scholarly journals Studying the genetic structure of Quercus robur forest stands on anthropogenically transformed territories using introns of the β-tubulin gene

2018 ◽  
Vol 26 (4) ◽  
pp. 269-275
Author(s):  
Y. V. Pirko ◽  
A. E. Demkovich ◽  
L. O. Kalafat ◽  
Y. B. Blume ◽  
О. А. Lykholat
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Quercus Robur ◽  
Spatial Genetic Structure ◽  
Anthropogenic Factors ◽  
Forest Stands ◽  
Individual Level ◽  
Information Index ◽  
Tubulin Genes ◽  
Β Tubulin

Based on the analysis of the intron polymorphism of β-tubulin genes, the genetic variability of old Quercus robur L. trees from “Holosiivsky” NPP was investigated. The genotyping of 55 old Q. robur trees was carried out; 40 polymorphic and one monomorphic (about 880 bp) TBR fragments were found. High frequency (70–90%) of occurrence of fragments with an approximate molecular weight of 275, 490, 500, and 1110 bp was observed.The genetic polymorphism of old Q. robur trees was assessed as quite high: РІС is 0.22 – 0.39, the effective number of alleles per locus was 1.174–1.268. The Shannon information index was in the range of 0.204–0.269.The geographical differentiation of the genetic structure of centuries-old oak trees from “Holosiivsky” NPP was not pronounced. The share of inter-selection genetic variability (AMOVA) accounts for about 6% of genetic variability, and the geographic component – about 1%. Around 93% of genetic variability is concentrated on the individual level. Using the ТВР method, we found that Q. robur forest stands do not have a stabilized genetic and visible spatial structure, but at the same time they possess a sufficiently large genetic diversity. The absence of a spatial genetic structure may indicate the artificial origin of Q. robur trees from different seed materials, and also that a small number of the plants have survived to this time. In this case, the main influence on the structure of oak stands in “Holosiivsky” NPP was from anthropogenic factors, both in the form of cutting down trees and, possibly, the introduction of alien seed material.

Generalist dispersal and gene flow of an endangered keystone specialist (Dipodomys ingens)

2019 ◽  
Vol 100 (5) ◽  
pp. 1533-1545
Author(s):  
Nathan B Alexander ◽  
Mark J Statham ◽  
Benjamin N Sacks ◽  
William T Bean
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Movement Ecology ◽  
Anthropogenic Factors ◽  
Kangaroo Rats ◽  
Cost Paths ◽  
Landscape Genetic ◽  
The Individual ◽  
Dipodomys Ingens

Abstract Movement ecology and dispersal capabilities inherently drive genetic structure across landscapes. Through understanding dispersal and gene flow of giant kangaroo rats (Dipodomys ingens), conservation efforts can be focused, and we can further understand how genetic structure persists in this highly endemic small mammal. Here, we genetically identify parent–offspring and sibship relationships among 239 giant kangaroo rats using 15 microsatellites in the northern part of the species range and describe the individual genetic-spatial variation using a Moran eigenvector map (MEM). We further employ two landscape genetic analyses (isolation by resistance [IBR] and least cost paths [LCPs]) and two individual-based genetic metrics (Dps and a codominant marker distance from GenAlEx) to determine landscape factors (precipitation, slope, vegetation community, and roads) that influence gene flow. We found 19 pairs of related individuals, of which 18 were less than 250 m apart, but one sibling pair was 5.52 km apart, suggesting greater dispersal capabilities than previously noted. We found hierarchal spatial genetic structure using a MEM, with 3–4 genetically similar regions and two genetically similar subregions. Finally, we found low correlative strength between landscape features and gene flow. IBR consistently outperformed LCPs, and there was evidence that regions with 250–350 mm of precipitation and slope ≤ 5° promoted connectivity. We recommend that managers focus on habitat protection rather than corridor maintenance, with the caveat that anthropogenic factors were minimally considered in this study.

scholarly journals Patterns of genetic variation in leading-edge populations of Quercus robur: genetic patchiness due to family clusters

2020 ◽  
Vol 16 (5) ◽  
Author(s):  
Pekka Vakkari ◽  
Mari Rusanen ◽  
Juha Heikkinen ◽  
Tea Huotari ◽  
Katri Kärkkäinen
Keyword(s):  
Population Structure ◽  
Genetic Structure ◽  
Genetic Differentiation ◽  
Population Genetic ◽  
Quercus Robur ◽  
Spatial Genetic Structure ◽  
Medium Size ◽  
Pedunculate Oak ◽  
Genetic Structures ◽  
Genetic Patchiness

Abstract The genetic structure of populations at the edge of species distribution is important for species adaptation to environmental changes. Small populations may experience non-random mating and differentiation due to genetic drift but larger populations, too, may have low effective size, e.g., due to the within-population structure. We studied spatial population structure of pedunculate oak, Quercus robur, at the northern edge of the species’ global distribution, where oak populations are experiencing rapid climatic and anthropogenic changes. Using 12 microsatellite markers, we analyzed genetic differentiation of seven small to medium size populations (census sizes 57–305 reproducing trees) and four populations for within-population genetic structures. Genetic differentiation among seven populations was low (Fst = 0.07). We found a strong spatial genetic structure in each of the four populations. Spatial autocorrelation was significant in all populations and its intensity (Sp) was higher than those reported in more southern oak populations. Significant genetic patchiness was revealed by Bayesian structuring and a high amount of spatially aggregated full and half sibs was detected by sibship reconstruction. Meta-analysis of isoenzyme and SSR data extracted from the (GD)2 database suggested northwards decreasing trend in the expected heterozygosity and an effective number of alleles, thus supporting the central-marginal hypothesis in oak populations. We suggest that the fragmented distribution and location of Finnish pedunculate oak populations at the species’ northern margin facilitate the formation of within-population genetic structures. Information on the existence of spatial genetic structures can help conservation managers to design gene conservation activities and to avoid too strong family structures in the sampling of seeds and cuttings for afforestation and tree improvement purposes.

scholarly journals Spatio-temporal genetic structure of the rodent Calomys venustus in linear, fragmented habitats

2015 ◽  
Vol 97 (2) ◽  
pp. 424-435 ◽  
Author(s):  
Marina B. Chiappero ◽  
Lucía V. Sommaro ◽  
José W. Priotto ◽  
María Paula Wiernes ◽  
Andrea R. Steinmann ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Spatial Genetic Structure ◽  
Geographic Distance ◽  
Sampling Period ◽  
Causal Modeling ◽  
Genetic Connectivity ◽  
Small Scale ◽  
Linear Habitats ◽  
Spatio Temporal

Abstract Studies about habitat fragmentation, in terms of how it affects gene flow and genetic variability, have traditionally been conducted on island-like systems in which the remaining habitats form patches embedded in a matrix. However, in agroecosystems, remaining habitats usually form linear strips along fence lines, roads, and water courses (“border” habitats). We used the rodent Calomys venustus , a species inhabiting borders in central Argentina agroecosystems, as a model to address how genetic variability is structured in linear habitats. A total of 359 rodents were captured seasonally from spring 2005 to winter 2006. Genetic variability at microsatellite loci was uniformly high, despite significant variation in population size during the sampling period. Genetic differentiation, spatial autocorrelation, and causal modeling analyses suggested that dispersion patterns in this species depend mainly on geographic distance, with unfavorable habitat like dirt roads and crop fields posing only weak (or no) resistance to dispersal. Small-scale spatial genetic structure was related to different space use patterns by females and males. Our results showed that, although greatly reduced in area, border habitats can support stable populations of species without loss of either variability or genetic connectivity. Los efectos de la fragmentación del hábitat sobre el flujo génico y la variabilidad genética, se han estudiado tradicionalmente en sistemas tipo islas, en los cuales los hábitats remanentes forman parches embebidos en una matriz. Sin embargo, en los agroecosistemas, éstos suelen tener forma lineal a lo largo de alambrados, caminos y corrientes de agua (hábitats de “borde”). En este trabajo, utilizamos al roedor Calomys venustus , especie típica de ambientes de borde en los agroecosistemas del centro de Argentina, como modelo para estudiar cómo la variabilidad genética se estructura en hábitats lineales. Un total de 359 roedores se capturaron estacionalmente desde la primavera de 2005 hasta el invierno de 2006. La variabilidad genética encontrada en loci de microsatélites fue siempre alta, a pesar de una variación significativa del tamaño poblacional a lo largo del período de estudio. Los análisis de diferenciación genética, autocorrelación genética espacial y modelado causal sugieren que los patrones de dispersión en esta especie dependen principalmente de la distancia geográfica, y que los hábitats desfavorables como caminos de tierra y campos de cultivo representan una barrera débil (o nula) para la dispersión. La estructura genética a escala pequeña estuvo relacionada al diferente uso del espacio por parte de machos y hembras. Nuestros resultados mostraron que a pesar de tener un área reducida, los hábitat de bordes pueden mantener poblaciones estables sin pérdida de variabilidad genética o reducción del flujo génico.

scholarly journals Intron length polymorphism of beta-tubulin genes in Ulmus pumila L. plants in the Steppe Prydniprov'ia

2018 ◽  
Vol 16 (1) ◽  
pp. 28-34
Author(s):  
Ya. V. Pirko ◽  
L. O. Kalafat ◽  
N. M. Pirko ◽  
A. N. Rabokon ◽  
S. N. Privalikhin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Polymorphism ◽  
Natural Populations ◽  
Intron Length ◽  
Ulmus Pumila ◽  
Intron Length Polymorphism ◽  
Information Index ◽  
Tubulin Genes ◽  
Genes Encoding ◽  
Β Tubulin

Aim. Using DNA markers related to the genes encoding β-tubulin in plants, to evaluate the intraspecific genetic polymorphism of Ulmus pumila L. in the Steppe Prydniprov'yia and compare it with the polymorphism of this species within the natural range. Method. Analysis of the intron length of polymorphism of β-tubulin genes (TBPmethod). Results. It was established that the plants differ from each other slightly in terms of the number of identified amplicons and the nature of their distribution when comparing electrophoretic profiles obtained on the basis of the TBP analysis for U. pumila. Half of the fragments found in the samples are rare. The average number of fragments (alleles) on the locus (Ne), Shannon information index (I) and polymorphism information content value (PIC) amounted respectively: 1.26, 0.27, 0.21, and were lower than in natural populations, analyzed using microsatellite markers. Conclusions. U. pumila plants growing in the Steppe Prydniprov'yi for the TBP markers have a lower level of genetic diversity than was found during the analysis of natural populations using other molecular markers. Among the possible reasons may be the nature (methodology) of the creation and age of the tree stands examined, as well as the nature of the genetic markers used to analyze the genetic polymorphism of the species.Keywords: TBP-method, introns, β-tubulin, Ulmus pumila, genetic diversity.

scholarly journals The Patterns and Puzzles of Genetic Diversity of Endangered Freshwater Mussel Unio crassus Philipsson, 1788 Populations from Vistula and Neman Drainages (Eastern Central Europe)

Life ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 119
Author(s):  
Adrianna Kilikowska ◽  
Monika Mioduchowska ◽  
Anna Wysocka ◽  
Agnieszka Kaczmarczyk-Ziemba ◽  
Joanna Rychlińska ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Spatial Scales ◽  
Freshwater Mussel ◽  
Its Region ◽  
Strong Relationship ◽  
Mantel Test ◽  
Freshwater Ecosystems ◽  
Hierarchical Organization ◽  
Anthropogenic Factors

Mussels of the family Unionidae are important components of freshwater ecosystems. Alarmingly, the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species identifies almost 200 unionid species as extinct, endangered, or threatened. Their decline is the result of human impact on freshwater habitats, and the decrease of host fish populations. The Thick Shelled River Mussel Unio crassus Philipsson, 1788 is one of the examples that has been reported to show a dramatic decline of populations. Hierarchical organization of riverine systems is supposed to reflect the genetic structure of populations inhabiting them. The main goal of this study was an assessment of the U. crassus genetic diversity in river ecosystems using hierarchical analysis. Different molecular markers, the nuclear ribosomal internal transcribed spacer ITS region, and mitochondrial DNA genes (cox1 and ndh1), were used to examine the distribution of U. crassus among-population genetic variation at multiple spatial scales (within rivers, among rivers within drainages, and between drainages of the Neman and Vistula rivers). We found high genetic structure between both drainages suggesting that in the case of the analyzed U. crassus populations we were dealing with at least two different genetic units. Only about 4% of the mtDNA variation was due to differences among populations within drainages. However, comparison of population differentiation within drainages for mtDNA also showed some genetic structure among populations within the Vistula drainage. Only one haplotype was shared among all Polish populations whereas the remainder were unique for each population despite the hydrological connection. Interestingly, some haplotypes were present in both drainages. In the case of U. crassus populations under study, the Mantel test revealed a relatively strong relationship between genetic and geographical distances. However, in detail, the pattern of genetic diversity seems to be much more complicated. Therefore, we suggest that the observed pattern of U. crassus genetic diversity distribution is shaped by both historical and current factors i.e. different routes of post glacial colonization and history of drainage systems, historical gene flow, and more recent habitat fragmentation due to anthropogenic factors.

Inferring establishment histories in populations of Quercus dentata (Fagaceae) from the analysis of spatial genetic structure

2005 ◽  
Vol 250 (3-4) ◽  
pp. 231-242 ◽  
Author(s):  
M. Y. Chung ◽  
K.-J. Kim ◽  
J.-H. Pak ◽  
C.-W. Park ◽  
B.-Y. Sun ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Quercus Dentata

scholarly journals Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Kelly B. Klingler ◽  
Joshua P. Jahner ◽  
Thomas L. Parchman ◽  
Chris Ray ◽  
Mary M. Peacock
Keyword(s):  
Genetic Variation ◽  
Genetic Structure ◽  
Sierra Nevada ◽  
Spatial Genetic Structure ◽  
Spatial Scales ◽  
Thermal Sensitivity ◽  
Genomic Variation ◽  
Genome Wide ◽  
A Genome ◽  
American Pika

Abstract Background Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada. Results Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θW = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θW = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θW = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide. Conclusions Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

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