FST Estimates Research Articles

The genome sequence and genomic diversity of soybean tentiform leafminer (Macrosaccus morrisella).

The soybean tentiform leafminer, Macrosaccus morrisella (Fitch) (Lepidoptera: Gracillariidae), is native to North America where it was known to feed on American hogpeanut and slickseed fuzzybean. However, it has recently expanded its host range to include soybean, an important agricultural crop. Here we report a new, highly contiguous genome for this species with a length of 245 Mb, N50 of 9 Mb, and 96.33% BUSCO completeness. The mitochondrial genome shares only 81% identity to its nearest relative in the NCBI nucleotide database indicating long-standing divergence or sparse sequencing in this clade. To determine whether host plant choice is genetically driven, we sequenced 18 individuals across three locations in Minnesota, United States, collected from both American hogpeanut and soybean plants. Genetic variation did not correlate with population structure based on either geography or host plant species (weighted FST estimate: 0.0058). As a secondary measure, we independently assembled complete mitochondrial genomes from all individuals and observed no delineation between host or location. Overall lack of detectable population structure at the nuclear and mitochondrial genome levels suggests a large population with flexible dietary preferences and does not show evidence of genetically driven host preference.

Genome scans reveal extensive population structure in three neritic tuna and tuna-like species in the Indian Ocean

Abstract Neritic tunas and tuna-like species are an important resource for many coastal nations1 worldwide supporting both commercial and artisanal fisheries, but little is known about their population structure at a spatial scale required for effective fisheries management. In this study, we use Next Generation Sequencing methods to investigate the genetic connectivity of three major neritic tuna and tuna-like species in the Indian Ocean: Longtail Tuna (Thunnus tonggol), Kawakawa (Euthynnus affinis), and narrow-barred Spanish mackerel (Scomberomorus commerson). We sampled 293 Longtail Tuna from three locations, 362 Kawakawa from seven locations, and 210 narrow-barred Spanish mackerel from six locations. Genetic data showed clear evidence of heterogeneity in all three species, and patterns of isolation-by-distance were detected in Kawakawa and narrow-barred Spanish mackerel. Pairwise FST estimates of population differentiation and model-based grouping (mixture models) revealed that (i) individuals of Longtail Tuna from each sampling location belonged to a distinct genetic group, (ii) at least two different groups of Kawakawa were identified, and (iii) at least four groups of narrow-barred Spanish mackerel were identified across the sampled range within the north and eastern Indian Ocean. These results demonstrate that neritic tunas exhibit genetic structuring at small to medium spatial scales that need to be considered in the design of monitoring and assessment systems for fisheries management purposes in the northern and eastern parts of their range in the Indian Ocean. Further sampling, at a finer spatial resolution within the range of the current study, and across the north-western and western parts of their range of the Indian Ocean that were not covered in the current study, is required to provide a comprehensive understanding of the number of populations present and the spatial extent of individual populations in the Indian Ocean and adjacent seas.

Evaluation of Aedes aegypti control intervention with pyriproxyfen by lcWGS in Manacapuru, Amazonas, Brazil.

Ae. aegypti mosquitoes are considered a global threat to public health due to its ability to transmit arboviruses such as yellow fever, dengue, Zika and Chikungunya to humans. The lack of effective arboviral vaccines and etiological treatments make vector control strategies fundamental in interrupting the transmission cycle of these pathogens. This study evaluated Ae. aegypti mosquito populations pre- and post-intervention period with disseminating stations of the larvicide pyriproxyfen to understand its potential influence on the genetic structure and population diversity of these vectors. This study was conducted in Manacapuru city, Amazonas, Brazil, where 1,000 pyriproxyfen dissemination stations were deployed and monitored from FEB/2014 to FEB/2015 (pre-intervention) and AUG/2015 to JAN/2016 (post-intervention). Low-coverage whole genome sequencing of 36 individuals was performed, revealing significant stratification between pre- and post-intervention groups (pairwise FST estimate of 0.1126; p-value < 0.033). Tajima's D estimates were -3.25 and -3.07 (both p-value < 0.01) for pre- and post-intervention groups, respectively. Molecular diversity estimates (Theta(S) and Theta(Pi)) also showed divergences between pre- and post-intervention groups. PCA and K-means analysis showed clustering for SNP frequency matrix and SNP genotype matrix, respectively, being both mainly represented by the first principal component. PCA and K-means clustering also showed significant results that corroborate the impact of pyriproxyfen intervention on genetic structure populations of Ae. aegypti mosquitoes. The results revealed a bottleneck effect and reduced mosquito populations during intervention, followed by reintroduction from adjacent and unaffected populations by this vector. We highlighted that low-coverage whole genome sequencing can contribute to genetic and structure population data, and also generate important information to aid in genomic and epidemiological surveillance.

Genetic diversity and population structure of wild Salvia miltiorrhiza in China revealed by microsatellite markers and implication for conservation

AbstractSalvia miltiorrhiza is an outcrossing and perennial herb native to China. Although well-known for its medicinal value, there is a lack of knowledge regarding its natural population genetics. Here, we used 12 microsatellite markers to investigated population genetic diversity and structure of 215 samples from populations naturally distributed in central eastern China. A moderate level of genetic diversity was detected probably due to the over-mining of its roots. The allelic richness (AR) ranged from 3.034 to 4.889 with an average of 3.891. Moreover, pairwise estimates of FST among the populations of S. miltiorrhiza varied from 0.036 to 0.312 and two clusters were obtained by STRUCTURE and discriminant analysis of principal components. It is likely that the genetic differentiation of these two clusters was formed during glacial periods. Our result provides insights into the conservation of this valuable medicinal plant.

Genomic characterization of the Brazilian Crioulo Lageano: Insights for conservation of a Brazilian local bovine breed

Genomic characterization of the Brazilian Crioulo Lageano: Insights for conservation of a Brazilian local bovine breed

An overview of autosomal STRs and identity SNPs in a Norwegian population using massively parallel sequencing

In recent years, probabilistic genotyping software has been adapted for the analysis of massively parallel sequencing (MPS) forensic data. Likelihood ratios (LR) are based on allele frequencies selected from populations of interest. This study provides an outline of sequence-based (SB) allele frequencies for autosomal short tandem repeats (aSTRs) and identity single nucleotide polymorphisms (iSNPs) in 371 individuals from Southern Norway. 27 aSTRs and 94 iSNPs were previously analysed with the ForenSeq™ DNA Signature Prep Kit (Verogen). The number of alleles with frequencies less than 0.05 for sequenced-based alleles was 4.6 times higher than for length-based alleles. Consistent with previous studies, it was observed that sequence-based data (both with and without flanks) exhibited higher allele diversity compared to length-based (LB) data; random match probabilities were lower for SB alleles confirming their advantage to discriminate between individuals. Two alleles in markers D22S1045 and Penta D were observed with SNPs in the 3´ flanking region, which have not been reported before. Also, a novel SNP with a minor allele frequency (MAF) of 0.001, was found in marker TH01. The impact of the sample size on minor allele frequency (MAF) values was studied in 88 iSNPs from Southern Norway (n = 371). The findings were then compared to a larger Norwegian population dataset (n = 15,769). The results showed that the smaller Southern Norway dataset provided similar results, and it was a representative sample. Population structure was analyzed for regions within Southern Norway; FST estimates for aSTR and iSNPs did not indicate any genetic structure. Finally, we investigated the genetic differences between Southern Norway and two other populations: Northern Norway and Denmark. Allele frequencies between these populations were compared, and we found no significant frequency differences (p-values > 0.0001). We also calculated the pairwise FST values per marker and comparisons between Southern and Northern Norway showed small differences. In contrast, the comparisons between Southern Norway and Denmark showed higher FST values for some markers, possibly driven by distinct alleles that were present in only one of the populations. In summary, we propose that allele frequencies from each population considered in this study could be used interchangeably to calculate genotype probabilities.

Genetics, geography, and subspecies status of American mink in Florida, with an emphasis on Neogale vison evergladensis

Historical records of American mink (Neogale vison) in Florida suggest they occur in four populations, each currently recognized as a separate subspecies. The Everglades mink (N. v. evergladensis) is a state-listed threatened subspecies, and the Atlantic salt marsh mink (N. v. lutensis) and Gulf salt marsh mink (N. v. halilimnetes) are both Species of Greatest Conservation Need, but support for their taxonomic status is limited. We acquired 62 samples of mink for genetic analysis using mtDNA and microsatellite data with the objective of assessing the subspecies status of mink in Florida with an emphasis on evergladensis. We also compared historical and current range estimates of mink subspecies in Florida using museum specimens, public sightings, and detection records from scientific studies. All estimates of FST were significant when evergladensis was paired with other subspecies and both assignment tests and the Principal Coordinate Analysis separated evergladensis from other subspecies. The single mtDNA haplotype from evergladensis was not found elsewhere in Florida but was present in a subspecies outside of Florida (vulgivaga). Genetic diversity was lowest in evergladensis and highest for vulgivaga from Louisiana. We found support for lutensis as a separate taxonomic unit and assignment tests found some support for the genetic distinctiveness of halilimnetes. Sample sizes limited analyses in halilimnetes and prevented any conclusions about the subspecies status of mink in the Panhandle. Based on current range estimates, mink from evergladensis, lutensis, and halilimnetes are geographically isolated from one another and supports the genetic analysis. Using a more modern definition of subspecies that includes genetics, distribution, and ecology, we conclude that the data supports multiple subspecies of mink in Florida.

Phylogeography and climate shape the quantitative genetic landscape and range‐wide plasticity of a prevalent conifer

AbstractThe contribution of genetic adaptation and plasticity to intraspecific phenotypic variability remains insufficiently studied in long‐lived plants, as well as the relevance of neutral versus adaptive processes determining such divergence. We examined the importance of phylogeographic structure and climate in modulating genetic and plastic changes and their interdependence in fitness‐related traits of a widespread Mediterranean conifer (Pinus pinaster). Four marker‐based, previously defined neutral classifications along with two ad hoc climate‐based categorizations of 123 range‐wide populations were analyzed for their capacity to summarize genetic and plastic effects of height growth and survival (age 20) in 15 common gardens. The plasticity of tree height and differential survival were interpreted through mixed modeling accounting for heteroscedasticity in the genotype‐by‐environment dataset. The analysis revealed a slight superiority of phylogeographic classifications over climate categorizations on the explanation of genetic and plastic effects, which suggests that neutral processes can be at least as important as isolation by climate as a driving factor of evolutionary divergence in a prevalent pine. The best phylogeographic classification involved eight geographically discrete genetic groups, which explained 92% (height) and 52% (survival) of phenotypic variability, including between‐group mean differentiation and differential expression across trials. For height growth, there was high predictability of plastic group responses described by different reaction norm slopes, which were unrelated to between‐group mean differentiation. The latter differences (amounting to ca. 40% among groups) dominated intraspecific performance across trials. Local adaptation was evident for genetic groups tested in their native environments in terms of tree height and, especially, survival. This finding was supported by QST &gt; FST estimates. Additionally, our range‐wide evaluation did not support a general adaptive syndrome by which less reactive groups to ameliorated conditions would be associated with high survival and low growth. In fact, a lack of relationship between mean group differentiation, indicative of genetic adaptation, and predictable group plasticity for height growth suggests different evolutionary trajectories of these mechanisms of phenotypic divergence. Altogether, the existence of predictable adaptive‐trait phenotypic variation for the species, involving both genetic differentiation and plastic effects, should facilitate integrating genomics and environment into decision‐making tools to assist forests in coping with climate change.

Investigating temporal bone variation of colonial populations from St-Lawrence Valley, Quebec: A 3D geometric morphometric approach.

In Quebec, genetic and genealogical research are used to document migratory events and family structures since colonial times, because bioarchaeological analysis is limited by poor skeletal preservation. This article aims to fill this gap by exploring past population structure in the St-Lawrence Valley from the French (1683-1760) and British (1760-1867) regimes using morphological variation of well-preserved temporal bones. 3D geometric morphometrics shape data from seven populations (five Catholics of French descent and two Protestants of British descent; n = 214) were collected from temporal bones. Using Procrustes distances and both MANOVA and Discriminant Function Analysis, morphological differences were measured to calculate affinities patterns among populations. Shape variations were explored with between-group analysis, Mahalanobis distances and quantified by means of Fst estimates using Relethford-Blangero analysis. Despite strong affinities between all Catholic cemeteries, all show divergent morphological regional diversity -especially Montreal and the fortified villages dedicated to its defense. Montreal exhibits low increase in morphological variance over three centuries. As our results show no morphological differences between the Catholic and the Protestant cemeteries in Montreal, this fact may highlight the potential presence of Irish or admixed individuals in Montreal cemeteries after the British takeover. Patterns of morphological diversity highlighted that French colonists did not equally contribute to the descendant populations as reflected by significant interregional variation. Although historical records show that French and English-speaking populations did not tend to admix, morphological affinities between Protestants and Catholics in the beginning of the industrial era in Montreal could reflect the genetic contribution of Catholic Irish migrants. All Catholic cemeteries display distinct morphologies, highlighting differential contributions from French colonists and founder effects, which have increased regional differences. Montreal Catholic (French descent) and Protestant (English colonists) cemeteries show significant morphological affinities at the beginning of the industrial era. The Irish migration following the British conquest may explain morphological similarities observed between Catholic and Protestant cemeteries.

Genetic diversity and phylogeny of Anopheles nuneztovari C and Anopheles albimanus, vectors of malaria in the department of Córdoba, Colombia

Genetic diversity and phylogeny of Anopheles nuneztovari C and Anopheles albimanus, vectors of malaria in the department of Córdoba, Colombia

Open areas associated with traditional agriculture promote functional connectivity among amphibian demes in Mediterranean agrosystems

ContextFunctional connectivity across fragmented habitat patches is essential for the conservation of animal populations in humanized landscapes. Given their low dispersal capacity, amphibians in the Mediterranean region are threatened by habitat fragmentation and loss due to changes in land use, including agricultural intensification.ObjectivesWe assessed patterns of functional connectivity of a Near Threatened Mediterranean amphibian, the sharp ribbed newt (Pleurodeles waltl), in an agricultural landscape matrix in NW Spain subject to different intensification regimes.MethodsWe sampled newts in 17 ponds embedded in a terrestrial habitat matrix dominated by agricultural land uses. Genome-wide molecular markers (1390 SNPs) were used to assess patterns of genetic diversity and gene flow among ponds. We tested the role of landscape features on functional connectivity using isolation by resistance models incorporating information on Normalized Difference Vegetation Index (NDVI) data.ResultsWe found low levels of genetic diversity in all sampled populations. Global FST estimates and cluster analyses revealed shallow but significant genetic structure in the study area, with NDVI-based resistance models showing that open areas (rainfed crops and grasslands) offer lower resistance to gene flow and thus promote functional connectivity among demes.ConclusionsOur study highlights the important role of landscape features, such as open areas resulting from traditional rainfed agriculture, in promoting functional connectivity between amphibian populations in Mediterranean agrosystems. Conservation policies must adopt a functional network strategy and protect groups of inter-connected temporary ponds across the traditional agricultural matrix to efficiently preserve their associated biotic communities.

Population structure and genetic diversity of rainbow trout (Oncorhynchus mykiss) broodstocks from Brazil using SNP markers

Population structure and genetic diversity of rainbow trout (Oncorhynchus mykiss) broodstocks from Brazil using SNP markers

Population Genomics of Plasmodium falciparum and Malaria Control Implications in Abidjan (Cote d’ivoire)

Introduction: The onset of Plasmodium falciparum (P. falciparum) resistance to antimalarial drugs requires the careful surveillance of African parasite populations. Genomic tools are implemented to detect evolutionary changes that could impact malaria control and elimination strategies. Here, we evaluate the genome-wide pattern of selection and sequence variation in P. falciparum populations in Abidjan, Côte d’Ivoire. Methods: The study was conducted in three localities of Abidjan from 2013 to 2014. We collected 70 blood samples after receiving written informed consent from patients above two years of age. After extracting P. falciparum and human DNA from isolates, we performed whole-genome sequencing and used population genomics approaches to investigate the genetic diversity and complexity of infections and identify loci under positive directional selection. Results: We observed an excess of rare variants in the population, showing a clear mutation process in the isolates. Moderate Fst estimates (0.3) was detected for surfin, an immune invasion gene family. Seven iHS regions that had at least two SNPs with a score &gt; 3.2 were identified. These regions code for genes that have been under strong directional selection. Two of these genes were the chloroquine resistance transporter (crt) on chromosome 7 and the dihydropteroate reductase (dhps) on chromosome 8. Our analyses showed that a recent selective sweep occurred for the erythrocyte membrane protein (Pfemp1). Conclusion: Our analyses identified genes under selective drug pressure and balancing selection on protective immune-specific genes. These findings demonstrate the effectiveness of genomics analyses to follow the evolution of malaria parasites and adopt appropriate strategies to eliminate malaria in Côte d’Ivoire.

FST estimates of 94 populations in China based on STR markers

The proper assessment of DNA evidence in cases of personal identification is a recurring theme in forensics. It is common practice to evaluate the strength of DNA evidence using the likelihood ratio (LR). The accurate use of population allele frequencies is a crucial problem in LR calculation. Allele frequency differences among different populations could be estimated by the FST values. Thus, FST would also affect LR values by correcting the allele frequencies. In this study, Chinese population allele frequency data were selected from population reports published in Chinese and English journals. The population-specific FST values of each population, the overall FST values of each province, each region, and the whole country, and the locus-specific FST values of different loci were calculated. The LRs using different allele frequencies and different FST values were compared based on the combination of simulated genotypes. As a result, the FST values of 94 populations, 19 provinces, 7 regions, and the whole country were obtained. The LR was overestimated using allele frequencies of the combined population containing multiple populations rather than using allele frequencies of a population, and the LRs after FST correction were lower than those without correction. Conclusively, the correction in conjunction with corresponding FST values can make the LRs more accurate and reasonable.

Genetic structure of common bottlenose dolphins (Tursiops truncatus) inhabiting adjacent South Florida estuaries – Biscayne Bay and Florida Bay

Coastal common bottlenose dolphins show a variety of migration and residency patterns adding to the difficulty of defining stocks for management purposes. Genetic structure plays an important role in identifying population stocks of dolphins. This study examines genetic differentiation in common bottlenose dolphins both between two social groups occurring in Biscayne Bay, Florida and between Biscayne Bay and an adjacent group of dolphins in Florida Bay. Skin biopsy samples were sequenced at the mitochondrial DNA (mtDNA) control region and genotyped at microsatellite loci. Significant genetic differentiation was found between bottlenose dolphins in Biscayne Bay and Florida Bay (mtDNA FST = 0.139, p ≤ 0.001; microsatellite FST = 0.042, p ≤ 0.001) supporting independent management stock status for these two populations. Within Biscayne Bay, evidence of weak but significant population differentiation was found between the two social groups using microsatellite markers (FST = 0.0149, p ≤ 0.009); however, differentiation was not evident from the mtDNA-based estimates of FST and φST. The lack of differentiation at mtDNA coupled with field observations indicating overlapping home ranges for these two groups suggests ongoing, though perhaps low, levels of interbreeding. These data are insufficient to warrant splitting the Biscayne Bay management stock at this time.

Cryptic Lineage and Genetic Structure of Acanthopagrus pacificus Populations in a Natural World Heritage Site Revealed by Population Genetic Analysis

Recent studies have revealed extensive genetic differentiation among some populations of marine taxa that were previously believed to be essentially homogeneous because larvae are widely dispersed in ocean currents. Acanthopagrus pacificus is a commercially and ecologically important teleost fish that is endemic to shallow coastal waters and estuaries of some tropical and sub-tropical areas in the West Pacific Ocean. Here, we examined genetic structure and the inferred demographic history of A. pacificus populations from mtDNA control region sequence data. A 677–678 base-pair fragment was sequenced from 159 individuals sampled at three localities across the West Pacific Ocean. Haplotype diversity was high, ranging from 0.915 to 0.989, while nucleotide diversity was low to medium, ranging from 0.8% to 2.60%. Analysis of molecular variance (AMOVA) showed significant genetic subdivision (FST = 0.155, p &lt; 0.05) among sampled populations while pairwise FST estimates also revealed strong genetic differentiation among populations indicating that gene flow was restricted. Two distinct cryptic lineages were identified that were estimated to have diverged during the Pleistocene. In summary, contemporary factors including regional oceanic currents and self-recruitment are considered to have played significant roles in producing the population structure in this fish. In particular, the genetic information generated in the current study will allow appropriate fisheries management and conservation strategies to be developed for this important local fish in the waters around Iriomotejima Island, a World Heritage site.

Effects of fifty years of shelterwood harvesting on genetic diversity and population structure of Oriental beech (Fagus orientalis L.) in the relict Hyrcanian forest

Effects of fifty years of shelterwood harvesting on genetic diversity and population structure of Oriental beech (Fagus orientalis L.) in the relict Hyrcanian forest

Genome-Wide Genetic Diversity and Population Structure of Local Sudanese Sheep Populations Revealed by Whole-Genome Sequencing

Local Sudanese sheep populations inhabiting diverse environmental conditions and holding opposing morphologies provide opportunities for molecular-genetic research. Characterizing their genome is crucial for sustainable breeding improvement and targeting favorable genes in breeding programs. However, the genome of these sheep populations, which comprises several subtypes, remains uncharacterized using whole-genome sequence data. This study aimed to elucidate genome-wide genetic diversity and population structure of 11 local Sudanese sheep populations, namely, Hammari, Kabbashi, Meidobe, Ashgar, Dubasi, Watish, Bega, Naili, Fulani, Zagawi, and Garag. Ninety whole blood samples were collected, and we extracted DNA using a Qiagen DNeasy® extraction kit. We used the Illumina HiSeq 2000 platform to sequence all the DNA samples. We included whole-genome sequence data of three Ethiopian sheep (Doyogena, Kefis, and Gafera) and one Libyan sheep (Libyan Barbary) in the study to infer the genetic relationships of local Sudanese sheep populations from a continental perspective. A total of 44.8 million bi-allelic autosomal SNPs were detected; 28.5% and 63.3% occur in introns and intergenic regions, respectively. The mean genetic diversity ranged from 0.276 for Garag to 0.324 for Kabbashi sheep populations. The lowest FST estimates were observed between Kabbashi and Ashgar and the highest between Bega and Fulani local Sudanese sheep populations. The principal component and population structure analyses of the 11 local Sudanese sheep populations indicated three separate genetic groups categorized following their tail morphotype, geographical distribution, and population subtype. The thin-tailed local Sudanese sheep populations exhibited independent clustering from the fat-tailed Ethiopian and Libyan sheep. We also observed distinct clustering between the fat-tailed Ethiopian and Libyan sheep. The present study’s findings demonstrated the population structure and principal components related to tail morphotype, geographical distribution, and population subtype of local Sudanese sheep populations. A clear signature of admixture was observed among the studied local Sudanese sheep populations.

Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds

Copy number variation (CNV) is one of the main sources of variation between different individuals that has recently attracted much researcher interest as a major source for heritable variation in complex traits. The aim of this study was to identify CNVs in Afghan indigenous sheep consisting of three Arab, Baluchi, and Gadik breeds using genomic arrays containing 53,862 single nucleotide polymorphism (SNP) markers. Data were analyzed using the Hidden Markov Model (HMM) of PennCNV software. In this study, out of 45 sheep studied, 97.8% (44 animals) have shown CNVs. In total, 411 CNVs were observed for autosomal chromosomes and the entire sequence length of around 144 Mb was identified across the genome. The average number of CNVs per each sheep was 9.13. The identified CNVs for Arab, Baluchi, and Gadik breeds were 306, 62, and 43, respectively. After merging overlapped regions, a total of 376 copy number variation regions (CNVR) were identified, which are 286, 50, and 40 for Arab, Baluchi, and Gadik breeds, respectively. Bioinformatics analysis was performed to identify the genes and QTLs reported in these regions and the biochemical pathways involved by these genes. The results showed that many of these CNVRs overlapped with the genes or QTLs that are associated with various pathways such as immune system development, growth, reproduction, and environmental adaptions. Furthermore, to determine a genome-wide pattern of selection signatures in Afghan sheep breeds, the unbiased estimates of FST was calculated and the results indicated that 37 of the 376 CNVRs (~ 10%) have been also under selection signature, most of those overlapped with the genes influencing production, reproduction and immune system. Finally, the statistical methods used in this study was applied in an external dataset including 96 individuals of the Iranian sheep breed. The results indicated that 20 of the 114 CNVRs (18%) identified in Iranian sheep breed were also identified in our study, most of those overlapped with the genes influencing production, reproduction and immune system. Overall, this is the first attempts to develop the genomic map of loss and gain variation in the genome of Afghan indigenous sheep breeds, and may be important to shed some light on the genomic regions associated with some economically important traits in these breeds.

Genetic Diversity and Fine-Scale Spatial Genetic Structure of the Endangered Shrub Birch (Betula humilis Schrk.) Populations in Protected and Unprotected Areas

The genetic diversity of natural populations is a key factor in the success of long-term ecosystem protection. We studied the genetic diversity and spatial genetic structure (SGS) in three endangered shrub birch (Betula humilis) populations using seven nuclear microsatellite loci. The highest genetic variation was found in the restored Szuszalewo population in Biebrza National Park, where active prevention of thicket forest succession was recently conducted. The results of bottleneck tests were not statistically significant in each locality, although a genetic indication for population reduction was detected in the Rospuda stand, which is not actively protected. The Bayesian clustering, principal coordinates analysis, and FST estimates revealed the greatest difference between Magdzie Bagno and Rospuda samples. SGS was found in all B. humilis stands; however, it was the strongest in the Rospuda locality, where pollen and seed dispersal was limited by dense clusters of shrub birch ramets scattered among forest and brushwood plants. The weakest SGS, also supported by finding some sibling pairs in distant locations, was observed in the Szuszalewo population. The aforementioned results indicate that the active protection practices may impose an immediate beneficial effect on the restoration and maintenance of the B. humilis populations.