1
|
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:e14254. [PMID: 38563102 DOI: 10.1111/cobi.14254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [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.
Collapse
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
| |
Collapse
|
2
|
Davis RP, Simmons LM, Shaw SL, Sass GG, Sard NM, Isermann DA, Larson WA, Homola JJ. Demographic patterns of walleye ( Sander vitreus) reproductive success in a Wisconsin population. Evol Appl 2024; 17:e13665. [PMID: 38468712 PMCID: PMC10925830 DOI: 10.1111/eva.13665] [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: 08/08/2023] [Revised: 12/21/2023] [Accepted: 01/17/2024] [Indexed: 03/13/2024] Open
Abstract
Harvest in walleye Sander vitreus fisheries is size-selective and could influence phenotypic traits of spawners; however, contributions of individual spawners to recruitment are unknown. We used parentage analyses using single nucleotide polymorphisms to test whether parental traits were related to the probability of offspring survival in Escanaba Lake, Wisconsin. From 2017 to 2020, 1339 adults and 1138 juveniles were genotyped and 66% of the offspring were assigned to at least one parent. Logistic regression indicated the probability of reproductive success (survival of age-0 to first fall) was positively (but weakly) related to total length and growth rate in females, but not age. No traits analyzed were related to reproductive success for males. Our analysis identified the model with the predictors' growth rate and year for females and the models with year and age and year for males as the most likely models to explain variation in reproductive success. Our findings indicate that interannual variation (i.e., environmental conditions) likely plays a key role in determining the probability of reproductive success in this population and provide limited support that female age, length, and growth rate influence recruitment.
Collapse
Affiliation(s)
- Robert P. Davis
- Wisconsin Cooperative Fishery Research UnitUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - Levi M. Simmons
- Wisconsin Cooperative Fishery Research UnitUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - Stephanie L. Shaw
- Office of Applied Science, Wisconsin Department of Natural ResourcesEscanaba Lake Research StationBoulder JunctionWisconsinUSA
| | - Greg G. Sass
- Office of Applied Science, Wisconsin Department of Natural ResourcesEscanaba Lake Research StationBoulder JunctionWisconsinUSA
| | - Nicholas M. Sard
- Department of Biological SciencesState University of New York‐OswegoOswegoNew YorkUSA
| | - Daniel A. Isermann
- U.S. Geological Survey, Wisconsin Cooperative Fishery Research UnitUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| | - Wesley A. Larson
- National Marine Fisheries Service, Alaska Fisheries Science Center, Auke Bay LaboratoriesNational Oceanic and Atmospheric AdministrationJuneauAlaskaUSA
| | - Jared J. Homola
- U.S. Geological Survey, Wisconsin Cooperative Fishery Research UnitUniversity of Wisconsin‐Stevens PointStevens PointWisconsinUSA
| |
Collapse
|
3
|
Ropp AJ, Reece KS, Snyder RA, Song J, Biesack EE, McDowell JR. Fine-scale population structure of the northern hard clam ( Mercenaria mercenaria) revealed by genome-wide SNP markers. Evol Appl 2023; 16:1422-1437. [PMID: 37622097 PMCID: PMC10445094 DOI: 10.1111/eva.13577] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 08/26/2023] Open
Abstract
Aquaculture is growing rapidly worldwide, and sustainability is dependent on an understanding of current genetic variation and levels of connectivity among populations. Genetic data are essential to mitigate the genetic and ecological impacts of aquaculture on wild populations and guard against unintended human-induced loss of intraspecific diversity in aquacultured lines. Impacts of disregarding genetics can include loss of diversity within and between populations and disruption of local adaptation patterns, which can lead to a decrease in fitness. The northern hard clam, Mercenaria mercenaria (Linnaeus, 1758), is an economically valuable aquaculture species along the North American Atlantic and Gulf coasts. Hard clams have a pelagic larval phase that allows for dispersal, but the level of genetic connectivity among geographic areas is not well understood. To better inform the establishment of site-appropriate aquaculture brood stocks, this study used DArTseq™ genotyping by sequencing to characterize the genetic stock structure of wild clams sampled along the east coast of North America and document genetic diversity within populations. Samples were collected from 15 locations from Prince Edward Island, Canada, to South Carolina, USA. Stringent data filtering resulted in 4960 single nucleotide polymorphisms from 448 individuals. Five genetic breaks separating six genetically distinct populations were identified: Canada, Maine, Massachusetts, Mid-Atlantic, Chesapeake Bay, and the Carolinas (F ST 0.003-0.046; p < 0.0001). This is the first study to assess population genetic structure of this economically important hard clam along a large portion of its native range with high-resolution genomic markers, enabling identification of previously unrecognized population structure. Results of this study not only broaden insight into the factors shaping the current distribution of M. mercenaria but also reveal the genetic population dynamics of a species with a long pelagic larval dispersal period along the North American Atlantic and Gulf coasts.
Collapse
Affiliation(s)
- Ann J. Ropp
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Kimberly S. Reece
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Richard A. Snyder
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Jingwei Song
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Ellen E. Biesack
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| | - Jan R. McDowell
- Virginia Institute of Marine Science, William & MaryGloucester PointVirginiaUSA
| |
Collapse
|
4
|
Iannucci A, Benazzo A, Natali C, Arida EA, Zein MSA, Jessop TS, Bertorelle G, Ciofi C. Population structure, genomic diversity and demographic history of Komodo dragons inferred from whole-genome sequencing. Mol Ecol 2021; 30:6309-6324. [PMID: 34390519 PMCID: PMC9292392 DOI: 10.1111/mec.16121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 07/28/2021] [Accepted: 08/03/2021] [Indexed: 02/07/2023]
Abstract
Population and conservation genetics studies have greatly benefited from the development of new techniques and bioinformatic tools associated with next-generation sequencing. Analysis of extensive data sets from whole-genome sequencing of even a few individuals allows the detection of patterns of fine-scale population structure and detailed reconstruction of demographic dynamics through time. In this study, we investigated the population structure, genomic diversity and demographic history of the Komodo dragon (Varanus komodoensis), the world's largest lizard, by sequencing the whole genomes of 24 individuals from the five main Indonesian islands comprising the entire range of the species. Three main genomic groups were observed. The populations of the Island of Komodo and the northern coast of Flores, in particular, were identified as two distinct conservation units. Degrees of genomic divergence among island populations were interpreted as a result of changes in sea level affecting connectivity across islands. Demographic inference suggested that Komodo dragons probably experienced a relatively steep population decline over the last million years, reaching a relatively stable Ne during the Saalian glacial cycle (400-150 thousand years ago) followed by a rapid Ne decrease. Genomic diversity of Komodo dragons was similar to that found in endangered or already extinct reptile species. Overall, this study provides an example of how whole-genome analysis of a few individuals per population can help define population structure and intraspecific demographic dynamics. This is particularly important when applying population genomics data to conservation of rare or elusive endangered species.
Collapse
Affiliation(s)
| | - Andrea Benazzo
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
| | - Chiara Natali
- Department of BiologyUniversity of FlorenceFirenzeItaly
| | - Evy Ayu Arida
- Research Center for BiologyThe Indonesian Institute of Sciences (LIPI)Cibinong Science CenterCibinongIndonesia
| | - Moch Samsul Arifin Zein
- Research Center for BiologyThe Indonesian Institute of Sciences (LIPI)Cibinong Science CenterCibinongIndonesia
| | - Tim S. Jessop
- School of Life and Environmental SciencesDeakin UniversityGeelongVic.Australia
| | - Giorgio Bertorelle
- Department of Life Sciences and BiotechnologyUniversity of FerraraFerraraItaly
| | - Claudio Ciofi
- Department of BiologyUniversity of FlorenceFirenzeItaly
| |
Collapse
|
5
|
O'Grady CJ, Dhandapani V, Colbourne JK, Frisch D. Refining the evolutionary time machine: An assessment of whole genome amplification using single historical Daphnia eggs. Mol Ecol Resour 2021; 22:946-961. [PMID: 34672105 DOI: 10.1111/1755-0998.13524] [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] [Received: 04/17/2021] [Revised: 09/03/2021] [Accepted: 09/07/2021] [Indexed: 12/14/2022]
Abstract
Whole genome sequencing is instrumental for the study of genome variation in natural populations, delivering important knowledge on genomic modifications and potential targets of natural selection at the population level. Large dormant eggbanks of aquatic invertebrates such as the keystone herbivore Daphnia, a microcrustacean widespread in freshwater ecosystems, provide detailed sedimentary archives to study genomic processes over centuries. To overcome the problem of limited DNA amounts in single Daphnia dormant eggs, we developed an optimized workflow for whole genome amplification (WGA), yielding sufficient amounts of DNA for downstream whole genome sequencing of individual historical eggs, including polyploid lineages. We compare two WGA kits, applied to recently produced Daphnia magna dormant eggs from laboratory cultures, and to historical dormant eggs of Daphnia pulicaria collected from Arctic lake sediment between 10 and 300 years old. Resulting genome coverage breadth in most samples was ~70%, including those from >100-year-old isolates. Sequence read distribution was highly correlated among samples amplified with the same kit, but less correlated between kits. Despite this, a high percentage of genomic positions with single nucleotide polymorphisms in one or more samples (maximum of 74% between kits, and 97% within kits) were recovered at a depth required for genotyping. As a by-product of sequencing we obtained 100% coverage of the mitochondrial genomes even from the oldest isolates (~300 years). The mitochondrial DNA provides an additional source for evolutionary studies of these populations. We provide an optimized workflow for WGA followed by whole genome sequencing including steps to minimize exogenous DNA.
Collapse
Affiliation(s)
- Christopher James O'Grady
- School of Life Sciences, University of Warwick, Coventry, UK.,Cell and Gene Therapy Catapult, London, UK.,School of Biosciences, University of Birmingham, Birmingham, UK
| | | | | | - Dagmar Frisch
- School of Biosciences, University of Birmingham, Birmingham, UK.,Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, Germany
| |
Collapse
|
6
|
Farleigh K, Vladimirova SA, Blair C, Bracken JT, Koochekian N, Schield DR, Card DC, Finger N, Henault J, Leaché AD, Castoe TA, Jezkova T. The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard (Phrynosoma platyrhinos). Mol Ecol 2021; 30:4481-4496. [PMID: 34245067 DOI: 10.1111/mec.16070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 11/30/2022]
Abstract
Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization routes. Based on our analyses of a large SNP data set, we find evidence that both climate and demographic history have shaped the genetic structure of populations. Pronounced genetic differentiation was evident between populations occupying cold versus hot deserts, and we detected numerous loci with significant associations with climate. The genetic signal of founder effects, however, is still present in the genomes of the recently expanded populations, which comprise subsets of genetic variation found in the southern populations.
Collapse
Affiliation(s)
- Keaka Farleigh
- Department of Biology, Miami University, Oxford, Ohio, USA
| | | | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, Brooklyn, New York, USA.,Biology PhD Program, CUNY Graduate Center, New York, New York, USA
| | | | | | - Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts, USA
| | - Nicholas Finger
- Department of Biological Sciences, New York City College of Technology, The City University of New York, Brooklyn, New York, USA
| | | | - Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas, USA
| | - Tereza Jezkova
- Department of Biology, Miami University, Oxford, Ohio, USA
| |
Collapse
|
7
|
Seaborn T, Andrews KR, Applestein CV, Breech TM, Garrett MJ, Zaiats A, Caughlin TT. Integrating genomics in population models to forecast translocation success. Restor Ecol 2021. [DOI: 10.1111/rec.13395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Travis Seaborn
- Department of Fish and Wildlife Sciences University of Idaho Moscow ID U.S.A
| | - Kimberly R. Andrews
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID U.S.A
| | | | - Tyler M. Breech
- Department of Biological Sciences Idaho State University Pocatello ID U.S.A
| | - Molly J. Garrett
- Department of Fish and Wildlife Sciences University of Idaho Moscow ID U.S.A
| | - Andrii Zaiats
- Biological Sciences Boise State University Boise ID U.S.A
| | | |
Collapse
|
8
|
Schweizer RM, Saarman N, Ramstad KM, Forester BR, Kelley JL, Hand BK, Malison RL, Ackiss AS, Watsa M, Nelson TC, Beja-Pereira A, Waples RS, Funk WC, Luikart G. Big Data in Conservation Genomics: Boosting Skills, Hedging Bets, and Staying Current in the Field. J Hered 2021; 112:313-327. [PMID: 33860294 DOI: 10.1093/jhered/esab019] [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: 10/16/2020] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
A current challenge in the fields of evolutionary, ecological, and conservation genomics is balancing production of large-scale datasets with additional training often required to handle such datasets. Thus, there is an increasing need for conservation geneticists to continually learn and train to stay up-to-date through avenues such as symposia, meetings, and workshops. The ConGen meeting is a near-annual workshop that strives to guide participants in understanding population genetics principles, study design, data processing, analysis, interpretation, and applications to real-world conservation issues. Each year of ConGen gathers a diverse set of instructors, students, and resulting lectures, hands-on sessions, and discussions. Here, we summarize key lessons learned from the 2019 meeting and more recent updates to the field with a focus on big data in conservation genomics. First, we highlight classical and contemporary issues in study design that are especially relevant to working with big datasets, including the intricacies of data filtering. We next emphasize the importance of building analytical skills and simulating data, and how these skills have applications within and outside of conservation genetics careers. We also highlight recent technological advances and novel applications to conservation of wild populations. Finally, we provide data and recommendations to support ongoing efforts by ConGen organizers and instructors-and beyond-to increase participation of underrepresented minorities in conservation and eco-evolutionary sciences. The future success of conservation genetics requires both continual training in handling big data and a diverse group of people and approaches to tackle key issues, including the global biodiversity-loss crisis.
Collapse
Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT
| | - Norah Saarman
- Department of Biology, Utah State University, Logan, UT
| | - Kristina M Ramstad
- Department of Biology and Geology, University of South Carolina Aiken, Aiken, SC
| | | | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA
| | - Brian K Hand
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Rachel L Malison
- Flathead Lake Biological Station, University of Montana, Polson, MT
| | - Amanda S Ackiss
- Wisconsin Cooperative Fishery Research Unit, University of Wisconsin Stevens Point, Stevens Point, WI
| | | | | | - Albano Beja-Pereira
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO-UP), InBIO, Universidade do Porto, Vairão, Portugal.,DGAOT, Faculty of Sciences, University of Porto, Porto, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Faculty of Sciences, University of Porto, Porto, Portugal
| | - Robin S Waples
- Northwest Fisheries Science Center, NOAA Fisheries, Seattle, WA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO
| | - Gordon Luikart
- Division of Biological Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, University of Montana, Polson, MT
| |
Collapse
|
9
|
Comparative Analysis of SNP Discovery and Genotyping in Fagus sylvatica L. and Quercus robur L. Using RADseq, GBS, and ddRAD Methods. FORESTS 2021. [DOI: 10.3390/f12020222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Next-generation sequencing of reduced representation genomic libraries (RRL) is capable of providing large numbers of genetic markers for population genetic studies at relatively low costs. However, one major concern of these types of markers is the precision of genotyping, which is related to the common problem of missing data, which appears to be particularly important in association and genomic selection studies. We evaluated three RRL approaches (GBS, RADseq, ddRAD) and different SNP identification methods (de novo or based on a reference genome) to find the best solutions for future population genomics studies in two economically and ecologically important broadleaved tree species, namely F. sylvatica and Q. robur. We found that the use of ddRAD method coupled with SNP calling based on reference genomes provided the largest numbers of markers (28 k and 36 k for beech and oak, respectively), given standard filtering criteria. Using technical replicates of samples, we demonstrated that more than 80% of SNP loci should be considered as reliable markers in GBS and ddRAD, but not in RADseq data. According to the reference genomes’ annotations, more than 30% of the identified ddRAD loci appeared to be related to genes. Our findings provide a solid support for using ddRAD-based SNPs for future population genomics studies in beech and oak.
Collapse
|
10
|
Kraft DW, Conklin EE, Barba EW, Hutchinson M, Toonen RJ, Forsman ZH, Bowen BW. Genomics versus mtDNA for resolving stock structure in the silky shark ( Carcharhinus falciformis). PeerJ 2020; 8:e10186. [PMID: 33150082 PMCID: PMC7585369 DOI: 10.7717/peerj.10186] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022] Open
Abstract
Conservation genetic approaches for elasmobranchs have focused on regions of the mitochondrial genome or a handful of nuclear microsatellites. High-throughput sequencing offers a powerful alternative for examining population structure using many loci distributed across the nuclear and mitochondrial genomes. These single nucleotide polymorphisms are expected to provide finer scale and more accurate population level data; however, there have been few genomic studies applied to elasmobranch species. The desire to apply next-generation sequencing approaches is often tempered by the costs, which can be offset by pooling specimens prior to sequencing (pool-seq). In this study, we assess the utility of pool-seq by applying this method to the same individual silky sharks, Carcharhinus falciformis, previously surveyed with the mtDNA control region in the Atlantic and Indian Oceans. Pool-seq methods were able to recover the entire mitochondrial genome as well as thousands of nuclear markers. This volume of sequence data enabled the detection of population structure between regions of the Atlantic Ocean populations, undetected in the previous study (inter-Atlantic mitochondrial SNPs FST values comparison ranging from 0.029 to 0.135 and nuclear SNPs from 0.015 to 0.025). Our results reinforce the conclusion that sampling the mitochondrial control region alone may fail to detect fine-scale population structure, and additional sampling across the genome may increase resolution for some species. Additionally, this study shows that the costs of analyzing 4,988 loci using pool-seq methods are equivalent to the standard Sanger-sequenced markers and become less expensive when large numbers of individuals (>300) are analyzed.
Collapse
Affiliation(s)
- Derek W. Kraft
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Emily E. Conklin
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Evan W. Barba
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Melanie Hutchinson
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
- Joint Institute of Marine and Atmospheric Research, Pacific Islands Fisheries Science Center, NOAA, University of Hawai’i, Honolulu, HI, USA
| | - Robert J. Toonen
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Zac H. Forsman
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| | - Brian W. Bowen
- Hawai’i Institute of Marine Biology, University of Hawai’i, Kaneohe, HI, USA
| |
Collapse
|
11
|
Leung K, Ras E, Ferguson KB, Ariëns S, Babendreier D, Bijma P, Bourtzis K, Brodeur J, Bruins MA, Centurión A, Chattington SR, Chinchilla-Ramírez M, Dicke M, Fatouros NE, González-Cabrera J, Groot TVM, Haye T, Knapp M, Koskinioti P, Le Hesran S, Lyrakis M, Paspati A, Pérez-Hedo M, Plouvier WN, Schlötterer C, Stahl JM, Thiel A, Urbaneja A, van de Zande L, Verhulst EC, Vet LEM, Visser S, Werren JH, Xia S, Zwaan BJ, Magalhães S, Beukeboom LW, Pannebakker BA. Next-generation biological control: the need for integrating genetics and genomics. Biol Rev Camb Philos Soc 2020; 95:1838-1854. [PMID: 32794644 PMCID: PMC7689903 DOI: 10.1111/brv.12641] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/12/2022]
Abstract
Biological control is widely successful at controlling pests, but effective biocontrol agents are now more difficult to import from countries of origin due to more restrictive international trade laws (the Nagoya Protocol). Coupled with increasing demand, the efficacy of existing and new biocontrol agents needs to be improved with genetic and genomic approaches. Although they have been underutilised in the past, application of genetic and genomic techniques is becoming more feasible from both technological and economic perspectives. We review current methods and provide a framework for using them. First, it is necessary to identify which biocontrol trait to select and in what direction. Next, the genes or markers linked to these traits need be determined, including how to implement this information into a selective breeding program. Choosing a trait can be assisted by modelling to account for the proper agro‐ecological context, and by knowing which traits have sufficiently high heritability values. We provide guidelines for designing genomic strategies in biocontrol programs, which depend on the organism, budget, and desired objective. Genomic approaches start with genome sequencing and assembly. We provide a guide for deciding the most successful sequencing strategy for biocontrol agents. Gene discovery involves quantitative trait loci analyses, transcriptomic and proteomic studies, and gene editing. Improving biocontrol practices includes marker‐assisted selection, genomic selection and microbiome manipulation of biocontrol agents, and monitoring for genetic variation during rearing and post‐release. We conclude by identifying the most promising applications of genetic and genomic methods to improve biological control efficacy.
Collapse
Affiliation(s)
- Kelley Leung
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Erica Ras
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria
| | - Kim B Ferguson
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Simone Ariëns
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | | | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University & Research, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria
| | - Jacques Brodeur
- Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke Est, Montréal, Quebec, Canada, H1X 2B2
| | - Margreet A Bruins
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Alejandra Centurión
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | - Sophie R Chattington
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | - Milena Chinchilla-Ramírez
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Marcel Dicke
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Nina E Fatouros
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Joel González-Cabrera
- Department of Genetics, Estructura de Recerca Interdisciplinar en Biotecnología i Biomedicina (ERI-BIOTECMED), Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Universitat de València, Dr Moliner 50, 46100, Burjassot, Valencia, Spain
| | - Thomas V M Groot
- Koppert Biological Systems, Veilingweg 14, 2651 BE, Berkel en Rodenrijs, The Netherlands
| | - Tim Haye
- CABI, Rue des Grillons 1, 2800, Delémont, Switzerland
| | - Markus Knapp
- Koppert Biological Systems, Veilingweg 14, 2651 BE, Berkel en Rodenrijs, The Netherlands
| | - Panagiota Koskinioti
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna International Centre, P.O. Box 100, 1400, Vienna, Austria.,Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - Sophie Le Hesran
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Koppert Biological Systems, Veilingweg 14, 2651 BE, Berkel en Rodenrijs, The Netherlands
| | - Manolis Lyrakis
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Angeliki Paspati
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Meritxell Pérez-Hedo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Wouter N Plouvier
- INRA, CNRS, UMR 1355-7254, 400 Route des Chappes, BP 167 06903, Sophia Antipolis Cedex, France
| | - Christian Schlötterer
- Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Judith M Stahl
- CABI, Rue des Grillons 1, 2800, Delémont, Switzerland.,Kearney Agricultural Research and Extension Center, University of California Berkeley, 9240 South Riverbend Avenue, Parlier, CA, 93648, USA
| | - Andra Thiel
- Group for Population and Evolutionary Ecology, FB 02, Institute of Ecology, University of Bremen, Leobener Str. 5, 28359, Bremen, Germany
| | - Alberto Urbaneja
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, Unidad Mixta Gestión Biotecnológica de Plagas UV-IVIA, Carretera CV-315, Km 10'7, 46113, Moncada, Valencia, Spain
| | - Louis van de Zande
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Eveline C Verhulst
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Louise E M Vet
- Laboratory of Entomology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.,Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Sander Visser
- Institute of Entomology, Biology Centre CAS, Branišovská 31, 370 05, České Budějovice, Czech Republic.,Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05, České Budějovice, Czech Republic
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Shuwen Xia
- Animal Breeding and Genomics, Wageningen University & Research, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Sara Magalhães
- cE3c: Centre for Ecology, Evolution, and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Edifício C2, Campo Grande, 1749-016, Lisbon, Portugal
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, PO Box 11103, 9700 CC, Groningen, The Netherlands
| | - Bart A Pannebakker
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| |
Collapse
|
12
|
Chong VK, Stinchcombe JR. Evaluating Population Genomic Candidate Genes Underlying Flowering Time in Arabidopsis thaliana Using T-DNA Insertion Lines. J Hered 2020; 110:445-454. [PMID: 31158286 DOI: 10.1093/jhered/esz026] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 04/16/2019] [Indexed: 12/14/2022] Open
Abstract
Population genomic scans have emerged as a powerful tool to detect regions of the genome that are potential targets of selection. Despite the success of genomic scans in identifying novel lists of loci potentially underlying adaptation, few studies proceed to validate the function of these candidate genes. In this study, we used transfer-DNA (T-DNA) insertion lines to evaluate the effects of 27 candidate genes on flowering time in North American accessions of Arabidopsis thaliana. We compared the flowering time of T-DNA insertion lines that knock out the function of a candidate gene obtained from population genomic studies to a wild type under long- and short-day conditions. We also did the same for a collection of randomly chosen genes that had not been identified as candidates. We validated the well-known effect of long-day conditions in accelerating flowering time and found that gene disruption caused by insertional mutagenesis tends to delay flowering. Surprisingly, we found that knockouts in random genes were just as likely to produce significant phenotypic effects as knockouts in candidate genes. T-DNA insertions at a handful of candidate genes that had previously been identified as outlier loci showed significant delays in flowering time under both long and short days, suggesting that they are promising candidates for future investigation.
Collapse
Affiliation(s)
- Veronica K Chong
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
13
|
Cortinovis G, Frascarelli G, Di Vittori V, Papa R. Current State and Perspectives in Population Genomics of the Common Bean. PLANTS (BASEL, SWITZERLAND) 2020; 9:E330. [PMID: 32150958 PMCID: PMC7154925 DOI: 10.3390/plants9030330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/27/2020] [Accepted: 03/03/2020] [Indexed: 11/17/2022]
Abstract
* Correspondence: r [...].
Collapse
Affiliation(s)
| | | | | | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali (D3A), Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy; (G.C.); (G.F.); (V.D.V.)
| |
Collapse
|
14
|
Vendrami DLJ, De Noia M, Telesca L, Handal W, Charrier G, Boudry P, Eberhart-Phillips L, Hoffman JI. RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories. Sci Rep 2019; 9:7455. [PMID: 31092869 PMCID: PMC6520335 DOI: 10.1038/s41598-019-43939-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/30/2019] [Indexed: 12/25/2022] Open
Abstract
Recent developments in genomics are advancing our understanding of the processes shaping population structure in wild organisms. In particular, reduced representation sequencing has facilitated the generation of dense genetic marker datasets that provide greater power for resolving population structure, investigating the role of selection and reconstructing demographic histories. We therefore used RAD sequencing to study the great scallop Pecten maximus and its sister species P. jacobeus along a latitudinal cline in Europe. Analysis of 219 samples genotyped at 82,439 single nucleotide polymorphisms clearly resolved an Atlantic and a Norwegian group within P. maximus as well as P. jacobeus, in support of previous studies. Fine-scale structure was also detected, including pronounced differences involving Mulroy Bay in Ireland, where scallops are commercially cultured. Furthermore, we identified a suite of 279 environmentally associated loci that resolved a contrasting phylogenetic pattern to the remaining neutral loci, consistent with ecologically mediated divergence. Finally, demographic inference provided support for the two P. maximus groups having diverged during the last glacial maximum and subsequently expanded, whereas P. jacobeus diverged around 95,000 generations ago and experienced less pronounced expansion. Our results provide an integrative perspective on the factors shaping genome-wide differentiation in a commercially important marine invertebrate.
Collapse
Affiliation(s)
- David L J Vendrami
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33615, Bielefeld, Germany.
| | - Michele De Noia
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33615, Bielefeld, Germany.,Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Luca Telesca
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EQ, United Kingdom.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, United Kingdom
| | - William Handal
- University of Brest, Laboratoire des Sciences de l'Environnement Marin (LEMAR, UMR 6539, UBO/CNRS/IRD/Ifremer), European University Institute for the Sea (IUEM), rue Dumont d'Urville, 29280, Plouzané, France
| | - Grégory Charrier
- University of Brest, Laboratoire des Sciences de l'Environnement Marin (LEMAR, UMR 6539, UBO/CNRS/IRD/Ifremer), European University Institute for the Sea (IUEM), rue Dumont d'Urville, 29280, Plouzané, France
| | - Pierre Boudry
- Ifremer, Laboratoire des Sciences de l'Environnement Marin (UBO/CNRS/IRD/Ifremer), Plouzané, France
| | - Luke Eberhart-Phillips
- Department of Evolutionary Ecology and Behavioural Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Joseph I Hoffman
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33615, Bielefeld, Germany.,British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, United Kingdom
| |
Collapse
|
15
|
Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|