Genetic diversity and population structure of red spruce (Picea rubens)

1994 ◽  
Vol 72 (12) ◽  
pp. 1778-1786 ◽  
Author(s):  
Gary J. Hawley ◽  
Donald H. DeHayes
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Genetic Drift ◽  
Black Spruce ◽  
Allozyme Variation ◽  
Picea Rubens ◽  
Red Spruce ◽  
Isolated Populations ◽  
Cool Temperate

Allozyme variation at 36 loci was estimated for 19 populations of red spruce (Picea rubens Sarg.) from throughout its natural range. Average estimates of polymorphic loci (95% criterion), effective number of alleles per locus, and observed and expected heterozygosities are 23%, 1.13, 7.47%, and 7.89%, respectively. Mean genetic distance among populations is 0.007, and 93% of the genetic diversity resides within red spruce populations. Comparisons with other species indicate that red spruce is less genetically variable than most other north-temperate woody plant species. Observed heterozygosity varied significantly among geographic regions, with northern cool-temperate populations having the highest mean observed heterozygosity, followed by central montane populations, then southern isolated populations with the lowest observed heterozygosity. Regional differences in genetic variability could be due to several factors, including migration from different glacial refugia, introgression of red spruce with more genetically variable black spruce in areas of sympatry in the north, and genetic drift followed by higher than expected levels of inbreeding in small isolated southern red spruce populations. Based on genetic distance, northern cool-temperate red spruce are more closely related to nonintrogressed red spruce than to nonintrogressed black spruce, suggesting that introgression is not a major factor contributing to greater genetic variability in the northern portion of the red spruce range. Relatively high genetic differentiation among populations, higher than expected levels of inbreeding, and evidence of reduced gene flow among populations suggest that low genetic variability evident in southern red spruce populations may be a result of genetic drift followed by inbreeding. Key words: Picea rubens, genetic diversity, isozymes, population genetic structure.

A Major Disjunction in Genetic Diversity Over the Geographic Range of Acacia melanoxylon R.Br

1993 ◽  
Vol 41 (3) ◽  
pp. 355 ◽  
Author(s):  
J Playford ◽  
JC Bell ◽  
GF Moran
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Allozyme Variation ◽  
Geographic Range ◽  
Considerable Time ◽  
High Genetic Diversity ◽  
Acacia Melanoxylon ◽  
River Region ◽  
High Level

A study of allozyme variation in Acacia melanoxylon R. Br. in 27 populations from across the geographic range of the species indicated high genetic diversity compared to other Australian trees and plants generally. Clines of increasing genetic variability with increasing latitude were found for four measures of genetic diversity. Most of the genetic diversity is found within populations but there was an unusually high level of the variation between populations (37.7%). A distinct genetic separation between the northern and southern populations was located approximately at the Hunter River region, where there is also a disjunction in the distribution of the species. The Nei (1978) genetic distance between these populations within this species is larger than observed between some plant species. Clearly the species has evolved separately in the two regions for a considerable time.

Allozyme variation in three closely related species of Caucasian rock lizards (Lacerta)

1995 ◽  
Vol 16 (4) ◽  
pp. 331-340 ◽  
Author(s):  
Ross D. MacCulloch ◽  
F.D. Danielyan ◽  
Ilya S. Darevsky ◽  
Robert W. Murphy ◽  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Related Species ◽  
Allozyme Variation ◽  
Direct Count ◽  
Closely Related Species ◽  
Polymorphic Loci ◽  
Allozyme Loci ◽  
Insular Populations

AbstractGenetic diversity at 37 allozyme loci was surveyed from Lacerta valentini (4 populations), L. portschinskii and L. rudis (1 population each). The number of polymorphic loci ranged from 1 (L. valentini) to 11 (L. rudis). Mean heterozygosity (direct count) ranged from 0.003 (L. valentini) to 0.071 (L. rudis). Nei's (1978) genetic distance ranged from 0-0.03 among populations of L. valentini, 0.127-0.163 between L. valentini and L. rudis and 0.366-0.487 between L. portschinskii and the two other taxa. Indices of genetic variability for species having disjunct distributions were lower than in species with contiguous distributions, similar to the case of insular populations, which have lower values than do mainland populations.

Indicators of population viability in red spruce, Picea rubens. II. Genetic diversity, population structure, and mating behavior

2000 ◽  
Vol 78 (7) ◽  
pp. 941-956 ◽  
Author(s):  
Om P Rajora ◽  
Alex Mosseler ◽  
John E Major
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Picea Rubens ◽  
Red Spruce ◽  
Past Century ◽  
Stage Of Development ◽  
Outcrossing Rates ◽  
Population Sizes ◽  
Allozyme Loci ◽  
Filled Seeds

Red spruce (Picea rubens Sarg.) has become increasingly rare across large portions of its range in eastern North America as a result of a general and widespread decline over the past century. Genetic diversity, population genetic structure, outcrossing rates in the filled seeds, and actual inbreeding levels were characterized in five small, isolated, remnant red spruce populations from the disjunct northwestern limits of its range in Ontario and five populations from the larger, more extensive Maritime populations of Nova Scotia and New Brunswick to determine genetic and reproductive status, to provide some benchmarks for monitoring genetic changes resulting from isolation and restricted population sizes, and to assist the development of restoration and conservation strategies. Thirty-seven allozyme loci coding for 15 enzymes were used for genetic diversity assessments, and six of the most polymorphic loci were used for mating system determination. On average, 29.1% (95% criterion) of the loci were polymorphic, the number of alleles per locus was 1.60, and the observed and expected heterozygosities were 0.097 and 0.100, respectively. The Ontario populations were comparable to or slightly less genetically variable than those from the Maritimes. Only 4.7% of the detected genetic variation was among stands; the remainder was among individuals within stands. The Maritime populations were genetically less differentiated from each other than those in Ontario. With the exception of three Maritime populations clustering tightly in one group, there was no clear separation of Ontario red spruce populations from Maritime red spruce populations based on genetic distance as well as canonical discriminant analyses. The average multilocus (tm) and single-locus (ts) population outcrossing rates were 0.595 and 0.558, respectively, indicating a comparatively high tolerance for inbreeding up to the filled seed stage of development in red spruce. The Ontario populations, on average, showed higher outcrossing rates (tm = 0.654, ts = 0.641) than the Maritime populations (tm = 0.535, ts = 0.475). Individual family outcrossing rates were similar to their respective population outcrossing rates and no significant differences were observed among families within populations for the multilocus estimates. When such high levels of inbreeding in filled seeds were combined with the proportions of empty (post-pollination-aborted) seeds, it appears that actual inbreeding levels may vary from 48 to 86%. The highest inbreeding levels occurred in the smallest, most isolated Ontario populations and in those populations most likely to have been affected by poorer pollination conditions. Allozyme variation indicates that in the short term, extant remnants of Ontario red spruce have maintained their genetic diversity and integrity. For artificial restoration of red spruce in Ontario, local seed sources could be used without undue concern over losses of genetic diversity. However, over the longer term, genetic drift and inbreeding may be expected to result in further losses of genetic diversity and (or) reproductive fitness if population sizes, numbers, and distribution continue to decline.Key words: Picea rubens, allozymes, gene conservation, restoration, genetic diversity, population structure, outcrossing rates, inbreeding.

scholarly journals Associative Overdominance and Negative Epistasis Shape Genome-Wide Ancestry Landscape in Supplemented Fish Populations

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 524
Author(s):  
Maeva Leitwein ◽  
Hugo Cayuela ◽  
Louis Bernatchez
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Recombination Rate ◽  
Management Strategies ◽  
Population Level ◽  
Negative Effects ◽  
Isolated Populations ◽  
Positive Effects ◽  
Genome Wide ◽  
Negative Epistasis

The interplay between recombination rate, genetic drift and selection modulates variation in genome-wide ancestry. Understanding the selective processes at play is of prime importance toward predicting potential beneficial or negative effects of supplementation with domestic strains (i.e., human-introduced strains). In a system of lacustrine populations supplemented with a single domestic strain, we documented how population genetic diversity and stocking intensity produced lake-specific patterns of domestic ancestry by taking the species’ local recombination rate into consideration. We used 552 Brook Charr (Salvelinus fontinalis) from 22 small lacustrine populations, genotyped at ~32,400 mapped SNPs. We observed highly variable patterns of domestic ancestry between each of the 22 populations without any consistency in introgression patterns of the domestic ancestry. Our results suggest that such lake-specific ancestry patterns were mainly due to variable associative overdominance (AOD) effects among populations (i.e., potential positive effects due to the masking of possible deleterious alleles in low recombining regions). Signatures of AOD effects were also emphasized by highly variable patterns of genetic diversity among and within lakes, potentially driven by predominant genetic drift in those small isolated populations. Local negative effects such as negative epistasis (i.e., potential genetic incompatibilities between the native and the introduced population) potentially reflecting precursory signs of outbreeding depression were also observed at a chromosomal scale. Consequently, in order to improve conservation practices and management strategies, it became necessary to assess the consequences of supplementation at the population level by taking into account both genetic diversity and stocking intensity when available.

A high-density genetic linkage map of a black spruce (Picea mariana) × red spruce (Picea rubens) interspecific hybrid

Genome ◽  
2011 ◽  
Vol 54 (2) ◽  
pp. 128-143 ◽  
Author(s):  
Bum-Yong Kang ◽  
John E. Major ◽  
Om P. Rajora
Keyword(s):  
Picea Mariana ◽  
Interspecific Hybrid ◽  
Genetic Linkage ◽  
Genetic Linkage Map ◽  
Black Spruce ◽  
Picea Rubens ◽  
Red Spruce ◽  
Linkage Groups ◽  
Genomic Resource ◽  
Map Distance

Genetic maps provide an important genomic resource of basic and applied significance. Spruce ( Picea ) has a very large genome size (between 0.85 × 1010 and 2.4 × 1010 bp; 8.5–24.0 pg/1C, a mean of 17.7 pg/1C ). We have constructed a near-saturated genetic linkage map for an interspecific backcross (BC1) hybrid of black spruce (BS; Picea mariana (Mill.) B.S.P.) and red spruce (RS; Picea rubens Sarg.), using selectively amplified microsatellite polymorphic loci (SAMPL) markers. A total of 2284 SAMPL markers were resolved using 31 SAMPL–MseI selective nucleotide primer combinations. Of these, 1216 SAMPL markers showing Mendelian segregation were mapped, whereas 1068 (46.8%) SAMPL fragments showed segregation distortion at α = 0.05. Maternal, paternal, and consensus maps consistently coalesced into 12 linkage groups, corresponding to the haploid chromosome number (1n = 1x = 12) of 12 in the genus Picea. The maternal BS map consisted of 814 markers distributed over 12 linkage groups, covering 1670 cM, with a mean map distance of 2.1 cM between adjacent markers. The paternal BS × RS map consisted of 773 markers distributed over 12 linkage groups, covering 1563 cM, with a mean map distance of 2.0 cM between adjacent markers. The consensus interspecific hybrid BC1 map consisted of 1216 markers distributed over 12 linkage groups, covering 1865 cM (98% genome coverage), with a mean map distance of 1.5 cM between adjacent markers. The genetic map reported here provides an important genomic resource in Picea, Pinaceae, and conifers.

scholarly journals PSIII-15 Genetic variability of Russian domestic reindeer populations (Rangifer Tarandus) by microsatellites

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 237-238
Author(s):  
Veronika R Kharzinova ◽  
Arsen V Dotsev ◽  
Anastasiya D Solovieva ◽  
Valeriy I Fedorov ◽  
Larisa D Shimit ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Indigenous Peoples ◽  
Rangifer Tarandus ◽  
R Package ◽  
Komi Republic ◽  
Middle Level ◽  
Taiga Zone ◽  
Isolated Populations ◽  
Mountain Taiga

Abstract Domestic reindeer are bred across the Russian tundra from the Kola Peninsula to Chukotka and in the mountain-taiga zone. To understand the genetic diversity and population structure of domestic reindeer, 528 individuals were analyzed using 14 microsatellites. The sample included the Nenets breed of the Komi Republic (NEN_K, n = 42), Nenets (NEN_N, n = 148), Yamalo-Nenets (NEN_Y, n = 46), Archangelsk (NEN_A, n = 47), Murmansk (NEN_M, n = 43), Taymyr (NEN_T, n = 52) regions; the Even (EVN, n = 33), the Evenk (EVK, n = 31), the Chukotka (CHUY, n = 33) breeds of Yakutia; the Chukotka breed (CHU, n = 40) of Chukotka Region; the Tuvinian (TUV, n = 32) and Mongolian (MGL, n = 21) populations of the Tuva Republic and Mongolia. Calculations were done in R package “diveRsity,” software SplitsTree 4.14.6., Structure 2.3.4. Possibly due to permanent exchanges with animals among farms of the Nenets region and thus introduction of “foreign” alleles into the herds, a higher level of genetic diversity was found in NEN_N (HE=0.699; AR =6.086). All groups had a significant homozygote excess with the maximal value of FIS in geographically isolated populations MGL (0.326) and TUV (0.229). Neighbor-Net tree showed formation of three main clusters according to breed origin and breeding region: (1) the Nenets reindeer from different regions, (2) three breeds of Yakutia and (3) TUV and MGL populations. CHU branched individually with a distance from others. At K=11 of STRUCTURE, we observed a clear clustering of CHU, MGL, TUV, NEN_T. A middle level of admixture was detected in NEN_A, NEN_Y, NEN_M and NEN_N with NEN_K and CHUY with EVN/EVK, which formed one cluster. Here, we obtained more detailed information on genetic variability of Russian domestic reindeer, which would assist to fill current gaps in knowledge about this essential species for many indigenous peoples of the Far North. The study was funded by the RSF within Project no. 16-16-10068-P.

scholarly journals The Sensitiveness of Expected Heterozygosity and Allelic Richness Estimates for Analyzing Population Genetic Diversity

2021 ◽  
Author(s):  
María Eugenia Barrandeguy ◽  
María Victoria García
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Variability ◽  
Population Size ◽  
Genetic Drift ◽  
Population Genetic ◽  
Allelic Richness ◽  
Theoretical Background ◽  
Computational Simulations ◽  
Expected Heterozygosity

Genetic diversity comprises the total of genetic variability contained in a population and it represents the fundamental component of changes since it determines the microevolutionary potential of populations. There are several measures for quantifying the genetic diversity, most notably measures based on heterozygosity and measures based on allelic richness, i.e. the expected number of alleles in populations of same size. These measures differ in their theoretical background and, in consequence, they differ in their ecological and evolutionary interpretations. Therefore, in the present chapter these measures of genetic diversity were jointly analyzed, highlighting the changes expected as consequence of gene flow and genetic drift. To develop this analysis, computational simulations of extreme scenarios combining changes in the levels of gene flow and population size were performed.

Diversity of Washoe pine and comparisons with allozymes of ponderosa pine races

1990 ◽  
Vol 20 (3) ◽  
pp. 298-308 ◽  
Author(s):  
Charles R. Niebling ◽  
M. Thompson Conkle
Keyword(s):  
Genetic Distance ◽  
Great Basin ◽  
Ponderosa Pine ◽  
Rocky Mountain ◽  
Electrophoretic Analysis ◽  
Allozyme Variation ◽  
Genetic Distances ◽  
Isolated Populations ◽  
The North ◽  
The Pacific

Washoe pine (Pinuswashoensis Mason and Stockwell), a narrow endemic native to mountains on the western rim of the Great Basin in northeastern California and northwestern Nevada, may be on the verge of extinction. Lowered genetic diversity and increased interpopulation differentiation are expected evolutionary consequences for small, isolated populations like those of Washoe pine. But the species has levels of allozyme variation (estimated average heterozygosity for 26 loci equals 0.148) similar to those for widespread geographic races of ponderosa pine (Pinusponderosa Laws.), which are likely to be its closest extant relatives. Heterozygosity in ponderosa pine was 0.144 in the Pacific race, 0.178 in the North Plateau race, and 0.164 in the Rocky Mountain race. Electrophoretic analysis of trees in the three well-documented populations of Washoe pine revealed only minor and nonsignificant population to population differentiation (98.4% of allozyme variation was among samples within populations). Pair-wise genetic distances between the Washoe populations and the three northern races of ponderosa pine indicated that its closest similarity was with the North Plateau race (Nei's unbiased genetic distance averaged 0.004); the next closest similarity was with samples of the Pacific race (genetic distance 0.013). Washoe pine and the Pacific and North Plateau races of ponderosa pine were all strongly differentiated from the Rocky Mountain race of ponderosa pine (genetic distances were 0.066, 0.082, and 0.060, respectively. The few remaining populations of Washoe pine may be a potentially valuable gene source for the yellow pines of North America.

scholarly journals Does marine geospatial/environmental variation affect genetic variation? A meta-analysis

2021 ◽  
Author(s):  
◽  
Daniel Cárcamo
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
New Zealand ◽  
Genetic Variability ◽  
Genetic Distance ◽  
Meta Analysis ◽  
Environmental Variation ◽  
Environmental Data ◽  
Seascape Genetics ◽  
Species Specific

<p>Genetic information is important to inform management and conservation. However, few studies have tested the relationship between genetic variation and geospatial/environmental variation across marine species. Here, I test two genetics-based ideas in evolutionary theory using data from 55 New Zealand coastal marine taxa. The Core-Periphery Hypothesis (CPH) states that populations at the centre of a species’ distribution exhibit greater genetic variability than populations at the periphery (the ‘normal’ model). Variants of this model include the ‘ramped north’ (greatest variation in the north), the ‘ramped south’ (greatest variation in the south), and the ‘abundant edge’ (greatest variation at the distributional edges, least variation at the centre). The Seascape Genetics Test (SGT) null hypothesis predicts no association between genetic variation and environmental variation. I conducted a meta-analysis of published/unpublished material on population genetic connectivity and diversity and marine environmental data to test both hypotheses. To assess the CPH, genetic data were fitted to four models (Normal, Ramped North, Ramped South, Abundant Edge). I also conducted a descriptive analysis between the genetic outcomes of the CPH and abundance records for a subset of species. The SGT involved GLM analyses using eleven geospatial/environmental variables and species-specific FST-ΦST (genetic distance) estimates plus a smaller subset of genetic diversity data. The CPH results showed that 55 of 249 tests (evaluating on average 2.9 ± 1.3 genetic indices in each of the 84 studies) fitted at least one of the four models: Ramped North (10%), Ramped South (8%), Normal (2%) and Abundant Edge (2.4%). Species-specific abundance records followed the same patterns detected by the CPH. These results indicate that edge populations (Ramped North, Ramped South, Abundant Edge) exhibit greater genetic variability than central populations amongst marine taxa from New Zealand, but that most taxa do not conform to any model (~78% of all tests were not statistically significant). For the seascape genetics multi-species analysis (comprising 498 individual tests), the FST-ΦST estimates (genetic distance estimates between pairs of populations) were mostly affected by four factors related to sea surface temperature. For genetic diversity indices the most significant predictors were latitude and longitude. Whilst different factors (e.g., physical oceanography, food availability, life-history traits and harvesting), either acting alone or acting synergistically, are likely to be important in explaining patterns of genetic diversity in New Zealand’s marine coastal species, my results indicate that variables including SST and to a lesser extent the geospatial variables (latitude and longitude) explain much of the variation in the genetic indices tested here.</p>

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