1
|
Scott AM, Kovach AI. FecalSeq enrichment with RAD Sequencing from non-invasive environmental samples holds promise for genetic monitoring of an imperiled lagomorph. Sci Rep 2024; 14:17575. [PMID: 39080335 PMCID: PMC11289273 DOI: 10.1038/s41598-024-67764-6] [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: 11/23/2023] [Accepted: 07/15/2024] [Indexed: 08/02/2024] Open
Abstract
Despite advances in genomic sequencing and bioinformatics, conservation genomics is still often hindered by a reliance on non-invasive samples. The presence of exogenous DNA and the low quantity and poor quality of DNA in non-invasive samples have been a roadblock to sequencing, thereby limiting the potential for genomic monitoring of endangered species. Recent molecular advances, such as host DNA enrichment, hold promise for facilitating sequencing from non-invasive samples. We used the FecalSeq method to enrich DNA extracted from wild-collected fecal pellets of the imperiled New England cottontail and identified SNPs from 3RAD Sequencing. We obtained SNPs from rabbit pellets, including pellets that were collected in poor environmental conditions and samples that performed poorly with microsatellites. Measures of sequencing success improved with greater amounts of starting DNA and 32% of samples generated SNP genotypes that passed quality control filtering. Genotyping error rates were high, however, and the approach was unable to consistently distinguish unique individuals or matching genotypes, while it was suitable for recovering the expected population structure. Pairing FecalSeq enrichment with RADseq is a promising low-cost method for monitoring wild populations using non-invasive samples in an environmental context, but it may be better suited for informing conservation through population genomics.
Collapse
Affiliation(s)
- Amy M Scott
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA.
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA
| |
Collapse
|
2
|
Choi TY, Son DC, Oh A, Lee SR. Unveiling a potential threat to forest ecosystems: molecular diagnosis of Alliaria petiolata, a newly introduced alien plant in Korea. FRONTIERS IN PLANT SCIENCE 2024; 15:1395676. [PMID: 39011305 PMCID: PMC11246967 DOI: 10.3389/fpls.2024.1395676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 06/14/2024] [Indexed: 07/17/2024]
Abstract
Identifying stages of a species invasion in a new habitat (i.e., colonization, establishment, and landscape spread) and their primary determinants in biological invasion warrants attention, as it provides vital insights for preventing non-native species from becoming pervasive invaders. However, delineating invasion stages and their associated factors can pose significant challenges due to the ambiguous distinctions between these stages. Alliaria petiolata, one of the most noxious weeds in woodland habitats, has recently been introduced to Korea and observed in a few distant locations. Although the plant's spread has been relatively slow thus far, rapid spread is highly likely in the future, given the high invasive potential reported elsewhere. We indirectly diagnose the current status of A. petiolata invasion in Korea through the assessment of genetic diversity and phylogenetic inferences using genome-wide molecular markers and cytological data. We analyzed 86 individual samples collected from two native and six introduced populations, employing 1,172 SNPs. Our analysis estimated within- and among-population genetic diversity and included two clustering analyses. Furthermore, we investigated potential gene flow and reticulation events among the sampled populations. Our data unraveled that Korean garlic mustard exhibits a hexaploid ploidy level with two distinct chromosome numbers, 2n = 36 and 42. The extent of genetic diversity measured in Korean populations was comparable to that of native populations. Using genome-wide SNP data, we identified three distinct clusters with minor gene flow, while failing to detect indications of reticulation among Korean populations. Based on the multifaceted analyses, our study provides valuable insights into the colonization process and stressed the importance of closely monitoring A. petiolata populations in Korea.
Collapse
Affiliation(s)
- Tae-Young Choi
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, Republic of Korea
| | - Ami Oh
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
| | - Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, Republic of Korea
| |
Collapse
|
3
|
Veale A, Reudink MW, Burg TM. Neutral markers reveal complex population structure across the range of a widespread songbird. Ecol Evol 2024; 14:e11638. [PMID: 38979005 PMCID: PMC11228359 DOI: 10.1002/ece3.11638] [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: 01/22/2024] [Revised: 05/17/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024] Open
Abstract
Understanding how both contemporary and historical physical barriers influence gene flow is key to reconstructing evolutionary histories and can allow us to predict species' resilience to changing environmental conditions. During the last glacial maximum (LGM), many high latitude North American bird species were forced into glacial refugia, including mountain bluebirds (Silia currucoides). Within their current breeding range, mountain bluebirds still experience a wide variety of environmental conditions and barriers that may disrupt gene flow and isolate populations. Using single nucleotide polymorphisms (SNPs) obtained through restriction site-associated DNA sequencing, we detected at least four genetically distinct mountain bluebird populations. Based on this structure, we determined that isolation-by-distance, the northern Rocky Mountains, and discontinuous habitat are responsible for the low connectivity and the overall history of each population going back to the last glacial maximum. Finally, we identified five candidate genes under balancing selection and three loci under diversifying selection. This study provides the first look at connectivity and gene flow across the range of these high-altitude and high latitude songbirds.
Collapse
Affiliation(s)
- Aaron Veale
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Matthew W. Reudink
- Department of Biological SciencesThompson Rivers UniversityKamloopsBritish ColumbiaCanada
| | - Theresa M. Burg
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Lee S, Choi T, Son D. Multiple introductions of divergent lineages and admixture conferred the high invasiveness in a widespread weed ( Hypochaeris radicata). Evol Appl 2024; 17:e13740. [PMID: 38911265 PMCID: PMC11192970 DOI: 10.1111/eva.13740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 05/21/2024] [Accepted: 05/27/2024] [Indexed: 06/25/2024] Open
Abstract
Biological invasion consists of spatially and temporally varying stages, accompanied by ecological and evolutionary changes. Understanding the genomics underlying invasion dynamics provides critical insights into the geographic sources and genetic diversity, contributing to successful invasions across space and time. Here, we used genomic data and model-based approaches to characterize the invasion dynamics of Hypochaeris radicata L., a noxious weed in Korea. Genetic diversity and assignment patterns were investigated using 3563 SNPs of 283 individuals sampled from 22 populations. We employed a coalescent-based simulation method to estimate demographic changes for each population and inferred colonization history using both phylogenetic and population genetic model-based approaches. Our data suggest that H. radicata has been repeatedly been introduced to Korea from multiple genetic sources within the last 50 years, experiencing weak population bottlenecks followed by subsequent population expansions. These findings highlight the potential for further range expansion, particularly in the presence of human-mediated dispersal. Our study represents the first population-level genomic research documenting the invasion dynamics of the successful worldwide invader, H. radicata, outside of Europe.
Collapse
Affiliation(s)
- Soo‐Rang Lee
- Department of Biology Education, College of EducationChosun UniversityGwangjuSouth Korea
| | - Tae‐Young Choi
- Department of Biology Education, College of EducationChosun UniversityGwangjuSouth Korea
| | - Dong‐Chan Son
- Division of Forest Biodiversity and HerbariumKorea National ArboretumPocheonKorea
| |
Collapse
|
6
|
Babik W, Marszałek M, Dudek K, Antunes B, Palomar G, Zając B, Taugbøl A, Pabijan M. Limited evidence for genetic differentiation or adaptation in two amphibian species across replicated rural-urban gradients. Evol Appl 2024; 17:e13700. [PMID: 38832082 PMCID: PMC11146147 DOI: 10.1111/eva.13700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Urbanization leads to complex environmental changes and poses multiple challenges to organisms. Amphibians are highly susceptible to the effects of urbanization, with land use conversion, habitat destruction, and degradation ranked as the most significant threats. Consequently, amphibians are declining in urban areas, in both population numbers and abundance, however, the effect of urbanization on population genetic parameters remains unclear. Here, we studied the genomic response to urbanization in two widespread European species, the common toad Bufo bufo (26 localities, 480 individuals), and the smooth newt Lissotriton vulgaris (30 localities, 516 individuals) in three geographic regions: southern and northern Poland and southern Norway. We assessed genome-wide SNP variation using RADseq (ca. 42 and 552 thousand SNPs in toads and newts, respectively) and adaptively relevant major histocompatibility complex (MHC) class I and II genes. The results linked most of the genetic differentiation in both marker types to regional (latitudinal) effects, which also correspond to historical biogeography. Further, we did not find any association between genetic differentiation and level of urbanization at local scales for either species. However, urban smooth newts, but not toads, have lower levels of within-population genome-wide diversity, suggesting higher susceptibility to the negative effects of urbanization. A decreasing level of genetic diversity linked to increasing urbanization was also found for MHC II in smooth newts, while the relationship between MHC class I diversity and urbanization differed between geographic regions. We did not find any effects of urbanization on MHC diversity in the toad populations. Although two genetic environment association analyses of genome-wide data, LFMM and BayPass, revealed numerous (219 in B. bufo and 7040 in L. vulgaris) SNPs statistically associated with urbanization, we found a marked lack of repeatability between geographic regions, suggesting a complex and multifaceted response to natural selection elicited by life in the city.
Collapse
Affiliation(s)
- W. Babik
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - M. Marszałek
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - K. Dudek
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - B. Antunes
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - G. Palomar
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
- Department of Genetics, Physiology and Microbiology, Faculty of Biological SciencesComplutense University of MadridMadridSpain
| | - B. Zając
- Faculty of Biology, Institute of Zoology and Biomedical ResearchJagiellonian UniversityKrakówPoland
| | - A. Taugbøl
- Norwegian Institute for Nature ResearchLillehammerNorway
| | - M. Pabijan
- Faculty of Biology, Institute of Zoology and Biomedical ResearchJagiellonian UniversityKrakówPoland
| |
Collapse
|
7
|
Pierson TW, Kozak KH, Glenn TC, Fitzpatrick BM. River Drainage Reorganization and Reticulate Evolution in the Two-Lined Salamander (Eurycea bislineata) Species Complex. Syst Biol 2024; 73:26-35. [PMID: 37879625 DOI: 10.1093/sysbio/syad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/14/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023] Open
Abstract
The origin and eventual loss of biogeographic barriers can create alternating periods of allopatry and secondary contact, facilitating gene flow among distinct metapopulations and generating reticulate evolutionary histories that are not adequately described by a bifurcating evolutionary tree. One such example may exist in the two-lined salamander (Eurycea bislineata) species complex, where discordance among morphological and molecular datasets has created a "vexing taxonomic challenge." Previous phylogeographic analyses of mitochondrial DNA (mtDNA) suggested that the reorganization of Miocene paleodrainages drove vicariance and dispersal, but the inherent limitations of a single-locus dataset precluded the evaluation of subsequent gene flow. Here, we generate triple-enzyme restriction site-associated DNA sequencing (3RAD) data for > 100 individuals representing all major mtDNA lineages and use a suite of complementary methods to demonstrate that discordance among earlier datasets is best explained by a reticulate evolutionary history influenced by river drainage reorganization. Systematics of such groups should acknowledge these complex histories and relationships that are not strictly hierarchical. [Amphibian; hybridization; introgression; Plethodontidae; stream capture.].
Collapse
Affiliation(s)
- Todd W Pierson
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Kennesaw, GA 30144, USA
| | - Kenneth H Kozak
- Bell Museum and Department of Fisheries, Wildlife and Conservation Biology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Travis C Glenn
- Department of Environmental Health Science and Institute of Bioinformatics, University of Georgia, Athens, GA 30609, USA
| | - Benjamin M Fitzpatrick
- Department of Ecology and Evolutionary Biology, University of Tennessee Knoxville, Knoxville, TN 37996, USA
| |
Collapse
|
8
|
Souza LHB, Pierson TW, Tenório RO, Ferro JM, Gatto KP, Silva BC, de Andrade GV, Suárez P, Haddad CFB, Lourenço LB. Multiple contact zones and karyotypic evolution in a neotropical frog species complex. Sci Rep 2024; 14:1119. [PMID: 38212602 PMCID: PMC10784582 DOI: 10.1038/s41598-024-51421-z] [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: 07/10/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024] Open
Abstract
Previous studies of DNA sequence and karyotypic data have revealed high genetic diversity in the Physalaemus cuvieri - Physalaemus ephippifer species complex-a group of small leptodactylid frogs in South America. To date, seven major genetic lineages have been recognized in this group, with species delimitation tests supporting four to seven of them as valid species. Among these, only P. ephippifer shows heteromorphic sex chromosomes, but the implications of cytogenetic divergence for the evolution of this group are unknown. We analyzed karyotypic, mitochondrial DNA, and 3RAD genomic data to characterize a putative contact zone between P. ephippifer and P. cuvieri Lineage 1, finding evidence for admixture and karyotypic evolution. We also describe preliminary evidence for admixture between two other members of this species complex-Lineage 1 and Lineage 3 of P. cuvieri. Our study sheds new light on evolutionary relationships in the P. cuvieri - P. ephippifer species complex, suggesting an important role of karyotypic divergence in its evolutionary history and underscoring the importance of hybridization as a mechanism of sex chromosome evolution in amphibians.
Collapse
Affiliation(s)
- Lucas H B Souza
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil.
| | - Todd W Pierson
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Kennesaw, GA, USA
| | - Renata O Tenório
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
| | - Juan M Ferro
- Laboratorio de Genética Evolutiva "Dr. Claudio J. Bidau", Instituto de Biología Subtropical (CONICET-UNaM), Facultad de Ciencias Exactas, Químicas y Naturales, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Kaleb P Gatto
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
| | - Bruno C Silva
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
| | - Gilda V de Andrade
- Departamento de Biologia, Centro de Ciências Biológicas e da Saúde, Universidade Federal do Maranhão (UFMA), Campus do Bacanga, São Luís, MA, 65080-040, Brazil
| | - Pablo Suárez
- Instituto de Biología Subtropical (CONICET-UNaM), Puerto Iguazú, Argentina
| | - Célio F B Haddad
- Departamento de Biodiversidade and Centro de Aquicultura (CAUNESP), Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Luciana B Lourenço
- Laboratório de Estudos Cromossômicos (LabEsC), Departamento de Biologia Estrutural e Funcional, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, 13083-863, Brazil
| |
Collapse
|
9
|
Reyes-Moya I, Sánchez-Montes G, Babik W, Dudek K, Martínez-Solano Í. Assessing fine-scale pondscape connectivity with amphibian eyes: An integrative approach using genomic and capture-mark-recapture data. Mol Ecol 2024; 33:e17206. [PMID: 37997532 DOI: 10.1111/mec.17206] [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: 11/04/2022] [Revised: 10/20/2023] [Accepted: 10/24/2023] [Indexed: 11/25/2023]
Abstract
In the face of habitat loss, preserving functional connectivity is essential to maintain genetic diversity and the demographic dynamics required for the viability of biotic communities. This requires knowledge of the dispersal behaviour of target species, which can be modelled as kernels, or probability density functions of dispersal distances at increasing geographic distances. We present an integrative approach to investigate the relationships between genetic connectivity and demographic parameters in organisms with low vagility focusing on five syntopic pond-breeding amphibians. We genotyped 1056 individuals of two anuran and three urodele species (1732-3913 SNPs per species) from populations located in a landscape comprising 64 ponds to characterize fine-scale genetic structure in a comparative framework, and combined these genetic data with information obtained in a previous 2-year capture-mark-recapture (CMR) study. Specifically, we contrasted graphs reconstructed from genomic data with connectivity graphs based on dispersal kernels and demographic information obtained from CMR data from previous studies, and assessed the effects of population size, population density, geographical distances, inverse movement probabilities and the presence of habitat patches potentially functioning as stepping stones on genetic differentiation. Our results show a significant effect of local population sizes on patterns of genetic differentiation at small spatial scales. In addition, movement records and cluster-derived kernels provide robust inferences on most likely dispersal paths that are consistent with genomic inferences on genetic connectivity. The integration of genetic and CMR data holds great potential for understanding genetic connectivity at spatial scales relevant to individual organisms, with applications for the implementation of management actions at the landscape level.
Collapse
Affiliation(s)
- Ismael Reyes-Moya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Gregorio Sánchez-Montes
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| | - Wieslaw Babik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Katarzyna Dudek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Íñigo Martínez-Solano
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
| |
Collapse
|
10
|
Klein JD, Maduna SN, Dicken ML, da Silva C, Soekoe M, McCord ME, Potts WM, Hagen SB, Bester‐van der Merwe AE. Local adaptation with gene flow in a highly dispersive shark. Evol Appl 2024; 17:e13628. [PMID: 38283610 PMCID: PMC10810256 DOI: 10.1111/eva.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/06/2023] [Accepted: 11/27/2023] [Indexed: 01/30/2024] Open
Abstract
Adaptive divergence in response to environmental clines are expected to be common in species occupying heterogeneous environments. Despite numerous advances in techniques appropriate for non-model species, gene-environment association studies in elasmobranchs are still scarce. The bronze whaler or copper shark (Carcharhinus brachyurus) is a large coastal shark with a wide distribution and one of the most exploited elasmobranchs in southern Africa. Here, we assessed the distribution of neutral and adaptive genomic diversity in C. brachyurus across a highly heterogeneous environment in southern Africa based on genome-wide SNPs obtained through a restriction site-associated DNA method (3RAD). A combination of differentiation-based genome-scan (outflank) and genotype-environment analyses (redundancy analysis, latent factor mixed models) identified a total of 234 differentiation-based outlier and candidate SNPs associated with bioclimatic variables. Analysis of 26,299 putatively neutral SNPs revealed moderate and evenly distributed levels of genomic diversity across sites from the east coast of South Africa to Angola. Multivariate and clustering analyses demonstrated a high degree of gene flow with no significant population structuring among or within ocean basins. In contrast, the putatively adaptive SNPs demonstrated the presence of two clusters and deep divergence between Angola and all other individuals from Namibia and South Africa. These results provide evidence for adaptive divergence in response to a heterogeneous seascape in a large, mobile shark despite high levels of gene flow. These results are expected to inform management strategies and policy at the national and regional level for conservation of C. brachyurus populations.
Collapse
Affiliation(s)
- Juliana D. Klein
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| | - Simo N. Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Matthew L. Dicken
- KwaZulu‐Natal Sharks BoardUmhlanga RocksSouth Africa
- Institute for Coastal and Marine Research (CMR), Ocean Sciences CampusNelson Mandela UniversityGqeberhaSouth Africa
| | - Charlene da Silva
- Department of Forestry, Fisheries and EnvironmentRogge BaySouth Africa
| | - Michelle Soekoe
- Division of Marine ScienceReel Science CoalitionCape TownSouth Africa
| | - Meaghen E. McCord
- South African Shark ConservancyHermanusSouth Africa
- Canadian Parks and Wilderness SocietyVancouverBritish ColumbiaCanada
| | - Warren M. Potts
- Department of Ichthyology and Fisheries ScienceRhodes UniversityMakhandaSouth Africa
- South African Institute for Aquatic BiodiversityMakhandaSouth Africa
| | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research StationNorwegian Institute of Bioeconomy Research—NIBIOSvanvikNorway
| | - Aletta E. Bester‐van der Merwe
- Molecular Breeding and Biodiversity Research Group, Department of GeneticsStellenbosch UniversityStellenboschSouth Africa
| |
Collapse
|
11
|
Vega-Sánchez YM, Oyama K, Mendoza-Cuenca LF, Gaytán-Legaria R, González-Rodríguez A. Genomic differentiation and niche divergence in the Hetaerina americana (Odonata) cryptic species complex. Mol Ecol 2024; 33:e17207. [PMID: 37975486 DOI: 10.1111/mec.17207] [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: 08/17/2023] [Revised: 10/11/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023]
Abstract
The evolution of reproductive barriers, that is, the speciation process, implies the limitation of gene flow between populations. Different patterns of genomic differentiation throughout the speciation continuum may provide insights into the causal evolutionary forces of species divergence. In this study, we analysed a cryptic species complex of the genus Hetaerina (Odonata). This complex includes H. americana and H. calverti; however, in H. americana two highly differentiated genetic groups have been previously detected, which, we hypothesize, may correspond to different species with low morphological variation. We obtained single nucleotide polymorphism (SNP) data for 90 individuals belonging to the different taxa in the complex and carried out differentiation tests to identify genetic isolation. The results from STRUCTURE and discriminant analysis of principal components (DAPC), based on almost 5000 SNPs, confirmed the presence of three highly differentiated taxa. Also, we found FST values above 0.5 in pairwise comparisons, which indicates a considerable degree of genetic isolation among the suggested species. We also found low climatic niche overlap among all taxa, suggesting that each group occurs at specific conditions of temperature, precipitation and elevation. We propose that H. americana comprises two cryptic species, which may be reproductively isolated by ecological barriers related to niche divergence, since the morphological variation is minimal and, therefore, mechanical barriers are probably less effective compared to other related species such as H. calverti.
Collapse
Affiliation(s)
- Yesenia Margarita Vega-Sánchez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Morelia, Mexico
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Morelia, Mexico
| | | | - Ricardo Gaytán-Legaria
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Morelia, Mexico
| | - Antonio González-Rodríguez
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México (UNAM), Morelia, Mexico
| |
Collapse
|
12
|
Guo L, Kruglyak L. Genetics and biology of coloration in reptiles: the curious case of the Lemon Frost geckos. Physiol Genomics 2023; 55:479-486. [PMID: 37642275 DOI: 10.1152/physiolgenomics.00015.2023] [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: 03/06/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 08/31/2023] Open
Abstract
Although there are more than 10,000 reptile species, and reptiles have historically contributed to our understanding of biology, genetics research into class Reptilia has lagged compared with other animals. Here, we summarize recent progress in genetics of coloration in reptiles, with a focus on the leopard gecko, Eublepharis macularius. We highlight genetic approaches that have been used to examine variation in color and pattern formation in this species as well as to provide insights into mechanisms underlying skin cancer. We propose that their long breeding history in captivity makes leopard geckos one of the most promising emerging reptilian models for genetic studies. More broadly, technological advances in genetics, genomics, and gene editing may herald a golden era for studies of reptile biology.
Collapse
Affiliation(s)
- Longhua Guo
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan, United States
- Geriatrics Center and Institute of Gerontology, University of Michigan, Ann Arbor, Michigan, United States
| | - Leonid Kruglyak
- Department of Human Genetics, University of California, Los Angeles, California, United States
- Department of Biological Chemistry, University of California, Los Angeles, California, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| |
Collapse
|
13
|
Reichard M, Koblmüller S, Blažek R, Zimmermann H, Katongo C, Bryjová A, Bryja J. Lack of host specialization despite selective host use in brood parasitic cuckoo catfish. Mol Ecol 2023; 32:6070-6082. [PMID: 37861460 DOI: 10.1111/mec.17173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 10/21/2023]
Abstract
Host-parasite dynamics involve coevolutionary arms races, which may lead to host specialization and ensuing diversification. Our general understanding of the evolution of host specialization in brood parasites is compromised by a restricted focus on bird and insect lineages. The cuckoo catfish (Synodontis multipunctatus) is an obligate parasite of parental care of mouthbrooding cichlids in Lake Tanganyika. Given the ecological and taxonomic diversity of mouthbrooding cichlids in the lake, we hypothesized the existence of sympatric host-specific lineages in the cuckoo catfish. In a sample of 779 broods from 20 cichlid species, we found four species parasitized by cuckoo catfish (with prevalence of parasitism of 2%-18%). All parasitized cichlids were from the tribe Tropheini, maternal mouthbrooders that spawn over a substrate (rather than in open water). Phylogenetic analysis based on genomic (ddRAD sequencing) and mitochondrial (Dloop) data from cuckoo catfish embryos showed an absence of host-specific lineages. This was corroborated by analyses of genetic structure and co-ancestry matrix. Within host species, parasitism was not associated with any individual characteristic we recorded (parent size, water depth), but was costly as parasitized parents carried smaller clutches of their own offspring. We conclude that the cuckoo catfish is an intermediate generalist and discuss costs, benefits and constraints of host specialization in this species and brood parasites in general.
Collapse
Affiliation(s)
- Martin Reichard
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | | | - Radim Blažek
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Holger Zimmermann
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Institute of Biology, University of Graz, Graz, Austria
| | - Cyprian Katongo
- Department of Biological Sciences, University of Zambia, Lusaka, Zambia
| | - Anna Bryjová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| |
Collapse
|
14
|
Babik W, Dudek K, Marszałek M, Palomar G, Antunes B, Sniegula S. The genomic response to urbanization in the damselfly Ischnura elegans. Evol Appl 2023; 16:1805-1818. [PMID: 38029064 PMCID: PMC10681423 DOI: 10.1111/eva.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/19/2023] [Indexed: 12/01/2023] Open
Abstract
The complex and rapid environmental changes brought about by urbanization pose significant challenges to organisms. The multifaceted effects of urbanization often make it difficult to define and pinpoint the very nature of adaptive urban phenotypes. In such situations, scanning genomes for regions differentiated between urban and non-urban populations may be an attractive approach. Here, we investigated the genomic signatures of adaptation to urbanization in the damselfly Ischnura elegans sampled from 31 rural and urban localities in three geographic regions: southern and northern Poland, and southern Sweden. Genome-wide variation was assessed using more than 370,000 single nucleotide polymorphisms (SNPs) genotyped by ddRADseq. Associations between SNPs and the level of urbanization were tested using two genetic environment association methods: Latent Factors Mixed Models and BayPass. While we found numerous candidate SNPs and a highly significant overlap between candidates identified by the two methods within the geographic regions, there was a distinctive lack of repeatability between the geographic regions both at the level of individual SNPs and of genomic regions. However, we found "synapse organization" at the top of the functional categories enriched among the genes located in the proximity of the candidate urbanization SNPs. Interestingly, the overall significance of "synapse organization" was built up by the accretion of different genes associated with candidate SNPs in different geographic regions. This finding is consistent with the highly polygenic nature of adaptation, where the response may be achieved through a subtle adjustment of allele frequencies in different genes that contribute to adaptive phenotypes. Taken together, our results point to a polygenic adaptive response in the nervous system, specifically implicating genes involved in synapse organization, which mirrors the findings from several genomic and behavioral studies of adaptation to urbanization in other taxa.
Collapse
Affiliation(s)
- W. Babik
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - K. Dudek
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - M. Marszałek
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - G. Palomar
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
- Department of Genetics, Physiology and Microbiology, Faculty of Biological SciencesComplutense University of MadridMadridSpain
| | - B. Antunes
- Faculty of Biology, Institute of Environmental SciencesJagiellonian UniversityKrakówPoland
| | - S. Sniegula
- Department of Ecosystem Conservation, Institute of Nature ConservationPolish Academy of SciencesKrakówPoland
| |
Collapse
|
15
|
Weber JN, Kojima W, Boisseau RP, Niimi T, Morita S, Shigenobu S, Gotoh H, Araya K, Lin CP, Thomas-Bulle C, Allen CE, Tong W, Lavine LC, Swanson BO, Emlen DJ. Evolution of horn length and lifting strength in the Japanese rhinoceros beetle Trypoxylus dichotomus. Curr Biol 2023; 33:4285-4297.e5. [PMID: 37734374 DOI: 10.1016/j.cub.2023.08.066] [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: 03/13/2023] [Revised: 06/28/2023] [Accepted: 08/23/2023] [Indexed: 09/23/2023]
Abstract
What limits the size of nature's most extreme structures? For weapons like beetle horns, one possibility is a tradeoff associated with mechanical levers: as the output arm of the lever system-the beetle horn-gets longer, it also gets weaker. This "paradox of the weakening combatant" could offset reproductive advantages of additional increases in weapon size. However, in contemporary populations of most heavily weaponed species, males with the longest weapons also tend to be the strongest, presumably because selection drove the evolution of compensatory changes to these lever systems that ameliorated the force reductions of increased weapon size. Therefore, we test for biomechanical limits by reconstructing the stages of weapon evolution, exploring whether initial increases in weapon length first led to reductions in weapon force generation that were later ameliorated through the evolution of mechanisms of mechanical compensation. We describe phylogeographic relationships among populations of a rhinoceros beetle and show that the "pitchfork" shaped head horn likely increased in length independently in the northern and southern radiations of beetles. Both increases in horn length were associated with dramatic reductions to horn lifting strength-compelling evidence for the paradox of the weakening combatant-and these initial reductions to horn strength were later ameliorated in some populations through reductions to horn length or through increases in head height (the input arm for the horn lever system). Our results reveal an exciting geographic mosaic of weapon size, weapon force, and mechanical compensation, shedding light on larger questions pertaining to the evolution of extreme structures.
Collapse
Affiliation(s)
- Jesse N Weber
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Wataru Kojima
- Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8511, Japan
| | - Romain P Boisseau
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Teruyuki Niimi
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Shinichi Morita
- Division of Evolutionary Developmental Biology, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Shuji Shigenobu
- Trans-Scale Biology Center, National Institute for Basic Biology, 38 Nishigonaka Myodaiji, Okazaki 444-8585, Japan
| | - Hiroki Gotoh
- Department of Science, Graduate School of Integrated Science and Technology, Shizuoka University, 836 Oya, Suruga Ward, Shizuoka, Japan
| | - Kunio Araya
- Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka-city Fukuoka 819-0395, Japan
| | - Chung-Ping Lin
- Department of Life Science, National Taiwan Normal University, No.88 Sec. 4, Tingzhou Rd, Taipei 11677, Taiwan
| | - Camille Thomas-Bulle
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA; Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Cerisse E Allen
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
| | - Wenfei Tong
- Cornell Laboratory of Ornithology, Ithaca, NY 14850, USA
| | - Laura Corley Lavine
- Department of Entomology, Washington State University, Pullman, WA 99164, USA
| | - Brook O Swanson
- Department of Biology, Gonzaga University, 502 East Boone Avenue, Spokane, WA 99258-0102, USA
| | - Douglas J Emlen
- Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA.
| |
Collapse
|
16
|
Hopper KR. Reduced-representation libraries in insect genetics. CURRENT OPINION IN INSECT SCIENCE 2023; 59:101084. [PMID: 37442341 DOI: 10.1016/j.cois.2023.101084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 05/04/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023]
Abstract
Genotyping-by-sequencing of reduced-representation libraries has ushered in an era where genome-wide data can be gotten for any species. Here, I review research on this topic during the last two years, report meta-analysis of the results, and discuss analysis methods and issues. Scanning the literature from 2021 to 2022 identified 21 papers, the majority of which were on population differences, including local adaptation and migration, but several papers were on genetic maps and their use in assembly scaffolding or analysis of quantitative trait loci, on the origin of incursions of pest insects, or on infection rates of a pathogen in a disease vector. The research reviewed includes 33 species from 25 families and 11 orders. Meta-analysis showed that less than 16%, and most often, less than 1% of the genome was implicated in local adaptation and that the number of adaptive loci correlated with genetic divergence among populations.
Collapse
Affiliation(s)
- Keith R Hopper
- Beneficial Insect Introductions Research Unit, ARS, USDA, Newark, DE, United States.
| |
Collapse
|
17
|
Sromek L, Ylinen E, Kunnasranta M, Maduna SN, Sinisalo T, Michell CT, Kovacs KM, Lydersen C, Ieshko E, Andrievskaya E, Alexeev V, Leidenberger S, Hagen SB, Nyman T. Loss of species and genetic diversity during colonization: Insights from acanthocephalan parasites in northern European seals. Ecol Evol 2023; 13:e10608. [PMID: 37869427 PMCID: PMC10585441 DOI: 10.1002/ece3.10608] [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: 06/27/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Abstract
Studies on host-parasite systems that have experienced distributional shifts, range fragmentation, and population declines in the past can provide information regarding how parasite community richness and genetic diversity will change as a result of anthropogenic environmental changes in the future. Here, we studied how sequential postglacial colonization, shifts in habitat, and reduced host population sizes have influenced species richness and genetic diversity of Corynosoma (Acanthocephala: Polymorphidae) parasites in northern European marine, brackish, and freshwater seal populations. We collected Corynosoma population samples from Arctic, Baltic, Ladoga, and Saimaa ringed seal subspecies and Baltic gray seals, and then applied COI barcoding and triple-enzyme restriction-site associated DNA (3RAD) sequencing to delimit species, clarify their distributions and community structures, and elucidate patterns of intraspecific gene flow and genetic diversity. Our results showed that Corynosoma species diversity reflected host colonization histories and population sizes, with four species being present in the Arctic, three in the Baltic Sea, two in Lake Ladoga, and only one in Lake Saimaa. We found statistically significant population-genetic differentiation within all three Corynosoma species that occur in more than one seal (sub)species. Genetic diversity tended to be high in Corynosoma populations originating from Arctic ringed seals and low in the landlocked populations. Our results indicate that acanthocephalan communities in landlocked seal populations are impoverished with respect to both species and intraspecific genetic diversity. Interestingly, the loss of genetic diversity within Corynosoma species seems to have been less drastic than in their seal hosts, possibly due to their large local effective population sizes resulting from high infection intensities and effective intra-host population mixing. Our study highlights the utility of genomic methods in investigations of community composition and genetic diversity of understudied parasites.
Collapse
Affiliation(s)
- Ludmila Sromek
- Department of Marine Ecosystems Functioning, Institute of OceanographyUniversity of GdanskGdyniaPoland
| | - Eeva Ylinen
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
| | - Mervi Kunnasranta
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Natural Resources Institute FinlandJoensuuFinland
| | - Simo N. Maduna
- Department of Ecosystem in the Barents RegionNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Tuula Sinisalo
- Department of Biological and Environmental SciencesUniversity of JyväskyläJyväskyläFinland
| | - Craig T. Michell
- Department of Environmental and Biological SciencesUniversity of Eastern FinlandJoensuuFinland
- Red Sea Research CenterKing Abdullah University of Science and TechnologyJeddahSaudi Arabia
| | | | | | - Evgeny Ieshko
- Institute of Biology, Karelian Research CentreRussian Academy of SciencesPetrozavodskRussia
| | | | | | - Sonja Leidenberger
- Department of Biology and Bioinformatics, School of BioscienceUniversity of SkövdeSkövdeSweden
| | - Snorre B. Hagen
- Department of Ecosystem in the Barents RegionNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Tommi Nyman
- Department of Ecosystem in the Barents RegionNorwegian Institute of Bioeconomy ResearchSvanvikNorway
| |
Collapse
|
18
|
Maduna SN, Jónsdóttir ÓDB, Imsland AKD, Gíslason D, Reynolds P, Kapari L, Hangstad TA, Meier K, Hagen SB. Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish-Implications for Broodstock Provenance Sourcing and Larval Production. Genes (Basel) 2023; 14:1870. [PMID: 37895225 PMCID: PMC10606024 DOI: 10.3390/genes14101870] [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: 08/21/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for "cleaner fish" to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype-environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our 'global' sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway.
Collapse
Affiliation(s)
- Simo Njabulo Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
| | | | - Albert Kjartan Dagbjartarson Imsland
- Akvaplan-Niva Iceland Office, Akralind 6, 201 Kópavogur, Iceland; (Ó.D.B.J.); (A.K.D.I.)
- Department of Biological Sciences, High Technology Centre, University of Bergen, 5020 Bergen, Norway
| | | | | | - Lauri Kapari
- Akvaplan-Niva, Framsenteret, 9296 Tromsø, Norway;
| | | | | | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Oksanen S, Saarinen R, Korkiakoski A, Lamminmäki U, Huovinen T. Genotyped functional screening of soluble Fab clones enables in-depth analysis of mutation effects. Sci Rep 2023; 13:13107. [PMID: 37567990 PMCID: PMC10421887 DOI: 10.1038/s41598-023-40241-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
Monoclonal antibodies (mAbs) and their fragments are widely used in therapeutics, diagnostics and basic research. Although display methods such as phage display offer high-throughput, affinities of individual antibodies need to be accurately measured in soluble format. We have developed a screening platform capable of providing genotyped functional data from a total of 9216 soluble, individual antigen binding fragment (Fab) clones by employing next-generation sequencing (NGS) with hierarchical indexing. Full-length, paired variable domain sequences (VL-VH) are linked to functional screening data, enabling in-depth analysis of mutation effects. The platform was applied to four phage display-selected scFv/Fab screening projects and one site-saturation VH affinity maturation project. Genotyped functional screening simultaneously enabled the identification of affinity improving mutations in the VH domain of Fab 49A3 recognizing Dengue virus non-structural protein 1 (NS1) serotype 2 and informed on VH residue positions which cannot be changed from wild-type without decreasing the affinity. Genotype-based identification revealed to us the extent of intraclonal signal variance inherent to single point screening data, a phenomenon often overlooked in the field. Moreover, genotyped screening eliminated the redundant selection of identical genotypes for further study and provided a new analysis tool to evaluate the success of phage display selections and remaining clonal diversity in the screened repertoires.
Collapse
Affiliation(s)
- Sami Oksanen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland.
| | - Roope Saarinen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland
| | | | - Urpo Lamminmäki
- Department of Life Sciences, University of Turku, 20520, Turku, Finland
| | - Tuomas Huovinen
- Department of Life Sciences, University of Turku, 20520, Turku, Finland.
| |
Collapse
|
21
|
Gallego-García N, Vargas-Ramírez M, Shaffer HB. The importance of cryptic diversity in the conservation of wide-ranging species: The red-footed tortoise Chelonoidis carbonarius in Colombia. Mol Ecol 2023; 32:4531-4545. [PMID: 37340598 DOI: 10.1111/mec.17052] [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: 12/27/2022] [Revised: 05/23/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023]
Abstract
Wide-ranging species are seldom considered conservation priorities, yet they have the potential to harbour genetically deeply differentiated units across environments or ecological barriers, including some that warrant taxonomic recognition. Documenting such cryptic genetic diversity is especially important for wide-ranging species that are in decline, as they may comprise a set of even more endangered lineages or species with small distributions. However, studies of wide-ranging species, particularly when they cross political borders, are extremely challenging. One approach to overcoming these challenges is to conduct detailed local analyses in combination with less detailed, range-wide studies. We used this approach with the red-footed tortoise (Chelonoidis carbonarius), a threatened species likely to contain cryptic diversity given its vast range and the distinctive ecoregions that it inhabits. Previous single-gene molecular studies indicated the presence of at least five lineages, two of which occur in different ecoregions separated by the Andes within Colombia. We used a comprehensive genomic analysis to test the hypothesis of cryptic diversity within the single jurisdiction of Colombia. We used a combination of restriction-site-associated DNA sequencing and environmental niche modelling to provide three independent lines of evidence that support the presence of important cryptic diversity that may deserve taxonomic recognition: allopatric reproductive isolation, local adaptation and ecological divergence. We also provide a fine-scale genetic map with the distribution of conservation units in Colombia. As we complete ongoing range-wide analyses and make taxonomic adjustments, we recommend that the two lineages in Colombia be treated as separate units for conservation purposes.
Collapse
Affiliation(s)
- Natalia Gallego-García
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
| | - Mario Vargas-Ramírez
- Biodiversidad y Conservación Genética, Instituto de Genética, Universidad Nacional de Colombia, Bogotá, Colombia
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, University of California, Los Angeles, Los Angeles, California, USA
| |
Collapse
|
22
|
Mendoza-Portillo V, García-De León FJ, von der Heyden S. Responses of population structure and genomic diversity to climate change and fishing pressure in a pelagic fish. GLOBAL CHANGE BIOLOGY 2023; 29:4107-4125. [PMID: 37078996 DOI: 10.1111/gcb.16732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/28/2023] [Accepted: 04/16/2023] [Indexed: 05/03/2023]
Abstract
The responses of marine species to environmental changes and anthropogenic pressures (e.g., fishing) interact with ecological and evolutionary processes that are not well understood. Knowledge of changes in the distribution range and genetic diversity of species and their populations into the future is essential for the conservation and sustainable management of resources. Almaco jack (Seriola rivoliana) is a pelagic fish with high importance to fisheries and aquaculture in the Pacific Ocean. In this study, we assessed contemporary genomic diversity and structure in loci that are putatively under selection (outlier loci) and determined their potential functions. Using a combination of genotype-environment association, spatial distribution models, and demogenetic simulations, we modeled the effects of climate change (under three different RCP scenarios) and fishing pressure on the species' geographic distribution and genomic diversity and structure to 2050 and 2100. Our results show that most of the outlier loci identified were related to biological and metabolic processes that may be associated with temperature and salinity. The contemporary genomic structure showed three populations-two in the Eastern Pacific (Cabo San Lucas and Eastern Pacific) and one in the Central Pacific (Hawaii). Future projections suggest a loss of suitable habitat and potential range contractions for most scenarios, while fishing pressure decreased population connectivity. Our results suggest that future climate change scenarios and fishing pressure will affect the genomic structure and genotypic composition of S. rivoliana and lead to loss of genomic diversity in populations distributed in the eastern-central Pacific Ocean, which could have profound effects on fisheries that depend on this resource.
Collapse
Affiliation(s)
- Verónica Mendoza-Portillo
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
| | - Francisco J García-De León
- Laboratorio de Genética para la Conservación, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
| | - Sophie von der Heyden
- Evolutionary Genomics Group, Department of Botany and Zoology, Stellenbosch University, Matieland, South Africa
- School of Climate Studies, Stellenbosch University, Matieland, South Africa
| |
Collapse
|
23
|
van Riemsdijk I, Arntzen JW, Bucciarelli GM, McCartney-Melstad E, Rafajlović M, Scott PA, Toffelmier E, Shaffer HB, Wielstra B. Two transects reveal remarkable variation in gene flow on opposite ends of a European toad hybrid zone. Heredity (Edinb) 2023; 131:15-24. [PMID: 37106116 PMCID: PMC10313803 DOI: 10.1038/s41437-023-00617-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 03/27/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Speciation entails a reduction in gene flow between lineages. The rates at which genomic regions become isolated varies across space and time. Barrier markers are linked to putative genes involved in (processes of) reproductive isolation, and, when observed over two transects, indicate species-wide processes. In contrast, transect-specific putative barrier markers suggest local processes. We studied two widely separated transects along the 900 km hybrid zone between Bufo bufo and B. spinosus, in northern and southern France, for ~1200 RADseq markers. We used genomic and geographic cline analyses to identify barrier markers based on their restricted introgression, and found that some markers are transect-specific, while others are shared between transects. Twenty-six barrier markers were shared across both transects, of which some are clustered in the same chromosomal region, suggesting that their associated genes are involved in reduced gene flow across the entire hybrid zone. Transect-specific barrier markers were twice as numerous in the southern than in the northern transect, suggesting that the overall barrier effect is weaker in northern France. We hypothesize that this is consistent with a longer period of secondary contact in southern France. The smaller number of introgressed genes in the northern transect shows considerably more gene flow towards the southern (B. spinosus) than the northern species (B. bufo). We hypothesize that hybrid zone movement in northern France and hybrid zone stability in southern France explain this pattern. The Bufo hybrid zone provides an excellent opportunity to separate a general barrier effect from localized gene flow-reducing conditions.
Collapse
Affiliation(s)
- I van Riemsdijk
- Naturalis Biodiversity Center, Leiden, the Netherlands.
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands.
- Institute for Evolution and Ecology, Plant Evolutionary Ecology, Tübingen University, Tübingen, Germany.
| | - J W Arntzen
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - G M Bucciarelli
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
- Institute of the Environment, UC Davis, Davis, CA, USA
- Department of Wildlife, Fish, and Conservation Biology, UC Davis, Davis, CA, USA
| | - E McCartney-Melstad
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - M Rafajlović
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
- The Linnaeus Centre for Marine Evolutionary Biology, University of Gothenburg, Gothenburg, Sweden
| | - P A Scott
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Natural Sciences Collegium, Eckerd College, 4200 54 Ave S, St Petersburg, FL, 33711, USA
| | - E Toffelmier
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - H B Shaffer
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- La Kretz Center for California Conservation Science, Institute of the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - B Wielstra
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| |
Collapse
|
24
|
Frederick JC, Thompson AT, Sharma P, Dharmarajan G, Ronai I, Pesapane R, Smith RC, Sundstrom KD, Tsao JI, Tuten HC, Yabsley MJ, Glenn TC. Phylogeography of the blacklegged tick (Ixodes scapularis) throughout the USA identifies candidate loci for differences in vectorial capacity. Mol Ecol 2023; 32:3133-3149. [PMID: 36912202 DOI: 10.1111/mec.16921] [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: 08/22/2022] [Revised: 02/25/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023]
Abstract
The blacklegged tick (Ixodes scapularis (Journal of the Academy of Natural Sciences of Philadelphia, 1821, 2, 59)) is a vector of Borrelia burgdorferi sensu stricto (s.s.) (International Journal of Systematic Bacteriology, 1984, 34, 496), the causative bacterial agent of Lyme disease, part of a slow-moving epidemic of Lyme borreliosis spreading across the northern hemisphere. Well-known geographical differences in the vectorial capacity of these ticks are associated with genetic variation. Despite the need for detailed genetic information in this disease system, previous phylogeographical studies of these ticks have been restricted to relatively few populations or few genetic loci. Here we present the most comprehensive phylogeographical study of genome-wide markers in I. scapularis, conducted by using 3RAD (triple-enzyme restriction-site associated sequencing) and surveying 353 ticks from 33 counties throughout the species' range. We found limited genetic variation among populations from the Northeast and Upper Midwest, where Lyme disease is most common, and higher genetic variation among populations from the South. We identify five spatially associated genetic clusters of I. scapularis. In regions where Lyme disease is increasing in frequency, the I. scapularis populations genetically group with ticks from historically highly Lyme-endemic regions. Finally, we identify 10 variable DNA sites that contribute the most to population differentiation. These variable sites cluster on one of the chromosome-scale scaffolds for I. scapularis and are within identified genes. Our findings illuminate the need for additional research to identify loci causing variation in the vectorial capacity of I. scapularis and where additional tick sampling would be most valuable to further understand disease trends caused by pathogens transmitted by I. scapularis.
Collapse
Affiliation(s)
- Julia C Frederick
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, 30602, USA
| | - Alec T Thompson
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, 30602, USA
- Center for the Ecology of Infectious Diseases, Odom School of Ecology, University of Georgia, Athens, Georgia, 30602, USA
| | - Prisha Sharma
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, 30602, USA
| | - Guha Dharmarajan
- Savannah River Ecology Laboratory, University of Georgia, Aiken, South Carolina, 29808, USA
- Division of Sciences, School of Interwoven Arts and Sciences, Krea University, Sri City, Andhra Pradesh, India
| | - Isobel Ronai
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, USA
| | - Risa Pesapane
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, 43210, USA
- School of Environment and Natural Resources, The Ohio State University, Columbus, Ohio, 43210, USA
| | - Ryan C Smith
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, Iowa, 50011, USA
| | - Kellee D Sundstrom
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Oklahoma State University, Stillwater, Oklahoma, 74078, USA
| | - Jean I Tsao
- Department of Wildlife and Fisheries, Michigan State University, East Lansing, Michigan, 48824, USA
| | - Holly C Tuten
- Illinois Natural History Survey, University of Illinois Urbana-Champaign, Champaign, Illinois, 61820, USA
| | - Michael J Yabsley
- Southeastern Cooperative Wildlife Disease Study, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, Georgia, 30602, USA
- Center for the Ecology of Infectious Diseases, Odom School of Ecology, University of Georgia, Athens, Georgia, 30602, USA
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, 30602, USA
| | - Travis C Glenn
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, 30602, USA
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, 30602, USA
| |
Collapse
|
25
|
Alkemade JA, Baroncelli R, Messmer MM, Hohmann P. Attack of the clones: Population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose. MOLECULAR PLANT PATHOLOGY 2023; 24:616-627. [PMID: 37078402 DOI: 10.1111/mpp.13332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Colletotrichum lupini, the causative agent of lupin anthracnose, affects lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the diversity, evolutionary dynamics, and molecular basis of the interaction of this notorious lupin pathogen with its host. A collection of globally representative C. lupini isolates was genotyped through triple digest restriction site-associated DNA sequencing, resulting in a data set of unparalleled resolution. Phylogenetic and structural analysis could distinguish four independent lineages (I-IV). The strong population structure and high overall standardized index of association (r̅d ) indicates that C. lupini reproduces clonally. Different morphologies and virulence patterns on white lupin (Lupinus albus) and Andean lupin (Lupinus mutabilis) were observed between and within clonal lineages. Isolates belonging to lineage II were shown to have a minichromosome that was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this minichromosome could imply a role in host-pathogen interaction. All four lineages were present in the South American Andes region, which is suggested to be the centre of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seedborne pathogen, C. lupini has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.
Collapse
Affiliation(s)
- Joris A Alkemade
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
- Centre for Studies on Bioinspired Agro-Enviromental Technology, Università di Napoli Federico II, Portici, 80055, Italy
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Bonaplanta, BioCrops Innovations SL, Manresa, Spain
| |
Collapse
|
26
|
Whelan NV, Strong EE, Gladstone NS, Mays JW. Using genomics, morphometrics, and environmental niche modeling to test the validity of a narrow-range endemic snail, Pateranantahala (Gastropoda, Polygyridae). Zookeys 2023; 1158:91-120. [PMID: 37234252 PMCID: PMC10208601 DOI: 10.3897/zookeys.1158.94152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 03/13/2023] [Indexed: 05/27/2023] Open
Abstract
Terrestrial gastropods are among the most imperiled groups of organisms on Earth. Many species have a complex taxonomic history, often including poorly defined subspecies, most of which have not been the focus of modern systematics research. Genomic tools, geometric morphometrics, and environmental niche modeling were used to assess the taxonomic status of Pateraclarkiinantahala (Clench & Banks, 1932), a subspecies of high conservation concern with a restricted range of approximately 3.3 km2 in North Carolina, USA. A genome-scale dataset was generated that included individuals with morphologies matching P.c.nantahala, P.c.clarkii, and one individual with an intermediate form between P.c.nantahala and P.c.clarkii that was initially hypothesized as a potential hybrid. Mitochondrial phylogenetics, nuclear species tree inference, and phylogenetic networks were used to assess relationships and gene flow. Differences in shell shape via geometric morphometrics and whether the environmental niches of the two subspecies were significantly different were also examined. Molecular analyses indicated an absence of gene flow among lineages of P.clarkii sensu lato. Analyses rejected our hypothesis that the intermediate shelled form represented a hybrid, but instead indicated that it was a distinct lineage. Environmental niche models indicated significant differences in environmental niche between P.c.clarkii and P.c.nantahala, and geometric morphometrics indicated that P.c.nantahala had a significantly different shell shape. Given multiple lines of evidence, species-level recognition of P.nantahala is warranted.
Collapse
Affiliation(s)
- Nathan V. Whelan
- Southeast Conservation Genetics Lab, Warm Springs Fish Technology Center, US Fish and Wildlife Service, 203 Swingle Hall, Auburn, Alabama, 36849, USAAuburn UniversityAuburnUnited States of America
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USAWarm Springs Fish Technology Center, US Fish and Wildlife ServiceAuburnUnited States of America
| | - Ellen E. Strong
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, PO Box 37012, MRC 163, Washington, DC 20013, USANational Museum of Natural History, Smithsonian InstitutionWashingtonUnited States of America
| | - Nicholas S. Gladstone
- School of Fisheries, Aquaculture, and Aquatic Sciences, College of Agriculture, Auburn University, 203 Swingle Hall, Auburn, Alabama, 36849, USAWarm Springs Fish Technology Center, US Fish and Wildlife ServiceAuburnUnited States of America
| | - Jason W. Mays
- Asheville Ecological Services Field Office, United States Fish and Wildlife Service, 160 Zillicoa ST, Asheville, NC 28801, USAAsheville Ecological Services Field Office, United States Fish and Wildlife ServiceAshevilleUnited States of America
| |
Collapse
|
27
|
Kim HN, Lee O, Lee HJ, Kim GC, Kim HS, Derbridge JJ, Jo YS. The Origin and Invasion Pathway of Brown Rats Rattus norvegicus on Dok-Do Island Revealed by Genome-Wide Markers from 3-RADseq Approach. Animals (Basel) 2023; 13:ani13071243. [PMID: 37048499 PMCID: PMC10093337 DOI: 10.3390/ani13071243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/12/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
Biological invasions are known to cause local extinctions on islands. Dok-do, a small, remote volcanic island in the East Sea of Korea in the western Pacific, has recently been invaded by rats, posing ecological problems. To infer their origin and invasion pathway, we collected rats from Dok-do and from the potential introduction source locations, Ulleung-do in the Pacific Ocean, and four east coastal ports. First, we identified that the brown rat (Rattus norvegicus) was the only rat species occurring at collecting sites based on the key morphological characteristics. To determine the population-level genetic diversity pattern, we applied the 3-RADseq approach. After a series of filtrations (minor allele frequency < 0.05, Hardy–Weinberg equilibrium p < 1 × 10−7), 4042 SNPs were retained for the final dataset from the 25,439 SNPs initially isolated. The spatial structure and genetic diversity pattern of brown rats suggested that the rat population on Dok-do was likely introduced from Ulleung-do. Our work provides practical information that will assist in the management of invasive brown rats in vulnerable island ecosystems.
Collapse
Affiliation(s)
- Han-Na Kim
- Department of Biology Education, Daegu University, Gyeongsan 38453, Republic of Korea
| | - Ohsun Lee
- Department of Biology Education, Daegu University, Gyeongsan 38453, Republic of Korea
| | - Hwa-Jin Lee
- Department of Biology Education, Daegu University, Gyeongsan 38453, Republic of Korea
| | - Gyu-Cheol Kim
- Department of Biology Education, Daegu University, Gyeongsan 38453, Republic of Korea
| | - Hyeon-Soo Kim
- Department of Biology Education, Daegu University, Gyeongsan 38453, Republic of Korea
| | | | - Yeong-Seok Jo
- Department of Biology Education, Daegu University, Gyeongsan 38453, Republic of Korea
| |
Collapse
|
28
|
Mar-Silva AF, Diaz-Jaimes P, Domínguez-Mendoza C, Domínguez-Domínguez O, Valdiviezo-Rivera J, Espinoza-Herrera E. Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific. PeerJ 2023; 11:e15029. [PMID: 37009151 PMCID: PMC10062342 DOI: 10.7717/peerj.15029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/17/2023] [Indexed: 03/29/2023] Open
Abstract
Background
The lack of barriers in the marine environment has promoted the idea of panmixia in marine organisms. However, oceanographic conditions and habitat characteristics have recently been linked to genetic structure in marine species. The Tropical Eastern Pacific (TEP) is characterized by dynamic current systems and heterogeneous oceanographic conditions. The Gulf of Panama (part of the equatorial segment for the TEP) is influenced by a complex current system and heterogeneous environment, which has been shown to limit the gene flow for shoreline species. Next Generation Sequencing (NGS) has contributed to detect genetic differences in previously reported panmictic species by the assessment of loci associated with selection and to understand how selection acts affects marine populations. Lutjanus guttatus is a species distributed in the TEP for which previous studies using mitochondrial data recovered a panmictic pattern along its distributional range. In this study, we used SNP data of L. guttatus individuals sampled along its range to evaluate population genetic structure and investigate whether oceanographic factors influence the species’ genetic architecture. Finally, we assessed the role of adaptive selection by evaluating the contribution of outlier and neutral loci to genetic divergence.
Methods
The RADcap method was used to obtain 24 million paired reads for 123 individuals of L. guttatus covering nearly all its distributional area. Genetic variation was assessed using both spatial and non-spatial methods by comparing three different data sets: (i) a Combined Loci (CL dataset = 2003 SNPs); a search for putative loci under selection allowed the evaluation of (ii) Neutral Loci (NL dataset = 1858 SNPs) and (iii) Outlier Loci (OL dataset = 145 SNPs). We used the estimating effective migration surface (EEMS) approach to detect possible barriers to gene flow.
Results
Genetic differences were found in the OL dataset, showing two clusters (Northern and Southern), whereas NL showed no differences. This result may be related to the Selection-Migration balance model. The limit between the Northern and Southern groups was in the Gulf of Panama, which has been previously identified as a barrier to gene flow for other species, mainly due to its heterogeneous oceanographic conditions. The results suggest that selection plays an important role in generating genetic differences in Lutjanus guttatus. A migration corridor was detected that coincides with the Costa Rica Coastal Current that flows from Central America to the Gulf of California, allowing the homogenization of the northern population. In the Southern cluster, a migration corridor was observed with the OL from Panama to Colombia, which could be associated with the currents found in the Gulf of Panama. Genetic variation found in the OL of Lutjanus guttatus highlights the usefulness of NGS data in evaluating the role of selection in population differentiation.
Collapse
Affiliation(s)
- Adán F. Mar-Silva
- Posgrado en Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Pindaro Diaz-Jaimes
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Cristina Domínguez-Mendoza
- Unidad de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Omar Domínguez-Domínguez
- Laboratorio de Biología Acuática, Facultad de Biología, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, Mexico
- Instituto Nacional de Biodiversidad, Quito, Ecuador
| | | | | |
Collapse
|
29
|
Benites P, Zaldívar-Riverón A, Meza-Lázaro RN, Samacá-Sáenz E, Gutiérrez-Rodríguez J, Hernández-López A. Multiple introgression events during the diversification history of the edible mexican grasshopper genus sphenarium (orthoptera: pyrgomorphidae). Mol Phylogenet Evol 2023; 183:107774. [PMID: 36972795 DOI: 10.1016/j.ympev.2023.107774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 03/07/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Speciation with gene flow often leads to ambiguous phylogenetic reconstructions, reticulate patterns of relatedness and conflicting nuclear versus mitochondrial (mt) lineages. Here we employed a fragment of the COI mtDNA gene and nuclear genome-wide data (3RAD) to assess the diversification history of Sphenarium, an orthopteran genus of great economic importance in Mexico that is presumed to have experienced hybridisation events in some of its species. We carried out separate phylogenetic analyses to evaluate the existence of mito-nuclear discordance in the species relationships, and also assessed the genomic diversity and population genomic structure and investigated the existence of interspecific introgression and species limits of the taxa involved based on the nuclear dataset. The species delineation analyses discriminated all the currently recognised species, but also supported the existence of four undescribed species. The mt and nuclear topologies had four discordant species relationships that can be explained by mt introgression, where the mt haplotypes of S. purpurascens appear to have replaced those of S. purpurascens A and B, S. variabile and S. zapotecum. Moreover, our analyses supported the existence of nuclear introgression events between four species pairs that are distributed in the Sierra Madre del Sur province in southeast Mexico, with three of them occurring in the Tehuantepec Isthmus region. Our study highlights the relevance of genomic data to address the relative importance of allopatric isolation versus gene flow in speciation.
Collapse
Affiliation(s)
- Pilar Benites
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Rubi N Meza-Lázaro
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Ernesto Samacá-Sáenz
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Copilco, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México; Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Cd. Universitaria, Coyoacán, 04510 Ciudad de México, México
| | | | - Antonio Hernández-López
- Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Guanajuato, México
| |
Collapse
|
30
|
Evans SA, Whigham DF, Hartvig I, McCormick MK. Hybridization in the Fringed Orchids: An Analysis of Species Boundaries in the Face of Gene Flow. DIVERSITY 2023. [DOI: 10.3390/d15030384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Natural hybridization between closely related species in sympatry is an evolutionary process that is common in orchids. Once seen as a threat to parent species, interspecific genetic change is increasingly viewed as a source of novel variation in some ecological contexts. Terrestrial fringed orchids in the genus Platanthera contain several clades with high genetic compatibility among species and many putative hybrids. We used biallelic SNPs generated with 3RAD sequencing to study the hybrid complex formed from the parent species P. blephariglottis, P. ciliaris, and P. cristata with high resolution. The genetic structure and phylogenetic relationship of the hybrid complex revealed site-dependent gene flow between species. We documented extensive hybridization and cryptic hybrids in sympatric sites. Interspecific genetic exchange is particularly common between P. blephariglottis and P. ciliaris, with cryptic hybrids among putative P. ciliaris samples being more common than parental assignments in sympatric sites. Hybridization across the triad species complex can reticulate lineages and introduce adaptive alleles. Conversely, it can reduce diversification rates and introduce maladaptive alleles. Investigation into whether anthropogenic forces are eroding species boundaries, particularly the permeable P. blephariglottis and P. ciliaris boundary, is appropriate for conservation efforts.
Collapse
|
31
|
Chambers EA, Tarvin RD, Santos JC, Ron SR, Betancourth-Cundar M, Hillis DM, Matz MV, Cannatella DC. 2b or not 2b? 2bRAD is an effective alternative to ddRAD for phylogenomics. Ecol Evol 2023; 13:e9842. [PMID: 36911313 PMCID: PMC9994478 DOI: 10.1002/ece3.9842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 03/10/2023] Open
Abstract
Restriction-site-associated DNA sequencing (RADseq) has become an accessible way to obtain genome-wide data in the form of single-nucleotide polymorphisms (SNPs) for phylogenetic inference. Nonetheless, how differences in RADseq methods influence phylogenetic estimation is poorly understood because most comparisons have largely relied on conceptual predictions rather than empirical tests. We examine how differences in ddRAD and 2bRAD data influence phylogenetic estimation in two non-model frog groups. We compare the impact of method choice on phylogenetic information, missing data, and allelic dropout, considering different sequencing depths. Given that researchers must balance input (funding, time) with output (amount and quality of data), we also provide comparisons of laboratory effort, computational time, monetary costs, and the repeatability of library preparation and sequencing. Both 2bRAD and ddRAD methods estimated well-supported trees, even at low sequencing depths, and had comparable amounts of missing data, patterns of allelic dropout, and phylogenetic signal. Compared to ddRAD, 2bRAD produced more repeatable datasets, had simpler laboratory protocols, and had an overall faster bioinformatics assembly. However, many fewer parsimony-informative sites per SNP were obtained from 2bRAD data when using native pipelines, highlighting a need for further investigation into the effects of each pipeline on resulting datasets. Our study underscores the importance of comparing RADseq methods, such as expected results and theoretical performance using empirical datasets, before undertaking costly experiments.
Collapse
Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA.,Department of Environmental Science, Policy, and Management and Museum of Vertebrate Zoology University of California Berkeley Berkeley California USA
| | - Rebecca D Tarvin
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA.,Department of Integrative Biology and Museum of Vertebrate Zoology University of California Berkeley Berkeley California USA
| | - Juan C Santos
- Department of Biological Sciences St John's University New York New York USA
| | - Santiago R Ron
- Museo de Zoología, Escuela de Ciencias Biológicas Pontificia Universidad Católica del Ecuador Quito Ecuador
| | | | - David M Hillis
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
| | - Mikhail V Matz
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
| | - David C Cannatella
- Department of Integrative Biology and Biodiversity Center University of Texas at Austin Austin Texas USA
| |
Collapse
|
32
|
Bernos TA, Avlijaš S, Hill J, Morissette O, Ricciardi A, Mandrak NE, Jeffries KM. Genetic diversity and structure of a recent fish invasion: Tench ( Tinca tinca) in eastern North America. Evol Appl 2023; 16:173-188. [PMID: 36699124 PMCID: PMC9850014 DOI: 10.1111/eva.13520] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/22/2022] [Accepted: 12/02/2022] [Indexed: 01/20/2023] Open
Abstract
Introduced and geographically expanding populations experience similar eco-evolutionary challenges, including founder events, genetic bottlenecks, and novel environments. Theory predicts that reduced genetic diversity resulting from such phenomena limits the success of introduced populations. Using 1900 SNPs obtained from restriction-site-associated DNA sequencing, we evaluated hypotheses related to the invasion history and connectivity of an invasive population of Tench (Tinca tinca), a Eurasian freshwater fish that has been expanding geographically in eastern North America for three decades. Consistent with the reported history of a single introduction event, our findings suggest that multiple introductions from distinct genetic sources are unlikely as Tench had a small effective population size (~114 [95% CI = 106-123] individuals), no strong population subdivision across time and space, and evidence of a recent genetic bottleneck. The large genetic neighbourhood size (220 km) and weak within-population genetic substructure suggested high connectivity across the invaded range, despite the relatively large area occupied. There was some evidence for a small decay in genetic diversity as the species expanded northward, but not southward, into new habitats. As eradicating the species within a ~112 km radius would be necessary to prevent recolonization, eradicating Tench is likely not feasible at watershed-and possibly local-scales. Management should instead focus on reducing abundance in priority conservation areas to mitigate adverse impacts. Our study indicates that introduced populations can thrive and exhibit relatively high levels of genetic diversity despite severe bottlenecks (<1.5% of the ancestral effective population size) and suggests that landscape heterogeneity and population demographics can generate variability in spatial patterns of genetic diversity within a single range expansion.
Collapse
Affiliation(s)
- Thaïs A. Bernos
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
- Department of Biological SciencesUniversity of Toronto ScarboroughScarboroughOntarioCanada
| | - Sunčica Avlijaš
- Redpath MuseumMcGill UniversityMontrealQuébecCanada
- Department of BiologyMcGill UniversityMontrealQuébecCanada
| | - Jaclyn Hill
- Maurice Lamontagne InstituteFisheries and Oceans CanadaMont‐JoliQuébecCanada
| | - Olivier Morissette
- Département des Sciences FondamentalesUniversité du Québec à ChicoutimiChicoutimiQuébecCanada
| | | | - Nicholas E. Mandrak
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoOntarioCanada
| | - Kenneth M. Jeffries
- Department of Biological SciencesUniversity of ManitobaWinnipegManitobaCanada
| |
Collapse
|
33
|
Lee SR, Son DC. Genetic diversity pattern reveals the primary determinant of burcucumber ( Sicyos angulatus L.) invasion in Korea. FRONTIERS IN PLANT SCIENCE 2022; 13:997521. [PMID: 36457533 PMCID: PMC9706109 DOI: 10.3389/fpls.2022.997521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Biological invasion is a complex process associated with propagule pressure, dispersal ability, environmental constraints, and human interventions, which leave genetic signatures. The population genetics of an invasive species thus provides invaluable insights into the patterns of invasion. Burcucumber, one of the most detrimental weeds for soybean production in US, has recently colonized Korea and rapidly spread posing a great threat to the natural ecosystem. We aim to infer the determinants of the rapid burcucumber invasion by examining the genetic diversity, demography, and spread pattern with advanced genomic tools. We employed 2,696 genome-wide single-nucleotide polymorphisms to assess the level of diversity and the spatial pattern associated with the landscape factors and to infer the demographic changes of 24 populations (364 genotypes) across four major river basins with the east coastal streams in South Korea. Through the approximate Bayesian computation, we inferred the likely invasion scenario of burcucumber in Korea. The landscape genetics approach adopting the circuit theory and MaxEnt model was applied to determine the landscape contributors. Our data suggested that most populations have experienced population bottlenecks, which led to lowered within-population genetic diversity and inflated population divergences. Burcucumber colonization in Korea has strongly been affected by demographic bottlenecks and multiple introductions, whereas environmental factors were not the primary determinant of the invasion. Our work highlighted the significance of preventing secondary introductions, particularly for aggressive weedy plants such as the burcucumber.
Collapse
Affiliation(s)
- Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, South Korea
| | - Dong Chan Son
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, South Korea
| |
Collapse
|
34
|
Martin Cerezo ML, Raval R, de Haro Reyes B, Kucka M, Chan FY, Bryk J. Identification and quantification of chimeric sequencing reads in a highly multiplexed RAD-seq protocol. Mol Ecol Resour 2022; 22:2860-2870. [PMID: 35668693 PMCID: PMC9796921 DOI: 10.1111/1755-0998.13661] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/29/2022] [Accepted: 05/23/2022] [Indexed: 01/07/2023]
Abstract
Highly multiplexed approaches have become common in genomic studies. They have improved the cost-effectiveness of genotyping hundreds of individuals using combinatorially barcoded adapters. These strategies, however, can potentially misassigned reads to incorrect samples. Here, we used a modified quaddRAD protocol to analyse the occurrence of index hopping and PCR chimeras in a series of experiments with up to 100 multiplexed samples per sequencing lane (639 samples in total). We created two types of sequencing libraries: four libraries of type A, where PCRs were run on individual samples before multiplexing, and three libraries of type B, where PCRs were run on pooled samples. We used fixed pairs of inner barcodes to identify chimeric reads. Type B libraries show a higher percentage of misassigned reads (1.15%) than type A libraries (0.65%). We also quantify the commonly undetectable chimeric sequences that occur whenever multiplexed groups of samples with different outer barcodes are sequenced together on a single flow cell. Our results suggest that these types of chimeric sequences represent up to 1.56% and 1.29% of reads in type A and B libraries, respectively. We also show that increasing the number of mismatches allowed for barcode rescue to above 2 dramatically increases the number of recovered chimeric reads. We provide recommendations for developing highly multiplexed RAD-seq protocols and analysing the resulting data to minimize the generation of chimeric sequences, allowing their quantification and a finer control on the number of PCR cycles necessary to generate enough input DNA for library preparation.
Collapse
Affiliation(s)
- Maria Luisa Martin Cerezo
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK,IFM BiologyLinköping UniversityLinköpingSweden
| | - Rohan Raval
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
| | - Bernardo de Haro Reyes
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK,IFM BiologyLinköping UniversityLinköpingSweden
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck SocietyTübingenGermany
| | | | - Jarosław Bryk
- Department of Biological and Geographical Sciences, School of Applied SciencesUniversity of HuddersfieldHuddersfieldUK
| |
Collapse
|
35
|
Halsey MK, Stuhler JD, Bayona-Vásquez NJ, Platt RN, Goetze JR, Martin RE, Matocha KG, Bradley RD, Stevens RD, Ray DA. Comparison of genetic variation between rare and common congeners of Dipodomys with estimates of contemporary and historical effective population size. PLoS One 2022; 17:e0274554. [PMID: 36099283 PMCID: PMC9469943 DOI: 10.1371/journal.pone.0274554] [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: 01/27/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Species with low effective population sizes are at greater risk of extinction because of reduced genetic diversity. Such species are more vulnerable to chance events that decrease population sizes (e.g. demographic stochasticity). Dipodomys elator, (Texas kangaroo rat) is a kangaroo rat that is classified as threatened in Texas and field surveys from the past 50 years indicate that the distribution of this species has decreased. This suggests geographic range reductions that could have caused population fluctuations, potentially impacting effective population size. Conversely, the more common and widespread D. ordii (Ord’s kangaroo rat) is thought to exhibit relative geographic and demographic stability. We assessed the genetic variation of D. elator and D. ordii samples using 3RAD, a modified restriction site associated sequencing approach. We hypothesized that D. elator would show lower levels of nucleotide diversity, observed heterozygosity, and effective population size when compared to D. ordii. We were also interested in identifying population structure within contemporary samples of D. elator and detecting genetic variation between temporal samples to understand demographic dynamics. We analyzed up to 61,000 single nucleotide polymorphisms. We found that genetic variability and effective population size in contemporary D. elator populations is lower than that of D. ordii. There is slight, if any, population structure within contemporary D. elator samples, and we found low genetic differentiation between spatial or temporal historical samples. This indicates little change in nuclear genetic diversity over 30 years. Results suggest that genetic diversity of D. elator has remained stable despite reduced population size and/or abundance, which may indicate a metapopulation-like system, whose fluctuations might counteract species extinction.
Collapse
Affiliation(s)
- Michaela K. Halsey
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- Department of Natural Resources Management, Texas Tech University, Lubbock, Texas, United States of America
| | - John D. Stuhler
- Department of Natural Resources Management, Texas Tech University, Lubbock, Texas, United States of America
| | - Natalia J. Bayona-Vásquez
- Department of Environmental Health Science, University of Georgia, Athens, Georgia, United States of America
- Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Roy N. Platt
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Jim R. Goetze
- Natural Sciences Department, Laredo College, Laredo, Texas, United States of America
| | - Robert E. Martin
- Department of Biology, McMurry University, Abilene, Texas, United States of America
| | - Kenneth G. Matocha
- Department of Biology, South Arkansas Community College, El Dorado, Arkansas, United States of America
| | - Robert D. Bradley
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- Natural Science Research Laboratory, Museum of Texas Tech, Lubbock, Texas, United States of America
| | - Richard D. Stevens
- Department of Natural Resources Management, Texas Tech University, Lubbock, Texas, United States of America
- Natural Science Research Laboratory, Museum of Texas Tech, Lubbock, Texas, United States of America
| | - David A. Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
- * E-mail:
| |
Collapse
|
36
|
Clark JD, Benham PM, Maldonado JE, Luther DA, Lim HC. Maintenance of local adaptation despite gene flow in a coastal songbird. Evolution 2022; 76:1481-1494. [PMID: 35700208 PMCID: PMC9545442 DOI: 10.1111/evo.14538] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 03/09/2022] [Accepted: 03/19/2022] [Indexed: 01/22/2023]
Abstract
Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) is a widespread, polytypic passerine that occurs in shrubland habitats throughout North America. We examined the population structure of two parapatric subspecies that inhabit different environments: the Atlantic song sparrow (M. m. atlantica), a coastal specialist, and the eastern song sparrow (M. m. melodia), a shrubland generalist. These populations lacked clear mitochondrial population structure, yet coastal birds formed a distinct nuclear genetic cluster. We found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or a combination thereof. There was a steep genetic cline at the transition to coastal habitats, consistent with isolation by environment, not isolation by distance. A phenotype under divergent selection, bill size, varied with the amount of coastal ancestry in transitional areas, but larger bill size was maintained in coastal habitats regardless of ancestry, further supporting a role for selection in the maintenance of these subspecies. Demographic modeling suggested a divergence history of limited gene flow followed by secondary contact, which has emerged as a common theme in adaptive divergence across taxa.
Collapse
Affiliation(s)
- Jonathan D. Clark
- Department of Environmental Science and PolicyGeorge Mason UniversityFairfaxVirginia22030,Current Address: Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew Hampshire03824
| | - Phred M. Benham
- Museum of Vertebrate ZoologyUniversity of California, BerkeleyBerkeleyCalifornia94720
| | - Jesus E. Maldonado
- Department of Environmental Science and PolicyGeorge Mason UniversityFairfaxVirginia22030,Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonD.C.20013
| | - David A. Luther
- Department of BiologyGeorge Mason UniversityFairfaxVirginia22030
| | - Haw Chuan Lim
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteWashingtonD.C.20013,Department of BiologyGeorge Mason UniversityFairfaxVirginia22030
| |
Collapse
|
37
|
Grismer J, Scott P, Toffelmier E, Hinds B, Klabacka R, Stewart G, White V, Oaks J, Bradley Shaffer H. Genomic data reveal local endemism in Southern California Rubber Boas (Serpentes: Boidae, Charina) and the critical need for enhanced conservation actions. Mol Phylogenet Evol 2022; 174:107542. [PMID: 35690376 DOI: 10.1016/j.ympev.2022.107542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 05/25/2022] [Accepted: 05/31/2022] [Indexed: 10/18/2022]
Abstract
The mountains of southern California represent unique, isolated ecosystems that support distinct high-elevation habitats found nowhere else in the area. Analyses of several moisture-dependent species across these sky-islands indicate they exist as locally endemic lineages that occur across these fragmented mountains ranges. The Rubber Boa is a semi-fossorial snake species that is widely distributed in the cooler and more moist ecoregions regions of western North America, including isolated populations across southern California mountain ranges. We developed a genomic and ecological dataset to examine genetic diversity within Rubber Boas and to determine if the endemic Southern Rubber Boa represents a distinct lineage. We quantified current and future habitat suitability under a range of climate change scenarios, and discuss the possible environmental threats facing these unique montane isolates. Our results support four major lineages within Rubber Boas, with genetic breaks that are consistent with biogeographic boundaries observed in other co-distributed, cool-temperature, moisture adapted species. Our data support previous studies that the Southern Rubber Boa is an independent evolutionary unit and now includes multiple locally endemic sky-island populations, restricted to isolated mountain tops and ranges across southern California. Analyses of future habitat suitability indicate that many of these sky-island populations will lose most of their suitable habitat over the next 70 years given predicted increases in drought, rising temperatures, and wildfires. Collectively these data emphasize the critical conservation needs of these montane ecosystems in southern California under current and projected climate change conditions.
Collapse
Affiliation(s)
- Jesse Grismer
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA; Department of Biology, La Sierra University, Riverside, CA 92515, USA.
| | - Peter Scott
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA; Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, TX 79016, USA
| | - Erin Toffelmier
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Brian Hinds
- Department of Biology, La Sierra University, Riverside, CA 92515, USA
| | - Randy Klabacka
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Glenn Stewart
- Department of Biological Sciences, California State Polytechnic University, Pomona, CA 91768, USA
| | - Virginia White
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - Jamie Oaks
- Department of Biological Sciences and Museum of Natural History, Auburn University, Auburn, AL 36849, USA
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, La Kretz Center for Californian Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| |
Collapse
|
38
|
Cui M, Wu Y, Javal M, Giguère I, Roux G, Andres JA, Keena M, Shi J, Wang B, Braswell E, Pfister SE, Hamelin R, Roe A, Porth I. Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky). Evol Appl 2022; 15:934-953. [PMID: 35782014 PMCID: PMC9234632 DOI: 10.1111/eva.13381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 02/12/2022] [Accepted: 03/21/2022] [Indexed: 11/26/2022] Open
Abstract
Human-assisted movement has allowed the Asian longhorned beetle (ALB, Anoplophora glabripennis (Motschulsky)) to spread beyond its native range and become a globally regulated invasive pest. Within its native range of China and the Korean peninsula, human-mediated dispersal has also caused cryptic translocation of insects, resulting in population structure complexity. Previous studies used genetic methods to detangle this complexity but were unable to clearly delimit native populations which is needed to develop downstream biosurveillance tools. We used genome-wide markers to define historical population structure in native ALB populations and contemporary movement between regions. We used genotyping-by-sequencing to generate 6102 single-nucleotide polymorphisms (SNPs) and amplicon sequencing to genotype 53 microsatellites. In total, we genotyped 712 individuals from ALB's native distribution. We observed six distinct population clusters among native ALB populations, with a clear delineation between northern and southern groups. Most of the individuals from South Korea were distinct from populations in China. Our results also indicate historical divergence among populations and suggest limited large-scale admixture, but we did identify a restricted number of cases of contemporary movement between regions. We identified SNPs under selection and describe a clinal allele frequency pattern in a missense variant associated with glycerol kinase, an important enzyme in the utilization of an insect cryoprotectant. We further demonstrate that small numbers of SNPs can assign individuals to geographic regions with high probability, paving the way for novel ALB biosurveillance tools.
Collapse
Affiliation(s)
- Mingming Cui
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
| | - Yunke Wu
- Forest Pest Methods LaboratoryPlant Protection and Quarantine Science and TechnologyAnimal and Plant Health Inspection ServiceUnited States Department of AgricultureBuzzards BayMassachusettsUSA
| | - Marion Javal
- Centre d'Écologie Fonctionnelle et ÉvolutiveUniversité MontpellierMontpellierFrance
| | - Isabelle Giguère
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
| | - Géraldine Roux
- Institut National de la Recherche AgronomiqueUR633 Zoologie ForestièreOrléansFrance
- COSTUniversité d’OrléansOrléansFrance
| | - Jose A. Andres
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew YorkUSA
| | - Melody Keena
- United States Department of AgricultureForest ServiceNorthern Research StationHamdenConnecticutUSA
| | - Juan Shi
- Key Laboratory for Silviculture and Conservation of Ministry of EducationBeijing Forestry UniversityBeijingChina
| | - Baode Wang
- Forest Pest Methods LaboratoryPlant Protection and Quarantine Science and TechnologyAnimal and Plant Health Inspection ServiceUnited States Department of AgricultureBuzzards BayMassachusettsUSA
| | - Evan Braswell
- Insect Management and Molecular Diagnostics LaboratoryPlant Protection and Quarantine Science and Technology, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureEdinburgTexasUSA
| | - Scott E. Pfister
- Forest Pest Methods LaboratoryPlant Protection and Quarantine Science and TechnologyAnimal and Plant Health Inspection ServiceUnited States Department of AgricultureBuzzards BayMassachusettsUSA
| | - Richard Hamelin
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
- Department of Forest and Conservation SciencesThe University of British ColumbiaVancouverBritish ColumbiaCanada
| | - Amanda Roe
- Canadian Forest ServiceGreat Lakes Forestry CentreNatural Resources CanadaSault Ste. MarieOntarioCanada
| | - Ilga Porth
- Institut de Biologie Intégrative et des SystèmesUniversité LavalQuébecQuébecCanada
- Département des sciences du bois et de la forêtUniversité LavalQuébecQuébecCanada
| |
Collapse
|
39
|
Guo L, Bloom JS, Dols-Serrate D, Boocock J, Ben-David E, Schubert OT, Kozuma K, Ho K, Warda E, Chui C, Wei Y, Leighton D, Lemus Vergara T, Riutort M, Sánchez Alvarado A, Kruglyak L. Island-specific evolution of a sex-primed autosome in a sexual planarian. Nature 2022; 606:329-334. [PMID: 35650439 PMCID: PMC9177419 DOI: 10.1038/s41586-022-04757-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 04/12/2022] [Indexed: 12/26/2022]
Abstract
The sexual strain of the planarian Schmidtea mediterranea, indigenous to Tunisia and several Mediterranean islands, is a hermaphrodite1,2. Here we isolate individual chromosomes and use sequencing, Hi-C3,4 and linkage mapping to assemble a chromosome-scale genome reference. The linkage map reveals an extremely low rate of recombination on chromosome 1. We confirm suppression of recombination on chromosome 1 by genotyping individual sperm cells and oocytes. We show that previously identified genomic regions that maintain heterozygosity even after prolonged inbreeding make up essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicates that this phenomenon has evolved specifically in populations from Sardinia and Corsica. We find that most known master regulators5-13 of the reproductive system are located on chromosome 1. We used RNA interference14,15 to knock down a gene with haplotype-biased expression, which led to the formation of a more pronounced female mating organ. On the basis of these observations, we propose that chromosome 1 is a sex-primed autosome primed for evolution into a sex chromosome.
Collapse
Affiliation(s)
- Longhua Guo
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Joshua S Bloom
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Daniel Dols-Serrate
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - James Boocock
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Eyal Ben-David
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University of Jerusalem-Hadassah Medical School, Jerusalem, Israel
| | - Olga T Schubert
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Kaiya Kozuma
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Katarina Ho
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Emily Warda
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Clarice Chui
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yubao Wei
- Institute of Reproductive Medicine, Henan Provincial People's Hospital, Zhengzhou University, Zhengzhou, China
| | - Daniel Leighton
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzitziki Lemus Vergara
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Marta Riutort
- Departament de Genètica, Microbiologia i Estadística, Institut de Recerca de la Biodiversitat, Universitat de Barcelona, Barcelona, Spain
| | - Alejandro Sánchez Alvarado
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Leonid Kruglyak
- Department of Human Genetics and Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| |
Collapse
|
40
|
Lujan NK, Colm JE, Weir JT, Montgomery FA, Noonan BP, Lovejoy NR, Mandrak NE. Genomic population structure of Grass Pickerel (Esox americanus vermiculatus) in Canada: management guidance for an at-risk fish at its northern range limit. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01450-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
41
|
Niemiller ML, Davis MA, Tan M, Apodaca JJ, Dooley KE, Cucalón RV, Benito JB, Niemiller KDK, Hardman RH, Istvanko D, Thames D. Mitochondrial DNA and Population Genomics Reveal Additional Cryptic Diversity in the Green Salamander (Subgenus Castaneides) Species Complex. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.890859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cryptic species present particular challenges to biodiversity conservation, as true species diversity and distributional boundaries remain obscured. However, modern molecular tools have afforded unparalleled opportunities to elucidate cryptic species, define their distributions, and, ultimately, develop conservation interventions to extend their evolutionary trajectories into the future. The Green Salamander (Aneides aeneus) complex provides an evolutionary focal point and the Appalachian Highlands an ecological context for the exploration of cryptic speciation in an imperiled taxon. A recent study uncovered significant levels of genetic and genomic variation geographically structured across the Appalachian Highlands, including up to four lineages, one of which (A. caryaensis) was described therein. Here we extend the genetic and genomic examination of the Castaneides species complex by intensive sampling of additional populations along Cumberland Plateau and Appalachian Valley and Ridge of Alabama and Tennessee, employing both mtDNA and RADseq species delimitation approaches to delineate cryptic diversity and boundaries in this region. Analyses of two mitochondrial loci (nd4 and cytb) identified two reciprocally monophyletic lineages, which are also supported by population clustering and phylogenetic analyses of SNPs, that identified two population clusters with no evidence of gene flow. Our genetic and genomic results support the recognition of two additional cryptic lineages in the Castaneides species complex. Ultimately, this information is critical in developing successful adaptive management strategies for this important and endemic component of Appalachian Highland biodiversity.
Collapse
|
42
|
Kurata NP, Hickerson MJ, Hoffberg SL, Gardiner N, Stiassny MLJ, Alter SE. Riverscape genomics of cichlid fishes in the lower Congo: Uncovering mechanisms of diversification in an extreme hydrological regime. Mol Ecol 2022; 31:3516-3532. [PMID: 35532943 DOI: 10.1111/mec.16495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 04/10/2022] [Accepted: 05/04/2022] [Indexed: 11/28/2022]
Abstract
Freshwater fishes are notably diverse, given that freshwater habitat represents a tiny fraction of the earth's surface, but the mechanisms generating this diversity remain poorly understood. Rivers provide excellent models to understand how freshwater diversity is generated and maintained across heterogeneous habitats. In particular, the lower Congo River (LCR) consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, morphological and ecological specialization. Previous studies have suggested that the numerous high-energy rapids throughout the LCR form physical barriers to gene flow, thus facilitating diversification and speciation, generating ichthyofaunal diversity. However, this hypothesis has not been fully explored using genome-wide SNPs for fish species distributed across the LCR. Here, we examined four lamprologine cichlids endemic to the LCR that are distributed along the river without range overlap. Using genome-wide SNP data, we tested the hypotheses that high-energy rapids serve as physical barriers to gene flow that generate genetic divergence at inter- and intraspecific levels, and that gene flow occurs primarily in a downstream direction. Our results are consistent with the prediction that powerful rapids sometimes act as a barrier to gene flow but also suggest that, at certain temporal and spatial scales, they may provide multidirectional dispersal opportunities for riverine rheophilic cichlid fishes. These results highlight the complexity of diversification processes in rivers and the importance of assessing such processes across different riverscapes.
Collapse
Affiliation(s)
- Naoko P Kurata
- The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.,Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - Michael J Hickerson
- The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY, 10016, USA.,The City College of New York, 160 Convent Ave, New York, NY, 10031, USA.,Division of Invertebrate Zoology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - Sandra L Hoffberg
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY, 10027, USA
| | - Ned Gardiner
- Department of Geography, University of Georgia, 210 Field St #204, Athens, Georgia, GA, 30602, USA
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.,The Sackler Institute for Comparative Genomics, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA
| | - S Elizabeth Alter
- Department of Ichthyology, American Museum of Natural History, 79th Street and Central Park West, New York, NY, 10024, USA.,Department of Biology and Chemistry, California State University Monterey Bay, Seaside, California, CA, 93955, USA
| |
Collapse
|
43
|
Moncrieff AE, Faircloth BC, Brumfield RT. Systematics of Lepidothrix manakins (Aves: Passeriformes: Pipridae) using RADcap markers. Mol Phylogenet Evol 2022; 173:107525. [DOI: 10.1016/j.ympev.2022.107525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/06/2022] [Accepted: 04/26/2022] [Indexed: 10/18/2022]
|
44
|
Meza‐Lázaro RN, Peña‐Carrillo KI, Poteaux C, Lorenzi MC, Wetterer JK, Zaldívar‐Riverón A. Genome and cuticular hydrocarbon-based species delimitation shed light on potential drivers of speciation in a Neotropical ant species complex. Ecol Evol 2022; 12:e8704. [PMID: 35342602 PMCID: PMC8928884 DOI: 10.1002/ece3.8704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/02/2022] [Accepted: 02/18/2022] [Indexed: 12/03/2022] Open
Abstract
Geographic separation that leads to the evolution of reproductive isolation between populations generally is considered the most common form of speciation. However, speciation may also occur in the absence of geographic barriers due to phenotypic and genotypic factors such as chemical cue divergence, mating signal divergence, and mitonuclear conflict. Here, we performed an integrative study based on two genome-wide techniques (3RAD and ultraconserved elements) coupled with cuticular hydrocarbon (CHC) and mitochondrial (mt) DNA sequence data, to assess the species limits within the Ectatomma ruidum species complex, a widespread and conspicuous group of Neotropical ants for which heteroplasmy (i.e., presence of multiple mtDNA variants in an individual) has been recently discovered in some populations from southeast Mexico. Our analyses indicate the existence of at least five distinct species in this complex: two widely distributed across the Neotropics, and three that are restricted to southeast Mexico and that apparently have high levels of heteroplasmy. We found that species boundaries in the complex did not coincide with geographic barriers. We therefore consider possible roles of alternative drivers that may have promoted the observed patterns of speciation, including mitonuclear incompatibility, CHC differentiation, and colony structure. Our study highlights the importance of simultaneously assessing different sources of evidence to disentangle the species limits of taxa with complicated evolutionary histories.
Collapse
Affiliation(s)
- Rubi N. Meza‐Lázaro
- Colección Nacional de InsectosInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Kenzy I. Peña‐Carrillo
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
- INIFAPCampo Experimental General TeránGeneral TeránMexico
| | - Chantal Poteaux
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
| | - Maria Cristina Lorenzi
- Laboratoire d’Ethologie Expérimentale et ComparéeUR 4443LEECUniversité Sorbonne Paris NordClémentFrance
| | - James K. Wetterer
- Harriet L. Wilkes Honors CollegeFlorida Atlantic UniversityJupiterFloridaUSA
| | - Alejandro Zaldívar‐Riverón
- Colección Nacional de InsectosInstituto de BiologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| |
Collapse
|
45
|
Lee SR, Choi TY, Jung SY. Genetic Diversity on a Rare Terrestrial Orchid, Habenaria linearifolia in South Korea: Implications for Conservation Offered by Genome-Wide Single Nucleotide Polymorphisms. FRONTIERS IN PLANT SCIENCE 2022; 13:772621. [PMID: 35283866 PMCID: PMC8907889 DOI: 10.3389/fpls.2022.772621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Monitoring intraspecific diversity offers invaluable insights on conservation practices as the variation is the product of species evolution. Accordingly, the role of population genetic diversity has drawn great attention over the last century responding to the biodiversity loss induced by a series of anthropogenic changes. Orchids are one of the most diverse, yet ironically most rapidly disappearing plant groups due to the specialized habitat preferences. Thus, population-level genetic diversity studies may offer a powerful tool for orchid conservation programs. Using the 3 restriction site-associated DNA (3RAD) approach, 2,734 genome-wide single nucleotide polymorphisms (SNPs) were isolated. With the 2,734 SNPs, we investigated genetic diversity and population structure on 72 individuals of Habenaria linearifolia and Habenaria cruciformis in South Korea. Overall, the genetic diversity was well maintained in South Korean Habenaria, but high F ST values were estimated suggesting large population diversification with limited gene flow. Bayesian assignment analysis revealed a morphologically cryptic diversity pattern in Jeju Island populations, which might serve as an evolutionarily significant unit.
Collapse
Affiliation(s)
- Soo-Rang Lee
- Department of Biology Education, College of Education, Chosun University, Gwangju, South Korea
| | - Tae-Young Choi
- Department of Biology Education, College of Education, Chosun University, Gwangju, South Korea
| | - Su-Young Jung
- Division of Forest Biodiversity and Herbarium, Korea National Arboretum, Pocheon, South Korea
| |
Collapse
|
46
|
Gutiérrez-Rodríguez J, Zaldívar-Riverón A, Weissman DB, Vandergast AG. Extensive species diversification and marked geographic phylogenetic structure in the Mesoamerican genus Stenopelmatus (Orthoptera: Stenopelmatidae: Stenopelmatinae) revealed by mitochondrial and nuclear 3RAD data. INVERTEBR SYST 2022. [DOI: 10.1071/is21022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Jerusalem cricket subfamily Stenopelmatinae is distributed from south-western Canada through the western half of the United States to as far south as Ecuador. Recently, the generic classification of this subfamily was updated to contain two genera, the western North American Ammopelmatus, and the Mexican, and central and northern South American Stenopelmatus. The taxonomy of the latter genus was also revised, with 5, 13 and 14 species being respectively validated, declared as nomen dubium and described as new. Despite this effort, the systematics of Stenopelmatus is still far from complete. Here, we generated sequences of the mitochondrial DNA barcoding locus and performed two distinct DNA sequence-based approaches to assess the species’ limits among several populations of Stenopelmatus, with emphasis on populations from central and south-east Mexico. We reconstructed the phylogenetic relationships among representative species of the main clades within the genus using nuclear 3RAD data and carried out a molecular clock analysis to investigate its biogeographic history. The two DNA sequence-based approaches consistently recovered 34 putative species, several of which are apparently undescribed. Our estimates of phylogeny confirmed the recent generic update of Stenopelmatinae and revealed a marked phylogeographic structure within Stenopelmatus. Based on our results, we propose the existence of four species-groups within the genus (the faulkneri, talpa, Central America and piceiventris species-groups). The geographic distribution of these species-groups and our molecular clock estimates are congruent with the geological processes that took place in mountain ranges along central and southern Mexico, particularly since the Neogene. Our study emphasises the necessity to continue performing more taxonomic and phylogenetic studies on Stenopelmatus to clarify its actual species richness and evolutionary history in Mesoamerica.
Collapse
|
47
|
Jacobs SJ, Grundler MC, Henriquez CL, Zapata F. An integrative genomic and phenomic analysis to investigate the nature of plant species in Escallonia (Escalloniaceae). Sci Rep 2021; 11:24013. [PMID: 34907249 PMCID: PMC8671583 DOI: 10.1038/s41598-021-03419-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
What we mean by species and whether they have any biological reality has been debated since the early days of evolutionary biology. Some biologists even suggest that plant species are created by taxonomists as a subjective, artificial division of nature. However, the nature of plant species has been rarely tested critically with data while ignoring taxonomy. We integrate phenomic and genomic data collected across hundreds of individuals at a continental scale to investigate this question in Escallonia (Escalloniaceae), a group of plants which includes 40 taxonomic species (the species proposed by taxonomists). We first show that taxonomic species may be questionable as they match poorly to patterns of phenotypic and genetic variation displayed by individuals collected in nature. We then use explicit statistical methods for species delimitation designed for phenotypic and genomic data, and show that plant species do exist in Escallonia as an objective, discrete property of nature independent of taxonomy. We show that such species correspond poorly to current taxonomic species (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$< 20\%$$\end{document}<20%) and that phenomic and genomic data seldom delimit congruent entities (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$< 20\%$$\end{document}<20%). These discrepancies suggest that evolutionary forces additional to gene flow can maintain the cohesion of species. We propose that phenomic and genomic data analyzed on an equal footing build a broader perspective on the nature of plant species by helping delineate different ‘types of species’. Our results caution studies which take the accuracy of taxonomic species for granted and challenge the notion of plant species without empirical evidence. Note: A version of the complete manuscript in Spanish is available in the Supplemental Materials.
Collapse
Affiliation(s)
- Sarah J Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.,Department of Botany, California Academy of Sciences, San Francisco, CA, 94118, USA
| | - Michael C Grundler
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Claudia L Henriquez
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Felipe Zapata
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA.
| |
Collapse
|
48
|
How challenging RADseq data turned out to favor coalescent-based species tree inference. A case study in Aichryson (Crassulaceae). Mol Phylogenet Evol 2021; 167:107342. [PMID: 34785384 DOI: 10.1016/j.ympev.2021.107342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 07/05/2021] [Accepted: 10/29/2021] [Indexed: 12/24/2022]
Abstract
Analysing multiple genomic regions while incorporating detection and qualification of discordance among regions has become standard for understanding phylogenetic relationships. In plants, which usually have comparatively large genomes, this is feasible by the combination of reduced-representation library (RRL) methods and high-throughput sequencing enabling the cost effective acquisition of genomic data for thousands of loci from hundreds of samples. One popular RRL method is RADseq. A major disadvantage of established RADseq approaches is the rather short fragment and sequencing range, leading to loci of little individual phylogenetic information. This issue hampers the application of coalescent-based species tree inference. The modified RADseq protocol presented here targets ca. 5,000 loci of 300-600nt length, sequenced with the latest short-read-sequencing (SRS) technology, has the potential to overcome this drawback. To illustrate the advantages of this approach we use the study group Aichryson Webb & Berthelott (Crassulaceae), a plant genus that diversified on the Canary Islands. The data analysis approach used here aims at a careful quality control of the long loci dataset. It involves an informed selection of thresholds for accurate clustering, a thorough exploration of locus properties, such as locus length, coverage and variability, to identify potential biased data and a comparative phylogenetic inference of filtered datasets, accompanied by an evaluation of resulting BS support, gene and site concordance factor values, to improve overall resolution of the resulting phylogenetic trees. The final dataset contains variable loci with an average length of 373nt and facilitates species tree estimation using a coalescent-based summary approach. Additional improvements brought by the approach are critically discussed.
Collapse
|
49
|
Gallego-García N, Caballero S, Shaffer HB. Are genomic updates of well-studied species worth the investment for conservation? A case study of the Critically Endangered Magdalena River turtle. J Hered 2021; 112:575-589. [PMID: 34628509 DOI: 10.1093/jhered/esab063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 10/08/2021] [Indexed: 11/13/2022] Open
Abstract
As genomic-scale data sets become economically feasible for most organisms, a key question for conservation biology is whether the increased resolution offered by new genomic approaches justifies repeating earlier studies based on traditional markers, rather than investing those same time and monetary resources in less-known species. Genomic studies offer clear advantages when the objective is to identify adaptive loci that may be critical to conservation policy-makers. However, the answer is far less certain for the population and landscape studies based on neutral loci that dominate the conservation genetics research agenda. We used RADseq to revisit earlier molecular studies of the IUCN Critically Endangered Magdalena River turtle (Podocnemis lewyana), documenting the conservation insights gained by increasing the number of neutral markers by several orders of magnitude. Earlier research indicated that P. lewyana has the lowest genetic diversity known for any chelonian, and little or no population differentiation among independent rivers. In contrast, the RADseq data revealed discrete population structure with isolation-by-distance within river segments and identified precise population breaks clearly delineating management units. It also confirmed that the species does not have extremely low heterozygosity and that effective population sizes are probably sufficient to maintain long-term evolutionary potential. Contrary to earlier inferences from more limited population genetic markers, our genomic data suggest that management strategies should shift from active genetic rescue to more passive protection without extreme interventions. We conclude with a list of examples of conservation studies in other vertebrates indicating that for many systems a genomic update is worth the investment.
Collapse
Affiliation(s)
- Natalia Gallego-García
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,Departamento de Ciencias Biológicas, Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Universidad de los Andes, Bogotá, Colombia
| | - Susana Caballero
- Departamento de Ciencias Biológicas, Laboratorio de Ecología Molecular de Vertebrados Acuáticos LEMVA, Universidad de los Andes, Bogotá, Colombia
| | - H Bradley Shaffer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.,La Kretz Center for California Conservation Science, and Institute of the Environment and Sustainability, University of California, Los Angeles, CA, USA
| |
Collapse
|
50
|
O'Connor TK, Sandoval MC, Wang J, Hans JC, Takenaka R, Child M, Whiteman NK. Ecological basis and genetic architecture of crypsis polymorphism in the desert clicker grasshopper (Ligurotettix coquilletti). Evolution 2021; 75:2441-2459. [PMID: 34370317 DOI: 10.1111/evo.14321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 11/28/2022]
Abstract
Color polymorphic species can offer exceptional insight into the ecology and genetics of adaptation. Although the genetic architecture of animal coloration is diverse, many color polymorphisms are associated with large structural variants and maintained by biotic interactions. Grasshoppers are notably polymorphic in both color and karyotype, which makes them excellent models for understanding the ecological drivers and genetic underpinnings of color variation. Banded and uniform morphs of the desert clicker grasshopper (Ligurotettix coquilletti) are found across the western deserts of North America. To address the hypothesis that predation maintains local color polymorphism and shapes regional crypsis variation, we surveyed morph frequencies and tested for covariation with two predation environments. Morphs coexisted at intermediate frequencies at most sites, consistent with local balancing selection. Morph frequencies covaried with the appearance of desert substrate-an environment used only by females-suggesting that ground-foraging predators are major agents of selection on crypsis. We next addressed the hypothesized link between morph variation and genome structure. To do so, we designed an approach for detecting inversions and indels using only RADseq data. The banded morph was perfectly correlated with a large putative indel. Remarkably, indel dominance differed among populations, a rare example of dominance evolution in nature.
Collapse
Affiliation(s)
- Timothy K O'Connor
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720.,Current Address: Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, 60637
| | - Marissa C Sandoval
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| | - Jiarui Wang
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| | - Jacob C Hans
- Department of Entomology, University of California, Riverside, Riverside, California, 92521
| | - Risa Takenaka
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington, 98195.,Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, 98109
| | - Myron Child
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, 84112
| | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, 94720
| |
Collapse
|