportion by which the heterozygosity of an individual is reduced by inbreeding. With the development of high-throughput sequencing, researchers were able to perform deep approaches to investigate which genes are affected by inbreeding and reveal some molecular underpinnings of inbreeding depression. As one commercially important species, Yesso scallop Patinopecten yessoensis confront the same dilemma of inbreeding depression. To examine how inbreeding affects gene expression, we compared the transcriptome of two experimentally selfing families with inbreeding coefficient f reached 0.5 as well as one natural population (f ≈ 0) of P. yessoensis. A total of 24 RNA-Seq libraries were constructed using scallop adductor muscle, and eventually 676.56 M (96.85%) HQ reads were acquired. Based on differential gene analysis, we were able to identify nine common differentially expressed genes (DEGs) across the top-ranked 30 DEGs in both selfing families in comparation with the natural population. Remarkable, through weighted gene co-expression network analysis (WGCNA), five common DEGs were found enriched in the most significant inbreeding related functional module M14 (FDR = 1.64E-156), including SREBP1, G3BP2, SBK1, KIAA1161, and AATs-Glupro. These five genes showed significantly higher expression in self-bred progeny. Suggested by the genetic functional analysis, up-regulated SREBP1, G3BP2, and KIAA1161 may suggest a perturbing lipid metabolism, a severe inframammary reaction or immune response, and a stress-responsive behavior. Besides, the significant higher SBK1 and AATs-Glupro may reflect the abnormal cellular physiological situation. Together, these genetic aberrant transcriptomic performances may contribute to inbreeding depression in P. yessoensis, deteriorating the stress tolerance and survival phenotype in self-bred progeny. Our results would lay a foundation for further comprehensive understanding of bivalve inbreeding depression, which may potentially benefit the genetic breeding for scallop aquaculture.
Collapse
Affiliation(s)
- Liang Zhao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Yangping Li
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Jiarun Lou
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Zhihui Yang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Huan Liao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Qiang Fu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Zhenyi Guo
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
| | - Shanshan Lian
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Xiaoli Hu
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| |
Collapse
|
222
|
Doekes HP, Veerkamp RF, Bijma P, de Jong G, Hiemstra SJ, Windig JJ. Inbreeding depression due to recent and ancient inbreeding in Dutch Holstein-Friesian dairy cattle. Genet Sel Evol 2019; 51:54. [PMID: 31558150 PMCID: PMC6764141 DOI: 10.1186/s12711-019-0497-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/19/2019] [Indexed: 02/01/2023] Open
Abstract
Background Inbreeding decreases animal performance (inbreeding depression), but not all inbreeding is expected to be equally harmful. Recent inbreeding is expected to be more harmful than ancient inbreeding, because selection decreases the frequency of deleterious alleles over time. Selection efficiency is increased by inbreeding, a process called purging. Our objective was to investigate effects of recent and ancient inbreeding on yield, fertility and udder health traits in Dutch Holstein–Friesian cows. Methods In total, 38,792 first-parity cows were included. Pedigree inbreeding (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$F_{PED}$$\end{document}FPED) was computed and 75 k genotype data were used to compute genomic inbreeding, among others based on regions of homozygosity (ROH) in the genome (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$F_{ROH}$$\end{document}FROH). Results Inbreeding depression was observed, e.g. a 1% increase in \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$F_{ROH}$$\end{document}FROH was associated with a 36.3 kg (SE = 2.4) decrease in 305-day milk yield, a 0.48 day (SE = 0.15) increase in calving interval and a 0.86 unit (SE = 0.28) increase in somatic cell score for day 150 through to 400. These effects equalled − 0.45, 0.12 and 0.05% of the trait means, respectively. When \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$F_{PED}$$\end{document}FPED was split into generation-based components, inbreeding on recent generations was more harmful than inbreeding on more distant generations for yield traits. When \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$F_{PED}$$\end{document}FPED was split into new and ancestral components, based on whether alleles were identical-by-descent for the first time or not, new inbreeding was more harmful than ancestral inbreeding, especially for yield traits. For example, a 1% increase in new inbreeding was associated with a 2.42 kg (SE = 0.41) decrease in 305-day fat yield, compared to a 0.03 kg (SE = 0.71) increase for ancestral inbreeding. There were no clear differences between effects of long ROH (recent inbreeding) and short ROH (ancient inbreeding). Conclusions Inbreeding depression was observed for yield, fertility and udder health traits. For yield traits and based on pedigree, inbreeding on recent generations was more harmful than inbreeding on distant generations and there was evidence of purging. Across all traits, long and short ROH contributed to inbreeding depression. In future work, inbreeding depression and purging should be assessed in more detail at the genomic level, using higher density information and genomic time series.
Collapse
Affiliation(s)
- Harmen P Doekes
- Wageningen University & Research, Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands. .,Wageningen University & Research, Centre for Genetic Resources the Netherlands, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
| | - Roel F Veerkamp
- Wageningen University & Research, Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Piter Bijma
- Wageningen University & Research, Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
| | - Gerben de Jong
- Cooperation CRV, Wassenaarweg 20, 6843 NW, Arnhem, The Netherlands
| | - Sipke J Hiemstra
- Wageningen University & Research, Centre for Genetic Resources the Netherlands, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Jack J Windig
- Wageningen University & Research, Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.,Wageningen University & Research, Centre for Genetic Resources the Netherlands, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| |
Collapse
|
223
|
Santos da Silva E, Marques Ponte JC, Barbosa da Silva M, Silva Pinheiro C, Carvalho Pacheco LG, Ferreira F, Briza P, Alcantara-Neves NM. Proteomic Analysis Reveals Allergen Variability among Breeds of the Dust Mite Blomia tropicalis. Int Arch Allergy Immunol 2019; 180:159-172. [PMID: 31563904 DOI: 10.1159/000501964] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/06/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The dawn of the "omics" technologies has changed allergy research, increasing the knowledge and identification of new allergens. However, these studies have been almost restricted to Dermatophagoides spp. Although Blomia tropicalis has long been established as a clinically important source of allergens, a thorough proteomic characterization is still lacking for this dust mite. OBJECTIVE To increase knowledge of B. tropicalis allergens through proteomic analysis. METHODS Eleven in-bred lineages of B. tropicalis were obtained from 11 unique different pregnant females. Their somatic extracts were analyzed and compared with a commercially available extract by liquid chromatography tandem mass spectrometry (LC-MS/MS). RESULTS Considerable differences in the protein expression profiles were found among the breeds, and most of them displayed higher expression levels of major allergens than the commercially available extract. Blo t 2 was the most prominent allergenic protein in the analyzed extracts. Six identified allergens and 14 isoforms have not yet been recognized by IUIS. Conversely, 3 previously recognized B. tropicalis allergens were not found. CONCLUSIONS The clear impact of inbreeding on allergen content shown by our study leads us to conclude that the quantification and/or identification of allergens from in-bred lines should be routinely considered for mite cultivation in order to select breeds with higher amounts of major allergens. In this sense, LC-MS/MS may be a useful method to achieve this quality control for research and commercial purposes.
Collapse
Affiliation(s)
- Eduardo Santos da Silva
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.,Department of Biosciences, University of Salzburg, Salzburg, Austria.,Programa de Pós-Graduação em Biotecnologia da Rede Nordeste de Biotecnologia (RENORBIO), Natal, Brazil
| | - João Carlos Marques Ponte
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.,Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Márcia Barbosa da Silva
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.,Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Carina Silva Pinheiro
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Luis Gustavo Carvalho Pacheco
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Fatima Ferreira
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Peter Briza
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Neuza Maria Alcantara-Neves
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil, .,Programa de Pós-Graduação em Biotecnologia da Rede Nordeste de Biotecnologia (RENORBIO), Natal, Brazil,
| |
Collapse
|
224
|
Thavornkanlapachai R, Mills HR, Ottewell K, Dunlop J, Sims C, Morris K, Donaldson F, Kennington WJ. Mixing Genetically and Morphologically Distinct Populations in Translocations: Asymmetrical Introgression in A Newly Established Population of the Boodie ( Bettongia lesueur). Genes (Basel) 2019; 10:E729. [PMID: 31546973 PMCID: PMC6770996 DOI: 10.3390/genes10090729] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 11/22/2022] Open
Abstract
The use of multiple source populations provides a way to maximise genetic variation and reduce the impacts of inbreeding depression in newly established translocated populations. However, there is a risk that individuals from different source populations will not interbreed, leading to population structure and smaller effective population sizes than expected. Here, we investigate the genetic consequences of mixing two isolated, morphologically distinct island populations of boodies (Bettongia lesueur) in a translocation to mainland Australia over three generations. Using 18 microsatellite loci and the mitochondrial D-loop region, we monitored the released animals and their offspring between 2010 and 2013. Despite high levels of divergence between the two source populations (FST = 0.42 and ϕST = 0.72), there was clear evidence of interbreeding between animals from different populations. However, interbreeding was non-random, with a significant bias towards crosses between the genetically smaller-sized Barrow Island males and the larger-sized Dorre Island females. This pattern of introgression was opposite to the expectation that male-male competition or female mate choice would favour larger males. This study shows how mixing diverged populations can bolster genetic variation in newly established mammal populations, but the ultimate outcome can be difficult to predict, highlighting the need for continued genetic monitoring to assess the long-term impacts of admixture.
Collapse
Affiliation(s)
- Rujiporn Thavornkanlapachai
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| | - Harriet R Mills
- Centre for Ecosystem Management, School of Science, Edith Cowan University, Joondalup, Western Australia 6027, Australia.
| | - Kym Ottewell
- Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Western Australia 6152, Australia.
| | - Judy Dunlop
- School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.
- Department of Biodiversity, Conservation and Attractions, PO Box 51, Wanneroo, Western Australia 6946, Australia.
| | - Colleen Sims
- Department of Biodiversity, Conservation and Attractions, PO Box 51, Wanneroo, Western Australia 6946, Australia.
| | - Keith Morris
- Department of Biodiversity, Conservation and Attractions, PO Box 51, Wanneroo, Western Australia 6946, Australia.
| | - Felicity Donaldson
- 360 Environmental, 10 Bermondsey Street, West Leederville, Western Australia 6007, Australia.
| | - W Jason Kennington
- School of Biological Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia.
| |
Collapse
|
225
|
Hasselgren M, Norén K. Inbreeding in natural mammal populations: historical perspectives and future challenges. Mamm Rev 2019. [DOI: 10.1111/mam.12169] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Malin Hasselgren
- Department of Zoology Stockholm University 106 91 Stockholm Sweden
| | - Karin Norén
- Department of Zoology Stockholm University 106 91 Stockholm Sweden
| |
Collapse
|
226
|
Inbreeding reduces long-term growth of Alpine ibex populations. Nat Ecol Evol 2019; 3:1359-1364. [PMID: 31477848 DOI: 10.1038/s41559-019-0968-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 07/26/2019] [Indexed: 11/08/2022]
Abstract
Many studies document negative inbreeding effects on individuals, and conservation efforts to preserve rare species routinely employ strategies to reduce inbreeding. Despite this, there are few clear examples in nature of inbreeding decreasing the growth rates of populations, and the extent of population-level effects of inbreeding in the wild remains controversial. Here, we take advantage of a long-term dataset of 26 reintroduced Alpine ibex (Capra ibex ibex) populations spanning nearly 100 years to show that inbreeding substantially reduced per capita population growth rates, particularly for populations in harsher environments. Populations with high average inbreeding (F ≈ 0.2) had population growth rates reduced by 71% compared with populations with no inbreeding. Our results show that inbreeding can have long-term demographic consequences even when environmental variation is large and deleterious alleles may have been purged during bottlenecks. Thus, efforts to guard against inbreeding effects in populations of endangered species have not been misplaced.
Collapse
|
227
|
Domínguez-García S, García C, Quesada H, Caballero A. Accelerated inbreeding depression suggests synergistic epistasis for deleterious mutations in Drosophila melanogaster. Heredity (Edinb) 2019; 123:709-722. [PMID: 31477803 PMCID: PMC6834575 DOI: 10.1038/s41437-019-0263-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 08/15/2019] [Accepted: 08/18/2019] [Indexed: 01/21/2023] Open
Abstract
Epistasis may have important consequences for a number of issues in quantitative genetics and evolutionary biology. In particular, synergistic epistasis for deleterious alleles is relevant to the mutation load paradox and the evolution of sex and recombination. Some studies have shown evidence of synergistic epistasis for spontaneous or induced deleterious mutations appearing in mutation-accumulation experiments. However, many newly arising mutations may not actually be segregating in natural populations because of the erasing action of natural selection. A demonstration of synergistic epistasis for naturally segregating alleles can be achieved by means of inbreeding depression studies, as deleterious recessive allelic effects are exposed in inbred lines. Nevertheless, evidence of epistasis from these studies is scarce and controversial. In this paper, we report the results of two independent inbreeding experiments carried out with two different populations of Drosophila melanogaster. The results show a consistent accelerated inbreeding depression for fitness, suggesting synergistic epistasis among deleterious alleles. We also performed computer simulations assuming different possible models of epistasis and mutational parameters for fitness, finding some of them to be compatible with the results observed. Our results suggest that synergistic epistasis for deleterious mutations not only occurs among newly arisen spontaneous or induced mutations, but also among segregating alleles in natural populations.
Collapse
Affiliation(s)
- Sara Domínguez-García
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain
| | - Carlos García
- CIBUS, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Galicia, Spain
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310, Vigo, Spain. .,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, 36310, Vigo, Spain.
| |
Collapse
|
228
|
Origin and Evolution of Deleterious Mutations in Horses. Genes (Basel) 2019; 10:genes10090649. [PMID: 31466279 PMCID: PMC6769756 DOI: 10.3390/genes10090649] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/24/2019] [Accepted: 08/26/2019] [Indexed: 01/04/2023] Open
Abstract
Domestication has changed the natural evolutionary trajectory of horses by favoring the reproduction of a limited number of animals showing traits of interest. Reduced breeding stocks hampered the elimination of deleterious variants by means of negative selection, ultimately inflating mutational loads. However, ancient genomics revealed that mutational loads remained steady during most of the domestication history until a sudden burst took place some 250 years ago. To identify the factors underlying this trajectory, we gather an extensive dataset consisting of 175 modern and 153 ancient genomes previously published, and carry out the most comprehensive characterization of deleterious mutations in horses. We confirm that deleterious variants segregated at low frequencies during the last 3500 years, and only spread and incremented their occurrence in the homozygous state during modern times, owing to inbreeding. This independently happened in multiple breeds, following both the development of closed studs and purebred lines, and the deprecation of horsepower in the 20th century, which brought many draft breeds close to extinction. Our work illustrates the paradoxical effect of some conservation and improvement programs, which reduced the overall genomic fitness and viability.
Collapse
|
229
|
Ksiazek-Mikenas K, Fant JB, Skogen KA. Pollinator-Mediated Gene Flow Connects Green Roof Populations Across the Urban Matrix: A Paternity Analysis of the Self-Compatible Forb Penstemon hirsutus. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00299] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
230
|
Poirier M, Coltman DW, Pelletier F, Jorgenson J, Festa‐Bianchet M. Genetic decline, restoration and rescue of an isolated ungulate population. Evol Appl 2019; 12:1318-1328. [PMID: 31417617 PMCID: PMC6691324 DOI: 10.1111/eva.12706] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/19/2018] [Accepted: 08/27/2018] [Indexed: 01/08/2023] Open
Abstract
Isolation of small populations is expected to reduce fitness through inbreeding and loss of genetic variation, impeding population growth and compromising population persistence. Species with long generation time are the least likely to be rescued by evolution alone. Management interventions that maintain or restore genetic variation to assure population viability are consequently of significant importance. We investigated, over 27 years, the genetic and demographic consequences of a demographic bottleneck followed by artificial supplementation in an isolated population of bighorn sheep (Ovis canadensis). Based on a long-term pedigree and individual monitoring, we documented the genetic decline, restoration and rescue of the population. Microsatellite analyses revealed that the demographic bottleneck reduced expected heterozygosity and allelic diversity by 6.2% and 11.3%, respectively, over two generations. Following supplementation, first-generation admixed lambs were 6.4% heavier at weaning and had 28.3% higher survival to 1 year compared to lambs of endemic ancestry. Expected heterozygosity and allelic diversity increased by 4.6% and 14.3% after two generations through new alleles contributed by translocated individuals. We found no evidence for outbreeding depression and did not see immediate evidence of swamping of local genes. Rapid intervention following the demographic bottleneck allowed the genetic restoration and rescue of this bighorn sheep population, likely preventing further losses at both the genetic and demographic levels. Our results provide further empirical evidence that translocation can be used to reduce inbreeding depression in nature and has the potential to mitigate the effect of human-driven environmental changes on wild populations.
Collapse
Affiliation(s)
- Marc‐Antoine Poirier
- Département de BiologieUniversité de SherbrookeSherbrookeQuébecCanada
- Centre d’Études Nordiques (CEN)Université LavalQuebec CityQuébecCanada
| | - David W. Coltman
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Fanie Pelletier
- Département de BiologieUniversité de SherbrookeSherbrookeQuébecCanada
| | | | - Marco Festa‐Bianchet
- Département de BiologieUniversité de SherbrookeSherbrookeQuébecCanada
- Centre d’Études Nordiques (CEN)Université LavalQuebec CityQuébecCanada
| |
Collapse
|
231
|
Lifetime Fitness Costs of Inbreeding and Being Inbred in a Critically Endangered Bird. Curr Biol 2019; 29:2711-2717.e4. [DOI: 10.1016/j.cub.2019.06.064] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/31/2019] [Accepted: 06/21/2019] [Indexed: 11/20/2022]
|
232
|
García-Fernández A, Manzano P, Seoane J, Azcárate FM, Iriondo JM, Peco B. Herbivore corridors sustain genetic footprint in plant populations: a case for Spanish drove roads. PeerJ 2019; 7:e7311. [PMID: 31341747 PMCID: PMC6637930 DOI: 10.7717/peerj.7311] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 06/17/2019] [Indexed: 11/20/2022] Open
Abstract
Habitat fragmentation is one of the greatest threats to biodiversity conservation and ecosystem productivity mediated by direct human impact. Its consequences include genetic depauperation, comprising phenomena such as inbreeding depression or reduction in genetic diversity. While the capacity of wild and domestic herbivores to sustain long-distance seed dispersal has been proven, the impact of herbivore corridors in plant population genetics remains to be observed. We conducted this study in the Conquense Drove Road in Spain, where sustained use by livestock over centuries has involved transhumant herds passing twice a year en route to winter and summer pastures. We compared genetic diversity and inbreeding coefficients of Plantago lagopus populations along the drove road with populations in the surrounding agricultural matrix, at varying distances from human settlements. We observed significant differences in coefficients of inbreeding between the drove road and the agricultural matrix, as well as significant trends indicative of higher genetic diversity and population nestedness around human settlements. Trends for higher genetic diversity along drove roads may be present, although they were only marginally significant due to the available sample size. Our results illustrate a functional landscape with human settlements as dispersal hotspots, while the findings along the drove road confirm its role as a pollinator reservoir observed in other studies. Drove roads may possibly also function as linear structures that facilitate long-distance dispersal across the agricultural matrix, while local P. lagopus populations depend rather on short-distance seed dispersal. These results highlight the role of herbivore corridors for conserving the migration capacity of plants, and contribute towards understanding the role of seed dispersal and the spread of invasive species related to human activities.
Collapse
Affiliation(s)
| | - Pablo Manzano
- Commission on Ecosystem Management, International Union for Conservation of Nature, Nairobi, Kenya.,Terrestrial Ecology Group-Departamento de Ecología, Centro de Investigación en Biodiversidad y Cambio Global (CIBC), Universidad Autónoma de Madrid, Madrid, Spain.,HELSUS, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Javier Seoane
- Terrestrial Ecology Group-Departamento de Ecología, Centro de Investigación en Biodiversidad y Cambio Global (CIBC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Francisco M Azcárate
- Terrestrial Ecology Group-Departamento de Ecología, Centro de Investigación en Biodiversidad y Cambio Global (CIBC), Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose M Iriondo
- Área de Biodiversidad y Conservación, Universidad Rey Juan Carlos, Móstoles, Madrid, Spain
| | - Begoña Peco
- Terrestrial Ecology Group-Departamento de Ecología, Centro de Investigación en Biodiversidad y Cambio Global (CIBC), Universidad Autónoma de Madrid, Madrid, Spain
| |
Collapse
|
233
|
Bell DA, Robinson ZL, Funk WC, Fitzpatrick SW, Allendorf FW, Tallmon DA, Whiteley AR. The Exciting Potential and Remaining Uncertainties of Genetic Rescue. Trends Ecol Evol 2019; 34:1070-1079. [PMID: 31296345 DOI: 10.1016/j.tree.2019.06.006] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/06/2019] [Accepted: 06/10/2019] [Indexed: 02/03/2023]
Abstract
Restoring gene flow into small, isolated populations can alleviate genetic load and decrease extinction risk (i.e., genetic rescue), yet gene flow is rarely augmented as a conservation strategy. Due to this discrepancy between opportunity and action, a recent call was made for widespread genetic rescue attempts. However, several aspects of augmenting gene flow are poorly understood, including the magnitude and duration of beneficial effects and when deleterious effects are likely to occur. We discuss the remaining uncertainties of genetic rescue in order to promote and direct future research and to hasten progress toward implementing this potentially powerful conservation strategy on a broader scale.
Collapse
Affiliation(s)
- Donovan A Bell
- Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA.
| | - Zachary L Robinson
- Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - W Chris Funk
- Department of Biology and Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Department of Integrative Biology, Michigan State University, Hickory Corners, MI, USA; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Fred W Allendorf
- Division of Biological Sciences, University of Montana, Missoula, MT, USA
| | - David A Tallmon
- Biology and Marine Biology Program, University of Alaska Southeast, Juneau, AK, USA
| | - Andrew R Whiteley
- Wildlife Biology Program, W.A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| |
Collapse
|
234
|
Nonaka E, Sirén J, Somervuo P, Ruokolainen L, Ovaskainen O, Hanski I. Scaling up the effects of inbreeding depression from individuals to metapopulations. J Anim Ecol 2019; 88:1202-1214. [PMID: 31077598 DOI: 10.1111/1365-2656.13011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 03/10/2019] [Indexed: 12/01/2022]
Abstract
Inbreeding is common in nature, and many laboratory studies have documented that inbreeding depression can reduce the fitness of individuals. Demonstrating the consequences of inbreeding depression on the growth and persistence of populations is more challenging because populations are often regulated by density- or frequency-dependent selection and influenced by demographic and environmental stochasticity. A few empirical studies have shown that inbreeding depression can increase extinction risk of local populations. The importance of inbreeding depression at the metapopulation level has been conjectured based on population-level studies but has not been evaluated. We quantified the impact of inbreeding depression affecting the fitness of individuals on metapopulation persistence in heterogeneous habitat networks of different sizes and habitat configuration in a context of natural butterfly metapopulations. We developed a spatial individual-based simulation model of metapopulations with explicit genetics. We used Approximate Bayesian Computation to fit the model to extensive demographic, genetic and life-history data available for the well-studied Glanville fritillary butterfly (Melitaea cinxia) metapopulations in the Åland islands in SW Finland. We compared 18 semi-independent habitat networks differing in size and fragmentation. The results show that inbreeding is more frequent in small habitat networks, and consequently, inbreeding depression elevates extinction risks in small metapopulations. Metapopulation persistence and neutral genetic diversity maintained in the metapopulations increase with the total habitat amount in and mean patch size of habitat networks. Dispersal and mating behaviour interact with landscape structure to determine how likely it is to encounter kin while looking for mates. Inbreeding depression can decrease the viability of small metapopulations even when they are strongly influenced by stochastic extinction-colonization dynamics and density-dependent selection. The findings from this study support that genetic factors, in addition to demographic factors, can contribute to extinctions of small local populations and also of metapopulations.
Collapse
Affiliation(s)
- Etsuko Nonaka
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland.,Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Jukka Sirén
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland
| | - Panu Somervuo
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland.,Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Lasse Ruokolainen
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland.,Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland
| | - Otso Ovaskainen
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland.,Organismal and Evolutionary Biology Research Programme, University of Helsinki, Helsinki, Finland.,Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ilkka Hanski
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, Helsinki, Finland
| |
Collapse
|
235
|
Gallego‐García N, Forero‐Medina G, Vargas‐Ramírez M, Caballero S, Shaffer HB. Landscape genomic signatures indicate reduced gene flow and forest‐associated adaptive divergence in an endangered neotropical turtle. Mol Ecol 2019; 28:2757-2771. [DOI: 10.1111/mec.15112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 03/20/2019] [Accepted: 04/15/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Natalia Gallego‐García
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
- Department of Ecology and Evolutionary Biology, California Conservation Science, Institute of the Environment and Sustainability University of California Los Angeles California USA
- Wildlife Conservation Society Turtle Survival Alliance Cali Colombia
| | | | - Mario Vargas‐Ramírez
- Biodiversidad y Conservación Genética, Instituto de Genética Universidad Nacional de Colombia Bogotá Colombia
| | - Susana Caballero
- Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
| | - Howard Bradley Shaffer
- Department of Ecology and Evolutionary Biology, California Conservation Science, Institute of the Environment and Sustainability University of California Los Angeles California USA
| |
Collapse
|
236
|
Esson C, Skerratt LF, Berger L, Malmsten J, Strand T, Lundkvist Å, Järhult JD, Michaux J, Mijiddorj TN, Bayrakçısmith R, Mishra C, Johansson Ö. Health and zoonotic Infections of snow leopards Panthera unica in the South Gobi desert of Mongolia. Infect Ecol Epidemiol 2019; 9:1604063. [PMID: 31231481 PMCID: PMC6567154 DOI: 10.1080/20008686.2019.1604063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/02/2019] [Indexed: 10/31/2022] Open
Abstract
Background: Snow leopards, Panthera uncia, are a threatened apex predator, scattered across the mountains of Central and South Asia. Disease threats to wild snow leopards have not been investigated.Methods and Results: Between 2008 and 2015, twenty snow leopards in the South Gobi desert of Mongolia were captured and immobilised for health screening and radio-collaring. Blood samples and external parasites were collected for pathogen analyses using enzyme-linked immunosorbent assay (ELISA), microscopic agglutination test (MAT), and next-generation sequencing (NGS) techniques. The animals showed no clinical signs of disease, however, serum antibodies to significant zoonotic pathogens were detected. These pathogens included, Coxiella burnetii, (25% prevalence), Leptospira spp., (20%), and Toxoplasma gondii (20%). Ticks collected from snow leopards contained potentially zoonotic bacteria from the genera Bacillus, Bacteroides, Campylobacter, Coxiella, Rickettsia, Staphylococcus and Streptococcus.Conclusions: The zoonotic pathogens identified in this study, in the short-term did not appear to cause illness in the snow leopards, but have caused illness in other wild felids. Therefore, surveillance for pathogens should be implemented to monitor for potential longer- term disease impacts on this snow leopard population.
Collapse
Affiliation(s)
- Carol Esson
- One Health Research Group, College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Australia
| | - Lee F Skerratt
- Melbourne Veterinary School, University of Melbourne, Parkville, Australia
| | - Lee Berger
- Melbourne Veterinary School, University of Melbourne, Parkville, Australia
| | - Jonas Malmsten
- Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden.,Department of Wildlife, Fish and Environment Science, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Tanja Strand
- Zoonosis Science Centre (ZSC), Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Åke Lundkvist
- Zoonosis Science Centre (ZSC), Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Josef D Järhult
- Zoonosis Science Centre (ZSC), Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Johan Michaux
- Génétique de la conservation Life Sciences, Liege, Belgium
| | | | | | | | - Örjan Johansson
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, Riddarhyttan, Sweden.,Snow Leopard Trust, Seattle, WA, USA
| |
Collapse
|
237
|
Roques S, Chancerel E, Boury C, Pierre M, Acolas M. From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon. Ecol Evol 2019; 9:7017-7029. [PMID: 31380030 PMCID: PMC6662312 DOI: 10.1002/ece3.5268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 02/12/2019] [Accepted: 04/04/2019] [Indexed: 01/06/2023] Open
Abstract
The use of genetic information is crucial in conservation programs for the establishment of breeding plans and for the evaluation of restocking success. Short tandem repeats (STRs) have been the most widely used molecular markers in such programs, but next-generation sequencing approaches have prompted the transition to genome-wide markers such as single nucleotide polymorphisms (SNPs). Until now, most sturgeon species have been monitored using STRs. The low diversity found in the critically endangered European sturgeon (Acipenser sturio), however, makes its future genetic monitoring challenging, and the current resolution needs to be increased. Here, we describe the discovery of a highly informative set of 79 SNPs using double-digest restriction-associated DNA (ddRAD) sequencing and its validation by genotyping using the MassARRAY system. Comparing with STRs, the SNP panel proved to be highly efficient and reproducible, allowing for more accurate parentage and kinship assignments' on 192 juveniles of known pedigree and 40 wild-born adults. We explore the effectiveness of both markers to estimated relatedness and inbreeding, using simulated and empirical datasets. Interestingly, we found significant correlations between STRs and SNPs at individual heterozygosity and inbreeding that give support to a reasonable representation of whole genome diversity for both markers. These results are useful for the conservation program of A. sturio in building a comprehensive studbook, which will optimize conservation strategies. This approach also proves suitable for other case studies in which highly discriminatory genetic markers are needed to assess parentage and kinship.
Collapse
Affiliation(s)
- Séverine Roques
- Aquatic Ecosystems and Global ChangesIRSTEA, EABX URCestasFrance
| | | | | | - Maud Pierre
- Aquatic Ecosystems and Global ChangesIRSTEA, EABX URCestasFrance
| | | |
Collapse
|
238
|
Murphy SM, Hast JT, Augustine BC, Weisrock DW, Clark JD, Kocka DM, Ryan CW, Sajecki JL, Cox JJ. Early genetic outcomes of American black bear reintroductions in the Central Appalachians, USA. URSUS 2019. [DOI: 10.2192/ursu-d-18-00011.1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Sean M. Murphy
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
| | - John T. Hast
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
| | - Ben C. Augustine
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
| | - David W. Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Joseph D. Clark
- United States Geological Survey, Northern Rocky Mountain Science Center, Southern Appalachian Research Branch, University of Tennessee, Knoxville, TN 37996, USA
| | - David M. Kocka
- Virginia Department of Game and Inland Fisheries, Verona, VA 24482, USA
| | - Christopher W. Ryan
- West Virginia Division of Natural Resources, South Charleston, WV 25303, USA
| | - Jaime L. Sajecki
- Virginia Department of Game and Inland Fisheries, Verona, VA 24482, USA
| | - John J. Cox
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY 40546, USA
| |
Collapse
|
239
|
López-Cortegano E, Pérez-Figueroa A, Caballero A. metapop2: Re-implementation of software for the analysis and management of subdivided populations using gene and allelic diversity. Mol Ecol Resour 2019; 19:1095-1100. [PMID: 30938911 DOI: 10.1111/1755-0998.13015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 03/07/2019] [Accepted: 03/19/2019] [Indexed: 01/06/2023]
Abstract
Management programmes often have to make decisions based on the analysis of the genetic properties and diversity of populations. Expected heterozygosity (or gene diversity) and population structure parameters are often used to make recommendations for conservation, such as avoidance of inbreeding or migration across subpopulations. Allelic diversity, however, can also provide complementary and useful information for conservation programmes, as it is highly sensitive to population bottlenecks, and is more related to long-term selection response than heterozygosity. Here we present a completely revised and updated re-implementation of the software metapop for the analysis of diversity in subdivided populations, as well as a tool for the management and dynamic estimation of optimal contributions in conservation programmes. This new update includes computation of allelic diversity for population analysis and management, as well as a simulation mode to forecast the consequences of taking different management strategies over time. Furthermore, the new implementation in C++ includes code optimization and improved memory usage, allowing for fast analysis of large data sets including single nucleotide polymorphism markers, as well as enhanced cross-software and cross-platform compatibility.
Collapse
Affiliation(s)
- Eugenio López-Cortegano
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigaciones Biomédicas (CINBIO), Universidade de Vigo, Vigo, Spain
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, Vigo, Spain.,Centro de Investigación Marina (CIM-UVIGO), Universidade de Vigo, Vigo, Spain
| |
Collapse
|
240
|
Inbreeding depression causes reduced fecundity in Golden Retrievers. Mamm Genome 2019; 30:166-172. [PMID: 31115595 PMCID: PMC6606663 DOI: 10.1007/s00335-019-09805-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/15/2019] [Indexed: 01/09/2023]
Abstract
Inbreeding depression has been demonstrated to impact vital rates, productivity, and performance in human populations, wild and endangered species, and in recent years, the domestic species. In all cases, standardized, high-quality phenotype data on all individuals are invaluable for longitudinal analyses such as those required to evaluate vital rates of a study cohort. Further, many investigators agree upon the preference for and utility of genomic measures of inbreeding in lieu of pedigree-based estimates of inbreeding. We evaluated the association of measures of reproductive fitness in 93 Golden Retrievers enrolled in the Golden Retriever Lifetime Study with a genomic measurement of inbreeding, FROH. We demonstrate a statistically significant negative correlation between fecundity and FROH. This work sets the stage for larger scale analyses to investigate genomic regions associated with fecundity and other measures of fitness.
Collapse
|
241
|
Jantzen F, Wozniak N, Kappel C, Sicard A, Lenhard M. A high-throughput amplicon-based method for estimating outcrossing rates. PLANT METHODS 2019; 15:47. [PMID: 31131016 PMCID: PMC6525360 DOI: 10.1186/s13007-019-0433-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCR-genotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming. RESULTS We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd's Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons. CONCLUSIONS This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.
Collapse
Affiliation(s)
- Friederike Jantzen
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, House 26, 14476 Potsdam-Golm, Germany
| | - Natalia Wozniak
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, House 26, 14476 Potsdam-Golm, Germany
- Present Address: Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, Building ND North, 44801 Bochum, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, House 26, 14476 Potsdam-Golm, Germany
| | - Adrien Sicard
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, House 26, 14476 Potsdam-Golm, Germany
- Present Address: Department of Plant Biology, Swedish University of Agricultural, Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, House 26, 14476 Potsdam-Golm, Germany
| |
Collapse
|
242
|
Mating structure of the blue and red shrimp, Aristeus antennatus (Risso, 1816) characterized by relatedness analysis. Sci Rep 2019; 9:7227. [PMID: 31076585 PMCID: PMC6510731 DOI: 10.1038/s41598-019-43523-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 04/03/2019] [Indexed: 11/09/2022] Open
Abstract
Understanding life history variation and strategies is crucial for stock assessment and fisheries management due to the direct effects on population dynamics, effective population size, sex-ratios, levels of inbreeding, and relatedness among individuals. Aristeus antennatus (En ─ Blue and red shrimp; Fr ─ Crevette rouge; Sp ─ Gamba rosada) is one of the most exploited demersal resources in the Western Mediterranean Sea. However, information regarding the mating system and mate choice preferences remains largely unknown. Advances in molecular genetic markers and methods of inferring biological relationships among individuals have facilitated new insights into the reproductive dynamics of the species in the wild. Here, we used microsatellite markers to examine the A. antennatus mating system and putative mate choice preferences. Our results provided clear evidence of polyandry and polygyny. Relatedness analyses, together with FST and DAPC values showed females exhibited a mating bias towards unrelated males. Mating males were inferred from spermatophores and suggested males were sympatric with females and were also from other spawning grounds. Our findings provided the first description of the reproductive behavior of blue and red shrimp.
Collapse
|
243
|
Hasselgren M, Angerbjörn A, Eide NE, Erlandsson R, Flagstad Ø, Landa A, Wallén J, Norén K. Genetic rescue in an inbred Arctic fox ( Vulpes lagopus) population. Proc Biol Sci 2019; 285:rspb.2017.2814. [PMID: 29593110 DOI: 10.1098/rspb.2017.2814] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/02/2018] [Indexed: 12/22/2022] Open
Abstract
Isolation of small populations can reduce fitness through inbreeding depression and impede population growth. Outcrossing with only a few unrelated individuals can increase demographic and genetic viability substantially, but few studies have documented such genetic rescue in natural mammal populations. We investigate the effects of immigration in a subpopulation of the endangered Scandinavian arctic fox (Vulpes lagopus), founded by six individuals and isolated for 9 years at an extremely small population size. Based on a long-term pedigree (105 litters, 543 individuals) combined with individual fitness traits, we found evidence for genetic rescue. Natural immigration and gene flow of three outbred males in 2010 resulted in a reduction in population average inbreeding coefficient (f), from 0.14 to 0.08 within 5 years. Genetic rescue was further supported by 1.9 times higher juvenile survival and 1.3 times higher breeding success in immigrant first-generation offspring compared with inbred offspring. Five years after immigration, the population had more than doubled in size and allelic richness increased by 41%. This is one of few studies that has documented genetic rescue in a natural mammal population suffering from inbreeding depression and contributes to a growing body of data demonstrating the vital connection between genetics and individual fitness.
Collapse
Affiliation(s)
- Malin Hasselgren
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Anders Angerbjörn
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Nina E Eide
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Rasmus Erlandsson
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | | | - Arild Landa
- Norwegian Institute for Nature Research, 7485 Trondheim, Norway
| | - Johan Wallén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| | - Karin Norén
- Department of Zoology, Stockholm University, 10691 Stockholm, Sweden
| |
Collapse
|
244
|
Robinson JA, Räikkönen J, Vucetich LM, Vucetich JA, Peterson RO, Lohmueller KE, Wayne RK. Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction. SCIENCE ADVANCES 2019; 5:eaau0757. [PMID: 31149628 PMCID: PMC6541468 DOI: 10.1126/sciadv.aau0757] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 04/23/2019] [Indexed: 05/08/2023]
Abstract
The observation that small isolated populations often suffer reduced fitness from inbreeding depression has guided conservation theory and practice for decades. However, investigating the genome-wide dynamics associated with inbreeding depression in natural populations is only now feasible with relatively inexpensive sequencing technology and annotated reference genomes. To characterize the genome-wide effects of intense inbreeding and isolation, we performed whole-genome sequencing and morphological analysis of an iconic inbred population, the gray wolves (Canis lupus) of Isle Royale. Through population genetic simulations and comparison with wolf genomes from a variety of demographic histories, we find evidence that severe inbreeding depression in this population is due to increased homozygosity of strongly deleterious recessive mutations. Our results have particular relevance in light of the recent translocation of wolves from the mainland to Isle Royale, as well as broader implications for management of genetic variation in the fragmented landscape of the modern world.
Collapse
Affiliation(s)
- Jacqueline A. Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Corresponding author.
| | - Jannikke Räikkönen
- Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
| | - Leah M. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - John A. Vucetich
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Rolf O. Peterson
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
245
|
Olito C, Connallon T. Sexually Antagonistic Variation and the Evolution of Dimorphic Sexual Systems. Am Nat 2019; 193:688-701. [DOI: 10.1086/702847] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
246
|
Charlton SJ, Nielsen MB, Pedersen CR, Thomsen L, Kristjansen MP, Sørensen TB, Pertoldi C, Strand J. Strong Heterogeneity in Advances in Cryopreservation Techniques in the Mammalian Orders. Zoolog Sci 2019; 35:1-22. [PMID: 29417894 DOI: 10.2108/zs170037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Between 1970 and 2012, vertebrate abundance has declined by 58% with an average annual decline of 2%, calling for serious action to prevent a mass extinction and an irreversible loss of biodiversity. Cryobanks and cryopreservation have the potential to assist and improve ex situ and in situ conservation strategies by storing valuable genetic material. A great deal of studies concerning cryopreservation have been performed within the class Mammalia, although no systematic overview has previously been presented. The objective of this study is therefore to evaluate the status, pattern and future of cryopreservation within Mammalia. A strong disproportional distribution of studies in examined orders is displayed. For the majority of examined orders less than 10% of species has been examined. However, the cryopreservation of germplasm has in several cases been successful and resulted in successful applications of assisted reproductive techniques (ARTs). Various obstacles are associated with the development of cryopreservation protocols, and among them the most prominent is interspecific differences in cryotolerance. Extrapolation of protocols in closely related species is considered the most applicable procedure, and a future supplement to overcome this problem is the examination and comparison of cryobiological traits. Successful protocols have been developed for the vast majority of domesticated mammals, which gives incentive for the further extrapolation of protocols in threatened species.
Collapse
Affiliation(s)
- Sebastian J Charlton
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Mikkel B Nielsen
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Carina R Pedersen
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Lisette Thomsen
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Mads P Kristjansen
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Thomas B Sørensen
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark
| | - Cino Pertoldi
- 1 Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220 Aalborg, Denmark.,2 Aalborg Zoo, Aalborg, Mølleparkvej 63, 9000 Aalborg, Denmark
| | - Julie Strand
- 3 Randers Regnskov, Randers, Tørvebryggen 11, 8900 Randers, Denmark
| |
Collapse
|
247
|
|
248
|
Inbreeding load and inbreeding depression estimated from lifetime reproductive success in a small, dispersal-limited population. Heredity (Edinb) 2019; 123:192-201. [PMID: 30809076 DOI: 10.1038/s41437-019-0197-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 02/11/2019] [Accepted: 02/12/2019] [Indexed: 11/08/2022] Open
Abstract
The fitness consequences of inbreeding and the individual behaviors that prevent its detrimental effects can be challenging to document in wild populations. Here, we use field and molecular data from a 17-year study of banner-tailed kangaroo rats (Dipodomys spectabilis) to quantify the relationship between inbreeding, mate kinship, and lifetime reproductive success. Using a pedigree that was reconstructed using genetic and field data within a Bayesian framework (median probability of parental assignment = 0.92, mean pedigree depth = 6 generations), we estimated both inbreeding coefficients and kinship between individuals that produced offspring (mean inbreeding coefficient = 0.07, mean mate kinship = 0.08). We also used the pedigree, in combination with census data, to generate a series of fitness estimates, ranging from survival to reproductive maturity to lifetime reproductive success. We found that the population's inbreeding load was low to moderate (0.98-4.66 haploid lethal equivalents) and increased with the time frame over which fitness was estimated (lowest for survival to maturity, highest for adult-to-adult reproductive success). Fitness decreased with increasing inbreeding coefficients. For example, lifetime reproductive success was reduced by 24% for individuals with inbreeding coefficients greater than twice the population mean. Within full sibling pairs, the sibling with less-related mates produced an average of 30% more offspring over its lifetime. These data further illustrate that inbreeding can have a negative effect on lifetime reproductive success.
Collapse
|
249
|
Mensch EL, Kronenberger JA, Broder ED, Fitzpatrick SW, Funk WC, Angeloni LM. A potential role for immigrant reproductive behavior in the outcome of population augmentations. Anim Conserv 2019. [DOI: 10.1111/acv.12486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- E. L. Mensch
- Department of Biology Colorado State University Fort Collins CO USA
| | - J. A. Kronenberger
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - E. D. Broder
- Department of Biology Colorado State University Fort Collins CO USA
- Biology Department St. Ambrose University Davenport IA USA
| | - S. W. Fitzpatrick
- W.K. Kellogg Biological Station Department of Integrative Biology Michigan State University Hickory Corners MI USA
| | - W. C. Funk
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| | - L. M. Angeloni
- Department of Biology Colorado State University Fort Collins CO USA
- Graduate Degree Program in Ecology Colorado State University Fort Collins CO USA
| |
Collapse
|
250
|
Lichtenauer W, van de Pol M, Cockburn A, Brouwer L. Indirect fitness benefits through extra-pair mating are large for an inbred minority, but cannot explain widespread infidelity among red-winged fairy-wrens. Evolution 2019; 73:467-480. [PMID: 30666623 PMCID: PMC7172280 DOI: 10.1111/evo.13684] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 12/30/2018] [Accepted: 01/03/2019] [Indexed: 11/30/2022]
Abstract
Extra‐pair paternity (EPP) has been suggested to improve the genetic quality of offspring, but evidence has been equivocal. Benefits of EPP may be only available to specific individuals or under certain conditions. Red‐winged fairy‐wrens have extremely high levels of EPP, suggesting fitness benefits might be large and available to most individuals. Furthermore, extreme philopatry commonly leads to incestuous social pairings, so inbreeding avoidance may be an important selection pressure. Here, we quantified the fitness benefits of EPP under varying conditions and across life‐stages. Extra‐pair offspring (EPO) did not appear to have higher fitness than within‐pair offspring (WPO), neither in poor years nor in the absence of helpers‐at‐the‐nest. However, EPP was beneficial for closely related social pairs, because inbred WPO suffered an overall 75% reduction in fitness. Inbreeding depression was nonlinear and reduced nestling body condition, first year survival and reproductive success. Our comprehensive study indicates that EPP should be favored for the 17% of females paired incestuously, but cannot explain the widespread infidelity in this species. Furthermore, our finding that fitness benefits of EPP only become apparent for a small part of the population could potentially explain the apparent absence of fitness differences in population wide comparisons of EPO and WPO.
Collapse
Affiliation(s)
- Wendy Lichtenauer
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Martijn van de Pol
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Andrew Cockburn
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Lyanne Brouwer
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands.,Department of Animal Ecology and Physiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| |
Collapse
|