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Elbers JP, Brown MB, Taylor SS. Identifying genome-wide immune gene variation underlying infectious disease in wildlife populations - a next generation sequencing approach in the gopher tortoise. BMC Genomics 2018; 19:64. [PMID: 29351737 PMCID: PMC5775545 DOI: 10.1186/s12864-018-4452-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 01/15/2018] [Indexed: 11/25/2022] Open
Abstract
Background Infectious disease is the single greatest threat to taxa such as amphibians (chytrid fungus), bats (white nose syndrome), Tasmanian devils (devil facial tumor disease), and black-footed ferrets (canine distemper virus, plague). Although understanding the genetic basis to disease susceptibility is important for the long-term persistence of these groups, most research has been limited to major-histocompatibility and Toll-like receptor genes. To better understand the genetic basis of infectious disease susceptibility in a species of conservation concern, we sequenced all known/predicted immune response genes (i.e., the immunomes) in 16 Florida gopher tortoises, Gopherus polyphemus. All tortoises produced antibodies against Mycoplasma agassizii (an etiologic agent of infectious upper respiratory tract disease; URTD) and, at the time of sampling, either had (n = 10) or lacked (n = 6) clinical signs. Results We found several variants associated with URTD clinical status in complement and lectin genes, which may play a role in Mycoplasma immunity. Thirty-five genes deviated from neutrality according to Tajima’s D. These genes were enriched in functions relating to macromolecule and protein modifications, which are vital to immune system functioning. Conclusions These results are suggestive of genetic differences that might contribute to disease severity, a finding that is consistent with other mycoplasmal diseases. This has implications for management because tortoises across their range may possess genetic variation associated with a more severe response to URTD. More generally: 1) this approach demonstrates that a broader consideration of immune genes is better able to identify important variants, and; 2) this data pipeline can be adopted to identify alleles associated with disease susceptibility or resistance in other taxa, and therefore provide information on a population’s risk of succumbing to disease, inform translocations to increase genetic variation for disease resistance, and help to identify potential treatments. Electronic supplementary material The online version of this article (10.1186/s12864-018-4452-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jean P Elbers
- School of Renewable Natural Resources, 227 RNR Bldg., Louisiana State University and AgCenter, Baton Rouge, LA, 70803, USA.
| | - Mary B Brown
- Department of Infectious Diseases and Pathology, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Sabrina S Taylor
- School of Renewable Natural Resources, 227 RNR Bldg., Louisiana State University and AgCenter, Baton Rouge, LA, 70803, USA
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Elbers JP, Clostio RW, Taylor SS. Neutral Genetic Processes Influence MHC Evolution in Threatened Gopher Tortoises (Gopherus polyphemus). J Hered 2017; 108:515-523. [PMID: 28387863 DOI: 10.1093/jhered/esx034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/04/2017] [Indexed: 11/12/2022] Open
Abstract
Levels of adaptive genetic variation influence how species deal with environmental and ecological change, but these levels are frequently inferred using neutral genetic markers. Major histocompatibility complex (MHC) genes play a key role in the adaptive branch of the immune system and have been used extensively to estimate levels of adaptive genetic variation. Parts of the peptide binding region, sites where MHC molecules directly interact with pathogen and self-proteins, were sequenced from a MHC class I (95/441 tortoises) and class II (245/441 tortoises) gene in threatened and nonthreatened populations of gopher tortoises (Gopherus polyphemus), and adaptive genetic variation at MHC genes was compared to neutral genetic variation derived from 10 microsatellite loci (441 tortoises). Genetic diversity at the MHC class II locus and microsatellites was greater in populations in the nonthreatened portion of the gopher tortoise's range (MHC class II difference in mean A = 8.11, AR = 0.79, HO = 0.51, and HE = 0.16; microsatellite difference in mean A = 1.05 and AR = 0.47). Only MHC class II sequences showed evidence of positive selection (dN/dS > 1, Z = 1.81, P = 0.04). Historical gene flow as estimated with Migrate-N was greater than recent migration estimated with BayesAss, suggesting that populations were better connected in the past when habitat was less fragmented. MHC genetic differentiation was correlated with microsatellite differentiation (Mantel r = 0.431, P = 0.001) suggesting neutral genetic processes are influencing MHC evolution, and advantageous MHC alleles could be lost due to genetic drift.
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Affiliation(s)
- Jean P Elbers
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Bldg., Baton Rouge, LA 70803; and Department of Biology, University of Louisiana at Lafayette, Lafayette, LA
| | - Rachel W Clostio
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Bldg., Baton Rouge, LA 70803; and Department of Biology, University of Louisiana at Lafayette, Lafayette, LA
| | - Sabrina S Taylor
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Bldg., Baton Rouge, LA 70803; and Department of Biology, University of Louisiana at Lafayette, Lafayette, LA
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Ennen JR, Matamoros WA, Agha M, Lovich JE, Sweat SC, Hoagstrom CW. Hierarchical, Quantitative Biogeographic Provinces for All North American Turtles and Their Contribution to the Biogeography of Turtles and the Continent. HERPETOLOGICAL MONOGRAPHS 2017. [DOI: 10.1655/herpmonographs-d-16-00013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Joshua R. Ennen
- Tennessee Aquarium Conservation Institute, Tennessee Aquarium, 175 Baylor School Road, Chattanooga, TN 37405, USA
| | - Wilfredo A. Matamoros
- Facultad de Ciencias Biológicas, Universidad de Ciencias y Artes de Chiapas, Museo de Zoología, Tuxtla Gutiérrez, Chiapas, México Apartado Postal 29000, México
| | - Mickey Agha
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jeffrey E. Lovich
- U.S. Geological Survey, Southwest Biological Science Center, 2255 North Gemini Drive, Flagstaff, AZ 86001, USA
| | - Sarah C. Sweat
- Tennessee Aquarium Conservation Institute, Tennessee Aquarium, 175 Baylor School Road, Chattanooga, TN 37405, USA
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Population Genetics Between an Insular and Coastal Population of Gopher Tortoises (Gopherus polyphemus) in Southwest Florida. SOUTHEAST NAT 2017. [DOI: 10.1656/058.016.0305] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Range-Wide and Regional Patterns of Population Structure and Genetic Diversity in the Gopher Tortoise. JOURNAL OF FISH AND WILDLIFE MANAGEMENT 2017. [DOI: 10.3996/022017-jfwm-010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Abstract
The gopher tortoise (Gopherus polyphemus) has experienced dramatic population declines throughout its distribution in the southeastern United States and is federally listed as threatened in the area west of the Tombigbee and Mobile rivers. While there is molecular support for recognizing the listed portion of the range as genetically distinct, other research has suggested that additional population structure exists at both range-wide and regional scales. In this study, we sought to comprehensively define genetic population structure at both spatial scales by doubling the data available in terms of the number of sampling sites, individuals, and microsatellite loci compared to previously published work. We also compared patterns of genetic diversity, gene flow, and demographic history across the range. We collected 933 individuals from 47 sampling sites across the range and genotyped them for 20 microsatellite loci. Our range-wide analyses supported the recognition of five genetic groups (or regions) delineated by the Tombigbee and Mobile rivers, Apalachicola and Chattahoochee rivers, and the transitional areas between several physiographic province sections of the Coastal Plains (i.e., Eastern Gulf, Sea Island, and Floridian). We found genetic admixture at sampling sites along the boundaries of these genetically defined groups. We detected some degree of additional genetic structure within each of the five regions. Notably, within the range listed as threatened under the Endangered Species Act, we found some support for two additional genetic groups loosely delineated by the Pascagoula and Chickasawhay rivers, and we detected four more genetic groups within the Florida region that seemed to reflect the influence of the local physiography. Additionally, our range-wide analysis found the periphery of the range had lower levels of genetic diversity relative to the core. We suggest that the five main genetic groups delineated in our study warrant recognition as management units in terms of conservation planning. Intraregional population structure also points to the potential importance of other barriers to gene flow at finer spatial scales, although additional work is needed to better delineate these genetic groups.
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Elbers JP, Clostio RW, Taylor SS. Population genetic inferences using immune gene SNPs mirror patterns inferred by microsatellites. Mol Ecol Resour 2016; 17:481-491. [PMID: 27488693 DOI: 10.1111/1755-0998.12591] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 07/25/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are replacing microsatellites for population genetic analyses, but it is not apparent how many SNPs are needed or how well SNPs correlate with microsatellites. We used data from the gopher tortoise, Gopherus polyphemus-a species with small populations, to compare SNPs and microsatellites to estimate population genetic parameters. Specifically, we compared one SNP data set (16 tortoises from four populations sequenced at 17 901 SNPs) to two microsatellite data sets, a full data set of 101 tortoises and a partial data set of 16 tortoises previously genotyped at 10 microsatellites. For the full microsatellite data set, observed heterozygosity, expected heterozygosity and FST were correlated between SNPs and microsatellites; however, allelic richness was not. The same was true for the partial microsatellite data set, except that allelic richness, but not observed heterozygosity, was correlated. The number of clusters estimated by structure differed for each data set (SNPs = 2; partial microsatellite = 3; full microsatellite = 4). Principle component analyses (PCA) showed four clusters for all data sets. More than 800 SNPs were needed to correlate with allelic richness, observed heterozygosity and expected heterozygosity, but only 100 were needed for FST . The number of SNPs typically obtained from next-generation sequencing (NGS) far exceeds the number needed to correlate with microsatellite parameter estimates. Our study illustrates that diversity, FST and PCA results from microsatellites can mirror those obtained with SNPs. These results may be generally applicable to small populations, a defining feature of endangered and threatened species, because theory predicts that genetic drift will tend to outweigh selection in small populations.
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Affiliation(s)
- Jean P Elbers
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Bldg., Baton Rouge, LA, 70803, USA
| | - Rachel W Clostio
- Department of Biology, University of Louisiana at Lafayette, 300 E. Street Mary Blvd., Lafayette, LA, 70503, USA
| | - Sabrina S Taylor
- School of Renewable Natural Resources, Louisiana State University and AgCenter, 227 RNR Bldg., Baton Rouge, LA, 70803, USA
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Edwards T, Karl AE, Vaughn M, Rosen PC, Torres CM, Murphy RW. The desert tortoise trichotomy: Mexico hosts a third, new sister-species of tortoise in the Gopherus morafkai-G. agassizii group. Zookeys 2016:131-58. [PMID: 27006625 PMCID: PMC4768471 DOI: 10.3897/zookeys.562.6124] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 01/06/2016] [Indexed: 02/08/2023] Open
Abstract
Desert tortoises (Testudines; Testudinidae; Gopherusagassizii group) have an extensive distribution throughout the Mojave, Colorado, and Sonoran desert regions. Not surprisingly, they exhibit a tremendous amount of ecological, behavioral, morphological and genetic variation. Gopherusagassizii was considered a single species for almost 150 years but recently the species was split into the nominate form and Morafka’s desert tortoise, Gopherusmorafkai, the latter occurring south and east of the Colorado River. Whereas a large body of literature focuses on tortoises in the United States, a dearth of investigations exists for Mexican animals. Notwithstanding, Mexican populations of desert tortoises in the southern part of the range of Gopherusmorafkai are distinct, particularly where the tortoises occur in tropical thornscrub and tropical deciduous forest. Recent studies have shed light on the ecology, morphology and genetics of these southern ‘desert’ tortoises. All evidence warrants recognition of this clade as a distinctive taxon and herein we describe it as Gopherusevgoodeisp. n. The description of the new species significantly reduces and limits the distribution of Gopherusmorafkai to desertscrub habitat only. By contrast, Gopherusevgoodeisp. n. occurs in thornscrub and tropical deciduous forests only and this leaves it with the smallest range of the three sister species. We present conservation implications for the newly described Gopherusevgoodei, which already faces impending threats.
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Affiliation(s)
- Taylor Edwards
- School of Natural Resources and the Environment. The University of Arizona, Tucson, AZ 85721 USA; University of Arizona Genetics Core, University of Arizona, Tucson, AZ 85721 USA
| | | | | | - Philip C Rosen
- School of Natural Resources and the Environment. The University of Arizona, Tucson, AZ 85721 USA
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Cerame B, Cox JA, Brumfield RT, Tucker JW, Taylor SS. Adaptation to ephemeral habitat may overcome natural barriers and severe habitat fragmentation in a fire-dependent species, the Bachman's Sparrow (Peucaea aestivalis). PLoS One 2014; 9:e105782. [PMID: 25180939 PMCID: PMC4152175 DOI: 10.1371/journal.pone.0105782] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/18/2014] [Indexed: 01/05/2023] Open
Abstract
Bachman's Sparrow (Peucaea aestivalis) is a fire-dependent species that has undergone range-wide population declines in recent decades. We examined genetic diversity in Bachman's Sparrows to determine whether natural barriers have led to distinct population units and to assess the effect of anthropogenic habitat loss and fragmentation. Genetic diversity was examined across the geographic range by genotyping 226 individuals at 18 microsatellite loci and sequencing 48 individuals at mitochondrial and nuclear genes. Multiple analyses consistently demonstrated little genetic structure and high levels of genetic variation, suggesting that populations are panmictic. Based on these genetic data, separate management units/subspecies designations or translocations to promote gene flow among fragmented populations do not appear to be necessary. Panmixia in Bachman's Sparrow may be a consequence of an historical range expansion and retraction. Alternatively, high vagility in Bachman's Sparrow may be an adaptation to the ephemeral, fire-mediated habitat that this species prefers. In recent times, high vagility also appears to have offset inbreeding and loss of genetic diversity in highly fragmented habitat.
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Affiliation(s)
- Blain Cerame
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
| | - James A Cox
- Tall Timbers Research Station and Land Conservancy, Tallahassee, Florida, United States of America
| | - Robb T Brumfield
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - James W Tucker
- Archbold Biological Station, Venus, Florida, United States of America
| | - Sabrina S Taylor
- School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, Louisiana, United States of America
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Averill-Murray RC, Hagerty BE. Translocation Relative to Spatial Genetic Structure of the Mojave Desert Tortoise,Gopherus agassizii. CHELONIAN CONSERVATION AND BIOLOGY 2014. [DOI: 10.2744/ccb-1050.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Matala AP, Ackerman MW, Campbell MR, Narum SR. Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes. Evol Appl 2014; 7:682-701. [PMID: 25067950 PMCID: PMC4105918 DOI: 10.1111/eva.12174] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 05/06/2014] [Indexed: 12/25/2022] Open
Abstract
Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non-neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non-neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad-scale population structure consistent with previous studies, but fine-scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non-neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non-neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long-term conservation of this species.
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Affiliation(s)
- Andrew P Matala
- Columbia River Inter-Tribal Fish Commission Hagerman, ID, USA
| | - Michael W Ackerman
- Eagle Fish Genetic Laboratory, Pacific States Marine Fisheries Commission Eagle, ID, USA
| | - Matthew R Campbell
- Eagle Fish Genetic Laboratory, Idaho Department of Fish and Game Eagle, ID, USA
| | - Shawn R Narum
- Columbia River Inter-Tribal Fish Commission Hagerman, ID, USA
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Richter SC, O'Neill EM, Nunziata SO, Rumments A, Gustin ES, Young JE, Crother BI. Cryptic Diversity and Conservation of Gopher Frogs across the Southeastern United States. COPEIA 2014. [DOI: 10.1643/cg-13-040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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