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Peñafiel Loaiza N, Chafe AH, Moraes R M, Oleas NH, Roncal J. Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products. Evol Appl 2024; 17:e13765. [PMID: 39091352 PMCID: PMC11291087 DOI: 10.1111/eva.13765] [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: 04/06/2023] [Revised: 06/30/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus Parajubaea (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, P. torallyi and P. sunkha, are non-timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, P. cocoides, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of Parajubaea species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3753 bp) challenged the hypothesis that P. cocoides is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single-nucleotide polymorphism markers by genotyping-by-sequencing of 194 wild Parajubaea individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.
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Affiliation(s)
- Nicolás Peñafiel Loaiza
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
- Present address:
Chone y BabahoyoLojaEcuador
| | - Abigail H. Chafe
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Mónica Moraes R
- Herbario Nacional de Bolivia, Instituto de EcologíaUniversidad Mayor de San AndrésLa PazBolivia
| | - Nora H. Oleas
- Centro de Investigación de la Biodiversidad y Cambio Climático – BioCamb e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio AmbienteUniversidad IndoaméricaQuitoEcuador
| | - Julissa Roncal
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
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2
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Lowe WH, Addis BR, Cochrane MM. Outbreeding reduces survival during metamorphosis in a headwater stream salamander. Mol Ecol 2024; 33:e17375. [PMID: 38699973 DOI: 10.1111/mec.17375] [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: 03/06/2023] [Revised: 02/22/2024] [Accepted: 03/01/2024] [Indexed: 05/05/2024]
Abstract
Assessing direct fitness effects of individual genetic diversity is challenging due to the intensive and long-term data needed to quantify survival and reproduction in the wild. But resolving these effects is necessary to determine how inbreeding and outbreeding influence eco-evolutionary processes. We used 8 years of capture-recapture data and single nucleotide polymorphism genotypes for 1906 individuals to test for effects of individual heterozygosity on stage-specific survival probabilities in the salamander Gyrinophilus porphyriticus. The life cycle of G. porphyriticus includes an aquatic larval stage followed by metamorphosis into a semi-aquatic adult stage. In our study populations, the larval stage lasts 6-10 years, metamorphosis takes several months, and lifespan can reach 20 years. Previous studies showed that metamorphosis is a sensitive life stage, leading us to predict that fitness effects of individual heterozygosity would occur during metamorphosis. Consistent with this prediction, monthly probability of survival during metamorphosis declined with multi-locus heterozygosity (MLH), from 0.38 at the lowest MLH (0.10) to 0.06 at the highest MLH (0.38), a reduction of 84%. Body condition of larvae also declined significantly with increasing MLH. These relationships were consistent in the three study streams. With evidence of localised inbreeding within streams, these results suggest that outbreeding disrupts adaptations in pre-metamorphic and metamorphic individuals to environmental gradients along streams, adding to evidence that headwater streams are hotspots of microgeographic adaptation. Our results also underscore the importance of incorporating life history in analyses of the fitness effects of individual genetic diversity and suggest that metamorphosis and similar discrete life stage transitions may be critical periods of viability selection.
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Affiliation(s)
- Winsor H Lowe
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Brett R Addis
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
| | - Madaline M Cochrane
- Division of Biological Sciences, University of Montana, Missoula, Montana, USA
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3
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Trumbo DR, Hardy BM, Crockett HJ, Muths E, Forester BR, Cheek RG, Zimmerman SJ, Corey-Rivas S, Bailey LL, Funk WC. Conservation genomics of an endangered montane amphibian reveals low population structure, low genomic diversity and selection pressure from disease. Mol Ecol 2023; 32:6777-6795. [PMID: 37864490 DOI: 10.1111/mec.17175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/23/2023]
Abstract
Wildlife diseases are a major global threat to biodiversity. Boreal toads (Anaxyrus [Bufo] boreas) are a state-endangered species in the southern Rocky Mountains of Colorado and New Mexico, and a species of concern in Wyoming, largely due to lethal skin infections caused by the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). We performed conservation and landscape genomic analyses using single nucleotide polymorphisms from double-digest, restriction site-associated DNA sequencing in combination with the development of the first boreal toad (and first North American toad) reference genome to investigate population structure, genomic diversity, landscape connectivity and adaptive divergence. Genomic diversity (π = 0.00034-0.00040) and effective population sizes (Ne = 8.9-38.4) were low, likely due to post-Pleistocene founder effects and Bd-related population crashes over the last three decades. Population structure was also low, likely due to formerly high connectivity among a higher density of geographically proximate populations. Boreal toad gene flow was facilitated by low precipitation, cold minimum temperatures, less tree canopy, low heat load and less urbanization. We found >8X more putatively adaptive loci related to Bd intensity than to all other environmental factors combined, and evidence for genes under selection related to immune response, heart development and regulation and skin function. These data suggest boreal toads in habitats with Bd have experienced stronger selection pressure from disease than from other, broad-scale environmental variations. These findings can be used by managers to conserve and recover the species through actions including reintroduction and supplementation of populations that have declined due to Bd.
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Affiliation(s)
- D R Trumbo
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - B M Hardy
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - H J Crockett
- Colorado Parks and Wildlife, Fort Collins, Colorado, USA
| | - E Muths
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - B R Forester
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
| | - R G Cheek
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - S J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - S Corey-Rivas
- Department of Biology, New Mexico Highlands University, Las Vegas, New Mexico, USA
| | - L L Bailey
- Department of Fish, Wildlife and Conservation Biology, Colorado State University, Fort Collins, Colorado, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
| | - W C Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado, USA
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, USA
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4
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Arantes LS, Caccavo JA, Sullivan JK, Sparmann S, Mbedi S, Höner OP, Mazzoni CJ. Scaling-up RADseq methods for large datasets of non-invasive samples: Lessons for library construction and data preprocessing. Mol Ecol Resour 2023. [PMID: 37646753 DOI: 10.1111/1755-0998.13859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 08/12/2023] [Accepted: 08/16/2023] [Indexed: 09/01/2023]
Abstract
Genetic non-invasive sampling (gNIS) is a critical tool for population genetics studies, supporting conservation efforts while imposing minimal impacts on wildlife. However, gNIS often presents variable levels of DNA degradation and non-endogenous contamination, which can incur considerable processing costs. Furthermore, the use of restriction-site-associated DNA sequencing methods (RADseq) for assessing thousands of genetic markers introduces the challenge of obtaining large sets of shared loci with similar coverage across multiple individuals. Here, we present an approach to handling large-scale gNIS-based datasets using data from the spotted hyena population inhabiting the Ngorongoro Crater in Tanzania. We generated 3RADseq data for more than a thousand individuals, mostly from faecal mucus samples collected non-invasively and varying in DNA degradation and contamination level. Using small-scale sequencing, we screened samples for endogenous DNA content, removed highly contaminated samples, confirmed overlap fragment length between libraries, and balanced individual representation in a sequencing pool. We evaluated the impact of (1) DNA degradation and contamination of non-invasive samples, (2) PCR duplicates and (3) different SNP filters on genotype accuracy based on Mendelian error estimated for parent-offspring trio datasets. Our results showed that when balanced for sequencing depth, contaminated samples presented similar genotype error rates to those of non-contaminated samples. We also showed that PCR duplicates and different SNP filters impact genotype accuracy. In summary, we showed the potential of using gNIS for large-scale genetic monitoring based on SNPs and demonstrated how to improve control over library preparation by using a weighted re-pooling strategy that considers the endogenous DNA content.
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Affiliation(s)
- Larissa S Arantes
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
| | - Jilda A Caccavo
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-sur-Yvette, France
- Laboratoire d'Océanographie et du Climat: Expérimentations et Approches Numériques, LOCEAN/IPSL, UPMC-CNRS-IRD-MNHN, Sorbonne Université, Paris, France
| | - James K Sullivan
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Freie Universität, Berlin, Germany
| | - Sarah Sparmann
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Leibniz-Institut für Gewässerökologie und Binnenfischerei (IGB), Berlin, Germany
| | - Susan Mbedi
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Museum für Naturkunde, Berlin, Germany
| | - Oliver P Höner
- Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
| | - Camila J Mazzoni
- Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Berlin, Germany
- Leibniz-Institut für Zoo- und Wildtierforschung (IZW), Berlin, Germany
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5
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Afonso RO, Pina-Martins F, Friesen V, Sun Z, Campioni L, Madeiros J, Silva MC. No evidence of inbreeding depression despite a historical severe bottleneck in the endangered Bermuda petrel (Pterodroma cahow). J Hered 2023; 114:459-469. [PMID: 37162284 DOI: 10.1093/jhered/esad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/08/2023] [Indexed: 05/11/2023] Open
Abstract
The Bermuda petrel Pterodroma cahow is an island endemic seabird that belongs to the Procellariiformes, one of the most endangered orders of birds. Historical records suggest a significant population size decline following human settlement in Bermuda, bringing the species to near extinction. Since the 1950s, the population has been recovering aided by the implementation of an ongoing conservation plan. However, it still faces several threats, and negative genetic effects resulting from that drastic decline are to be expected, including inbreeding and genetic drift. We studied genetic diversity and levels of inbreeding, and their effects on individual fitness and mating choice. We also tested for a genetic signature of the recent demographic bottleneck. For this, we analyzed variation in thousands of nuclear single-nucleotide polymorphisms derived from double digest restriction site-associated DNA sequencing and 1 mitochondrial gene (cytochrome oxidase I). The results revealed that the Bermuda petrel suffered a recent genetic bottleneck and shows low mitochondrial diversity compared with other petrel species. Conversely, nuclear diversity was similar to that of other endangered petrels. Inbreeding levels were not high overall, although some individuals were highly inbred. However, we found no evidence that individual inbreeding or relatedness between mates affected hatching success, or that mate choice is influenced by kinship in this very small population.
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Affiliation(s)
- Rita O Afonso
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Francisco Pina-Martins
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Vicki Friesen
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Zhengxin Sun
- Department of Biology, Queen's University, Kingston, ON, Canada
| | - Letizia Campioni
- MARE-Marine and Environmental Sciences Centre, Ispa-Instituto Universitário, Lisboa, Portugal
| | - Jeremy Madeiros
- Department of Environment and Natural Resources, Government of Bermuda, Hamilton, Bermuda
| | - Mónica C Silva
- cE3c-Centre for Ecology, Evolution and Environmental Changes & CHANGE-Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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6
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Grossfurthner LP, Milano ER, Hohenlohe PA, Waits LP, Richardson BA. Population structure and hybridization under contemporary and future climates in a heteroploid foundational shrub species ( Artemisia tridentata). FRONTIERS IN PLANT SCIENCE 2023; 14:1155868. [PMID: 37284723 PMCID: PMC10239881 DOI: 10.3389/fpls.2023.1155868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/20/2023] [Indexed: 06/08/2023]
Abstract
Current and past climatic changes can shift plant climatic niches, which may cause spatial overlap or separation between related taxa. The former often leads to hybridization and introgression, which may generate novel variation and influence the adaptive capacity of plants. An additional mechanism facilitating adaptations to novel environments and an important evolutionary driver in plants is polyploidy as the result of whole genome duplication. Artemisia tridentata (big sagebrush) is a landscape-dominating foundational shrub in the western United States which occupies distinct ecological niches, exhibiting diploid and tetraploid cytotypes. Tetraploids have a large impact on the species' landscape dominance as they occupy a preponderance of the arid spectrum of A. tridentata range. Three distinct subspecies are recognized, which co-occur in ecotones - the transition zone between two or more distinct ecological niches - allowing for hybridization and introgression. Here we assess the genomic distinctiveness and extent of hybridization among subspecies at different ploidies under both contemporary and predicted future climates. We sampled five transects throughout the western United States where a subspecies overlap was predicted using subspecies-specific climate niche models. Along each transect, we sampled multiple plots representing the parental and the potential hybrid habitats. We performed reduced representation sequencing and processed the data using a ploidy-informed genotyping approach. Population genomic analyses revealed distinct diploid subspecies and at least two distinct tetraploid gene pools, indicating independent origins of the tetraploid populations. We detected low levels of hybridization (2.5%) between the diploid subspecies, while we found evidence for increased admixture between ploidy levels (18%), indicating hybridization has an important role in the formation of tetraploids. Our analyses highlight the importance of subspecies co-occurrence within these ecotones to maintain gene exchange and potential formation of tetraploid populations. Genomic confirmations of subspecies in the ecotones support the subspecies overlap predicted by the contemporary climate niche models. However, future mid-century projections of subspecies niches predict a substantial loss in range and subspecies overlap. Thus, reductions in hybridization potential could affect new recruitment of genetically variable tetraploids that are vital to this species' ecological role. Our results underscore the importance of ecotone conservation and restoration.
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Affiliation(s)
- Lukas P. Grossfurthner
- Bioinformatics and Computational Biology Graduate Program, University of Idaho, Moscow, ID, United States
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Elizabeth R. Milano
- Rocky Mountain Research Station, United States Department of Agriculture (USDA) Forest Service, Moscow, ID, United States
| | - Paul A. Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, United States
| | - Bryce A. Richardson
- Rocky Mountain Research Station, United States Department of Agriculture (USDA) Forest Service, Moscow, ID, United States
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7
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Hupało K, Copilaș-Ciocianu D, Leese F, Weiss M. Morphology, nuclear SNPs and mate selection reveal that COI barcoding overestimates species diversity in a Mediterranean freshwater amphipod by an order of magnitude. Cladistics 2023; 39:129-143. [PMID: 36576962 DOI: 10.1111/cla.12520] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/29/2022] Open
Abstract
DNA sequence information has revealed many morphologically cryptic species worldwide. For animals, DNA-based assessments of species diversity usually rely on the mitochondrial cytochrome c oxidase subunit I (COI) gene. However, a growing amount of evidence indicate that mitochondrial markers alone can lead to misleading species diversity estimates due to mito-nuclear discordance. Therefore, reports of putative species based solely on mitochondrial DNA should be verified by other methods, especially in cases where COI sequences are identical for different morphospecies or where divergence within the same morphospecies is high. Freshwater amphipods are particularly interesting in this context because numerous putative cryptic species have been reported. Here, we investigated the species status of the numerous mitochondrial molecular operational taxonomic units (MOTUs) found within Echinogammarus sicilianus. We used an integrative approach combining DNA barcoding with mate selection observations, detailed morphometrics and genome-wide double digest restriction site-associated DNA sequencing (ddRAD-seq). Within a relatively small sampling area, we detected twelve COI MOTUs (divergence = 1.8-20.3%), co-occurring in syntopy at two-thirds of the investigated sites. We found that pair formation was random and there was extensive nuclear gene flow among the ten MOTUs co-occurring within the same river stretch. The four most common MOTUs were also indistinguishable with respect to functional morphology. Therefore, the evidence best fits the hypothesis of a single, yet genetically diverse, species within the main river system. The only two MOTUs sampled outside the focal area were genetically distinct at the nuclear level and may represent distinct species. Our study reveals that COI-based species delimitation can significantly overestimate species diversity, highlighting the importance of integrative taxonomy for species validation, especially in hyperdiverse complexes with syntopically occurring mitochondrial MOTUs.
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Affiliation(s)
- Kamil Hupało
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany
| | - Denis Copilaș-Ciocianu
- Nature Research Centre, Laboratory of Evolutionary Ecology of Hydrobionts, Akademijos 2, Vilnius, 08412, Lithuania
| | - Florian Leese
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 2, Essen, 45141, Germany
| | - Martina Weiss
- Aquatic Ecosystem Research, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, Essen, 45141, Germany.,Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstr. 2, Essen, 45141, Germany
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8
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Forester BR, Murphy M, Mellison C, Petersen J, Pilliod DS, Van Horne R, Harvey J, Funk WC. Genomics-informed delineation of conservation units in a desert amphibian. Mol Ecol 2022; 31:5249-5269. [PMID: 35976166 PMCID: PMC9804278 DOI: 10.1111/mec.16660] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 07/28/2022] [Indexed: 01/05/2023]
Abstract
Delineating conservation units (CUs, e.g., evolutionarily significant units, ESUs, and management units, MUs) is critical to the recovery of declining species because CUs inform both listing status and management actions. Genomic data have strengths and limitations in informing CU delineation and related management questions in natural systems. We illustrate the value of using genomic data in combination with landscape, dispersal and occupancy data to inform CU delineation in Nevada populations of the Great Basin Distinct Population Segment of the Columbia spotted frog (Rana luteiventris). R. luteiventris occupies naturally fragmented aquatic habitats in this xeric region, but beaver removal, climate change and other factors have put many of these populations at high risk of extirpation without management intervention. We addressed three objectives: (i) assessing support for ESUs within Nevada; (ii) evaluating and revising, if warranted, the current delineation of MUs; and (iii) evaluating genetic diversity, effective population size, adaptive differentiation and functional connectivity to inform ongoing management actions. We found little support for ESUs within Nevada but did identify potential revisions to MUs based on unique landscape drivers of connectivity that distinguish these desert populations from those in the northern portion of the species range. Effective sizes were uniformly small, with low genetic diversity and weak signatures of adaptive differentiation. Our findings suggest that management actions, including translocations and genetic rescue, might be warranted. Our study illustrates how a carefully planned genetic study, designed to address priority management goals that include CU delineation, can provide multiple insights to inform conservation action.
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Affiliation(s)
- Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Melanie Murphy
- Department of Ecosystem Science and Management, Program in Ecology, University of Wyoming, Laramie, WY, USA
| | | | | | - David S Pilliod
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
| | | | | | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
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9
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Piñeros VJ, Del R Pedraza-Marrón C, Betancourt-Resendes I, Calderón-Cortés N, Betancur-R R, Domínguez-Domínguez O. Genome-wide species delimitation analyses of a silverside fish species complex in central Mexico indicate taxonomic over-splitting. BMC Ecol Evol 2022; 22:108. [PMID: 36104671 PMCID: PMC9472351 DOI: 10.1186/s12862-022-02063-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Delimiting species across a speciation continuum is a complex task, as the process of species origin is not generally instantaneous. The use of genome-wide data provides unprecedented resolution to address convoluted species delimitation cases, often unraveling cryptic diversity. However, because genome-wide approaches based on the multispecies coalescent model are known to confound population structure with species boundaries, often resulting in taxonomic over-splitting, it has become increasingly evident that species delimitation research must consider multiple lines of evidence. In this study, we used phylogenomic, population genomic, and coalescent-based species delimitation approaches, and examined those in light of morphological and ecological information, to investigate species numbers and boundaries comprising the Chirostoma "humboltianum group" (family Atherinidae). The humboltianum group is a taxonomically controversial species complex where previous morphological and mitochondrial studies produced conflicting species delimitation outcomes. We generated ddRADseq data for 77 individuals representing the nine nominal species in the group, spanning their distribution range in the central Mexican plateau. RESULTS Our results conflict with the morphospecies and ecological delimitation hypotheses, identifying four independently evolving lineages organized in three geographically cohesive clades: (i) chapalae and sphyraena groups in Lake Chapala, (ii) estor group in Lakes Pátzcuaro and Zirahuén, and (iii) humboltianum sensu stricto group in Lake Zacapu and Lerma river system. CONCLUSIONS Overall, our study provides an atypical example where genome-wide analyses delineate fewer species than previously recognized on the basis of morphology. It also highlights the influence of the geological history of the Chapala-Lerma hydrological system in driving allopatric speciation in the humboltianum group.
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Affiliation(s)
- Victor Julio Piñeros
- Laboratorio de Ecología Molecular, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacán, Mexico
| | | | - Isaí Betancourt-Resendes
- Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, Avenida de Las Ciencias S/N Juriquilla, Delegación Santa Rosa Jáuregui, 76230, Querétaro, Mexico
| | - Nancy Calderón-Cortés
- Laboratorio de Ecología Molecular, Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Antigua Carretera a Pátzcuaro 8701, Ex-Hacienda de San José de La Huerta, 58190, Morelia, Michoacán, Mexico.
| | - Ricardo Betancur-R
- Department of Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK, 73019, USA
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Edificio "R" Planta Baja, Ciudad Universitaria, 58030, Morelia, Michoacán, Mexico.
- Laboratorio Nacional de Análisis y Síntesis Ecológica Para la Conservación de Recursos Genéticos de México, Escuela Nacional de Estudios Superiores, Unidad Morelia, Universidad Nacional Autónoma de México, Apartado Postal 27-3 (Xangari), 58089, Michoacán, Morelia, Mexico.
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10
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Addis BR, Lowe WH. Environmentally associated variation in dispersal distance affects inbreeding risk in a stream salamander. Am Nat 2022; 200:802-814. [DOI: 10.1086/721763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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11
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Weigand H, Cross Lopez de Llergo J, Frantz AC. Genomic basis for an informed conservation management of
Pelophylax
water frogs in Luxembourg. Ecol Evol 2022; 12:e8810. [PMID: 35432923 PMCID: PMC9001158 DOI: 10.1002/ece3.8810] [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: 09/23/2021] [Revised: 03/14/2022] [Accepted: 03/24/2022] [Indexed: 11/17/2022] Open
Abstract
Genetic identification methods have become increasingly important for species that are difficult to identify in the field. A case in point is Pelophylax water frogs. While their morphological determination is highly complex, they include species protected under EU law and some that are classified as invasive. Additionally, genetic data can provide insights into their complex breeding systems, which may or may not involve the reproductive dependency of one species on another. Here, we generate baseline data for water frog monitoring in Luxembourg. We applied a countrywide sampling approach and used SNPs generated by ddRAD sequencing to identify individuals and infer the breeding systems present in the country. We found Pelophylax lessonae and P. kl. esculentus throughout Luxembourg, mostly living in syntopy. In general, a reproductive dependency of P. kl. esculentus on P. lessonae (L‐E system) was revealed. Besides this general system, we detected triploid P. kl. esculentus in six ponds. This indicates a modified L‐E system with reproductive dependency of the triploids on the diploid P. kl. esculentus. The invasive P. cf. bedriagae was detected in three ponds in southern Luxembourg, with evidence for hybridization with native water frogs. In addition to the ddRAD data, we tested a simple genetic method for future monitoring based on the MND1 marker. It showed in almost all cases, an identical species identification as the ddRAD data and was successfully applied to DNA extracts from mouth swabs. Combining this method with our baseline data will enable informed choices for the protection of native water frog species in Luxembourg.
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Affiliation(s)
- Hannah Weigand
- Musée National d'Histoire Naturelle de Luxembourg Luxembourg City Luxembourg
- Fondation faune‐flore Luxembourg City Luxembourg
| | | | - Alain C. Frantz
- Musée National d'Histoire Naturelle de Luxembourg Luxembourg City Luxembourg
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12
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Bendall EE, Bagley RK, Sousa VC, Linnen CR. Faster-haplodiploid evolution under divergence-with-gene-flow: simulations and empirical data from pine-feeding hymenopterans. Mol Ecol 2022; 31:2348-2366. [PMID: 35231148 DOI: 10.1111/mec.16410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 11/28/2022]
Abstract
Although haplodiploidy is widespread in nature, the evolutionary consequences of this mode of reproduction are not well characterized. Here, we examine how genome-wide hemizygosity and a lack of recombination in haploid males affects genomic differentiation in populations that diverge via natural selection while experiencing gene flow. First, we simulated diploid and haplodiploid "genomes" (500-kb loci) evolving under an isolation-with-migration model with mutation, drift, selection, migration, and recombination; and examined differentiation at neutral sites both tightly and loosely linked to a divergently selected site. So long as there is divergent selection and migration, sex-limited hemizygosity and recombination cause elevated differentiation (i.e., produce a "faster-haplodiploid effect") in haplodiploid populations relative to otherwise equivalent diploid populations, for both recessive and codominant mutations. Second, we used genome-wide SNP data to model divergence history and describe patterns of genomic differentiation between sympatric populations of Neodiprion lecontei and N. pinetum, a pair of pine sawfly species (order: Hymenoptera; family: Diprionidae) that are specialized on different pine hosts. These analyses support a history of continuous gene exchange throughout divergence and reveal a pattern of heterogeneous genomic differentiation that is consistent with divergent selection on many unlinked loci. Third, using simulations of haplodiploid and diploid populations evolving according to the estimated divergence history of N. lecontei and N. pinetum, we found that divergent selection would lead to higher differentiation in haplodiploids. Based on these results, we hypothesize that haplodiploids undergo divergence-with-gene-flow and sympatric speciation more readily than diploids.
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Affiliation(s)
- Emily E Bendall
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Robin K Bagley
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA.,Department of Evolution, Ecology, and Organismal Biology, The Ohio State University at Lima, Lima, OH, 45804, USA
| | - Vitor C Sousa
- CE3C - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculdade de Ciências da Universidade de Lisboa, University of Lisbon, Campo Grande 1749-016, Lisboa, Portugal
| | - Catherine R Linnen
- Department of Biology, University of Kentucky, Lexington, Kentucky, 40506, USA
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13
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Cayuela H, Dorant Y, Forester BR, Jeffries DL, Mccaffery RM, Eby LA, Hossack BR, Gippet JMW, Pilliod DS, Chris Funk W. Genomic signatures of thermal adaptation are associated with clinal shifts of life history in a broadly distributed frog. J Anim Ecol 2021; 91:1222-1238. [PMID: 34048026 PMCID: PMC9292533 DOI: 10.1111/1365-2656.13545] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022]
Abstract
Temperature is a critical driver of ectotherm life‐history strategies, whereby a warmer environment is associated with increased growth, reduced longevity and accelerated senescence. Increasing evidence indicates that thermal adaptation may underlie such life‐history shifts in wild populations. Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) can help uncover the molecular mechanisms of temperature‐driven variation in growth, longevity and senescence. However, our understanding of these mechanisms is still limited, which reduces our ability to predict the response of non‐model ectotherms to global temperature change. In this study, we examined the potential role of thermal adaptation in clinal shifts of life‐history traits (i.e. life span, senescence rate and recruitment) in the Columbia spotted frog Rana luteiventris along a broad temperature gradient in the western United States. We took advantage of extensive capture–recapture datasets of 20,033 marked individuals from eight populations surveyed annually for 14–18 years to examine how mean annual temperature and precipitation influenced demographic parameters (i.e. adult survival, life span, senescence rate, recruitment and population growth). After showing that temperature was the main climatic predictor influencing demography, we used RAD‐seq data (50,829 SNPs and 6,599 putative CNVs) generated for 352 individuals from 31 breeding sites to identify the genomic signatures of thermal adaptation. Our results showed that temperature was negatively associated with annual adult survival and reproductive life span and positively associated with senescence rate. By contrast, recruitment increased with temperature, promoting the long‐term viability of most populations. These temperature‐dependent demographic changes were associated with strong genomic signatures of thermal adaptation. We identified 148 SNP candidates associated with temperature including three SNPs located within protein‐coding genes regulating resistance to cold and hypoxia, immunity and reproduction in ranids. We also identified 39 CNV candidates (including within 38 transposable elements) for which normalized read depth was associated with temperature. Our study indicates that both SNPs and structural variants are associated with temperature and could eventually be found to play a functional role in clinal shifts in senescence rate and life‐history strategies in R. luteiventris. These results highlight the potential role of different sources of molecular variation in the response of ectotherms to environmental temperature variation in the context of global warming.
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Affiliation(s)
- Hugo Cayuela
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Yann Dorant
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, Canada
| | - Brenna R Forester
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Dan L Jeffries
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Rebecca M Mccaffery
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Port Angeles, WA, USA
| | - Lisa A Eby
- Wildlife Biology Program, W. A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT, USA
| | - Blake R Hossack
- US Geological Survey, Northern Rocky Mountain Science Center, Missoula, MT, USA
| | - Jérôme M W Gippet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - David S Pilliod
- US Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
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14
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Stahlke A, Bell D, Dhendup T, Kern B, Pannoni S, Robinson Z, Strait J, Smith S, Hand BK, Hohenlohe PA, Luikart G. Population Genomics Training for the Next Generation of Conservation Geneticists: ConGen 2018 Workshop. J Hered 2021; 111:227-236. [PMID: 32037446 PMCID: PMC7117792 DOI: 10.1093/jhered/esaa001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 01/06/2020] [Indexed: 12/30/2022] Open
Abstract
The increasing availability and complexity of next-generation sequencing (NGS) data sets make ongoing training an essential component of conservation and population genetics research. A workshop entitled “ConGen 2018” was recently held to train researchers in conceptual and practical aspects of NGS data production and analysis for conservation and ecological applications. Sixteen instructors provided helpful lectures, discussions, and hands-on exercises regarding how to plan, produce, and analyze data for many important research questions. Lecture topics ranged from understanding probabilistic (e.g., Bayesian) genotype calling to the detection of local adaptation signatures from genomic, transcriptomic, and epigenomic data. We report on progress in addressing central questions of conservation genomics, advances in NGS data analysis, the potential for genomic tools to assess adaptive capacity, and strategies for training the next generation of conservation genomicists.
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Affiliation(s)
- Amanda Stahlke
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Donavan Bell
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Tashi Dhendup
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Department of Forest and Park Services, Ugyen Wangchuck Institute for Conservation and Environmental Research, Bumthang, Bhutan
| | - Brooke Kern
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN
| | - Samuel Pannoni
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| | - Zachary Robinson
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Jeffrey Strait
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT
| | - Seth Smith
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI
| | - Brian K Hand
- Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID
| | - Gordon Luikart
- Wildlife Biology Program, College of Forestry and Conservation, University of Montana, Missoula, MT.,Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT.,Flathead Lake Biological Station, Division of Biological Sciences, College of Humanities and Sciences, University of Montana, Missoula, MT
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15
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Bouzid NM, Archie JW, Anderson RA, Grummer JA, Leaché AD. Evidence for ephemeral ring species formation during the diversification history of western fence lizards (Sceloporus occidentalis). Mol Ecol 2021; 31:620-631. [PMID: 33565164 DOI: 10.1111/mec.15836] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/18/2021] [Accepted: 02/02/2021] [Indexed: 12/31/2022]
Abstract
Divergence is often ephemeral, and populations that diverge in response to regional topographic and climatic factors may not remain reproductively isolated when they come into secondary contact. We investigated the geographical structure and evolutionary history of population divergence within Sceloporus occidentalis (western fence lizard), a habitat generalist with a broad distribution that spans the major biogeographical regions of Western North America. We used double digest RAD sequencing to infer population structure, phylogeny and demography. Population genetic structure is hierarchical and geographically structured with evidence for gene flow between biogeographical regions. Consistent with the isolation-expansion model of divergence during Quaternary glacial-interglacial cycles, gene flow and secondary contact are supported as important processes explaining the demographic histories of populations. Although populations may have diverged as they spread northward in a ring-like manner around the Sierra Nevada and southern Cascade Ranges, there is strong evidence for gene flow among populations at the northern terminus of the ring. We propose the concept of an "ephemeral ring species" and contrast S. occidentalis with the classic North American ring species, Ensatina eschscholtzii. Contrary to expectations of lower genetic diversity at northern latitudes following post-Quaternary-glaciation expansion, the ephemeral nature of divergence in S. occidentalis has produced centres of high genetic diversity for different reasons in the south (long-term stability) vs. the north (secondary contact).
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Affiliation(s)
- Nassima M Bouzid
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
| | - James W Archie
- Biological Sciences, California State University, Long Beach, CA, USA
| | - Roger A Anderson
- Biology Department, Western Washington University, Bellingham, WA, USA
| | - Jared A Grummer
- Department of Zoology, University of British Columbia, Beaty Biodiversity Museum, Vancouver, BC, Canada
| | - Adam D Leaché
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, WA, USA
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16
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Reiter T, Brooks† PT, Irber† L, Joslin† SEK, Reid† CM, Scott† C, Brown CT, Pierce-Ward NT. Streamlining data-intensive biology with workflow systems. Gigascience 2021; 10:giaa140. [PMID: 33438730 PMCID: PMC8631065 DOI: 10.1093/gigascience/giaa140] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/14/2022] Open
Abstract
As the scale of biological data generation has increased, the bottleneck of research has shifted from data generation to analysis. Researchers commonly need to build computational workflows that include multiple analytic tools and require incremental development as experimental insights demand tool and parameter modifications. These workflows can produce hundreds to thousands of intermediate files and results that must be integrated for biological insight. Data-centric workflow systems that internally manage computational resources, software, and conditional execution of analysis steps are reshaping the landscape of biological data analysis and empowering researchers to conduct reproducible analyses at scale. Adoption of these tools can facilitate and expedite robust data analysis, but knowledge of these techniques is still lacking. Here, we provide a series of strategies for leveraging workflow systems with structured project, data, and resource management to streamline large-scale biological analysis. We present these practices in the context of high-throughput sequencing data analysis, but the principles are broadly applicable to biologists working beyond this field.
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Affiliation(s)
- Taylor Reiter
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Phillip T Brooks†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Luiz Irber†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Shannon E K Joslin†
- Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Charles M Reid†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Camille Scott†
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - C Titus Brown
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - N Tessa Pierce-Ward
- Department of Population Health and Reproduction, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA
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17
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Wegner KM, Lokmer A, John U. Genomic and Transcriptomic Differentiation of Independent Invasions of the Pacific Oyster Crassostrea gigas. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.567049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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18
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Colston-Nepali L, Provencher JF, Mallory ML, Franckowiak RP, Sun Z, Robertson GJ, Friesen VL. Using genomic tools to inform management of the Atlantic northern fulmar. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01309-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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19
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Postel U, Glemser B, Salazar Alekseyeva K, Eggers SL, Groth M, Glöckner G, John U, Mock T, Klemm K, Valentin K, Beszteri B. Adaptive divergence across Southern Ocean gradients in the pelagic diatom
Fragilariopsis kerguelensis. Mol Ecol 2020; 29:4913-4924. [DOI: 10.1111/mec.15554] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/20/2020] [Accepted: 07/08/2020] [Indexed: 01/16/2023]
Affiliation(s)
- Ute Postel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
- Institute for Biochemistry I University Cologne Cologne Germany
- University of Duisburg‐Essen Essen Germany
| | - Barbara Glemser
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Katherine Salazar Alekseyeva
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
- Department of Functional and Evolutionary Ecology University of Vienna Vienna Austria
| | - Sarah Lena Eggers
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Marco Groth
- Leibniz Institute on Aging ‐ Fritz Lipmann Institute (FLI) Jena Germany
| | - Gernot Glöckner
- Institute for Biochemistry I University Cologne Cologne Germany
| | - Uwe John
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg Oldenburg Germany
| | - Thomas Mock
- University of East AngliaNorwich Research Park Norwich UK
| | - Kerstin Klemm
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Klaus Valentin
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
| | - Bánk Beszteri
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research Bremerhaven Germany
- University of Duisburg‐Essen Essen Germany
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20
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Ogiso-Tanaka E, Yabe S, Tanaka T. IonBreeders: bioinformatics plugins toward genomics-assisted breeding. BREEDING SCIENCE 2020; 70:396-401. [PMID: 32714063 PMCID: PMC7372021 DOI: 10.1270/jsbbs.19141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/07/2020] [Indexed: 06/11/2023]
Abstract
Polymorphism information generated by next-generation sequencing (NGS) technologies has enabled applications of genome-wide markers assisted breeding. However, handling such large-scale data remains a challenge for experimental researchers and breeders, calling for the urgent development of a flexible and straightforward analysis tool for NGS data. We developed "IonBreeders" as bioinformatics plugins that implement general analysis steps from genotyping to genomic prediction. IonBreeders comprises three plugins, "ABH", "IMPUTATION", and "GENOMIC PREDICTION", for format conversion of genotyping data, preprocessing and imputation of genotyping data, and genomic prediction, respectively. "ABH" converts genotyping data derived from NGS into the ABH format, which is acceptable for our further plugins and with other breeding software tools, R/qtl, MapMaker, and AntMap. "IMPUTATION" filters out non-informative markers and imputes missing marker genotypes. In "GENOMIC PREDICTION", users can use four statistical methods based on their target trait, quantitative trait locus effect, and number of markers, and construct a prediction model for genomic selection. IonBreeders is operated in Torrent Suite, but can also handle genotype data in standard formats, e.g., Variant Call Format (VCF), by format conversion using free software or our provided scripts.
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Affiliation(s)
- Eri Ogiso-Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shiori Yabe
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tsuyoshi Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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21
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Norrell AE, Jones KL, Saillant EA. Development and characterization of genomic resources for a non-model marine teleost, the red snapper (Lutjanus campechanus, Lutjanidae): Construction of a high-density linkage map, anchoring of genome contigs and comparative genomic analysis. PLoS One 2020; 15:e0232402. [PMID: 32348345 PMCID: PMC7190162 DOI: 10.1371/journal.pone.0232402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 04/15/2020] [Indexed: 11/19/2022] Open
Abstract
The red snapper Lutjanus campechanus is an exploited reef fish of major economic importance in the Gulf of Mexico region. Studies of genome wide genetic variation are needed to understand the structure of wild populations and develop breeding programs for aquaculture but interpretation of these genome scans is limited by the absence of reference genome. In this work, the first draft of a reference genome was developed and characterized for the red snapper. P-454 and Illumina sequencing were conducted to produce paired-end reads that were assembled into reference contigs and scaffolds. The current assembly spans over 770 Mb, representing an estimated 69% of the red snapper genome in 67,254 scaffolds (N50 = 16,803 bp). The genome contigs were applied to map double digest Restriction-Site Associated DNA Tags and characterize Single Nucleotide Polymorphisms (SNPs) in five outbred full-sib families. The identified SNPs and 97 microsatellite loci were used to generate a high-density linkage map that includes 7,420 markers distributed across 24 linkage groups and spans 1,346.64 cM with an average inter–marker distance of 0.18 cM. Sex-specific maps revealed a 1.10:1 female to male map length ratio. A total of 4,422 genome contigs (10.5% of the assembly) were anchored to the map and used in a comparative genomic analysis of the red snapper and two model teleosts. Red snapper showed a high degree of chromosome level syntenic conservation with both medaka and spotted green puffer and a near one to one correspondence between the 24 red snapper linkage groups and corresponding medaka chromosomes was observed. This work established the first draft of a reference genome for a lutjanid fish. The obtained genomic resources will serve as a framework for the interpretation of genome scans during studies of wild populations and captive breeding programs.
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Affiliation(s)
- Adrienne E. Norrell
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, United States of America
| | - Kenneth L. Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Eric A. Saillant
- School of Ocean Science and Engineering, Gulf Coast Research Laboratory, University of Southern Mississippi, Ocean Springs, MS, United States of America
- * E-mail:
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22
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Bresadola L, Link V, Buerkle CA, Lexer C, Wegmann D. Estimating and accounting for genotyping errors in RAD‐seq experiments. Mol Ecol Resour 2020; 20:856-870. [DOI: 10.1111/1755-0998.13153] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Luisa Bresadola
- Department of Biology University of Fribourg Fribourg Switzerland
| | - Vivian Link
- Department of Biology University of Fribourg Fribourg Switzerland
- Swiss Institute of Bioinformatics Fribourg Switzerland
| | | | - Christian Lexer
- Department of Botany and Biodiversity Research University of Vienna Vienna Austria
| | - Daniel Wegmann
- Department of Biology University of Fribourg Fribourg Switzerland
- Swiss Institute of Bioinformatics Fribourg Switzerland
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23
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Jensen EL, Tschritter C, de Groot PVC, Hayward KM, Branigan M, Dyck M, Clemente‐Carvalho RBG, Lougheed SC. Canadian polar bear population structure using genome-wide markers. Ecol Evol 2020; 10:3706-3714. [PMID: 32313629 PMCID: PMC7160183 DOI: 10.1002/ece3.6159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/23/2020] [Accepted: 02/18/2020] [Indexed: 12/01/2022] Open
Abstract
Predicting the consequences of environmental changes, including human-mediated climate change on species, requires that we quantify range-wide patterns of genetic diversity and identify the ecological, environmental, and historical factors that have contributed to it. Here, we generate baseline data on polar bear population structure across most Canadian subpopulations (n = 358) using 13,488 genome-wide single nucleotide polymorphisms (SNPs) identified with double-digest restriction site-associated DNA sequencing (ddRAD). Our ddRAD dataset showed three genetic clusters in the sampled Canadian range, congruent with previous studies based on microsatellites across the same regions; however, due to a lack of sampling in Norwegian Bay, we were unable to confirm the existence of a unique cluster in that subpopulation. These data on the genetic structure of polar bears using SNPs provide a detailed baseline against which future shifts in population structure can be assessed, and opportunities to develop new noninvasive tools for monitoring polar bears across their range.
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Affiliation(s)
- Evelyn L. Jensen
- Department of BiologyQueen’s UniversityKingstonONCanada
- Present address:
Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCTUSA
| | | | | | | | - Marsha Branigan
- Department of Environment and Natural ResourcesGovernment of the Northwest TerritoriesInuvikNTCanada
| | - Markus Dyck
- Department of EnvironmentGovernment of NunavutIgloolikNUCanada
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24
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Rochette NC, Rivera‐Colón AG, Catchen JM. Stacks 2: Analytical methods for paired‐end sequencing improve RADseq‐based population genomics. Mol Ecol 2019; 28:4737-4754. [DOI: 10.1111/mec.15253] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Nicolas C. Rochette
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐Champaign Urbana IL USA
| | - Angel G. Rivera‐Colón
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐Champaign Urbana IL USA
| | - Julian M. Catchen
- Department of Evolution, Ecology, and Behavior University of Illinois at Urbana‐Champaign Urbana IL USA
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25
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Bayona-Vásquez NJ, Glenn TC, Kieran TJ, Pierson TW, Hoffberg SL, Scott PA, Bentley KE, Finger JW, Louha S, Troendle N, Diaz-Jaimes P, Mauricio R, Faircloth BC. Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD). PeerJ 2019; 7:e7724. [PMID: 31616583 PMCID: PMC6791345 DOI: 10.7717/peerj.7724] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/22/2019] [Indexed: 11/24/2022] Open
Abstract
Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially because it is difficult to multiplex sufficient numbers of samples to fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for the construction of dual-digest RADseq libraries that build on adapters and primers designed in Adapterama I. Major features of our method include: (1) minimizing the number of processing steps; (2) focusing on a single strand of sample DNA for library construction, allowing the use of a non-phosphorylated adapter on one end; (3) ligating adapters in the presence of active restriction enzymes, thereby reducing chimeras; (4) including an optional third restriction enzyme to cut apart adapter-dimers formed by the phosphorylated adapter, thus increasing the efficiency of adapter ligation to sample DNA, which is particularly effective when only low quantity/quality DNA samples are available; (5) interchangeable adapter designs; (6) incorporating variable-length internal indexes within the adapters to increase the scope of sample indexing, facilitate pooling, and increase sequence diversity; (7) maintaining compatibility with universal dual-indexed primers and thus, Illumina sequencing reagents and libraries; and, (8) easy modification for the identification of PCR duplicates. We present eight adapter designs that work with 72 restriction enzyme combinations. We demonstrate the efficiency of our approach by comparing it with existing methods, and we validate its utility through the discovery of many variable loci in a variety of non-model organisms. Our 2RAD/3RAD method is easy to perform, has low startup costs, has increased utility with low-concentration input DNA, and produces libraries that can be highly-multiplexed and pooled with other Illumina libraries.
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Affiliation(s)
- Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Travis C. Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
| | - Troy J. Kieran
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
| | - Todd W. Pierson
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, United States of America
| | - Sandra L. Hoffberg
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, United States of America
| | - Peter A. Scott
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States of America
- Current affiliation: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, United States of America
| | - Kerin E. Bentley
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: LeafWorks Inc., Sebastopol, CA, United States of America
| | - John W. Finger
- Department of Environmental Health Science, University of Georgia, Athens, GA, United States of America
- Interdisciplinary Toxicology Program, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Biological Sciences, Auburn University, Auburn, AL, United States of America
| | - Swarnali Louha
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Nicholas Troendle
- Department of Genetics, University of Georgia, Athens, GA, United States of America
- Current affiliation: Department of Natural, Health, and Mathematical Sciences, MidAmerica Nazarene University, Olathe, KS, United States of America
| | - Pindaro Diaz-Jaimes
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rodney Mauricio
- Department of Genetics, University of Georgia, Athens, GA, United States of America
| | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA, United States of America
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26
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Euclide PT, McKinney GJ, Bootsma M, Tarsa C, Meek MH, Larson WA. Attack of the PCR clones: Rates of clonality have little effect on RAD‐seq genotype calls. Mol Ecol Resour 2019; 20:66-78. [DOI: 10.1111/1755-0998.13087] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/12/2019] [Accepted: 08/16/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Peter T. Euclide
- Wisconsin Cooperative Fishery Research Unit College of Natural Resources University of Wisconsin‐Stevens Point Stevens Point WI USA
| | - Garrett J. McKinney
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - Matthew Bootsma
- Wisconsin Cooperative Fishery Research Unit College of Natural Resources University of Wisconsin‐Stevens Point Stevens Point WI USA
| | - Charlene Tarsa
- Department of Integrative Biology and AgBio Research Michigan State University East Lansing MI USA
| | - Mariah H. Meek
- Department of Integrative Biology and AgBio Research Michigan State University East Lansing MI USA
| | - Wesley A. Larson
- U.S. Geological Survey Wisconsin Cooperative Fishery Research Unit College of Natural Resources University of Wisconsin‐Stevens Point Stevens Point WI USA
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27
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Zimmerman SJ, Aldridge CL, Oh KP, Cornman RS, Oyler‐McCance SJ. Signatures of adaptive divergence among populations of an avian species of conservation concern. Evol Appl 2019; 12:1661-1677. [PMID: 31462921 PMCID: PMC6708427 DOI: 10.1111/eva.12825] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the genetic underpinning of adaptive divergence among populations is a key goal of evolutionary biology and conservation. Gunnison sage-grouse (Centrocercus minimus) is a sagebrush obligate species with a constricted range consisting of seven discrete populations, each with distinctly different habitat and climatic conditions. Though geographically close, populations have low levels of natural gene flow resulting in relatively high levels of differentiation. Here, we use 15,033 SNP loci in genomic outlier analyses, genotype-environment association analyses, and gene ontology enrichment tests to examine patterns of putatively adaptive genetic differentiation in an avian species of conservation concern. We found 411 loci within 5 kbp of 289 putative genes associated with biological functions or pathways that were overrepresented in the assemblage of outlier SNPs. The identified gene set was enriched for cytochrome P450 gene family members (CYP4V2, CYP2R1, CYP2C23B, CYP4B1) and could impact metabolism of plant secondary metabolites, a critical challenge for sagebrush obligates. Additionally, the gene set was also enriched with members potentially involved in antiviral response (DEAD box helicase gene family and SETX). Our results provide a first look at local adaption for isolated populations of a single species and suggest adaptive divergence in multiple metabolic and biochemical pathways may be occurring. This information can be useful in managing this species of conservation concern, for example, to identify unique populations to conserve, avoid translocation or release of individuals that may swamp locally adapted genetic diversity, or guide habitat restoration efforts.
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Affiliation(s)
- Shawna J. Zimmerman
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University in Cooperation with U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Cameron L. Aldridge
- Department of Ecosystem Science and Sustainability and Natural Resource Ecology Laboratory, Colorado State University in Cooperation with U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Kevin P. Oh
- U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
| | - Robert S. Cornman
- U.S. Geological SurveyFort Collins Science CenterFort CollinsColorado
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28
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Vasconcellos MM, Colli GR, Weber JN, Ortiz EM, Rodrigues MT, Cannatella DC. Isolation by instability: Historical climate change shapes population structure and genomic divergence of treefrogs in the Neotropical Cerrado savanna. Mol Ecol 2019; 28:1748-1764. [DOI: 10.1111/mec.15045] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 01/17/2019] [Accepted: 01/23/2019] [Indexed: 12/30/2022]
Affiliation(s)
| | - Guarino R. Colli
- Departamento de Zoologia Universidade de Brasília Brasília Brazil
| | - Jesse N. Weber
- Department of Biological Sciences University of Alaska Anchorage Anchorage, Alaska
| | - Edgardo M. Ortiz
- Department of Integrative Biology The University of Texas at Austin Austin Texas
- Plant Biodiversity Research Department of Ecology and Ecosystem Management Technical University of Munich Freising Germany
| | - Miguel T. Rodrigues
- Departamento de Zoologia, Instituto de Biociências Universidade de São Paulo São Paulo Brazil
| | - David C. Cannatella
- Department of Integrative Biology The University of Texas at Austin Austin Texas
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29
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Rey-Iglesia A, Gopalakrishan S, Carøe C, Alquezar-Planas DE, Ahlmann Nielsen A, Röder T, Bruhn Pedersen L, Naesborg-Nielsen C, Sinding MHS, Fredensborg Rath M, Li Z, Petersen B, Gilbert MTP, Bunce M, Mourier T, Hansen AJ. MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements. Mol Ecol Resour 2019; 19:512-525. [PMID: 30575257 DOI: 10.1111/1755-0998.12984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022]
Abstract
In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome-scale studies to characterize both model and non-model organisms. Most of these methods rely on the use of restriction enzymes to obtain DNA sequences at a genome-wide level. These approaches have been widely used to sequence thousands of markers across individuals for many organisms at a reasonable cost, revolutionizing the field of population genomics. However, there are still some limitations associated with these methods, in particular the high molecular weight DNA required as starting material, the reduced number of common loci among investigated samples, and the short length of the sequenced site-associated DNA. Here, we present MobiSeq, a RRL protocol exploiting simple laboratory techniques, that generates genomic data based on PCR targeted enrichment of transposable elements and the sequencing of the associated flanking region. We validate its performance across 103 DNA extracts derived from three mammalian species: grey wolf (Canis lupus), red deer complex (Cervus sp.) and brown rat (Rattus norvegicus). MobiSeq enables the sequencing of hundreds of thousands loci across the genome and performs SNP discovery with relatively low rates of clonality. Given the ease and flexibility of MobiSeq protocol, the method has the potential to be implemented for marker discovery and population genomics across a wide range of organisms-enabling the exploration of diverse evolutionary and conservation questions.
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Affiliation(s)
- Alba Rey-Iglesia
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Shyam Gopalakrishan
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - David E Alquezar-Planas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Anne Ahlmann Nielsen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Timo Röder
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lene Bruhn Pedersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | | | - Mikkel-Holger S Sinding
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | | | - Zhipeng Li
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Faculty of Applied Sciences, Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), AIMST University, Kedah, Malaysia
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Michael Bunce
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Tobias Mourier
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
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30
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Weigand H, Weiss M, Cai H, Li Y, Yu L, Zhang C, Leese F. Fishing in troubled waters: Revealing genomic signatures of local adaptation in response to freshwater pollutants in two macroinvertebrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:875-891. [PMID: 29602123 DOI: 10.1016/j.scitotenv.2018.03.109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 03/02/2018] [Accepted: 03/09/2018] [Indexed: 06/08/2023]
Abstract
Local adaptation is of fundamental importance for populations to cope with fast, human-mediated environmental changes. In the past, analyses of local adaptation were restricted to few model species. Nowadays, due to the increased affordability of high-throughput sequencing, local adaptation can be studied much easier by searching for patterns of positive selection using genomic data. In the present study, we analysed effects of wastewater treatment plant and ore mining effluents on stream invertebrate populations. The two different anthropogenic stressors have impacted on stream ecosystems over different time scales and with different potencies. As target organisms we selected two macroinvertebrate species with different life histories and dispersal capacities: the caddisfly Glossosoma conformis and the flatworm Dugesia gonocephala. We applied a genome-wide genetic marker technique, termed ddRAD (double digest restriction site associated DNA) sequencing, to identify local adaptation. Ten and 18% of all loci were identified as candidate loci for local adaptation in D. gonocephala and G. conformis, respectively. However, after stringent re-evaluation of the genomic data, strong evidence for local adaptation remained only for one population of the flatworm D. gonocephala affected by high copper concentration from ore mining. One of the corresponding candidate loci is arnt, a gene associated with the response to xenobiotics and potentially involved in metal detoxification. Our results support the hypotheses that local adaptation is more likely to play a central role in environments impacted by a stronger stressor for a longer time and that it is more likely to occur in species with lower migration rates. However, these findings have to be interpreted cautiously, as several confounding factors may have limited the possibility to detect local adaptation. Our study highlights how genomic tools can be used to study the adaptability and thus resistance of natural populations to changing environments and we discuss prospects and limitations of the methods.
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Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, 45141 Essen, Germany.
| | - Martina Weiss
- Aquatic Ecosystem Research, University of Duisburg-Essen, 45141 Essen, Germany
| | - Huimin Cai
- Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China
| | | | - Lili Yu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, 45141 Essen, Germany
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31
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Robledo D, Palaiokostas C, Bargelloni L, Martínez P, Houston R. Applications of genotyping by sequencing in aquaculture breeding and genetics. REVIEWS IN AQUACULTURE 2018; 10:670-682. [PMID: 30220910 PMCID: PMC6128402 DOI: 10.1111/raq.12193] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/27/2016] [Indexed: 05/18/2023]
Abstract
Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high-density single-nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction-site associated DNA sequencing (RAD-Seq) and subsequent variations have been extensively applied to generate population-level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD-Seq techniques have included generation of genetic linkage maps, performing genome-wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.
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Affiliation(s)
- Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Christos Palaiokostas
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroPadovaItaly
| | - Paulino Martínez
- Department of ZoologyGenetics and Physical AnthropologyFaculty of VeterinaryUniversity of Santiago de CompostelaLugoSpain
| | - Ross Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
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32
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O'Leary SJ, Puritz JB, Willis SC, Hollenbeck CM, Portnoy DS. These aren't the loci you'e looking for: Principles of effective SNP filtering for molecular ecologists. Mol Ecol 2018; 27:3193-3206. [PMID: 29987880 DOI: 10.1111/mec.14792] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 12/16/2022]
Abstract
Sequencing reduced-representation libraries of restriction site-associated DNA (RADseq) to identify single nucleotide polymorphisms (SNPs) is quickly becoming a standard methodology for molecular ecologists. Because of the scale of RADseq data sets, putative loci cannot be assessed individually, making the process of filtering noise and correctly identifying biologically meaningful signal more difficult. Artefacts introduced during library preparation and/or bioinformatic processing of SNP data can create patterns that are incorrectly interpreted as indicative of population structure or natural selection. Therefore, it is crucial to carefully consider types of errors that may be introduced during laboratory work and data processing, and how to minimize, detect and remove these errors. Here, we discuss issues inherent to RADseq methodologies that can result in artefacts during library preparation and locus reconstruction resulting in erroneous SNP calls and, ultimately, genotyping error. Further, we describe steps that can be implemented to create a rigorously filtered data set consisting of markers accurately representing independent loci and compare the effect of different combinations of filters on four RAD data sets. At last, we stress the importance of publishing raw sequence data along with final filtered data sets in addition to detailed documentation of filtering steps and quality control measures.
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Affiliation(s)
- Shannon J O'Leary
- Department of Life Sciences, Texas A&M University - Corpus Christi, Texas
| | - Jonathan B Puritz
- Biological Sciences, University of Rhode Island, Kingston, Rhode Island
| | - Stuart C Willis
- Department of Life Sciences, Texas A&M University - Corpus Christi, Texas
- Department of Ichthyology, California Academy of Sciences, San Francisco, California
| | | | - David S Portnoy
- Department of Life Sciences, Texas A&M University - Corpus Christi, Texas
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33
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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34
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Weiss M, Weigand H, Weigand AM, Leese F. Genome-wide single-nucleotide polymorphism data reveal cryptic species within cryptic freshwater snail species-The case of the Ancylus fluviatilis species complex. Ecol Evol 2018; 8:1063-1072. [PMID: 29375779 PMCID: PMC5773296 DOI: 10.1002/ece3.3706] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/20/2017] [Accepted: 11/10/2017] [Indexed: 01/01/2023] Open
Abstract
DNA barcoding utilizes short standardized DNA sequences to identify species and is increasingly used in biodiversity assessments. The technique has unveiled an unforeseeably high number of morphologically cryptic species. However, if speciation has occurred relatively recently and rapidly, the use of single gene markers, and especially the exclusive use of mitochondrial markers, will presumably fail in delimitating species. Therefore, the true number of biological species might be even higher. One mechanism that can result in rapid speciation is hybridization of different species in combination with polyploidization, that is, allopolyploid speciation. In this study, we analyzed the population genetic structure of the polyploid freshwater snail Ancylus fluviatilis, for which allopolyploidization was postulated as a speciation mechanism. DNA barcoding has already revealed four cryptic species within A. fluviatilis (i.e., A. fluviatilis s. str., Ancylus sp. A-C), but early allozyme data even hint at the presence of additional cryptic lineages in Central Europe. We combined COI sequencing with high-resolution genome-wide SNP data (ddRAD data) to analyze the genetic structure of A. fluviatilis populations in a Central German low mountain range (Sauerland). The ddRAD data results indicate the presence of three cryptic species within A. fluviatilis s. str. occurring in sympatry and even syntopy, whereas mitochondrial sequence data only support the existence of one species, with shared haplotypes between species. Our study hence points to the limitations of DNA barcoding when dealing with organismal groups where speciation is assumed to have occurred rapidly, for example, through the process of allopolyploidization. We therefore emphasize that single marker DNA barcoding can underestimate the true species diversity and argue in strong favor of using genome-wide data for species delimitation in such groups.
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Affiliation(s)
- Martina Weiss
- Aquatic Ecosystem ResearchUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Hannah Weigand
- Aquatic Ecosystem ResearchUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
| | - Alexander M. Weigand
- Aquatic Ecosystem ResearchUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
- Musée National d'Histoire NaturelleLuxembourgLuxembourg
| | - Florian Leese
- Aquatic Ecosystem ResearchUniversity of Duisburg‐EssenEssenGermany
- Centre for Water and Environmental Research (ZWU)University of Duisburg‐EssenEssenGermany
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35
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Timm H, Weigand H, Weiss M, Leese F, Rahmann S. ddrage
: A data set generator to evaluate ddRADseq analysis software. Mol Ecol Resour 2017; 18:681-690. [DOI: 10.1111/1755-0998.12743] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Henning Timm
- Genome Informatics; Institute of Human Genetics; University of Duisburg-Essen, University Hospital Essen; Essen Germany
| | - Hannah Weigand
- Aquatic Ecosystem Research; Faculty of Biology; University of Duisburg-Essen; Essen Germany
| | - Martina Weiss
- Aquatic Ecosystem Research; Faculty of Biology; University of Duisburg-Essen; Essen Germany
| | - Florian Leese
- Aquatic Ecosystem Research; Faculty of Biology; University of Duisburg-Essen; Essen Germany
| | - Sven Rahmann
- Genome Informatics; Institute of Human Genetics; University of Duisburg-Essen, University Hospital Essen; Essen Germany
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36
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Flanagan SP, Jones AG. Substantial differences in bias between single‐digest and double‐digest RAD‐seq libraries: A case study. Mol Ecol Resour 2017; 18:264-280. [DOI: 10.1111/1755-0998.12734] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/29/2017] [Accepted: 10/06/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Sarah P. Flanagan
- Biology Department Texas A&M University College Station TX USA
- National Institute for Mathematical and Biological Synthesis University of Tennessee Knoxville TN USA
| | - Adam G. Jones
- Biology Department Texas A&M University College Station TX USA
- Department of Biological Sciences University of Idaho Moscow ID USA
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37
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Weigand H, Weiss M, Cai H, Li Y, Yu L, Zhang C, Leese F. Deciphering the origin of mito-nuclear discordance in two sibling caddisfly species. Mol Ecol 2017; 26:5705-5715. [PMID: 28792677 DOI: 10.1111/mec.14292] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/20/2017] [Accepted: 08/03/2017] [Indexed: 01/15/2023]
Abstract
An increasing number of phylogenetic studies have reported discordances among nuclear and mitochondrial markers. These discrepancies are highly relevant to widely used biodiversity assessment approaches, such as DNA barcoding, that rely almost exclusively on mitochondrial markers. Although the theoretical causes of mito-nuclear discordances are well understood, it is often extremely challenging to determine the principal underlying factor in a given study system. In this study, we uncovered significant mito-nuclear discordances in a pair of sibling caddisfly species. Application of genome sequencing, ddRAD and DNA barcoding revealed ongoing hybridization, as well as historical hybridization in Pleistocene refugia, leading us to identify introgression as the ultimate cause of the observed discordance pattern. Our novel genomic data, the discovery of a European-wide hybrid zone and the availability of established techniques for laboratory breeding make this species pair an ideal model system for studying species boundaries with ongoing gene flow.
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Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Martina Weiss
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Huimin Cai
- BGI-Shenzhen, Shenzhen, China.,Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | | | - Lili Yu
- BGI-Shenzhen, Shenzhen, China
| | | | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
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38
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Franchini P, Monné Parera D, Kautt AF, Meyer A. quaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage. Mol Ecol 2017; 26:2783-2795. [PMID: 28247584 DOI: 10.1111/mec.14077] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Paolo Franchini
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Daniel Monné Parera
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Andreas F. Kautt
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
| | - Axel Meyer
- Zoology and Evolutionary Biology; Department of Biology; University of Konstanz; Universitätsstraße 10 78457 Konstanz Germany
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39
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Vendrami DLJ, Telesca L, Weigand H, Weiss M, Fawcett K, Lehman K, Clark MS, Leese F, McMinn C, Moore H, Hoffman JI. RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160548. [PMID: 28386419 PMCID: PMC5367306 DOI: 10.1098/rsos.160548] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/04/2017] [Indexed: 05/07/2023]
Abstract
The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.
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Affiliation(s)
- David L. J. Vendrami
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
| | - Luca Telesca
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge, Cambridgeshire, CB2 3EQ, UK
| | - Hannah Weigand
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Universitaetsstrasse 5, 45141 Essen, Germany
| | - Martina Weiss
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Universitaetsstrasse 5, 45141 Essen, Germany
| | - Katie Fawcett
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
| | - Katrin Lehman
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
| | - M. S. Clark
- British Antarctic Survey, Natural Environment Research Council, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Florian Leese
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Universitaetsstrasse 5, 45141 Essen, Germany
| | - Carrie McMinn
- Agri-Food and Biosciences Institute, Fisheries and Aquatic Ecosystems, 18a Newforge Lane, Belfast BT9 5PX, UK
| | - Heather Moore
- Agri-Food and Biosciences Institute, Fisheries and Aquatic Ecosystems, 18a Newforge Lane, Belfast BT9 5PX, UK
| | - Joseph I. Hoffman
- Department of Animal Behavior, University of Bielefeld, Postfach 100131, 33501 Bielefeld, Germany
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40
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Vendrami DLJ, Telesca L, Weigand H, Weiss M, Fawcett K, Lehman K, Clark MS, Leese F, McMinn C, Moore H, Hoffman JI. RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160548. [PMID: 28386419 DOI: 10.5061/dryad.mk860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/04/2017] [Indexed: 05/23/2023]
Abstract
The field of molecular ecology is transitioning from the use of small panels of classical genetic markers such as microsatellites to much larger panels of single nucleotide polymorphisms (SNPs) generated by approaches like RAD sequencing. However, few empirical studies have directly compared the ability of these methods to resolve population structure. This could have implications for understanding phenotypic plasticity, as many previous studies of natural populations may have lacked the power to detect genetic differences, especially over micro-geographic scales. We therefore compared the ability of microsatellites and RAD sequencing to resolve fine-scale population structure in a commercially important benthic invertebrate by genotyping great scallops (Pecten maximus) from nine populations around Northern Ireland at 13 microsatellites and 10 539 SNPs. The shells were then subjected to morphometric and colour analysis in order to compare patterns of phenotypic and genetic variation. We found that RAD sequencing was superior at resolving population structure, yielding higher Fst values and support for two distinct genetic clusters, whereas only one cluster could be detected in a Bayesian analysis of the microsatellite dataset. Furthermore, appreciable phenotypic variation was observed in size-independent shell shape and coloration, including among localities that could not be distinguished from one another genetically, providing support for the notion that these traits are phenotypically plastic. Taken together, our results suggest that RAD sequencing is a powerful approach for studying population structure and phenotypic plasticity in natural populations.
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Affiliation(s)
- David L J Vendrami
- Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany
| | - Luca Telesca
- Department of Earth Sciences , University of Cambridge , Downing Street, Cambridge, Cambridgeshire, CB2 3EQ , UK
| | - Hannah Weigand
- Faculty of Biology, Aquatic Ecosystem Research , University of Duisburg-Essen , Universitaetsstrasse 5, 45141 Essen , Germany
| | - Martina Weiss
- Faculty of Biology, Aquatic Ecosystem Research , University of Duisburg-Essen , Universitaetsstrasse 5, 45141 Essen , Germany
| | - Katie Fawcett
- Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany
| | - Katrin Lehman
- Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany
| | - M S Clark
- British Antarctic Survey , Natural Environment Research Council , High Cross, Madingley Road, Cambridge CB3 0ET , UK
| | - Florian Leese
- Faculty of Biology, Aquatic Ecosystem Research , University of Duisburg-Essen , Universitaetsstrasse 5, 45141 Essen , Germany
| | - Carrie McMinn
- Agri-Food and Biosciences Institute , Fisheries and Aquatic Ecosystems , 18a Newforge Lane, Belfast BT9 5PX , UK
| | - Heather Moore
- Agri-Food and Biosciences Institute , Fisheries and Aquatic Ecosystems , 18a Newforge Lane, Belfast BT9 5PX , UK
| | - Joseph I Hoffman
- Department of Animal Behavior , University of Bielefeld , Postfach 100131, 33501 Bielefeld , Germany
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41
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Bagley RK, Sousa VC, Niemiller ML, Linnen CR. History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (
Neodiprion lecontei
). Mol Ecol 2017; 26:1022-1044. [DOI: 10.1111/mec.13972] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/10/2016] [Accepted: 12/01/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Robin K. Bagley
- Department of Biology University of Kentucky Lexington KY 40506 USA
| | - Vitor C. Sousa
- cE3c ‐ Centre for Ecology, Evolution and Environmental Changes Faculdade de Ciências Universidade de Lisboa 1749‐016 Lisboa Portugal
| | - Matthew L. Niemiller
- Illinois Natural History Survey Prairie Research Institute University of Illinois Urbana‐Champaign Champaign IL 61820 USA
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42
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Lowry DB, Hoban S, Kelley JL, Lotterhos KE, Reed LK, Antolin MF, Storfer A. Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Mol Ecol Resour 2016; 17:142-152. [PMID: 27860289 DOI: 10.1111/1755-0998.12635] [Citation(s) in RCA: 232] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/23/2016] [Accepted: 09/02/2016] [Indexed: 12/26/2022]
Abstract
Understanding how and why populations evolve is of fundamental importance to molecular ecology. Restriction site-associated DNA sequencing (RADseq), a popular reduced representation method, has ushered in a new era of genome-scale research for assessing population structure, hybridization, demographic history, phylogeography and migration. RADseq has also been widely used to conduct genome scans to detect loci involved in adaptive divergence among natural populations. Here, we examine the capacity of those RADseq-based genome scan studies to detect loci involved in local adaptation. To understand what proportion of the genome is missed by RADseq studies, we developed a simple model using different numbers of RAD-tags, genome sizes and extents of linkage disequilibrium (length of haplotype blocks). Under the best-case modelling scenario, we found that RADseq using six- or eight-base pair cutting restriction enzymes would fail to sample many regions of the genome, especially for species with short linkage disequilibrium. We then surveyed recent studies that have used RADseq for genome scans and found that the median density of markers across these studies was 4.08 RAD-tag markers per megabase (one marker per 245 kb). The length of linkage disequilibrium for many species is one to three orders of magnitude less than density of the typical recent RADseq study. Thus, we conclude that genome scans based on RADseq data alone, while useful for studies of neutral genetic variation and genetic population structure, will likely miss many loci under selection in studies of local adaptation.
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Affiliation(s)
- David B Lowry
- Plant Biology Laboratories, Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Sean Hoban
- The Morton Arboretum, Lisle, IL, USA.,National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, TN, USA
| | - Joanna L Kelley
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Katie E Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, 430 Nahant Rd., Nahant, MA, 01908, USA
| | - Laura K Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, 35406, USA
| | - Michael F Antolin
- Department of Biology, Colorado State University, Fort Collins, CO, 80523-1878, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
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43
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Hoban S, Kelley JL, Lotterhos KE, Antolin MF, Bradburd G, Lowry DB, Poss ML, Reed LK, Storfer A, Whitlock MC. Finding the Genomic Basis of Local Adaptation: Pitfalls, Practical Solutions, and Future Directions. Am Nat 2016; 188:379-97. [PMID: 27622873 PMCID: PMC5457800 DOI: 10.1086/688018] [Citation(s) in RCA: 438] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.
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Affiliation(s)
- Sean Hoban
- Morton Arboretum, Lisle, Illinois 60532; and National Institute for Mathematical and Biological Synthesis (NIMBioS), Knoxville, Tennessee 37966
| | - Joanna L. Kelley
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
| | - Katie E. Lotterhos
- Department of Marine and Environmental Sciences, Northeastern University Marine Science Center, Nahant, Massachusetts 01908
| | - Michael F. Antolin
- Department of Biology, Colorado State University, Fort Collins, Colorado 80523
| | - Gideon Bradburd
- Museum of Vertebrate Zoology and Department of Environmental Science, Policy, and Management, University of California, Berkeley, California 94720
| | - David B. Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824
| | - Mary L. Poss
- Department of Biology and Veterinary and Biomedical Sciences, Penn State University, University Park, Pennsylvania 16802
| | - Laura K. Reed
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama 35406
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, Washington 99164
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44
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Hoffberg SL, Kieran TJ, Catchen JM, Devault A, Faircloth BC, Mauricio R, Glenn TC. RAD
cap: sequence capture of dual‐digest
RAD
seq libraries with identifiable duplicates and reduced missing data. Mol Ecol Resour 2016; 16:1264-78. [DOI: 10.1111/1755-0998.12566] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | - Troy J. Kieran
- Department of Environmental Health Science University of Georgia Athens GA 30602 USA
| | - Julian M. Catchen
- Department of Animal Biology University of Illinois Urbana IL 61801 USA
| | | | - Brant C. Faircloth
- Department of Biological Sciences and Museum of Natural Science Louisiana State University Baton Rouge LA 70803 USA
| | - Rodney Mauricio
- Department of Genetics University of Georgia Athens GA 30602 USA
| | - Travis C. Glenn
- Department of Genetics University of Georgia Athens GA 30602 USA
- Department of Environmental Health Science University of Georgia Athens GA 30602 USA
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45
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Mora-Márquez F, García-Olivares V, Emerson BC, López de Heredia U. ddradseqtools: a software package for in silico simulation and testing of double-digest RADseq experiments. Mol Ecol Resour 2016; 17:230-246. [DOI: 10.1111/1755-0998.12550] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/11/2016] [Accepted: 05/31/2016] [Indexed: 12/29/2022]
Affiliation(s)
- F. Mora-Márquez
- Forest Genetics and Physiology Research Group; Technical University of Madrid (UPM); Ciudad Universitaria s/n Madrid Spain
| | - V. García-Olivares
- Island Ecology and Evolution Research Group; IPNA-CSIC; Tenerife Canary Islands Spain
| | - B. C. Emerson
- Island Ecology and Evolution Research Group; IPNA-CSIC; Tenerife Canary Islands Spain
- School of Biological Sciences; University of East Anglia; Norwich Research Park Norwich NR4 7TJ UK
| | - U. López de Heredia
- Forest Genetics and Physiology Research Group; Technical University of Madrid (UPM); Ciudad Universitaria s/n Madrid Spain
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46
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Digital gene expression analysis with sample multiplexing and PCR duplicate detection: A straightforward protocol. Biotechniques 2016; 61:26-32. [PMID: 27401671 DOI: 10.2144/000114434] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 04/12/2016] [Indexed: 11/23/2022] Open
Abstract
Tag-Seq is a high-throughput approach used for discovering SNPs and characterizing gene expression. In comparison to RNA-Seq, Tag-Seq eases data processing and allows detection of rare mRNA species using only one tag per transcript molecule. However, reduced library complexity raises the issue of PCR duplicates, which distort gene expression levels. Here we present a novel Tag-Seq protocol that uses the least biased methods for RNA library preparation combined with a novel approach for joint PCR template and sample labeling. In our protocol, input RNA is fragmented by hydrolysis, and poly(A)-bearing RNAs are selected and directly ligated to mixed DNA-RNA P5 adapters. The P5 adapters contain i5 barcodes composed of sample-specific (moderately) degenerate base regions (mDBRs), which later allow detection of PCR duplicates. The P7 adapter is attached via reverse transcription with individual i7 barcodes added during the amplification step. The resulting libraries can be sequenced on an Illumina sequencer. After sample demultiplexing and PCR duplicate removal with a free software tool we designed, the data are ready for downstream analysis. Our protocol was tested on RNA samples from predator-induced and control Daphnia microcrustaceans.
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47
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Harvey MG, Smith BT, Glenn TC, Faircloth BC, Brumfield RT. Sequence Capture versus Restriction Site Associated DNA Sequencing for Shallow Systematics. Syst Biol 2016; 65:910-24. [PMID: 27288477 DOI: 10.1093/sysbio/syw036] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 04/15/2016] [Indexed: 01/08/2023] Open
Abstract
Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies. At shallow timescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species. We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RAD-Seq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of historical processes across biotas. We argue that sequence capture should be given greater attention as a method of obtaining data for studies in shallow systematics and comparative phylogeography.
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Affiliation(s)
- Michael G Harvey
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA,
| | - Brian Tilston Smith
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA, and
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, GA 30602, USA
| | - Brant C Faircloth
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Robb T Brumfield
- Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA, Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
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48
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Lohman BK, Weber JN, Bolnick DI. Evaluation of TagSeq, a reliable low-cost alternative for RNAseq. Mol Ecol Resour 2016; 16:1315-1321. [DOI: 10.1111/1755-0998.12529] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/18/2016] [Accepted: 03/18/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Brian K. Lohman
- Department of Integrative Biology; University of Texas at Austin; One University Station C0990 Austin TX 78712 USA
| | - Jesse N. Weber
- Department of Integrative Biology; University of Texas at Austin; One University Station C0990 Austin TX 78712 USA
| | - Daniel I. Bolnick
- Department of Integrative Biology; University of Texas at Austin; One University Station C0990 Austin TX 78712 USA
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49
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Pandey RV, Pabinger S, Kriegner A, Weinhäusel A. ClinQC: a tool for quality control and cleaning of Sanger and NGS data in clinical research. BMC Bioinformatics 2016; 17:56. [PMID: 26830926 PMCID: PMC4735967 DOI: 10.1186/s12859-016-0915-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/28/2016] [Indexed: 01/07/2023] Open
Abstract
Background Traditional Sanger sequencing has been used as a gold standard method for genetic testing in clinic to perform single gene test, which has been a cumbersome and expensive method to test several genes in heterogeneous disease such as cancer. With the advent of Next Generation Sequencing technologies, which produce data on unprecedented speed in a cost effective manner have overcome the limitation of Sanger sequencing. Therefore, for the efficient and affordable genetic testing, Next Generation Sequencing has been used as a complementary method with Sanger sequencing for disease causing mutation identification and confirmation in clinical research. However, in order to identify the potential disease causing mutations with great sensitivity and specificity it is essential to ensure high quality sequencing data. Therefore, integrated software tools are lacking which can analyze Sanger and NGS data together and eliminate platform specific sequencing errors, low quality reads and support the analysis of several sample/patients data set in a single run. Results We have developed ClinQC, a flexible and user-friendly pipeline for format conversion, quality control, trimming and filtering of raw sequencing data generated from Sanger sequencing and three NGS sequencing platforms including Illumina, 454 and Ion Torrent. First, ClinQC convert input read files from their native formats to a common FASTQ format and remove adapters, and PCR primers. Next, it split bar-coded samples, filter duplicates, contamination and low quality sequences and generates a QC report. ClinQC output high quality reads in FASTQ format with Sanger quality encoding, which can be directly used in down-stream analysis. It can analyze hundreds of sample/patients data in a single run and generate unified output files for both Sanger and NGS sequencing data. Our tool is expected to be very useful for quality control and format conversion of Sanger and NGS data to facilitate improved downstream analysis and mutation screening. Conclusions ClinQC is a powerful and easy to handle pipeline for quality control and trimming in clinical research. ClinQC is written in Python with multiprocessing capability, run on all major operating systems and is available at https://sourceforge.net/projects/clinqc. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-0915-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ram Vinay Pandey
- Health & Environment Department, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Vienna, Austria. .,Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, A-1210, Vienna, Austria.
| | - Stephan Pabinger
- Health & Environment Department, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Vienna, Austria.
| | - Albert Kriegner
- Health & Environment Department, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Vienna, Austria.
| | - Andreas Weinhäusel
- Health & Environment Department, Molecular Diagnostics, AIT Austrian Institute of Technology GmbH, Vienna, Austria.
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50
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Abstract
High-throughput techniques based on restriction site-associated DNA sequencing (RADseq) are enabling the low-cost discovery and genotyping of thousands of genetic markers for any species, including non-model organisms, which is revolutionizing ecological, evolutionary and conservation genetics. Technical differences among these methods lead to important considerations for all steps of genomics studies, from the specific scientific questions that can be addressed, and the costs of library preparation and sequencing, to the types of bias and error inherent in the resulting data. In this Review, we provide a comprehensive discussion of RADseq methods to aid researchers in choosing among the many different approaches and avoiding erroneous scientific conclusions from RADseq data, a problem that has plagued other genetic marker types in the past.
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