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Cobo-Simón I, Méndez-Cea B, Portillo H, Elvir F, Vega H, Gallego FJ, Fontecha G. Testing the effectiveness of conservation management within biosphere reserves: the case of the Mexican deer mouse (Peromyscus mexicanus) as a bioindicator. Integr Zool 2018; 14:422-434. [PMID: 30585414 DOI: 10.1111/1749-4877.12371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Biosphere reserves are protected areas whose purpose is to combine conservation and sustainable development. However, their effectiveness has not been tested sufficiently, especially from an ecological and genetic approach. In this sense, the Peromyscus genus represents an excellent bioindicator to address these questions, due to its short life and high evolutionary rate and fecundity. For conservation managers, genetic structure can increase the rate of loss of genetic diversity because alleles exclusive of a subpopulation are more likely to disappear as a consequence of genetic drift in comparison with a panmictic population. Here we analyzed the abundance, movement distances, morphology/morphometry and genetic structure of 3 populations of Mexican deer mouse (Peromyscus mexicanus) located in different protected zones of La Tigra National Park (Honduras). Our results are consistent among the 3 approaches and showed the highest values of abundance, morphometry and genetic diversity in the population located at the core zone, whereas non-statistically significant differences were found between buffer and transition zone populations, suggesting suitable effectiveness of conservation management in the core zone but a lack of ecological buffering function of the other zones. In addition, the low movement distances and high genetic structure among the studied populations provide evidence of poor conservation management in the buffer and transition zone. Thus, we discuss the utility of the novel methodology used in this work, combining morphometry, abundance and genetics, in testing the effectiveness of conservation strategies in biosphere reserves, and the value of the Peromyscus genus as a bioindicator.
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Affiliation(s)
- Irene Cobo-Simón
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain.,Department of Physical, Chemical and Natural Systems, University Pablo de Olavide, Seville, Spain
| | - Belén Méndez-Cea
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Héctor Portillo
- Grupo de Investigación Para La Biodiversidad de Honduras GIBH-BALAM, National Autonomous University of Honduras, Tegucigalpa, Honduras
| | - Fausto Elvir
- Grupo de Investigación Para La Biodiversidad de Honduras GIBH-BALAM, National Autonomous University of Honduras, Tegucigalpa, Honduras
| | - Hermes Vega
- Grupo de Investigación Para La Biodiversidad de Honduras GIBH-BALAM, National Autonomous University of Honduras, Tegucigalpa, Honduras
| | - Francisco Javier Gallego
- Department of Genetics, Physiology and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Gustavo Fontecha
- Grupo de Investigación Para La Biodiversidad de Honduras GIBH-BALAM, National Autonomous University of Honduras, Tegucigalpa, Honduras
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Lion KA, Rice SE, Clark RW. Genetic patterns in fragmented habitats: a case study for two Peromyscus species in southern California. J Mammal 2018. [DOI: 10.1093/jmammal/gyy069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Kelly A Lion
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Stephen E Rice
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Rulon W Clark
- Department of Biology, San Diego State University, San Diego, CA, USA
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Delaney EK, Hoekstra HE. Sexual imprinting and speciation between two Peromyscus species. Evolution 2018; 72:274-287. [PMID: 29231989 DOI: 10.1111/evo.13409] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 11/11/2017] [Accepted: 11/21/2017] [Indexed: 12/30/2022]
Abstract
Sexual isolation, a reproductive barrier, can prevent interbreeding between diverging populations or species. Sexual isolation can have a clear genetic basis; however, it may also result from learned mate preferences that form via sexual imprinting. Here, we demonstrate that two sympatric species of mice-the white-footed mouse (Peromyscus leucopus) and its sister species, the cotton mouse (P. gossypinus)-hybridize only rarely in the wild despite co-occurrence in the same habitat and lack of any measurable intrinsic postzygotic barriers in laboratory crosses. We present evidence that strong conspecific mating preferences in each species result in significant sexual isolation. We find that these preferences are learned in at least one species: P. gossypinus sexually imprints on its parents, but in P. leucopus, additional factors influence mating preferences. Our study demonstrates that sexual imprinting contributes to reproductive isolation that reduces hybridization between otherwise interfertile species, supporting the role for learning in mammalian speciation.
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Affiliation(s)
- Emily K Delaney
- Howard Hughes Medical Institute, Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138.,Current Address: Department of Evolution and Ecology, University of California-Davis, Davis, California 95616
| | - Hopi E Hoekstra
- Howard Hughes Medical Institute, Department of Organismic and Evolutionary Biology, Department of Molecular and Cellular Biology, Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138
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Austin JD, Gore JA, Greene DU, Gotteland C. Conspicuous genetic structure belies recent dispersal in an endangered beach mouse (Peromyscus polionotus trissyllepsis). CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0710-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mabry KE. Effects of sex and population density on dispersal and spatial genetic structure in brush mice. J Mammal 2014. [DOI: 10.1644/14-mamm-a-008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Kenney-Hunt J, Lewandowski A, Glenn TC, Glenn JL, Tsyusko OV, O'Neill RJ, Brown J, Ramsdell CM, Nguyen Q, Phan T, Shorter KR, Dewey MJ, Szalai G, Vrana PB, Felder MR. A genetic map of Peromyscus with chromosomal assignment of linkage groups (a Peromyscus genetic map). Mamm Genome 2014; 25:160-79. [PMID: 24445420 DOI: 10.1007/s00335-014-9500-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 12/18/2013] [Indexed: 11/25/2022]
Abstract
The rodent genus Peromyscus is the most numerous and species-rich mammalian group in North America. The naturally occurring diversity within this genus allows opportunities to investigate the genetic basis of adaptation, monogamy, behavioral and physiological phenotypes, growth control, genomic imprinting, and disease processes. Increased genomic resources including a high quality genetic map are needed to capitalize on these opportunities. We produced interspecific hybrids between the prairie deer mouse (P. maniculatus bairdii) and the oldfield mouse (P. polionotus) and scored meiotic recombination events in backcross progeny. A genetic map was constructed by genotyping of backcross progeny at 185 gene-based and 155 microsatellite markers representing all autosomes and the X-chromosome. Comparison of the constructed genetic map with the molecular maps of Mus and Rattus and consideration of previous results from interspecific reciprocal whole chromosome painting allowed most linkage groups to be unambiguously assigned to specific Peromyscus chromosomes. Based on genomic comparisons, this Peromyscus genetic map covers ~83% of the Rattus genome and 79% of the Mus genome. This map supports previous results that the Peromyscus genome is more similar to Rattus than Mus. For example, coverage of the 20 Rattus autosomes and the X-chromosome is accomplished with only 28 segments of the Peromyscus map, but coverage of the 19 Mus autosomes and the X-chromosome requires 40 chromosomal segments of the Peromyscus map. Furthermore, a single Peromyscus linkage group corresponds to about 91% of the rat and only 76% of the mouse X-chromosomes.
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Affiliation(s)
- Jane Kenney-Hunt
- Department of Biological Sciences and Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, 29208, USA
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Mussali-Galante P, Tovar-Sánchez E, Valverde M, Valencia-Cuevas L, Rojas E. Evidence of population genetic effects in Peromyscus melanophrys chronically exposed to mine tailings in Morelos, Mexico. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:7666-79. [PMID: 23108757 DOI: 10.1007/s11356-012-1263-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/11/2012] [Indexed: 05/21/2023]
Abstract
Effects of environmental chemical pollution can be observed at all levels of biological organization. At the population level, genetic structure and diversity may be affected by exposure to metal contamination. This study was conducted in Huautla, Morelos, Mexico in a mining district where the main contaminants are lead and arsenic. Peromyscus melanophrys is a small mammal species that inhabits Huautla mine tailings and has been considered as a sentinel species. Metal bioaccumulation levels were examined by inductively coupled plasma mass spectrometry and genetic analyses were performed using eight microsatellite loci in 100 P. melanophrys individuals from 3 mine tailings and 2 control sites. The effect of metal bioaccumulation levels on genetic parameters (population and individual genetic diversity, genetic structure) was analyzed. We found a tissue concentration gradient for each metal and for the bioaccumulation index. The highest values of genetic differentiation (Fst and Rst) and the lowest number of migrants per generation (Nm) were registered among the exposed populations. Genetic distance analyses showed that the most polluted population was the most genetically distant among the five populations examined. Moreover, a negative and significant relationship was detected between genetic diversity (expected heterozygosity and internal relatedness) and each metal concentration and for the bioaccumulation index in P. melanophrys. This study highlights that metal stress is a major factor affecting the distribution and genetic diversity levels of P. melanophrys populations living inside mine tailings. We suggest the use of genetic population changes at micro-geographical scales as a population level biomarker.
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Affiliation(s)
- Patricia Mussali-Galante
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México, D.F., C.P. 04510, Mexico
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Glenn TC, Lance SL, McKee AM, Webster BL, Emery AM, Zerlotini A, Oliveira G, Rollinson D, Faircloth BC. Significant variance in genetic diversity among populations of Schistosoma haematobium detected using microsatellite DNA loci from a genome-wide database. Parasit Vectors 2013; 6:300. [PMID: 24499537 PMCID: PMC3874762 DOI: 10.1186/1756-3305-6-300] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 09/18/2013] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. METHODS We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. RESULTS We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse. CONCLUSIONS About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma species (i.e., using DNA sequences conserved among species), as well as other markers that are specific to species or species-groups (i.e., using DNA sequences that differ among species). Full genome-sequencing of additional species and specimens of S. haematobium, S. japonicum, and S. mansoni is desirable to better characterize differences within and among these species, to develop additional genetic markers, and to examine genes as well as conserved non-coding elements associated with drug resistance.
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Affiliation(s)
- Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens 30602 GA, USA
| | - Stacey L Lance
- Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken 29802 SC, USA
| | - Anna M McKee
- Department of Environmental Health Science, University of Georgia, Athens 30602 GA, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens 30602 GA, USA
| | - Bonnie L Webster
- Department of Life Sciences, Natural History Museum, Wolfson Wellcome Biomedical Laboratories, Cromwell Road, London, SW7 5BD, UK
- Present address; Department of Infectious Disease Epidemiology, Imperial College Faculty of Medicine (St Mary’s Campus), Norfolk Place, London W2 1PG, UK
| | - Aidan M Emery
- Department of Life Sciences, Natural History Museum, Wolfson Wellcome Biomedical Laboratories, Cromwell Road, London, SW7 5BD, UK
| | - Adhemar Zerlotini
- Rene Rachou Research Center, National Institute of Science and Technology in Tropical Diseases, Oswaldo Cruz Foundation, Av. Augusto de Lima 1715, BarroPreto, Belo Horizonte CEP 30190-002 MG, Brazil
- Present address: Embrapa Agricultural Informatics, Av. Andre Tosello, 209, Campinas 13083-886 SP, Brazil
| | - Guilherme Oliveira
- Rene Rachou Research Center, National Institute of Science and Technology in Tropical Diseases, Oswaldo Cruz Foundation, Av. Augusto de Lima 1715, BarroPreto, Belo Horizonte CEP 30190-002 MG, Brazil
| | - David Rollinson
- Department of Life Sciences, Natural History Museum, Wolfson Wellcome Biomedical Laboratories, Cromwell Road, London, SW7 5BD, UK
| | - Brant C Faircloth
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles 90095 CA, USA
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The changing brain--insights into the mechanisms of neural and behavioral adaptation to the environment. Neuroscience 2013; 247:412-22. [PMID: 23602885 DOI: 10.1016/j.neuroscience.2013.04.012] [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: 11/23/2022]
Abstract
The Kavli Prize in Neuroscience was awarded for the third time in September 2012, by the Norwegian Academy of Science and Letters in Oslo. The accompanying Kavli Prize Symposium on Neuroscience, held in Bergen and Trondheim, was a showcase of excellence in neuroscience research. The common theme of the Symposium presentations was the mechanisms by which animals adapt to their environment. The symposium speakers--Michael Greenberg, Erin Schuman, Chiara Cirelli, Michael Meaney, Catherine Dulac, Hopi Hoekstra, and Stanislas Dehaene--covered topics ranging from the molecular and cellular levels to the systems level and behavior. Thus a single amino acid change in a transcriptional repressor can disrupt gene regulation through neural activity (Greenberg). Deep sequencing analysis of the neuropil transcriptome indicates that a large fraction of the synaptic proteome is synthesized in situ in axons and dendrites, permitting local regulation (Schuman). The nature of the 'reset' function that makes animals dependent of sleep is being revealed (Cirelli). Maternal behavior can cause changes in gene expression that stably modify behavior in the offspring (Meaney). Removal of a single sensory channel protein in the vomero-nasal organ can switch off male-specific and switch on female-specific innate behavior of mice in response to environmental stimulation (Dulac). Innate behaviors can be stably transmitted from parent to offspring through generations even when those behaviors cannot be expressed, as illustrated by the elaborate burrowing behavior in a rodent species, in which independent genetic regions regulate distinct modules of the burrowing pattern (Hoekstra). Finally, at the other extreme of the nature-nurture scale, functional magnetic resonance imaging (fMRI) analysis in children and adults identified a brain area specifically involved in reading (Dehaene). As the area must originally have developed for a purpose other than reading, such as shape recognition, this illustrates the use of a previously formed neural structure to tackle a new challenge.
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Two different high throughput sequencing approaches identify thousands of de novo genomic markers for the genetically depleted Bornean elephant. PLoS One 2012. [PMID: 23185354 PMCID: PMC3504023 DOI: 10.1371/journal.pone.0049533] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
High throughput sequencing technologies are being applied to an increasing number of model species with a high-quality reference genome. The application and analyses of whole-genome sequence data in non-model species with no prior genomic information are currently under way. Recent sequencing technologies provide new opportunities for gathering genomic data in natural populations, laying the empirical foundation for future research in the field of conservation and population genomics. Here we present the case study of the Bornean elephant, which is the most endangered subspecies of Asian elephant and exhibits very low genetic diversity. We used two different sequencing platforms, the Roche 454 FLX (shotgun) and Illumina, GAIIx (Restriction site associated DNA, RAD) to evaluate the feasibility of the two methodologies for the discovery of de novo markers (single nucleotide polymorphism, SNPs and microsatellites) using low coverage data. Approximately, 6,683 (shotgun) and 14,724 (RAD) SNPs were detected within our elephant sequence dataset. Genotyping of a representative sample of 194 SNPs resulted in a SNP validation rate of ∼ 83 to 94% and 17% of the loci were polymorphic with a low diversity (Ho = 0.057). Different numbers of microsatellites were identified through shotgun (27,226) and RAD (868) techniques. Out of all di-, tri-, and tetra-microsatellite loci, 1,706 loci had sufficient flanking regions (shotgun) while only 7 were found with RAD. All microsatellites were monomorphic in the Bornean but polymorphic in another elephant subspecies. Despite using different sample sizes, and the well known differences in the two platforms used regarding sequence length and throughput, the two approaches showed high validation rate. The approaches used here for marker development in a threatened species demonstrate the utility of high throughput sequencing technologies as a starting point for the development of genomic tools in a non-model species and in particular for a species with low genetic diversity.
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Veres M, Duselis AR, Graft A, Pryor W, Crossland J, Vrana PB, Szalai G. The biology and methodology of assisted reproduction in deer mice (Peromyscus maniculatus). Theriogenology 2011; 77:311-9. [PMID: 21924468 DOI: 10.1016/j.theriogenology.2011.07.044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 07/27/2011] [Accepted: 07/28/2011] [Indexed: 11/17/2022]
Abstract
Although laboratory-reared species of the genus Peromyscus-including deer mice-are used as model animals in a wide range of research, routine manipulation of Peromyscus embryogenesis and reproduction has been lagging. The objective of the present study was to optimize conditions for oocyte and/or embryo retrieval and for in vitro culturing. On average, 6.4 oocytes per mouse were recovered when two doses of 15 IU of pregnant mare serum gonadotropin (PMSG) were given 24 h apart, followed by 15 IU of hCG 48 h later. Following this hormone priming, females mated overnight with a fertile male yielded an average of 9.1 two-cell stage embryos. Although two-cell stage embryos developed to 8-cell stage in Potassium Simplex Optimized Medium (KSOM; Millipore-Chemicon, Billerica, MA, USA) in vitro, but not further, embryos recovered at the 8- to 16-cell stages developed into fully expanded blastocysts when cultured in M16 media in vitro. These blastocysts had full potential to develop into late stage fetuses and possibly into live pups. As a result of the present work, all stages of Peromyscus preimplantation development are now obtainable in numbers sufficient for molecular or other analyses. These advances provide the opportunity for routine studies involving embryo transfer (e.g., chimeras, transgenics), and preservation of genetic lines by cryopreservation.
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Affiliation(s)
- Monika Veres
- Peromyscus Genetic Stock Center, Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, USA
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Rivadeneira C, Allen JM, Reed DL. Microsatellite loci for testing temporal changes in the population genetics of the Florida mouse (Podomys floridanus). CONSERV GENET RESOUR 2011. [DOI: 10.1007/s12686-010-9308-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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