scholarly journals Genetic structure and diversity of the selfing model grassBrachypodium stacei(Poaceae) in Western Mediterranean: out of the Iberian Peninsula and into the islands

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2407 ◽  
Author(s):  
Valeriia Shiposha ◽  
Pilar Catalán ◽  
Marina Olonova ◽  
Isabel Marques
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Iberian Peninsula ◽  
Canary Islands ◽  
Population Genetic ◽  
Western Mediterranean ◽  
Life Cycles ◽  
Detailed Knowledge ◽  
Genome Wide Association Studies

Annual Mediterranean species of the genusBrachypodiumare promising model plants for energy crops since their selfing nature and short-life cycles are an advantage in breeding programs. The false brome,B. distachyon, has already been sequenced and new genomic initiatives have triggered the de-novo genome sequencing of its close relatives such asB. stacei, a species that was until recently mistaken forB. distachyon. However, the success of these initiatives hinges on detailed knowledge about the distribution of genetic variation within and among populations for the effective use of germplasm in a breeding program. Understanding population genetic diversity and genetic structure is also an important prerequisite for designing effective experimental populations for genomic wide studies. However, population genetic data are still limited inB. stacei. We therefore selected and amplified 10 nuclear microsatellite markers to depict patterns of population structure and genetic variation among 181 individuals from 19 populations ofB. staceioccurring in its predominant range, the western Mediterranean area: mainland Iberian Peninsula, continental Balearic Islands and oceanic Canary Islands. Our genetic results support the occurrence of a predominant selfing system with extremely high levels of homozygosity across the analyzed populations. Despite the low level of genetic variation found, two different genetic clusters were retrieved, one clustering all SE Iberian mainland populations and the island of Minorca and another one grouping all S Iberian mainland populations, the Canary Islands and all Majorcan populations except one that clustered with the former group. These results, together with a high sharing of alleles (89%) suggest different colonization routes from the mainland Iberian Peninsula into the islands. A recent colonization scenario could explain the relatively low levels of genetic diversity and low number of alleles found in the Canary Islands populations while older colonization events are hypothesized to explain the high genetic diversity values found in the Majorcan populations. Our study provides widely applicable information about geographical patterns of genetic variation inB. stacei. Among others, the genetic pattern and the existence of local alleles will need to be adequately reflected in the germplasm collection ofB. staceifor efficient genome wide association studies.

Genetic Diversity and Population Genetic Structure in the Rare Chittering Grass Wattle, Acacia anomala Court

1988 ◽  
Vol 36 (3) ◽  
pp. 273 ◽  
Author(s):  
DJ Coates
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Genetic System ◽  
Small Population ◽  
Vegetative Multiplication ◽  
The Mean ◽  
Allozyme Loci

There are 10 known populations of Acacia anomala occurring in two small disjunct groups some 30 km apart. The Chittering populations reproduce sexually whereas the Kalamunda populations appear to reproduce almost exclusively by vegetative multiplication. The level and distribution of genetic variation were studied at 15 allozyme loci. Two loci were monomorphic in all populations. In the Chittering populations the mean number of alleles per locus was 2.0 and the expected panmictic heterozygosity (genetic diversity) 0.209. In the Kalamunda populations the mean number of alleles per locus was 1.15 and the expected panmictic heterozygosity 0.079, although the observed heterozygosity of 0.150 was only marginally less than the Chittering populations (0.177). These data support the contention that the Chittering populations are primarily outcrossing whereas the Kalamunda populations are clonal, with each population consisting of individuals with identical and, in three of the four populations, heterozygous, multilocus genotypes. The level of genetic diversity within the Chittering populations is high for plants in general even though most populations are relatively smsll and isolated. It is proposed that either the length of time these populations have been reduced in size and isolated is insufficient for genetic diversity to be reduced or the genetic system of this species is adapted to small population conditions. Strategies for the adequate conservation of the genetic resources of Acacia anomala are discussed.

scholarly journals Variable opportunities for outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Anna-Liisa Laine ◽  
Benoit Barrès ◽  
Elina Numminen ◽  
Jukka P Siren
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Fungal Pathogen ◽  
Population Genetic ◽  
Reproductive Strategies ◽  
Natural Populations ◽  
Pathogen Population ◽  
To Come ◽  
Pathogen Populations

Many pathogens possess the capacity for sex through outcrossing, despite being able to reproduce also asexually and/or via selfing. Given that sex is assumed to come at a cost, these mixed reproductive strategies typical of pathogens have remained puzzling. While the ecological and evolutionary benefits of outcrossing are theoretically well-supported, support for such benefits in pathogen populations are still scarce. Here, we analyze the epidemiology and genetic structure of natural populations of an obligate fungal pathogen, Podosphaera plantaginis. We find that the opportunities for outcrossing vary spatially. Populations supporting high levels of coinfection –a prerequisite of sex – result in hotspots of novel genetic diversity. Pathogen populations supporting coinfection also have a higher probability of surviving winter. Jointly our results show that outcrossing has direct epidemiological consequences as well as a major impact on pathogen population genetic diversity, thereby providing evidence of ecological and evolutionary benefits of outcrossing in pathogens.

scholarly journals Population Genetic Structure of Laurus nobilis L. Inferred From Transferred Nuclear Microsatellites

2009 ◽  
Vol 58 (1-6) ◽  
pp. 270-276 ◽  
Author(s):  
H. Marzouki ◽  
N. Nasri ◽  
B. Jouaud ◽  
C. Bonnet ◽  
A. Khaldi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Eastern Mediterranean ◽  
Western Mediterranean ◽  
Nuclear Microsatellites ◽  
Distribution Area ◽  
Gene Pools ◽  
Laurus Nobilis ◽  
The Mediterranean

Abstract Species with fragmented populations and low population size often display low within-population genetic diversity and strong among-population differentiation. Laurus nobilis L. (Lauraceae), common laurel, has a scattered distribution throughout the Mediterranean, with only few autochthonous populations. Our goal was to elucidate if this species has range-wide genetic structure and if planted material can be traced back to its origin. Genetic diversity was investigated using 4 polymorphic nuclear microsatellites (nSSR) transferred from two species of Lauraceae. Sixty-six laurel trees were selected from 7 widely separated populations within the Mediterranean distribution area of the species. A total of 34 alleles (9 alleles per locus on average) were found. Mean genetic diversity within-population (Hs), was 0.558. Genetic differentiation among populations (GST = 0.243) was high compared to that of other angiosperms. Laurus nobilis can be separated into two main gene pools, one from western (Tunisia, Algeria and France) and the other from eastern Mediterranean (Turkey). The Algerian, Tunisian and French populations presented a strong genetic similarity, compatible with the fact that North African laurel populations could be recently introduced from north-western Mediterranean stock.

scholarly journals Population genetic structure and connectivity patterns of the kanae (Mugil cephalus) in New Zealand inland and coastal waters

2021 ◽  
Author(s):  
◽  
Angel Jimenez Brito
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
New Zealand ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Coastal Waters ◽  
Population Genetic ◽  
Mugil Cephalus ◽  
Connectivity Patterns

<p>Mugil cephalus is a cosmopolitan fish species found in most coastal waters from tropical to temperate zones. It is a species common in the near-shore marine environment, and known to reside in estuarine and freshwater systems. Adult M. cephalus move out to sea to spawn in aggregations. Their larvae can drift on surface ocean currents for over a month before recruitment to nursery grounds. Mugil cephalus is a species that is closely associated with the coastal environment, but it is capable of interoceanic migrations. Population genetic studies have reported high levels of genetic differentiation among populations in the Mediterranean, Atlantic and western Pacific. However, there is no evidence to suggest reproductive incompatibility has arisen among populations. In New Zealand M. cephalus supports important recreational, commercial and customary fisheries, but very little is known about the distribution and connectivity among populations.  The aim of this study was to use nuclear microsatellite DNA (msatDNA) and mitochondrial DNA (mtDNA) markers to describe the population genetic structure, connectivity patterns and to determine the phylogeographic history of New Zealand M. cephalus populations. Total of 850 samples were collected (576 adults and 274 juveniles) during the summers of 2010 and 2014-2015 from 15 locations around coastal and inland waters of the North Island, and one location in Marlborough Sounds. In addition, 245 mtDNA sequences were added from previously published studies and used to outgroup the New Zealand population and place it into the context of the other Pacific populations.  Seven msatDNA loci were isolated and used to determine the population genetic structure and connectivity patterns of M. cephalus in New Zealand. Admixture of four genetically distinct groups or populations was identified and a chaotic spatial distribution of allele frequencies. Within each population there was significant gene flow among locations, no pattern of genetic isolation-by-distance was identified and there was a high proportion of non-migrant individuals. There was evidence of bottlenecks and seasonal reproductive variation of adults, which could explain the significant shifts in the effective population size among locations.  To test whether the pattern of genetic variation in M. cephalus populations was the result of seasonal variability in the reproductive success of adults, DNA from adult and juvenile samples were used to test for differences in the levels of genetic variation between generations (cohorts). Juveniles were grouped by age classes and compared to the adults. The levels of genetic diversity within the groups of juveniles were compared to the adult population and significant genetic bottlenecks between juveniles and adults were detected. This pattern was consistent with the Sweepstake-Reproductive-Success hypothesis. Two spawning groups in the adults were identified, an early spawning group and a late spawning group.  The analysis of DNA sequence data from the mtDNA Cytochrome Oxidase subunit 1 (COX1) gene and D-loop region showed two sympatric haplogroups of M. cephalus. New Zealand was most likely colonised by M. cephalus migrants from different population sources from the Pacific first ~50,000 and a second wave of migrants from Australia between ~20, 000 and ~16,000 years ago. High levels of gene flow were detected, but there has not been enough time for genetic drift to completely sort the lineages.  The findings of this thesis research will help with the understanding of aspects of M. cephalus dispersal and the genetic structure of populations. The patterns of connectivity can be used to better align the natural boundaries of wild populations to the fishery management stock structure. Understanding the reproductive units, levels of genetic diversity and the patterns of reproduction of M. cephalus will assist management efforts to focus on the key habitats threats, risks and the long-term sustainability of the species.</p>

scholarly journals Population genetic structure and connectivity patterns of the kanae (Mugil cephalus) in New Zealand inland and coastal waters

2021 ◽  
Author(s):  
◽  
Angel Jimenez Brito
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
New Zealand ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Coastal Waters ◽  
Population Genetic ◽  
Mugil Cephalus ◽  
Connectivity Patterns

<p>Mugil cephalus is a cosmopolitan fish species found in most coastal waters from tropical to temperate zones. It is a species common in the near-shore marine environment, and known to reside in estuarine and freshwater systems. Adult M. cephalus move out to sea to spawn in aggregations. Their larvae can drift on surface ocean currents for over a month before recruitment to nursery grounds. Mugil cephalus is a species that is closely associated with the coastal environment, but it is capable of interoceanic migrations. Population genetic studies have reported high levels of genetic differentiation among populations in the Mediterranean, Atlantic and western Pacific. However, there is no evidence to suggest reproductive incompatibility has arisen among populations. In New Zealand M. cephalus supports important recreational, commercial and customary fisheries, but very little is known about the distribution and connectivity among populations.  The aim of this study was to use nuclear microsatellite DNA (msatDNA) and mitochondrial DNA (mtDNA) markers to describe the population genetic structure, connectivity patterns and to determine the phylogeographic history of New Zealand M. cephalus populations. Total of 850 samples were collected (576 adults and 274 juveniles) during the summers of 2010 and 2014-2015 from 15 locations around coastal and inland waters of the North Island, and one location in Marlborough Sounds. In addition, 245 mtDNA sequences were added from previously published studies and used to outgroup the New Zealand population and place it into the context of the other Pacific populations.  Seven msatDNA loci were isolated and used to determine the population genetic structure and connectivity patterns of M. cephalus in New Zealand. Admixture of four genetically distinct groups or populations was identified and a chaotic spatial distribution of allele frequencies. Within each population there was significant gene flow among locations, no pattern of genetic isolation-by-distance was identified and there was a high proportion of non-migrant individuals. There was evidence of bottlenecks and seasonal reproductive variation of adults, which could explain the significant shifts in the effective population size among locations.  To test whether the pattern of genetic variation in M. cephalus populations was the result of seasonal variability in the reproductive success of adults, DNA from adult and juvenile samples were used to test for differences in the levels of genetic variation between generations (cohorts). Juveniles were grouped by age classes and compared to the adults. The levels of genetic diversity within the groups of juveniles were compared to the adult population and significant genetic bottlenecks between juveniles and adults were detected. This pattern was consistent with the Sweepstake-Reproductive-Success hypothesis. Two spawning groups in the adults were identified, an early spawning group and a late spawning group.  The analysis of DNA sequence data from the mtDNA Cytochrome Oxidase subunit 1 (COX1) gene and D-loop region showed two sympatric haplogroups of M. cephalus. New Zealand was most likely colonised by M. cephalus migrants from different population sources from the Pacific first ~50,000 and a second wave of migrants from Australia between ~20, 000 and ~16,000 years ago. High levels of gene flow were detected, but there has not been enough time for genetic drift to completely sort the lineages.  The findings of this thesis research will help with the understanding of aspects of M. cephalus dispersal and the genetic structure of populations. The patterns of connectivity can be used to better align the natural boundaries of wild populations to the fishery management stock structure. Understanding the reproductive units, levels of genetic diversity and the patterns of reproduction of M. cephalus will assist management efforts to focus on the key habitats threats, risks and the long-term sustainability of the species.</p>

Genetic variation in Trillium erectum (Melanthiaceae), a widespread forest herb in eastern North America

2004 ◽  
Vol 82 (3) ◽  
pp. 316-321 ◽  
Author(s):  
Steven R Griffin ◽  
Spencer CH Barrett
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
North America ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Eastern North America ◽  
Mixed Mating ◽  
Allozyme Loci

Trillium erectum L. is an insect-pollinated understory herb widespread in forests of eastern North America. Marker gene studies indicate that the species has a mixed mating system, but aspects of population genetic structure have not been investigated. Using 10 allozyme loci, we measured genetic variation within and among 23 populations sampled from throughout the species' range. Overall, T. erectum displayed moderate levels of genetic diversity in comparison with other herbaceous plants. The percentage of loci that were polymorphic was 52%, with average values (±SE) of 1.20 ± 0.02, 0.08 ± 0.01, and 0.13 ± 0.01 for the number of alleles per locus (A), observed heterozygosity (Ho), and expected heterozygosity (He), respectively. There was evidence of inbreeding within populations (Fis = 0.39, 95% CI 0.26–0.55) and significant population differentiation (Fst = 0.16, 0.05–0.24). Analysis of genetic data provided no evidence of isolation by distance, and together with the occurrence of population subdivision, this suggests that there is relatively limited contemporary gene flow among populations. Northern populations of T. erectum tended to have less genetic variability than southern populations, probably as a result of historical factors associated with post glacial migration. Limited opportunities for gene dispersal as a result of low plant densities, the capacity for self-fertilization, and local seed dispersal by ants are likely to be the main factors maintaining contemporary patterns of genetic variation in T. erectum. Key words: allozymes, genetic diversity, gene flow, population genetic structure, Trillium.

Significant genetic differences among Heterodera schachtii populations within and among sugar beet production areas

Nematology ◽  
2020 ◽  
Vol 22 (2) ◽  
pp. 165-177 ◽  
Author(s):  
Rasha Haj Nuaima ◽  
Johannes Roeb ◽  
Johannes Hallmann ◽  
Matthias Daub ◽  
Holger Heuer
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Spatial Scales ◽  
Geographic Distance ◽  
Heterodera Schachtii ◽  
Parasitic Nematodes ◽  
Neutral Genetic Variation ◽  
Production Areas

Summary Characterising the non-neutral genetic variation within and among populations of plant-parasitic nematodes is essential to determine factors shaping the population genetic structure. This study describes the genetic variation of the parasitism gene vap1 within and among geographic populations of the beet cyst nematode Heterodera schachtii. Forty populations of H. schachtii were sampled at four spatial scales: 695 km, 49 km, 3.1 km and 0.24 km. DGGE fingerprinting showed significant differences in vap1 patterns among populations. High similarity of vap1 patterns appeared between geographically close populations, and occasionally among distant populations. Analysis of spatially sampled populations within fields revealed an effect of tillage direction on the vap1 similarity for two of four studied fields. Overall, geographic distance and similarity of vap1 patterns of H. schachtii populations were negatively correlated. In conclusion, the population genetic structure was shaped by the interplay between the genetic adaptation and the passive transport of this nematode.

scholarly journals Intraspecific divergences and phylogeography of Panzerina lanata (Lamiaceae) in Northwest China

2018 ◽  
Author(s):  
Yanfen Zhao ◽  
Hongxiang Zhang ◽  
Borong Pan ◽  
Mingli Zhang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Population Genetic ◽  
Divergence Time ◽  
Northwest China ◽  
Northwestern China ◽  
Intraspecific Diversity ◽  
Early Pleistocene ◽  
Helan Mountains ◽  
The Impact

Climactic fluctuations during the Quaternary played a crucial role in genetic diversity and population genetic structure of many plant species in northwestern China. In order to understand the impact of climate change on herbaceous plants, we studied Panzerina lanata (Lamiaceae), a widely distributed species. Two chloroplast DNA intergenic spacers (trnH-psbA and rpoB-trnC) were used to sequence 269 individuals from 27 populations and seven haplotypes were identified. Genetic structure and demographic characteristics were estimated using AMOVA, neutrality tests, and mismatch distribution analyses. The divergence times between the seven haplotypes were estimated using Beast. Our results revealed high levels of total genetic diversity (HT = 0.673±0.0869) and low levels of average within-population genetic diversity (HS = 0.033±0.0214). The analysis of molecular variance indicated major genetic differentiation among the three groups: northern, central, and eastern group. The species distribution modeling and demographic analysis indicated that P. lanata has not experience a recent range expansion. The divergence time within P. lanata occurred between the early Pleistocene and the late Pleistocene, which coincides with aridification and the expansion of the deserts in northwestern China that resulted in species diversification and habitat fragmentation. In addition, we speculate that the deserts and the Helan Mountains acted as effective geographic barriers that led to intraspecific diversity.

scholarly journals Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications

2021 ◽  
Vol 9 ◽  
Author(s):  
Heather R. Kates ◽  
Fernando López Anido ◽  
Guillermo Sánchez-de la Vega ◽  
Luis E. Eguiarte ◽  
Pamela S. Soltis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Morphological Diversity ◽  
Cucurbita Maxima ◽  
Wild Progenitor ◽  
Breeding Potential ◽  
Trait Improvement ◽  
Wild Progenitors

Studies of domestication genetics enrich our understanding of how domestication shapes genetic and morphological diversity. We characterized patterns of genetic variation in two independently domesticated pumpkins and their wild progenitors to assess and compare genetic consequences of domestication. To compare genetic diversity pre- and post-domestication and to identify genes targeted by selection during domestication, we analyzed ∼15,000 SNPs of 48 unrelated accessions, including wild, landrace, and improved lines for each of two pumpkin species, Cucurbita argyrosperma and Cucurbita maxima. Genetic diversity relative to its wild progenitor was reduced in only one domesticated subspecies, C. argyrosperma ssp. argyrosperma. The two species have different patterns of genetic structure across domestication status. Only 1.5% of the domestication features identified for both species were shared between species. These findings suggest that ancestral genetic diversity, wild-crop gene flow, and domestication practices shaped the genetic diversity of two similar Cucurbita crops in different ways, adding to our understanding of how genetic diversity changes during the processes of domestication and how trait improvement impacts the breeding potential of modern crops.

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