1
|
Barratt CD, Preißler K, Jennert PR, Eckhardt F, Nadjafzadeh M, Steinfartz S. A decision-making framework to maximise the evolutionary potential of populations - Genetic and genomic insights from the common midwife toad (Alytes obstetricans) at its range limits. Heredity (Edinb) 2024; 133:249-261. [PMID: 39223228 PMCID: PMC11436998 DOI: 10.1038/s41437-024-00710-4] [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: 12/20/2023] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 09/04/2024] Open
Abstract
Anthropogenic habitat modification and climate change are fundamental drivers of biodiversity declines, reducing the evolutionary potential of species, particularly at their distributional limits. Supportive breeding or reintroductions of individuals are often made to replenish declining populations, sometimes informed by genetic analysis. However, most approaches utilised (i.e. single locus markers) do not have the resolution to account for local adaptation to environmental conditions, a crucial aspect to consider when selecting donor and recipient populations. Here, we incorporate genetic (microsatellite) and genome-wide SNP (ddRAD-seq) markers, accounting for both neutral and putative adaptive genetic diversity, to inform the conservation management of the threatened common midwife toad, Alytes obstetricans at the northern and eastern edges of its range in Europe. We find geographically structured populations (n = 4), weak genetic differentiation and fairly consistent levels of genetic diversity across localities (observed heterozygosity and allelic richness). Categorising individuals based on putatively adaptive regions of the genome showed that the majority of localities are not strongly locally adapted. However, several localities present high numbers of private alleles in tandem with local adaptation to warmer conditions and rough topography. Combining genetic diversity and local adaptations with estimates of migration rates, we develop a decision-making framework for selecting donor and recipient populations which maximises the geographic dispersal of neutral and putatively adaptive genetic diversity. Our framework is generally applicable to any species, but especially to amphibians, so armed with this information, conservationists may avoid the reintroduction of unsuitable/maladapted individuals to new sites and increase the evolutionary potential of populations within species.
Collapse
Affiliation(s)
- Christopher D Barratt
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103, Leipzig, Germany.
- University of Leipzig, Ritterstrasse 26, 04109, Leipzig, Germany.
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands.
- Animal Breeding and Genomics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Kathleen Preißler
- University of Leipzig, Institute of Biology, Molecular Evolution and Systematics of Animals, Talstrasse 33, 04103, Leipzig, Germany
| | - Pauline R Jennert
- University of Leipzig, Institute of Biology, Molecular Evolution and Systematics of Animals, Talstrasse 33, 04103, Leipzig, Germany
| | - Falk Eckhardt
- NABU (Nature and Biodiversity Conservation Union) Lower Saxony, Alleestrasse 36, 30167, Hannover, Germany
| | - Mirjam Nadjafzadeh
- NABU (Nature and Biodiversity Conservation Union) Lower Saxony, Alleestrasse 36, 30167, Hannover, Germany
| | - Sebastian Steinfartz
- University of Leipzig, Institute of Biology, Molecular Evolution and Systematics of Animals, Talstrasse 33, 04103, Leipzig, Germany.
| |
Collapse
|
2
|
Babin CH, Leiva FP, Verberk WCEP, Rees BB. Evolution of Key Oxygen-Sensing Genes Is Associated with Hypoxia Tolerance in Fishes. Genome Biol Evol 2024; 16:evae183. [PMID: 39165136 PMCID: PMC11370800 DOI: 10.1093/gbe/evae183] [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: 11/15/2023] [Revised: 08/05/2024] [Accepted: 08/14/2024] [Indexed: 08/22/2024] Open
Abstract
Low dissolved oxygen (hypoxia) is recognized as a major threat to aquatic ecosystems worldwide. Because oxygen is paramount for the energy metabolism of animals, understanding the functional and genetic drivers of whole-animal hypoxia tolerance is critical to predicting the impacts of aquatic hypoxia. In this study, we investigate the molecular evolution of key genes involved in the detection of and response to hypoxia in ray-finned fishes: the prolyl hydroxylase domain (PHD)-hypoxia-inducible factor (HIF) oxygen-sensing system, also known as the EGLN (egg-laying nine)-HIF oxygen-sensing system. We searched fish genomes for HIFA and EGLN genes, discovered new paralogs from both gene families, and analyzed protein-coding sites under positive selection. The physicochemical properties of these positively selected amino acid sites were summarized using linear discriminants for each gene. We employed phylogenetic generalized least squares to assess the relationship between these linear discriminants for each HIFA and EGLN and hypoxia tolerance as reflected by the critical oxygen tension (Pcrit) of the corresponding species. Our results demonstrate that Pcrit in ray-finned fishes correlates with the physicochemical variation of positively selected sites in specific HIFA and EGLN genes. For HIF2A, two linear discriminants captured more than 90% of the physicochemical variation of these sites and explained between 20% and 39% of the variation in Pcrit. Thus, variation in HIF2A among fishes may contribute to their capacity to cope with aquatic hypoxia, similar to its proposed role in conferring tolerance to high-altitude hypoxia in certain lineages of terrestrial vertebrates.
Collapse
Affiliation(s)
- Courtney H Babin
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| | - Félix P Leiva
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven 27570, Germany
| | - Wilco C E P Verberk
- Department of Animal Ecology and Physiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Bernard B Rees
- Department of Biological Sciences, University of New Orleans, New Orleans, LA 70148, USA
| |
Collapse
|
3
|
Cohen DH, Fant JB, Skogen KA. Conservation genomics assessment of Tharp's bluestar ( Amsonia tharpii) with comparisons to widespread ( A. longilora) and narrowly endemic ( A. fugatei) congeners. Evol Appl 2024; 17:e13736. [PMID: 38903246 PMCID: PMC11186748 DOI: 10.1111/eva.13736] [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: 01/31/2024] [Accepted: 06/05/2024] [Indexed: 06/22/2024] Open
Abstract
Land-use change and habitat fragmentation are threats to biodiversity. The decrease in available habitat, increase in isolation, and mating within populations can lead to elevated inbreeding, lower genetic diversity, and poor fitness. Here we investigate the genetics of two rare and threatened plant species, Amsonia tharpii and A. fugatei, and we compare them to a widespread congener A. longiflora. We also report the first phylogenetic study of the genus Amsonia (Apocynaceae), including 10 of the 17 taxa and multiple sampling locations, to understand species relationships. We used a double digest restriction-site associated DNA sequencing (ddRADseq) approach to investigate the genetic diversity and gene flow of each species and to create a maximum likelihood phylogeny. The ddRADseq data was mapped to a reference genome to separate out the chloroplast and nuclear markers for population genetic analysis. Our results show that genetic diversity and inbreeding were low across all three species. The chloroplast and nuclear dataset in A. tharpii were highly structured, whereas they showed no structure for A. fugatei, while A. longiflora lacked structure for nuclear data but not chloroplast. Phylogenetic results revealed that A. tharpii is distinct and sister to A. fugatei, and together they are distantly related to A. longiflora. Our results demonstrated that evolutionary history and contemporary ecological processes largely influences genetic diversity within Amsonia. Interestingly, we show that in A. tharpii there was significant structure despite being pollinated by large, bodied hawkmoths that are known to be able to carry pollen long distances, suggesting that other factors are contributing to the structure observed among A. tharpii populations. Conservation efforts should focus on protecting all of the A. tharpii populations, as they contain unique genetic diversity, and a protection plan for A. fugatei needs to be established due to its limited distribution.
Collapse
Affiliation(s)
- Dylan H. Cohen
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic GardenGlencoeIllinoisUSA
- Plant Biology and ConservationNorthwestern UniversityEvanstonIllinoisUSA
| | - Jeremie B. Fant
- Negaunee Institute for Plant Conservation Science and ActionChicago Botanic GardenGlencoeIllinoisUSA
- Plant Biology and ConservationNorthwestern UniversityEvanstonIllinoisUSA
| | - Krissa A. Skogen
- Department of Biological SciencesClemson UniversityClemsonSouth CarolinaUSA
| |
Collapse
|
4
|
Muharromah AF, Carvajal TM, Regilme MAF, Watanabe K. Fine-scale adaptive divergence and population genetic structure of Aedes aegypti in Metropolitan Manila, Philippines. Parasit Vectors 2024; 17:233. [PMID: 38769579 PMCID: PMC11107013 DOI: 10.1186/s13071-024-06300-x] [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: 02/06/2024] [Accepted: 04/23/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND The adaptive divergence of Aedes aegypti populations to heterogeneous environments can be a driving force behind the recent expansion of their habitat distribution and outbreaks of dengue disease in urbanized areas. In this study, we investigated the population genomics of Ae. aegypti at a regional scale in Metropolitan Manila, Philippines. METHODS We used the Pool-Seq double digestion restriction-site association DNA sequencing (ddRAD-Seq) approach to generate a high number of single nucleotide polymorphisms (SNPs), with the aim to determine local adaptation and compare the population structure with 11 microsatellite markers. A total of 217 Ae. aegypti individuals from seven female and seven male populations collected from Metropolitan Manila were used in the assays. RESULTS We detected 65,473 SNPs across the populations, of which 76 were non-neutral SNPs. Of these non-neutral SNPs, the multivariate regression test associated 50 with eight landscape variables (e.g. open space, forest, etc.) and 29 with five climate variables (e.g. air temperature, humidity, etc.) (P-value range 0.005-0.045) in female and male populations separately. Male and female populations exhibited contrasting spatial divergence, with males exhibiting greater divergence than females, most likely reflecting the different dispersal abilities of male and female mosquitoes. In the comparative analysis of the same Ae. aegypti individuals, the pairwise FST values of 11 microsatellite markers were lower than those of the neutral SNPs, indicating that the neutral SNPs generated via pool ddRAD-Seq were more sensitive in terms of detecting genetic differences between populations at fine-spatial scales. CONCLUSIONS Overall, our study demonstrates the utility of pool ddRAD-Seq for examining genetic differences in Ae. aegypti populations in areas at fine-spatial scales that could inform vector control programs such as Wolbachia-infected mosquito mass-release programs. This in turn would provide information on mosquito population dispersal patterns and the potential barriers to mosquito movement within and around the release area. In addition, the potential of environmental adaptability observed in Ae. aegypti could help population control efforts.
Collapse
Affiliation(s)
- Atikah Fitria Muharromah
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
- Graduate School of Science and Engineering, Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
- Department of Tropical Biology, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, 55281, Indonesia
| | - Thaddeus M Carvajal
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
- Biological Control Research Unit, Center for Natural Sciences and Environmental Research, De La Salle University, 2401 Taft Avenue, 1004, Manila, Philippines
| | - Maria Angenica F Regilme
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan
| | - Kozo Watanabe
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama, Ehime, 7908577, Japan.
| |
Collapse
|
5
|
Olah G, Waples RS, Stojanovic D. Influence of molecular marker type on estimating effective population size and other genetic parameters in a critically endangered parrot. Ecol Evol 2024; 14:e11102. [PMID: 38524913 PMCID: PMC10961163 DOI: 10.1002/ece3.11102] [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: 08/01/2023] [Revised: 02/15/2024] [Accepted: 02/20/2024] [Indexed: 03/26/2024] Open
Abstract
Genetics is a fast-moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, Lathamus discolor, and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower H O than H E. We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100-SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size (N e) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated N e was higher for the full SNP dataset (2010-2019) than the smaller comparison data (2010-2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.
Collapse
Affiliation(s)
- George Olah
- Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
- King's Forensics, Department of Analytical, Environmental and Forensic Sciences, Faculty of Life Sciences and MedicineKing's College LondonLondonUK
| | - Robin S. Waples
- School of Aquatic and Fishery SciencesUniversity of WashingtonSeattleWashingtonUSA
| | - Dejan Stojanovic
- Fenner School of Environment and SocietyAustralian National UniversityCanberraAustralian Capital TerritoryAustralia
| |
Collapse
|
6
|
Sarakinis KG, Reis-Santos P, Donnellan SC, Ye Q, Earl J, Gillanders BM. Strong philopatry in an estuarine-dependent fish. Ecol Evol 2024; 14:e10989. [PMID: 38500851 PMCID: PMC10945236 DOI: 10.1002/ece3.10989] [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: 07/21/2023] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 03/20/2024] Open
Abstract
Understanding fish movement is critical in determining the spatial scales in which to appropriately manage wild populations. Genetic markers provide a natural tagging approach to assess the degree of gene flow and population connectivity across a species distribution. We investigated the genetic structure of black bream Acanthopagrus butcheri across its entire distribution range in Australia, as well as regional scale gene flow across south-eastern Australia by undertaking a comprehensive analysis of the populations in estuaries across the region. We applied genome-wide sampling of single-nucleotide polymorphism (SNP) markers generated from restriction site-associated DNA sequencing. Genetic structure and potential gene flow was assessed using principal component analyses and admixture analyses (STRUCTURE). Using 33,493 SNPs, we detected broad scale genetic structuring, with limited gene flow among regional clusters (i.e. Western Australia, South Australia and western Victoria; and eastern Victoria, Tasmania and New South Wales). This is likely the result of unsuitable habitats, strong ocean currents (e.g. the Leeuwin Current and the East Australian Current), large water bodies (e.g. Bass Strait) and known biogeographical provinces across the continent. Local-scale genetic structuring was also identified across the south-eastern Australian estuaries sampled, reflecting that the coexistence of both migratory and resident individuals within populations (i.e. partial migration), and the movement of fish into coastal waters, still results in strong philopatry across the region. Instances of movement among estuaries at this spatial scale were primarily found between adjacent estuaries and were likely attributed to lone migrants utilising inshore coastal currents for movement beyond nearby habitats. Targeting SNP markers in A. butcheri at this continental scale highlighted how neither spatial proximity of estuaries nor black bream's ability to move into coastal waters reflects increased gene flow. Overall, our findings highlight the importance of location-specific management.
Collapse
Affiliation(s)
- Koster G Sarakinis
- Southern Seas Ecology Laboratories, School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
| | - Patrick Reis-Santos
- Southern Seas Ecology Laboratories, School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
| | | | - Qifeng Ye
- South Australian Research and Development Institute Aquatic and Livestock Sciences Adelaide South Australia Australia
| | - Jason Earl
- South Australian Research and Development Institute Aquatic and Livestock Sciences Adelaide South Australia Australia
| | - Bronwyn M Gillanders
- Southern Seas Ecology Laboratories, School of Biological Sciences The University of Adelaide Adelaide South Australia Australia
| |
Collapse
|
7
|
Soares LS, Freitas LB. The phylogeographic journey of a plant species from lowland to highlands during the Pleistocene. Sci Rep 2024; 14:3825. [PMID: 38360894 PMCID: PMC10869790 DOI: 10.1038/s41598-024-53414-4] [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: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 02/17/2024] Open
Abstract
Phylogeographic history refers to how species evolve and diversify in response to historical, ecological, and demographic factors. The climate fluctuation during the Pleistocene period marked a crucial time in shaping many species' distribution and genetic structure, particularly those from southern South American grasslands. This work investigated the phylogeographic history of a highland grassland, Petunia altiplana T. Ando & Hashim. (Solanaceae), its diversity, and geographic distribution using a population genomic approach based on RAD-seq data. Our results indicated that, during the Pleistocene, when the grasslands expanded to highlands, the lowland populations of P. altiplana reached the higher open fields, enlarging their geographic distribution. We found that the P. altiplana genetic diversity followed the geographic division into eastern (E) and western (WE) population groups, with a subtle division in the E group regarding the Pelotas River headwater. The results also showed that isolation by distance was the main divergence pattern, with elevation playing a pivotal role in shaping WE and E groups. Our findings indicated that lowland-adapted populations quickly colonized highlands during the late Pleistocene.
Collapse
Affiliation(s)
- Luana Sousa Soares
- Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, Porto Alegre, 91501-970, Brazil
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, PoBox 15053, Porto Alegre, 91501-970, Brazil.
| |
Collapse
|
8
|
Payne N, Erwin JA, Morrison JL, Dwyer JF, Culver M. Genomic insights into isolation of the threatened Florida crested caracara (Caracara plancus). J Hered 2024; 115:45-56. [PMID: 37837958 DOI: 10.1093/jhered/esad057] [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: 06/07/2023] [Revised: 09/18/2023] [Accepted: 09/24/2023] [Indexed: 10/16/2023] Open
Abstract
We conducted a population genomic study of the crested caracara (Caracara plancus) using samples (n = 290) collected from individuals in Florida, Texas, and Arizona, United States. Crested caracaras are non-migratory raptors ranging from the southern tip of South America to the southern United States, including a federally protected relict population in Florida long thought to have been isolated since the last ice age. Our objectives were to evaluate genetic diversity and population structure of Florida's apparently isolated population and to evaluate taxonomic relationships of crested caracaras at the northern edge of their range. Using DNA purified from blood samples, we conducted double-digest restriction site associated DNA sequencing and sequenced the mitochondrial ND2 gene. Analyses of population structure using over 9,000 SNPs suggest that two major clusters are best supported, one cluster including only Florida individuals and the other cluster including Arizona and Texas individuals. Both SNPs and mitochondrial haplotypes reveal the Florida population to be highly differentiated genetically from Arizona and Texas populations, whereas, Arizona and Texas populations are moderately differentiated from each other. The Florida population's mitochondrial haplotypes form a separate monophyletic group, while Arizona and Texas populations share mitochondrial haplotypes. Results of this study provide substantial genetic evidence that Florida's crested caracaras have experienced long-term isolation from caracaras in Arizona and Texas and thus, represent a distinct evolutionary lineage possibly warranting distinction as an Evolutionarily Significant Unit (ESU) or subspecies. This study will inform conservation strategies focused on long-term survival of Florida's distinct, panmictic population.
Collapse
Affiliation(s)
- Natalie Payne
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85719, United States
| | - John A Erwin
- Florida International University College of Law, Miami, FL 33199, United States
| | - Joan L Morrison
- Department of Biology, Trinity College, 300 Summit Street, Hartford, CT 06106, United States
| | - James F Dwyer
- EDM International, Inc., Fort Collins, CO 80525, United States
| | - Melanie Culver
- Genetics Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ 85719, United States
- U.S. Geological Survey, Arizona Cooperative Fish and Wildlife Research Unit, University of Arizona, Tucson, AZ 85721, United States
- School of Natural Resources and the Environment, University of Arizona, Tucson, AZ 85721, United States
| |
Collapse
|
9
|
Masuda K, Setoguchi H, Nagasawa K, Hirota SK, Suyama Y, Sawa K, Fukumoto S, Ishihara MI, Abe H, Tsuboi H, Tango T, Mori S, Sakaguchi S. Genetic consequences of Last Glacial-Holocene changes in snowfall regime in Arnica mallotopus populations: A plant confined to heavy-snow areas of Japan. AMERICAN JOURNAL OF BOTANY 2024; 111:e16275. [PMID: 38303667 DOI: 10.1002/ajb2.16275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 02/03/2024]
Abstract
PREMISE Snow is an important environmental factor affecting plant distribution. Past changes in snowfall regimes may have controlled the demographies of snow-dependent plants. However, our knowledge of changes in the distribution and demographies of such plants is limited because of the lack of fossil records. METHODS Population genetic and landscape genetic analyses were used to investigate the response of population dynamics of Arnica mallotopus (Asteraceae)-a plant confined to heavy-snow areas of Japan-to changes in snowfall regimes from the Last Glacial Period to the Holocene. RESULTS The population genetic analysis suggested that the four geographic lineages diverged during the Last Glacial Period. The interaction between reduced snowfall and lower temperatures during this period likely triggered population isolation in separate refugia. Subpopulation differentiation in the northern group was lower than in the southern group. Our ecological niche model predicted that the current distribution was patchy in the southern region; that is, the populations were isolated by topologically flat and climatically unsuitable lowlands. The landscape genetic analysis suggested that areas with little snowfall acted as barriers to the Holocene expansion of species distribution and continued limiting gene flow between local populations. CONCLUSIONS These findings indicate that postglacial population responses vary among regions and are controlled by environmental and geographic factors. Thus, changes in snowfall regime played a major role in shaping the distribution and genetic structure of the snow-dependent plant.
Collapse
Affiliation(s)
- Kazutoshi Masuda
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo-ku, 606-8501, Kyoto, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo-ku, 606-8501, Kyoto, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, 606-8501, Kyoto, Japan
| | - Koki Nagasawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo-ku, 606-8501, Kyoto, Japan
| | - Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Aza-yomogida, Naruko Onsen, Osaki, 989-6711, Miyagi, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Aza-yomogida, Naruko Onsen, Osaki, 989-6711, Miyagi, Japan
| | | | | | - Masae I Ishihara
- Ashiu Forest Research Station, Kyoto University, Ashiu, Miyama-cho, Nantan, 601-0703, Kyoto, Japan
| | - Harue Abe
- Faculty of Agriculture, Niigata University, Sado, 952-2206, Niigata, Japan
| | - Hayato Tsuboi
- Hakubagoryu Alpine Botanical Garden, Hakuba, Kita-ado, Nagano, Japan
| | | | | | - Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-Nihonmatsu-cho, Sakyo-ku, 606-8501, Kyoto, Japan
- Graduate School of Global Environmental Studies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, 606-8501, Kyoto, Japan
| |
Collapse
|
10
|
Srikanthan P, Burg TM. Environmental drivers behind the genetic differentiation in mountain chickadees ( Poecile gambeli). Genome 2024; 67:53-63. [PMID: 37922513 DOI: 10.1139/gen-2023-0067] [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] [Indexed: 11/05/2023]
Abstract
Anthropogenic climate change has a large impact on wildlife populations and the scale of the impacts has been increasing. In this study, we utilised 3dRAD sequence data to investigate genetic divergence and identify the environmental drivers of genetic differentiation between 12 populations of mountain chickadees, family Paridae, sampled across North America. To examine patterns of genetic variation across the range, we conducted a discriminant analysis of principal components (DAPC), admixture analysis, and calculated pairwise Fst values. The DAPC revealed four clusters: southern California, eastern Rocky Mountains, northwestern Rocky Mountains, and Oregon/northern California. We then used BayeScEnv to highlight significant outlier SNPs associated with the five environmental variables. We identified over 150 genes linked to outlier SNPs associated with more than 15 pathways, including stress response and circadian rhythm. We also found a strong signal of isolation by distance and local temperature was highly correlated with genetic distance. Maxent simulations showed a northward range shift over the next 50 years and a decrease in suitable habitat, highlighting the need for immediate conservation action.
Collapse
Affiliation(s)
- P Srikanthan
- Department of Biology, University of Lethbridge, 4401 University Dr., Lethbridge, AB T1K 3M4, Canada
| | - T M Burg
- Department of Biology, University of Lethbridge, 4401 University Dr., Lethbridge, AB T1K 3M4, Canada
| |
Collapse
|
11
|
Haltiner L, Spaak P, Dennis SR, Feulner PGD. Population genetic insights into establishment, adaptation, and dispersal of the invasive quagga mussel across perialpine lakes. Evol Appl 2024; 17:e13620. [PMID: 38283608 PMCID: PMC10809192 DOI: 10.1111/eva.13620] [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: 04/25/2023] [Revised: 10/13/2023] [Accepted: 11/10/2023] [Indexed: 01/30/2024] Open
Abstract
Human activities have facilitated the invasion of freshwater ecosystems by various organisms. Especially, invasive bivalves such as the quagga mussels, Dreissena bugensis, have the potential to alter ecosystem function as they heavily affect the food web. Quagga mussels occur in high abundance, have a high filtration rate, quickly spread within and between waterbodies via pelagic larvae, and colonize various substrates. They have invaded various waterbodies across the Northern Hemisphere. In Central Europe, they have invaded multiple large and deep perialpine lakes with first recordings in Lake Geneva in 2015 and 2016 in Lake Constance. In the deep perialpine lakes, quagga mussels quickly colonized the littoral zone but are also abundant deeper (>80 m), where they are often thinner and brighter shelled. We analysed 675 quagga mussels using ddRAD sequencing to gain in-depth insights into the genetic population structure of quagga mussels across Central European lakes and across various sites and depth habitats in Lake Constance. We revealed substantial genetic differentiation amongst quagga mussel populations from three unconnected lakes, and all populations showed high genetic diversity and effective population size. In Lake Constance, we detected no genetic differentiation amongst quagga mussels sampled across different sites and depth habitats. We also did not identify any convincing candidate loci evidential for adaptation along a depth gradient and a transplant experiment showed no indications of local adaptation to living in the deep based on investigating growth and survival. Hence, the shallow-water and the deep-water morphotypes seem to be a result of phenotypic plasticity rather than local adaptation to depth. In conclusion, our ddRAD approach revealed insight into the establishment of genetically distinct quagga mussel populations in three perialpine lakes and suggests that phenotypic plasticity and life history traits (broadcast spawner with high fecundity and dispersing pelagic larvae) facilitate the fast spread and colonization of various depth habitats by the quagga mussel.
Collapse
Affiliation(s)
- Linda Haltiner
- Aquatic EcologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
- Environmental Systems SciencesETH ZürichZürichSwitzerland
| | - Piet Spaak
- Aquatic EcologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
- Environmental Systems SciencesETH ZürichZürichSwitzerland
| | - Stuart R. Dennis
- Aquatic EcologySwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
- Present address:
Department IT servicesSwiss Federal Institute of Aquatic Science and Technology (Eawag)DübendorfSwitzerland
| | - Philine G. D. Feulner
- Fish Ecology and Evolution, Center for Ecology, Evolution and BiogeochemistrySwiss Federal Institute of Aquatic Science and Technology (Eawag)KastanienbaumSwitzerland
- Aquatic Ecology, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| |
Collapse
|
12
|
Hopken MW, Piaggio AJ, Abdo Z, Chipman RB, Mankowski CP, Nelson KM, Hilton MS, Thurber C, Tsuchiya MTN, Maldonado JE, Gilbert AT. Are rabid raccoons ( Procyon lotor) ready for the rapture? Determining the geographic origin of rabies virus-infected raccoons using RADcapture and microhaplotypes. Evol Appl 2023; 16:1937-1955. [PMID: 38143904 PMCID: PMC10739080 DOI: 10.1111/eva.13613] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/06/2023] [Accepted: 10/18/2023] [Indexed: 12/26/2023] Open
Abstract
North America is recognized for the exceptional richness of rabies virus (RV) wildlife reservoir species. Management of RV is accomplished through vaccination targeting mesocarnivore reservoir populations, such as the raccoon (Procyon lotor) in Eastern North America. Raccoons are a common generalist species, and populations may reach high densities in developed areas, which can result in contact with humans and pets with potential exposures to the raccoon variant of RV throughout the eastern United States. Understanding the spatial movement of RV by raccoon populations is important for monitoring and refining strategies supporting the landscape-level control and local elimination of this lethal zoonosis. We developed a high-throughput genotyping panel for raccoons based on hundreds of microhaplotypes to identify population structure and genetic diversity relevant to rabies management programs. Throughout the eastern United States, we identified hierarchical population genetic structure with clusters that were connected through isolation-by-distance. We also illustrate that this genotyping approach can be used to support real-time management priorities by identifying the geographic origin of a rabid raccoon that was collected in an area of the United States that had been raccoon RV-free for 8 years. The results from this study and the utility of the microhaplotype panel and genotyping method will provide managers with information on raccoon ecology that can be incorporated into future management decisions.
Collapse
Affiliation(s)
- Matthew W. Hopken
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Antoinette J. Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Richard B. Chipman
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Rabies Management ProgramConcordNew HampshireUSA
| | - Clara P. Mankowski
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Kathleen M. Nelson
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Rabies Management ProgramConcordNew HampshireUSA
| | - Mikaela Samsel Hilton
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
| | - Christine Thurber
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Rabies Management ProgramConcordNew HampshireUSA
| | - Mirian T. N. Tsuchiya
- Data Science Lab, Office of the Chief Information OfficerSmithsonian InstitutionWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian National Zoo and Conservation Biology InstituteWashingtonDCUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian National Zoo and Conservation Biology InstituteWashingtonDCUSA
| | - Amy T. Gilbert
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
| |
Collapse
|
13
|
Li H, Song K, Li B, Zhang X, Wang D, Dong S, Yang L. CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis. Int J Mol Sci 2023; 24:15317. [PMID: 37894996 PMCID: PMC10607008 DOI: 10.3390/ijms242015317] [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: 08/31/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
CRISPR/Cas9 is an efficient genome-editing tool, and the identification of editing sites and potential influences in the Camellia sinensis genome have not been investigated. In this study, bioinformatics methods were used to characterise the Camellia sinensis genome including editing sites, simple sequence repeats (SSRs), G-quadruplexes (GQ), gene density, and their relationships. A total of 248,134,838 potential editing sites were identified in the genome, and five PAM types, AGG, TGG, CGG, GGG, and NGG, were observed, of which 66,665,912 were found to be specific, and they were present in all structural elements of the genes. The characteristic region of high GC content, GQ density, and PAM density in contrast to low gene density and SSR density was identified in the chromosomes in the joint analysis, and it was associated with secondary metabolites and amino acid biosynthesis pathways. CRISPR/Cas9, as a technology to drive crop improvement, with the identified editing sites and effector elements, provides valuable tools for functional studies and molecular breeding in Camellia sinensis.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
| |
Collapse
|
14
|
Holmes IA, Monagan IV, Westphal MF, Johnson PJ, Rabosky ARD. Parsing variance by marker type: Testing biogeographic hypotheses and differential contribution of historical processes to population structure in a desert lizard. Mol Ecol 2023; 32:4880-4897. [PMID: 37466017 PMCID: PMC10530499 DOI: 10.1111/mec.17076] [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: 10/10/2021] [Revised: 06/19/2023] [Accepted: 07/04/2023] [Indexed: 07/20/2023]
Abstract
A fundamental goal of population genetic studies is to identify historical biogeographic patterns and understand the processes that generate them. However, localized demographic events can skew population genetic inference. Assessing populations with multiple types of genetic markers, each with unique mutation rates and responses to changes in population size, can help to identify potentially confounding population-specific demographic processes. Here, we compared population structure and connectivity inferred from microsatellites and restriction site-associated DNA loci among 17 populations of an arid-specialist lizard, the desert night lizard, Xantusia vigilis, in central California to test among historical processes structuring population genetic diversity. We found that both marker types yielded generally concordant insights into population genetic structure including a major phylogenetic break maintained between two populations separated by less than 10 km, suggesting that either marker type could be used to understand generalized demographic patterns across the region for management purposes. However, we also found that the effects of demography on marker discordance could be used to elucidate population histories and distinguish among competing biogeographic hypotheses. Our results suggest that comparisons of within-population diversity across marker types provide powerful opportunities for leveraging marker discordance, particularly for understanding the creation and maintenance of contact zones among clades.
Collapse
Affiliation(s)
- Iris A. Holmes
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Cornell Institute of Host Microbe Interactions and Disease and Department of Microbiology, Cornell University, Ithaca, NY 14853 USA
| | - Ivan V. Monagan
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Department of Ecology, Evolution, and Environmental Biology, Columbia University and American Museum of Natural History, NY, USA
| | | | | | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI USA
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, CA USA
| |
Collapse
|
15
|
Martina M, Acquadro A, Portis E, Barchi L, Lanteri S. Diversity analyses in two ornamental and large-genome Ranunculaceae species based on a low-cost Klenow NGS-based protocol. FRONTIERS IN PLANT SCIENCE 2023; 14:1187205. [PMID: 37360724 PMCID: PMC10289064 DOI: 10.3389/fpls.2023.1187205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Persian buttercup (Ranunculus asiaticus L.) and poppy anemone (Anemone coronaria L.) are ornamental, outcrossing, perennial species belonging to the Ranunculaceae family, characterized by large and highly repetitive genomes. We applied K-seq protocol in both species to generate high-throughput sequencing data and produce a large number of genetic polymorphisms. The technique entails the application of Klenow polymerase-based PCR using short primers designed by analyzing k-mer sets in the genome sequence. To date the genome sequence of both species has not been released, thus we designed primer sets based on the reference the genome sequence of the related species Aquilegia oxysepala var. kansuensis (Brühl). A whole of 11,542 SNPs were selected for assessing genetic diversity of eighteen commercial varieties of R. asiaticus, while 1,752 SNPs for assessing genetic diversity in six cultivars of A. coronaria. UPGMA dendrograms were constructed and in R. asiaticus integrated in with PCA analysis. This study reports the first molecular fingerprinting within Persian buttercup, while the results obtained in poppy anemone were compared with a previously published SSR-based fingerprinting, proving K-seq to be an efficient protocol for the genotyping of complex genetic backgrounds.
Collapse
|
16
|
Chaput R, Quigley CN, Weppe SB, Jeffs AG, de Souza JMAC, Gardner JPA. Identifying the source populations supplying a vital economic marine species for the New Zealand aquaculture industry. Sci Rep 2023; 13:9344. [PMID: 37291180 PMCID: PMC10250383 DOI: 10.1038/s41598-023-36224-y] [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: 01/17/2023] [Accepted: 05/31/2023] [Indexed: 06/10/2023] Open
Abstract
Aquaculture of New Zealand's endemic green-lipped mussel (Perna canaliculus) is an industry valued at NZ$ 336 M per annum and is ~ 80% reliant on the natural supply of wild mussel spat harvested at a single location-Te Oneroa-a-Tōhē-Ninety Mile Beach (NMB)-in northern New Zealand. Despite the economic and ecological importance of this spat supply, little is known about the population connectivity of green-lipped mussels in this region or the location of the source population(s). In this study, we used a biophysical model to simulate the two-stage dispersal process of P. canaliculus. A combination of backward and forward tracking experiments was used to identify primary settlement areas and putative source populations. The model was then used to estimate the local connectivity, revealing two geographic regions of connectivity in northern New Zealand, with limited larval exchange between them. Although secondary dispersal can double the dispersal distance, our simulations show that spat collected at NMB originate from neighbouring mussel beds, with large contributions from beds located at Ahipara (southern end of NMB). These results provide information that may be used to help monitor and protect these important source populations to ensure the ongoing success of the New Zealand mussel aquaculture industry.
Collapse
Affiliation(s)
- Romain Chaput
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand.
- Cawthron Institute, Nelson, New Zealand.
| | - Calvin N Quigley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Simon B Weppe
- MetOcean Solutions, Division of Meteorological Service of New Zealand, Raglan, New Zealand
| | - Andrew G Jeffs
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - João M A C de Souza
- MetOcean Solutions, Division of Meteorological Service of New Zealand, Raglan, New Zealand
| | - Jonathan P A Gardner
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| |
Collapse
|
17
|
Hassett K, Muria-Gonzalez MJ, Turner A, McLean MS, Wallwork H, Martin A, Ellwood SR. Widespread genetic heterogeneity and genotypic grouping associated with fungicide resistance among barley spot form net blotch isolates in Australia. G3 (BETHESDA, MD.) 2023; 13:jkad076. [PMID: 37002913 PMCID: PMC10151411 DOI: 10.1093/g3journal/jkad076] [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: 02/13/2023] [Revised: 02/13/2023] [Accepted: 03/10/2023] [Indexed: 04/04/2023]
Abstract
Spot form net blotch, caused by Pyrenophora teres f. maculata, is a major foliar disease of barley worldwide. Knowledge of the pathogen's genetic diversity and population structure is critical for a better understanding of inherent evolutionary capacity and for the development of sustainable disease management strategies. Genome-wide, single nucleotide polymorphism data of 254 Australian isolates revealed genotypic diversity and an absence of population structure, either between states, or between fields and cultivars in different agro-ecological zones. This indicates there is little geographical isolation or cultivar directional selection and that the pathogen is highly mobile across the continent. However, two cryptic genotypic groups were found only in Western Australia, predominantly associated with genes involved in fungicide resistance. The findings in this study are discussed in the context of current cultivar resistance and the pathogen's adaptive potential.
Collapse
Affiliation(s)
- Kealan Hassett
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | | | - Aleesha Turner
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| | - Mark S McLean
- Field Crops Pathology, Agriculture Victoria, Horsham, Victoria 3401, Australia
| | - Hugh Wallwork
- Cereal Pathology Laboratory, South Australian Research and Development Institute, Hartley Grove, Urrbrae, SA 5064, Australia
| | - Anke Martin
- Centre for Crop Health, University of Southern Queensland, Toowoomba, Queensland 4350, Australia
| | - Simon R Ellwood
- Centre for Crop and Disease Management, Curtin University, Bentley, WA 6102, Australia
| |
Collapse
|
18
|
Skey ED, Ottewell KM, Spencer PB, Shaw RE. Empirical landscape genetic comparison of single nucleotide polymorphisms and microsatellites in three arid-zone mammals with high dispersal capacity. Ecol Evol 2023; 13:e10037. [PMID: 37153020 PMCID: PMC10154367 DOI: 10.1002/ece3.10037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 05/09/2023] Open
Abstract
Landscape genetics is increasingly transitioning away from microsatellites, with single nucleotide polymorphisms (SNPs) providing increased resolution for detecting patterns of spatial-genetic structure. This is particularly pertinent for research in arid-zone mammals due to challenges associated with unique life history traits, such as boom-bust population dynamics and long-distance dispersal capacities. Here, we provide a case study comparing SNPs versus microsatellites for testing three explicit landscape genetic hypotheses (isolation-by-distance, isolation-by-barrier, and isolation-by-resistance) in a suite of small, arid-zone mammals in the Pilbara region of Western Australia. Using clustering algorithms, Mantel tests, and linear mixed effects models, we compare functional connectivity between genetic marker types and across species, including one marsupial, Ningaui timealeyi, and two native rodents, Pseudomys chapmani and P. hermannsburgensis. SNPs resolved subtle genetic structuring not detected by microsatellites, particularly for N. timealeyi where two genetic clusters were identified. Furthermore, stronger signatures of isolation-by-distance and isolation-by-resistance were detected when using SNPs, and model selection based on SNPs tended to identify more complex resistance surfaces (i.e., composite surfaces of multiple environmental layers) in the best-performing models. While we found limited evidence for physical barriers to dispersal across the Pilbara for all species, we found that topography, substrate, and soil moisture were the main environmental drivers shaping functional connectivity. Our study demonstrates that new analytical and genetic tools can provide novel ecological insights into arid landscapes, with potential application to conservation management through identifying dispersal corridors to mediate the impacts of ongoing habitat fragmentation in the region.
Collapse
Affiliation(s)
- Ebony D. Skey
- Environmental & Conservation SciencesMurdoch UniversityPerthWestern AustraliaAustralia
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Kym M. Ottewell
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
| | - Peter B. Spencer
- Environmental & Conservation SciencesMurdoch UniversityPerthWestern AustraliaAustralia
| | - Robyn E. Shaw
- Environmental & Conservation SciencesMurdoch UniversityPerthWestern AustraliaAustralia
- Biodiversity and Conservation ScienceDepartment of Biodiversity, Conservation and AttractionsPerthWestern AustraliaAustralia
- Present address:
Division of Ecology and Evolution, Research School of BiologyThe Australian National UniversityCanberraAustralian Capital TerritoryAustralia
| |
Collapse
|
19
|
Maas DL, Prost S, de Leeuw CA, Bi K, Smith LL, Purwanto P, Aji LP, Tapilatu RF, Gillespie RG, Becking LE. Sponge diversification in marine lakes: Implications for phylogeography and population genomic studies on sponges. Ecol Evol 2023; 13:e9945. [PMID: 37066063 PMCID: PMC10099488 DOI: 10.1002/ece3.9945] [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: 12/06/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 04/18/2023] Open
Abstract
The relative influence of geography, currents, and environment on gene flow within sessile marine species remains an open question. Detecting subtle genetic differentiation at small scales is challenging in benthic populations due to large effective population sizes, general lack of resolution in genetic markers, and because barriers to dispersal often remain elusive. Marine lakes can circumvent confounding factors by providing discrete and replicated ecosystems. Using high-resolution double digest restriction-site-associated DNA sequencing (4826 Single Nucleotide Polymorphisms, SNPs), we genotyped populations of the sponge Suberites diversicolor (n = 125) to test the relative importance of spatial scales (1-1400 km), local environmental conditions, and permeability of seascape barriers in shaping population genomic structure. With the SNP dataset, we show strong intralineage population structure, even at scales <10 km (average F ST = 0.63), which was not detected previously using single markers. Most variation was explained by differentiation between populations (AMOVA: 48.8%) with signatures of population size declines and bottlenecks per lake. Although the populations were strongly structured, we did not detect significant effects of geographic distance, local environments, or degree of connection to the sea on population structure, suggesting mechanisms such as founder events with subsequent priority effects may be at play. We show that the inclusion of morphologically cryptic lineages that can be detected with the COI marker can reduce the obtained SNP set by around 90%. Future work on sponge genomics should confirm that only one lineage is included. Our results call for a reassessment of poorly dispersing benthic organisms that were previously assumed to be highly connected based on low-resolution markers.
Collapse
Affiliation(s)
- Diede L. Maas
- Marine Animal EcologyWageningen University & ResearchWageningenThe Netherlands
| | - Stefan Prost
- LOEWE Centre for Translational Biodiversity GenomicsSenckenberg Natural History MuseumFrankfurt am MainGermany
- South African National Biodiversity InstituteNational Zoological Gardens of South AfricaPretoriaSouth Africa
| | | | - Ke Bi
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Computational Genomics Resource Laboratory, California Institute for Quantitative BiosciencesUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Lydia L. Smith
- Museum of Vertebrate ZoologyUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | | | - Ludi P. Aji
- Marine Animal EcologyWageningen University & ResearchWageningenThe Netherlands
- Research Centre for Oceanography, Indonesian Institute of SciencesLembaga Ilmu Pengetahuan IndonesiaJakartaIndonesia
| | - Ricardo F. Tapilatu
- Marine Science and Fisheries Departments and Research Center of Pacific Marine ResourcesState University of PapuaManokwariIndonesia
| | - Rosemary G. Gillespie
- Department of Environmental Science, Policy and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | - Leontine E. Becking
- Department of Environmental Science, Policy and ManagementUniversity of California BerkeleyBerkeleyCaliforniaUSA
- Aquaculture and Fisheries, Naturalis Biodiversity CenterWageningen University & ResearchWageningenThe Netherlands
| |
Collapse
|
20
|
Bilska-Zając E, Korpysa-Dzirba W, Bełcik A, Karamon J, Sroka J, Cencek T. Scheme of Effective Epidemiological Investigations in Trichinella Outbreaks on Pig Farms. Foods 2023; 12:foods12061320. [PMID: 36981247 PMCID: PMC10048642 DOI: 10.3390/foods12061320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
Trichinellosis is a parasitic, zoonotic disease caused by larvae of the genus Trichinella. Infection occurs via the consumption of raw or undercooked meat containing this parasite. Symptoms of the disease manifest as intestinal disorders, followed by facial swelling, fever, muscle pain and other symptoms, eventually leading to neurological and cardiac complications and even death. In Europe, trichinellosis is most often associated with the consumption of meat from wild boars, pigs and horses. In recent years, wild boars that are hunted illegally and not tested for Trichinella spp. have been the most common cause of trichinellosis in humans; however, there have also been cases where infected pigs have been the source of infection. When trichinellosis is suspected in humans, epidemiological measures are taken to identify the source. Similarly, an epidemiological investigation should be initiated whenever Trichinella spp. has been detected in pigs. However, commonly used actions do not provide sufficient data to determine the source of infection for pigs and to prevent further transmission. Therefore, in this article, we propose a scheme for effective epidemiological investigations into Trichinella outbreaks on pig farms that can help trace the transmission mechanisms of the parasite and that takes into account currently available testing tools. The proposed pathway can be easily adopted for epidemiological investigations in routine veterinary inspection work.
Collapse
|
21
|
Sibly RM, Curnow RN. Allele frequencies and selection coefficients in locally adapted populations. J Theor Biol 2023; 565:111463. [PMID: 36914112 DOI: 10.1016/j.jtbi.2023.111463] [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: 07/19/2022] [Revised: 12/22/2022] [Accepted: 03/08/2023] [Indexed: 03/15/2023]
Abstract
Understanding the role of natural selection in driving evolutionary change requires accurate estimates of the strength of selection acting at the genetic level in the wild. This is challenging to achieve but may be easier in the case of populations in migration-selection balance. When two populations are at equilibrium under migration-selection balance, there exist loci whose alleles are selected different ways in the two populations. Such loci can be identified from genome sequencing by their high values of FST. This raises the question of what is the strength of selection on locally-adaptive alleles. To answer this question we analyse a 1-locus 2-allele model of a population distributed between two niches. We show by simulation of selected cases that the outputs from finite-population models are essentially the same as those from deterministic infinite-population models. We then derive theory for the infinite-population model showing the dependence of selection coefficients on equilibrium allele frequencies, migration rates, dominance and relative population sizes in the two niches. An Excel spreadsheet is provided for the calculation of selection coefficients and their approximate standard errors from observed values of population parameters. We illustrate our results with a worked example, with graphs showing the dependence of selection coefficients on equilibrium allele frequencies, and graphs showing how FST depends on the selection coefficients acting on the alleles at a locus. Given the extent of recent progress in ecological genomics, we hope our methods may help those studying migration-selection balance to quantify the advantages conferred by adaptive genes.
Collapse
Affiliation(s)
| | - Robert N Curnow
- Department of Mathematics and Statistics, University of Reading, UK.
| |
Collapse
|
22
|
Scariolo F, Palumbo F, Farinati S, Barcaccia G. Pipeline to Design Inbred Lines and F1 Hybrids of Leaf Chicory (Radicchio) Using Male Sterility and Genotyping-by-Sequencing. PLANTS (BASEL, SWITZERLAND) 2023; 12:1242. [PMID: 36986929 PMCID: PMC10055022 DOI: 10.3390/plants12061242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Chicory, a horticultural crop cultivated worldwide, presents many botanical varieties and local biotypes. Among these, cultivars of the Italian radicchio group of the pure species Cichorium intybus L. and its interspecific hybrids with Cichorium endivia L.-as the "Red of Chioggia" biotype-includes several phenotypes. This study uses a pipeline to address the marker-assisted breeding of F1 hybrids: it presents the genotyping-by-sequencing results of four elite inbred lines using a RADseq approach and an original molecular assay based on CAPS markers for screening mutants with nuclear male sterility in the radicchio of Chioggia. A total of 2953 SNP-carrying RADtags were identified and used to compute the actual estimates of homozygosity and overall genetic similarity and uniformity of the populations, as well as to determine their genetic distinctiveness and differentiation. Molecular data were further used to investigate the genomic distribution of the RADtags among the two Cichorium species, allowing their mapping in 1131 and 1071 coding sequences in chicory and endive, respectively. Paralleling this, an assay to screen the genotype at the male sterility locus Cims-1 was developed to discriminate wild-type and mutant alleles of the causative gene myb80-like. Moreover, a RADtag mapped close to this genomic region proved the potential application of this method for future marker-assisted selection tools. Finally, after combining the genotype information of the core collection, the best 10 individuals from each inbred line were selected to compute the observed genetic similarity as a measure of uniformity as well as the expected homozygosity and heterozygosity estimates scorable by the putative progenies derived from selfing (pollen parent) and full-sibling (seed parent) or pair-wise crossing (F1 hybrids). This predictive approach was conducted as a pilot study to understand the potential application of RADseq in the fine tuning of molecular marker-assisted breeding strategies aimed at the development of inbred lines and F1 hybrids in leaf chicory.
Collapse
|
23
|
Dufresnes C, Dutoit L, Brelsford A, Goldstein-Witsenburg F, Clément L, López-Baucells A, Palmeirim J, Pavlinić I, Scaravelli D, Ševčík M, Christe P, Goudet J. Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe. Sci Rep 2023; 13:1523. [PMID: 36707640 PMCID: PMC9883447 DOI: 10.1038/s41598-023-27988-4] [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: 07/10/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing (RAD-seq) analyses to investigate population structure in the declining bent-winged bat (Miniopterus schreibersii) across Europe. Both markers retrieved general patterns of weak range-wide differentiation, little sex-biased dispersal, and strong isolation by distance that associated with significant genetic structure between the three Mediterranean Peninsulas, which could have acted as glacial refugia. Microsatellites proved uninformative in individual-based analyses, but the resolution offered by genomic SNPs illuminated on regional substructures within several countries, with colonies sharing migrators of distinct ancestry without admixture. This finding is consistent with a marked philopatry and spatial partitioning between mating and rearing grounds in the species, which was suspected from marked-recaptured data. Our study advocates that genomic data are necessary to properly unveil the genetic footprints left by biogeographic processes and social organization in long-distant flyers, which are otherwise rapidly blurred by their high levels of gene flow.
Collapse
Affiliation(s)
- Christophe Dufresnes
- Laboratory for Amphibian Systematic and Evolutionary Research, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China.
| | - Ludovic Dutoit
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.,Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | | | - Laura Clément
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Adria López-Baucells
- Bat Research Area, Granollers Museum of Natural Sciences, Carrer Palaudaries 102, 08402, Granollers, Spain
| | - Jorge Palmeirim
- Department of Animal Biology, Centre for Ecology, Evolution and Environmental Change - cE3c, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Igor Pavlinić
- Department of Zoology, Croatian Natural History Museum, Demetrova 1, 10000, Zagreb, Croatia
| | - Dino Scaravelli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Martin Ševčík
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague 2, Czech Republic
| | - Philippe Christe
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
| |
Collapse
|
24
|
Osborne MJ, Caeiro-Dias G, Turner TF. Transitioning from microsatellites to SNP-based microhaplotypes in genetic monitoring programmes: Lessons from paired data spanning 20 years. Mol Ecol 2023; 32:316-334. [PMID: 36321869 DOI: 10.1111/mec.16760] [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: 04/27/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/18/2022]
Abstract
Many long-term genetic monitoring programmes began before next-generation sequencing became widely available. Older programmes can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programmes should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (Hybognathus amarus) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.
Collapse
Affiliation(s)
- Megan J Osborne
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Guilherme Caeiro-Dias
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Thomas F Turner
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| |
Collapse
|
25
|
Rivera HE, Cohen AL, Thompson JR, Baums IB, Fox MD, Meyer-Kaiser KS. Palau's warmest reefs harbor thermally tolerant corals that thrive across different habitats. Commun Biol 2022; 5:1394. [PMID: 36543929 PMCID: PMC9772186 DOI: 10.1038/s42003-022-04315-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
Ocean warming is killing corals, but heat-tolerant populations exist; if protected, they could replenish affected reefs naturally or through restoration. Palau's Rock Islands experience consistently higher temperatures and extreme heatwaves, yet their diverse coral communities bleach less than those on Palau's cooler outer reefs. Here, we combined genetic analyses, bleaching histories and growth rates of Porites cf. lobata colonies to identify thermally tolerant genotypes, map their distribution, and investigate potential growth trade-offs. We identified four genetic lineages of P. cf. lobata. On Palau's outer reefs, a thermally sensitive lineage dominates. The Rock Islands harbor two lineages with enhanced thermal tolerance; one of which shows no consistent growth trade-off and also occurs on several outer reefs. This suggests that the Rock Islands provide naturally tolerant larvae to neighboring areas. Finding and protecting such sources of thermally-tolerant corals is key to reef survival under 21st century climate change.
Collapse
Affiliation(s)
- Hanny E. Rivera
- grid.116068.80000 0001 2341 2786MIT-WHOI Joint Program in Oceanography/Applied Ocean Science & Engineering, Cambridge and Woods Hole, MA USA ,grid.56466.370000 0004 0504 7510Woods Hole Oceanographic Institution, Woods Hole, MA USA ,grid.116068.80000 0001 2341 2786Massachusetts Institute of Technology, Cambridge, MA USA
| | - Anne L. Cohen
- grid.56466.370000 0004 0504 7510Woods Hole Oceanographic Institution, Woods Hole, MA USA
| | - Janelle R. Thompson
- grid.116068.80000 0001 2341 2786Massachusetts Institute of Technology, Cambridge, MA USA ,grid.59025.3b0000 0001 2224 0361Asian School of the Environment, Nanyang Technological University, Singapore (NTU), Singapore ,grid.484638.50000 0004 7703 9448Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Singapore, Singapore
| | - Iliana B. Baums
- grid.29857.310000 0001 2097 4281Pennsylvania State University, State College, PA USA
| | - Michael D. Fox
- grid.56466.370000 0004 0504 7510Woods Hole Oceanographic Institution, Woods Hole, MA USA ,grid.45672.320000 0001 1926 5090Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | |
Collapse
|
26
|
Mijangos JL, Bino G, Hawke T, Kolomyjec SH, Kingsford RT, Sidhu H, Grant T, Day J, Dias KN, Gongora J, Sherwin WB. Fragmentation by major dams and implications for the future viability of platypus populations. Commun Biol 2022; 5:1127. [PMID: 36329312 PMCID: PMC9633709 DOI: 10.1038/s42003-022-04038-9] [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: 03/16/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily unique platypus (Ornithorhynchus anatinus) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation (FST) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers; FST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, FST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.
Collapse
Affiliation(s)
- Jose L. Mijangos
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia ,grid.1039.b0000 0004 0385 7472Centre for Conservation Ecology and Genomics, Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Gilad Bino
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Tahneal Hawke
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Stephen H. Kolomyjec
- grid.258898.60000 0004 0462 9201College of Science and the Environment, Lake Superior State University, Sault Sainte Marie, USA
| | - Richard T. Kingsford
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Harvinder Sidhu
- grid.1005.40000 0004 4902 0432School of Science, UNSW, Canberra, Australia
| | - Tom Grant
- grid.1005.40000 0004 4902 0432Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, Australia
| | - Jenna Day
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Kimberly N. Dias
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - Jaime Gongora
- grid.1013.30000 0004 1936 834XSydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, Australia
| | - William B. Sherwin
- grid.1005.40000 0004 4902 0432Evolution & Ecology Research Centre, UNSW, Sydney, Australia
| |
Collapse
|
27
|
Sibly RM, Curnow RN. Sexual imprinting leads to speciation in locally adapted populations. Ecol Evol 2022; 12:e9479. [PMID: 36381395 PMCID: PMC9643133 DOI: 10.1002/ece3.9479] [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: 09/12/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/10/2022] Open
Abstract
Sexual imprinting is widespread in birds and other species but its existence requires explanation. Our results suggest that sexual imprinting leads to speciation in locally-adapted populations if a neutral mating cue-e.g., novel plumage coloration-arises through mutation. Importantly, the mating cue locus is not linked to adaptation loci. Local adaptation is a necessary precursor to speciation and occurs when evolution results in stable genetic polymorphisms with one allele predominating in some areas while others predominate elsewhere. Here we use a deterministic two-niche population genetic model to map the set of migration and selection rates for which polymorphic evolutionary outcomes, i.e., local adaptations, can occur. Approximate equations for the boundaries of the set of polymorphic evolutionary outcomes were derived by Bulmer (American Naturalist, 106, 254, 1972), but our results, obtained by deterministic simulation of the evolutionary process, show that one of Bulmer's equations is inaccurate except when the level of dominance is 0.5, and fails if one of the alleles is dominant. Having an accurate map of the set of migration and selection rates for which polymorphic evolutionary outcomes can occur, we then show using the model of Sibly et al. (Ecology and Evolution, 9, 13506, 2019) that local adaptation in all analyzed cases leads to speciation if a new neutral mating cue arises by mutation. We finish by considering how genome sequencing makes possible testing our model and its predictions.
Collapse
Affiliation(s)
| | - Robert N. Curnow
- Department of Mathematics and StatisticsUniversity of ReadingReadingUK
| |
Collapse
|
28
|
Poelstra JW, Montero BK, Lüdemann J, Yang Z, Rakotondranary SJ, Hohenlohe P, Stetter N, Ganzhorn JU, Yoder AD. RADseq data reveal a lack of admixture in a mouse lemur contact zone contrary to previous microsatellite results. Proc Biol Sci 2022; 289:20220596. [PMID: 35946151 PMCID: PMC9364002 DOI: 10.1098/rspb.2022.0596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Microsatellites have been a workhorse of evolutionary genetic studies for decades and are still commonly in use for estimating signatures of genetic diversity at the population and species level across a multitude of taxa. Yet, the very high mutation rate of these loci is a double-edged sword, conferring great sensitivity at shallow levels of analysis (e.g. paternity analysis) but yielding considerable uncertainty for deeper evolutionary comparisons. For the present study, we used reduced representation genome-wide data (restriction site-associated DNA sequencing (RADseq)) to test for patterns of interspecific hybridization previously characterized using microsatellite data in a contact zone between two closely related mouse lemur species in Madagascar (Microcebus murinus and Microcebus griseorufus). We revisit this system by examining populations in, near, and far from the contact zone, including many of the same individuals that had previously been identified as hybrids with microsatellite data. Surprisingly, we find no evidence for admixed nuclear ancestry. Instead, re-analyses of microsatellite data and simulations suggest that previously inferred hybrids were false positives and that the program NewHybrids can be particularly sensitive to erroneously inferring hybrid ancestry. Combined with results from coalescent-based analyses and evidence for local syntopic co-occurrence, we conclude that the two mouse lemur species are in fact completely reproductively isolated, thus providing a new understanding of the evolutionary rate whereby reproductive isolation can be achieved in a primate.
Collapse
Affiliation(s)
- Jelmer W. Poelstra
- Department of Biology, Duke University, Durham, NC 27708, USA,Molecular and Cellular Imaging Center, Ohio State University, Wooster, OH 44691, USA
| | - B. Karina Montero
- Institute of Zoology, Department of Animal Ecology and Conservation, Universität Hamburg, Hamburg, 20146, Germany
| | - Jan Lüdemann
- Institute of Zoology, Department of Animal Ecology and Conservation, Universität Hamburg, Hamburg, 20146, Germany
| | - Ziheng Yang
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - S. Jacques Rakotondranary
- Institute of Zoology, Department of Animal Ecology and Conservation, Universität Hamburg, Hamburg, 20146, Germany,Anthropobiologie et Développement Durable, Faculté des Sciences, Université d'Antananarivo, PO Box 906, Antananarivo 101, Madagascar
| | - Paul Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Nadine Stetter
- Institute of Zoology, Department of Animal Ecology and Conservation, Universität Hamburg, Hamburg, 20146, Germany,Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
| | - Jörg U. Ganzhorn
- Institute of Zoology, Department of Animal Ecology and Conservation, Universität Hamburg, Hamburg, 20146, Germany
| | - Anne D. Yoder
- Department of Biology, Duke University, Durham, NC 27708, USA
| |
Collapse
|
29
|
Ellerstrand SJ, Choudhury S, Svensson K, Andersson MN, Kirkeby C, Powell D, Schlyter F, Jönsson AM, Brydegaard M, Hansson B, Runemark A. Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden. Ecol Evol 2022; 12:e9078. [PMID: 35822111 PMCID: PMC9260063 DOI: 10.1002/ece3.9078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 01/05/2023] Open
Abstract
The Eurasian spruce bark beetle, Ips typographus, is a major pest, capable of killing spruce forests during large population outbreaks. Recorded dispersal distances of individual beetles are typically within hundreds of meters or a few kilometers. However, the connectivity between populations at larger distances and longer time spans and how this is affected by the habitat is less studied, despite its importance for understanding at which distances local outbreaks may spread. Previous population genetic studies in I. typographus typically used low resolution markers. Here, we use genome-wide data to assess population structure and connectivity of I. typographus in Sweden. We used 152 individuals from 19 population samples, distributed over 830 km from Strömsund (63° 46' 8″ N) in the north to Nyteboda (56° 8' 50″ N) in the south, to capture processes at a large regional scale, and a transect sampling design adjacent to a recent outbreak to capture processes at a smaller scale (76 km). Using restriction site-associated DNA sequencing (RADseq) markers capturing 1409-1997 SNPs throughout the genome, we document a weak genetic structure over the large scale, potentially indicative of high connectivity with extensive gene flow. No differentiation was detected at the smaller scale. We find indications of isolation-by-distance both for relative (F ST) and absolute divergence (Dxy). The two northernmost populations are most differentiated from the remaining populations, and diverge in parallel to the southern populations for a set of outlier loci. In conclusion, the population structure of I. typographus in Sweden is weak, suggesting a high capacity to disperse and establish outbreak populations in new territories.
Collapse
Affiliation(s)
| | - Shruti Choudhury
- Department of BiologyLund UniversityLundSweden
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science CentreSwedish University of Agricultural SciencesUmeåSweden
| | | | | | - Carsten Kirkeby
- Excellent Team for Mitigation, Faculty of Forestry & Wood SciencesCzech University of Life Sciences PragueSuchdolCzech Republic
| | - Daniel Powell
- Animal Welfare and Disease ControlCopenhagen UniversityFrederiksberg CDenmark
| | - Fredrik Schlyter
- Global Change Ecology Research GroupUniversity of the Sunshine CoastSippy DownsQueenslandAustralia
- Department of Plant Protection BiologySwedish University of Agricultural SciencesLommaSweden
| | - Anna Maria Jönsson
- Department of Physical Geography and Ecosystem ScienceLund UniversityLundSweden
| | | | | | | |
Collapse
|
30
|
Virrueta Herrera S, Johnson KP, Sweet AD, Ylinen E, Kunnasranta M, Nyman T. High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal. Mol Ecol 2022; 31:4593-4606. [PMID: 35726520 PMCID: PMC9544963 DOI: 10.1111/mec.16569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 02/02/2023]
Abstract
Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis), which is endemic to Lake Saimaa in Finland, and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.
Collapse
Affiliation(s)
- Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, Illinois, USA.,Program in Ecology, Evolution, and Conservation, University of Illinois, Urbana, Illinois, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, Illinois, USA
| | - Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
| | - Eeva Ylinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland, Joensuu, Finland
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| |
Collapse
|
31
|
Ruocco M, Jahnke M, Silva J, Procaccini G, Dattolo E. 2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation. Front Genet 2022; 13:866758. [PMID: 35651946 PMCID: PMC9149362 DOI: 10.3389/fgene.2022.866758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.
Collapse
Affiliation(s)
| | - Marlene Jahnke
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - João Silva
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
| | | | | |
Collapse
|
32
|
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
|
33
|
White NFD, Mennell H, Power G, Edwards D, Chrimes L, Woolaver L, Velosoa J, Randriamahita, Mozavelo R, Rafeliarisoa TH, Kuchling G, Lopez J, Bekarany E, Charles N, Young R, Lewis R, Bruford MW, Orozco-terWengel P. A population genetic analysis of the Critically Endangered Madagascar big-headed turtle, Erymnochelys madagascariensis across captive and wild populations. Sci Rep 2022; 12:8740. [PMID: 35610259 PMCID: PMC9130144 DOI: 10.1038/s41598-022-12422-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/14/2022] [Indexed: 12/31/2022] Open
Abstract
Erymnochelys madagascariensis is a Critically Endangered turtle endemic to Madagascar. Anthropogenic activity has depleted the wild population by 70% in the last century, and effective conservation management is essential to ensuring its persistence. Captive breeding was implemented to augment depleted populations in the southern part of Ankarafantsika National Park (ANP), when no genetic data were available for E. madagascariensis. It is unknown how much of the natural population's diversity is encapsulated in captivity. We used eight microsatellite loci and fragments of two mitochondrial genes to identify the genetic structure of E. madagascariensis in the wild. Captive bred turtles were compared with wild populations in order to assess the representativeness of this ex situ conservation strategy for ANP. Six microsatellite clusters, ten cytochrome b, and nine COI haplotypes were identified across wild populations, with high genetic divergence found between populations in two groups of watersheds. Captive bred individuals represent three out of six sampled microsatellite clusters found in the wild and just one mitochondrial haplotype, possibly due to genetic drift. To improve genetic representation, the strategy of frequent interchange between captive and wild breeders within ANP should be revitalised and, as originally planned, hatchlings or juveniles should not be released beyond ANP.
Collapse
Affiliation(s)
- Nina F D White
- School of Biosciences, Cardiff University, Cardiff, UK
- Institute of Zoology, Zoological Society of London, London, UK
| | - Holly Mennell
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Georgia Power
- School of Biosciences, Cardiff University, Cardiff, UK
| | | | - Luke Chrimes
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Lance Woolaver
- Durrell Wildlife Conservation Trust, Les Augrès Manor, UK
- Wildlife Preservation Canada, Guelph, Canada
| | | | - Randriamahita
- Durrell Wildlife Conservation Trust, Les Augrès Manor, UK
| | | | - Tsilavo Hasina Rafeliarisoa
- Durrell Wildlife Conservation Trust, Les Augrès Manor, UK
- Biodiversity Conservation Madagascar, Antananarivo, Madagascar
| | - Gerald Kuchling
- School of Biological Sciences, University of Western Australia, Perth, Australia
| | - Javier Lopez
- Animal Health Department, Chester Zoo, Cheshire, UK
| | | | | | - Richard Young
- Durrell Wildlife Conservation Trust, Les Augrès Manor, UK
| | - Richard Lewis
- Durrell Wildlife Conservation Trust, Les Augrès Manor, UK
| | | | | |
Collapse
|
34
|
Mounger JM, van Riemsdijk I, Boquete MT, Wagemaker CAM, Fatma S, Robertson MH, Voors SA, Oberstaller J, Gawehns F, Hanley TC, Grosse I, Verhoeven KJF, Sotka EE, Gehring CA, Hughes AR, Lewis DB, Schmid MW, Richards CL. Genetic and Epigenetic Differentiation Across Intertidal Gradients in the Foundation Plant Spartina alterniflora. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.868826] [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
Ecological genomics approaches have informed us about the structure of genetic diversity in natural populations that might underlie patterns in trait variation. However, we still know surprisingly little about the mechanisms that permit organisms to adapt to variable environmental conditions. The salt marsh foundation plant Spartina alterniflora exhibits a dramatic range in phenotype that is associated with a pronounced intertidal environmental gradient across a narrow spatial scale. Both genetic and non-genetic molecular mechanisms might underlie this phenotypic variation. To investigate both, we used epigenotyping-by-sequencing (epiGBS) to evaluate the make-up of natural populations across the intertidal environmental gradient. Based on recent findings, we expected that both DNA sequence and DNA methylation diversity would be explained by source population and habitat within populations. However, we predicted that epigenetic variation might be more strongly associated with habitat since similar epigenetic modifications could be rapidly elicited across different genetic backgrounds by similar environmental conditions. Overall, with PERMANOVA we found that population of origin explained a significant amount of the genetic (8.6%) and epigenetic (3.2%) variance. In addition, we found that a small but significant amount of genetic and epigenetic variance (<1%) was explained by habitat within populations. The interaction of population and habitat explained an additional 2.9% of the genetic variance and 1.4% of the epigenetic variance. By examining genetic and epigenetic variation within the same fragments (variation in close-cis), we found that population explained epigenetic variation in 9.2% of 8,960 tested loci, even after accounting for differences in the DNA sequence of the fragment. Habitat alone explained very little (<0.1%) of the variation in these close-cis comparisons, but the interaction of population and habitat explained 2.1% of the epigenetic variation in these loci. Using multiple matrix regression with randomization (MMRR) we found that phenotypic differences in natural populations were correlated with epigenetic and environmental differences even when accounting for genetic differences. Our results support the contention that sequence variation explains most of the variation in DNA methylation, but we have provided evidence that DNA methylation distinctly contributes to plant responses in natural populations.
Collapse
|
35
|
Labiros DA, Catalig AMP, Ymbong RRJ, Sakuntabhai A, Lluisma AO, Edillo FE. Novel and Broadly Applicable Microsatellite Markers in Identified Chromosomes of the Philippine Dengue Mosquitoes, Aedes aegypti (Diptera: Culicidae). JOURNAL OF MEDICAL ENTOMOLOGY 2022; 59:545-553. [PMID: 35134978 PMCID: PMC8924974 DOI: 10.1093/jme/tjab194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 05/12/2023]
Abstract
Dengue is the leading arboviral infection in the Philippines. Its endemicity in the country is due to the presence of its primary mosquito vector, Aedes aegypti (L.). This species has limited microsatellite markers. This study characterized microsatellite markers screened in silico from intergenic regions of the updated reference genome of Ae. aegypti from Liverpool, U.K. Criteria for good markers are: polymorphic, inherited in a Mendelian codominant manner, no null alleles, selectively neutral, randomly associated, and broadly applicable across different regions. Genotypes were scored using ABI Peak Scanner and were screened for the presence of null alleles. Hardy-Weinberg equilibrium, linkage disequilibrium, and robustness of the markers were determined by GENEPOP using Ae. aegypti samples from selected highland and lowland sites (n = 30 each) in the Philippines and outgroups (Thailand and Vietnam). Mendelian codominant inheritance was examined using F1 offspring of Ae. aegypti family (n = 30 each) derived from samples collected from Cebu city highlands and Maramag, Bukidnon. From the 63 randomly selected markers, nine were polymorphic. Two markers (Aaeg1-3D of chromosome 1 and Aaeg3-4C of chromosome 3) satisfied all criteria, hence, are good broadly useful microsatellite markers. Two other markers (Aaeg2-2E of chromosome 2 and Aaeg3-2A of chromosome 3) met all criteria but deviated from Mendelian codominant inheritance. These new markers of the Philippine Ae. aegypti with their chromosomal locations relative to the other published markers are presented, and will ultimately be useful in a variety of population genetic studies of Ae. aegypti to protect the public health.
Collapse
Affiliation(s)
- Dinesse A Labiros
- Department of Biology, University of San Carlos—Talamban Campus, Talamban, Cebu city, 6000, Philippines
| | - Antonio Mari P Catalig
- Marine Science Institute, University of the Philippines Diliman, Diliman, Quezon city, Philippines
| | - Rhoniel Ryan J Ymbong
- Department of Biology, University of San Carlos—Talamban Campus, Talamban, Cebu city, 6000, Philippines
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, Rue de Docteur Roux, 75015, Paris, France
- Centre National de la Recherche Scientifique, 75015, Paris, France
| | - Arturo O Lluisma
- Marine Science Institute, University of the Philippines Diliman, Diliman, Quezon city, Philippines
| | - Frances E Edillo
- Department of Biology, University of San Carlos—Talamban Campus, Talamban, Cebu city, 6000, Philippines
- Corresponding author, e-mail:
| |
Collapse
|
36
|
Genome-wide SSR markers in bottle gourd: development, characterization, utilization in assessment of genetic diversity of National Genebank of India and synteny with other related cucurbits. J Appl Genet 2022; 63:237-263. [PMID: 35106708 DOI: 10.1007/s13353-022-00684-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/06/2022] [Accepted: 01/15/2022] [Indexed: 10/19/2022]
Abstract
Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, flower, and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance, informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding genetic improvement, cultivar identification, and phylogenetic studies. Next-generation sequencing has revolutionized the approaches for discovery, assessment, and validation of molecular markers. We conducted a genome-wide analysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data obtained from NCBI. By performing in silico mining of microsatellite repeat motifs, we developed 45,066 perfect SSR markers. Of which 207 markers were successfully validated and 120 (57.97%) polymorphic primer pairs were utilized for an in-depth genetic diversity and population structure analysis of 96 accessions from the National Genebank of India. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%), further 21.03%, 9.6%, and 4.3% of di-, penta-, and hexa-nucleotide repeats in the bottle gourd genome, respectively. Synteny of SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber (93.2%), 12 chromosomes of melon (87.4%), and 11 of watermelon (90.8%). The generated SSR markers provide a valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, gene discovery, and for breeding in bottle gourd and other cucurbits species. KEY MESSAGE: Development of 45,066 perfect microsatellite markers as a valuable tool for marker assisted selection (MAS) in plant breeding.
Collapse
|
37
|
Conservation genomics of an Australian cycad Cycas calcicola, and the Absence of Key Genotypes in Botanic Gardens. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01428-8] [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]
|
38
|
Bowles E, Jeon HB, Marin K, MacLeod P, Fraser DJ. Freshwater fisheries monitoring in northern ecosystems using Indigenous ecological knowledge, genomics, and life history: Insights for community decision-making. Facets (Ott) 2022. [DOI: 10.1139/facets-2021-0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Natural resources in northern regions are often data-limited because they are difficult and expensive to access. Indigenous ecological knowledge (IEK) can provide information similar to, different from, or complementary to Western scientific data (WSD). We evaluated the general hypothesis that congruence in outcomes of IEK and WSD for population monitoring parameters is determined by temporal and spatial scale of the knowledge type. Parameters included population structure, degree of philopatry, morphological variation (and conservation status for one species), and genomics was a key Western scientific method. We evaluated this hypothesis in three subsistence and recreational fisheries (walleye, lake trout, and northern pike) in Mistassini Lake, Quebec, Canada. Concordance of outcomes was varied. IEK provided richer information on the biology, distribution, and morphological variation observable with the eyes. However, IEK cannot “see” into the genome, and WSD identified population structure and history more precisely than IEK. Both knowledge types could “see” change in populations, and the nature of what was seen both converged and was complementary. Determining when IEK and WSD are complementary or reach common conclusions may allow Indigenous communities to use both together, or one knowledge type over another when either is more desired, appropriate, or time- or cost-efficient to adopt.
Collapse
Affiliation(s)
- Ella Bowles
- Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
- Current affiliation: Canadian Wildlife Service, 351 Boulevard St. Joseph, Gatineau, QC J8Y 3Z5, Canada
| | - Hyung-Bae Jeon
- Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
| | - Kia Marin
- Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
| | - Pamela MacLeod
- Cree Nation of Mistissini, 187 Main Street, Mistissini, QC G0W 1C0, Canada
| | - Dylan J. Fraser
- Concordia University, 7141 Sherbrooke St. West, Montreal, QC H4B 1R6, Canada
| |
Collapse
|
39
|
Luiken JM, Gamble T, Berendzen PB. Comparative riverscape genomics of the rainbow darter ( Etheostoma caeruleum) in glaciated and unglaciated environments. Ecol Evol 2021; 11:18305-18318. [PMID: 35003674 PMCID: PMC8717317 DOI: 10.1002/ece3.8422] [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: 08/03/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 11/11/2022] Open
Abstract
Periodic glaciation during the Quaternary period shaped the contemporary riverscape and distribution of freshwater fishes in the Mississippi River drainage of central North America. The rainbow darter (Etheostoma caeruleum) is a member of this ichthyofauna and has a disjunct distribution in glaciated and unglaciated environments west of the Mississippi River. Based on glacial history of the region, there are different expectations on the observed spatial genetic structure of populations in these environments. The aim of this study was to utilize genome-wide SNP data to compare the population genomic structure of the rainbow darter in river networks with disparate glacial histories; the Volga River in the glaciated upper Mississippi River basin and the Meramec River in the unglaciated Ozark Plateau. Individuals were sampled from localities within each river system at distances dictated by the organismal life history and habitat preferences. Riverscape analyses were performed on three datasets: total combined localities of both rivers and one for each river independently. The results revealed a lasting influence of historic glaciation on the population genomic structure of rainbow darter populations. There was evidence of population expansion into the glaciated northern region following glacial retreat. The population genetic signature within the Volga River did not fit expectations of the stream hierarchy model, but revealed a pattern of repeated colonization and extirpation due to cyclic glaciation. The population within the unglaciated Meramec River adhered to the stream hierarchy model, with a directional order of genetic diversity based on the life history and habitat preferences of the species. These results demonstrate the importance of considering the geologic and climatic history of a region as well as the life history of an organism when interpreting spatial genetic patterns.
Collapse
Affiliation(s)
- Jon M. Luiken
- Department of BiologyUniversity of Northern IowaCedar FallsIowaUSA
| | - Tony Gamble
- Department of Biological SciencesMarquette UniversityMilwaukeeWisconsinUSA
| | | |
Collapse
|
40
|
Genome-wide assessment of population structure in Florida’s coastal seaside sparrows. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01411-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
41
|
Kovach JD, Long JC, Barbosa LM, Moura ARSS, Silva LK, Reis MG, Blanton RE. A Schistosoma mansoni tri- and tetramer microsatellite catalog for genetic population diversity and differentiation. Int J Parasitol 2021; 51:1007-1014. [PMID: 34022195 DOI: 10.1016/j.ijpara.2021.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 02/08/2023]
Abstract
All Schistosoma mansoni tri- and tetranucleotide repeat microsatellites published as of December 2018 were identified. All 52 were evaluated for autosomal location, strength of amplification, scorability and behavior as single-copy loci by polyacrylamide and capillary gel electrophoresis. Of these, 27 were unique, autosomal, polymorphic, easily scored and single copy as assessed on pooled adult worm DNA from two different continental origins and adult worm clones. These microsatellites were distributed across all seven autosomal chromosomes. On laboratory strains their heterozygosity ranged from 0.22 to 0.77. Individual markers had 5-13 alleles, allelic richness of 2-10 and an effective allele number of 1.3-8.14. Those infected by Schistosoma mansoni carry many genetically distinct, sexually reproducing parasites, therefore, for an individual infection the complete allele frequency profile of their progeny consists of a pool of DNA from multiple diploid eggs. Using a set of 25 microsatellites, we calculated allele frequency profiles of eggs in fecal samples from people in two Brazilian communities separated by 6 km: Jenipapo (n = 80) and Volta do Rio (n = 38). There were no a priori characteristics that could predict the performance of markers in natural infections based on their performance with laboratory strains. Increasing marker number did not change accuracy for differentiation and diversity but did improve precision. Our data suggest that using a random set of 10-20 microsatellites appears to result in values that exhibit low standard deviations for diversity and differentiation indices. All identified microsatellites as well as PCR conditions, allele size, primer sequences and references for all tri- and tetramer microsatellites markers presented in this work are available at: https://sites.google.com/case.edu/cwru-and-fiocruz-wdrc/home.
Collapse
Affiliation(s)
- Jeffrey D Kovach
- Center for Global Health and Diseases, Case Western Reserve University, Biomedical Research Building, 2109 Adelbert Rd., Cleveland, OH 44106, USA
| | - Jeffrey C Long
- University of New Mexico, Department of Anthropology, Albuquerque, 1 University of New Mexico, NM 87131, USA
| | - Lúcio M Barbosa
- Bahiana School of Medicine and Public Health, Av. Silveira Martins, n° 3386, Salvador, Bahia 41150-100, Brazil; Gonçalo Moniz Research Centre, Oswaldo Cruz Foundation, Rua Waldemar Falcão, 121 Brotas, Salvador, Bahia 40296-710, Brazil
| | - Ana Rafaela Silva Simões Moura
- Gonçalo Moniz Research Centre, Oswaldo Cruz Foundation, Rua Waldemar Falcão, 121 Brotas, Salvador, Bahia 40296-710, Brazil
| | - Luciano K Silva
- Gonçalo Moniz Research Centre, Oswaldo Cruz Foundation, Rua Waldemar Falcão, 121 Brotas, Salvador, Bahia 40296-710, Brazil
| | - Mitermayer G Reis
- Gonçalo Moniz Research Centre, Oswaldo Cruz Foundation, Rua Waldemar Falcão, 121 Brotas, Salvador, Bahia 40296-710, Brazil; School of Medicine, Federal University of Bahia, Salvador, Bahia, Brazil; Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Ronald E Blanton
- Department of Tropical Medicine, Tulane School of Public Health and Tropical Medicine, Tidewater Building, 1440 Canal Street, New Orleans, LA 70112, USA.
| |
Collapse
|
42
|
Bilska-Zając E, Rosenthal B, Thompson P. Trich-tracker - a practical tool to trace Trichinella spiralis transmission based on rapid, cost-effective sampling of genome-wide genetic variation. Int J Parasitol 2021; 52:145-155. [PMID: 34543631 DOI: 10.1016/j.ijpara.2021.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/12/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022]
Abstract
Molecular epidemiology using traditional sequencing has been notoriously difficult in inbred parasites due to a lack of genetic variation available for discriminating among parasites. Next generation sequencing techniques offer a solution to this problem by increasing the number of loci that can be sequenced. Here, we introduce Trich-tracker, a tool that makes efficient use of diagnostic variation distributed throughout the genome of Trichinella spiralis to more rapidly, and conclusively, resolve connections and distinctions among focal outbreaks of T. spiralis. In particular, we rapidly characterised genetic variation among a sample of parasites from Polish farms and wildlife, sampling genomic variation using double digest restriction site-associated DNA sequencing (ddRADseq). Approximately 400,000 bases of sequence were generated from each sample and shown to be distributed across the genome with single nucleotide polymorphisms occurring at a frequency of approximately one base in 10,000. Both phylogenetic and Bayesian clustering analyses indicated that ddRADseq genotypes formed distinct clusters for specific outbreaks and were quite distinct from wild boar samples. Two of the investigated outbreaks were more similar to each other than to other outbreak samples, suggesting a link between these outbreaks. Hence, the Trich-tracker procedure identified informative genomic variation which afforded unprecedented epidemiological resolution. Trich-tracker is very flexible tool, quickly and inexpensively mining genomes of even highly inbred populations of T. spiralis to support outbreak investigations. The simplicity of the entire procedure, and time and cost effectiveness of Trich-tracker support its practical application in ongoing Trichinella outbreaks. The discriminating power of this tool is tunable and scalable, allowing application in a variety of epidemiological contexts, and is easily adapted to other parasite systems.
Collapse
Affiliation(s)
- Ewa Bilska-Zając
- National Veterinary Research Institute in Puławy, Department of Parasitology and Invasive Diseases, Aleja Partyzantów 56, 24-100 Puławy, Poland
| | - Benjamin Rosenthal
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, BARC-East Building 1040, 10300 Baltimore Avenue, 10705 Beltsville, MD, USA
| | - Peter Thompson
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, BARC-East Building 1040, 10300 Baltimore Avenue, 10705 Beltsville, MD, USA
| |
Collapse
|
43
|
Gariepy TD, Musolin DL, Konjević A, Karpun NN, Zakharchenko VY, Zhuravleva EN, Tavella L, Bruin A, Haye T. Diversity and distribution of cytochrome oxidase I (COI) haplotypes of the brown marmorated stink bug, Halyomorpha halys Stål (Hemiptera, Pentatomidae), along the eastern front of its invasive range in Eurasia. NEOBIOTA 2021. [DOI: 10.3897/neobiota.68.68915] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The arrival, establishment and pest status of Halyomorpha halys in Europe and non-native countries in Asia have been well-documented, with thorough characterisation of the genetic diversity and occurrence of cytochrome oxidase I (COI) haplotypes in Switzerland, France, Hungary, Italy and Greece. However, a number of gaps exist in terms of the characterisation of the haplotype diversity and occurrence of H. halys along the invasion front that covers eastern Europe, western and central Asia. To contribute towards filling this gap, the COI haplotype diversity and distribution were investigated for H. halys collected in Serbia, Ukraine, Russia, Georgia and Kazakhstan. A total of 646 specimens were analysed and five haplotypes were found (H1, H3, H8, H33 and H80). Haplotype H1 was present in all five countries investigated and was the only haplotype detected amongst > 500 specimens collected from Ukraine, Russia and Georgia. H1 (82%) was the dominant haplotype found in Kazakhstan, alongside H3 (18%). In contrast to the low or no diversity observed in these four countries, Serbia had higher haplotype diversity and was represented by five haplotypes. Although H3 was dominant (47%) in Serbia, H1 was also prevalent (40%); the remaining haplotypes (H8, H33 and H80) were minor contributors (1–11%) to the haplotype composition. The results are discussed in context with other known populations in neighbouring countries and patterns of haplotype diversity indicate the movement of successful invasive populations in Europe to generate secondary invasions along the eastern front of the invasion in Eurasia. Possible scenarios regarding the spread of particular haplotypes in these regions are discussed, along with suggestions for future research to fill existing gaps.
Collapse
|
44
|
Bilska-Zając E, Thompson P, Rosenthal B, Różycki M, Cencek T. Infection, genetics, and evolution of Trichinella: Historical insights and applications to molecular epidemiology. INFECTION GENETICS AND EVOLUTION 2021; 95:105080. [PMID: 34509647 DOI: 10.1016/j.meegid.2021.105080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 11/26/2022]
Abstract
Genetic variation in pathogen populations provides the means to answer questions in disease ecology and transmission, illuminating interactions between genetic traits, environmental exposures, and disease. Such studies elucidate the phylogeny, evolution, transmission and pathogenesis of viruses, bacteria and parasites. Here, we review how such studies have fostered understanding of the biology and epidemiology of zoonotic nematode parasites in the genus Trichinella spp., which impose considerable economic and health burdens by infecting wildlife, livestock, and people. To use such data to define ongoing chains of local transmission and source traceback, researchers first must understand the extent and distribution of genetic variation resident in regional parasite populations. Thus, genetic variability illuminates a population's past as well as its present. Here we review how such data have helped define population dynamics of Trichinella spp. in wild and domesticated hosts, creating opportunities to harness genetic variation in the quest to prevent, track, and contain future outbreaks.
Collapse
Affiliation(s)
| | - Peter Thompson
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, Beltsville, MD, USA
| | - Benjamin Rosenthal
- USDA-Agricultural Research Service, Animal Parasitic Diseases Lab, Beltsville, MD, USA
| | | | - Tomasz Cencek
- National Veterinary Research Institute in Puławy, Poland
| |
Collapse
|
45
|
Szatmári L, Cserkész T, Laczkó L, Lanszki J, Pertoldi C, Abramov AV, Elmeros M, Ottlecz B, Hegyeli Z, Sramkó G. A comparison of microsatellites and genome-wide SNPs for the detection of admixture brings the first molecular evidence for hybridization between Mustela eversmanii and M. putorius (Mustelidae, Carnivora). Evol Appl 2021; 14:2286-2304. [PMID: 34603499 PMCID: PMC8477604 DOI: 10.1111/eva.13291] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 07/28/2021] [Accepted: 08/02/2021] [Indexed: 11/30/2022] Open
Abstract
Introgressive hybridization can pose a serious threat to endangered species which have an overlapping distribution such as in the case of two polecat species, Mustela eversmanii and M. putorius, in Europe. The population size of steppe polecat is known to continuously shrink, whereas its sister species, the European polecat, is still somehow widespread. In this study, we perform an analysis using microsatellite (SSR) and genomic (SNP) data sets to identify natural hybrids between polecats. Four populations were genotyped for eight polymorphic SSR loci, and thousands of unlinked SNPs were generated using a reduced-representation sequencing approach, RADseq, to characterize the genetic make-up of allopatric populations and to identify hybrids in the sympatric area. We applied standard population genetic analyses to characterize the populations based on their SSR allelic frequency. Only a single sample out of 48 sympatric samples showed exact intermediacy that we identified as an F1 hybrid. Additionally, one specimen was indicated in the genomic data sets as backcrossed. Other backcrosses, indicated by SSRs, were not validated by SNPs, which highlights the higher efficacy of the genomic method to identify backcrossed individuals. The low frequency of hybridization suggests that the difference in habitat preference of the two species may act as a barrier to admixture. Therefore, it is apparently unlikely that polecat populations are threatened by significant introgression. The two species showed a clear genetic differentiation using both techniques. We found higher genetic diversity values in the sympatric steppe polecat population than in the other studies on polecat populations. Although M. putorius is a hunted species in most countries, genetic diversity values indicate worse conditions in Europe than in the protected sibling species M. eversmanii. Suspending hunting and providing protected status of the former seems to be reasonable and timely.
Collapse
Affiliation(s)
- Lajos Szatmári
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
| | - Tamás Cserkész
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
- Bükk Mammalogical Society Eger Hungary
| | - Levente Laczkó
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
| | - József Lanszki
- Carnivore Ecology Research Group Szent István University, Kaposvár Campus Kaposvár Hungary
| | - Cino Pertoldi
- Department of Chemistry and Bioscience Aalborg University Aalborg Øst Denmark
- Aalborg Zoo Aalborg Denmark
| | - Alexei V Abramov
- Zoological Institute Russian Academy of Sciences Saint Petersburg Russia
| | - Morten Elmeros
- Department of Bioscience - Wildlife Ecology Aarhus University Rønde Denmark
| | | | - Zsolt Hegyeli
- Milvus Group Bird and Nature Protection Association Tîrgu Mureș Romania
| | - Gábor Sramkó
- MTA-DE "Lendület" Evolutionary Phylogenomics Research Group Debrecen Hungary
- Department of Botany University of Debrecen Debrecen Hungary
| |
Collapse
|
46
|
Genetic Diversity and Population Differentiation of Kashgarian Loach ( Triplophysa yarkandensis) in Xinjiang Tarim River Basin. BIOLOGY 2021; 10:biology10080734. [PMID: 34439966 PMCID: PMC8389669 DOI: 10.3390/biology10080734] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary The distribution of Kashgarian loach (Triplophysa yarkandensis) is limited to the Tarim River basin, which is the largest inland river in China. However, the population size of T. yarkandensis has been diminishing, and it is critically endangered in the Tarim River basin due to the gradual depletion of water resources, together with alien invasion and agricultural cultivation in Tarim River. In this study, we adopted the RAD-seq method to investigate the population genetics of T. yarkandensis, and a high degree of genetic variations and significant genetic differentiation was detected among T. yarkandensis populations in the Tarim River basin. The obtained data contribute to understanding the genetic status of T. yarkandensis, and help to provide the scientific management strategies and direct future monitoring and utilization of the genetic resource in Xinjiang region. Abstract The distribution of Triplophysa yarkandensis is restricted to Xinjiang’s Tarim River basin. We collected 119 T. yarkandensis samples from nine geographic populations in the Tarim River basin and utilized the RAD-seq method for SNP genotyping. In this study, a total of 164.81 Gb bases were generated with the Illumina platform, and 129,873 candidate SNPs were obtained with the Stacks pipeline for population genetic analyses. High levels of genetic diversity were detected among nine populations. The AMOVA results showed that the majority of genetic variations originated from among populations (FST = 0.67), and the pairwise FST values ranged from 0.4579 to 0.8736, indicating high levels of genetic differentiation among these populations. The discriminate analysis of principal components (DAPCs) and neighbor joining (NJ) tree revealed that the nine populations could be separated into two clusters (i.e., south and north populations), and modest genetic differentiation between south and north populations was observed, while the individuals from several populations were not clustered together by geographical location. The evidence of two genetic boundaries between south and north populations (except TTM) was supported by barrier analysis. The Bayesian skyline plotting indicated that T. yarkandensis populations in the Tarim River basin had not experienced genetic bottlenecks, and the effective population size remained stable. This study first clarified the genetic diversity and differentiation of T. yarkandensis populations in the Tarim River basin, and it provided valuable molecular data for conservation and management of natural populations.
Collapse
|
47
|
How well do genetic markers inform about responses to intraspecific admixture? A comparative analysis of microsatellites and RADseq. BMC Genom Data 2021; 22:22. [PMID: 34182923 PMCID: PMC8237422 DOI: 10.1186/s12863-021-00974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/20/2021] [Indexed: 11/21/2022] Open
Abstract
Background Fitness consequences of intraspecific genetic admixture can vary from positive to negative depending on the genetic composition of the populations and environmental conditions. Because admixture has potential to influence the success of management and conservation efforts, genetic similarity has been suggested to be used as a proxy to predict the outcome. Studies utilizing microsatellites (a neutral marker) to investigate associations between genetic distance and admixture effects show conflicting results. Marker types that yield information on genome-wide and/or adaptive variation might be more useful for predicting responses to inter-population hybridization. In this study we utilized published data for three populations of pike (Esox lucius) to investigate associations between offspring performance (hatching success) and parental genetic similarity in experimentally purebred and admixed families, based on neutral (microsatellites), genome-wide neutral (RADseq SNPs), and adaptive (SNPs under selection) markers. Results Estimated similarity varied among the markers, likely reflecting differences in their inherent properties, but was consistently higher in purebred than admixed families. A significant interaction between marker type and admixture treatment reflected that neutral SNPs yielded higher estimates than adaptive SNPs for admixed families whereas no difference was found for purebred families, which indicates that neutral similarity was not reflective of adaptive similarity. When all samples were pooled, no association between similarity and performance was found for any marker. For microsatellites, similarity was positively correlated with hatching success in purebred families, whereas no association was found in admixed families; however, the direction of the effect differed between the population combinations. Conclusions The results strengthen the notion that, as of today, there is no proxy that can reliably predicted the outcome of admixture. This emphasizes the need of further studies to advance knowledge that can shed light on how to safeguard against negative consequences of admixture, and thereby inform management and promote conservation of biological diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-00974-3.
Collapse
|
48
|
Taylor LU, Benavides E, Simmons JW, Near TJ. Genomic and phenotypic divergence informs translocation strategies for an endangered freshwater fish. Mol Ecol 2021; 30:3394-3407. [PMID: 33960044 DOI: 10.1111/mec.15947] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/28/2021] [Accepted: 04/19/2021] [Indexed: 12/31/2022]
Abstract
Translocation, the movement of organisms for conservation purposes, can result in unintended introgression if genetic material flows between populations in new ways. The Bluemask Darter Etheostoma akatulo is a federally endangered species of freshwater fish inhabiting the Caney Fork River system and three of its tributaries (Collins River, Rocky River, and Cane Creek) in Tennessee. The current conservation strategy for Bluemask Darters involves translocating the progeny of broodstock from the Collins River (in the west) to the Calfkiller River (in the east) where the species had been extirpated. In this study, we use ddRAD sequence data from across the extant range to assess this translocation strategy in light of population structure, phylogeny, and demography. We also include museum specimen data to assess morphological variation among extant and extirpated populations. Our analyses reveal substantial genetic and phenotypic disparities between a western population in the Collins River and an eastern population encompassing the Rocky River, Cane Creek, and upper Caney Fork, the two of which shared common ancestry more than 100,000 years ago. Furthermore, morphological analyses classify 12 of 13 Calfkiller River specimens with phenotypes consistent with the eastern population. These results suggest that current translocations perturb the evolutionary boundaries between two delimited populations. Instead, we suggest that repopulating the Calfkiller River using juveniles from the Rocky River could balance conflicting signatures of demography, diversity, and divergence. Beyond conservation, the microgeographic structure of Bluemask Darter populations adds another puzzle to the phylogeography of the hyperdiverse freshwater fishes in eastern North America.
Collapse
Affiliation(s)
- Liam U Taylor
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Edgar Benavides
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | | | - Thomas J Near
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.,Yale Peabody Museum of Natural History, New Haven, CT, USA
| |
Collapse
|
49
|
Luan P, Huo T, Ma B, Song D, Zhang X, Hu G. Genomic inbreeding and population structure of northern pike ( Esox lucius) in Xinjiang, China. Ecol Evol 2021; 11:5657-5668. [PMID: 34026037 PMCID: PMC8131772 DOI: 10.1002/ece3.7469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/28/2021] [Accepted: 03/03/2021] [Indexed: 11/21/2022] Open
Abstract
Northern pike (Esox lucius) was widely distributed in the high latitudes of the northern hemisphere. In China, northern pike was originally distributed only in the upper reaches of the Irtysh River in Xinjiang and has appeared in many water bodies outside the Irtysh River Basin in Northern Xinjiang. A total of four populations were collected from north to south in Xinjiang, including Irtysh River (RIR), Ulungu Lake (LUL), a small lake nearby Ulungu River (LJD), and Bosten Lake (LBO). We estimated population genomic parameters, performed gene flow analysis, and estimated the effective population size of each population. The proportion of individuals with high inbreeding coefficient (F ≥ 0.0625) accounted for 36.4% (44/121) of all sequenced individuals, approximately 4.5% (1/22) in LUL, 25.9% (7/27) in LBO, 42.9% (18/42) in RIR, and 60% (18/30) in LJD. RIR had the highest mean of genomic relatedness (coancestry coefficient = 0.025 ± 0.040, IBD = 0.036 ± 0.078). Gene flow results showed that the population spreading was from RIR into two branches, one was LBO, and the other continued to split into LUL and LJD, and migration signal from LBO to LUL was detected. Our results suggested that the extinction risk of northern pike was very low in Xinjiang of China, and the controlled capture fishery of northern pike could be developed reasonably.
Collapse
Affiliation(s)
- Peixian Luan
- Heilongjiang River Fisheries Research InstituteChinese Academy of Fishery SciencesHarbinChina
- Key Laboratory of Freshwater Aquatic Biotechnology and BreedingMinistry of Agriculture and Rural AffairsHeilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesHarbinChina
| | - Tangbin Huo
- Heilongjiang River Fisheries Research InstituteChinese Academy of Fishery SciencesHarbinChina
- Key Laboratory of Freshwater Aquatic Biotechnology and BreedingMinistry of Agriculture and Rural AffairsHeilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesHarbinChina
| | - Bo Ma
- Heilongjiang River Fisheries Research InstituteChinese Academy of Fishery SciencesHarbinChina
- Key Laboratory of Freshwater Aquatic Biotechnology and BreedingMinistry of Agriculture and Rural AffairsHeilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesHarbinChina
| | - Dan Song
- Heilongjiang River Fisheries Research InstituteChinese Academy of Fishery SciencesHarbinChina
- Key Laboratory of Freshwater Aquatic Biotechnology and BreedingMinistry of Agriculture and Rural AffairsHeilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesHarbinChina
| | - Xiaofeng Zhang
- Heilongjiang River Fisheries Research InstituteChinese Academy of Fishery SciencesHarbinChina
- Key Laboratory of Freshwater Aquatic Biotechnology and BreedingMinistry of Agriculture and Rural AffairsHeilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesHarbinChina
| | - Guo Hu
- Heilongjiang River Fisheries Research InstituteChinese Academy of Fishery SciencesHarbinChina
- Key Laboratory of Freshwater Aquatic Biotechnology and BreedingMinistry of Agriculture and Rural AffairsHeilongjiang River Fisheries Research Institute, Chinese Academy of Fishery SciencesHarbinChina
| |
Collapse
|
50
|
Nam BH, Kim H, Seol D, Kim H, Noh ES, Kim EM, Noh JK, Kim YO, Park JY, Kwak W. Genotyping-by-Sequencing of the regional Pacific abalone (Haliotis discus) genomes reveals population structures and patterns of gene flow. PLoS One 2021; 16:e0247815. [PMID: 33826655 PMCID: PMC8026068 DOI: 10.1371/journal.pone.0247815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 02/12/2021] [Indexed: 01/05/2023] Open
Abstract
Continuous monitoring of the present genetic status is essential to preserve the genetic resource of wild populations. In this study, we sequenced regional Pacific abalone Haliotis discus samples from three different locations around the Korean peninsula to assess population structure, utilizing Genotyping-by-Sequencing (GBS) method. Using PstI enzyme for genome reduction, we demonstrated the resultant library represented the whole genome region with even spacing, and as a result 16,603 single nucleotide variants (SNVs) were produced. Genetic diversity and population structure were investigated using several methods, and a strong genetic heterogeneity was observed in the Korean abalone populations. Additionally, by comparison of the variant sets among population groups, we were able to discover 26 Korean abalone population-specific SNVs, potentially associated with phenotype differences. This is the first study demonstrating the feasibility of GBS for population genetic study on H. discus. Our results will provide valuable data for the genetic conservation and management of wild abalone populations in Korea and help future GBS studies on the marine mollusks.
Collapse
Affiliation(s)
- Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Hyaekang Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyeok Seol
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Genome, Inc, Seoul, Republic of Korea
| | - Eun Soo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Eun Mi Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jae Koo Noh
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Jung Youn Park
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Republic of Korea
| | - Woori Kwak
- Genome, Inc, Seoul, Republic of Korea
- * E-mail:
| |
Collapse
|