Genetic variation and population structure of moose (Alces alces) at neutral and functional DNA loci

2003 ◽  
Vol 81 (4) ◽  
pp. 670-683 ◽  
Author(s):  
Paul J Wilson ◽  
Sonya Grewal ◽  
Art Rodgers ◽  
Rob Rempel ◽  
Jacques Saquet ◽  
...  
Keyword(s):  
Genetic Variation ◽  
National Parks ◽  
Dna Markers ◽  
Isolation By Distance ◽  
Alces Alces ◽  
Allelic Diversity ◽  
Isle Royale ◽  
Exon 2 ◽  
Local Selection ◽  
Functional Dna

Genetic variation was examined for moose (Alces alces) from Riding Mountain, Isle Royale, and Pukaskwa national parks; northwestern, Nipigon, northeastern, and central Ontario; New Brunswick; and Newfoundland. The national parks were identified as maintaining potentially different local selection pressures due to the absence of hunting and the presence or absence of the parasite Parelaphostrongylus tenuis. Genetic variation was estimated using neutral DNA markers, assessed by multilocus DNA fingerprinting and five microsatellite loci, and the functional antigen binding region (ARS) (exon 2) of the major histocompatibility complex (MHC) gene DRB. There was discordance in the allelic diversity observed at the neutral loci compared with the MHC DRB locus in a number of populations. Ontario populations demonstrated higher levels of variability at the neutral loci and relatively low levels at the DRB locus. Conversely, the Isle Royale population has the lowest genetic variability, consistent with a historic small founding event, at the neutral DNA markers and relatively high variability at the MHC gene. Relatively high levels of genetic variation at the DRB locus were observed in protected park populations concomitant with the absence of white-tailed deer (Odocoileus virginianus) or the parasite P. tenuis and an absence of hunting. Gene flow was observed among the neighboring geographic regions within Ontario, including Pukaskwa National Park, with evidence of isolation-by-distance among more distant regions within Ontario. The discordant patterns between DNA markers suggest that neutral DNA markers may not accurately reflect adaptive variation present at functional loci.

Population genetic structure of the Gulf of St. Lawrence aster, Symphyotrichum laurentianum (Asteraceae), a threatened coastal endemic

Botany ◽  
2009 ◽  
Vol 87 (11) ◽  
pp. 1089-1095 ◽  
Author(s):  
Stephen B. Heard ◽  
Linley K. Jesson ◽  
Kirby Tulk
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Threatened Species ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Population Decline ◽  
Allelic Diversity ◽  
Magdalen Islands

The Gulf of St. Lawrence aster ( Symphyotrichum laurentianum (Fernald) G.L. Nesom) is an endemic annual of saline habitats in the southern Gulf of St. Lawrence. It is listed as a threatened species, and has recently experienced population declines in much of its range. We used 11 allozyme markers to assay population genetic variation in six wild populations of S. laurentianum from the Magdalen Islands, Quebec (QC), the only remaining wild population from Prince Edward Island National Park (PEI), and a greenhouse population founded in 1999 with seed collected from PEI. Symphyotrichum laurentianum harbours moderate genetic diversity (Ps = 0.36, As = 1.54), with only modest spatial genetic structure (pairwise FST < 0.15) and no significant isolation by distance. The PEI population had greatly reduced allelic diversity compared with the populations from the Magdalen Islands, which likely act as a reservoir of genetic variation in S. laurentianum. Recent loss of alleles during population decline in PEI is suggested by the retention of greater allelic diversity in the greenhouse population. Estimates of breeding structure suggest small but nonzero rates of outcross pollination (FIS = 0.73, 95% CI = 0.48–0.97; outcrossing rate ∼16%). Population genetic structure in S. laurentianum can inform those forming and carrying out conservation and recovery plans for this threatened species.

scholarly journals Population genomic consequences of novel life history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers (Mimulus guttatus)

2021 ◽  
Author(s):  
Kory M. Kolis ◽  
Colette S. Berg ◽  
Thomas C. Nelson ◽  
Lila Fishman
Keyword(s):  
Genetic Variation ◽  
Life History ◽  
Mating System ◽  
Isolation By Distance ◽  
Geographic Region ◽  
Mimulus Guttatus ◽  
Inbreeding Coefficients ◽  
Local Selection ◽  
System Adaptation ◽  
The One

Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been particularly proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200m geographical gap. Individual inbreeding coefficients (FIS) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1km) scales. Finally, YNP adaptation does not re-use a widespread inversion polymorphism diagnostic of annual vs. perennial M. guttatus range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.

scholarly journals Environmental and geographic data optimize ex situ collections and the preservation of adaptive evolutionary potential

2020 ◽  
Author(s):  
Lionel N. Di Santo ◽  
Jill A. Hamilton
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Plant Species ◽  
Isolation By Distance ◽  
Allelic Diversity ◽  
Genetic Data ◽  
Ex Situ ◽  
Evolutionary Potential ◽  
Isolation By Environment ◽  
The Impact

AbstractMaintenance of biodiversity, through seed banks and botanical gardens where the wealth of species’ genetic variation may be preserved ex situ, is a major goal of conservation. However, challenges can persist in optimizing ex situ collections where trade-offs exist between expense, effort, and conserving species evolutionary potential, particularly when genetic data is not available. Within this context, we evaluate the genetic consequences of guiding population preservation using geographic (isolation-by-distance, IBD) and environmental (isolation-by-environment, IBE) data for ex situ collections where provenance data is available. We use 19 genetic and genomic datasets from 15 plant species to (i) assess the proportion of population genetic differentiation explained by geographic and environmental factors, and (ii) simulate ex situ collections prioritizing source populations based on pairwise geographic or environmental distances. Specifically, we test the impact prioritizing sampling based on environmental and geographic distances may have on capturing neutral, functional or putatively adaptive genetic diversity and differentiation. We find that collectively IBD and IBE explain a substantial proportion of genetic differences among functional (median 45%) and adaptive (median 71%) loci, but not for neutral loci (median 21.5%). Simulated ex situ collections reveal that inclusion of IBD and IBE increases both allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections using environmental and geographic distance data can impact genetic variation captured ex situ. This provides value for the vast majority of plant species for which we have no genetic data, informing conservation of genetic variation needed to maintain evolutionary potential within collections.

scholarly journals Developing First Microsatellites and Analysing Genetic Diversity in Six Chia Cultivars

2021 ◽  
Author(s):  
GH Yue ◽  
CC Lai ◽  
M Lee ◽  
L Wang ◽  
ZJ Song
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Dna Sequences ◽  
Dna Markers ◽  
Gene Diversity ◽  
Allelic Diversity ◽  
Founder Population ◽  
Southern Mexico ◽  
Polymorphic Microsatellites ◽  
Promising Source

Abstract Chia (Salvia hispanica L.), originated in central and southern Mexico and Guatemala, is an emerging industry crop due to its high content of omega‐3 fatty acids and dietary fiber in its seeds. The seeds also have a high concentration of proteins and essential amino acids, and are becoming a promising source of bioactive peptides. Polymorphic DNA markers are essential tools to analyse genetic diversity and to accelerate genetic improvement. However, in Chia, polymorphic and codominant DNA markers are still lacking. In this study, fourteen polymorphic microsatellites were identified from DNA sequences and were characterized. The average allele number was 4.8 while the expected and observed heterozygosity was 0.24 and 0.34, respectively. The average PI was 0.50 while the combined PI was 9 ×10-6. These first 14 microsatellites in Chia are useful in genetic analysis and traceability. These 14 polymorphic microsatellites were used in analysing genetic diversity and population relationships in six cultivars originating in Mexico, Australia and Bolivia. Results showed that allelic diversity and gene diversity were low and ranged from 2.79 to 3.64 and 0.27 to 0.38, respectively. The Mexico black cultivar showed the highest allelic (3.64) and gene diversity (0.38). The six cultivars were closely related with high identity (> 0.893). Taken together, these Chia cultivars contain low genetic variation. Therefore, to initiate a breeding program for improving traits, it is essential to use seeds from multiple cultivars to enlarge genetic variation in the founder population.

Genetic Relationships of Cory's Shearwater: Parentage, Mating Assortment, and Geographic Differentiation Revealed by DNA Fingerprinting

The Auk ◽  
2000 ◽  
Vol 117 (3) ◽  
pp. 651-662 ◽  
Author(s):  
Corinne Rabouam ◽  
Vincent Bretagnolle ◽  
Yves Bigot ◽  
Georges Periquet
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Dna Fingerprinting ◽  
Genetic Relatedness ◽  
Isolation By Distance ◽  
Genetic Relationships ◽  
Cory’S Shearwater ◽  
Genetic Structure Of Populations ◽  
The Social ◽  
Calonectris Diomedea

Abstract We used DNA fingerprinting to assess genetic structure of populations in Cory's Shearwater (Calonectris diomedea). We analyzed mates and parent-offspring relationships, as well as the amount and distribution of genetic variation within and among populations, from the level of subcolony to subspecies. We found no evidence of extrapair fertilization, confirming that the genetic breeding system matches the social system that has been observed in the species. Mates were closely related, and the level of genetic relatedness within populations was within the range usually found in inbred populations. In contrast to previous studies based on allozymes and mtDNA polymorphism, DNA fingerprinting using microsatellites revealed consistent levels of genetic differentiation among populations. However, analyzing the two subspecies separately revealed that the pattern of genetic variation among populations did not support the model of isolation by distance. Natal dispersal, as well as historic and/or demographic events, probably contributed to shape the genetic structure of populations in the species.

Significant population genetic structure detected for a new and highly restricted species of Atriplex (Chenopodiaceae) from Western Australia, and implications for conservation management

2012 ◽  
Vol 60 (1) ◽  
pp. 32 ◽  
Author(s):  
Laurence J. Clarke ◽  
Duncan I. Jardine ◽  
Margaret Byrne ◽  
Kelly Shepherd ◽  
Andrew J. Lowe
Keyword(s):  
Genetic Variation ◽  
New Species ◽  
Genetic Structure ◽  
Western Australia ◽  
Sequence Data ◽  
Isolation By Distance ◽  
Conservation Strategies ◽  
New Taxon ◽  
Near Surface ◽  
Two Populations

Atriplex sp. Yeelirrie Station (L. Trotter & A. Douglas LCH 25025) is a highly restricted, potentially new species of saltbush, known from only two sites ~30 km apart in central Western Australia. Knowledge of genetic structure within the species is required to inform conservation strategies as both populations occur within a palaeovalley that contains significant near-surface uranium mineralisation. We investigate the structure of genetic variation within populations and subpopulations of this taxon using nuclear microsatellites. Internal transcribed spacer sequence data places this new taxon within a clade of polyploid Atriplex species, and the maximum number of alleles per locus suggests it is hexaploid. The two populations possessed similar levels of genetic diversity, but exhibited a surprising level of genetic differentiation given their proximity. Significant isolation by distance over scales of less than 5 km suggests dispersal is highly restricted. In addition, the proportion of variation between the populations (12%) is similar to that among A. nummularia populations sampled at a continent-wide scale (several thousand kilometres), and only marginally less than that between distinct A. nummularia subspecies. Additional work is required to further clarify the exact taxonomic status of the two populations. We propose management recommendations for this potentially new species in light of its highly structured genetic variation.

scholarly journals Spatial genetic structure of the sea sandwort (<i>Honckenya peploides</i>) on Surtsey: an immigrant's journey

2014 ◽  
Vol 11 (22) ◽  
pp. 6495-6507 ◽  
Author(s):  
S. H. Árnason ◽  
Ǽ. Th. Thórsson ◽  
B. Magnússon ◽  
M. Philipp ◽  
H. Adsersen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Early Stage ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Rapid Expansion ◽  
Aflp Markers ◽  
Plant Colonization ◽  
Southern Coast ◽  
Binary Matrix

Abstract. Sea sandwort (Honckenya peploides) was one of the first plants to successfully colonize and reproduce on the volcanic island Surtsey, formed in 1963 off the southern coast of Iceland. Using amplified fragment length polymorphic (AFLP) markers, we examined levels of genetic variation and differentiation among populations of H. peploides on Surtsey in relation to populations on the nearby island Heimaey and from the southern coast of Iceland. Selected populations from Denmark and Greenland were used for comparison. In addition, we tested whether the effects of isolation by distance could be seen in the Surtsey populations. Using two primer combinations, we obtained 173 AFLP markers from a total of 347 plant samples. The resulting binary matrix was then analysed statistically. The main results include the following: (i) Surtsey had the highest proportion of polymorphic markers as well as a comparatively high genetic diversity (55.5% proportion of polymorphic loci, PLP; 0.1974 HE) and Denmark the lowest (31.8% PLP; 0.132 HE), indicating rapid expansion during an early stage of population establishment on Surtsey and/or multiple origins of immigrants; (ii) the total genetic differentiation (FST) among Surtsey (0.0714) and Heimaey (0.055) populations was less than half of that found among the mainland populations in Iceland (0.1747), indicating substantial gene flow on the islands; (iii) most of the genetic variation (79%, p < 0.001) was found within localities, possibly due to the outcrossing and subdioecious nature of the species; (iv) a significant genetic distance was found within Surtsey, among sites, and this appeared to correlate with the age of plant colonization; and (v) the genetic structure analysis indicated multiple colonization episodes on Surtsey, whereby H. peploides most likely immigrated from the nearby island of Heimaey and directly from the southern coast of Iceland.

scholarly journals Genetic structure and dispersal patterns of the invasive psocid Liposcelis decolor (Pearman) in Australian grain storage systems

2010 ◽  
Vol 100 (5) ◽  
pp. 521-527 ◽  
Author(s):  
K.M. Mikac ◽  
N.N. FitzSimmons
Keyword(s):  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Allelic Diversity ◽  
Mantel Test ◽  
Null Alleles ◽  
Dispersal Patterns ◽  
Long Distance ◽  
Population Comparisons ◽  
Low Levels

AbstractMicrosatellite markers were used to investigate the genetic structure among invasive L. decolor populations from Australia and a single international population from Kansas, USA to determine patterns of dispersal. Six variable microsatellites displayed an average of 2.5–4.2 alleles per locus per population. Observed (HO) heterozygosity ranged from 0.12–0.65 per locus within populations; but, in 13 of 36 tests, HO was less than expected. Despite low levels of allelic diversity, genetic structure estimated as θ was significant for all pairwise comparisons between populations (θ=0.05–0.23). Due to suspected null alleles at four loci, ENA (excluding null alleles) corrected FST estimates were calculated overall and for pairwise population comparisons. The ENA-corrected FST values (0.02–0.10) revealed significant overall genetic structure, but none of the pairwise values were significantly different from zero. A Mantel test of isolation by distance indicated no relationship between genetic structure and geographic distance among all populations (r2=0.12, P=0.18) and for Australian populations only (r2=0.19, P=0.44), suggesting that IBD does not describe the pattern of gene flow among populations. This study supports a hypothesis of long distance dispersal by L. decolor at moderate to potentially high levels.

scholarly journals Population genetic structure of European wildcats inhabiting the area between the Dinaric Alps and the Scardo-Pindic mountains

2021 ◽  
Author(s):  
Felicita Urzi ◽  
Nikica Šprem ◽  
Hubert Potočnik ◽  
Magda Sindičić ◽  
Dean Konjević ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Population Genetic ◽  
Allelic Richness ◽  
Isolation By Distance ◽  
Domestic Cats ◽  
Genetic Purity ◽  
Eastern Group ◽  
Two Samples ◽  
European Wildcat ◽  
Genetic Clusters

Abstract Habitat fragmentation and loss have contributed significantly to the demographic decline of European wildcat populations and hybridization with domestic cats poses a threat to the loss of genetic purity of the species. In this study we used microsatellite markers to analyse genetic variation and structure of the wildcat populations from the area between the Dinaric Alps and the Scardo-Pindic mountains in Slovenia, Croatia, Serbia and North Macedonia. We also investigated hybridisation between populations of wildcats and domestic cats in the area. One hundred and thirteen samples from free-leaving European wildcats and thirty-two samples from domestic cats were analysed. Allelic richness across populations ranged from 3.61 to 3.98. The observed Ho values ranged between 0.57 and 0.71. The global FST value for the four populations was 0.080 (95% CI 0.056–0.109) and differed significantly from zero (P < 0.001). The highest FST value was observed between the populations North Macedonia and Slovenia and the lowest between Slovenia and Croatia. We also found a signal for the existence of isolation by distance between populations. Our results showed that wildcats are divided in two genetic clusters largely consistent with a geographic division into a genetically diverse northern group (Slovenia, Croatia) and genetically eroded south-eastern group (Serbia, N. Macedonia). Hybridisation rate between wildcats and domestic cats varied between 13% and 52% across the regions.

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