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Schiebelhut LM, Guillaume AS, Kuhn A, Schweizer RM, Armstrong EE, Beaumont MA, Byrne M, Cosart T, Hand BK, Howard L, Mussmann SM, Narum SR, Rasteiro R, Rivera-Colón AG, Saarman N, Sethuraman A, Taylor HR, Thomas GWC, Wellenreuther M, Luikart G. Genomics and conservation: Guidance from training to analyses and applications. Mol Ecol Resour 2024; 24:e13893. [PMID: 37966259 DOI: 10.1111/1755-0998.13893] [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: 06/10/2022] [Revised: 10/25/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.
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Affiliation(s)
- Lauren M Schiebelhut
- Life and Environmental Sciences, University of California, Merced, California, USA
| | - Annie S Guillaume
- Geospatial Molecular Epidemiology group (GEOME), Laboratory for Biological Geochemistry (LGB), École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Arianna Kuhn
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
- Virginia Museum of Natural History, Martinsville, Virginia, USA
| | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | | | - Mark A Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Margaret Byrne
- Department of Biodiversity, Conservation and Attractions, Biodiversity and Conservation Science, Perth, Western Australia, Australia
| | - Ted Cosart
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Brian K Hand
- Flathead Lake Biological Station, University of Montana, Polson, Montana, USA
| | - Leif Howard
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
| | - Steven M Mussmann
- Southwestern Native Aquatic Resources and Recovery Center, U.S. Fish & Wildlife Service, Dexter, New Mexico, USA
| | - Shawn R Narum
- Hagerman Genetics Lab, University of Idaho, Hagerman, Idaho, USA
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Norah Saarman
- Department of Biology and Ecology Center, Utah State University, Logan, Utah, USA
| | - Arun Sethuraman
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Helen R Taylor
- Royal Zoological Society of Scotland, Edinburgh, Scotland
| | - Gregg W C Thomas
- Informatics Group, Harvard University, Cambridge, Massachusetts, USA
| | - Maren Wellenreuther
- Plant and Food Research, Nelson, New Zealand
- University of Auckland, Auckland, New Zealand
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
- Flathead Lake Biology Station, University of Montana, Missoula, Montana, USA
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2
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Genetic structure of American bullfrog populations in Brazil. Sci Rep 2022; 12:9927. [PMID: 35705600 PMCID: PMC9200760 DOI: 10.1038/s41598-022-13870-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/30/2022] [Indexed: 11/15/2022] Open
Abstract
Non-native species are a major problem affecting numerous biomes around the globe. Information on their population genetics is crucial for understanding their invasion history and dynamics. We evaluated the population structure of the non-native American bullfrog, Aquarana catesbeiana, in Brazil on the basis of 324 samples collected from feral and captive groups at 38 sites in seven of the nine states where feral populations occur. We genotyped all samples using previously developed, highly polymorphic microsatellite loci and performed a discriminant analysis of principal components together with Jost’s D index to quantify pairwise differentiation between populations. We then amplified 1,047 base pairs of the mitochondrial cytochrome b (cytb) gene from the most divergent samples from each genetic population and calculated their pairwise differences. Both the microsatellite and cytb data indicated that bullfrogs comprise two populations. Population grouping 1 is widespread and possesses two cytb haplotypes. Population grouping 2 is restricted to only one state and possesses only one of the haplotypes from Population grouping 1. We show that there were two imports of bullfrogs to Brazil and that there is low genetic exchange between population groupings. Also, we find that there is no genetic divergence among feral and captive populations suggesting continuous releases. The limited genetic variability present in the country is associated to the small number of introductions and founders. Feral bullfrogs are highly associated to leaks from farms, and control measures should focus on preventing escapes using other resources than genetics, as feral and captive populations do not differ.
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Tang D, Cai W, Yang W, Chen S, Li L. Effectiveness of Health-Related Behavior Interventions on Physical Activity-Related Injuries in Junior Middle School Students. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:4049. [PMID: 35409732 PMCID: PMC8997892 DOI: 10.3390/ijerph19074049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 02/05/2023]
Abstract
The objective of this study was to determine the effectiveness of an intervention program based on Health-Related Behavior Theory (HRBT) in reducing physical activity-related injuries (PARIs) occurrence and individual risk-taking behaviors, as well as improving PA-related behaviors. A total of 1044 students from six junior middle schools in Shantou city were included and divided randomly into an intervention group (n = 550) and a control group (n = 494), respectively. The intervention group followed a prescribed PARIs intervention program based on HRBT, and the control group performed a common health education program, consisting of seven sessions and lasting seven months from May to November 2018. After the intervention, both groups showed a significantly lower prevalence of PARIs (intervention group: from 25.45% to 10.91%, control group: from 29.76% to 11.74%, both p < 0.05), but no significant between-group differences could be observed in the post-intervention PARIs prevalence (p > 0.05). Compared with the control group, students in the intervention group had a higher improvement in PA-related behaviors and a lower score of risk-taking behaviors (both p < 0.05). Thus, it could be concluded that the HRBT intervention program had a positive effect on PA-related and risk-taking behaviors in junior middle school students, though its effectiveness in reducing the occurrence of PARIs was not significant.
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Affiliation(s)
- Dongchun Tang
- School of Public Health, Shantou University, Shantou 515041, China
- Injury Prevention Research Center, Shantou University Medical College, Shantou 515041, China
- Department of Non-communicable Diseases Control, Futian District Institute for Prevention and Control of Chronic Diseases, Shenzhen 518048, China
| | - Weicong Cai
- School of Public Health, Shantou University, Shantou 515041, China
- Injury Prevention Research Center, Shantou University Medical College, Shantou 515041, China
- Shenzhen Center for Chronic Disease Control, Shenzhen 518020, China
- The George Institute for Global Health, University of New South Wales, Newtown, NSW 2042, Australia
| | - Wenda Yang
- School of Public Health, Shantou University, Shantou 515041, China
- Injury Prevention Research Center, Shantou University Medical College, Shantou 515041, China
| | - Shangmin Chen
- School of Public Health, Shantou University, Shantou 515041, China
- Injury Prevention Research Center, Shantou University Medical College, Shantou 515041, China
| | - Liping Li
- School of Public Health, Shantou University, Shantou 515041, China
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4
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Zhang H, Wong TY, Broekman BFP, Chong YS, Shek LP, Gluckman PD, Tan KH, Meaney MJ, Fortier MV, Qiu A. Maternal Adverse Childhood Experience and Depression in Relation with Brain Network Development and Behaviors in Children: A Longitudinal Study. Cereb Cortex 2021; 31:4233-4244. [PMID: 33825872 DOI: 10.1093/cercor/bhab081] [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: 12/06/2020] [Revised: 02/14/2021] [Accepted: 03/10/2021] [Indexed: 01/28/2023] Open
Abstract
Maternal childhood maltreatment and depression increase risks for the psychopathology of the offspring. This study employed a longitudinal dataset of mother-child dyads to investigate the developmental trajectories of brain functional networks and behaviors of children in relation with maternal childhood adverse experience and depression. Maternal childhood trauma was retrospectively assessed via childhood trauma questionnaire, whereas maternal depressive symptoms were prospectively evaluated during pregnancy and after delivery (n = 518). Child brain scans were acquired at age of 4.5, 6, and 7.5 years (n = 163) and behavioral problems were measured at 7.5 years using the Child Behavior Checklist. We found the functional connectivity of the language network with the sensorimotor, frontal, and attentional networks as a function of maternal adverse experience that interacted with sex and age. Girls exposed to mothers with depressive symptoms or childhood abuse showed the increased development of the functional connectivity of the language network with the visual networks, which was associated with social problems. Girls exposed to mothers with depressive symptoms showed the slower growth of the functional connectivity of the language network with the sensorimotor networks. Our findings, in a community sample, suggest the language network organization as neuroendophenotypes for maternal childhood trauma and depression.
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Affiliation(s)
- Han Zhang
- School of Computer Engineering and Science, Shanghai University, Shanghai 200444, China.,Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Ting-Yat Wong
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore
| | - Birit F P Broekman
- Singapore Institute for Clinical Sciences, Singapore 117609, Singapore.,Department of Psychiatry, OLVG and Amsterdam UMC, VU University, Amsterdam 1081 HJ, the Netherlands
| | - Yap-Seng Chong
- Singapore Institute for Clinical Sciences, Singapore 117609, Singapore.,Department of Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore 119228, Singapore
| | - Lynette P Shek
- Department of Pediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University of Singapore, Singapore 119228, Singapore
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences, Singapore 117609, Singapore
| | - Kok Hian Tan
- Department of Maternal Fetal Medicine, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Michael J Meaney
- Singapore Institute for Clinical Sciences, Singapore 117609, Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.,Douglas Mental Health University Institute, McGill University, Montreal H4H 1R3, Canada
| | - Marielle V Fortier
- Department of Diagnostic and Interventional Imaging, KK Women's and Children's Hospital, Singapore 229899, Singapore
| | - Anqi Qiu
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,The N.1 Institute for Health, National University of Singapore, Singapore 117456, Singapore.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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5
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White TJH, Frazier JA, Althoff RR, Novins DK. What the Journal of the American Academy of Child and Adolescent Psychiatry Is Looking for in Neuroimaging Submissions. J Am Acad Child Adolesc Psychiatry 2021; 60:324-328. [PMID: 33307124 DOI: 10.1016/j.jaac.2020.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/02/2020] [Indexed: 02/06/2023]
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6
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Mayoke A, Ouma JO, Mireji PO, Omondi SF, Muya SM, Itoua A, Okoth SO, Bateta R. Population Structure and Migration Patterns of the Tsetse Fly Glossina fuscipes in Congo-Brazzaville. Am J Trop Med Hyg 2020; 104:917-927. [PMID: 33372648 PMCID: PMC7941806 DOI: 10.4269/ajtmh.20-0774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/17/2020] [Indexed: 11/07/2022] Open
Abstract
Tsetse flies of the palpalis group, particularly Glossina fuscipes, are the main vectors of human African trypanosomiasis or sleeping sickness in Congo-Brazzaville. They transmit the deadly human parasite, Trypanosoma brucei gambiense and other trypanosomes that cause animal trypanosomiasis. Knowledge on diversity, population structure, population size, and gene flow is a prerequisite for designing effective tsetse control strategies. There is limited published information on these parameters including migration patterns of G. fuscipes in Congo-Brazzaville. We genotyped 288 samples of G. fuscipes from Bomassa (BMSA), Bouemba (BEMB), and Talangai (TLG) locations at 10 microsatellite loci and determined levels of genetic diversity, differentiation, structuring, and gene flow among populations. We observed high genetic diversity in all three localities. Mean expected heterozygosity was 0.77 ± 0.04, and mean allelic richness was 11.2 ± 1.35. Deficiency of heterozygosity was observed in all populations with positive and significant F IS values (0.077-0.149). Structure analysis revealed three clusters with genetic admixtures, evidence of closely related but potentially different taxa within G. fuscipes. Genetic differentiation indices were low but significant (F ST = 0.049, P < 0.05), indicating ongoing gene flow countered with a stronger force of drift. We recorded significant migration from all the three populations, suggesting exchange of genetic information between and among locations. Ne estimates revealed high and infinite population sizes in BEMB and TLG. These critical factors should be considered when planning area-wide tsetse control interventions in the country to prevent resurgence of tsetse from relict populations and/or reinvasion of cleared habitats.
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Affiliation(s)
- Abraham Mayoke
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology and Innovation, Nairobi, Kenya
- Kenya Forestry Research Institute, Nairobi, Kenya
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
- Marien Ngouabi University, Brazzaville, Congo
| | - Johnson O. Ouma
- African Technical Research Centre, Vector Health International, Arusha, Tanzania
| | - Paul O. Mireji
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
| | | | - Shadrack M. Muya
- School of Biological Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Andre Itoua
- Laboratoire de Parasitologie, Centre de Recherche Veterinaire et Zootechniques, Brazzaville, Congo
| | - Sylvance O. Okoth
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
| | - Rosemary Bateta
- Biotechnology Research Institute, Kenya Agricultural and Livestock Research Organization, Kikuyu, Kenya
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7
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White T, van der Ende J, Nichols TE. Beyond Bonferroni revisited: concerns over inflated false positive research findings in the fields of conservation genetics, biology, and medicine. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01178-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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8
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Sethuraman A, Gonzalez NM, Grenier CE, Kansagra KS, Mey KK, Nunez-Zavala SB, Summerhays BEW, Wulf GK. Continued misuse of multiple testing correction methods in population genetics-A wake-up call? Mol Ecol Resour 2019; 19:23-26. [PMID: 30701708 DOI: 10.1111/1755-0998.12969] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/02/2018] [Accepted: 11/12/2018] [Indexed: 11/29/2022]
Abstract
Population geneticists often use multiple independent hypothesis tests of Hardy-Weinberg Equilibrium (HWE), Linkage Disequilibrium (LD), and population differentiation, to make broad inferences about their systems of choice. However, correcting for Family-Wise Error Rates (FWER) that are inflated due to multiple comparisons, is sparingly reported in our current literature. In this issue of Molecular Ecology Resources, perform a meta-analysis of 215 population genetics studies published between 2011 and 2013 to show (i) scarce use of FWER corrections across all three classes of tests, and (ii) when used, inconsistent application of correction methods with a clear bias towards less-conservative corrections for tests of population differentiation, than for tests of HWE, and LD. Here we replicate this meta-analysis using 205 population genetics studies published between 2013 and 2018, to show the same continued disuse, and inconsistencies. We hope that both studies serve as a wake-up call to population geneticists, reviewers, and editors to be rigorous about consistently correcting for FWER inflation.
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Affiliation(s)
- Arun Sethuraman
- Department of Biological Sciences, California State University San Marcos, San Marcos, California
| | - Nicolette M Gonzalez
- Department of Biological Sciences, California State University San Marcos, San Marcos, California
| | - Christy E Grenier
- Department of Biological Sciences, California State University San Marcos, San Marcos, California
| | - Khyati S Kansagra
- Department of Biological Sciences, California State University San Marcos, San Marcos, California
| | - Ken K Mey
- Department of Biological Sciences, California State University San Marcos, San Marcos, California
| | - Stefany B Nunez-Zavala
- Department of Biological Sciences, California State University San Marcos, San Marcos, California
| | - Bryce E W Summerhays
- Department of Biological Sciences, California State University San Marcos, San Marcos, California
| | - Gwendalyn K Wulf
- Department of Biological Sciences, California State University San Marcos, San Marcos, California
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