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.

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.

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 Habitat Connectivity for Jaguar (Panthera onca) Conservation in Central Belize.

2019 ◽  
Author(s):  
Angelica Menchaca ◽  
Natalia Rossi ◽  
Jeremy Froidevaux ◽  
Isabela Dias-freedman ◽  
Anthony Caragiulo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Genetic Connectivity ◽  
Suitable Habitat ◽  
Fine Scale ◽  
Panthera Onca ◽  
Wildlife Sanctuary ◽  
Landscape Permeability ◽  
Forest Reserve

Abstract Connectivity among jaguar (Panthera onca) populations will ensure natural gene flow and the long-term survival of the species throughout its range. Jaguar conservation efforts have focused primarily on connecting suitable habitat in a broad-scale. Accelerated habitat reduction, human-wildlife conflict, limited funding, and the complexity of jaguar behaviour have proven challenging to maintain connectivity between populations effectively. Here, we used non-invasive genetic sampling and individual-based conservation genetic analyses to assess genetic diversity and levels of genetic connectivity between individuals in the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We used expert knowledge and scientific literature to develop models of landscape permeability based on circuit theory with fine-scale landscape features as ecosystem types, distance to human settlements and roads to predict the most probable jaguar movement across central Belize. Results We used 12 highly polymorphic microsatellite loci to identify 50 individual jaguars. We detected high levels of genetic diversity across loci (HE= 0.61, HO= 0.55, and NA=9.33). Using Bayesian clustering and multivariate models to assess gene flow and genetic structure, we identified one single group of jaguars (K = 1). We identified critical areas for jaguar movement that fall outside the boundaries of current protected areas in central Belize. We detected two main areas of high landscape permeability in a stretch of approximately 18 km between Sittee River Forest Reserve and Manatee Forest Reserve that may increase functional connectivity and facilitate jaguar dispersal from and to Cockscomb Basin Wildlife Sanctuary. Our analysis provides important insights on fine-scale genetic and landscape connectivity of jaguars in central Belize, an area of conservation concern. Conclusions The results of our study demonstrate high levels of relatively recent gene flow for jaguars between two study sites in central Belize. Our landscape analysis detected corridors of expected jaguar movement between the Cockscomb Basin Wildlife Sanctuary and the Maya Forest Corridor. We highlight the importance of maintaining already established corridors and consolidating new areas that further promote jaguar movement across suitable habitat beyond the boundaries of currently protected areas. Continued conservation efforts within identified corridors will further maintain and increase genetic connectivity in central Belize.

scholarly journals Landscape permeability and individual variation in a dispersal-linked gene jointly determine genetic structure in the Glanville fritillary butterfly

2018 ◽  
Author(s):  
Michelle F. DiLeo ◽  
Arild Husby ◽  
Marjo Saastamoinen
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Individual Variation ◽  
Landscape Fragmentation ◽  
Landscape Matrix ◽  
Fragmented Landscapes ◽  
Dispersal Traits ◽  
Glanville Fritillary Butterfly ◽  
Large Decline

AbstractThere is now clear evidence that species across a broad range of taxa harbour extensive heritable variation in dispersal. While studies suggest that this variation can facilitate demographic outcomes such as range expansion and invasions, few have considered the consequences of intraspecific variation in dispersal for the maintenance and distribution of genetic variation across fragmented landscapes. Here we examine how landscape characteristics and individual variation in dispersal combine to predict genetic structure using genomic and spatial data from the Glanville fritillary butterfly. We used linear and latent factor mixed models to identify the landscape features that best predict spatial sorting of alleles in the dispersal-related gene phosphoglucose isomerase (Pgi). We next used structural equation modeling to test if variation in Pgi mediated gene flow as measured by Fst at putatively neutral loci. In a year when the population was expanding following a large decline, individuals with a genotype associated with greater dispersal ability were found at significantly higher frequencies in populations isolated by water and forest, and these populations showed lower levels of genetic differentiation at neutral loci. These relationships disappeared in the next year when metapopulation density was high, suggesting that the effects of individual variation are context dependent. Together our results highlight that 1) more complex aspects of landscape structure beyond just the configuration of habitat can be important for maintaining spatial variation in dispersal traits, and 2) that individual variation in dispersal plays a key role in maintaining genetic variation across fragmented landscapes.Impact summaryUnderstanding how fragmentation affects dispersal and gene flow across human-modified landscapes has long been a goal in evolutionary biology. It is typically assumed that individuals of the same species respond to the landscape in the same way, however growing evidence suggests that individuals can vary considerably in their dispersal traits. While the effects of this individual dispersal variation on range expansions and invasions have been well-characterized, knowledge of how it might mediate genetic responses to landscape fragmentation are almost entirely lacking. Here we demonstrate that individual variation in dispersal is key to the maintenance of genetic variation during a population expansion following a large decline in a butterfly metapopulation. We further show that spatial variation in dispersal is not maintained by the configuration of habitat patches alone, but by a more complex genotype-environment interaction involving the landscape matrix (i.e. landscape features found between habitat patches). This challenges the simplified landscape representations typically used in studies of dispersal evolution that ignore heterogeneity in the landscape matrix. More broadly, our results highlight the interplay of adaptive and neutral processes across fragmented landscapes, suggesting that an understanding of species vulnerability to landscape fragmentation requires consideration of both.

scholarly journals Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247586
Author(s):  
Christine E. Edwards ◽  
Brooke C. Tessier ◽  
Joel F. Swift ◽  
Burgund Bassüner ◽  
Alexander G. Linan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Plant Species ◽  
Genetic Drift ◽  
Rare Species ◽  
Ex Situ ◽  
Ouachita Mountains ◽  
Genetic Diversity And Structure ◽  
Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

scholarly journals Geographic patterns of human allele frequency variation: a variant-centric perspective

2020 ◽  
Author(s):  
Arjun Biddanda ◽  
Daniel P. Rice ◽  
John Novembre
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Allele Frequency ◽  
Human Genetics ◽  
Geographic Region ◽  
Frequency Variation ◽  
Human Genetic Variation ◽  
Alternative Representation ◽  
Geographic Patterns

AbstractA key challenge in human genetics is to describe and understand the distribution of human genetic variation. Often genetic variation is described by showing relationships among populations or individuals, in each case drawing inferences over a large number of variants. Here, we present an alternative representation of human genetic variation that reveals the relative abundance of different allele frequency patterns across populations. This approach allows viewers to easily see several features of human genetic structure: (1) most variants are rare and geographically localized, (2) variants that are common in a single geographic region are more likely to be shared across the globe than to be private to that region, and (3) where two individuals differ, it is most often due to variants that are common globally, regardless of whether the individuals are from the same region or different regions. To guide interpretation of the results, we also apply the visualization to contrasting theoretical scenarios with varying levels of divergence and gene flow. Our variant-centric visualization clarifies the major geographic patterns of human variation and can be used to help correct potential misconceptions about the extent and nature of genetic differentiation among populations.

Mitochondrial DNA variation within and among populations of the mosquito Aedes albopictus

Genome ◽  
1991 ◽  
Vol 34 (2) ◽  
pp. 288-292 ◽  
Author(s):  
Srinivas Kambhampati ◽  
Karamjit S. Rai
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Hong Kong ◽  
Gene Flow ◽  
Genetic Structure ◽  
Aedes Albopictus ◽  
Range Expansion ◽  
Dna Variation ◽  
Restriction Fragment Polymorphism ◽  
Mtdna Polymorphism

A survey of restriction fragment polymorphism in mitochondrial DNA (mtDNA) of 17 populations of the mosquito Aedes albopictus was undertaken. The mtDNA size was estimated to be about 17.5 kbp. The level of polymorphism was low, with over 99% of the fragments being shared in common among the 17 populations. Three populations, Mauritius, Singapore, and Hong Kong, contained individuals with both the ancestral and novel mtDNA haplotypes. We conclude that the low level of mtDNA polymorphism in A. albopictus is a result of recent range expansion and that the mixture of haplotypes is a likely result of human-aided gene flow among populations.Key words: mitochondrial DNA, genetic variation, genetic structure, Aedes albopictus.

Intact genetic structure and high levels of genetic diversity in bottlenecked sockeye salmon (Oncorhynchus nerka) populations of the Fraser River, British Columbia, Canada

2000 ◽  
Vol 57 (10) ◽  
pp. 1985-1998 ◽  
Author(s):  
Ruth E Withler ◽  
Khai D Le ◽  
R John Nelson ◽  
Kristina M Miller ◽  
Terry D Beacham
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Sockeye Salmon ◽  
Oncorhynchus Nerka ◽  
Allelic Diversity ◽  
Lower Proportion ◽  
Fraser River ◽  
Rare Alleles ◽  
Genetic Bottlenecks

Analysis of six microsatellite loci in 5800 sockeye salmon (Oncorhynchus nerka) from 29 Fraser River populations provided little evidence of genetic bottlenecks or mass straying in upper Fraser sockeye salmon resulting from reduced abundances following 1913-1914 rockslides in the Fraser canyon and successive decades of high exploitation. Upper Fraser populations were not characterized by a paucity of rare alleles, a sensitive indicator of populations in which effective size has been recently reduced. Heterozygosity and allelic diversity did not differ consistently between lower and upper Fraser populations. Throughout the watershed, early-migrating populations had lower allelic diversity and a lower proportion of rare alleles than did late-migrating ones. Genetic differentiation between upper and lower Fraser populations and heterogeneity among lower Fraser populations supported the suggestion that Fraser sockeye salmon are descendants of at least two postglacial "races." Variation among lakes within regions was the strongest component of genetic structure, accounting for five times the variation among populations within lakes and more than two times the variation among regions. Extensive historical transplants of eggs and juveniles apparently resulted in lit tle gene flow among regions, but three populations were reestablished or rebuilt as the result of more recent transplants.

scholarly journals Absence of Population Genetic Structure Among Breeding Colonies of the Waved Albatross

The Condor ◽  
2006 ◽  
Vol 108 (2) ◽  
pp. 440-445 ◽  
Author(s):  
Kathryn P. Huyvaert ◽  
Patricia G. Parker
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Breeding Population ◽  
Genetic Structuring ◽  
Galapagos Archipelago ◽  
Phoebastria Irrorata ◽  
Waved Albatrosses

Abstract We used four variable microsatellite loci to examine the distribution of genetic variation and degree of genetic structuring among three subcolonies of Waved Albatrosses (Phoebastria irrorata). The breeding population of this species is almost entirely limited to the island of Española in the Galápagos Archipelago. Such strong philopatry could lead to population genetic structure among subcolonies on the island. Pairwise values of the FST analog, θ, calculated from microsatellite genotypes, were all less than 0.012, indicating little genetic differentiation and the presence of gene flow throughout the population.

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