scholarly journals Habitat Fragmentation Reduces Genetic Diversity and Connectivity of the Mexican Spotted Owl: A Simulation Study Using Empirical Resistance Models

Genes ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 403 ◽  
Author(s):  
Ho Wan ◽  
Samuel Cushman ◽  
Joseph Ganey
Keyword(s):  
Genetic Diversity ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Geographic Area ◽  
Negative Influence ◽  
Landscape Resistance ◽  
Effective Population ◽  
Habitat Amount ◽  
Spotted Owl ◽  
Habitat Patches

We evaluated how differences between two empirical resistance models for the same geographic area affected predictions of gene flow processes and genetic diversity for the Mexican spotted owl (Strix occidentalis lucida). The two resistance models represented the landscape under low- and high-fragmentation parameters. Under low fragmentation, the landscape had larger but highly concentrated habitat patches, whereas under high fragmentation, the landscape had smaller habitat patches that scattered across a broader area. Overall habitat amount differed little between resistance models. We tested eight scenarios reflecting a factorial design of three factors: resistance model (low vs. high fragmentation), isolation hypothesis (isolation-by-distance, IBD, vs. isolation-by-resistance, IBR), and dispersal limit of species (200 km vs. 300 km). Higher dispersal limit generally had a positive but small influence on genetic diversity. Genetic distance increased with both geographic distance and landscape resistance, but landscape resistance displayed a stronger influence. Connectivity was positively related to genetic diversity under IBR but was less important under IBD. Fragmentation had a strong negative influence on the spatial patterns of genetic diversity and effective population size (Ns). Despite habitats being more concentrated and less widely distributed, the low-fragmentation landscape had greater genetic diversity than the high-fragmentation landscape, suggesting that highly concentrated but larger habitat patches may provide a genetic refuge for the Mexican spotted owl.

Spatial and temporal genetic diversity of the Texas kangaroo rat, Dipodomys elator (Rodentia: Heteromyidae)

2019 ◽  
Vol 100 (4) ◽  
pp. 1169-1181 ◽  
Author(s):  
Russell S Pfau ◽  
Jim R Goetze ◽  
Robert E Martin ◽  
Kenneth G Matocha ◽  
Allan D Nelson
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Isolation By Distance ◽  
Extinction Risk ◽  
Allelic Diversity ◽  
Effective Population ◽  
Kangaroo Rat ◽  
Time Periods ◽  
Mtdna Diversity ◽  
Using Data

Abstract The Texas kangaroo rat (Dipodomys elator) is listed as a threatened species in Texas because of its scarcity and small geographic range. We assessed patterns of genetic diversity in D. elator that could affect extinction risk or influence management decisions. Specific objectives included: 1) document levels of genetic diversity, 2) document the degree and patterns of genetic divergence among localities, and 3) compare levels of genetic diversity between different time periods at the same locality. Portions of the mitochondrial genome (mtDNA; control region, cytochrome c oxidase subunit I, and cytochrome b) were sequenced and nuclear microsatellites were examined. Low mtDNA diversity was observed, which could be explained by an historical, species-wide genetic bottleneck. In contrast, microsatellites exhibited ample variation, and analyses were conducted using data from 11 loci and four populations (designated Quanah, Iowa Park, Vernon, and Harrold). Allelic diversity and heterozygosity were similar between populations and temporal samples. Estimates of effective population size (Ne) ranged from 5 to 856, depending on method and population, with Iowa Park showing consistently lower values than Quanah. All methods addressing population structure indicated that the Iowa Park population was divergent from the others, with Vernon and Harrold showing a somewhat intermediate relationship but with a closer affiliation with Quanah than Iowa Park, despite their closer proximity to Iowa Park. This pattern did not conform to isolation by distance, thus genetic drift appears to have played a greater role than gene flow in establishing genetic structure. There was much less difference between temporal samples compared to geographic samples, indicating that genetic drift has had only minimal impacts in shifting allelic frequencies over the time periods examined (17–36 years).

Genetic diversity and gene flow patterns in two riverine plant species with contrasting life-history traits and distributions across a large inland floodplain

2020 ◽  
Vol 68 (5) ◽  
pp. 384
Author(s):  
William Higgisson ◽  
Dianne Gleeson ◽  
Linda Broadhurst ◽  
Fiona Dyer
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Water Resource ◽  
Isolation By Distance ◽  
Spatial Genetic Structure ◽  
Geographic Distance ◽  
Resource Development ◽  
Water Resource Development ◽  
Floodplain River

Gene flow is a key evolutionary driver of spatial genetic structure, reflecting demographic processes and dispersal mechanisms. Understanding how genetic structure is maintained across a landscape can assist in setting conservation objectives. In Australia, floodplains naturally experience highly variable flooding regimes that structure the vegetation communities. Flooding plays an important role, connecting communities on floodplains and enabling dispersal via hydrochory. Water resource development has changed the lateral-connectivity of floodplain-river systems. One possible consequence of these changes is reduced physical and subsequent genetic connections. This study aimed to identify and compare the population structure and dispersal patterns of tangled lignum (Duma florulenta) and river cooba (Acacia stenophylla) across a large inland floodplain using a landscape genetics approach. Both species are widespread throughout flood prone areas of arid and semiarid Australia. Tangled lignum occurs on floodplains while river cooba occurs along rivers. Leaves were collected from 144 tangled lignum plants across 10 sites and 84 river cooba plants across 6 sites, on the floodplain of the lower and mid Lachlan River, and the Murrumbidgee River, NSW. DNA was extracted and genotyped using DArTseq platforms (double digest RADseq). Genetic diversity was compared with floodplain-river connection frequency, and genetic distance (FST) was compared with river distance, geographic distance and floodplain-river connection frequency between sites. Genetic similarity increased with increasing floodplain-river connection frequency in tangled lignum but not in river cooba. In tangled lignum, sites that experience more frequent flooding had greater genetic diversity and were more genetically homogenous. There was also an isolation by distance effect where increasing geographic distance correlated with increasing genetic differentiation in tangled lignum, but not in river cooba. The distribution of river cooba along rivers facilitates regular dispersal of seeds via hydrochory regardless of river level, while the dispersal of seeds of tangled lignum between patches is dependent on flooding events. The genetic impact of water resource development may be greater for species which occur on floodplains compared with species along river channels.

scholarly journals Fine-scale genetic structure of the overwintering Chilo suppressalis in the typical bivoltine areas of northern China

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243999
Author(s):  
Ke-Xin Zhu ◽  
Shan Jiang ◽  
Lei Han ◽  
Ming-Ming Wang ◽  
Xing-Ya Wang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Isolation By Distance ◽  
Genetic Relationships ◽  
Management Strategies ◽  
Geographic Distance ◽  
Northern China ◽  
Economic Losses ◽  
Chilo Suppressalis

The rice stem borer (RSB), Chilo suppressalis (Lepidoptera: Pyralidae), is an important agricultural pest that has caused serious economic losses in the major rice-producing areas of China. To effectively control this pest, we investigated the genetic diversity, genetic differentiation and genetic structure of 16 overwintering populations in the typical bivoltine areas of northern China based on 12 nuclear microsatellite loci. Moderate levels of genetic diversity and genetic differentiation among the studied populations were detected. Neighbour-joining dendrograms, Bayesian clustering and principal coordinate analysis (PCoA) consistently divided these populations into three genetic clades: western, eastern and northern/central. Isolation by distance (IBD) and spatial autocorrelation analyses demonstrated no correlation between genetic distance and geographic distance. Bottleneck analysis illustrated that RSB populations had not undergone severe bottleneck effects in these regions. Accordingly, our results provide new insights into the genetic relationships of overwintering RSB populations and thus contribute to developing effective management strategies for this pest.

scholarly journals Genetic Divergence of Two Sitobion avenae Biotypes on Barley and Wheat in China

Insects ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 117
Author(s):  
Da Wang ◽  
Xiaoqin Shi ◽  
Deguang Liu ◽  
Yujing Yang ◽  
Zheming Shang
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Host Plant ◽  
Genetic Divergence ◽  
Isolation By Distance ◽  
Critical Role ◽  
Geographic Distance ◽  
Sitobion Avenae ◽  
Insect Populations

Host plant affinity and geographic distance can play critical roles in the genetic divergence of insect herbivores and evolution of insect biotypes, but their relative importance in the divergence of insect populations is still poorly understood. We used microsatellite markers to test the effects of host plant species and geographic distance on divergence of two biotypes of the English grain aphid, Sitobion avenae (Fabricius). We found that clones of S. avenae from western provinces (i.e., Xinjiang, Gansu, Qinghai and Shaanxi) had significantly higher genetic diversity than those from eastern provinces (i.e., Anhui, Henan, Hubei, Zhejiang and Jiangsu), suggesting their differentiation between both areas. Based on genetic diversity and distance estimates, biotype 1 clones of eastern provinces showed high genetic divergence from those of western provinces in many cases. Western clones of S. avenae also showed higher genetic divergence among themselves than eastern clones. The Mantel test identified a significant isolation-by-distance (IBD) effect among different geographic populations of S. avenae, providing additional evidence for a critical role of geography in the genetic structure of both S. avenae biotypes. Genetic differentiation (i.e., FST) between the two biotypes was low in all provinces except Shaanxi. Surprisingly, in our analyses of molecular variance, non-significant genetic differentiation between both biotypes or between barley and wheat clones of S. avenae was identified, showing little contribution of host-plant associated differentiation to the divergence of both biotypes in this aphid. Thus, it is highly likely that the divergence of the two S. avenae biotypes involved more geographic isolation and selection of some form than host plant affinity. Our study can provide insights into understanding of genetic structure of insect populations and the divergence of insect biotypes.

scholarly journals Genetic structure of natural populations of Cryptocarya moschata Nees (Lauraceae) from southeastern Brazilian Atlantic rain forest

2004 ◽  
Vol 4 (1) ◽  
pp. 01-16 ◽  
Author(s):  
Pedro Luís Rodrigues de Moraes ◽  
Maria Teresa Vitral de Carvalho Derbyshire
Keyword(s):  
Genetic Structure ◽  
Rain Forest ◽  
Evolutionary Dynamics ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Natural Populations ◽  
Conservation Strategies ◽  
Atlantic Rain Forest ◽  
Effective Population ◽  
Allozyme Loci

This study was accomplished on a more comprehensive basis to evaluate previous questions that were raised from a preliminary article about the genetic structure of Cryptocarya moschata populations. Thus, through the analysis of 40 polymorphic allozyme loci, allele frequencies were estimated from 335 individuals of 11 natural populations of C. moschata from six hydrographic basins of São Paulo state and Serra da Estrela, Rio de Janeiro, Brazil. Estimates of Wright's F statistics were done through the analysis of variance, presenting average values of <img border=0 width=32 height=32 id="_x0000_i1026" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f).jpg" align=absmiddle > or = 0.352, <img border=0 width=32 height=32 id="_x0000_i1027" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle > or = 0.285 and <img border=0 width=32 height=32 id="_x0000_i1028" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f2).jpg" align=absmiddle > or = 0.097. These results indicated that individuals within populations must be panmitic, and that the diversity among populations is fairly high, being superior to what would be expected for groups of plants having a full-sib family structure. From estimates of <img border=0 width=32 height=32 id="_x0000_i1029" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>obtained for populations taken two at a time, the model of isolation by distance was tested; data did not fit the model, showing that <img border=0 width=32 height=32 id="_x0000_i1030" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>did not increase by the respective increasing of the geographic distance. The estimated gene flow of 0.55 migrants per generation corroborated the pronounced populational differentiation, indicating that drift effects should be more important than the selection ones. The effective population sizes found from the sampled populations showed that there was an adequate genetic representativeness of the samples for those with relatively low values of <img border=0 width=32 height=32 id="_x0000_i1031" src="../../../../../../img/revistas/bn/v4n1/img/a04car(f2).jpg" align=absmiddle>. Though, under a metapopulation context, the effective population size was 17.07 individuals, indicating that sampling performed for the species corresponded to 88.44% of the maximum effective size obtained from 11 populations with a <img border=0 width=32 height=32 id="_x0000_i1032" src="../../../../../../img/revistas/bn/v4n1/img/a04car(0p).jpg" align=absmiddle>of 0.285, equivalent to only 5.09% individuals for the total sampled. Management and conservation strategies aimed at preserving high intrapopulation genetic variation in C. moschata would imply in the maintenance of populations with great number of individuals. Moreover, for the preservation of the species as a whole, the maintenance of many such populations would be mandatorily recommended, which denotes that the conservation of large areas of Atlantic rain forest should be necessary to hold its evolutionary dynamics.

The influence of hydrographic structure and seasonal run timing on genetic diversity and isolation-by-distance in chum salmon (Oncorhynchus keta)

2008 ◽  
Vol 65 (9) ◽  
pp. 2026-2042 ◽  
Author(s):  
Jeffrey B. Olsen ◽  
Blair G. Flannery ◽  
Terry D. Beacham ◽  
Jeffrey F. Bromaghin ◽  
Penelope A. Crane ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Chum Salmon ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Population Connectivity ◽  
Oncorhynchus Keta ◽  
Chum Salmon Oncorhynchus Keta ◽  
Yukon River ◽  
Run Timing

We used 20 microsatellite loci to compare genetic diversity and patterns of isolation-by-distance among three groups of chum salmon ( Oncorhynchus keta ) from two physically distinct watersheds in western Alaska, USA. The results were consistent with the hypothesis that gene flow decreases as the complexity of the hydrographic system increases. Specifically, higher gene flow was inferred among 11 populations from a nonhierarchical collection of short coastal rivers in Norton Sound compared with 29 populations from a complex hierarchical network of inland tributaries of the Yukon River. Within the Yukon River, inferred gene flow was highest among 15 summer-run populations that spawn in the lower drainage, compared with 14 fall-run populations that spawn in the upper drainage. The results suggest that the complexity of the hydrographic system may influence population connectivity and hence the level of genetic diversity of western Alaska chum salmon. Finally, evidence of isolation-by-time, when controlling for geographic distance, supported the hypothesis that genetic divergence in Yukon River chum salmon is influenced by seasonal run timing. However, evidence of isolation-by-distance, when controlling for season run timing, indicated the populations are not sufficiently isolated, spatially or temporally, to prevent gene flow. Dispersal among summer- and fall-run populations may play a role in maintaining genetic diversity.

Genetic diversity and population structure of Piceaglauca on an altitudinal gradient in interior Alaska

1987 ◽  
Vol 17 (12) ◽  
pp. 1519-1526 ◽  
Author(s):  
John Alden ◽  
Carol Loopstra
Keyword(s):  
Genetic Diversity ◽  
Sea Level ◽  
Geographic Distance ◽  
White Spruce ◽  
Geographic Area ◽  
Allozyme Variation ◽  
Interior Alaska ◽  
Provenance Research ◽  
Tree Limit ◽  
Upper Slope

Allozyme variation at 13 loci for 11 enzyme systems was studied in four white spruce (Piceaglauca (Moench) Voss) populations extending from a floodplain at 120 m above sea level to the altitudinal tree limit at 750 m above sea level in interior Alaska. Although 97% of the total genetic diversity was among trees within stands and 1% was among stands within populations, frequencies of several allozymes and allozyme genotypes were significantly different (P < 0.05) among populations. Ninety-two percent of the loci were polymorphic. Total heterozygosity was 0.276. Heterozygosity and allozyme frequencies were not related to altitude. The population at the tree limit was as genetically diverse as populations at low elevations [Formula: see text] and contained four of seven rare alleles observed in all populations. These observations suggested that white spruce is genetically diverse in interior Alaska and the tree-limit population will continue to colonize new habitats. Genetic distance was not related to altitude and geographic distance and was less between the tree-limit and upper slope populations than among other populations A detectable gene substitution rate was estimated at 10−6 per year. Populations on the upper slope and at the tree limit may have diverged about 2500 years ago and reached tree-limit altitudes only recently. Populations at low altitudes may have diverged during early Holocene white spruce expansion. We concluded that white spruce is genetically diverse in a small geographic area in interior Alaska. Results suggested that local white spruce populations should be regenerated from indigenous seed and that provenance research is needed to support afforestation programs.

scholarly journals Genetic Structure of Mexican Spotted Owl (Strix Occidentalis Lucida) Populations in a Fragmented Landscape

The Auk ◽  
2006 ◽  
Vol 123 (4) ◽  
pp. 1090-1102 ◽  
Author(s):  
George F. Barrowclough ◽  
Jeff G. Groth ◽  
Lisa A. Mertz ◽  
R. J. Gutiérrez
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Variance Partitioning ◽  
Fragmented Landscape ◽  
Spotted Owl ◽  
Strix Occidentalis ◽  
Strix Occidentalis Lucida ◽  
Central Arizona

Abstract We used mitochondrial DNA control-region sequences to investigate the genetic structure of Mexican Spotted Owl (Strix occidentalis lucida) populations in the southwestern United States. This subspecies is federally listed as threatened, and its preferred habitat is naturally fragmented. We found that intrapopulation genetic diversity was high in all but the southeastern Arizona “sky island” populations, where it was variable. Genetic variance partitioning indicated that ≈17% of the variation was distributed among populations and 7.5% was distributed among physiographic regions. Patterns of genetic correlation with geographic distance indicated that gene flow was substantial among populations within the relatively continuous habitat zone of the Mogollon Rim-Upper Gila Mountains in central Arizona and west-central New Mexico. However, there was significant isolation-by-distance elsewhere, and estimates of genetic divergence increased exponentially with geographic distance among fragmented populations on the scale of a few hundreds of kilometers; this implies that gene flow is restricted among those habitat fragments. Genetic heterogeneity among southeastern Arizona populations suggest that they have regularly received immigrants from the central Arizona populations. The Colorado population either was larger than thought or, more likely, has continuously received immigrants from elsewhere and is not a self-sustaining population. Estructura Genética de las Poblaciones de Strix occidentalis lucida en un Paisaje Fragmentado

scholarly journals First genome-wide analysis of an endangered lichen reveals isolation by distance and strong population structure

2017 ◽  
Author(s):  
Jessica L. Allen ◽  
Sean K. McKenzie ◽  
Robin S. Sleith ◽  
S. Elizabeth Alter
Keyword(s):  
Genetic Diversity ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Distribution Models ◽  
Extrinsic Factors ◽  
Biogeographic Patterns ◽  
Ecological Requirements ◽  
Genome Wide ◽  
Isolation By Environment

AbstractLichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes driving diversification and genetic differentiation in these lineages. Though few studies have examined population genetic patterns in lichens, their geographic distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, while their reproductive structures are observable, the lack of information about recombination mechanisms and rates can make inferences about reproductive strategies difficult. Here we investigate the population genomics ofCetradonia linearis, an endangered lichen narrowly endemic to the southern Appalachians of eastern North America, to test the relative contributions of environmental factors and geographic distance in shaping genetic structure, and to gain insights into the demography and reproductive biology of range restricted fungi. Analysis of genome-wide SNP data indicated strong evidence for both low rates of recombination and for strong isolation by distance, but did not support isolation by environment. Hindcast species distribution models and the spatial distribution of genetic diversity also suggested thatC. linearishad a larger range during the last glacial maximum, especially in the southern portion of its current extent, consistent with previous findings in other southern Appalachian taxa. These results contribute to our understanding of intrinsic and extrinsic factors shaping genetic diversity and biogeographic patterns inC. linearis, and more broadly, in rare and endangered fungi.

scholarly journals Levels and patterns of genetic diversity differ between two closely related endemicArabidopsisspecies

2016 ◽  
Author(s):  
Julie Jacquemin ◽  
Nora Hohmann ◽  
Matteo Buti ◽  
Alberto Selvaggi ◽  
Thomas Müller ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Endemic Species ◽  
Isolation By Distance ◽  
Demographic History ◽  
Adaptive Potential ◽  
Effective Population ◽  
Distribution Ranges ◽  
Small Effective Population Size

AbstractTheory predicts that a small effective population size leads to slower accumulation of mutations, increased levels of genetic drift and reduction in the efficiency of natural selection. Therefore endemic species should harbor low levels of genetic diversity and exhibit a reduced ability of adaptation to environmental changes.Arabidopsis pedemontanaandArabidopsis cebennensis, two endemic species from Italy and France respectively, provide an excellent model to study the adaptive potential of species with small distribution ranges. To evaluate the genome-wide levels and patterns of genetic variation, effective population size and demographic history of both species, we genotyped 53A. pedemontanaand 28A. cebennensisindividuals across the entire species ranges with Genotyping-by-Sequencing. SNPs data confirmed a low genetic diversity forA. pedemontanaalthough its effective population size is relatively high. Only a weak population structure was observed over the small distribution range ofA. pedemontana, resulting from an isolation-by-distance pattern of gene flow. In contrary,A. cebennensisindividuals clustered in three populations according to their geographic distribution. Despite this and a larger distribution, the overall genetic diversity was even lower forA. cebennensisthan forA. pedemontana.A demographic analysis demonstrated that both endemics have undergone a strong population size decline in the past, without recovery. The more drastic decline observed inA. cebennensispartially explains the very small effective population size observed in the present population. In light of these results, we discuss the adaptive potential of these endemic species in the context of rapid climate change.

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