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Westphal D, Mancini AN, Baden AL. Primate landscape genetics: A review and practical guide. Evol Anthropol 2021; 30:171-184. [PMID: 33720482 DOI: 10.1002/evan.21891] [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: 04/15/2019] [Revised: 06/12/2020] [Accepted: 02/17/2021] [Indexed: 11/06/2022]
Abstract
Landscape genetics is an emerging field that integrates population genetics, landscape ecology, and spatial statistics to investigate how geographical and environmental features and evolutionary processes such as gene flow, genetic drift, and selection structure genetic variation at both the population and individual levels, with implications for ecology, evolution, and conservation biology. Despite being particularly well suited for primatologists, this method is currently underutilized. Here, we synthesize the current state of research on landscape genetics in primates. We begin by outlining how landscape genetics has been used to disentangle the drivers of diversity, followed by a review of how landscape genetic methods have been applied to primates. This is followed by a section highlighting special considerations when applying the methods to primates, and a practical guide to facilitate further landscape genetics studies using both existing and de novo datasets. We conclude by exploring future avenues of inquiry that could be facilitated by recent developments as well as underdeveloped applications of landscape genetics to primates.
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Affiliation(s)
- Darice Westphal
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Amanda N Mancini
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA
| | - Andrea L Baden
- Department of Anthropology, The Graduate Center, City University of New York, New York, New York, USA.,The New York Consortium in Evolutionary Primatology (NYCEP), New York, New York, USA.,Department of Anthropology, Hunter College, New York, New York, USA
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3
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Jasinska AJ, Dong TS, Lagishetty V, Katzka W, Jacobs JP, Schmitt CA, Cramer JD, Ma D, Coetzer WG, Grobler JP, Turner TR, Freimer N, Pandrea I, Apetrei C. Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys. MICROBIOME 2020; 8:154. [PMID: 33158452 PMCID: PMC7648414 DOI: 10.1186/s40168-020-00928-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 10/06/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The microbiota plays an important role in HIV pathogenesis in humans. Microbiota can impact health through several pathways such as increasing inflammation in the gut, metabolites of bacterial origin, and microbial translocation from the gut to the periphery which contributes to systemic chronic inflammation and immune activation and the development of AIDS. Unlike HIV-infected humans, SIV-infected vervet monkeys do not experience gut dysfunction, microbial translocation, and chronic immune activation and do not progress to immunodeficiency. Here, we provide the first reported characterization of the microbial ecosystems of the gut and genital tract in a natural nonprogressing host of SIV, wild vervet monkeys from South Africa. RESULTS We characterized fecal, rectal, vaginal, and penile microbiomes in vervets from populations heavily infected with SIV from diverse locations across South Africa. Geographic site, age, and sex affected the vervet microbiome across different body sites. Fecal and vaginal microbiome showed marked stratification with three enterotypes in fecal samples and two vagitypes, which were predicted functionally distinct within each body site. External bioclimatic factors, biome type, and environmental temperature influenced microbiomes locally associated with vaginal and rectal mucosa. Several fecal microbial taxa were linked to plasma levels of immune molecules, for example, MIG was positively correlated with Lactobacillus and Escherichia/Shigella and Helicobacter, and IL-10 was negatively associated with Erysipelotrichaceae, Anaerostipes, Prevotella, and Anaerovibrio, and positively correlated with Bacteroidetes and Succinivibrio. During the chronic phase of infection, we observed a significant increase in gut microbial diversity, alterations in community composition (including a decrease in Proteobacteria/Succinivibrio in the gut) and functionality (including a decrease in genes involved in bacterial invasion of epithelial cells in the gut), and partial reversibility of acute infection-related shifts in microbial abundance observed in the fecal microbiome. As part of our study, we also developed an accurate predictor of SIV infection using fecal samples. CONCLUSIONS The vervets infected with SIV and humans infected with HIV differ in microbial responses to infection. These responses to SIV infection may aid in preventing microbial translocation and subsequent disease progression in vervets, and may represent host microbiome adaptations to the virus. Video Abstract.
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Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
- Eye on Primates, Los Angeles, CA, USA.
| | - Tien S Dong
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Venu Lagishetty
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - William Katzka
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Jonathan P Jacobs
- The Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Division of Gastroenterology, Hepatology and Parenteral Nutrition, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
- UCLA Microbiome Center, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Jennifer Danzy Cramer
- Department of Sociology, Anthropology, and General Studies, American Public University System, Charles Town, WV, USA
| | - Dongzhu Ma
- Department of Orthopedic Surgery, University of Pittsburgh, Pittsburgh, PA, USA
| | - Willem G Coetzer
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Trudy R Turner
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
- Department of Anthropology, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Nelson Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Ivona Pandrea
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Cristian Apetrei
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Ham-Dueñas JG, Canales-del-Castillo R, Voelker G, Ruvalcaba-Ortega I, Aguirre-Calderón CE, González-Rojas JI. Adaptive genetic diversity and evidence of population genetic structure in the endangered Sierra Madre Sparrow (Xenospiza baileyi). PLoS One 2020; 15:e0232282. [PMID: 32352998 PMCID: PMC7192469 DOI: 10.1371/journal.pone.0232282] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/10/2020] [Indexed: 12/13/2022] Open
Abstract
The magnitude and distribution of genetic diversity through space and time can provide useful information relating to evolutionary potential and conservation status in threatened species. In assessing genetic diversity in species that are of conservation concern, several studies have focused on the use of Toll-like receptors (TLRs). TLRs are innate immune genes related to pathogen resistance, and polymorphisms may reflect not only levels of functional diversity, but may also be used to assess genetic diversity within and among populations. Here, we combined four potentially adaptive markers (TLRs) with one mitochondrial (COI) marker to evaluate genetic variation in the endangered Sierra Madre Sparrow (Xenospiza baileyi). This species offers an ideal model to investigate population and evolutionary genetic processes that may be occurring in a habitat restricted endangered species with disjunct populations (Mexico City and Durango), the census sizes of which differ by an order of magnitude. TLRs diversity in the Sierra Madre Sparrow was relatively high, which was not expected given its two small, geographically isolated populations. Genetic diversity was different (but not significantly so) between the two populations, with less diversity seen in the smaller Durango population. Population genetic structure between populations was due to isolation and different selective forces acting on different TLRs; population structure was also evident in COI. Reduction of genetic diversity in COI was observed over 20 years in the Durango population, a result likely caused by habitat loss, a factor which may be the main cause of diversity decline generally. Our results provide information related to the ways in which adaptive variation can be altered by demographic changes due to human-mediated habitat alterations. Furthermore, our findings may help to guide conservation schemes for both populations and their restricted habitat.
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Affiliation(s)
- José G. Ham-Dueñas
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
| | - Ricardo Canales-del-Castillo
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
- * E-mail:
| | - Gary Voelker
- Department of Wildlife and Fisheries Sciences, Biodiversity Research and Teaching Collections, Texas A&M University, College Station, Texas, United States of America
| | - Irene Ruvalcaba-Ortega
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
| | | | - José I. González-Rojas
- Laboratorio de Biología de la Conservación y Desarrollo Sustentable. Cd. Universitaria, Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, San Nicolás de los Garza, Nuevo León, México
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Purifying selection shaping the evolution of the Toll-like receptor 2 TIR domain in brown hares (Lepus europaeus) from Europe and the Middle East. Mol Biol Rep 2020; 47:2975-2984. [PMID: 32236892 DOI: 10.1007/s11033-020-05382-x] [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: 08/24/2019] [Accepted: 03/19/2020] [Indexed: 10/24/2022]
Abstract
Toll-like receptors (TLRs) are transmembrane proteins of the innate immune system, composed of the ectodomain involved in pathogen recognition and the intracellular Toll/interleukin-1 receptor (TIR) domain important for downstream signal transduction. Here, we analyze the genetic variability of TIR nucleotide and amino-acid sequences of the TLR2 gene in 243 brown hares from Europe and the Middle East and tested for the presence of selection signals and spatial structuring. TLR2 TIR domain sequences were PCR amplified and sequenced, while genotyping was performed by phasing. Genetic diversity indices were calculated in DnaSP and Arlequin, while presence of selection signals was tested using MEGA and the Datamonkey web server. The presence of spatial patterns in TIR sequence distribution was tested by spatial Principal Component Analysis (sPCA) in adegenet. A total of 13 haplotypes were revealed with haplotype diversity of 0.424, and nucleotide diversity (π) of 0.00138. Two spatial clusters were revealed: "Anatolia/Middle East" and "Europe". In Anatolia the two most prevalent amino-acid variants, A and B (the latter being the most ancestral) were maintained at similar frequencies; but in Europe a shift in genotype frequencies was observed as well as a higher number of nonsynonymous substitutions giving rise to novel amino-acid protein variants originating from the evolutionarily younger protein variant. Molecular diversity (haplotype and nucleotide diversity) indices were significantly higher in the "Anatolia/Middle East" cluster. A signal of purifying selection was detected acting on the TIR sequences.
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Jasinska AJ. Resources for functional genomic studies of health and development in nonhuman primates. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 171 Suppl 70:174-194. [PMID: 32221967 DOI: 10.1002/ajpa.24051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Revised: 01/22/2020] [Accepted: 02/26/2020] [Indexed: 01/01/2023]
Abstract
Primates display a wide range of phenotypic variation underlaid by complex genetically regulated mechanisms. The links among DNA sequence, gene function, and phenotype have been of interest from an evolutionary perspective, to understand functional genome evolution and its phenotypic consequences, and from a biomedical perspective to understand the shared and human-specific roots of health and disease. Progress in methods for characterizing genetic, transcriptomic, and DNA methylation (DNAm) variation is driving the rapid development of extensive omics resources, which are now increasingly available from humans as well as a growing number of nonhuman primates (NHPs). The fast growth of large-scale genomic data is driving the emergence of integrated tools and databases, thus facilitating studies of gene functionality across primates. This review describes NHP genomic resources that can aid in exploration of how genes shape primate phenotypes. It focuses on the gene expression trajectories across development in different tissues, the identification of functional genetic variation (including variants deleterious for protein function and regulatory variants modulating gene expression), and DNAm profiles as an emerging tool to understand the process of aging. These resources enable comparative functional genomics approaches to identify species-specific and primate-shared gene functionalities associated with health and development.
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Affiliation(s)
- Anna J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, California, USA.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Eye on Primates, Los Angeles, California, USA
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