Population genetic variation in the New Zealand greenshell mussel: locus-dependent conflicting signals of weak structure and high gene flow balanced against pronounced structure and high self-recruitment

Abstract Background and Aims Mikania micrantha, a climbing perennial weed of the family Asteraceae, is native to Latin America and is highly invasive in the tropical belt of Asia, Oceania and Australia. This study was framed to investigate the population structure of M. micrantha at a large spatial scale in Asia and to identify how introduction history, evolutionary forces and landscape features influenced the genetic pattern of the species in this region. Methods We assessed the genetic diversity and structure of 1052 individuals from 46 populations for 12 microsatellite loci. The spatial pattern of genetic variation was investigated by estimating the relationship between genetic distance and geographical, climatic and landscape resistances hypothesized to influence gene flow between populations. Key Results We found high genetic diversity of M. micrantha in this region, as compared with the genetic diversity parameters of other invasive species. Spatial and non-spatial clustering algorithms identified the presence of multiple genetic clusters and admixture between populations. Most of the populations showed heterozygote deficiency, primarily due to inbreeding, and the founder populations showed evidence of a genetic bottleneck. Persistent gene flow throughout the invasive range caused low genetic differentiation among populations and provided beneficial genetic variation to the marginal populations in a heterogeneous environment. Environmental suitability was found to buffer the detrimental effects of inbreeding at the leading edge of range expansion. Both linear and non-linear regression models demonstrated a weak relationship between genetic distance and geographical distance, as well as bioclimatic variables and environmental resistance surfaces. Conclusions These findings provide evidence that extensive gene flow and admixture between populations have influenced the current genetic pattern of M. micrantha in this region. High gene flow across the invaded landscape may facilitate adaptation, establishment and long-term persistence of the population, thereby indicating the range expansion ability of the species.

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Using population genetic tools to develop a control strategy for feral cats (Felis catus) in Hawai'i

Wildlife Research ◽

10.1071/wr07043 ◽

2007 ◽

Vol 34 (8) ◽

pp. 587 ◽

Cited By ~ 17

Author(s):

Heidi Hansen ◽

Steven C. Hess ◽

David Cole ◽

Paul C. Banko

Keyword(s):

Genetic Diversity ◽

Invasive Species ◽

Population Genetics ◽

Gene Flow ◽

Population Genetic ◽

Effective Control ◽

Feral Cats ◽

Genetic Tools ◽

High Gene Flow ◽

High Gene

Population genetics can provide information about the demographics and dynamics of invasive species that is beneficial for developing effective control strategies. We studied the population genetics of feral cats on Hawai‘i Island by microsatellite analysis to evaluate genetic diversity and population structure, assess gene flow and connectivity among three populations, identify potential source populations, characterise population dynamics, and evaluate sex-biased dispersal. High genetic diversity, low structure, and high number of migrants per generation supported high gene flow that was not limited spatially. Migration rates revealed that most migration occurred out of West Mauna Kea. Effective population size estimates indicated increasing cat populations despite control efforts. Despite high gene flow, relatedness estimates declined significantly with increased geographic distance and Bayesian assignment tests revealed the presence of three population clusters. Genetic structure and relatedness estimates indicated male-biased dispersal, primarily from Mauna Kea, suggesting that this population should be targeted for control. However, recolonisation seems likely, given the great dispersal ability that may not be inhibited by barriers such as lava flows. Genetic monitoring will be necessary to assess the effectiveness of future control efforts. Management of other invasive species may benefit by employing these population genetic tools.

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

10.26686/wgtn.17072060.v1 ◽

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>

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Host movement and the genetic structure of populations of parasitic nematodes.

Genetics ◽

10.1093/genetics/141.3.1007 ◽

1995 ◽

Vol 141 (3) ◽

pp. 1007-1014 ◽

Cited By ~ 10

Author(s):

M S Blouin ◽

C A Yowell ◽

C H Courtney ◽

J B Dame

Keyword(s):

Gene Flow ◽

Genetic Structure ◽

Population Genetic ◽

Isolation By Distance ◽

Parasitic Nematodes ◽

Great Opportunity ◽

High Gene Flow ◽

Mtdna Sequence ◽

High Gene ◽

Host Movement

Abstract Mitochondrial DNA (mtDNA) sequence data were used to compare the population genetic structures of five species of parasitic nematodes from three different hosts: Ostertagia ostertagi and Haemonchus placei from cattle, H. contortus and Teladorsagia circumcincta from sheep, and Mazamastrongylus odocoilei from white-tailed deer. The parasites of sheep and cattle showed a pattern consistent with high gene flow among populations. The parasite of deer showed a pattern of substantial population subdivision and isolation by distance. It appears that host movement is an important determinant of population genetic structure in these nematodes. High gene flow in the parasites of livestock also indicates great opportunity for the spread of rare alleles that confer resistance to anthelmintic drugs. All species, including the parasite of deer, had unusually high within-population diversities (averages of 0.019-0.027 substitutions per site between pairs of individuals from the same population). Large effective population sizes (Ne), perhaps in combination with rapid mtDNA evolution, appear to be the most likely explanation for these high within-population diversities.

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

10.26686/wgtn.17072060 ◽

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>

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Microsatellite markers from Peronospora tabacina, the cause of blue mold of tobacco, reveal species origin, population structure, and high gene flow

Phytopathology ◽

10.1094/phyto-03-21-0092-r ◽

2021 ◽

Author(s):

Marcin Nowicki ◽

Denita Hadziabdic Guerry ◽

Robert N Trigiano ◽

Fabian Runge ◽

Marco Thines ◽

...

Keyword(s):

Population Structure ◽

Genetic Variation ◽

Gene Flow ◽

Blue Mold ◽

Long Distance ◽

Peronospora Tabacina ◽

Species Origin ◽

High Gene Flow ◽

High Gene ◽

Wind Currents

Peronospora tabacina is an obligate parasite that causes blue mold of tobacco. The pathogen reproduces primarily asexually by sporangia, and sexual oospores are a rarely observed form of propagation. A collection of 122 isolates of P. tabacina was genotyped using nine microsatellites to assess the population structure of individuals from subpopulations collected from Central, Southern, and Eastern Europe, the Middle East, Central and North America, and Australia. Genetic variation among the six subpopulations accounted for about 8% of total variation with moderate levels of genetic differentiation, high gene flow among these subpopulations, and a positive correlation between geographic and genetic distance (r = 0.225; P<0.001). Evidence of linkage disequilibrium (P<0.001) showed that populations contained partially clonal subpopulations, except subpopulations from Australia and Mediterranean Europe. High genetic variation and population structure among samples could be explained by continuous gene flow across continents via infected transplant exchange and/or long-distance dispersal of sporangia via wind currents. This study analyzed the most numerous P. tabacina collection to date and allowed conclusions on the migration, mutation, and evolutionary history of this obligate biotrophic oomycete. The evidence pointed to the species origin in Australia and identified intra- and inter-continental migration patterns of this important pathogen.

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Standing genetic variation and chromosomal rearrangements facilitate local adaptation in a marine fish

10.1101/782201 ◽

2019 ◽

Cited By ~ 4

Author(s):

Hugo Cayuela ◽

Quentin Rougemont ◽

Martin Laporte ◽

Claire Mérot ◽

Eric Normandeau ◽

...

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Local Adaptation ◽

Marine Fish ◽

Environmental Conditions ◽

Chromosomal Rearrangements ◽

Northwest Atlantic ◽

High Gene Flow ◽

High Gene ◽

Spawning Sites

AbstractPopulation genetic theory states that adaptation most frequently occurs from standing genetic variation, which results from the interplay between different evolutionary processes including mutation, chromosomal rearrangements, drift, gene flow and selection. To date, empirical work focusing on the contribution of standing genetic variation to local adaptation in the presence of high gene flow has been limited to a restricted number of study systems. Marine organisms are excellent biological models to address this issue since many species have to cope with variable environmental conditions acting as selective agents despite high dispersal abilities. In this study, we examined how, demographic history, standing genetic variation linked to chromosomal rearrangements and shared polymorphism among glacial lineages contribute to local adaptation to environmental conditions in the marine fish, the capelin (Mallotus villosus). We used a comprehensive dataset of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,359 individuals collected from 31 spawning sites in the northwest Atlantic (North America and Greenland waters). First, we reconstructed the history of divergence among three glacial lineages and showed that they diverged from 3.8 to 1.8 MyA. Depending on the pair of lineages considered, historical demographic modelling provided evidence for divergence with gene flow and secondary contacts, shaped by barriers to gene flow and linked selection. We next identified candidate loci associated with reproductive isolation of these lineages. Given the absence of physical or geographic barriers, we thus propose that these lineages may represent three cryptic species of capelin. Within each of these, our analyses provided evidence for large Ne and high gene flow at both historical and contemporary time scales among spawning sites. Furthermore, we detected a polymorphic chromosomal rearrangement leading to the coexistence of three haplogroups within the Northwest Atlantic lineage, but absent in the other two clades. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Altogether, our study shows that standing genetic variation associated with both chromosomal rearrangements and ancestral polymorphism contribute to local adaptation in the presence of high gene flow.

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Population Genetic of Anopheles Arabiensis Patton(Diptera: Culicidae) the Malaria Vector in the Republic of Sudan.

10.21203/rs.3.rs-131539/v1 ◽

2020 ◽

Author(s):

Mashair Mustafa ◽

Zairi Jaal ◽

Sumia Abu Kashawa ◽

Siti Azizah Mohd Nor

Keyword(s):

Population Structure ◽

Gene Flow ◽

Malaria Vector ◽

Microsatellite Loci ◽

Population Genetic ◽

Anopheles Arabiensis ◽

Isolation By Distance ◽

Gene Pools ◽

High Gene Flow ◽

High Gene

Abstract Background Anopheles arabiensis is a member of An. gambiae complex and a main malaria vector in Sudan. There is no sufficient An. arabiensis population genetic data available an understanding of vector population structure and genetics are important to the malaria vector control programs. The objective of this investigation is to study the population structure, gene flow and isolation by distance among An. arabiensis for developing control strategies Methods Mosquitoes were collected from six sites in Sudan using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitos were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven microsatellite loci published An. gambiae primers were used to amplify the DNA of An. arabiensis samples. Results PCR confirmed that An. arabiensis was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy-Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygotes deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant F ST was observed between all An. arabiensis populations . Kr population indicated high genetic differentiation (F ST ranged from 0.17 to 0.24). High gene flow (Nm= 1.6–8.2) was detected between clusters. There was evidence of a bottleneck event in the Hj population. No isolation by distance pattern was detected among populations. Conclusions This study revealed low levels of population differentiation with high gene flow among six An. arabiensis populations in Sudan.

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High gene flow maintains genetic diversity following selection for high EPSPS copy number in the weed kochia (Amaranthaceae)

Scientific Reports ◽

10.1038/s41598-020-75345-6 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Sara L. Martin ◽

Leshawn Benedict ◽

Wei Wei ◽

Connie A. Sauder ◽

Hugh J. Beckie ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Gene Flow ◽

Herbicide Resistance ◽

Random Mating ◽

Weed Species ◽

Canadian Prairie ◽

High Gene Flow ◽

High Gene ◽

Selection For

Abstract Kochia, a major weed species, has evolved resistance to four herbicide modes of action. Herbicide resistance appears to spread quickly, which could result in diminished standing genetic variation, reducing the ability of populations to adapt further. Here we used double digest restriction enzyme associated sequencing to determine the level of gene flow among kochia populations and whether selection for glyphosate resistance reduces genetic variation. Canadian Prairie populations show little to no genetic differentiation (FST = 0.01) and no correlation between genetic and geographic distance (r2 = − 0.02 p = 0.56), indicating high gene flow and no population structure. There is some evidence that kochia populations are genetically depauperate compared to other weed species, but genetic diversity did not differ between glyphosate susceptible and resistant populations or individuals. The inbreeding coefficients suggest there are 23% fewer heterozygotes in these populations than expected with random mating, and no variation was found within the chloroplast. These results indicate that any alleles for herbicide resistance can be expected to spread quickly through kochia populations, but there is little evidence this spread will reduce the species’ genetic variation or limit the species’ ability to respond to further selection pressure.

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