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Hirota SK, Yasumoto AA, Nitta K, Tagane M, Miki N, Suyama Y, Yahara T. Evolutionary history of Hemerocallis in Japan inferred from chloroplast and nuclear phylogenies and levels of interspecific gene flow. Mol Phylogenet Evol 2021; 164:107264. [PMID: 34273506 DOI: 10.1016/j.ympev.2021.107264] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 06/22/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
The perennial herb genus Hemerocallis (Asphodelaceae) shows four flowering types: diurnal half-day, diurnal one-day, nocturnal half-day, and nocturnal one-day flowering. These flowering types are corresponding to their main pollinators, and probably act as a primary mechanism of reproductive isolation. To examine how the four flowering types diverged, we reconstructed the phylogeny of the Japanese species of Hemerocallis using 1615 loci of nuclear genome-wide SNPs and 2078 bp sequences of four cpDNA regions. We also examined interspecific gene flows among taxa by an Isolation-with-Migration model and a population structure analysis. Our study revealed an inconsistency between chloroplast and nuclear genome phylogenies, which may have resulted from chloroplast capture. Each of the following five clusters is monophyletic and clearly separated on the nuclear genome-wide phylogenetic tree: (I) two nocturnal flowering species with lemon-yellow flowers, H. citrina (half-day flowering) and H. lilioasphodelus (one-day flowering); (II) a diurnal one-day flowering species with yellow-orange flowers, H. middendorffii; (III) a variety of a diurnal half-day flowering species with reddish orange flowers, H. fulva var. disticha; (IV) another variety of a diurnal half-day flowering species with reddish orange flowers, H. fulva var. aurantiaca, and a diurnal one-day flowering species with yellow-orange flowers, H. major; (V) a diurnal half-day flowering species with yellow-orange flowers, H. hakuunensis. The five clusters are consistent with traditional phenotype-based taxonomy (cluster I, cluster II, and clusters III-V correspond to Hemerocallis sect. Hemerocallis, Capitatae, and Fulvae, respectively). These findings could indicate that three flowering types (nocturnal flowering, diurnal one-day flowering, and diurnal half-day flowering) diverged in early evolutionary stages of Hemerocallis and subsequently a change from diurnal half-day flowering to diurnal one-day flowering occurred in a lineage of H. major. While genetic differentiation among the five clusters was well maintained, significant gene flow was detected between most pairs of taxa, suggesting that repeated hybridization played a role in the evolution of those taxa.
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Affiliation(s)
- Shun K Hirota
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Aza-yomogida, Naruko Onsen, Osaki, Miyagi 989-6711, Japan.
| | - Akiko A Yasumoto
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Kozue Nitta
- Department of Environmental Science, School of Life and Environmental Science, Azabu University, 1-17-71 Fuchinobe, Chuo, Sagamihara, Kanagawa 252-5201, Japan
| | - Misa Tagane
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Nozomu Miki
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
| | - Yoshihisa Suyama
- Field Science Center, Graduate School of Agricultural Science, Tohoku University, 232-3 Aza-yomogida, Naruko Onsen, Osaki, Miyagi 989-6711, Japan
| | - Tetsukazu Yahara
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Fukuoka 819-0395, Japan
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102
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Alves MF, Pinheiro F, Nunes CEP, Prosdocimi F, Sarzi DS, Furtado C, Mayer JLS. Reproductive development and genetic structure of the mycoheterotrophic orchid Pogoniopsis schenckii Cogn. BMC PLANT BIOLOGY 2021; 21:332. [PMID: 34253186 PMCID: PMC8276481 DOI: 10.1186/s12870-021-03118-y] [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: 04/08/2021] [Accepted: 06/29/2021] [Indexed: 05/17/2023]
Abstract
BACKGROUND Pogoniopsis schenckii Cogn. is a mycoheterotrophic orchid that can be used as a model to understand the influence of mycoheterotrophy at different stages of the reproductive cycle. We aimed to verify the presence of endophytic and epiphytic fungi at each stage of the reproductive process and investigated how the breeding system may relate to genetic structure and diversity of populations. In this study we performed anatomical and ultrastructural analyses of the reproductive organs, field tests to confirm the breeding system, and molecular analysis to assess genetic diversity and structure of populations. RESULTS During the development of the pollen grain, embryo sac and embryogenesis, no fungal infestation was observed. The presence of endophytic fungal hyphae was observed just within floral stems and indehiscent fruit. Beyond assuring the presence of fungus that promote seed germination, specific fungi hyphae in the fruit may affect other process, such as fruit ripening. As other mycoheterotrophic orchids, P. schenckii is autogamous, which may explain the low genetic diversity and high genetic structure in populations. CONCLUSIONS We discuss an interesting interaction: fungal hyphae in the indehiscent fruit. These fungal hyphae seem to play different roles inside fruit tissues, such as acting in the fruit maturation process and increasing the proximity between fungi and plant seeds even before dispersion occurs. As other mycoheterotrophic orchids, P. schenckii is autogamous, which may explain the low genetic diversity and high genetic structure in populations. Altogether, our findings provide important novel information about the mechanisms shaping ecology and evolution of fragmented populations of mycoheterotrophic plant.
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Affiliation(s)
- Mariana Ferreira Alves
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil.
| | - Fabio Pinheiro
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, São Paulo, Brazil
| | | | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Deise Schroder Sarzi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal Do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carolina Furtado
- Departamento de Genética, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
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103
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Gene flow in phylogenomics: Sequence capture resolves species limits and biogeography of Afromontane forest endemic frogs from the Cameroon Highlands. Mol Phylogenet Evol 2021; 163:107258. [PMID: 34252546 DOI: 10.1016/j.ympev.2021.107258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 11/21/2022]
Abstract
Puddle frogs of the Phrynobatrachus steindachneri species complex are a useful group for investigating speciation and phylogeography in Afromontane forests of the Cameroon Volcanic Line, western Central Africa. The species complex is represented by six morphologically relatively cryptic mitochondrial DNA lineages, only two of which are distinguished at the species level - southern P. jimzimkusi and Lake Oku endemic P. njiomock, leaving the remaining four lineages identified as 'P. steindachneri'. In this study, the six mtDNA lineages are subjected to genomic sequence capture analyses and morphological examination to delimit species and to study biogeography. The nuclear DNA data (387 loci; 571,936 aligned base pairs) distinguished all six mtDNA lineages, but the topological pattern and divergence depths supported only four main clades: P. jimzimkusi, P. njiomock, and only two divergent evolutionary lineages within the four 'P. steindachneri' mtDNA lineages. One of the two lineages is herein described as a new species, P. amieti sp. nov. Reticulate evolution (hybridization) was detected within the species complex with morphologically intermediate hybrid individuals placed between the parental species in phylogenomic analyses, forming a ladder-like phylogenetic pattern. The presence of hybrids is undesirable in standard phylogenetic analyses but is essential and beneficial in the network multispecies coalescent. This latter approach provided insight into the reticulate evolutionary history of these endemic frogs. Introgressions likely occurred during the Middle and Late Pleistocene climatic oscillations, due to the cyclic connections (likely dominating during cold glacials) and separations (during warm interglacials) of montane forests. The genomic phylogeographic pattern supports the separation of the southern (Mt. Manengouba to Mt. Oku) and northern mountains at the onset of the Pleistocene. Further subdivisions occurred in the Early Pleistocene, separating populations from the northernmost (Tchabal Mbabo, Gotel Mts.) and middle mountains (Mt. Mbam, Mt. Oku, Mambilla Plateau), as well as the microendemic lineage restricted to Lake Oku (Mt. Oku). This unique model system is highly threatened as all the species within the complex have exhibited severe population declines in the past decade, placing them on the brink of extinction. In addition, Mount Oku is identified to be of particular conservation importance because it harbors three species of this complex. We, therefore, urge for conservation actions in the Cameroon Highlands to preserve their diversity before it is too late.
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104
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Duplouy A, Nair A, Nyman T, van Nouhuys S. Long-term spatiotemporal genetic structure of an accidental parasitoid introduction, and local changes in prevalence of its associated Wolbachia symbiont. Mol Ecol 2021; 30:4368-4380. [PMID: 34233062 DOI: 10.1111/mec.16065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 06/14/2021] [Accepted: 07/02/2021] [Indexed: 11/30/2022]
Abstract
Population bottlenecks associated with founder events strongly impact the establishment and genetic makeup of populations. In addition to their genotype, founding individuals also bring along parasites, as well as symbionts that can manipulate the phenotype of their host, affecting the host population establishment, dynamics and evolution. Thus, to understand introduction, invasion, and spread, we should identify the roles played by accompanying symbionts. In 1991, the parasitoid wasp, Hyposoter horticola, and its associated hyperparasitoid were accidentally introduced from the main Åland islands, Finland, to an isolated island in the archipelago, along with their host, the Glanville fritillary butterfly. Though the receiving island was unoccupied, the butterfly was present on some of the small islands in the vicinity. The three introduced species have persisted locally ever since. A strain of the endosymbiotic bacterium Wolbachia has an intermediate prevalence in the parasitoid H. horticola across the main Åland population. The infection increases its susceptibility of to hyperparasitism. We investigated the establishment and spread of the parasitoid, along with patterns of prevalence of its symbiont using 323 specimens collected between 1992 and 2013, from five localities across Åland, including the source and introduced populations. Using 14 microsatellites and one mitochondrial marker, we suggest that the relatively diverse founding population and occasional migration between islands might have facilitated the persistence of all isolated populations, despite multiple local population crashes. We also show that where the hyperparasitoid is absent, and thus selection against infected wasp genotypes is relaxed, there is near-fixation of Wolbachia.
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Affiliation(s)
- Anne Duplouy
- Department of Biology, Lund University, Lund, Sweden.,Organismal and Evolutionary Biology Research Program, The University of Helsinki, Helsinki, Finland
| | - Abhilash Nair
- Organismal and Evolutionary Biology Research Program, The University of Helsinki, Helsinki, Finland
| | - Toshka Nyman
- Organismal and Evolutionary Biology Research Program, The University of Helsinki, Helsinki, Finland
| | - Saskya van Nouhuys
- Organismal and Evolutionary Biology Research Program, The University of Helsinki, Helsinki, Finland.,Department of Ecology and Evolutionary Biology, Ithaca, New York, USA
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105
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Dallaire X, Normandeau É, Mainguy J, Tremblay J, Bernatchez L, Moore J. Genomic data support management of anadromous Arctic Char fisheries in Nunavik by highlighting neutral and putatively adaptive genetic variation. Evol Appl 2021; 14:1880-1897. [PMID: 34295370 PMCID: PMC8287999 DOI: 10.1111/eva.13248] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 04/12/2021] [Accepted: 04/26/2021] [Indexed: 11/29/2022] Open
Abstract
Distinguishing neutral and adaptive genetic variation is one of the main challenges in investigating processes shaping population structure in the wild, and landscape genomics can help identify signatures of adaptation to contrasting environments. Arctic Char (Salvelinus alpinus) is an anadromous salmonid and the most harvested fish species by Inuit people, including in Nunavik (Québec, Canada), one of the most recently deglaciated regions in the world. Unlike many other anadromous salmonids, Arctic Char occupy coastal habitats near their natal rivers during their short marine phase restricted to the summer ice-free period. Our main objective was to document putatively neutral and adaptive genomic variation in anadromous Arctic Char populations from Nunavik and bordering regions to inform local fisheries management. We used genotyping by sequencing (GBS) to genotype 18,112 filtered single nucleotide polymorphisms (SNP) in 650 individuals from 23 sampling locations along >2000 km of coastline. Our results reveal a hierarchical genetic structure, whereby neighboring hydrographic systems harbor distinct populations grouped by major oceanographic basins: Hudson Bay, Hudson Strait, Ungava Bay, and Labrador Sea. We found genetic diversity and differentiation to be consistent both with the expected postglacial recolonization history and with patterns of isolation-by-distance reflecting contemporary gene flow. Results from three gene-environment association methods supported the hypothesis of local adaptation to both freshwater and marine environments (strongest associations with sea surface and air temperatures during summer and salinity). Our results support a fisheries management strategy at a regional scale, and other implications for hatchery projects and adaptation to climate change are discussed.
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Affiliation(s)
- Xavier Dallaire
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Centre d’Études Nordiques (CEN)Université LavalQuébecQCCanada
- Département de Biologie, Université LavalQuébecQCCanada
| | - Éric Normandeau
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Julien Mainguy
- Ministère des Forêts, de la Faune et des ParcsQuébecQCCanada
| | - Jean‐Éric Tremblay
- Département de Biologie, Université LavalQuébecQCCanada
- Ministère des Forêts, de la Faune et des ParcsQuébecQCCanada
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Département de Biologie, Université LavalQuébecQCCanada
| | - Jean‐Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
- Centre d’Études Nordiques (CEN)Université LavalQuébecQCCanada
- Département de Biologie, Université LavalQuébecQCCanada
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106
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Shier DM, Navarro AY, Tobler M, Thomas SM, King SND, Mullaney CB, Ryder OA. Genetic and ecological evidence of long‐term translocation success of the federally endangered Stephens' kangaroo rat. CONSERVATION SCIENCE AND PRACTICE 2021. [DOI: 10.1111/csp2.478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Debra M. Shier
- Recovery Ecology, San Diego Zoo Wildlife Alliance San Diego California USA
- Department of Ecology & Evolutionary Biology University of California Los Angeles Los Angeles California USA
| | - Asako Y. Navarro
- Conservation Genetics, San Diego Zoo Wildlife Alliance San Diego California USA
| | - Mathias Tobler
- Population Sustainability, San Diego Zoo Wildlife Alliance San Diego California USA
| | - Steven M. Thomas
- Conservation Genetics, San Diego Zoo Wildlife Alliance San Diego California USA
| | - Shauna N. D. King
- Recovery Ecology, San Diego Zoo Wildlife Alliance San Diego California USA
| | - Claire B. Mullaney
- Conservation Genetics, San Diego Zoo Wildlife Alliance San Diego California USA
| | - Oliver A. Ryder
- Conservation Genetics, San Diego Zoo Wildlife Alliance San Diego California USA
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107
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Fernández-López J, Fernández-Cruz J, Míguez-Soto B. The demographic history of Castanea sativa Mill. in southwest Europe: A natural population structure modified by translocations. Mol Ecol 2021; 30:3930-3947. [PMID: 34101923 DOI: 10.1111/mec.16013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 05/26/2021] [Accepted: 05/28/2021] [Indexed: 11/30/2022]
Abstract
In domesticated species, translocation of materials can alter natural demographic patterns; this may have occurred in Castanea sativa (European chestnut), a species conserved in several refuges, with a long domestication history for nut production. Bayesian analysis of population genetic structure in marginal areas and in the centre of C. sativa range, considering spatial information and making corrections for unbalanced size, allowed visualization of a genetic structure that was subsequently analysed by approximate Bayesian computation to assess its natural demographic history and test the origin of some hypothetical translocated germplasm. We obtained evidence of C. sativa population contraction during the earliest Pleistocene, resulting in a split into eastern (Greek) and western (Italian and Iberian) populations. The northern Iberian population, in the Eurosiberian area, is one of the vestiges that remained after the contraction that split the global Tertiary population. A secondary encounter, occurred from Middle to Upper Pleistocene, which explains the hybrid origin of the Western Mediterranean population present in Italy and in the centre and south of the Iberian Peninsula. It has been demonstrated that a germplasm translocation from Italy to the Central Iberian Range may have occurred. Recent translocations have hybridized with the local northern Iberian population, producing naturalized populations with high diversity. The populations of C. sativa in southwestern Europe have a genetic structure compatible with a natural origin, in which signs of population contractions and expansions caused by climatic oscillations since the Late Miocene have been imprinted.
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Affiliation(s)
| | | | - Beatriz Míguez-Soto
- Forest Research Centre Lourizán, AGACAL, Xunta de Galicia, Pontevedra, Spain
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108
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Andersen JC, Havill NP, Caccone A, Elkinton JS. Four times out of Europe: Serial invasions of the winter moth, Operophtera brumata, to North America. Mol Ecol 2021; 30:3439-3452. [PMID: 34033202 DOI: 10.1111/mec.15983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 11/30/2022]
Abstract
Reconstructing the geographic origins of non-native species is important for studying the factors that influence invasion success, however; these analyses can be constrained by the amount of diversity present in the native and invaded regions, and by changes in the genetic background of the invading population following bottlenecks and/or hybridization events. Here we explore the geographical origins of the invasive winter moth (Operopthera brumata L.) that has caused widespread defoliation to forests, orchards, and crops in Nova Scotia, British Columbia, Oregon, and the northeastern United States. It is not known whether these represent independent introductions to North America, or a "stepping stone" spread among regions. Using a combination of Bayesian assignment and approximate Bayesian computation methods, we analysed a population genetic data set of 24 microsatellite loci. We estimate that winter moth was introduced to North America on at least four occasions, with the Nova Scotian and British Columbian populations probably being introduced from France and Sweden, respectively; the Oregonian population probably being introduced from either the British Isles or northern Fennoscandia; and the population in the northeastern United States probably being introduced from somewhere in Central Europe. We discuss the impact of genetic bottlenecks on analyses meant to determine region of origin.
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Affiliation(s)
- Jeremy C Andersen
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Nathan P Havill
- Northern Research Station, USDA Forest Service, Hamden, CT, USA
| | - Adalgisa Caccone
- Department of Ecology & Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Joseph S Elkinton
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
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109
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Blyth C, Christmas MJ, Bickerton DC, Breed MF, Foster NR, Guerin GR, Mason ARG, Lowe AJ. Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy. Life (Basel) 2021; 11:553. [PMID: 34208381 PMCID: PMC8231295 DOI: 10.3390/life11060553] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/01/2022] Open
Abstract
Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from habitat fragmentation and climate change. We analysed range-wide genomic data and leaf shape variation to assess population diversity and divergence and to inform conservation management strategies. We detected three distinct genetic groupings and a likely cryptic species. Samples identified as O. pannosa subsp. cardiophylla from the Flinders Ranges in South Australia were genetically distinct from all other samples and likely form a separate, range-restricted species. Remaining samples formed two genetic clusters, which aligned with leaf shape differences but not fully with current subspecies classifications. Levels of genetic diversity and inbreeding differed between the three genetic groups, suggesting each requires a separate management strategy. Additionally, we tested for associations between genetic and environmental variation and carried out habitat suitability modelling for O. pannosa subsp. pannosa populations. We found mean annual maximum temperature explained a significant proportion of genomic variance. Habitat suitability modelling identified mean summer maximum temperature, precipitation seasonality and mean annual rainfall as constraints on the distribution of O. pannosa subsp. pannosa, highlighting increasing aridity as a threat for populations located near suitability thresholds. Our results suggest maximum temperature is an important agent of selection on O. pannosa subsp. pannosa and should be considered in conservation strategies. We recommend taxonomic revision of O. pannosa and provide conservation management recommendations.
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Affiliation(s)
- Colette Blyth
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
| | - Matthew J. Christmas
- Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
| | | | - Martin F. Breed
- College of Science and Engineering, Flinders University, Bedford Park 5042, Australia;
| | - Nicole R. Foster
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
- College of Science and Engineering, Flinders University, Bedford Park 5042, Australia;
| | - Greg R. Guerin
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
- Terrestrial Ecosystem Research Network (TERN), University of Adelaide, Adelaide 5005, Australia
| | - Alex R. G. Mason
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
| | - Andrew J. Lowe
- School of Biological Sciences, University of Adelaide, Adelaide 5005, Australia; (N.R.F.); (G.R.G.); (A.R.G.M.); (A.J.L.)
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110
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Abstract
The Antarctic environment is famously inhospitable to most terrestrial biodiversity, traditionally viewed as a driver of species extinction. Combining population- and species-level molecular data, we show that beetles on islands along the Antarctic Polar Front diversified in response to major climatic events over the last 50 Ma in surprising synchrony with the region’s marine organisms. Unique algae- and moss-feeding habits enabled beetles to capitalize on cooling conditions, which resulted in a decline in flowering plants—the typical hosts for beetles elsewhere. Antarctica’s cooling paleoclimate thus fostered the diversification of both terrestrial and marine life. Climatically driven evolutionary processes since the Miocene may underpin much of the region’s diversity, are still ongoing, and should be further investigated among Antarctic biota. Global cooling and glacial–interglacial cycles since Antarctica’s isolation have been responsible for the diversification of the region’s marine fauna. By contrast, these same Earth system processes are thought to have played little role terrestrially, other than driving widespread extinctions. Here, we show that on islands along the Antarctic Polar Front, paleoclimatic processes have been key to diversification of one of the world’s most geographically isolated and unique groups of herbivorous beetles—Ectemnorhinini weevils. Combining phylogenomic, phylogenetic, and phylogeographic approaches, we demonstrate that these weevils colonized the sub-Antarctic islands from Africa at least 50 Ma ago and repeatedly dispersed among them. As the climate cooled from the mid-Miocene, diversification of the beetles accelerated, resulting in two species-rich clades. One of these clades specialized to feed on cryptogams, typical of the polar habitats that came to prevail under Miocene conditions yet remarkable as a food source for any beetle. This clade’s most unusual representative is a marine weevil currently undergoing further speciation. The other clade retained the more common weevil habit of feeding on angiosperms, which likely survived glaciation in isolated refugia. Diversification of Ectemnorhinini weevils occurred in synchrony with many other Antarctic radiations, including penguins and notothenioid fishes, and coincided with major environmental changes. Our results thus indicate that geo-climatically driven diversification has progressed similarly for Antarctic marine and terrestrial organisms since the Miocene, potentially constituting a general biodiversity paradigm that should be sought broadly for the region’s taxa.
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111
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Carroll EL, Ott PH, McMillan LF, Galletti Vernazzani B, Neveceralova P, Vermeulen E, Gaggiotti OE, Andriolo A, Baker CS, Bamford C, Best P, Cabrera E, Calderan S, Chirife A, Fewster RM, Flores PAC, Frasier T, Freitas TRO, Groch K, Hulva P, Kennedy A, Leaper R, Leslie MS, Moore M, Oliveira L, Seger J, Stepien EN, Valenzuela LO, Zerbini A, Jackson JA. Genetic Diversity and Connectivity of Southern Right Whales (Eubalaena australis) Found in the Brazil and Chile-Peru Wintering Grounds and the South Georgia (Islas Georgias del Sur) Feeding Ground. J Hered 2021; 111:263-276. [PMID: 32347944 PMCID: PMC7238439 DOI: 10.1093/jhered/esaa010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/21/2020] [Indexed: 01/05/2023] Open
Abstract
As species recover from exploitation, continued assessments of connectivity and population structure are warranted to provide information for conservation and management. This is particularly true in species with high dispersal capacity, such as migratory whales, where patterns of connectivity could change rapidly. Here we build on a previous long-term, large-scale collaboration on southern right whales (Eubalaena australis) to combine new (nnew) and published (npub) mitochondrial (mtDNA) and microsatellite genetic data from all major wintering grounds and, uniquely, the South Georgia (Islas Georgias del Sur: SG) feeding grounds. Specifically, we include data from Argentina (npub mtDNA/microsatellite = 208/46), Brazil (nnew mtDNA/microsatellite = 50/50), South Africa (nnew mtDNA/microsatellite = 66/77, npub mtDNA/microsatellite = 350/47), Chile-Peru (nnew mtDNA/microsatellite = 1/1), the Indo-Pacific (npub mtDNA/microsatellite = 769/126), and SG (npub mtDNA/microsatellite = 8/0, nnew mtDNA/microsatellite = 3/11) to investigate the position of previously unstudied habitats in the migratory network: Brazil, SG, and Chile-Peru. These new genetic data show connectivity between Brazil and Argentina, exemplified by weak genetic differentiation and the movement of 1 genetically identified individual between the South American grounds. The single sample from Chile-Peru had an mtDNA haplotype previously only observed in the Indo-Pacific and had a nuclear genotype that appeared admixed between the Indo-Pacific and South Atlantic, based on genetic clustering and assignment algorithms. The SG samples were clearly South Atlantic and were more similar to the South American than the South African wintering grounds. This study highlights how international collaborations are critical to provide context for emerging or recovering regions, like the SG feeding ground, as well as those that remain critically endangered, such as Chile-Peru.
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Affiliation(s)
- Emma L Carroll
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,School of Biology, University of St Andrews, St Andrews, UK
| | - Paulo H Ott
- Grupo de Estudos de Mamíferos Aquáticos do Rio Grande do Sul, Torres, RS, Brazil.,Universidade Estadual do Rio Grande do Sul, Osório, RS, Brazil
| | - Louise F McMillan
- School of Mathematics and Statistics, Victoria University of Wellington, Wellington, New Zealand
| | | | - Petra Neveceralova
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Ivanhoe Sea Safaris, Gansbaai, South Africa.,Dyer Island Conservation Trust, Great White House, Kleinbaai, Gansbaai, South Africa
| | - Els Vermeulen
- Mammal Research Institute Whale Unit, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | | | - Artur Andriolo
- Departamento de Zoologia, Instituto de Ciências Biológicas, Universidade Federal de Juiz de Fora, Campus Universitário, Juiz de Fora, MG, Brazil.,Instituto Aqualie, Juiz de Fora, MG, Brazil
| | - C Scott Baker
- Marine Mammal Institute and Department of Fisheries and Wildlife, Oregon State University, Newport, OR
| | - Connor Bamford
- British Antarctic Survey, Cambridge, UK.,University of Southampton, Southampton, UK
| | | | - Elsa Cabrera
- Centro de Conservación Cetacea-Casilla 19178 Correo 19, Santiago, Chile
| | | | - Andrea Chirife
- Instituto de Ciencias Biomédicas (ICB), Universidad Andrés Bello, Chile
| | - Rachel M Fewster
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Paulo A C Flores
- Área de Proteção Ambiental (Environmental Protection Area) Anhatomirim, ICMBio, MMA, Florianópolis, SC, Brazil
| | - Timothy Frasier
- Department of Biology, Saint Mary's University, Halifax, Nova Scotia, Canada
| | - Thales R O Freitas
- Programa de Pós-Graduação em Genética e Biologia Molecular- Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Karina Groch
- Instituto Australis, Imbituba, Santa Catarina, Brazil
| | - Pavel Hulva
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.,Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Amy Kennedy
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA
| | | | | | - Michael Moore
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA
| | - Larissa Oliveira
- Universidade Estadual do Rio Grande do Sul, Osório, RS, Brazil.,Laboratório de Ecologia de Mamíferos, Universidade do Vale do Rio dos Sinos, Centro de Ciências da Saúde, Sao Leopoldo, RS, Brazil
| | - Jon Seger
- School of Biological Sciences, University of Utah, Salt Lake City, UT
| | - Emilie N Stepien
- Section of Marine Mammal Research, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Luciano O Valenzuela
- School of Biological Sciences, University of Utah, Salt Lake City, UT.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Laboratorio de Ecología Evolutiva Humana, UNCPBA, Quequén, Buenos Aires Province, Argentina.,Instituto de Conservación de Ballenas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Alexandre Zerbini
- Marine Mammal Laboratory, Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA, Seattle, WA.,Marine Ecology and Telemetry Research, Seabeck, WA.,Joint Institute for the Study of the Atmosphere and Ocean (JISAO), University of Washington, Seattle, WA
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112
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High genetic differentiation in the endemic and endangered freshwater fish Achondrostoma salmantinum Doadrio and Elvira, 2007 from Spain, as revealed by mitochondrial and SNP markers. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01381-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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113
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Genetic structure and essential oil composition in wild populations of Salvia multicaulis Vahl. BIOCHEM SYST ECOL 2021. [DOI: 10.1016/j.bse.2021.104269] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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114
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Pylidis C, Anijalg P, Saarma U, Dawson DA, Karaiskou N, Butlin R, Mertzanis Y, Giannakopoulos A, Iliopoulos Y, Krupa A, Burke TA. Multisource noninvasive genetics of brown bears ( Ursus arctos) in Greece reveals a highly structured population and a new matrilineal contact zone in southern Europe. Ecol Evol 2021; 11:6427-6443. [PMID: 34141229 PMCID: PMC8207399 DOI: 10.1002/ece3.7493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/14/2021] [Accepted: 02/22/2021] [Indexed: 11/21/2022] Open
Abstract
In human-dominated landscapes, connectivity is crucial for maintaining demographically stable mammalian populations. Here, we provide a comprehensive noninvasive genetic study for the brown bear population in the Hellenic Peninsula. We analyze its population structuring and connectivity, estimate its population size throughout its distribution, and describe its phylogeography in detail for the first time. Our results, based on 150 multilocus genotypes and on 244-bp sequences of the mtDNA control region, show the population is comprised by three highly differentiated genetic clusters, consistent with geographical populations of Pindos, Peristeri, and Rhodope. By detecting two male bears with Rhodopean ancestry in the western demes, we provide strong evidence for the ongoing genetic connectivity of the geographically fragmented eastern and western distributions, which suggests connectivity of the larger East Balkan and Pindos-Dinara populations. Total effective population size (N e) was estimated to be 199 individuals, and total combined population size (N C) was 499, with each cluster showing a relatively high level of genetic variability, suggesting that migration has been sufficient to counteract genetic erosion. The mtNDA results were congruent with the microsatellite data, and the three genetic clusters were matched predominantly with an equal number of mtDNA haplotypes that belong to the brown bear Western mitochondrial lineage (Clade 1), with two haplotypes being globally new and endemic. The detection of a fourth haplotype that belongs to the Eastern lineage (Clade 3a1) in three bears from the western distribution places the southernmost secondary contact zone between the Eastern and Western lineages in Greece and generates new hypotheses about postglacial maxima migration routes. This work indicates that the genetic composition and diversity of Europe's low-latitude fringe population are the outcome of ancient and historical events and highlight its importance for the connectivity and long-term persistence of the species in the Balkans.
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Affiliation(s)
- Charilaos Pylidis
- School of Biological SciencesUniversity of BristolBristolUK
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldUK
- Callisto Wildlife and Nature Conservation SocietyThessalonikiGreece
| | - Peeter Anijalg
- Department of ZoologyInstitute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Urmas Saarma
- Department of ZoologyInstitute of Ecology and Earth SciencesUniversity of TartuTartuEstonia
| | - Deborah A. Dawson
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldUK
| | - Nikoleta Karaiskou
- Department of Genetics, Developmental and Molecular BiologySchool of BiologyAristotle University of ThessalonikiThessalonikiGreece
| | - Roger Butlin
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Yorgos Mertzanis
- Callisto Wildlife and Nature Conservation SocietyThessalonikiGreece
| | | | | | - Andrew Krupa
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Terence A. Burke
- NERC Biomolecular Analysis FacilityDepartment of Animal and Plant SciencesUniversity of SheffieldUK
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115
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Xuereb A, D'Aloia CC, Andrello M, Bernatchez L, Fortin MJ. Incorporating putatively neutral and adaptive genomic data into marine conservation planning. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:909-920. [PMID: 32785955 DOI: 10.1111/cobi.13609] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 07/17/2020] [Accepted: 08/09/2020] [Indexed: 06/11/2023]
Abstract
The availability of genomic data for an increasing number of species makes it possible to incorporate evolutionary processes into conservation plans. Recent studies show how genetic data can inform spatial conservation prioritization (SCP), but they focus on metrics of diversity and distinctness derived primarily from neutral genetic data sets. Identifying adaptive genetic markers can provide important information regarding the capacity for populations to adapt to environmental change. Yet, the effect of including metrics based on adaptive genomic data into SCP in comparison to more widely used neutral genetic metrics has not been explored. We used existing genomic data on a commercially exploited species, the giant California sea cucumber (Parastichopus californicus), to perform SCP for the coastal region of British Columbia (BC), Canada. Using a RAD-seq data set for 717 P. californicus individuals across 24 sampling locations, we identified putatively adaptive (i.e., candidate) single nucleotide polymorphisms (SNPs) based on genotype-environment associations with seafloor temperature. We calculated various metrics for both neutral and candidate SNPs and compared SCP outcomes with independent metrics and combinations of metrics. Priority areas varied depending on whether neutral or candidate SNPs were used and on the specific metric used. For example, targeting sites with a high frequency of warm-temperature-associated alleles to support persistence under future warming prioritized areas in the southern coastal region. In contrast, targeting sites with high expected heterozygosity at candidate loci to support persistence under future environmental uncertainty prioritized areas in the north. When combining metrics, all scenarios generated intermediate solutions, protecting sites that span latitudinal and thermal gradients. Our results demonstrate that distinguishing between neutral and adaptive markers can affect conservation solutions and emphasize the importance of defining objectives when choosing among various genomic metrics for SCP.
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Affiliation(s)
- Amanda Xuereb
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Cassidy C D'Aloia
- Department of Biological Sciences, University of New Brunswick Saint John, 100 Tucker Park Road, Saint John, NB, E2L 4L5, Canada
| | - Marco Andrello
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Sète, France
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval, 1030 Avenue de la Médecine, Québec, QC, G1V 0A6, Canada
| | - Marie-Josée Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
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116
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Morris AB, Trostel K, Scalf C, Burleyson A, Call G, Albrecht MA. Genetic variation and structure in natural and reintroduced populations of the endangered legume, Pyne’s ground plum (Astragalus bibullatus). CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01346-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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117
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Benestan L, Fietz K, Loiseau N, Guerin PE, Trofimenko E, Rühs S, Schmidt C, Rath W, Biastoch A, Pérez-Ruzafa A, Baixauli P, Forcada A, Arcas E, Lenfant P, Mallol S, Goñi R, Velez L, Höppner M, Kininmonth S, Mouillot D, Puebla O, Manel S. Restricted dispersal in a sea of gene flow. Proc Biol Sci 2021; 288:20210458. [PMID: 34004134 PMCID: PMC8131118 DOI: 10.1098/rspb.2021.0458] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022] Open
Abstract
How far do marine larvae disperse in the ocean? Decades of population genetic studies have revealed generally low levels of genetic structure at large spatial scales (hundreds of kilometres). Yet this result, typically based on discrete sampling designs, does not necessarily imply extensive dispersal. Here, we adopt a continuous sampling strategy along 950 km of coast in the northwestern Mediterranean Sea to address this question in four species. In line with expectations, we observe weak genetic structure at a large spatial scale. Nevertheless, our continuous sampling strategy uncovers a pattern of isolation by distance at small spatial scales (few tens of kilometres) in two species. Individual-based simulations indicate that this signal is an expected signature of restricted dispersal. At the other extreme of the connectivity spectrum, two pairs of individuals that are closely related genetically were found more than 290 km apart, indicating long-distance dispersal. Such a combination of restricted dispersal with rare long-distance dispersal events is supported by a high-resolution biophysical model of larval dispersal in the study area, and we posit that it may be common in marine species. Our results bridge population genetic studies with direct dispersal studies and have implications for the design of marine reserve networks.
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Affiliation(s)
- L. Benestan
- CEFE, PSL EPHE, Université Montpellier, CNRS, IRD, Université Paul-Valéry Montpellier 3, Montpellier, France
| | - K. Fietz
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - N. Loiseau
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - P. E. Guerin
- CEFE, PSL EPHE, Université Montpellier, CNRS, IRD, Université Paul-Valéry Montpellier 3, Montpellier, France
| | - E. Trofimenko
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - S. Rühs
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - C. Schmidt
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - W. Rath
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - A. Biastoch
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - A. Pérez-Ruzafa
- Department of Ecology and Hydrology, Faculty of Biology, Espinardo, Regional Campus of International Excellence ‘Mare Nostrum’, University of Murcia, Murcia 30100, Spain
| | - P. Baixauli
- Department of Ecology and Hydrology, Faculty of Biology, Espinardo, Regional Campus of International Excellence ‘Mare Nostrum’, University of Murcia, Murcia 30100, Spain
| | - A. Forcada
- Department of Marine Sciences and Applied Biology, University of Alicante, P.O. Box 99, 03080 Alicante, Spain
| | - E. Arcas
- Department of Marine Sciences and Applied Biology, University of Alicante, P.O. Box 99, 03080 Alicante, Spain
| | - P. Lenfant
- Centre de Formation et de Recherche sur les Environnements Méditerranéens, Université Perpignan Via Domitia, CNRS, 66100 Perpignan, France
| | - S. Mallol
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Moll de Ponent s/n, 07015 Palma de Mallorca, Spain
| | - R. Goñi
- Instituto Español de Oceanografía, Centro Oceanográfico de Baleares, Moll de Ponent s/n, 07015 Palma de Mallorca, Spain
| | - L. Velez
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
| | - M. Höppner
- Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - S. Kininmonth
- School of Marine Studies, University of the South Pacific, Fiji
| | - D. Mouillot
- MARBEC, Univ Montpellier, CNRS, IFREMER, IRD, Montpellier, France
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia
| | - O. Puebla
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany
- Ecology Department, Leibniz-Centre for Tropical Marine Research, Fahrenheitstraße 6, 28359 Bremen, Germany
| | - S. Manel
- CEFE, PSL EPHE, Université Montpellier, CNRS, IRD, Université Paul-Valéry Montpellier 3, Montpellier, France
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118
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Genome-wide SNPs redefines species boundaries and conservation units in the freshwater mussel genus Cyprogenia of North America. Sci Rep 2021; 11:10752. [PMID: 34031525 PMCID: PMC8144384 DOI: 10.1038/s41598-021-90325-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/10/2021] [Indexed: 11/08/2022] Open
Abstract
Detailed information on species delineation and population genetic structure is a prerequisite for designing effective restoration and conservation strategies for imperiled organisms. Phylogenomic and population genomic analyses based on genome-wide double digest restriction-site associated DNA sequencing (ddRAD-Seq) data has identified three allopatric lineages in the North American freshwater mussel genus Cyprogenia. Cyprogenia stegaria is restricted to the Eastern Highlands and displays little genetic structuring within this region. However, two allopatric lineages of C. aberti in the Ozark and Ouachita highlands exhibit substantial levels (mean uncorrected FST = 0.368) of genetic differentiation and each warrants recognition as a distinct evolutionary lineage. Lineages of Cyprogenia in the Ouachita and Ozark highlands are further subdivided reflecting structuring at the level of river systems. Species tree inference and species delimitation in a Bayesian framework using single nucleotide polymorphisms (SNP) data supported results from phylogenetic analyses, and supports three species of Cyprogenia over the currently recognized two species. A comparison of SNPs generated from both destructively and non-destructively collected samples revealed no significant difference in the SNP error rate, quality and amount of ddRAD sequence reads, indicating that nondestructive or trace samples can be effectively utilized to generate SNP data for organisms for which destructive sampling is not permitted.
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119
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VanWallendael A, Alvarez M, Franks SJ. Patterns of population genomic diversity in the invasive Japanese knotweed species complex. AMERICAN JOURNAL OF BOTANY 2021; 108:857-868. [PMID: 33942283 DOI: 10.1002/ajb2.1653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Invasive species are expected to undergo a reduction in genetic diversity due to founder effects, which should limit their ability to adapt to new habitats. Still, many invasive species achieve widespread distributions and dense populations. This paradox of invasions could potentially be overcome through multiple introductions or hybridization, both of which increase genetic diversity. We conducted a population genomics study of Japanese knotweed (Reynoutria japonica), which is a polyploid, clonally reproducing invasive species that has been notoriously successful worldwide despite supposedly low genetic diversity. METHODS We used genotyping by sequencing to collect 12,912 SNP markers from 88 samples collected at 38 locations across North America for the species complex. We used alignment-free k-mer hashing analysis in addition to traditional population genetic analyses to account for the challenges of genotyping polyploids. RESULTS Genotypes conformed to three genetic clusters, likely representing Japanese knotweed, giant knotweed, and hybrid bohemian knotweed. We found that, contrary to previous findings, the Japanese knotweed cluster had substantial genetic diversity, though it had no apparent genetic structure across the landscape. In contrast, giant knotweed and hybrids showed distinct population groups. We did not find evidence of isolation by distance in the species complex, likely reflecting the stochastic introduction history of this species complex. CONCLUSIONS The results indicate that clonal invasive species can show substantial genetic diversity and can be successful at colonizing a variety of habitats without showing evidence of local adaptation or genetic structure.
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Affiliation(s)
- Acer VanWallendael
- Biology Department, Fordham University, 441 E. Fordham Road, Bronx, NY, 10458, USA
- Biology Department, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| | - Mariano Alvarez
- Biology Department, Duke University, 130 Science Drive, Durham, NC, 27708, USA
| | - Steven J Franks
- Biology Department, Fordham University, 441 E. Fordham Road, Bronx, NY, 10458, USA
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Genetic Distinctiveness but Low Diversity Characterizes Rear-Edge Thuja standishii (Gordon) Carr. (Cupressaceae) Populations in Southwest Japan. DIVERSITY 2021. [DOI: 10.3390/d13050185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in life-history traits, demographic histories and human impacts. Using 13 EST-microsatellites, we investigated the genetic diversity and differentiation of rear-edge populations of the Japanese endemic conifer Thuja standishii (Gordon) Carr. in southwest Japan from the core-range in northeast Japan. Range-wide genetic differentiation was moderate (Fst = 0.087), with northeast populations weakly differentiated (Fst = 0.047), but harboring high genetic diversity (average population-level Ar = 4.76 and Ho = 0.59). In contrast, rear-edge populations were genetically diverged (Fst = 0.168), but contained few unique alleles with lower genetic diversity (Ar = 3.73, Ho = 0.49). The divergence between rear-edge populations exceeding levels observed in the core-range and results from ABC analysis and species distribution modelling suggest that these populations are most likely relicts of the Last Glacial Maximum. However, despite long term persistence, low effective population size, low migration between populations and genetic drift have worked to promote the genetic differentiation of southwest Japan populations of T. standishii without the accumulation of unique alleles.
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121
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Trumbo DR, Funk WC, Pauly GB, Robertson JM. Conservation genetics of an island-endemic lizard: low Ne and the critical role of intermediate temperatures for genetic connectivity. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01362-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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122
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Can species distribution models and molecular tools help unravel disjunct distribution of Rhododendron arboreum? J Genet 2021. [DOI: 10.1007/s12041-021-01270-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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123
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The palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae) exhibits high genetic diversity despite Quaternary range contraction and post glacial bottlenecking. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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124
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Tu VT, Görföl T, Csorba G, Arai S, Kikuchi F, Fukui D, Koyabu D, Furey NM, Bawm S, Lin KS, Alviola P, Hang CT, Son NT, Tuan TA, Hassanin A. Integrative taxonomy and biogeography of Asian yellow house bats (Vespertilionidae:
Scotophilus
) in the Indomalayan Region. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Vuong Tan Tu
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Sorbonne UniversitéMNHNCNRSEPHE, UA ‐ Muséum National d’Histoire Naturelle Paris France
- Service de Systématique Moléculaire UMS 2700 Muséum national d’Histoire naturelle Paris France
| | - Tamás Görföl
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
- National Laboratory of Virology Szentágothai Research Centre University of Pécs Pécs Hungary
| | - Gábor Csorba
- Department of Zoology Hungarian Natural History Museum Budapest Hungary
| | - Satoru Arai
- Infectious Disease Surveillance Center National Institute of Infectious Diseases Shinjuku, Tokyo Japan
| | - Fuka Kikuchi
- Infectious Disease Surveillance Center National Institute of Infectious Diseases Shinjuku, Tokyo Japan
- Tokyo University of Science Shinjuku, Tokyo Japan
- Research and Education Center for Prevention of Global Infectious Diseases of Animals Tokyo University of Agriculture and Technology Fuchu, Tokyo Japan
| | - Dai Fukui
- The University of Tokyo Hokkaido Forest Graduate School of Agricultural and Life Sciences The University of Tokyo Hokkaido Japan
| | - Daisuke Koyabu
- Jockey Club College of Veterinary Medicine and Life Sciences City University of Hong Kong Kowloon Hong Kong
- Department of Molecular Craniofacial Embryology Graduate School of Medical and Dental Sciences Tokyo Medical and Dental University Bunkyo‐ku, Tokyo Japan
| | - Neil M. Furey
- Fauna & Flora International, Cambodia Programme Chamkarmorn, Phnom Penh Cambodia
- Harrison InstituteBowerwood House Sevenoaks Kent UK
| | - Saw Bawm
- University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
| | - Kyaw San Lin
- University of Veterinary Science Yezin, Nay Pyi Taw Myanmar
| | - Phillip Alviola
- Institute of Biological Sciences and Museum of Natural History University of the Philippines Los Banos Laguna Philippines
| | - Chu Thi Hang
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
| | - Nguyen Truong Son
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
| | - Tran Anh Tuan
- Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam
- Graduate University of Science and TechnologyVietnam Academy of Science and Technology Hanoi Vietnam
| | - Alexandre Hassanin
- Institut de Systématique, Évolution, Biodiversité (ISYEB) Sorbonne UniversitéMNHNCNRSEPHE, UA ‐ Muséum National d’Histoire Naturelle Paris France
- Service de Systématique Moléculaire UMS 2700 Muséum national d’Histoire naturelle Paris France
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Levin RA, Miller JS. Molecular signatures of long-distance oceanic dispersal and the colonization of Pacific islands in Lycium carolinianum. AMERICAN JOURNAL OF BOTANY 2021; 108:694-710. [PMID: 33811320 DOI: 10.1002/ajb2.1626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Long-distance dispersal has been important in explaining the present distributions of many plant species. Despite being infrequent, such dispersal events have considerable evolutionary consequences, because bottlenecks during colonization can result in reduced genetic diversity. We examined the phylogeographic history of Lycium carolinianum, a widespread taxon that ranges from southeastern North America to several Pacific islands, with intraspecific diversity in sexual and mating systems. METHODS We used Bayesian, likelihood, and coalescent approaches with nuclear and plastid sequence data and genome-wide single nucleotide polymorphisms to reconstruct the dispersal history of this species. We also compared patterns of genetic variation in mainland and island populations using single nucleotide polymorphisms and allelic diversity at the S-RNase mating system gene. RESULTS Lycium carolinianum is monophyletic and dispersed once from the North American mainland, colonizing the Pacific islands ca. 40,100 years ago. This dispersal was accompanied by a loss of genetic diversity in SNPs and the S-RNase locus due to a colonization bottleneck and the loss of self-incompatibility. Additionally, we documented at least two independent transitions to gynodioecy: once following the colonization of the Hawaiian Islands and loss of self-incompatibility, and a second time associated with polyploidy in the Yucatán region of Mexico. CONCLUSIONS Long-distance dispersal via fleshy, bird dispersed fruits best explains the unusually widespread distribution of L. carolinianum. The collapse of diversity at the S-RNase locus in island populations suggests that self-fertilization may have facilitated the subsequent colonization of Pacific islands following a single dispersal from mainland North America.
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Affiliation(s)
- Rachel A Levin
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
| | - Jill S Miller
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
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Genetic structure of Malus sylvestris and potential link with preference/performance by the rosy apple aphid pest Dysaphis plantaginea. Sci Rep 2021; 11:5732. [PMID: 33707470 PMCID: PMC7970975 DOI: 10.1038/s41598-021-85014-x] [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: 07/27/2020] [Accepted: 02/09/2021] [Indexed: 01/31/2023] Open
Abstract
The European crabapple Malus sylvestris, a crop wild relative of Malus domestica, is a major contributor to the cultivated apple genome and represents a potential source of interesting alleles or genes, particularly pest resistance traits. An original approach was used to explore the trophic interaction between M. sylvestris populations and its pest, the rosy apple aphid (Dysaphis plantaginea). Using 13 microsatellite markers, population genetic structure and level of crop-to-wild introgressions were inferred between M. sylvestris seedlings from three sites in Europe (Denmark, France, Romania), and M. domestica seedlings. Genetically characterized plants were also used to analyze aphid feeding behavior and fitness parameters. First, aphids submitted to two genetically close M. sylvestris populations (the Danish and French) exhibited similar behavioral parameters, suggesting similar patterns of resistance in these host plants. Second, the Romanian M. sylvestris population was most closely genetically related to M. domestica. Although the two plant genetic backgrounds were significantly differentiated, they showed comparable levels of sensitivity to D. plantaginea infestation. Third, aphid fitness parameters were not significantly impacted by the host plant's genetic background. Finally, crop-to-wild introgression seemed to significantly drive resistance to D. plantaginea independent of host plant population genetic structure, with hybrids being less suitable hosts.
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127
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Silva CNS, Young EF, Murphy NP, Bell JJ, Green BS, Morley SA, Duhamel G, Cockcroft AC, Strugnell JM. Climatic change drives dynamic source-sink relationships in marine species with high dispersal potential. Ecol Evol 2021; 11:2535-2550. [PMID: 33767820 PMCID: PMC7981208 DOI: 10.1002/ece3.7204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 12/14/2022] Open
Abstract
While there is now strong evidence that many factors can shape dispersal, the mechanisms influencing connectivity patterns are species-specific and remain largely unknown for many species with a high dispersal potential. The rock lobsters Jasus tristani and Jasus paulensis have a long pelagic larval duration (up to 20 months) and inhabit seamounts and islands in the southern Atlantic and Indian Oceans, respectively. We used a multidisciplinary approach to assess the genetic relationships between J. tristani and J. paulensis, investigate historic and contemporary gene flow, and inform fisheries management. Using 17,256 neutral single nucleotide polymorphisms we found low but significant genetic differentiation. We show that patterns of connectivity changed over time in accordance with climatic fluctuations. Historic migration estimates showed stronger connectivity from the Indian to the Atlantic Ocean (influenced by the Agulhas Leakage). In contrast, the individual-based model coupled with contemporary migration estimates inferred from genetic data showed stronger inter-ocean connectivity in the opposite direction from the Atlantic to the Indian Ocean driven by the Subtropical Front. We suggest that the J. tristani and J. paulensis historical distribution might have extended further north (when water temperatures were lower) resulting in larval dispersal between the ocean basis being more influenced by the Agulhas Leakage than the Subtropical Front. As water temperatures in the region increase in accordance with anthropogenic climate change, a southern shift in the distribution range of J. tristani and J. paulensis could further reduce larval transport from the Indian to the Atlantic Ocean, adding complexity to fisheries management.
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Affiliation(s)
- Catarina N. S. Silva
- Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQldAustralia
| | | | | | - James J. Bell
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Bridget S. Green
- Institute for Marine and Antarctic StudiesUniversity of TasmaniaHobartTASAustralia
| | | | - Guy Duhamel
- Département Adaptations du VivantBOREAMNHNParisFrance
| | - Andrew C. Cockcroft
- Department of Agriculture, Forestry and FisheriesSouth African GovernmentCape TownSouth Africa
| | - Jan M. Strugnell
- Centre for Sustainable Tropical Fisheries and AquacultureJames Cook UniversityTownsvilleQldAustralia
- Department of EcologyLa Trobe UniversityMelbourneVic.Australia
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128
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River drying influences genetic variation and population structure in an Arctic freshwater fish. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01339-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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129
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Wachi N, Gau JJ, Fujie S, Fukano K, Maeto K. Genomic population structure of sympatric sexual and asexual populations in a parasitic wasp, Meteorus pulchricornis (Hymenoptera: Braconidae), inferred from six hundred single-nucleotide polymorphism loci. Mol Ecol 2021; 30:1612-1623. [PMID: 33634920 DOI: 10.1111/mec.15834] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 01/22/2021] [Accepted: 02/04/2021] [Indexed: 11/28/2022]
Abstract
In spite of the two-fold reproductive advantage, asexual reproduction is not common in nature, probably due to the associated genetic deterioration or reduced genetic variation. To understand how genetic diversity is maintained in existing asexual populations, we investigated the genetic diversity and population structure of sympatric sexual and asexual populations of a parasitic wasp, Meteorus pulchricornis, using 614 genome-wide single nucleotide polymorphisms. The genetic structures of the apomictic asexual populations were distinct, showing considerable genetic differentiation among them. Most of the asexual populations were highly differentiated from the sympatric sexual population; some asexual individuals could not be distinguished from members of the sexual population. Furthermore, significantly fewer multilocus genotypes were identified in the asexual populations (1-7) compared to the sexual population (42), which is consistent with their apomictic nature. The observed patterns of fixed heterozygous sites suggest that most asexual populations had the same evolutionary origin and have long since evolved individually; the detected gene flow between the sexual population and a few asexual population may indicate independent origins of asexuality. The potential role of occasional males in apomictic wasps is also discussed.
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Affiliation(s)
- Nakatada Wachi
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Jin-Je Gau
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Shunpei Fujie
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan.,Osaka Museum of Natural History, Higashisumiyoshi, Osaka, Japan
| | - Kenya Fukano
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
| | - Kaoru Maeto
- Graduate School of Agricultural Science, Kobe University, Nada, Kobe, Japan
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130
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Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops. PLANTS 2021; 10:plants10020415. [PMID: 33672381 PMCID: PMC7926561 DOI: 10.3390/plants10020415] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/12/2022]
Abstract
Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.
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131
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Canty SWJ, Fox G, Rowntree JK, Preziosi RF. Genetic structure of a remnant Acropora cervicornis population. Sci Rep 2021; 11:3523. [PMID: 33568733 PMCID: PMC7876111 DOI: 10.1038/s41598-021-83112-4] [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: 02/19/2020] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
Amongst the global decline of coral reefs, hope spots such as Cordelia Bank in Honduras, have been identified. This site contains dense, remnant thickets of the endangered species Acropora cervicornis, which local managers and conservation organizations view as a potential source population for coral restoration projects. The aim of this study was to determine the genetic diversity of colonies across three banks within the protected area. We identified low genetic diversity (FST = 0.02) across the three banks, and genetic similarity of colonies ranged from 91.3 to 95.8% between the banks. Clonality rates were approximately 30% across the three banks, however, each genotype identified was unique to each bank. Despite the low genetic diversity, subtle genetic differences within and among banks were demonstrated, and these dense thickets were shown not to be comprised of a single or a few genotypes. The presence of multiple genotypes suggests A. cervicornis colonies from these banks could be used to maintain and enhance genetic diversity in restoration projects. Management of hope spots, such as Cordelia Bank, and the incorporation of genetic information into restoration projects to ensure genetic diversity within out-planted populations, will be critical in the ongoing challenge of conserving and preserving coral reefs.
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Affiliation(s)
- Steven W. J. Canty
- grid.1214.60000 0000 8716 3312Working Land and Seascapes, Conservation Commons, Smithsonian Institution, Washington, DC 20013 USA ,grid.452909.30000 0001 0479 0204Smithsonian Marine Station, 701 Seaway Drive, Fort Pierce, FL 34949 USA ,grid.25627.340000 0001 0790 5329Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, M1 5GD UK ,Centro de Estudios Marinos, Tegucigalpa, Honduras
| | - Graeme Fox
- grid.25627.340000 0001 0790 5329Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, M1 5GD UK
| | - Jennifer K. Rowntree
- grid.25627.340000 0001 0790 5329Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, M1 5GD UK
| | - Richard F. Preziosi
- grid.25627.340000 0001 0790 5329Department of Natural Sciences, Ecology and Environment Research Centre, Manchester Metropolitan University, Manchester, M1 5GD UK
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132
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Benestan LM, Rougemont Q, Senay C, Normandeau E, Parent E, Rideout R, Bernatchez L, Lambert Y, Audet C, Parent GJ. Population genomics and history of speciation reveal fishery management gaps in two related redfish species ( Sebastes mentella and Sebastes fasciatus). Evol Appl 2021; 14:588-606. [PMID: 33664797 PMCID: PMC7896722 DOI: 10.1111/eva.13143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 08/27/2020] [Accepted: 09/01/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the processes shaping population structure and reproductive isolation of marine organisms can improve their management and conservation. Using genomic markers combined with estimation of individual ancestries, assignment tests, spatial ecology, and demographic modeling, we (i) characterized the contemporary population structure, (ii) assessed the influence of space, fishing depth, and sampling years on contemporary distribution, and (iii) reconstructed the speciation history of two cryptic redfish species, Sebastes mentella and S. fasciatus. We genotyped 860 individuals in the Northwest Atlantic Ocean using 24,603 filtered single nucleotide polymorphisms (SNPs). Our results confirmed the clear genetic distinctiveness of the two species and identified three ecotypes within S. mentella and five populations in S. fasciatus. Multivariate analyses highlighted the influence of spatial distribution and depth on the overall genomic variation, while demographic modeling revealed that secondary contact models best explained inter- and intragenomic divergence. These species, ecotypes, and populations can be considered as a rare and wide continuum of genomic divergence in the marine environment. This acquired knowledge pertaining to the evolutionary processes driving population divergence and reproductive isolation will help optimizing the assessment of demographic units and possibly to refine fishery management units.
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Affiliation(s)
- Laura M. Benestan
- CEFEUniv Montpellier, CNRS, EPHE‐PSL UniversityIRD, Univ Paul Valéry Montpellier 3MontpellierFrance
| | - Quentin Rougemont
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Caroline Senay
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Eric Normandeau
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Eric Parent
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Rick Rideout
- Fisheries and Oceans CanadaNorthwest Atlantic Fisheries CentreN.L.St. John’sCanada
| | - Louis Bernatchez
- Département de biologie, Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Yvan Lambert
- Fisheries and Oceans CanadaMaurice‐Lamontagne InstituteMont‐JoliQCCanada
| | - Céline Audet
- Institut des sciences de la mer de RimouskiUniversité du Québec à RimouskiRimouskiQCCanada
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133
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Ryan WH, Aida J, Krueger-Hadfield SA. The Contribution of Clonality to Population Genetic Structure in the Sea Anemone, Diadumene lineata. J Hered 2021; 112:122-139. [PMID: 33507264 DOI: 10.1093/jhered/esaa050] [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: 02/06/2020] [Accepted: 12/22/2020] [Indexed: 01/06/2023] Open
Abstract
Ecological and evolutionary processes differ depending on how genetic diversity is organized in space. For clonal organisms, the organization of both genetic and genotypic diversity can influence the fitness effects of competition, the mating system, and reproductive mode, which are key drivers of life cycle evolution. Understanding how individual reproductive behavior contributes to population genetic structure is essential for disentangling these forces, particularly in species with complex and plastic life cycles. The widespread sea anemone, Diadumene lineata, exhibits temperature-dependent fission, which contributes to predictable variation in clonal rate along the Atlantic coast of the United States, part of its non-native range. Because warmer conditions lead to higher rates of clonality, we expected to find lower genotypic and genetic diversity in lower versus higher latitude populations. We developed primers for 11 microsatellite loci and genotyped 207 anemones collected from 8 sites ranging from Florida to Massachusetts. We found clonal influence at all sites, and as predicted, the largest clones were found at lower latitude sites. We also found genetic signatures of sex in the parts of the range where gametogenesis is most common. Evidence of sex outside the native range is novel for this species and provides insights into the dynamics of this successful invader. Our findings also illustrate challenges that partially clonal taxa pose for eco-evolutionary studies, such as difficulty sampling statistically robust numbers of genets and interpretating common population genetic metrics. For example, we found high among-locus variation in FIS, which makes the meaning of mean multilocus FIS unclear.
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Affiliation(s)
- Will H Ryan
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL.,Department of Biological Science, Florida State University, Tallahassee, FL
| | - Jaclyn Aida
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL
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134
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Rengefors K, Gollnisch R, Sassenhagen I, Härnström Aloisi K, Svensson M, Lebret K, Čertnerová D, Cresko WA, Bassham S, Ahrén D. Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species. Mol Ecol 2021; 30:912-925. [PMID: 33386639 DOI: 10.1111/mec.15787] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/04/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Species invasion and range expansion are currently under scrutiny due to increasing anthropogenic impact on the natural environment. This is also true for harmful algal blooms, which have been reported to have increased in frequency. However, this research is challenging due to the ephemeral nature, small size and mostly low concentrations of microalgae in the environment. One such species is the nuisance microalga Gonyostomum semen (Raphidophyceae), which has increased in occurrence in northern Europe in recent decades. The question of whether the species has expanded its habitat range or if it was already present in the lakes but was too rare to be detected remains unanswered. The aim of the present study was to determine the genetic structure and dispersal pathways of G. semen using RAD (restriction-site-associated DNA) tag sequencing. For G. semen, which has a huge genome (32 Gbp), we faced particular challenges, but were nevertheless able to recover over 1000 single nucleotide polymorphisms at high coverage. Our data revealed a distinct population genetic structure, demonstrating a divide of western and eastern populations that probably represent different lineages. Despite significant genetic differentiation among lakes, we found only limited isolation-by-distance. While we had expected a pattern of recent expansion northwards, the data demonstrated gene flow from the northeast/east towards the southwest/west. This genetic signature suggests that the observed gene flow may be due to dispersal by autumn migratory birds, which act as dispersal vectors of resistant resting propagules that form at the end of the G. semen blooms.
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Affiliation(s)
| | | | - Ingrid Sassenhagen
- Department of Biology, Lund University, Lund, Sweden.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Karolina Härnström Aloisi
- Department of Biology, Lund University, Lund, Sweden.,Nordic Genetic Resource Centre (NordGen), Alnarp, Sweden
| | | | - Karen Lebret
- Department of Biology, Lund University, Lund, Sweden
| | - Dora Čertnerová
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - William A Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Dag Ahrén
- Department of Biology, National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Lund, Sweden
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135
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Ha YH, Oh SH, Lee SR. Genetic Admixture in the Population of Wild Apple ( Malus Sieversii) from the Tien Shan Mountains, Kazakhstan. Genes (Basel) 2021; 12:104. [PMID: 33467767 PMCID: PMC7829876 DOI: 10.3390/genes12010104] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/01/2021] [Accepted: 01/12/2021] [Indexed: 01/14/2023] Open
Abstract
There is growing attention given to gene flow between crops and the wild relatives as global landscapes have been rapidly converted into agricultural farm fields over the past century. Crop-to-wild introgression may advance the extinction risks of rare plants through demographic swamping and/or genetic swamping. Malus sieversii, the progenitor of the apple, is exclusively distributed along the Tien Shan mountains. Habitat fragmentation and hybridization between M. sieversii and the cultivated apples have been proposed to be the causal mechanism of the accelerated extinction risk. We examined the genetic diversity pattern of eleven wild and domesticated apple populations and assessed the gene flow between M. sieversii and the cultivated apples in Kazakhstan using thirteen nuclear microsatellite loci. On average, apple populations harbored fairly high within-population diversity, whereas population divergences were very low suggesting likely influence of human-mediated dispersal. Assignment results showed a split pattern between the cultivated and wild apples and frequent admixture among the apple populations. Coupled with the inflated contemporary migration rates, the admixture pattern might be the signature of increased human intervention within the recent past. Our study highlighted the prevalent crop to wild gene flow of apples occurring in Kazakhstan, proposing an accelerated risk of genetic swamping.
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Affiliation(s)
- Young-Ho Ha
- Division of Forest Diversity, Korea National Arboretum, Pocheon 11186, Korea; (Y.-H.H.); (S.-H.O.)
- Department of Life Sciences, Gachon University, Seongnam 13120, Korea
| | - Seung-Hwan Oh
- Division of Forest Diversity, Korea National Arboretum, Pocheon 11186, Korea; (Y.-H.H.); (S.-H.O.)
| | - Soo-Rang Lee
- Department of Biology Education, College of Natural Sciences, 309 Pilmun-Daero, Dong-Gu, Gwangju 61452, Korea
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136
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Emel SL, Wang S, Metz RP, Spigler RB. Type and intensity of surrounding human land use, not local environment, shape genetic structure of a native grassland plant. Mol Ecol 2021; 30:639-655. [PMID: 33245827 DOI: 10.1111/mec.15753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 11/01/2020] [Accepted: 11/13/2020] [Indexed: 12/28/2022]
Abstract
Landscape heterogeneity can shape genetic structure and functional connectivity of populations. When this heterogeneity imposes variable costs of moving across the landscape, populations can be structured according to a pattern of "isolation by resistance" (IBR). At the same time, divergent local environmental filters can limit gene flow, creating an alternative pattern of "isolation by environment" (IBE). Here, we evaluate IBR and IBE in the insect-pollinated, biennial plant Sabatia angularis (L.) Pursh (Gentianaceae) across serpentine grasslands in the fragmented landscape of SE Pennsylvania, USA using ~4500 neutral SNP loci. Specifically, we test the extent to which radical alteration of the landscape matrix by humans has fundamentally altered the cost of movement, imprinting a pattern of IBR dictated by land use type and intensity, and the potential for IBE in relation to a gradient of heavy metal concentrations found in serpentine soil. We reveal a strong signal of IBR and a weak signal of IBE across sites, indicating the greater importance of the landscape matrix in shaping genetic structure of S. angularis populations in the study region. Based on Circuitscape and least cost path approaches, we find that both low- and high-intensity urbanization resist gene flow by orders of magnitude greater than "natural" habitats, although resistance to low-intensity urbanization weakens at larger spatial scales. While cropland presents a substantially lower barrier than urban development, cumulative human land use surrounding populations predicts within-population genetic diversity and inbreeding in S. angularis. Our results emphasize the role of forest buffers and corridors in facilitating gene flow between serpentine grassland patches and averting local extinction of plant populations.
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Affiliation(s)
- Sarah L Emel
- Department of Biology, Temple University, Philadelphia, PA, USA.,Department of Biology, Indiana University of Pennsylvania, Indiana, PA, USA
| | - Shichen Wang
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, TX, USA
| | - Richard P Metz
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, TX, USA
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137
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High genomic diversity maintained by populations of Carex scirpoidea subsp. convoluta, a paraphyletic Great Lakes ecotype. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01326-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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138
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Under the radar: genetic assessment of Rio Grande Shiner (Notropis jemezanus) and Speckled Chub (Macrhybopsis aestivalis), two Rio Grande basin endemic cyprinids that have experienced recent range contractions. CONSERV GENET 2021. [DOI: 10.1007/s10592-020-01328-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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139
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Banker SE, Lemmon AR, Hassinger AB, Dye M, Holland SD, Kortyna ML, Ospina OE, Ralicki H, Lemmon EM. Hierarchical Hybrid Enrichment: Multitiered Genomic Data Collection Across Evolutionary Scales, With Application to Chorus Frogs (Pseudacris). Syst Biol 2021; 69:756-773. [PMID: 31886503 PMCID: PMC7302053 DOI: 10.1093/sysbio/syz074] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/26/2019] [Accepted: 11/04/2019] [Indexed: 01/25/2023] Open
Abstract
Determining the optimal targets of genomic subsampling for phylogenomics, phylogeography, and population genomics remains a challenge for evolutionary biologists. Of the available methods for subsampling the genome, hybrid enrichment (sequence capture) has become one of the primary means of data collection for systematics, due to the flexibility and cost efficiency of this approach. Despite the utility of this method, information is lacking as to what genomic targets are most appropriate for addressing questions at different evolutionary scales. In this study, first, we compare the benefits of target loci developed for deep- and shallow scales by comparing these loci at each of three taxonomic levels: within a genus (phylogenetics), within a species (phylogeography), and within a hybrid zone (population genomics). Specifically, we target evolutionarily conserved loci that are appropriate for deeper phylogenetic scales and more rapidly evolving loci that are informative for phylogeographic and population genomic scales. Second, we assess the efficacy of targeting multiple-locus sets for different taxonomic levels in the same hybrid enrichment reaction, an approach we term hierarchical hybrid enrichment. Third, we apply this approach to the North American chorus frog genus Pseudacris to answer key evolutionary questions across taxonomic and temporal scales. We demonstrate that in this system the type of genomic target that produces the most resolved gene trees differs depending on the taxonomic level, although the potential for error is substantially lower for the deep-scale loci at all levels. We successfully recover data for the two different locus sets with high efficiency. Using hierarchical data targeting deep and shallow levels: we 1) resolve the phylogeny of the genus Pseudacris and introduce a novel visual and hypothesis testing method that uses nodal heat maps to examine the robustness of branch support values to the removal of sites and loci; 2) estimate the phylogeographic history of Pseudacris feriarum, which reveals up to five independent invasions leading to sympatry with congener Pseudacris nigrita to form replicated reinforcement contact zones with ongoing gene flow into sympatry; and 3) quantify with high confidence the frequency of hybridization in one of these zones between P. feriarum and P. nigrita, which is lower than microsatellite-based estimates. We find that the hierarchical hybrid enrichment approach offers an efficient, multitiered data collection method for simultaneously addressing questions spanning multiple evolutionary scales. [Anchored hybrid enrichment; heat map; hybridization; phylogenetics; phylogeography; population genomics; reinforcement; reproductive character displacement.].
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Affiliation(s)
- Sarah E Banker
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Integrative Biology, University of California, Berkeley, #3160 Berkeley, CA 94720-3160, USA
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University 400 Dirac Science Library, Tallahassee, FL 32306, USA
| | - Alyssa Bigelow Hassinger
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 318 W. 12th Avenue, 300 Aronoff Laboratory, Columbus, OH 43210, USA
| | - Mysia Dye
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Sean D Holland
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Michelle L Kortyna
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Oscar E Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
| | - Hannah Ralicki
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA.,Department of Biological Science, University of Connecticut, 91 North Eagleville Road, Storrs, CT 06268, USA
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL 32306, USA
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140
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Silva CNS, Murphy NP, Bell JJ, Green BS, Duhamel G, Cockcroft AC, Hernández CE, Strugnell JM. Global drivers of recent diversification in a marine species complex. Mol Ecol 2021; 30:1223-1236. [PMID: 33342039 DOI: 10.1111/mec.15780] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 11/03/2020] [Accepted: 12/14/2020] [Indexed: 02/06/2023]
Abstract
Investigating historical gene flow in species complexes can indicate how environmental and reproductive barriers shape genome divergence during speciation. The processes influencing species diversification under environmental change remain one of the central focal points of evolutionary biology, particularly for marine organisms with high dispersal potential. We investigated genome-wide divergence, introgression patterns and inferred demographic history between species pairs of all six extant rock lobster species (Jasus spp.), which have a long larval duration of up to two years and have populated continental shelf and seamount habitats around the globe at approximately 40o S. Genetic differentiation patterns reflected geographic isolation and the environment (i.e. habitat structure). Eastern Pacific species (J. caveorum and J. frontalis) were geographically more distant and genetically more differentiated from the remaining four species. Species associated with continental shelf habitats shared a common ancestry, but are geographically distant from one another. Similarly, species associated with island/seamount habitats in the Atlantic and Indian Oceans shared a common ancestry, but are also geographically distant. Benthic temperature was the environmental variable that explained most of the genetic differentiation (FST ), while controlling for the effects of geographic distance. Eastern Pacific species retained a signal of strict isolation following ancient migration, whereas species pairs from Australia and Africa, and seamounts in the Indian and Atlantic oceans, included events of introgression after secondary contact. Our results reveal important effects of habitat and demographic processes on the recent divergence of species within the genus Jasus, providing one of the first empirical studies of genome-wide drivers of diversification that incorporates all extant species in a marine genus with long pelagic larval duration.
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Affiliation(s)
- Catarina N S Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Nicholas P Murphy
- Department of Ecology, Environment & Evolution, La Trobe University, Melbourne, Vic, Australia
| | - James J Bell
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Bridget S Green
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Guy Duhamel
- Département Adaptations du Vivant, BOREA, MNHN, Paris, France
| | - Andrew C Cockcroft
- Department of Agriculture, Forestry and Fisheries, Cape Town, South Africa
| | - Cristián E Hernández
- Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile.,Universidad Católica de Santa María, Arequipa, Perú
| | - Jan M Strugnell
- Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Department of Ecology, Environment & Evolution, La Trobe University, Melbourne, Vic, Australia
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141
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Song Q, Magnuson R, Jalinsky J, Roseman M, Neiman M. Intraspecific genetic variation for anesthesia success in a New Zealand freshwater snail. Genetica 2021; 149:47-54. [PMID: 33389278 DOI: 10.1007/s10709-020-00110-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/20/2020] [Indexed: 11/26/2022]
Abstract
Intraspecific genetic variation can drive phenotypic variation even across very closely related individuals. Here, we demonstrate that genetic differences between snails are a major contributor to wide variation in menthol anesthesia success in an important freshwater snail model system, Potamopyrgus antipodarum. Anesthesia is used to immobilize organisms for experiments and surgical procedures and to humanely mitigate pain. This is the first example of which we are aware of a role for genetic variation in anesthesia success in a mollusk. These findings highlight the fact that using only one strain or lineage for many experiments will not provide a full picture of phenotypic variation, demonstrate the importance of optimizing biomedically relevant techniques and protocols across a variety of genetic backgrounds, illuminate a potential mechanism underlying previously documented challenges in molluscan anesthesia, and set the stage for powerful and humane manipulative experiments in P. antipodarum.
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Affiliation(s)
- Qiudong Song
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | | | - Joseph Jalinsky
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Marissa Roseman
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA.
- Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City, IA, USA.
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142
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Hirase S, Tezuka A, Nagano AJ, Sato M, Hosoya S, Kikuchi K, Iwasaki W. Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population. Evolution 2021; 75:176-194. [PMID: 33165944 PMCID: PMC7898790 DOI: 10.1111/evo.14120] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/14/2020] [Accepted: 09/30/2020] [Indexed: 12/28/2022]
Abstract
Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, that is, dysfunctional interactions between proteins encoded in the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we de novo sequenced the 747-Mb genome of the coastal goby, Chaenogobius annularis, and investigated its integrative genomic phylogeographics using RNA-sequencing, RAD-sequencing, genome resequencing, whole mitogenome sequencing, amplicon sequencing, and small RNA-sequencing. Chaenogobius annularis populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archipelago. Despite the divergence history and potential mitonuclear incompatibility between these lineages, the mitogenomes of the PO and SJ lineages have coexisted for generations in a hybrid population on the Sanriku Coast. Our analyses revealed accumulation of nonsynonymous substitutions in the PO-lineage mitogenomes, including two convergent substitutions, as well as signals of mitochondrial lineage-specific selection on mitochondria-related nuclear genes. Finally, our data implied that a microRNA gene was involved in resolving mitonuclear incompatibility. Our integrative genomic phylogeographic approach revealed that mitonuclear incompatibility can affect genome evolution in a natural hybrid population.
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Affiliation(s)
- Shotaro Hirase
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoBunkyo‐kuTokyo113‐0032Japan
- Fisheries LaboratoryGraduate School of Agricultural and Life SciencesThe University of TokyoHamamatsuShizuoka431‐0214Japan
| | - Ayumi Tezuka
- Faculty of AgricultureRyukoku UniversityOtsuShiga520–2194Japan
| | | | - Mana Sato
- Fisheries LaboratoryGraduate School of Agricultural and Life SciencesThe University of TokyoHamamatsuShizuoka431‐0214Japan
| | - Sho Hosoya
- Fisheries LaboratoryGraduate School of Agricultural and Life SciencesThe University of TokyoHamamatsuShizuoka431‐0214Japan
| | - Kiyoshi Kikuchi
- Fisheries LaboratoryGraduate School of Agricultural and Life SciencesThe University of TokyoHamamatsuShizuoka431‐0214Japan
| | - Wataru Iwasaki
- Department of Biological SciencesGraduate School of ScienceThe University of TokyoBunkyo‐kuTokyo113‐0032Japan
- Atmosphere and Ocean Research InstituteThe University of TokyoKashiwaChiba277–8564Japan
- Department of Computational Biology and Medical SciencesGraduate School of Frontier SciencesThe University of TokyoKashiwaChiba277–8561Japan
- Institute for Quantitative BiosciencesThe University of TokyoBunkyo‐kuTokyo113‐0032Japan
- Collaborative Research Institute for Innovative MicrobiologyThe University of TokyoBunkyo‐kuTokyo113‐0032Japan
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143
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Reproduction in Urbanised Coastal Waters: Shallow-Water Sea Anemones (Entacmaea quadricolor and Stichodactyla haddoni) Maintain High Genetic Diversity and Panmixia. DIVERSITY 2020. [DOI: 10.3390/d12120467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Sea anemones are sedentary marine animals that tend to disperse via planktonic larvae and are predicted to have high population connectivity in undisturbed habitats. We test whether two sea anemone species living in two different tidal zones of a highly disturbed marine environment can maintain high genetic connectivity. More than 1000 loci with single-nucleotide polymorphisms (SNPs) were obtained with double-digest RADseq for 81 Stichodactyla haddoni and 99 Entacmaea quadricolor individuals to test for population genetic structure. We find evidence that both species predominantly propagate via sexual reproduction, and asexual reproduction is limited. We observe panmixia that indicates the absence of effective dispersal barriers for these species living in a highly anthropogenically disturbed environment. This is positive news for both species that are also found in the aquarium trade. More fundamentally, our results suggest that inhabiting different parts of a shallow reef may not affect a species’ population connectivity nor favour asexual reproduction.
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144
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Pavičić M, Žužul I, Matić-Skoko S, Triantafyllidis A, Grati F, Durieux EDH, Celić I, Šegvić-Bubić T. Population Genetic Structure and Connectivity of the European Lobster Homarus gammarus in the Adriatic and Mediterranean Seas. Front Genet 2020; 11:576023. [PMID: 33365046 PMCID: PMC7750201 DOI: 10.3389/fgene.2020.576023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/11/2020] [Indexed: 11/13/2022] Open
Abstract
Highly selective fishing has the potential to permanently change the characteristics within a population and could drive the decline of genetic diversity. European lobster is an intensively fished crustacean species in the Adriatic Sea which reaches high market value. Since knowledge of population structure and dynamics is important for effective fisheries management, in this study, we used 14 neutral microsatellites loci and partial mitochondrial COI region sequencing to explore population connectivity and genetic structure by comparing samples from the Adriatic Sea and the adjacent basins of the Mediterranean Sea. The obtained results suggest that neutral genetic diversity has not been significantly affected by decrease in population size due to overfishing, habitat degradation and other anthropogenic activities. Global genetic differentiation across all populations was low (F ST = 0.0062). Populations from the Adriatic Sea were panmictic, while genetic differentiation was found among populations from different Mediterranean basins. Observed gene flow for European lobster suggest that populations in the north eastern Adriatic act as a source for surrounding areas, emphasizing the need to protect these populations by establishing interconnected MPAs that will be beneficial for both fisheries and conservation management.
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Affiliation(s)
- Mišo Pavičić
- Institute of Oceanography and Fisheries, Split, Croatia
| | - Iva Žužul
- Institute of Oceanography and Fisheries, Split, Croatia
| | | | | | - Fabio Grati
- Institute for Biological Resources and Marine Biotechnologies (IRBIM), National Research Council (CNR), Ancona, Italy
| | - Eric D. H. Durieux
- UMR CNRS 6134 Sciences Pour l’Environnement, Università di Corsica Pasquale Paoli, Corte, France
- UMS CNRS 3514 STELLA MARE, Università di Corsica Pasquale Paoli, Biguglia, France
| | - Igor Celić
- National Institute of Oceanography and Applied Geophysics – OGS, Trieste, Italy
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145
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Ospina OE, Tieu L, Apodaca JJ, Lemmon EM. Hidden Diversity in the Mountain Chorus Frog (Pseudacris brachyphona) and the Diagnosis of a New Species of Chorus Frog in the Southeastern United States. COPEIA 2020. [DOI: 10.1643/ch2020009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Oscar E. Ospina
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| | - Lynee Tieu
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
| | - Joseph J. Apodaca
- Tangled Bank Conservation, 128 Bingham Road, Suite 1150, Asheville, North Carolina 28806;
| | - Emily Moriarty Lemmon
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, Florida 32306; (EML) . Send reprint requests to this address
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146
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Manco R, Chiaiese P, Basile B, Corrado G. Comparative analysis of genomic- and EST-SSRs in European plum ( Prunus domestica L.): implications for the diversity analysis of polyploids. 3 Biotech 2020; 10:543. [PMID: 33235823 PMCID: PMC7679426 DOI: 10.1007/s13205-020-02513-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/27/2020] [Indexed: 11/23/2022] Open
Abstract
Simple sequence repeats (SSRs) are among the most useful DNA markers in plant science. The aim of this study was to compare the features and usefulness of genomic SSR (gSSR) and EST-SSRs in European plum (Prunus domestica L.), an economically important, hexaploid stone fruit crop globally cultivated to produce fleshy fruits and derived foodstuff. The analysis of an ample set of morphologically diverse varieties indicated that gSSRs and EST-SSRs provide different estimates of some of the locus-based indicators of diversity. Moreover, the two classes of SSRs gave different, weakly correlated, estimations of distance-based parameters with gSSRs being more powerful for discriminating purposes. The two SSR classes provide complementary information in European plum, making the contribution of EST-SSRs useful not only as non-neutral markers. The differences between SSR classes are discussed considering the neutral and non-neutral evolution, and the polyploidy and asexual propagation of the cultivated tree varieties.
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147
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Brauer CJ, Beheregaray LB. Recent and rapid anthropogenic habitat fragmentation increases extinction risk for freshwater biodiversity. Evol Appl 2020; 13:2857-2869. [PMID: 33294027 PMCID: PMC7691462 DOI: 10.1111/eva.13128] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 12/16/2022] Open
Abstract
Anthropogenic habitat fragmentation is often implicated as driving the current global extinction crisis, particularly in freshwater ecosystems. The genetic signal of recent population isolation can be confounded by the complex spatial arrangement of dendritic river systems. Consequently, many populations may presently be managed separately based on an incorrect assumption that they have evolved in isolation. Integrating landscape genomics data with models of connectivity that account for landscape structure, we show that the cumulative effects of multiple in-stream barriers have contributed to the recent decline of a freshwater fish from the Murray-Darling Basin, Australia. In addition, individual-based eco-evolutionary simulations further demonstrate that contemporary inferences about population isolation are consistent with the 160-year time frame since construction of in-stream barriers began in the region. Our findings suggest that the impact of very recent fragmentation may be often underestimated for freshwater biodiversity. We argue that proactive conservation measures to reconnect many riverine populations are urgently needed.
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Affiliation(s)
- Chris J. Brauer
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
| | - Luciano B. Beheregaray
- Molecular Ecology Laboratory, College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
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148
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Tyler J, Bonfitto MT, Clucas GV, Reddy S, Younger JL. Morphometric and genetic evidence for four species of gentoo penguin. Ecol Evol 2020; 10:13836-13846. [PMID: 33391684 PMCID: PMC7771148 DOI: 10.1002/ece3.6973] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/09/2020] [Accepted: 10/14/2020] [Indexed: 12/31/2022] Open
Abstract
Gentoo penguins (Pygoscelis papua) are found across the Southern Ocean with a circumpolar distribution and notable genetic and morphological variation across their geographic range. Whether this geographic variation represents species-level diversity has yet to be investigated in an integrative taxonomic framework. Here, we show that four distinct populations of gentoo penguins (Iles Kerguelen, Falkland Islands, South Georgia, and South Shetlands/Western Antarctic Peninsula) are genetically and morphologically distinct from one another. We present here a revised taxonomic treatment including formal nomenclatural changes. We suggest the designation of four species of gentoo penguin: P. papua in the Falkland Islands, P. ellsworthi in the South Shetland Islands/Western Antarctic Peninsula, P. taeniata in Iles Kerguelen, and a new gentoo species P. poncetii, described herein, in South Georgia. These findings of cryptic diversity add to many other such findings across the avian tree of life in recent years. Our results further highlight the importance of reassessing species boundaries as methodological advances are made, particularly for taxa of conservation concern. We recommend reassessment by the IUCN of each species, particularly P. taeniata and P. poncetii, which both show evidence of decline.
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Affiliation(s)
- Joshua Tyler
- Department of Biology & BiochemistryMilner Centre for EvolutionUniversity of BathBathUK
| | | | - Gemma V. Clucas
- Cornell Lab of OrnithologyCornell UniversityIthacaNYUSA
- Cornell Atkinson Center for a Sustainable FutureCornell UniversityIthacaNYUSA
| | - Sushma Reddy
- Bell Museum of Natural HistoryDepartment of Fisheries, Wildlife, and Conservation BiologyUniversity of MinnesotaSt. PaulMNUSA
| | - Jane L. Younger
- Department of Biology & BiochemistryMilner Centre for EvolutionUniversity of BathBathUK
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149
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Mizeriene G, Cerny K, Zyka V, Bakonyi J, Nagy ZÁ, Oliva J, Redondo MA, Corcobado T, Martín-García J, Prospero S. Patterns of Genetic Diversification in the Invasive Hybrid Plant Pathogen Phytophthora × alni and Its Parental Species P. uniformis. PHYTOPATHOLOGY 2020; 110:1959-1969. [PMID: 32633698 DOI: 10.1094/phyto-12-19-0475-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In pathogenic fungi and oomycetes, interspecific hybridization may lead to the formation of new species having a greater impact on natural ecosystems than the parental species. From the early 1990s, a severe alder (Alnus spp.) decline due to an unknown Phytophthora species was observed in several European countries. Genetic analyses revealed that the disease was caused by the triploid hybrid P. × alni, which originated in Europe from the hybridization of P. uniformis and P. × multiformis. Here, we investigated the population structure of P. × alni (158 isolates) and P. uniformis (85 isolates) in several European countries using microsatellite markers. Our analyses confirmed the genetic structure previously observed in other European populations, with P. uniformis populations consisting of at most two multilocus genotypes (MLGs) and P. × alni populations dominated by MLG Pxa-1. The genetic structure of P. × alni populations in the Czech Republic, Hungary and Sweden seemed to reflect the physical isolation of river systems. Most rare P. × alni MLGs showed a loss of heterozygosity (LOH) at one or a few microsatellite loci compared with other MLGs. This LOH may allow a stabilization within the P. × alni genome or a rapid adaptation to stress situations. Alternatively, alleles may be lost because of random genetic drift in small, isolated populations, with no effect on fitness of P. × alni. Additional studies would be necessary to confirm these patterns of population diversification and to better understand the factors driving it.
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Affiliation(s)
- Goda Mizeriene
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, CH-8903 Birmensdorf, Switzerland
- Institute of Botany at The Lithuanian State Research Institute Nature Research Centre, Žaliųjų Ežerų Str. 49, LT-08406 Vilnius, Lithuania
| | - Karel Cerny
- The Silva Tarouca Research Institute for Landscape and Ornamental Gardening (RILOG), Květnové náměstí 391, Průhonice 252 43, The Czech Republic
| | - Vladimir Zyka
- The Silva Tarouca Research Institute for Landscape and Ornamental Gardening (RILOG), Květnové náměstí 391, Průhonice 252 43, The Czech Republic
| | - József Bakonyi
- Plant Protection Institute, Centre for Agricultural Research, Herman Ottó Str. 15, H-1022 Budapest, Hungary
| | - Zoltán Árpád Nagy
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
| | - Jonas Oliva
- Department Crop and Forest Sciences, University of Lleida, Alcalde Rovira Roure 191, 25198, Lleida, Spain
- Joint Research Unit CTFC-Agrotecnio, Alcalde Rovira Roure 191 Lleida, 25198, Spain
| | - Miguel Angel Redondo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
| | - Tamara Corcobado
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
- Federal Research and Training Centre for Forests, Natural Hazards and Landscape (BFW), Seckendorff-Gudent-Weg 8, 1131 Vienna, Austria
| | - Jorge Martín-García
- Department of Biology, CESAM (Centre for Environmental and Marine Studies), University of Aveiro, Campus Universitario de Santiago, 3810-193 Aveiro, Portugal
- Department of Plant Production and Forest Resources, University of Valladolid, Avenida de Madrid 44, 34071 Palencia, Spain
| | - Simone Prospero
- Swiss Federal Research Institute WSL, Zuercherstrasse 111, CH-8903 Birmensdorf, Switzerland
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150
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Understanding the genetic diversity of the guayabillo (Psidium galapageium), an endemic plant of the Galapagos Islands. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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