Genetic Structure Of Natural Populations Research Articles

Genetic characterisation of Annona crassiflora as basis for conservation and breeding

Abstract Annona crassiflora is a fruit-bearing tree species native to the Cerrado that has ecological and economic potential, mainly due to the production of attractive and useful fruits for a number of species, including humans. To provide a basis for its conservation and breeding, the objective was to assess the diversity and genetic structure of natural populations of the species using inter-simple sequence repeat (ISSR) molecular markers. Eight populations were analysed in the state of Minas Gerais, Brazil, with 24 individuals randomly sampled in each population, reaching a total of 192 trees. Ten ISSR primers were used, resulting in high genetic diversity for the combined data (H* = 0.35 and I* = 0.52). However, a wide range of representative values was observed in the individual assessment of populations, with JAN, GM and MC standing out for their low genetic diversity, resulting in H* of 0.19, 0.23 and 0.24 and I* of 0.28, 0.34 and 0.35, respectively. An analysis of molecular variance showed greater variation within populations, indicating gene flow (Nm), but genetic differentiation between populations was moderate. Bayesian analysis, although resulting in four genetic groups, revealed the presence of a majority group for the GM and JAN populations. We propose measures to maintain these populations, such as raising awareness of local extractivism and planting genetically divergent seedlings. Furthermore, we recommend including of all populations in conservation and breeding programmes, aiming to cover the maximum genetic variation for the species.

Genomic DNA polymorphism in <i>Myrica gale</i> (Myricaceae) in the Lebyazhiy state Nature Reserve (the southern coast of the gulf of Finland)

The analysis of genomic DNA polymorphism is one of widely used approaches for studying the genetic structure of natural populations. It has been successfully applied to various plants. However, many species have not yet been studied, which is primarily due to methodological difficulties in isolating well-purified and non-degraded genomic DNA. These difficulties are due to the fact that plants possess numerous bioorganic compounds (polysaccharides, polyphenols, lipids, etc.) that contaminate DNA and significantly reduce its quality. Such species include marsh waxweed (Myrica gale L.), a perennial sub-Atlantic shrub with presumably vegetative propagation (in nature, waxweed seedlings are quite rare). We developed a simple protocol for isolation of high-quality genomic DNA from waxweed leaves and performed AFLP analysis of 42 plants of this species from three subpopulations in the Lebyazhiy Nature Reserve. Using three primer pairs, we isolated 22 amplification fragments, 8 of which were monomorphic. For the remaining 14 fragments, the average level of their polymorphism was low: depending on the subpopulation studied, it varied from 0.079 to 0.129. As shown by our analysis, all three studied subpopulations are polymorphic with a predominance of two common AFLP-genotypes. The corresponding plants are apparently the vegetative descendants of the founders. The rare AFLP-genotypes (represented by just one or two plants; a total of 12 such genotypes were identified) are likely the result of mutational and recombination processes. Our data give evidence that in the life cycle and dispersal of waxweed, the role of sexual reproduction is also noticeable.

Climate change effect on the genetics of a Mexican population of drosophila pseudoobscura

The chromosomal polymorphism present in populations of seveal species of Drosophila could be related with changes in time or ecological parameter. The aim of this work is to evaluate the long-term effect of climatic changes on the frequencies of D. pseudoobscura chromosomal arrangements. The population studied is located in a forest near Tulancingo, M?xico, the chromosomal analysis has been studied for more than 35 years. The relative frequencies found in that period were used to evaluate the changes. The climatic data of the National Meteorological Service were gather for the period from 1974 to 2011. A multiple analysis of variance was use to analyze the relationship between the changes in the chromosomal arrangement frequencies and the different climatic variables (maximum and minimum temperature, evaporation and pluvial precipitation). Results showed a significant correlation of several chromosome gene arrangements with one or more hydro-climatic variables modifying the genetic structure of the natural population. Comparisons with other populations shown and allow the establishment of the effect of climate change on the genetic structure of natural populations.

Population genetic characterization of (Aedes albopictus) mosquitoes (Diptera: Culicidae) from the Yangtze River Basin of China based on rDNA-ITS2.

Aedes albopictus is an important vector of many mosquito-borne viral diseases, including dengue fever and Zika. In recent years, it has spread and colonized tropical, subtropical and temperate regions worldwide. Monitoring of Ae. albopictus population dynamics is an important tool for early warning of mosquito-borne infections. Because the genetic diversity and genetic structure of natural populations are the genetic bases of population dynamics, studies of population genetics can reveal the origin, differentiation and dispersal characteristics of Ae. albopictus populations. Then, their evolutionary potential and environmental adaptability can be analyzed, providing a theoretical basis for the formulation of accurate Ae. albopictus surveillance and integrated control programs. In 2018, 552 Ae. albopictus larvae were collected during an invasive mosquito species surveillance project in China's Yangtze River Basin. Morphological analysis was performed to assign the adult mosquitoes to species, and then the genetic marker ITS2 was amplified and sequenced. There were 179 haplotypes among 552 ITS2 sequences. In total, 155/179 (86.59%) haplotypes were specific to individual populations, and 24/179 (13.41%) haplotypes were shared by populations. Hap4 (126), Hap7 (43), and Hap16 (34) were the most numerous haplotypes and the most widely distributed. The overall Hd was 0.928, π was 0.031, the mean nucleotide difference number (K) was 7.255, and the number of segregating sites was 169. TCS network maps mainly showed a single star-like scattered distribution. According to geographical location, there were no obvious haplotype groups, and the haplotypes were intricately connected. The genetic diversity of Ae. albopictus populations in the Yangtze River Basin was high. The molecular variance observed in the populations of Ae. albopictus mainly occurred among individuals within populations, accounting for 98.79% of the total, while that among populations accounted for only 1.21% of the total. Only the populations of Ae. albopictus in the Chongqing and Sichuan regions showed a moderate degree of population genetic differentiation, while genetic differentiation between the other regions were small, gene exchange was very common, and genetic differentiation within populations was minimal. According to this study, the genetic diversity of Ae. albopictus populations in the Yangtze River Basin is high, the genetic differentiation among populations is small, and gene exchange is common. In addition, frequent interregional exchange exacerbates the abnormal spread of vectors. This study highlighted the potential spread route of the vector Ae. albopictus in the Yangtze River Basin. There are three potential dispersal routes for Ae. albopictus populations in the Yangtze River Basin. The findings could be helpful for effective surveillance and early warning of Ae. albopictus vectors.

A Set of Highly Polymorphic Microsatellite Markers for Genetic Diversity Studies in the Genus Origanum

This study reports the development of a set of 20 highly polymorphic genomic SSR markers which can be used for both cultivar identification and genetic diversity studies in several Origanum species, including some of the most popular ones like Greek oregano (Origanum vulgare L. ssp. hirtum), common oregano (O. vulgare L. ssp. vulgare), and sweet marjoram (O. majorana L.). Analysis of the polymorphic information content (PIC) showed an average PIC value of 0.75 with a minimum of 0.41 and a maximum of 0.89, where 17 of the markers showed PIC values above 0.73. Comparative analysis of the genetic diversity of eight natural populations of Greek oregano in Bulgaria showed that six of the genomic SSR markers revealed significantly higher portions of genetic diversity in the populations, compared to 12 EST SSR markers used in our previous study. We also compared the performance of the same six genomic SSR markers with the results for eight SRAP primer combinations, which showed that SRAP markers captured more precisely the genetic structure in natural populations. The developed highly polymorphic genomic SSR markers can be successfully applied to evaluation of the genetic diversity in the genus Origanum, based on the expected and observed heterozygosity in the populations as well as for easy identification of breeding lines and cultivars based on unique SSR fingerprints.

Reference genome of the color polymorphic desert annual plant sandblossoms, Linanthus parryae.

Sandblossoms, Linanthus parryae is a widespread annual plant species found in washes and sandy open habitats across the Mojave Desert and Eastern Sierra Nevada of California. Studies in this species have played a central role in evolutionary biology, serving as the first test cases of the shifting balance theory of evolution, models of isolation by distance, and metrics to describe the genetic structure of natural populations. Despite the importance of L. parryae in the development of landscape genetics and phylogeography, there are no genomic resources available for the species. Through the California Conservation Genomics Project, we assembled the first genome in the genus Linanthus. Using PacBio HiFi long reads and Hi-C chromatin conformation capture, we assembled 123 scaffolds spanning 1.51 Gb of the 1.96 Gb estimated genome, with a contig N50 of 18.7 Mb and a scaffold N50 of 124.8 Mb. This assembly, with a BUSCO completeness score of 88.7%, will allow us to revisit foundational ideas central to our understanding of how evolutionary forces operate in a geographic landscape. In addition, it will be a new resource to uncover adaptations to arid environments in the fragile desert habitat threatened by urban and solar farm development, climate change, and off-road vehicles.

Genetic Differentiation and Widespread Mitochondrial Heteroplasmy among Geographic Populations of the Gourmet Mushroom Thelephora ganbajun from Yunnan, China.

The mitochondrial genomes are generally considered non-recombining and homoplasmic in nature. However, our previous study provided the first evidence of extensive and stable mitochondrial heteroplasmy in natural populations of the basidiomycete fungus Thelephora ganbajun from Yunnan province, China. The heteroplasmy was characterized by the presence of two types of introns residing at adjacent but different sites in the cytochrome oxidase subunits I (cox1) gene within an individual strain. However, the frequencies of these two introns among isolates from different geographical populations and the implications for the genetic structure in natural populations have not been investigated. In this study, we analyzed DNA sequence variation at the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster among 489 specimens from 30 geographic locations from Yunnan and compared that variation with distribution patterns of the two signature introns in the cox1 gene that are indicative of heteroplasmy in this species. In our samples, evidence for gene flow, abundant genetic diversity, and genotypic uniqueness among geographic samples in Yunnan were revealed by ITS sequence variation. While there was insignificant positive correlation between geographic distance and genetic differentiation among the geographic samples based on ITS sequences, a moderate significant correlation was found between ITS sequence variation, geographical distance of sampling sites, and distribution patterns of the two heteroplasmic introns in the cox1 gene. Interestingly, there was a significantly negative correlation between the copy numbers of the two co-existing introns. We discussed the implications of our results for a better understanding of the spread of stable mitochondrial heteroplasmy, mito-nuclear interactions, and conservation of this important gourmet mushroom.

Stand development stages and recruitment patterns influence fine-scale spatial genetic structure in two Patagonian Nothofagus species

Key messageNothofagus alpina (Poepp. et Endl.) Oerst. and Nothofagus obliqua (Mirb.) Oerst forests have strong fine-scale spatial genetic structures. The intensity of genetic structure patterns differed according to species, stand development stages, life stages, and spatial arrangement of regeneration groups. This data becomes useful for forest management as it provides an understanding of how populations evolve as well as of the consequences of disturbances and enables the establishment of sampling strategies.ContextThe understanding of fine-scale spatial genetic structure in natural populations is useful for forest management. Although Nothofagus alpina (Poepp. et Endl.) Oerst. and N. obliqua (Mirb.) are important species of the Patagonian forest, little is known about the genetic structure of their populations.AimsThe main objectives were to investigate the differences in fine-scale spatial genetic structure among mature tree populations of both species considering two stands at different development stages. Genetic structure was also evaluated among life stages and spatial distribution groups of regeneration within the old-growth stand.MethodsGenetic structure was examined by microsatellite DNA analysis of regeneration and mature tree populations of both species (around 1300 individuals). Gene dispersal distance was additionally estimated.ResultsIn both stands and species, strong fine-scale spatial genetic structure and short dispersal distance were found. This pattern was stronger in the early successional forest, in N. obliqua populations, in earlier life stages, and in scattered regeneration.ConclusionStand development stages and recruitment patterns influence the fine-scale spatial genetic structure of both Nothofagus species. However, the genetic structure also differs between species.

Comparing the population structure of the specialist Butler’s Gartersnake (Thamnophis butleri) and the generalist Eastern Gartersnake (Thamnophis sirtalis sirtalis) in Ontario (Canada) and Michigan (USA)

Species differing in life-history attributes vary in their responses to features within a shared landscape. We evaluated genetic structure of sympatric gartersnake species in southwestern Ontario (Canada) and southeastern Michigan (USA), where habitat fragmentation is high due to agriculture and urbanization. We surveyed genetic structure of a habitat specialist, Butler’s Gartersnake (Thamnophis butleri (Cope, 1889)), and a habitat generalist, Eastern Gartersnake (Thamnophis sirtalis sirtalis (Linnaeus, 1758)), using DNA microsatellites. Bayesian clustering, discriminant analysis of principal components, and pairwise population comparisons revealed genetic differentiation among three major regional clusters of Butler’s Gartersnake with evidence of further division within one. Genetic clustering of Butler’s Gartersnake suggest that inhospitable habitat limits dispersal. Eastern Gartersnakes showed less structure, with assignment tests implying a single genetic cluster. We found positive significant Mantel’s r for both species in the smallest distance class (<15 km), but significant isolation by distance for Butler’s Gartersnake only. These findings together imply that connectivity for Eastern Gartersnakes is less impacted by habitat loss and fragmentation or that we were less able to detect their effects. Our study shows the value of multispecies comparisons in studies seeking to understand the underlying causes of genetic structure in natural populations.

Genetic diversity and population structure in Vitis species illustrate phylogeographic patterns in eastern North America.

Geographical distribution and diversity of current plant species have been strongly shaped by climatic oscillations during the Quaternary. Analysing the resulting divergence among species and differentiation within species is crucial to understand the evolution of taxa like the Vitis genus, which provides very useful genetic resources for grapevine improvement and might reveal original recolonization patterns due to growth habit and dispersal mode. Here, we studied the genetic structure in natural populations of three species from eastern North America: Vitis aestivalis, V.cinerea and V.riparia using different marker types. Vitis aestivalis and V.cinerea showed higher diversity than V.riparia. The two former species are less differentiated, confirming an earlier divergence of V.riparia. V.aestivalis and V.riparia exhibited different genetic groups on both sides of the Appalachian Mountains that could mirror different recolonization routes from southern refugia. Genetic structure was stronger in V.cinerea, for which two varieties (var. berlandieri and var. cinerea) are morphologically recognized. Our results confirm this distinction and suggest the existence of three other lineages within var. cinerea. These discontinuities appear linked to adaptation of var. berlandieri to dry and limy areas of Texas and partially to the Mississippi River Valley. Rapid range expansions from refugia upon climate warming are also suggested by the low linkage disequilibrium values observed. Furthermore, large variation for downy mildew resistance was observed in the three species. Our findings appeared consistent with the vegetation history of eastern North America.

Genetic Structure in Populations of Euterpe precatoria Mart. in the Brazilian Amazon

Euterpe precatoriais a palm tree belonging to the Arecaceae family, occurring in Western and Central Brazilian Amazonia. Its fruit, which is very appreciated in the Amazon region, produces pulp that is consumed in fresh form. Its production is carried out almost exclusively by extractive farmers. In order to establish adequate strategies to sustain this genetic resource, we need knowledge about the diversity and genetic structure in natural populations. This study aimed to evaluate the influence of geographic distance on genetic structure in the main extractive populations ofE. precatoriain the Brazilian Amazon. Leaves from 377 plants were collected in 19 populations located in 16 municipalities in the State of Amazonas and three in the State of Rondônia. Twelve microsatellite loci were used to genotype the plants. The diversity and genetic structure among populations were estimated. The average number of alleles per locus was 5.97. The observed heterozygosity means (HO) were higher than expected (HE) at the population level (HO= 0.72,HE= 0.66) and fixation index (f= -0.100) was negative. TheFSTvalue (0.1820) and the AMOVA results (Φ= 0.1796) showed population structure. The populations were clustered into three groups (K= 3) in the Bayesian analysis. The Discriminant Analysis of Principal Components (DAPC) confirmed eight clusters, with the populations close to those identified by the Bayesian analysis. The geographic differentiation was confirmed by the groupings obtained in the Structure analysis and the DACP function. Information related to phenotypic, genetic and environmental characterization of populations is important to guide conservation and management strategies and the formulation of public species management policies in Amazonia.

ПОЛИМОРФИЗМ ДНК, ГЕНЕТИЧЕСКАЯ ОРИГИНАЛЬНОСТЬ И ИДЕНТИФИКАЦИЯ ПОПУЛЯЦИЙ И РЕМОНТНО-МАТОЧНЫХ СТАД СТЕРЛЯДИ (ACIPENSER RUTHENUS)

DNA polymorphism has been studied, indicators of genetic diversity and genetic originality have been de-termined for three natural populations and three replacement broodstocks of sterlet (Acipenser ruthenus Linnaeus, Acipenseridae) from the Volga Federal District. In the group of A. ruthenus replacement broodstock, 106 ISSR-PСR markers were identified, and in the group of natural populations, 103 ISSR-PСR markers. The indicators of genetic diversity and the coefficient of genetic originality (CGO) were slightly higher in the group of natural populations. Analysis of genetic structure of natural populations and groups of broodstock herds A. ruthenus showed that the coefficient of genetic differentiation are also slightly higher in the group of natural populations and equal 0,377. As a result of molecular genetic iden-tification, generic and species identification fragments of sterlet DNA were revealed, as well as combina-tions of polymorphic fragments for identification of the studied natural populations and stocks. The data obtained can be used to preserve the gene pool of populations, which is characteristic for a particular re-gion.

Genetic structure in natural populations of Dacrydium elatum (Roxb.) Wall. (Podocarpaceae) in the Central Highlands of Vietnam inferred by Microsatellites

To provide a reference for the conservation and application of breeding parentallines resource of Dacrydium elatum (Roxb.). Genetic diversity and population structure of eighty individuals from four populations (Kon Tum, Gia Lai, Dak Lak and Lam Dong) in Central Highlands were evaluated using eight SSR markers. Based on the SSR data, 21 alleles were detected by eight SSR with high polymorphism. The genetic diversity of levels within the populations were moderately high (Ho = 0.555, He = 0.429). The average number of shannon information index were 0.618 and genetic differentiation among populations was low (Fst=0.097). The AMOVA revealed high genetic variation within individuals (87%) compared among populations (13%). The UPGMA phenogram showed that the results of molecular clustering largely agreed with the pedigree and geographic origin. Three populations (NL, KCR and BDNB) were clustered together and CYS population was separated. The maximum quantity ΔK was observed for K=2 in population structure analysis, indicating that the entire collection could be divided into two main groups of genes. This study can provide a theoretical basis for genetic resource management and varieties identification of D. elatum resources, and provide reference basis for breeding.

Temporal migration rates affect the genetic structure of populations in the biennial Erysimum mediohispanicum with reproductive asynchrony.

Migration is a process with important implications for the genetic structure of populations. However, there is an aspect of migration seldom investigated in plants: migration between temporally isolated groups of individuals within the same geographic population. The genetic implications of temporal migration can be particularly relevant for semelparous organisms, which are those that reproduce only once in a lifetime after a certain period of growth. In this case, reproductive asynchrony in individuals of the same population generates demes of individuals differing in their developmental stage (non-reproductive and reproductive). These demes are connected by temporal migrants, that is, individuals that become annually asynchronous with respect to the rest of individuals of their same deme. Here, we investigated the extent of temporal migration and its effects on temporal genetic structure in the biennial plant Erysimum mediohispanicum. To this end, we conducted two independent complementary approaches. First, we empirically estimated temporal migration rates and temporal genetic structure in four populations of E. mediohispanicum during three consecutive years using nuclear microsatellites markers. Second, we developed a demographic genetic simulation model to assess genetic structure for different migration scenarios differing in temporal migration rates and their occurrence probabilities. We hypothesized that genetic structure decreased with increasing temporal migration rates due to the homogenizing effect of migration. Empirical and modelling results were consistent and indicated a U-shape relationship between genetic structure and temporal migration rates. Overall, they indicated the existence of temporal genetic structure and that such genetic structure indeed decreased with increasing temporal migration rates. However, genetic structure increased again at high temporal migration rates. The results shed light into the effects of reproductive asynchrony on important population genetic parameters. Our study contributes to unravel the complexity of some processes that may account for genetic diversity and genetic structure of natural populations.

Genetic structure of deltamethrin-resistant populations of Triatoma infestans (Hemiptera: Reduviidae) in the Gran Chaco.

The genetic structure of natural populations offers insight into the complexities of their dynamics, information that can be relevant to vector control strategies. Microsatellites are useful neutral markers to investigate the genetic structure and gene flow in Triatoma infestans, one of the main vectors of Chagas disease in South America. Recently, a heterogeneous pyrethroid-resistant hotspot was found in the Argentine Gran Chaco, characterized by the highest levels of deltamethrin resistance found at the present time. We applied population genetics analyses to microsatellite and village data and search for associations between the genetic variability and the heterogeneous toxicological pattern previously found. We genotyped 10 microsatellite loci in 67 T. infestans from 6 villages with no, low, and high pyrethroid resistance. The most genetically diverse populations were those susceptible or with low values of resistance. In contrast, high-resistance populations had lower herozygosity and some monomorphic loci. A negative association was found between variability and resistant ratios. Global and pairwise FSTs indicated significant differentiation between populations. The only susceptible population was discriminated in all the performed studies. Low-resistance populations were also differentiated by a discriminant analysis of principal components (DAPC) and were composed mostly by the same two genetic clusters according to STRUCTURE Bayesian algorithm. Individuals from the high-resistance populations were overlapped in the DAPC and shared significant proportions of a genetic cluster. These observations suggest that the resistant populations might have a common origin, although more genetic markers and samples are required to test this hypothesis more rigorously.

Detecting geospatial patterns of Plasmodium falciparum parasite migration in Cambodia using optimized estimated effective migration surfaces

BackgroundUnderstanding the genetic structure of natural populations provides insight into the demographic and adaptive processes that have affected those populations. Such information, particularly when integrated with geospatial data, can have translational applications for a variety of fields, including public health. Estimated effective migration surfaces (EEMS) is an approach that allows visualization of the spatial patterns in genomic data to understand population structure and migration. In this study, we developed a workflow to optimize the resolution of spatial grids used to generate EEMS migration maps and applied this optimized workflow to estimate migration of Plasmodium falciparum in Cambodia and bordering regions of Thailand and Vietnam.MethodsThe optimal density of EEMS grids was determined based on a new workflow created using density clustering to define genomic clusters and the spatial distance between genomic clusters. Topological skeletons were used to capture the spatial distribution for each genomic cluster and to determine the EEMS grid density; i.e., both genomic and spatial clustering were used to guide the optimization of EEMS grids. Model accuracy for migration estimates using the optimized workflow was tested and compared to grid resolutions selected without the optimized workflow. As a test case, the optimized workflow was applied to genomic data generated from P. falciparum sampled in Cambodia and bordering regions, and migration maps were compared to estimates of malaria endemicity, as well as geographic properties of the study area, as a means of validating observed migration patterns.ResultsOptimized grids displayed both high model accuracy and reduced computing time compared to grid densities selected in an unguided manner. In addition, EEMS migration maps generated for P. falciparum using the optimized grid corresponded to estimates of malaria endemicity and geographic properties of the study region that might be expected to impact malaria parasite migration, supporting the validity of the observed migration patterns.ConclusionsOptimized grids reduce spatial uncertainty in the EEMS contours that can result from user-defined parameters, such as the resolution of the spatial grid used in the model. This workflow will be useful to a broad range of EEMS users as it can be applied to analyses involving other organisms of interest and geographic areas.

Genetic structure of natural populations of endangered Tor mahseer, Tor tor (Hamilton, 1822) inferred from two mitochondrial DNA markers

Tor tor, Tor mahseer, an endangered cyprinid species, is important as a sport fish. Genetic divergence in natural populations of T. tor was investigated using two mitochondrial genes, Cytb (Cytochrome b) and ATPase6/8. Analysis of 140 sequences of Cytb (1121 bp) and ATPase6/8 (842 bp) genes revealed 12 and 7 haplotypes, respectively, whereas 23 haplotypes were found in concatenated sequences (1963 bp). Sequence analysis of mitochondrial regions revealed balancing selection and displayed low nucleotide and moderate haplotype diversities. Mantel tests identified a positive relationship between pairwise geographical and genetic distances for the study region. Results of AMOVA based on genes pointed out that the genetic variations were mainly due to variation in within populations (ATPase6/8: 62.73%, Cytb: 42.13%, concatenated sequences: 48.31%). The total Fst was found to be significant in both genes with a value of 0.5787 (p <0 .05) and 0.3726 (p <0 .05) for Cytb and ATPase6/8genes respectively, whereas 0.51687 (p <0 .05) was found in combined sequences, which revealed sub-structuring in the T. tor natural populations. Population pair-wise Fst ranged from 0.00901– to 0.85631 for Cytb and 0.09910– to 0.64731 for ATPase6/8genes, whereas 0.02039 to 0.85436 in combined sequences. Results indicated the presence of four genetic stocks in the populations studied. The baseline information about stock characterisation in this study would be applicable for planning strategies for conservation, management and sustainable fisheries of this species.

Variable opportunities for outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation.

Many pathogens possess the capacity for sex through outcrossing, despite being able to reproduce also asexually and/or via selfing. Given that sex is assumed to come at a cost, these mixed reproductive strategies typical of pathogens have remained puzzling. While the ecological and evolutionary benefits of outcrossing are theoretically well-supported, support for such benefits in pathogen populations are still scarce. Here, we analyze the epidemiology and genetic structure of natural populations of an obligate fungal pathogen, Podosphaera plantaginis. We find that the opportunities for outcrossing vary spatially. Populations supporting high levels of coinfection -a prerequisite of sex - result in hotspots of novel genetic diversity. Pathogen populations supporting coinfection also have a higher probability of surviving winter. Jointly our results show that outcrossing has direct epidemiological consequences as well as a major impact on pathogen population genetic diversity, thereby providing evidence of ecological and evolutionary benefits of outcrossing in pathogens.

The population genetic structure approach adds new insights into the evolution of plant LTR retrotransposon lineages.

Long terminal repeat retrotransposons (LTR-RTs) in plant genomes differ in abundance, structure and genomic distribution, reflecting the large number of evolutionary lineages. Elements within lineages can be considered populations, in which each element is an individual in its genomic environment. In this way, it would be reasonable to apply microevolutionary analyses to understand transposable element (TE) evolution, such as those used to study the genetic structure of natural populations. Here, we applied a Bayesian method to infer genetic structure of populations together with classical phylogenetic and dating tools to analyze LTR-RT evolution using the monocot Setaria italica as a model species. In contrast to a phylogeny, the Bayesian clusterization method identifies populations by assigning individuals to one or more clusters according to the most probabilistic scenario of admixture, based on genetic diversity patterns. In this work, each LTR-RT insertion was considered to be one individual and each LTR-RT lineage was considered to be a single species. Nine evolutionary lineages of LTR-RTs were identified in the S. italica genome that had different genetic structures with variable numbers of clusters and levels of admixture. Comprehensive analysis of the phylogenetic, clusterization and time of insertion data allowed us to hypothesize that admixed elements represent sequences that harbor ancestral polymorphic sequence signatures. In conclusion, application of microevolutionary concepts in genome evolution studies is suitable as a complementary approach to phylogenetic analyses to address the evolutionary history and functional features of TEs.

Associations between environmental variability and inversion polymorphism of Drosophila subobscura: meta-analysis of populations from the Central Balkans

CR Climate Research Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials CR 77:205-217 (2019) - DOI: https://doi.org/10.3354/cr01551 Associations between environmental variability and inversion polymorphism of Drosophila subobscura: meta-analysis of populations from the Central Balkans M. Stamenkovic-Radak1,*, B. Kenig2, M. Djurakic3, M. Jelic1, K. Eric1, M. Andjelkovic4 1Faculty of Biology, University of Belgrade, 11000 Belgrade, Republic of Serbia 2Institute of Biological Research ‘S. Stankovic’, University of Belgrade, 11000 Belgrade, Republic of Serbia 3Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, 21000 Novi Sad, Republic of Serbia 4Serbian Academy of Sciences and Arts, 11000 Belgrade, Republic of Serbia *Corresponding author: marina@bio.bg.ac.rs ABSTRACT: Ecological and evolutionary factors, together with abiotic conditions, affect biogeographic patterns of genetic entities. The spatial and temporal variability of chromosomal inversions of Drosophila subobscura suggests that this species can serve as a good model for studying the effects of environmental change on the genetic structure of natural populations. A comprehensive meta-analysis of the association of environmental and climatic variables with inversion diversity patterns was performed on 20 D. subobscura populations from the central part of the Balkan Peninsula. Environmental data consisted of 3 sets of variables related to temperature and precipitation, extracted from 2 climatic databases, averaged over a 3 month period, and using biological instead of calendar dates of sampling. Arrangement frequency patterns are likely driven by a synergistic effect of factors related to temperature and precipitation. The frequencies of standard chromosomal arrangements tend to co-vary positively with precipitation, whereas parameters related to temperature appear to favor higher frequencies of the inverted and more complex chromosomal arrangements. A complex relationship among local environmental variables is evident from the results and reflects the probable effect of an altitudinal shift; the altitudinal gradient of inversions is different from their latitudinal gradient. The pattern of inversions is generally not associated with environmental variables, and a particular inversion cannot be a predictive genetic marker of global climate change. Populations in different habitats are subjected to habitat-specific selection regimes, while demographic factors and population history also affect the genetic variability pattern observed. KEY WORDS: Adaptation · Climate · Chromosomal polymorphism · Thermal response Full text in pdf format Supplement 1Supplement 2 PreviousNextCite this article as: Stamenkovic-Radak M, Kenig B, Djurakic M, Jelic M, Eric K, Andjelkovic M (2019) Associations between environmental variability and inversion polymorphism of Drosophila subobscura: meta-analysis of populations from the Central Balkans. Clim Res 77:205-217. https://doi.org/10.3354/cr01551 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in CR Vol. 77, No. 3. Online publication date: March 28, 2019 Print ISSN: 0936-577X; Online ISSN: 1616-1572 Copyright © 2019 Inter-Research.