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Morland F, Ewen JG, Santure AW, Brekke P, Hemmings N. Demographic drivers of reproductive failure in a threatened bird: Insights from a decade of data. Proc Natl Acad Sci U S A 2024; 121:e2319104121. [PMID: 39186647 PMCID: PMC11388365 DOI: 10.1073/pnas.2319104121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 07/10/2024] [Indexed: 08/28/2024] Open
Abstract
Hatching failure affects up to 77% of eggs laid by threatened bird species, yet the true prevalence and drivers of egg fertilization failure versus embryo mortality as underlying mechanisms of hatching failure are unknown. Here, using ten years of data comprising 4,371 eggs laid by a population of a threatened bird, the hihi (Notiomystis cincta), we investigate the relative importance of infertility and embryo death as drivers of hatching failure and explore population-level factors associated with them. We show that of the 1,438 eggs that failed to hatch (33% of laid eggs) between 2010 and 2020, 83% failed due to embryo mortality, with the majority failing in the early stages of embryonic development. In the most comprehensive estimates of infertility rates in a wild bird population to date, we find that fertilization failure accounts for around 17% of hatching failure overall and is more prevalent in years where the population is smaller and more male biased. Male embryos are more likely to die during early development than females, but we find no overall effect of sex on the successful development of embryos. Offspring fathered by within-pair males have significantly higher inbreeding levels than extra-pair offspring; however, we find no effect of inbreeding nor extra-pair paternity on embryo mortality. Accurately distinguishing between infertility and embryo mortality in this study provides unique insight into the underlying causes of reproductive failure over a long-term scale and reveals the complex risks of small population sizes to the reproduction of threatened species.
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Affiliation(s)
- Fay Morland
- Department of Biosciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
- Institute of Zoology, Zoological Society of London, London NW8 7LS, United Kingdom
- Department of Anatomy, University of Otago, Dunedin 9016, New Zealand
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, London NW8 7LS, United Kingdom
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, London NW8 7LS, United Kingdom
| | - Nicola Hemmings
- Department of Biosciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
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2
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Zimmerman SJ, Aldridge CL, Schroeder MA, Fike JA, Cornman RS, Oyler-McCance SJ. The potential influence of genome-wide adaptive divergence on conservation translocation outcome in an isolated greater sage-grouse population. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2024; 38:e14254. [PMID: 38563102 DOI: 10.1111/cobi.14254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 12/20/2023] [Accepted: 01/20/2024] [Indexed: 04/04/2024]
Abstract
Conservation translocations are an important conservation tool commonly employed to augment declining or reestablish extirpated populations. One goal of augmentation is to increase genetic diversity and reduce the risk of inbreeding depression (i.e., genetic rescue). However, introducing individuals from significantly diverged populations risks disrupting coadapted traits and reducing local fitness (i.e., outbreeding depression). Genetic data are increasingly more accessible for wildlife species and can provide unique insight regarding the presence and retention of introduced genetic variation from augmentation as an indicator of effectiveness and adaptive similarity as an indicator of source and recipient population suitability. We used 2 genetic data sets to evaluate augmentation of isolated populations of greater sage-grouse (Centrocercus urophasianus) in the northwestern region of the species range (Washington, USA) and to retrospectively evaluate adaptive divergence among source and recipient populations. We developed 2 statistical models for microsatellite data to evaluate augmentation outcomes. We used one model to predict genetic diversity after augmentation and compared these predictions with observations of genetic change. We used the second model to quantify the amount of observed reproduction attributed to transplants (proof of population integration). We also characterized genome-wide adaptive divergence among source and recipient populations. Observed genetic diversity (HO = 0.65) was higher in the recipient population than predicted had no augmentation occurred (HO = 0.58) but less than what was predicted by our model (HO = 0.75). The amount of shared genetic variation between the 2 geographically isolated resident populations increased, which is evidence of periodic gene flow previously assumed to be rare. Among candidate adaptive genes associated with elevated fixation index (FST) (143 genes) or local environmental variables (97 and 157 genes for each genotype-environment association method, respectively), we found clusters of genes with related functions that may influence the ability of transplants to use local resources and navigate unfamiliar environments and their reproductive potential, all possible reasons for low genetic retention from augmentation.
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Affiliation(s)
- Shawna J Zimmerman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | - Cameron L Aldridge
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | | | - Jennifer A Fike
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | - Robert Scott Cornman
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
| | - Sara J Oyler-McCance
- Fort Collins Science Center, U.S. Geological Survey, Fort Collins, Colorado, USA
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3
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Snead AA, Tatarenkov A, Taylor DS, Marson K, Earley RL. Centrality to the metapopulation is more important for population genetic diversity than habitat area or fragmentation. Biol Lett 2024; 20:20240158. [PMID: 39044630 PMCID: PMC11267237 DOI: 10.1098/rsbl.2024.0158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/13/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024] Open
Abstract
Drift and gene flow affect genetic diversity. Given that the strength of genetic drift increases as population size decreases, management activities have focused on increasing population size through preserving habitats to preserve genetic diversity. Few studies have empirically evaluated the impacts of drift and gene flow on genetic diversity. Kryptolebias marmoratus, henceforth 'rivulus', is a small killifish restricted to fragmented New World mangrove forests with gene flow primarily associated with ocean currents. Rivulus form distinct populations across patches, making them a well-suited system to test the extent to which habitat area, fragmentation and connectivity are associated with genetic diversity. Using over 1000 individuals genotyped at 32 microsatellite loci, high-resolution landcover data and oceanographic simulations with graph theory, we demonstrate that centrality (connectivity) to the metapopulation is more strongly associated with genetic diversity than habitat area or fragmentation. By comparing models with and without centrality standardized by the source population's genetic diversity, our results suggest that metapopulation centrality is critical to genetic diversity regardless of the diversity of adjacent populations. While we find evidence that habitat area and fragmentation are related to genetic diversity, centrality is always a significant predictor with a larger effect than any measure of habitat configuration.
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Affiliation(s)
- Anthony A. Snead
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL35487, USA
- Department of Biology, New York University, New York, NY10003, USA
| | - Andrey Tatarenkov
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697, USA
| | - D. Scott Taylor
- The Environmentally Endangered Lands (EEL) Program, Brevard County, Melbourne, FL32904, USA
| | - Kristine Marson
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL35487, USA
| | - Ryan L. Earley
- Department of Biological Sciences, University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL35487, USA
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Li WJ, Chen PP, Sui LY, Sun SC. Temporal genetic variation mediated by climate change-induced salinity decline, a study on Artemia (Crustacea: Anostraca) from Kyêbxang Co, a high altitude salt lake on the Qinghai-Tibet Plateau. Gene 2024; 902:148160. [PMID: 38219874 DOI: 10.1016/j.gene.2024.148160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/11/2023] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
The Qinghai-Tibet Plateau is one of the areas the richest in salt lakes and Artemia sites. As a result of climate warming and wetting, the areas of salt lakes on the plateau have been increasing, and the salinities have decreased considerably since 1990s. However, the impact of salinity change on the genetic diversity of Artemia is still unknown. Kyêbxang Co is the highest (4620 m above sea level) salt lake currently with commercial harvesting of Artemia resting eggs in the world, and harbors the largest Artemia population on the plateau. Its salinity had dropped from ∼67 ppt in 1998 to ∼39 ppt in 2019. Using 13 microsatellite markers and the mitochondrial cytochrome oxidase submit I (COI) gene, we analyzed the temporal changes of genetic diversity, effective population size and genetic structure of this Artemia population based on samples collected in 1998, 2007 and 2019. Our results revealed a steady decline of genetic diversity and significant genetic differentiation among the sampling years, which may be a consequence of genetic drift and the selection of decreased salinity. A decline of effective population size was also detected, which may be relative to the fluctuation in census population size, skewed sex ratio, and selection of the declined salinity. In 2007 and 2019, the Artemia population showed an excess of heterozygosity and significant deviation from Hardy-Weinberg Equilibrium (p < 0.001), which may be associated with the heterozygote advantage under low salinity. To comprehensively understand the impact of climate warming and wetting on Artemia populations on the plateau, further investigation with broad and intensive sampling are needed.
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Affiliation(s)
- Wen-Jie Li
- Fisheries College, and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266000, China
| | - Pan-Pan Chen
- Fisheries College, and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266000, China
| | - Li-Ying Sui
- Asian Regional Artemia Reference Center, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Shi-Chun Sun
- Fisheries College, and Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266000, China.
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5
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Berigan LA, Aulicky CSH, Teige EC, Sullins DS, Fricke KA, Reitz JH, Rossi LG, Schultz KA, Rice MB, Tanner E, Fuhlendorf SD, Haukos DA. Lesser prairie-chicken dispersal after translocation: Implications for restoration and population connectivity. Ecol Evol 2024; 14:e10871. [PMID: 38304269 PMCID: PMC10828740 DOI: 10.1002/ece3.10871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024] Open
Abstract
Conservation translocations are frequently inhibited by extensive dispersal after release, which can expose animals to dispersal-related mortality or Allee effects due to a lack of nearby conspecifics. However, translocation-induced dispersals also provide opportunities to study how animals move across a novel landscape, and how their movements are influenced by landscape configuration and anthropogenic features. Translocation among populations is considered a potential conservation strategy for lesser prairie-chickens (Tympanuchus pallidicinctus). We determined the influence of release area on dispersal frequency by translocated lesser prairie-chickens and measured how lesser prairie-chickens move through grassland landscapes through avoidance of anthropogenic features during their dispersal movements. We translocated 411 lesser prairie-chickens from northwest Kansas to southeastern Colorado and southwestern Kansas in 2016-2019. We used satellite GPS transmitters to track 115 lesser prairie-chickens throughout their post-release dispersal movements. We found that almost all lesser prairie-chickens that survived from their spring release date until June undergo post-translocation dispersal, and there was little variation in dispersal frequency by release area (96% of all tracked birds, 100% in Baca County, Colorado, 94% in Morton County, Kansas, n = 55). Dispersal movements (male: 103 ± 73 km, female: 175 ± 108 km, n = 62) led to diffusion across landscapes, with 69% of birds settling >5 km from their release site. During dispersal movements, translocated lesser prairie-chickens usually travel by a single 3.75 ± 4.95 km dispersal flight per day, selecting for steps that end far from roads and in Conservation Reserve Program (CRP) grasslands. Due to this "stepping stone" method of transit, landscape connectivity is optimized when <5 km separates grassland patches on the landscape. Future persistence of lesser prairie-chicken populations can be aided through conservation of habitat and strategic placement of CRP to maximize habitat connectivity. Dispersal rates suggest that translocation is better suited to objectives for regional, rather than site-specific, population augmentation for this species.
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Affiliation(s)
- Liam A. Berigan
- Kansas Cooperative Fish and Wildlife Research Unit, Division of BiologyKansas State UniversityManhattanKansasUSA
| | - Carly S. H. Aulicky
- Kansas Cooperative Fish and Wildlife Research Unit, Division of BiologyKansas State UniversityManhattanKansasUSA
- Present address:
Native Prairies Association of TexasSan MarcosTexasUSA
| | - Elisabeth C. Teige
- Kansas Cooperative Fish and Wildlife Research Unit, Division of BiologyKansas State UniversityManhattanKansasUSA
| | - Daniel S. Sullins
- Kansas Cooperative Fish and Wildlife Research Unit, Division of BiologyKansas State UniversityManhattanKansasUSA
- Present address:
Department of Horticulture and Natural ResourcesKansas State UniversityManhattanKansasUSA
| | | | | | - Liza G. Rossi
- Colorado Parks and WildlifeSteamboat SpringsColoradoUSA
| | | | - Mindy B. Rice
- U.S. Fish and Wildlife Service, National Wildlife Refuge SystemFort CollinsColoradoUSA
| | - Evan Tanner
- Department of Rangeland and Wildlife Sciences, Caesar Kleberg Wildlife Research InstituteTexas A&M UniversityKingsvilleTexasUSA
| | - Samuel D. Fuhlendorf
- Natural Resource Ecology & ManagementOklahoma State UniversityStillwaterOklahomaUSA
| | - David A. Haukos
- U.S. Geological Survey, Kansas Cooperative Fish and Wildlife Research UnitKansas State UniversityManhattanKansasUSA
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6
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Mussmann SM, Wilson WD. Development of eighteen novel microsatellite loci for Masked Bobwhite, Colinus virginianus ridgwayi. Mol Biol Rep 2024; 51:210. [PMID: 38270754 DOI: 10.1007/s11033-023-09094-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 11/30/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND Masked Bobwhite (Colinus virginianus ridgwayi) is a critically-endangered New World quail species endemic to Sonoran Desert grasslands of North America. It suffered severe population declines during the nineteenth and twentieth centuries, with its persistence now reliant upon a captive breeding program that requires careful genetic management to maintain extant genetic diversity. Although nuclear microsatellite DNA markers existed for the closely related Northern Bobwhite (C. virginianus), none were available for Masked Bobwhite to inform necessary management decisions. METHODS AND RESULTS Paired-end Illumina© sequencing was conducted to screen the Masked Bobwhite genome for microsatellite loci. We identified 18 loci exhibiting high polymorphism and limited deviations from genetic equilibrium expectations. These loci were amplified in 78 individuals. Familial relationships were reconstructed via sibship methods and compared to manually-curated pedigree data. Thirteen of fifteen full-sibling groups in the pedigree were exactly reconstructed (86.6%). Three other full-sibling groups partially matched pedigree relationships with high statistical confidence, and likely represented pedigree inaccuracies. Four additional full-sibling pairs were identified with low statistical confidence and likely resulted from analytical artifacts. CONCLUSIONS The novel microsatellite loci accurately reconstructed parent-offspring and sibling relationships. These loci will be useful for guiding genetic management decisions and identifying pedigree inaccuracies in the captive breeding program.
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Affiliation(s)
- Steven M Mussmann
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish and Wildlife Service, 7116 Hatchery Rd., Dexter, NM, 88230, USA.
- Abernathy Fish Technology Center, U.S. Fish and Wildlife Service, 1440 Abernathy Creek Rd., Longview, WA, 98632, USA.
| | - Wade D Wilson
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish and Wildlife Service, 7116 Hatchery Rd., Dexter, NM, 88230, USA
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Benham PM, Walsh J, Bowie RCK. Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird. GLOBAL CHANGE BIOLOGY 2024; 30:e17126. [PMID: 38273486 DOI: 10.1111/gcb.17126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 11/22/2023] [Accepted: 12/13/2023] [Indexed: 01/27/2024]
Abstract
Combating the current biodiversity crisis requires the accurate documentation of population responses to human-induced ecological change. However, our ability to pinpoint population responses to human activities is often limited to the analysis of populations studied well after the fact. Museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure prior to the onset of human perturbation. Here, we leverage a spatially replicated time series of specimens to document population genomic responses to the destruction of nearly 90% of coastal habitats occupied by the Savannah sparrow (Passerculus sandwichensis) in California. We sequenced 219 sparrows collected from 1889 to 2017 across the state of California using an exome capture approach. Spatial-temporal analyses of genetic diversity found that the amount of habitat lost was not predictive of genetic diversity loss. Sparrow populations from southern California historically exhibited lower levels of genetic diversity and experienced the most significant temporal declines in genetic diversity. Despite experiencing the greatest levels of habitat loss, we found that genetic diversity in the San Francisco Bay area remained relatively high. This was potentially related to an observed increase in gene flow into the Bay Area from other populations. While gene flow may have minimized genetic diversity declines, we also found that immigration from inland freshwater-adapted populations into tidal marsh populations led to the erosion of divergence at loci associated with tidal marsh adaptation. Shifting patterns of gene flow through time in response to habitat loss may thus contribute to negative fitness consequences and outbreeding depression. Together, our results underscore the importance of tracing the genomic trajectories of multiple populations over time to address issues of fundamental conservation concern.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, California, USA
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, USA
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Johnson JA, Novak B, Athrey G, Sharo AG, Chase T, Toepfer J. Phylogenomics of the extinct Heath Hen provides support for sex-biased introgression among extant prairie grouse. Mol Phylogenet Evol 2023; 189:107927. [PMID: 37714443 DOI: 10.1016/j.ympev.2023.107927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/20/2023] [Accepted: 09/12/2023] [Indexed: 09/17/2023]
Abstract
Rapid divergence and subsequent reoccurring patterns of gene flow can complicate our ability to discern phylogenetic relationships among closely related species. To what degree such patterns may differ across the genome can provide an opportunity to extrapolate better how life history constraints may influence species boundaries. By exploring differences between autosomal and Z (or X) chromosomal-derived phylogenetic patterns, we can better identify factors that may limit introgression despite patterns of incomplete lineage sorting among closely related taxa. Here, using a whole-genome resequencing approach coupled with an exhaustive sampling of subspecies within the recently divergent prairie grouse complex (genus: Tympanuchus), including the extinct Heath Hen (T. cupido cupido), we show that their phylogenomic history differs depending on autosomal or Z-chromosome partitioned SNPs. Because the Heath Hen was allopatric relative to the other prairie grouse taxa, its phylogenetic signature should not be influenced by gene flow. In contrast, all the other extant prairie grouse taxa, except Attwater's Prairie-chicken (T. c. attwateri), possess overlapping contemporary geographic distributions and have been known to hybridize. After excluding samples that were likely translocated prairie grouse from the Midwest to the eastern coastal states or their resulting hybrids with mainland Heath Hens, species tree analyses based on autosomal SNPs consistently identified a paraphyletic relationship with regard to the Heath Hen with Lesser Prairie-chicken (T. pallidicinctus) sister to Greater Prairie-chicken (T. c. pinnatus) regardless of genic or intergenic partitions. In contrast, species trees based on the Z-chromosome were consistent with Heath Hen sister to a clade that included its conspecifics, Greater and Attwater's Prairie-chickens (T. c. attwateri). These results were further explained by historic gene flow, as shown with an excess of autosomal SNPs shared between Lesser and Greater Prairie-chickens but not with the Z-chromosome. Phylogenetic placement of Sharp-tailed Grouse (T. phasianellus), however, did not differ among analyses and was sister to a clade that included all other prairie grouse despite low levels of autosomal gene flow with Greater Prairie-chicken. These results, along with strong sexual selection (i.e., male hybrid behavioral isolation) and a lek breeding system (i.e., high variance in male mating success), are consistent with a pattern of female-biased introgression between prairie grouse taxa with overlapping geographic distributions. Additional study is warranted to explore how genomic components associated with the Z-chromosome influence the phenotype and thereby impact species limits among prairie grouse taxa despite ongoing contemporary gene flow.
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Affiliation(s)
- Jeff A Johnson
- The Peregrine Fund, Boise, ID 83709, USA; Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA.
| | - Ben Novak
- Revive & Restore, Sausalito, CA 94965, USA
| | - Giridhar Athrey
- Department of Poultry Science & Faculty of Ecology and Evolutionary Biology, Texas A&M University, College Station, TX 77843, USA
| | - Andrew G Sharo
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tom Chase
- Village and Wilderness, Martha's Vineyard, MA 02557, USA
| | - John Toepfer
- George Miksch Sutton Avian Research Center, Bartlesville, OK 74005, USA
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Maroso F, Padovani G, Muñoz Mora VH, Giannelli F, Trucchi E, Bertorelle G. Fitness consequences and ancestry loss in the Apennine brown bear after a simulated genetic rescue intervention. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2023; 37:e14133. [PMID: 37259604 DOI: 10.1111/cobi.14133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 03/14/2023] [Accepted: 03/22/2023] [Indexed: 06/02/2023]
Abstract
Reduction in population size, with its predicted effects on population fitness, is the most alarming anthropogenic impact on endangered species. By introducing compatible individuals, genetic rescue (GR) is a promising but debated approach for reducing the genetic load unmasked by inbreeding and for restoring the fitness of declining populations. Although GR can improve genetic diversity and fitness, it can also produce loss of ancestry, hampering local adaptation, or replace with introduced variants the unique genetic pools evolved in endemic groups. We used forward genetic simulations based on empirical genomic data to assess fitness benefits and loss of ancestry risks of GR in the Apennine brown bear (Ursus arctos marsicanus). There are approximately 50 individuals of this isolated subspecies, and they have lower genetic diversity and higher inbreeding than other European brown bears, and GR has been suggested to reduce extinction risks. We compared 10 GR scenarios in which the number and genetic characteristics of migrants varied with a non-GR scenario of simple demographic increase due to nongenetic factors. The introduction of 5 individuals of higher fitness or lower levels of deleterious mutations than the target Apennine brown bear from a larger European brown bear population produced a rapid 10-20% increase in fitness in the subspecies and up to 22.4% loss of ancestry over 30 generations. Without a contemporary demographic increase, fitness started to decline again after a few generations. Doubling the population size without GR gradually increased fitness to a comparable level, but without losing ancestry, thus resulting in the best strategy for the Apennine brown bear conservation. Our results highlight the importance for management of endangered species of realistic forward simulations grounded in empirical whole-genome data.
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Affiliation(s)
- Francesco Maroso
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- Department of Biology, University of Padova, Padova, Italy
| | - Giada Padovani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | | | - Francesco Giannelli
- Department of Life and Environmental Science, Marche Polytechnic University, Ancona, Italy
| | - Emiliano Trucchi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- Department of Life and Environmental Science, Marche Polytechnic University, Ancona, Italy
| | - Giorgio Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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10
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Bossu CM, Rodriguez M, Rayne C, Chromczak DA, Higgins PG, Trulio LA, Ruegg KC. Genomic approaches to mitigating genetic diversity loss in declining populations. Mol Ecol 2023; 32:5228-5240. [PMID: 37610278 DOI: 10.1111/mec.17109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/17/2023] [Accepted: 08/04/2023] [Indexed: 08/24/2023]
Abstract
The accelerating pace of global biodiversity loss is exacerbated by habitat fragmentation and subsequent inbreeding in small populations. To address this problem, conservation practitioners often turn to assisted breeding programmes with the aim of enhancing genetic diversity in declining populations. Although genomic information is infrequently included in these efforts, it has the potential to significantly enhance the success of such programmes. In this study, we showcase the value of genomic approaches for increasing genetic diversity in assisted breeding efforts, specifically focusing on a highly inbred population of Western burrowing owls. To maximize genetic diversity in the resulting offspring, we begin by creating an optimal pairing decision tree based on sex, kinship and patterns of homozygosity across the genome. To evaluate the effectiveness of our strategy, we compare genetic diversity, brood size and nestling success rates between optimized and non-optimized pairs. Additionally, we leverage recently discovered correlations between telomere length and fitness across species to investigate whether genomic optimization could have long-term fitness benefits. Our results indicate that pairing individuals with contrasting patterns of homozygosity across the genome is an effective way to increase genetic diversity in offspring. Although short-term field-based metrics of success did not differ significantly between optimized and non-optimized pairs, offspring from optimized pairs had significantly longer telomeres, suggesting that genetic optimization can help reduce the risk of inbreeding depression. These findings underscore the importance of genomic tools for informing efforts to preserve the adaptive potential of small, inbred populations at risk of further decline.
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Affiliation(s)
- Christen M Bossu
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Marina Rodriguez
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Christine Rayne
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
| | - Debra A Chromczak
- Burrowing Owl Researcher & Consultant, Riegelsville, Pennsylvania, USA
| | | | - Lynne A Trulio
- Department of Environmental Studies, San José State University, San Jose, California, USA
| | - Kristen C Ruegg
- Department of Biology, Colorado State University, Colorado, Fort Collins, USA
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11
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Shi L, Yang X, Cha M, Lyu T, Wang L, Zhou S, Dong Y, Dou H, Zhang H. Genetic diversity and structure of mongolian gazelle (Procapra gutturosa) populations in fragmented habitats. BMC Genomics 2023; 24:507. [PMID: 37648967 PMCID: PMC10469424 DOI: 10.1186/s12864-023-09574-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND The Mongolian gazelle (Procapra gutturosa) population has shown a considerable range of contractions and local extinctions over the last century, owing to habitat fragmentation and poaching. A thorough understanding of the genetic diversity and structure of Mongolian gazelle populations in fragmented habitats is critical for planning effective conservation strategies. RESULT In this study, we used eight microsatellite loci and mitochondrial cytochrome b (Cytb) to compare the levels of genetic diversity and genetic structure of Mongolian gazelle populations in the Hulun Lake National Nature Reserve (HLH) with those in the China-Mongolia border area (BJ). The results showed that the nucleotide diversity and observed heterozygosity of the HLH population were lower than those of the BJ population. Moreover, the HLH and BJ populations showed genetic differentiation. We concluded that the HLH population had lower genetic diversity and a distinct genetic structure compared with the BJ population. CONCLUSION The genetic diversity of fragmented Mongolian gazelle populations, can be improved by protecting these populations while reinforcing their gene exchange with other populations. For example, attempts can be made to introduce new individuals with higher genetic diversity from other populations to reduce inbreeding.
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Affiliation(s)
- Lupeng Shi
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Xiufeng Yang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Muha Cha
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Tianshu Lyu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Lidong Wang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Shengyang Zhou
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Yuehuan Dong
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China
| | - Huashan Dou
- Hulunbuir Academy of Inland Lakes in Northern Cold & Arid Areas, Hulunbuir, China
| | - Honghai Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong Province, China.
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12
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Lindsay-McGee V, Sanchez-Molano E, Banos G, Clark EL, Piercy RJ, Psifidi A. Genetic characterisation of the Connemara pony and the Warmblood horse using a within-breed clustering approach. Genet Sel Evol 2023; 55:60. [PMID: 37592264 PMCID: PMC10436415 DOI: 10.1186/s12711-023-00827-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/07/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND The Connemara pony (CP) is an Irish breed that has experienced varied selection by breeders over the last fifty years, with objectives ranging from the traditional hardy pony to an agile athlete. We compared these ponies with well-studied Warmblood (WB) horses, which are also selectively bred for athletic performance but with a much larger census population. Using genome-wide single nucleotide polymorphism (SNP) and whole-genome sequencing data from 116 WB (94 UK WB and 22 European WB) and 36 CP (33 UK CP and 3 US CP), we studied the genomic diversity, inbreeding and population structure of these breeds. RESULTS The k-means clustering approach divided both the CP and WB populations into four genetic groups, among which the CP genetic group 1 (C1) associated with non-registered CP, C4 with US CP, WB genetic group 1 (W1) with Holsteiners, and W3 with Anglo European and British WB. Maximum and mean linkage disequilibrium (LD) varied significantly between the two breeds (mean from 0.077 to 0.130 for CP and from 0.016 to 0.370 for WB), but the rate of LD decay was generally slower in CP than WB. The LD block size distribution peaked at 225 kb for all genetic groups, with most of the LD blocks not exceeding 1 Mb. The top 0.5% harmonic mean pairwise fixation index (FST) values identified ontology terms related to cancer risk when the four CP genetic groups were compared. The four CP genetic groups were less inbred than the WB genetic groups, but C2, C3 and C4 had a lower proportion of shorter runs of homozygosity (ROH) (74 to 76% < 4 Mb) than the four WB genetic groups (80 to 85% < 4 Mb), indicating more recent inbreeding. The CP and WB genetic groups had a similar ratio of effective number of breeders (Neb) to effective population size (Ne). CONCLUSIONS Distinct genetic groups of individuals were revealed within each breed, and in WB these genetic groups reflected population substructure better than studbook or country of origin. Ontology terms associated with immune and inflammatory responses were identified from the signatures of selection between CP genetic groups, and while CP were less inbred than WB, the evidence pointed to a greater degree of recent inbreeding. The ratio of Neb to Ne was similar in CP and WB, indicating the influence of popular sires is similar in CP and WB.
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Affiliation(s)
- Victoria Lindsay-McGee
- Royal Veterinary College, London, UK
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | | | | | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Edinburgh, UK
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13
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Fitzpatrick SW, Mittan-Moreau C, Miller M, Judson JM. Genetic rescue remains underused for aiding recovery of federally listed vertebrates in the United States. J Hered 2023; 114:354-366. [PMID: 36975379 PMCID: PMC10287150 DOI: 10.1093/jhered/esad002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Restoring gene flow among fragmented populations is discussed as a potentially powerful management strategy that could reduce inbreeding depression and cause genetic rescue. Yet, examples of assisted migration for genetic rescue remain sparse in conservation, prompting several outspoken calls for its increased use in genetic management of fragmented populations. We set out to evaluate the extent to which this strategy is underused and to determine how many imperiled species would realistically stand to benefit from genetic rescue, focusing on federally threatened or endangered vertebrate species in the United States. We developed a "genetic rescue suitability index (GR index)" based on concerns about small population problems relative to risks associated with outbreeding depression and surveyed the literature for 222 species. We found that two-thirds of these species were good candidates for consideration of assisted migration for the purpose of genetic rescue according to our suitability index. Good candidate species spanned all taxonomic groups and geographic regions, though species with more missing data tended to score lower on the suitability index. While we do not recommend a prescriptive interpretation of our GR index, we used it here to establish that assisted migration for genetic rescue is an underused strategy. For example, we found in total, "genetic rescue" was only mentioned in 11 recovery plans and has only been implemented in 3 of the species we surveyed. A potential way forward for implementation of this strategy is incorporating genetic rescue as a priority in USFWS recovery documentation. In general, our results suggest that although not appropriate for all imperiled species, many more species stand to benefit from a conservation strategy of assisted migration for genetic rescue than those for which it has previously been considered or implemented.
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Affiliation(s)
- Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Department of Integrative Biology, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Cinnamon Mittan-Moreau
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Madison Miller
- Savannah River Ecology Lab, University of Georgia, Aiken, SC, United States
- Division of Forestry and Natural Resources, West Virginia University, Morgantown, WV, United States
| | - Jessica M Judson
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI, United States
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, United States
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14
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Everson KM, Donohue ME, Weisrock DW. A Pervasive History of Gene Flow in Madagascar's True Lemurs (Genus Eulemur). Genes (Basel) 2023; 14:1130. [PMID: 37372308 DOI: 10.3390/genes14061130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
In recent years, it has become widely accepted that interspecific gene flow is common across the Tree of Life. Questions remain about how species boundaries can be maintained in the face of high levels of gene flow and how phylogeneticists should account for reticulation in their analyses. The true lemurs of Madagascar (genus Eulemur, 12 species) provide a unique opportunity to explore these questions, as they form a recent radiation with at least five active hybrid zones. Here, we present new analyses of a mitochondrial dataset with hundreds of individuals in the genus Eulemur, as well as a nuclear dataset containing hundreds of genetic loci for a small number of individuals. Traditional coalescent-based phylogenetic analyses of both datasets reveal that not all recognized species are monophyletic. Using network-based approaches, we also find that a species tree containing between one and three ancient reticulations is supported by strong evidence. Together, these results suggest that hybridization has been a prominent feature of the genus Eulemur in both the past and present. We also recommend that greater taxonomic attention should be paid to this group so that geographic boundaries and conservation priorities can be better established.
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Affiliation(s)
- Kathryn M Everson
- Department of Integrative Biology, Oregon State University, Corvallis, OR 97331, USA
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - Mariah E Donohue
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY 40506, USA
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15
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Alves F, Banks SC, Edworthy M, Stojanovic D, Langmore NE, Heinsohn R. Using conservation genetics to prioritise management options for an endangered songbird. Heredity (Edinb) 2023; 130:289-301. [PMID: 37016134 PMCID: PMC10162965 DOI: 10.1038/s41437-023-00609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
Genetic data can be highly informative for answering questions relevant to practical conservation efforts, but remain one of the most neglected aspects of species recovery plans. Framing genetic questions with reference to practical and tractable conservation objectives can help bypass this limitation of the application of genetics in conservation. Using a single-nucleotide polymorphism dataset from reduced-representation sequencing (DArTSeq), we conducted a genetic assessment of remnant populations of the endangered forty-spotted pardalote (Pardalotus quadragintus), a songbird endemic to Tasmania, Australia. Our objectives were to inform strategies for the conservation of genetic diversity in the species and estimate effective population sizes and patterns of inter-population movement to identify management units relevant to population conservation and habitat restoration. We show population genetic structure and identify two small populations on mainland Tasmania as 'satellites' of larger Bruny Island populations connected by migration. Our data identify management units for conservation objectives relating to genetic diversity and habitat restoration. Although our results do not indicate the immediate need to genetically manage populations, the small effective population sizes we estimated for some populations indicate that they are vulnerable to genetic drift, highlighting the urgent need to implement habitat restoration to increase population size and to conduct genetic monitoring. We discuss how our genetic assessment can be used to inform management interventions for the forty-spotted pardalote and show that by assessing contemporary genetic aspects, valuable information for conservation planning and decision-making can be produced to guide actions that account for genetic diversity and increase chances of recovery in species of conservation concern.
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Affiliation(s)
- Fernanda Alves
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia.
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia.
| | - Sam C Banks
- Research Institute for the Environment and Livelihoods, College of Engineering, IT and the Environment, Charles Darwin University, Darwin, NT, Australia
| | - Max Edworthy
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Dejan Stojanovic
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
| | - Naomi E Langmore
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Robert Heinsohn
- Fenner School of Environment and Society, Australian National University, Canberra, ACT, Australia
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16
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Eronen A, Hyvärinen P, Janhunen M, Kekäläinen J, Kortet R. Postrelease exploration and stress tolerance of landlocked and anadromous Atlantic salmon and their hybrids. CONSERVATION SCIENCE AND PRACTICE 2023. [DOI: 10.1111/csp2.12893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Aslak Eronen
- Department of Environmental and Biological Sciences University of Eastern Finland Joensuu Finland
| | - Pekka Hyvärinen
- Natural Resources Institute Finland (LUKE) Natural Resources, Migratory Fish and Regulated Rivers Joensuu Finland
| | - Matti Janhunen
- Natural Resources Institute Finland (LUKE) Natural Resources, Migratory Fish and Regulated Rivers Paltamo Finland
| | - Jukka Kekäläinen
- Department of Environmental and Biological Sciences University of Eastern Finland Joensuu Finland
| | - Raine Kortet
- Department of Environmental and Biological Sciences University of Eastern Finland Joensuu Finland
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17
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Pregler KC, Obedzinski M, Gilbert‐Horvath EA, White B, Carlson SM, Garza JC. Assisted gene flow from outcrossing shows the potential for genetic rescue in an endangered salmon population. Conserv Lett 2022. [DOI: 10.1111/conl.12934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Kasey C. Pregler
- Department of Environmental Science, Policy, and Management University of California, Berkeley Berkeley California USA
| | - Mariska Obedzinski
- Department of Environmental Science, Policy, and Management University of California, Berkeley Berkeley California USA
- California Sea Grant Windsor California USA
| | - Elizabeth A. Gilbert‐Horvath
- Southwest Fisheries Science Center National Marine Fisheries Service and University of California, Santa Cruz Santa Cruz California USA
| | - Benjamin White
- U.S. Army Corps of Engineers, Don Clausen/Warm Springs Hatchery Geyserville California USA
| | - Stephanie M. Carlson
- Department of Environmental Science, Policy, and Management University of California, Berkeley Berkeley California USA
| | - John Carlos Garza
- Southwest Fisheries Science Center National Marine Fisheries Service and University of California, Santa Cruz Santa Cruz California USA
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18
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Fameli AF, Edson J, Banfield JE, Rosenberry CS, Walter WD. Variability in prion protein genotypes by spatial unit to inform susceptibility to chronic wasting disease. Prion 2022; 16:254-264. [PMID: 36104983 PMCID: PMC9481152 DOI: 10.1080/19336896.2022.2117535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Chronic wasting disease (CWD) is a fatal encephalopathy affecting North American cervids. Certain alleles in a host's prion protein gene are responsible for reduced susceptibility to CWD. We assessed for the first time variability in the prion protein gene of elk (Cervus canadensis) present in Pennsylvania, United States of America, a reintroduced population for which CWD cases have never been reported. We sequenced the prion protein gene (PRNP) of 565 elk samples collected over 7 years (2014-2020) and found two polymorphic sites (codon 21 and codon 132). The allele associated with reduced susceptibility to CWD is present in the population, and there was no evidence of deviations from Hardy-Weinberg equilibrium in any of our sampling years (p-values between 0.14 and 1), consistent with the lack of selective pressure on the PRNP. The less susceptible genotypes were found in a frequency similar to the ones reported for elk populations in the states of Wyoming and South Dakota before CWD was detected. We calculated the proportion of less susceptible genotypes in each hunt zone in Pennsylvania as a proxy for their vulnerability to the establishment of CWD, and interpolated these results to obtain a surface representing expected proportion of the less susceptible genotypes across the area. Based on this analysis, hunt zones located in the southern part of our study area have a low proportion of less susceptible genotypes, which is discouraging for elk persistence in Pennsylvania given that these hunt zones are adjacent to the deer Disease Management Area 3, where CWD has been present since 2014.
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Affiliation(s)
- Alberto F. Fameli
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, University Park, PA, USA,CONTACT Alberto F. Fameli Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, University Park, PA16802, USA
| | - Jessie Edson
- Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, University Park, PA, USA
| | - Jeremiah E. Banfield
- Pennsylvania Game Commission, Bureau of Wildlife Management, 2001 Elmerton Avenue,Harrisburg, PA, USA
| | - Christopher S. Rosenberry
- Pennsylvania Game Commission, Bureau of Wildlife Management, 2001 Elmerton Avenue,Harrisburg, PA, USA
| | - W. David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, 403 Forest Resources Building, The Pennsylvania State University, University Park, PA, USA
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19
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Turghan MA, Jiang Z, Niu Z. An Update on Status and Conservation of the Przewalski's Horse ( Equus ferus przewalskii): Captive Breeding and Reintroduction Projects. Animals (Basel) 2022; 12:ani12223158. [PMID: 36428386 PMCID: PMC9686875 DOI: 10.3390/ani12223158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/06/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
This review summarizes studies on Przewalski's horse since its extinction in the wild in the 1960s, with a focus on the reintroduction projects in Mongolia and China, with current population status. Historical and present distribution, population trends, ecology and habitats, genetics, behaviors, conservation measures, actual and potential threats are also reviewed. Captive breeding and reintroduction projects have already been implemented, but many others are still under considerations. The review may help to understand the complexity of problem and show the directions for effective practice in the future.
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Affiliation(s)
- Mardan Aghabey Turghan
- State Key Laboratory of Oasis and Desert Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Graduate School, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (M.A.T.); (Z.J.)
| | - Zhigang Jiang
- Graduate School, University of Chinese Academy of Sciences, Beijing 100049, China
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (M.A.T.); (Z.J.)
| | - Zhongze Niu
- College of Biology and Geography Sciences, Yili Normal University, Yining 835000, China
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20
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Carley LN, Morris WF, Walsh R, Riebe D, Mitchell‐Olds T. Are genetic variation and demographic performance linked? Evol Appl 2022; 15:1888-1906. [PMID: 36426131 PMCID: PMC9679243 DOI: 10.1111/eva.13487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 09/12/2022] [Indexed: 12/13/2022] Open
Abstract
Quantifying relationships between genetic variation and population viability is important from both basic biological and applied conservation perspectives, yet few populations have been monitored with both long-term demographic and population genetics approaches. To empirically test whether and how genetic variation and population dynamics are related, we present one such paired approach. First, we use eight years of historical demographic data from five populations of Boechera fecunda (Brassicaceae), a rare, self-compatible perennial plant endemic to Montana, USA, and use integral projection models to estimate the stochastic population growth rate (λ S) and extinction risk of each population. We then combine these demographic estimates with previously published metrics of genetic variation in the same populations to test whether genetic diversity within populations is linked to demographic performance. Our results show that in this predominantly inbred species, standing genetic variation and demography are weakly positively correlated. However, the inbreeding coefficient was not strongly correlated with demographic performance, suggesting that more inbred populations are not necessarily less viable or at higher extinction risk than less inbred populations. A contemporary re-census of these populations revealed that neither genetic nor demographic parameters were consistently strong predictors of current population density, although populations showing lower probabilities of extinction in demographic models had larger population sizes at present. In the absence of evidence for inbreeding depression decreasing population viability in this species, we recommend conservation of distinct, potentially locally adapted populations of B. fecunda rather than alternatives such as translocations or reintroductions.
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Affiliation(s)
- Lauren N. Carley
- University Program in EcologyDuke UniversityDurhamNorth CarolinaUSA
- Biology DepartmentDuke UniversityDurhamNorth CarolinaUSA
- Department of Plant and Microbial BiologyUniversity of Minnesota Twin CitiesSt. PaulMinnesotaUSA
| | | | - Roberta Walsh
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Donna Riebe
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
| | - Tom Mitchell‐Olds
- Biology DepartmentDuke UniversityDurhamNorth CarolinaUSA
- Division of Biological SciencesUniversity of MontanaMissoulaMontanaUSA
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21
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Over 25 Years of Partnering to Conserve Chiricahua Leopard Frogs (Rana chiricahuensis) in Arizona, Combining Ex Situ and In Situ Strategies. JOURNAL OF ZOOLOGICAL AND BOTANICAL GARDENS 2022. [DOI: 10.3390/jzbg3040039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Phoenix Zoo has partnered with US Fish and Wildlife Service, Arizona Game and Fish Department, US Forest Service, and other organizations for more than 25 years to help recover Chiricahua leopard frogs (Rana [=Lithobates] chiricahuensis) in Arizona, USA. This federally threatened species faces declines due to habitat loss and degradation, long-term drought, disease, and invasive species. Over 26,000 larvae, froglets, and adults, as well as 26 egg masses produced by adults held at the Phoenix Zoo have been released to the wild, augmenting and/or re-establishing wild populations. Chiricahua leopard frog-occupied sites in Arizona have increased from 38 in 2007, when the species’ recovery plan was published, to a high of 155 in the last five years, as a result of ex situ and in situ conservation efforts. As one of the longest-running programs of its kind in the United States, communication among partners has been key to sustaining it. Recovery strategies and complex decisions are made as a team and we have worked through numerous management challenges together. Though Chiricahua leopard frogs still face significant threats and a long road to recovery, this program serves as a strong example of the positive effects of conservation partnerships for native wildlife.
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22
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Morrison RE, Hirwa JP, Ndagijimana F, Vecellio V, Eckardt W, Stoinski TS. Cascading effects of social dynamics on the reproduction, survival, and population growth of mountain gorillas. Anim Conserv 2022. [DOI: 10.1111/acv.12830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- R. E. Morrison
- Dian Fossey Gorilla Fund, Ellen DeGeneres Campus of the Dian Fossey Gorilla Fund Kinigi Rwanda
- Centre for Research in Animal Behaviour, Department of Psychology University of Exeter Exeter UK
| | - J. P. Hirwa
- Dian Fossey Gorilla Fund, Ellen DeGeneres Campus of the Dian Fossey Gorilla Fund Kinigi Rwanda
| | - F. Ndagijimana
- Dian Fossey Gorilla Fund, Ellen DeGeneres Campus of the Dian Fossey Gorilla Fund Kinigi Rwanda
| | - V. Vecellio
- Dian Fossey Gorilla Fund, Ellen DeGeneres Campus of the Dian Fossey Gorilla Fund Kinigi Rwanda
| | - W. Eckardt
- Dian Fossey Gorilla Fund, Ellen DeGeneres Campus of the Dian Fossey Gorilla Fund Kinigi Rwanda
| | - T. S. Stoinski
- Dian Fossey Gorilla Fund, Ellen DeGeneres Campus of the Dian Fossey Gorilla Fund Kinigi Rwanda
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23
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Campbell DC, Camak DT, Piller KR. Islands in the desert: assessing fine scale population genomic variation of a group of imperiled desert fishes. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01457-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Di Santo LN, Hoban S, Parchman TL, Wright JW, Hamilton JA. Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana Parry) with implications for rare species conservation. Mol Ecol 2022; 31:4622-4639. [PMID: 35822858 DOI: 10.1111/mec.16615] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
Abstract
Understanding the contribution of neutral and adaptive evolutionary processes to population differentiation is often necessary for better informed management and conservation of rare species. In this study, we focused on Pinus torreyana Parry (Torrey pine), one of the world's rarest pines, endemic to one island and one mainland population in California. Small population size, low genetic diversity, and susceptibility to abiotic and biotic stresses suggest Torrey pine may benefit from inter-population genetic rescue to preserve the species' evolutionary potential. We leveraged reduced representation sequencing to tease apart the respective contributions of stochastic and deterministic evolutionary processes to population differentiation. We applied these data to model spatial and temporal demographic changes in effective population sizes and genetic connectivity, to identify loci possibly under selection, and evaluate genetic rescue as a potential conservation strategy. Overall, we observed exceedingly low standing variation within both Torrey pine populations, reflecting consistently low effective population sizes across time, and limited genetic differentiation, suggesting maintenance of gene flow between populations following divergence. However, genome scans identified more than 2000 candidate SNPs potentially under divergent selection. Combined with previous observations indicating population phenotypic differentiation, this indicates natural selection has likely contributed to the evolution of population genetic differences. Thus, while reduced genetic diversity, small effective population size, and genetic connectivity between populations suggest genetic rescue could mitigate the adverse effects of rarity, evidence for adaptive differentiation suggests genetic mixing could disrupt adaptation. Further work evaluating the fitness consequences of inter-population admixture is necessary to empirically evaluate the trade-offs associated with genetic rescue in Torrey pine.
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Affiliation(s)
- Lionel N Di Santo
- North Dakota State University, Department of Biological Sciences, Fargo, ND, USA
| | | | | | - Jessica W Wright
- USDA- Forest Service, Pacific Southwest Research Station, Davis, CA, USA
| | - Jill A Hamilton
- North Dakota State University, Department of Biological Sciences, Fargo, ND, USA.,Pennsylvania State University, Department of Ecosystem Science and Management, University Park, PA, USA
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25
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Ju T, Han ZT, Ruhsam M, Li JL, Tao WJ, Tso S, Miehe G, Mao KS. Reproduction and genetic diversity of Juniperus squamata along an elevational gradient in the Hengduan Mountains. PLANT DIVERSITY 2022; 44:369-376. [PMID: 35967254 PMCID: PMC9363649 DOI: 10.1016/j.pld.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/06/2021] [Accepted: 12/06/2021] [Indexed: 06/15/2023]
Abstract
Elevation plays a crucial factor in the distribution of plants, as environmental conditions become increasingly harsh at higher elevations. Previous studies have mainly focused on the effects of large-scale elevational gradients on plants, with little attention on the impact of smaller-scale gradients. In this study we used 14 microsatellite loci to survey the genetic structure of 332 Juniperus squamata plants along elevation gradient from two sites in the Hengduan Mountains. We found that the genetic structure (single, clonal, mosaic) of J. squamata shrubs is affected by differences in elevational gradients of only 150 m. Shrubs in the mid-elevation plots rarely have a clonal or mosaic structure compared to shrubs in lower- or higher-elevation plots. Human activity can significantly affect genetic structure, as well as reproductive strategy and genetic diversity. Sub-populations at mid-elevations had the highest yield of seed cones, lower levels of asexual reproduction and higher levels of genetic diversity. This may be due to the trade-off between elevational stress and anthropogenic disturbance at mid-elevation since there is greater elevational stress at higher-elevations and greater intensity of anthropogenic disturbance at lower-elevations. Our findings provide new insights into the finer scale genetic structure of alpine shrubs, which may improve the conservation and management of shrublands, a major vegetation type on the Hengduan Mountains and the Qinghai-Tibet Plateau.
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Affiliation(s)
- Tsam Ju
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Zhi-Tong Han
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Jia-Liang Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Wen-Jing Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
| | - Sonam Tso
- College of Science, Tibet University, Lhasa, Tibet 850000, China
| | - Georg Miehe
- Department of Geography, Philipps-Universität Marburg, Deutschhausstraße 10, Marburg 35032, Hessen, Germany
| | - Kang-Shan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, Sichuan 610065, China
- College of Science, Tibet University, Lhasa, Tibet 850000, China
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GuibingaMickala A, Weber A, Ntie S, Gahlot P, Lehmann D, Mickala P, Abernethy K, Anthony N. Estimation of the census (Nc) and effective (Ne) population size of a wild mandrill (Mandrillus sphinx) horde in the Lopé National Park, Gabon using a non-invasive genetic approach. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01458-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Jørgensen DB, Ørsted M, Kristensen TN. Sustained positive consequences of genetic rescue of fitness and behavioural traits in inbred populations of Drosophila melanogaster. J Evol Biol 2022; 35:868-878. [PMID: 35532930 PMCID: PMC9325394 DOI: 10.1111/jeb.14015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
Abstract
One solution to alleviate the detrimental genetic effects associated with reductions in population size and fragmentation is to introduce immigrants from other populations. While the effects of this genetic rescue on fitness traits are fairly well known, it is less clear to what extent inbreeding depression and subsequent genetic rescue affect behavioural traits. In this study, replicated crosses between inbred lines of Drosophila melanogaster were performed in order to investigate the effects of inbreeding and genetic rescue on egg-to-adult viability and negative geotaxis behaviour-a locomotor response used to measure, e.g. the effects of physiological ageing. Transgenerational effects of outcrossing were investigated by examining the fitness consequences in both the F1 and F4 generation. The majority of inbred lines showed evidence for inbreeding depression for both egg-to-adult viability and behavioural performance (95% and 66% of lines, respectively), with inbreeding depression being more pronounced for viability compared with the locomotor response. Subsequent outcrossing with immigrants led to an alleviation of the negative effects for both viability and geotaxis response resulting in inbred lines being similar to the outbred controls, with beneficial effects persisting from F1 to F4 . Overall, the results clearly show that genetic rescue can provide transgenerational rescue of small, inbred populations by rapidly improving population fitness components. Thus, we show that even the negative effects of inbreeding on behaviour, similar to that of neurodegeneration associated with physiological ageing, can be reversed by genetic rescue.
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Affiliation(s)
| | - Michael Ørsted
- Department of Chemistry and Bioscience, Aalborg University, Aalborg E, Denmark.,Department of Biology, Aarhus University, Aarhus C, Denmark
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28
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Shafer CL. A greater yellowstone ecosystem grizzly bear case study: genetic reassessment for managers. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01262-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractThere are five grizzly bear (Ursus arctos horribilis) populations in the lower 48 states of the United States. My goal in this Commentary was to ascertain whether genetic diversity is being lost from the isolated GYE grizzly bear population and to better understand any viability implications. I reviewed the scientific literature, including two key genetic studies that the US Fish and Wildlife Service (USFWS) relied upon for their 2007 and current 2017 GYE grizzly bear genetics policy. I discovered that some studies reveal a loss of heterozygosity in the GYE bear population, both historically and in recent decades. Some had a statistically significant depletion rate. My review took place periodically between 2010 and 2021 and indicates that the genome of the GYE grizzly bear population is too small for long-term adaptation. The paper includes a discussion about evolutionary adaptation which invokes time frames rarely considered by nature conservation planners. I also examined genetic statements in the USFWS’s 2017 GYE grizzly bear delisting regulations and highlighted those that seem incongruent with current scientific thought. If this paper is read by some scientists, land managers, administrators, environmentalists, and others with some genetics background, they will better understand some USFWS decisions and policy statements. This case study illustrates that land management agencies can provide a one-sided treatment of some science when writing regulations about genetics.
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29
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Kardos M, Armstrong EE, Fitzpatrick SW, Hauser S, Hedrick PW, Miller JM, Tallmon DA, Funk WC. The crucial role of genome-wide genetic variation in conservation. Proc Natl Acad Sci U S A 2021; 118:e2104642118. [PMID: 34772759 PMCID: PMC8640931 DOI: 10.1073/pnas.2104642118] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2021] [Indexed: 12/30/2022] Open
Abstract
The unprecedented rate of extinction calls for efficient use of genetics to help conserve biodiversity. Several recent genomic and simulation-based studies have argued that the field of conservation biology has placed too much focus on conserving genome-wide genetic variation, and that the field should instead focus on managing the subset of functional genetic variation that is thought to affect fitness. Here, we critically evaluate the feasibility and likely benefits of this approach in conservation. We find that population genetics theory and empirical results show that conserving genome-wide genetic variation is generally the best approach to prevent inbreeding depression and loss of adaptive potential from driving populations toward extinction. Focusing conservation efforts on presumably functional genetic variation will only be feasible occasionally, often misleading, and counterproductive when prioritized over genome-wide genetic variation. Given the increasing rate of habitat loss and other environmental changes, failure to recognize the detrimental effects of lost genome-wide genetic variation on long-term population viability will only worsen the biodiversity crisis.
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Affiliation(s)
- Marty Kardos
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA 98112;
| | | | - Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060
- Department of Integrative Biology, Michigan State University, East Lansing, MI 48824
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI 48824
| | - Samantha Hauser
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211
| | - Philip W Hedrick
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Joshua M Miller
- San Diego Zoo Wildlife Alliance, Escondido, CA 92027
- Polar Bears International, Bozeman, MT 59772
- Department of Biological Sciences, MacEwan University, Edmonton, AB T5J 4S2, Canada
| | - David A Tallmon
- Biology and Marine Biology Program, University of Alaska Southeast, Juneau, AK 99801
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523
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30
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Reyne M, Dicks K, McFarlane C, Aubry A, Emmerson M, Marnell F, Reid N, Helyar S. Population genetic structure of the Natterjack toad (Epidalea calamita) in Ireland: implications for conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01421-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractMolecular methods can play a crucial role in species management and conservation. Despite the usefulness of genetic approaches, they are often not explicitly included as part of species recovery plans and conservation practises. The Natterjack toad (Epidalea calamita) is regionally Red-Listed as Endangered in Ireland. The species is declining and is now present at just seven sites within a highly restricted range. This study used 13 highly polymorphic microsatellite markers to analyse the population genetic diversity and structure. Genetic diversity was high with expected heterozygosity between 0.55 and 0.61 and allelic richness between 4.77 and 5.92. Effective population sizes were small (Ne < 100 individuals), but not abnormal for pond breeding amphibians. However, there was no evidence of historical or contemporary genetic bottlenecks or high levels of inbreeding. We identified a positive relationship between Ne and breeding pond surface area, suggesting that environmental factors are a key determinant of population size. Significant genetic structuring was detected throughout the species’ range, and we identified four genetic entities that should be considered in the species’ conservation strategies. Management should focus on preventing further population declines and future loss of genetic diversity overall and within genetic entities while maintaining adequate local effective population size through site-specific protection, human-mediated translocations and head-start programs. The apparent high levels of genetic variation give hope for the conservation of Ireland’s rarest amphibian if appropriately protected and managed.
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New developments in the field of genomic technologies and their relevance to conservation management. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01415-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractRecent technological advances in the field of genomics offer conservation managers and practitioners new tools to explore for conservation applications. Many of these tools are well developed and used by other life science fields, while others are still in development. Considering these technological possibilities, choosing the right tool(s) from the toolbox is crucial and can pose a challenging task. With this in mind, we strive to inspire, inform and illuminate managers and practitioners on how conservation efforts can benefit from the current genomic and biotechnological revolution. With inspirational case studies we show how new technologies can help resolve some of the main conservation challenges, while also informing how implementable the different technologies are. We here focus specifically on small population management, highlight the potential for genetic rescue, and discuss the opportunities in the field of gene editing to help with adaptation to changing environments. In addition, we delineate potential applications of gene drives for controlling invasive species. We illuminate that the genomic toolbox offers added benefit to conservation efforts, but also comes with limitations for the use of these novel emerging techniques.
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32
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Evaluating the genome-wide impacts of species translocations: the greater prairie-chicken as a case study. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01412-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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33
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Lehnen L, Jan PL, Besnard AL, Fourcy D, Kerth G, Biedermann M, Nyssen P, Schorcht W, Petit EJ, Puechmaille SJ. Genetic diversity in a long-lived mammal is explained by the past's demographic shadow and current connectivity. Mol Ecol 2021; 30:5048-5063. [PMID: 34402111 DOI: 10.1111/mec.16123] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 01/25/2023]
Abstract
Within-species genetic diversity is crucial for the persistence and integrity of populations and ecosystems. Conservation actions require an understanding of factors influencing genetic diversity, especially in the context of global change. Both population size and connectivity are factors greatly influencing genetic diversity; the relative importance of these factors can, however, change through time. Hence, quantifying the degree to which population size or genetic connectivity are shaping genetic diversity, and at which ecological time scale (past or present), is challenging, yet essential for the development of efficient conservation strategies. In this study, we estimated the genetic diversity of 42 colonies of Rhinolophus hipposideros, a long-lived mammal vulnerable to global change, sampling locations spanning its continental northern range. Here, we present an integrative approach that disentangles and quantifies the contribution of different connectivity measures in addition to contemporary colony size and historic bottlenecks in shaping genetic diversity. In our study, the best model explained 64% of the variation in genetic diversity. It included historic bottlenecks, contemporary colony size, connectivity and a negative interaction between the latter two. Contemporary connectivity explained most genetic diversity when considering a 65 km radius around the focal colonies, emphasizing the large geographic scale at which the positive impact of connectivity on genetic diversity is most profound and hence, the minimum scale at which conservation should be planned. Our results highlight that the relative importance of the two main factors shaping genetic diversity varies through time, emphasizing the relevance of disentangling them to ensure appropriate conservation strategies.
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Affiliation(s)
- Lisa Lehnen
- Applied Zoology and Nature Conservation, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Pierre-Loup Jan
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, France
| | | | - Damien Fourcy
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, France
| | - Gerald Kerth
- Applied Zoology and Nature Conservation, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
| | - Martin Biedermann
- Interessengemeinschaft für Fledermausschutz und -forschung in Thüringen (IFT) e.V, Bad Liebenstein, Germany
| | | | | | - Eric J Petit
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, France.,NACHTaktiv - Biologists for Bat research GbR, Erfurt, Germany
| | - Sebastien J Puechmaille
- Applied Zoology and Nature Conservation, Zoological Institute and Museum, University of Greifswald, Greifswald, Germany
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Shurba JA, Cole RA, Broadway MS, Roderick CL, Riddle JD, Dubay SA, Hull S. GAPEWORM (SYNGAMUS SPP.) PREVALENCE IN WISCONSIN GREATER PRAIRIE CHICKENS (TYMPANUCHUS CUPIDO PINNATUS). J Parasitol 2021; 107:600-605. [PMID: 34343317 DOI: 10.1645/19-138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Under Wisconsin state law, the greater prairie chicken (GRPC; Tympanuchus cupido pinnatus) has been listed as a threatened species since 1976. In 2014-15, we conducted a pilot study to determine the prevalence and intensity of gapeworms (Syngamus spp.) in female Wisconsin GRPCs collected from 2 monitored populations. We captured 62 female GRPCs using walk-in-style traps for females and night lighting for juveniles ≥45 days of age. From these individuals, we collected 15 carcasses of radio-marked birds, most of whom died due to predation events. Through dissection, we identified gapeworm in 20% of examined carcasses and report an intensity ranging between 4 and 74 worms.
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Affiliation(s)
- J A Shurba
- University of Wisconsin-Stevens Point, College of Natural Resources 800 Reserve Street, Stevens Point, Wisconsin 54481.,Department of Forestry and Environmental Conservation, Clemson University 261 Lehotsky Hall, Box 340317, Clemson, South Carolina 29634
| | - R A Cole
- U.S. Geological Survey-National Wildlife Health Center, 6006 Schroeder Road, Madison, Wisconsin 53711
| | - M S Broadway
- University of Wisconsin-Stevens Point, College of Natural Resources 800 Reserve Street, Stevens Point, Wisconsin 54481.,Indiana Department of Natural Resources Division of Fish and Wildlife, 402 W. Washington Street, Indianapolis, Indiana 46204
| | - C L Roderick
- U.S. Geological Survey-National Wildlife Health Center, 6006 Schroeder Road, Madison, Wisconsin 53711
| | - J D Riddle
- University of Wisconsin-Stevens Point, College of Natural Resources 800 Reserve Street, Stevens Point, Wisconsin 54481
| | - S A Dubay
- University of Wisconsin-Stevens Point, College of Natural Resources 800 Reserve Street, Stevens Point, Wisconsin 54481
| | - S Hull
- Wisconsin Department of Natural Resources, 101 S. Webster Street, PO Box 7921, Madison, Wisconsin 53707
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35
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LAWRENCE AJ, Carleton SA, Gould WR, Nichols CT. Lesser Prairie‐Chicken Survival in Varying Densities of Energy Development. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Andrew J. LAWRENCE
- Department of Biology New Mexico State University Las Cruces NM 88003 USA
| | - Scott A. Carleton
- Division of Migratory Birds United States Fish and Wildlife Service Albuquerque NM 87102 USA
| | - William R. Gould
- Applied Statistics Program, College of Business New Mexico State University Las Cruces NM 88003 USA
| | - Clay T. Nichols
- Ecological Services Division United States Fish and Wildlife Service Arlington TX 76006 USA
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36
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De Cahsan B, Westbury MV, Paraskevopoulou S, Drews H, Ott M, Gollmann G, Tiedemann R. Genomic consequences of human-mediated translocations in margin populations of an endangered amphibian. Evol Appl 2021; 14:1623-1634. [PMID: 34178108 PMCID: PMC8210794 DOI: 10.1111/eva.13229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/17/2021] [Accepted: 03/12/2021] [Indexed: 01/08/2023] Open
Abstract
Due to their isolated and often fragmented nature, range margin populations are especially vulnerable to rapid environmental change. To maintain genetic diversity and adaptive potential, gene flow from disjunct populations might therefore be crucial to their survival. Translocations are often proposed as a mitigation strategy to increase genetic diversity in threatened populations. However, this also includes the risk of losing locally adapted alleles through genetic swamping. Human-mediated translocations of southern lineage specimens into northern German populations of the endangered European fire-bellied toad (Bombina bombina) provide an unexpected experimental set-up to test the genetic consequences of an intraspecific introgression from central population individuals into populations at the species range margin. Here, we utilize complete mitochondrial genomes and transcriptome nuclear data to reveal the full genetic extent of this translocation and the consequences it may have for these populations. We uncover signs of introgression in four out of the five northern populations investigated, including a number of introgressed alleles ubiquitous in all recipient populations, suggesting a possible adaptive advantage. Introgressed alleles dominate at the MTCH2 locus, associated with obesity/fat tissue in humans, and the DSP locus, essential for the proper development of epidermal skin in amphibians. Furthermore, we found loci where local alleles were retained in the introgressed populations, suggesting their relevance for local adaptation. Finally, comparisons of genetic diversity between introgressed and nonintrogressed northern German populations revealed an increase in genetic diversity in all German individuals belonging to introgressed populations, supporting the idea of a beneficial transfer of genetic variation from Austria into North Germany.
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Affiliation(s)
- Binia De Cahsan
- Unit of Evolutionary Biology/Systematic ZoologyInstitute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- GLOBE InstituteUniversity of CopenhagenCopenhagenDenmark
| | | | - Sofia Paraskevopoulou
- Unit of Evolutionary Biology/Systematic ZoologyInstitute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
- Unit of ZoologyTel Aviv UniversityTel AvivIsrael
| | - Hauke Drews
- Stiftung Naturschutz Schleswig‐HolsteinMolfseeGermany
| | - Moritz Ott
- Stiftung Naturschutz Schleswig‐HolsteinMolfseeGermany
| | - Günter Gollmann
- Department of Evolutionary BiologyUniversity of ViennaViennaAustria
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic ZoologyInstitute for Biochemistry and BiologyUniversity of PotsdamPotsdamGermany
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37
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Sherry TW. Sensitivity of Tropical Insectivorous Birds to the Anthropocene: A Review of Multiple Mechanisms and Conservation Implications. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.662873] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Epigraph: “The house is burning. We do not need a thermometer. We need a fire hose.” (P. 102, Janzen and Hallwachs, 2019). Insectivorous birds are declining widely, and for diverse reasons. Tropical insectivorous birds, more than 60% of all tropical birds, are particularly sensitive to human disturbances including habitat loss and fragmentation, intensive agriculture and pesticide use, and climate change; and the mechanisms are incompletely understood. This review addresses multiple, complementary and sometimes synergistic explanations for tropical insectivore declines, by categorizing explanations into ultimate vs. proximate, and direct versus indirect. Ultimate explanations are diverse human Anthropocene activities and the evolutionary history of these birds. This evolutionary history, synthesized by the Biotic Challenge Hypothesis (BCH), explains tropical insectivorous birds' vulnerabilities to many proximate threats as a function of both these birds' evolutionary feeding specialization and poor dispersal capacity. These traits were favored evolutionarily by both the diversity of insectivorous clades competing intensely for prey and co-evolution with arthropods over long evolutionary time periods. More proximate, ecological threats include bottom-up forces like declining insect populations, top-down forces like meso-predator increases, plus the Anthropocene activities underlying these factors, especially habitat loss and fragmentation, agricultural intensification, and climate change. All these conditions peak in the lowland, mainland Neotropics, where insectivorous bird declines have been repeatedly documented, but also occur in other tropical locales and continents. This multiplicity of interacting evolutionary and ecological factors informs conservation implications and recommendations for tropical insectivorous birds: (1) Why they are so sensitive to global change phenomena is no longer enigmatic, (2) distinguishing ultimate versus proximate stressors matters, (3) evolutionary life-histories predispose these birds to be particularly sensitive to the Anthropocene, (4) tropical regions and continents vary with respect to these birds' ecological sensitivity, (5) biodiversity concepts need stronger incorporation of species' evolutionary histories, (6) protecting these birds will require more, larger reserves for multiple reasons, and (7) these birds have greater value than generally recognized.
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38
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Karamat S, Ashraf N, Akhtar T, Rahim F, Shafi N, Khalid S, Shahid B, Khawaja S, Rahim J, Majeed Z, Lateef Z, Mehmood M. CO1-Based DNA barcoding for assessing diversity of Pteropus giganteus from the state of Azad Jammu Kashmir, Pakistan. BRAZ J BIOL 2021; 81:584-591. [PMID: 32785466 DOI: 10.1590/1519-6984.226466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 02/21/2020] [Indexed: 11/22/2022] Open
Abstract
The flying fox (Pteropus giganteus) also familiar with the name of the greater Indian fruit Bat belongs to the order Chiroptera and family Pteropodidae. Current research emphasis on the DNA barcoding of P. giganteus in Azad Jammu Kashmir. Bat sequences were amplified and PCR products were sequenced and examined by bioinformatics software. Congeneric and conspecific, nucleotide composition and K2P nucleotide deviation, haplotype diversity and the number of haplotypes were estimated. The analysis showed that all of the five studied samples of P. giganteus had low G contents (G 19.8%) than C (27.8%), A (25.1%) and T (27.3%) contents. The calculated haplotype diversity was 0.60% and the mean intraspecific K2P distance was 0.001% having a high number of transitional substitutions. The study suggested that P. giganteus (R=0.00) do not deviate from the neutral evolution. It was determined from the conclusion that this mtDNA gene is a better marker for identification of Bat species than nuclear genes due to its distinctive characteristics and may serve as a landmark for the identification of interconnected species at the molecular level and in the determination of population genetics.
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Affiliation(s)
- Sana Karamat
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Nasra Ashraf
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Tasleem Akhtar
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Faisal Rahim
- Department of Agriculture Azad Jammu and Kashmir, Directorate of Agriculture Research, Muzaffarabad, Pakistan
| | - Nuzhat Shafi
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Saba Khalid
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Benish Shahid
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Sundas Khawaja
- University of Azad Jammu and Kashmir, Department of Biotechnology, Muzaffarabad, Pakistan
| | - Junaid Rahim
- University of Poonch Rawalakot, Faculty of Agriculture, Department of Entomology, Shamsabad, Rawalakot, Azad Jammu and Kashmir, Pakistan
| | - Zahid Majeed
- University of Azad Jammu and Kashmir, Department of Biotechnology, Muzaffarabad, Pakistan
| | - Zahid Lateef
- University of Azad Jammu and Kashmir, Department of Zoology, Muzaffarabad, Pakistan
| | - Majid Mehmood
- University of Poonch Rawalakot, Department of Zoology, Shamsabad, Rawalakot, Azad Jammu and Kashmir, Pakistan
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Demography, genetics, and decline of a spatially structured population of lekking bird. Oecologia 2021; 195:117-129. [PMID: 33392789 DOI: 10.1007/s00442-020-04808-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
Understanding the mechanisms underlying population decline is a critical challenge for conservation biologists. Both deterministic (e.g. habitat loss, fragmentation, and Allee effect) and stochastic (i.e. demographic and environmental stochasticity) demographic processes are involved in population decline. Simultaneously, a decrease of population size has far-reaching consequences for genetics of populations by increasing the risk of inbreeding and the strength of genetic drift, which together inevitably results in a loss of genetic diversity and a reduced effective population size ([Formula: see text]). These genetic factors may retroactively affect vital rates (a phenomenon coined 'inbreeding depression'), reduce population growth, and accelerate demographic decline. To date, most studies that have examined the demographic and genetic processes driving the decline of wild populations have neglected their spatial structure. In this study, we examined demographic and genetic factors involved in the decline of a spatially structured population of a lekking bird, the western capercaillie (Tetrao urogallus). To address this issue, we collected capture-recapture and genetic data over a 6-years period in the Vosges Mountains (France). Our study showed that the population of T. urogallus experienced a severe decline between 2010 and 2015. We did not detect any Allee effect on survival and recruitment. By contrast, individuals of both sexes dispersed to avoid small subpopulations, thus suggesting a potential behavioral response to a mate finding Allee effect. In parallel to this demographic decline, the population showed low levels of genetic diversity, high inbreeding and low effective population sizes at both subpopulation and population levels. Despite this, we did not detect evidence of inbreeding depression: neither adult survival nor recruitment were affected by individual inbreeding level. Our study underlines the benefit from combining demographic and genetic approaches to investigate processes that are involved in population decline.
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Adkins K, Roy CL, Wright RG, Andersen DE. Simulating Strategic Implementation of the CRP to Increase Greater Prairie‐Chicken Abundance. J Wildl Manage 2021. [DOI: 10.1002/jwmg.21960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kalysta Adkins
- Minnesota Cooperative Fish and Wildlife Research Unit University of Minnesota 1980 Folwell Avenue, 200 Hodson Hall St. Paul MN 55108 USA
| | - Charlotte L. Roy
- Minnesota Department of Natural Resources 1201 E Highway 2 Grand Rapids MN 55744 USA
| | - Robert G. Wright
- Minnesota Information Technology Services at Department of Natural Resources 5463‐C W Broadway Forest Lake MN 55025 USA
| | - David E. Andersen
- U.S. Geological Survey, Minnesota Cooperative Fish and Wildlife Research Unit 1980 Folwell Avenue, 200 Hodson Hall St. Paul MN 55108 USA
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41
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Botero-Delgadillo E, Quirici V, Vásquez RA, Kempenaers B. Heterozygosity-Fitness Correlations in a Continental Island Population of Thorn-Tailed Rayadito. J Hered 2020; 111:628-639. [PMID: 33277658 DOI: 10.1093/jhered/esaa056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/04/2020] [Indexed: 11/15/2022] Open
Abstract
Heterozygosity-fitness correlations (HFCs) have been used to monitor the effects of inbreeding in threatened populations. HFCs can also be useful to investigate the potential effects of inbreeding in isolated relict populations of long-term persistence and to better understand the role of inbreeding and outbreeding as drivers of changes in genetic diversity. We studied a continental island population of thorn-tailed rayadito (Aphrastura spinicauda) inhabiting the relict forest of Fray Jorge National Park, north-central Chile. This population has experienced a long-term, gradual process of isolation since the end of the Tertiary. Using 10 years of field data in combination with molecular techniques, we tested for HFCs to assess the importance of inbreeding depression. If inbreeding depression is important, we predict a positive relationship between individual heterozygosity and fitness-related traits. We genotyped 183 individuals at 12 polymorphic microsatellite loci and used 7 measures of reproductive success and estimates of apparent survival to calculate HFCs. We found weak to moderate statistical support (P-values between 0.05 and 0.01) for a linear effect of female multi-locus heterozygosity (MLH) on clutch size and nonlinear effects on laying date and fledging success. While more heterozygous females laid smaller clutches, nonlinear effects indicated that females with intermediate values of MLH started laying earlier and had higher fledging success. We found no evidence for effects of MLH on annual fecundity or on apparent survival. Our results along with the long-term demographic stability of the study population contradict the hypothesis that inbreeding depression occurs in this population.
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Affiliation(s)
- Esteban Botero-Delgadillo
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Verónica Quirici
- Departamento de Ecología y Biodiversidad, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Santiago, Chile.,Centro de investigación para la sustentabilidad, Universidad Andrés Bello, Santiago, Chile
| | - Rodrigo A Vásquez
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
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Foster RJ, Harmsen BJ, Urbina YL, Wooldridge RL, Doncaster CP, Quigley H, Figueroa OA. Jaguar ( Panthera onca) density and tenure in a critical biological corridor. J Mammal 2020; 101:1622-1637. [PMID: 33505226 PMCID: PMC7816682 DOI: 10.1093/jmammal/gyaa134] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 10/02/2020] [Indexed: 11/26/2022] Open
Abstract
We estimated jaguar density and tenure, and investigated ranging behavior, using camera traps across the Maya Forest Corridor, a human-influenced landscape in central Belize that forms the only remaining connection for jaguar populations inhabiting two regional forest blocks: the Selva Maya and the Maya Mountain Massif. Jaguars were ubiquitous across the study area. Similar to the neighboring Selva Maya, mean density ranged from 1.5 to 3.1 jaguars per 100 km2, estimated by spatial capture-recapture models. Cameras detected almost twice as many males as females, probably reflecting detection bias, and males ranged more widely than females within the camera grid. Both sexes crossed two major rivers, while highway crossings were rare and male-biased, raising concern that the highway could prevent female movement if traffic increases. Jaguars were more transient where the landscape was fragmented with settlements and agriculture than in contiguous forest. Compared with jaguars in the protected forests of the Maya Mountains, jaguars in central Belize displayed a lower potential for investment in intraspecific communication, indicative of a lower quality landscape; however, we did detect mating behavior and juveniles. Tenure of individuals was shorter than in the protected forests, with a higher turnover rate for males than females. At least three-quarters of reported jaguar deaths caused by people were male jaguars, and the majority was retaliation for livestock predation. Jaguars seem relatively tolerant to the human-influenced landscape of central Belize. However, intensification of game hunting and lethal control of predators would threaten population persistence, while increased highway traffic and clear-cutting riparian forest would severely limit the corridor function. Our results show that the viability of the corridor, and thus the long-term survival of jaguar populations in this region, will depend on appropriate land-use planning, nonlethal control of livestock predators, enforcement of game hunting regulations, and wildlife-friendly features in future road developments.
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Affiliation(s)
- R J Foster
- Panthera, New York, NY, USA
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
- Environmental Research Institute, University of Belize, Belmopan, Belize
| | - B J Harmsen
- Panthera, New York, NY, USA
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
- Environmental Research Institute, University of Belize, Belmopan, Belize
- Government of Belize, Market Square, Belmopan, Belize
| | - Y L Urbina
- Panthera, New York, NY, USA
- Environmental Research Institute, University of Belize, Belmopan, Belize
| | - R L Wooldridge
- Panthera, New York, NY, USA
- Environmental Research Institute, University of Belize, Belmopan, Belize
| | - C P Doncaster
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | - O A Figueroa
- Government of Belize, Market Square, Belmopan, Belize
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Yamachita AL, Pandolfi VCF, Souza FPD, Godoy SMD, Lima ECSD, Pereira UDP, Povh JA, Campos EC, Ayres DR, Bignardi AB, Ruas CDF, Lopera-Barrero NM. Evaluation of a panel of microsatellite markers to study their applications in Serrapinnus notomelas and to reveal the genetic diversity in Hyphessobrycon eques. Anim Biotechnol 2020; 33:701-709. [PMID: 33017262 DOI: 10.1080/10495398.2020.1826957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Jewel tetra (Hyphessobrycon eques) is a freshwater fish found in several rivers and basins in South America. The present study is the first study to create a panel of microsatellite markers for detecting genetic diversity in H. eques and evaluating the application of these markers in Serrapinnus notomelas. In total, 44 individuals were genotyped from the natural (WIL, n = 20) and stock in captivity (CAP, n = 24) population. Moreover, 19 microsatellite markers were obtained, of which only 8 loci presented a high degree polymorphism. In total, 45 alleles were detected, ranging from 126 bp (Hype2G2) to 420 bp (Hype2E2). The Hardy-Weinberg equilibrium (p < 0.05) revealed significant difference in one locus in WIL (Hype1G4) and three loci in CAP (Hype1F4, Hype2C3, and Hype2G2). Null alleles (p < 0.05) were present in only one locus (Hype1G4). The WIL and CAP populations revealed high genetic diversity during FST analysis. The cross-amplification test for S. notomelas revealed that only two loci (Hype2C3 and Hype2G2B) presented satisfactory transferability results. The developed microsatellite primers will be useful in studying the genetic diversity and population structure of H. eques in wild populations and fish farms in the Brazilian and other South American basins.
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Affiliation(s)
- Andrei Lincoln Yamachita
- Postgraduate Program in Biotechnology, Center of Exact Sciences, State University of Londrina, Londrina, Brazil
| | - Victor César Freitas Pandolfi
- Postgraduate Program in Animal Sciences, Center of Agricultural Sciences, State University of Londrina, Londrina, Brazil
| | - Felipe Pinheiro de Souza
- Postgraduate Program in Animal Sciences, Center of Agricultural Sciences, State University of Londrina, Londrina, Brazil
| | - Sara Mataroli de Godoy
- Postdoctoral Student in Genetics and Molecular Biology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Ed Christian Suzuki de Lima
- Postgraduate Program in Animal Sciences, Center of Agricultural Sciences, State University of Londrina, Londrina, Brazil
| | - Ulisses de Pádua Pereira
- Department of Preventive Veterinary Medicine and Postgraduate Program in Animal Sciences, Center of Agricultural Sciences, State University of Londrina, Londrina, Brazil
| | - Jayme Aparecido Povh
- Faculty of Veterinary Medicine and Animal Science, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Eric Costa Campos
- Postgraduate Program in Animal Sciences, Center of Agricultural Sciences, State University of Maringá, Maringá, Brazil
| | - Denise Rocha Ayres
- Institute of Agricultural and Technological Sciences, Federal University of Rondonópolis, Brazil
| | - Annaiza Braga Bignardi
- Institute of Agricultural and Technological Sciences, Federal University of Rondonópolis, Brazil
| | | | - Nelson Mauricio Lopera-Barrero
- Department of Animal Sciences and Postgraduate Program in Animal Sciences, Center of Agricultural Sciences, State University of Londrina, Londrina, Brazil
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La Haye MJJ, van Kats RJM, Müskens GJDM, Hallmann CA, Jongejans E. Predation and survival in reintroduced populations of the Common hamster Cricetus cricetus in the Netherlands. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00063-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractEuropean populations of Common hamster (Cricetus cricetus) have dramatically declined in the last decades, and in many EU countries, the species is on the brink of extinction. In the Netherlands, a research and reintroduction program was started in three areas with hamster-friendly management to reverse the decline of the species. Since 2002, more than 800 captive-bred and wild-born hamsters were monitored using implant radiotransmitters to quantify survival rates and discover the main causes of death after release compared to those of wild individuals. Individuals with a transmitter were regularly checked at their burrow. Predation by foxes, birds of prey, and small mustelids was the most important cause of mortality of this medium-sized rodent, while crop type and harvest regime were also likely to be important drivers as they influenced survival rates through the presence or absence of protective cover. The fitted weekly survival model showed that male hamsters had much lower survival rates during the active season than females, which corresponds with the ‘risky male hypothesis’. Survival rates of females appeared too low to keep populations at a stable level. To establish a viable population, more optimal environmental conditions for both survival and reproduction of the hamsters are necessary. Using electric fences around fields with hamsters significantly increased the survival of females. However, hamster conservationists need to consider not just subadult and adult survival rates, but also habitat connectivity, weather effects on reproduction, and alternative agricultural practices on a landscape scale.
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Kattawar J, Piller KR. Comparative population genetics of the federally endangered Relict Darter, and its sister taxon the Clarks Darter (Teleostei: Percidae). CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01300-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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46
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Wolf AL, Slater GL, Pearson SF, Anderson HE, Moore R. Range-Wide Patterns of Natal and Breeding Dispersal in the Streaked Horned Lark. NORTHWEST SCIENCE 2020. [DOI: 10.3955/046.094.0103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Adrian L. Wolf
- Center for Natural Lands Management, 120 Union Avenue SE #215, Olympia, Washington 98501
| | - Gary L. Slater
- Center for Natural Lands Management, 120 Union Avenue SE #215, Olympia, Washington 98501
| | - Scott F. Pearson
- Washington Department of Fish and Wildlife, 1111 Washington Street SE, 5th Floor, Olympia, Washington 98501 and
| | - Hannah E. Anderson
- Washington Department of Fish and Wildlife, 1111 Washington Street SE, 5th Floor, Olympia, Washington 98501 and
| | - Randall Moore
- Department of Fisheries and Wildlife, 104 Nash Hall, Oregon State University, Corvallis, Oregon 97331
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Abstract
AbstractTranslocation of conspecific individuals to reduce extinction risk of small, isolated populations and prevent genetic depletion is a powerful tool in conservation biology. An important question is how the translocated individuals influence the long-term genetic composition of the recipient population. Here, we experimentally reinforced a house sparrow (Passer domesticus) population, and examined the impact of this translocation on allele frequencies, levels of heterozygosity and genetic differentiation over six cohorts. We found no permanent increase in the mean number of alleles across loci or levels of observed heterozygosity, but a few alleles private to the translocated individuals remained in the population and we found a short-term increase in heterozygosity. Consequently, genetic differentiation of the recipient population compared to the genetic composition prior to reinforcement was small. The limited genetic impact was due to combined effects of a small probability of establishment and low mating success for the translocated individuals, together with increased genetic drift in the recipient population. Our findings emphasize the importance of selection and genetic drift as forces that may decrease the genetic contribution of reinforcement, especially in small populations. Conservation managers should aim to improve habitat quality in the recipient population to reduce genetic drift following translocation and thereby avoid the need for continued reinforcement. Furthermore, by facilitating establishment success and selecting individuals expected to have high mating success, possibly indicated by sexually selected traits, genetic contribution of released individuals is increased which in turn will decrease reproductive skew and genetic drift.
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48
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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]
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Potter S, Neaves LE, Lethbridge M, Eldridge MDB. Understanding Historical Demographic Processes to Inform Contemporary Conservation of an Arid zone Specialist: The Yellow-Footed Rock-Wallaby. Genes (Basel) 2020; 11:E154. [PMID: 32023869 PMCID: PMC7073556 DOI: 10.3390/genes11020154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/27/2020] [Accepted: 01/28/2020] [Indexed: 11/16/2022] Open
Abstract
Little genetic research has been undertaken on mammals across the vast expanse of the arid biome in Australia, despite continuing species decline and need for conservation management. Here, we evaluate the contemporary and historical genetic connectivity of the yellow-footed rock-wallaby, Petrogalexanthopusxanthopus, a threatened macropodid which inhabits rocky outcrops across the disconnected mountain range systems of the southern arid biome. We use 17 microsatellite loci together with mitochondrial control region data to determine the genetic diversity of populations and the evolutionary processes shaping contemporary population dynamics on which to base conservation recommendations. Our results indicate the highly fragmented populations have reduced diversity and limited contemporary gene flow, with most populations having been through population bottlenecks. Despite limited contemporary gene flow, the phylogeographic relationships of the mitochondrial control region indicate a lack of structure and suggests greater historical connectivity. This is an emerging outcome for mammals across this arid region. On the basis of our results, we recommend augmentation of populations of P. x.xanthopus, mixing populations from disjunct mountain range systems to reduce the chance of continued diversity loss and inbreeding depression, and therefore maximize the potential for populations to adapt and survive into the future.
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Affiliation(s)
- Sally Potter
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton ACT 2601, Australia
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney 2010, New South Wales, Australia (M.D.B.E.)
| | - Linda E. Neaves
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney 2010, New South Wales, Australia (M.D.B.E.)
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5 LR, UK
| | - Mark Lethbridge
- Biological Sciences, Flinders University, Adelaide 5001, Australia;
| | - Mark D. B. Eldridge
- Australian Museum Research Institute, Australian Museum, 1 William Street, Sydney 2010, New South Wales, Australia (M.D.B.E.)
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Fitzpatrick SW, Bradburd GS, Kremer CT, Salerno PE, Angeloni LM, Funk WC. Genomic and Fitness Consequences of Genetic Rescue in Wild Populations. Curr Biol 2020; 30:517-522.e5. [PMID: 31902732 DOI: 10.1016/j.cub.2019.11.062] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/11/2019] [Accepted: 11/20/2019] [Indexed: 10/25/2022]
Abstract
Gene flow is an enigmatic evolutionary force because it can limit adaptation but may also rescue small populations from inbreeding depression [1-3]. Several iconic examples of genetic rescue-increased population growth caused by gene flow [4, 5]-have reversed population declines [6, 7]. However, concerns about outbreeding depression and maladaptive gene flow limit the use of human-mediated gene flow in conservation [8, 9]. Rescue effects of immigration through demographic and/or genetic mechanisms have received theoretical and empirical support, but studies that monitor initial and long-term effects of gene flow on individuals and populations in the wild are lacking. Here, we used individual-based mark-recapture, multigenerational pedigrees, and genomics to test the demographic and evolutionary consequences of manipulating gene flow in two isolated, wild Trinidadian guppy populations. Recipient and source populations originated from environments with different predation, flow, and resource regimes [10]. We documented 10-fold increases in population size following gene flow and found that, on average, hybrids lived longer and reproduced more than residents and immigrants. Despite overall genomic homogenization, alleles potentially associated with local adaptation were not entirely swamped by gene flow. Our results suggest that genetic rescue was caused not just by increasing individual genetic diversity, rather new genomic variation from immigrants combined with alleles from the recipient population resulted in highly fit hybrids and subsequent increases in population size. Contrary to the classic view of maladaptive gene flow, our study reveals conditions under which immigration can produce long-term fitness benefits in small populations without entirely swamping adaptive variation.
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Affiliation(s)
- Sarah W Fitzpatrick
- W.K. Kellogg Biological Station, Michigan State University, 3700 E. Gull Lake Drive, Hickory Corners, MI 49060, USA; Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI 48824, USA; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA.
| | - Gideon S Bradburd
- Department of Integrative Biology, Michigan State University, 288 Farm Lane, East Lansing, MI 48824, USA; Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI 48824, USA
| | - Colin T Kremer
- W.K. Kellogg Biological Station, Michigan State University, 3700 E. Gull Lake Drive, Hickory Corners, MI 49060, USA
| | - Patricia E Salerno
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA; Universidad Regional Amazónica Ikiam, Km 7 Vía Muyuna, Tena, Napo, Ecuador
| | - Lisa M Angeloni
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA; Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
| | - W Chris Funk
- Department of Biology, Colorado State University, 1878 Campus Delivery, Fort Collins, CO 80523, USA; Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523, USA
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