Interpopulation Genetic Variation Research Articles

Genetic analyses reveal panmixia in Indian waters and population subdivision across Indian Ocean and Indo-Malay Archipelago for Decapterus russelli

The Indian Scad, Decapterus russelli is an important pelagic carangid widely distributed throughout the Indian Ocean and the Indo-West Pacific. Despite being widely distributed in the Indian Ocean, the information regarding genetic structuring and diversity has been lacking compared to its Indo Malay Archipelago counterparts. The present study was conducted to investigate the genetic stock structure of D. russelli based on mitochondrial (Cyt b) and nuclear (DrAldoB1) markers along Indian waters. The results indicated the presence of a single panmictic stock across the Indian Ocean region. High haplotype diversity associated with low nucleotide diversity suggested a population bottleneck followed by rapid population growth. Phylogenetic analysis revealed the absence of geographical clustering of lineages with the most common haplotype distributed globally. The pelagic life style, migratory capabilities, and larval dispersal may be the contributing factors to the observed spatial homogeneity of D. russelli. However, significant genetic differentiation was observed between the populations from Indian Ocean and Indo-Malay Archipelago. Hierarchical molecular variance analysis (AMOVA), pairwise FST comparisons and SAMOVA showed existence of two distinct genetic stocks of D. russelli in the Indian Ocean and IMA. The observed interpopulation genetic variation was high. A plausible explanation for the genetic differentiation observed between the Indo-Malay Archipelago and the Indian Ocean regions suggest the influence of historic isolation, ocean surface currents and biotic and abiotic features of the ocean. Also, there was a significant relationship between genetic distance and geographical distance between population pairs in a manner consistent with isolation-by-distance. These resulted in the evolution of a phylogeographic break for this species between these regions. The findings of these results suggest that D. russelli from the Indian Ocean shall be managed in its entire area of distribution as a single stock. Further, the Indian Ocean and Indo-Malayan stocks can be managed separately.

On the study of molecular markers of the genus <i>Picea</i> in Russia and Belarus

Currently, degradation of spruce stands is observed in various regions of Russia, which is associated with the transformation of climatic and environmental conditions of the environment. To ensure effective reforestation and afforestation of spruce forests, it is necessary to study the features of the population-genetic structure of plantations in order to preserve the genetic resources of valuable forest-forming tree species. The purpose of this work is to review modern achievements in the study of molecular markers of the genus Picea in Russia and Belarus. To characterize the genetic diversity of spruce populations, 9 ISSR primers with a high level of polymorphism (86,6%) were selected: (GA)9T, (AC)8C, (CA)6RY, (CA)6RG, (CA)6(GT), (CA)6(AC), (AG)8T, (GA)8C and (AG)8YT. The analysis of the mh44 locus of mitochondrial DNA revealed 13 allelic variants and is suitable for studying the genetic diversity of intra- and inter-population genetic variability of spruce. Experimental work with the mitochondrial Nad1 gene has shown the possibility of its application for phylogeographic studies of spruce. The assessment of the genetic variability of microsatellite loci Pt63718, Pt26081, Pt71936 revealed 19 allelic variants and is also suitable for phylogeographic studies. These results are very valuable and can form the basis for studying and characterizing the genetic structure of spruce plantations.

Conservation genetics of endangered Trillium govanianum Wall. ex D. Don – A pharmaceutically prized medicinal plant from the Himalaya and implications for species recovery

Understanding the genetic diversity and population structure of pharmaceutically important endangered plant species is crucial for their conservation and sustainable use. Despite the continuous population decline in Trillium govanianum Wall. ex D. Don, a highly prized medicinal plant endemic to the Himalaya, information regarding its conservation genetics has been lacking. Here, we employed a conservation genetics approach to investigate how drastically declining populations in natural habitats impact population genetic diversity and structure of this endangered species across the Kashmir Himalaya. We used Start codon targeted (SCoT) and Simple sequence repeat (SSR) markers to assess the intra- and inter-population genetic variation in seven sites across the study region. Based on these markers, we found a very low genetic diversity in T. govanianum populations. Very low levels of observed heterozygosity (Ho = 0.000) and that expected (He = 0.064) in the populations indicate high heterozygote deficiency and high levels of inbreeding depression (FIS = 1.000). A high genetic differentiation was observed among the populations for both SCoT (Gst = 0.719) and SSR (Fst = 0.707) markers. Both the markers showed low gene flow, SCoT (Nm = 0.195) and SSR (Nm = 0.119), depicting high among-population variation than within-population variation. Analysis of molecular variance also indicated a higher genetic variation between the populations than within populations. We also observed a significant positive correlation between genetic divergence and geographical distance, indicating that genetic differentiation in T. govanianum follows a pattern of isolation by distance. Bayesian structure and cluster analysis grouped the populations according to their geographical proximity. Further, redundancy analysis (RDA) revealed the presence of one polymorphic locus for each marker with high discriminatory power. Overall, our findings reveal a very low genetic diversity, high levels of inbreeding, and high genetic differentiation among the populations; likely resulting from habitat fragmentation, population isolation, bottleneck effect, low gene flow, and predominantly asexual reproduction currently operative in the species. Finally, based on the insights gained, we discuss the potential implications of our findings in guiding species recovery and habitat rehabilitation of T. govanianum in the Himalaya with conservation lessons for elsewhere in the world.

Genetic Variation of Ceiba pentandra (L.) Gaertn. from Three Populations in West Sumatra, Indonesia Based on RAPD Markers

Ceiba pentandra (L.) Gaertn. is one of the cotton-producing plants. However, there is a population decline in some areas, resulting in a decrease in genetic variation. This study aims to determine intrapopulation and interpopulation genetic variation and genetic differentiation of C. pentandra in three populations in West Sumatra. The research was conducted with the descriptive method using molecular data and sample collection with the survey method. Analysis of genetic variation using RAPD (Random Amplified Polymorphic DNA) markers on 15 individual plants collected from three populations, namely Solok, Pesisir Selatan, and Padang Pariaman. The results showed that primers OPA-01, OPA-02, and OPB-10 could detect polymorphism. The value of intrapopulation genetic variation was highest in the South Coastal population (H = 0.1857) and lowest in the Solok population (H = 0.1228). Interpopulation genetic variation (DST = 0.0326) was lower than intrapopulation genetic variation (Hs = 0.1607), with a low genetic differentiation value (GST = 0.1686) and a high gene flow value (Nm = 2.4660). Cluster analysis showed that the Pesisir Selatan and Solok populations had the farthest genetic distances (0.0580). UPGMA analysis shows that accessions do not cluster specifically based on their population.

Origin and History of Introduction of Rainbow Trout, Oncorhynchus mykiss (Walbaum, 1792) Stocks in Southern India As Inferred From Y-linked Marker

Rainbow trout, Oncorhynchus mykiss (Walbaum, 1792), is a popular cold-water fish widely distributed and farmed globally. In the nineteenth century, rainbow trout were introduced into India, and since then, it has gradually spread and established itself as one of the most prevalent non-native fish. In Southern India, rainbow trout were introduced from New Zealand in 1909 in the Ooty region of the Western Ghats, followed by introductions in other coldwater regions in the Peninsular uplands such as Munnar and Kodaikanal. Continuous introductions were done from various geographical locations at different periods to increase O. mykiss stocks in the Peninsular upland regions. Despite being regularly introduced in the streams of Munnar, Ooty, and Kodaikanal of Southern India, they still have not become self-sustaining, and genetic diversity has been suggested as a potential underlying factor. Therefore, this study aimed to resolve these questions and explore the structure and origin of Southern Indian stocks by conducting a population genetic study. The Y-linked marker of the trout stocks sampled from Munnar, Ooty, and Kodaikanal was compared with that of the native populations from North America. The results showed less proportion of inter-population genetic variation, suggesting that Southern Indian stocks were derived from multiple origins of population, with a great majority of parental populations belonging to the coastal rainbow trout from North America. This study revealed no considerable genetic differences among the Southern Indian stocks and reported the major ecotype as the Steelhead trout, Oncorhynchus mykiss irideus (Gibbons, 1955).

Genetic Diversity Analysis of the Red Swamp Crayfish Procambarus clarkii in Three Cultured Populations Based on Microsatellite Markers.

With the increasing scale of crayfish breeding, the self-propagation and "catch large and keep small" breeding patterns have led to serious degradation of the fry, so the selection and breeding of high-quality fry is very important. Selecting a population with a high genetic diversity as the base population for breeding can greatly improve the breeding efficiency. Fifteen microsatellite loci were used to understand the genetic structure and diversity of three Procambarus clarkii populations in Chongming, Shanghai; Gaoyou, Jiangsu; and Xuancheng, Anhui. The results indicated that the three populations were diverse and the number of alleles, observed heterozygosity, expected heterozygosity, Shannon information index, and polymorphic information content ranged from 4.8 to 6.2, 0.5567 to 0.6257, 0.6166 to 0.7086, 1.1292 to 1.3987, and 0.5446 to 0.6452, respectively. The Xuancheng population had the highest genetic diversity. The genetic differentiation coefficient and gene flow of the three populations were between 0.0553 and 0.1068 and 2.0908 and 4.2708, respectively, and there was extensive genetic exchange between the Chongming and Xuancheng populations. Analyses of molecular variance indicated that the genetic variation was mainly within the population (91.51%) and inter-population genetic variation accounted for 8.49%. The unweighted pair group method with an arithmetic mean clustering map was utilised based on the genetic distance between groups, and the results showed that the Gaoyou group was grouped alone, while the Chongming and Xuancheng groups were clustered together. The structural results indicated that the Chongming and Xuancheng groups had the same origin, although the Xuancheng group possessed a more complex genetic structure. This study indicated that all three populations had a high genetic diversity, with the Xuancheng population exhibiting the highest diversity. The results of the study provide a reference for the selection of base populations in breeding programs and confirm that the Xuancheng population in Anhui has a better genetic background. The selection of the Xuancheng population as one of the base populations for genetic breeding will be more efficient to accumulate superior traits.

Analysis of Genetic Variations of Ceiba pentandra (L.) Gaertn. on Several Critical Lands in West Sumatra Using RAPD Molecular Markers

Ceiba pentandra (L.) Gaertn. is a plant whose fruit is used to produce fiber and seeds for biofuel, which has the potential to be developed in critical land because it is adaptive to grow in critical land that is less fertile and lacks water. In West Sumatra, several critical land locations are overgrown by C. pentandra plants. This study aims to determine the genetic variation of C. pentandra in five critical land populations in West Sumatra as the basis for selecting superior seeds for development in critical land. The research was conducted by the descriptive method using molecular data with the molecular marker RAPD (random amplified polymorphic DNA). The results showed that the primers OPA-01, OPA-02, and OPB-10 could detect polymorphisms. Pangkalan Koto Baru in the regency Lima Puluh Kota (H = 0.1212) was the population with the highest intrapopulation genetic variation value. Interpopulation genetic variation (DST = 0.0321) was lower than intrapopulation genetic variation (HS = 0.1021), with a low genetic differentiation value (GST = 0.2392) and a high gene flow value (Nm = 1.5894). The genetic variation of C. pentandra can be used to select the parent in plant breeding programs.

Drivers of population divergence and genetic variation in Elymus breviaristatus (Keng) Keng f. (Poaceae: Triticeae), an endemic perennial herb of the Qinghai-Tibet plateau

Elymus breviaristatus, a rare grass species with excellent resistance and ecological importance, is narrowly distributed on the Qinghai-Tibet plateau. Populations of E. breviaristatus are declining due to habitat fragmentation, and thus far, characteristics of genetic differentiation and adaptive responses to climate change remain poorly understood in this species. Here, we explored the genetic structure of 18 natural populations (269 individuals) in the transition zone between Tibet and the Hengduan Mountains using 15 expressed sequence tag (EST)-SSR primer pairs and identified possible barriers to gene flow that might have caused genetic discontinuities. Additional analyses were performed to identify the environmental factors affecting genetic diversity and to test whether the patterns of genetic variation among populations were more consistent with the isolation by distance (IBD) or isolation by environment (IBE) model. Multiple measures of genetic diversity revealed that intra-population genetic variation was low, while inter-population genetic variation was high. Clustering, structure, and principal coordinate analyses identified three genetic groups: (a) Eastern Qamdo, (b) Nagqu and Western Qamdo, and (c) Lhasa and Nyingchi. A clear physical barrier to gene flow was formed by the Yarlung Zangbo Grand Canyon and the Tanggula Mountains. We found that both IBD and IBE contributed to the observed patterns of genetic variation, and the IBE model played a leading role. In addition, precipitation-related variables, soil phosphorus content and soil K:P ratio significantly affected population genetic variation. Overall, our results emphasized the genetic fragility of E. breviaristatus populations and showed that this species requires attention, as future climate changes and human activities may further threaten its survival. In addition, the genetic differences among E. breviaristatus populations should be considered when formulating conservation measures for E. breviaristatus populations in the study area.

Using genetic tools to inform conservation of fragmented populations of Asian elephants (Elephas maximus) across their range in China.

A herd of 15 Chinese elephants attracted international attention during their 2021 northward trek, motivating the government to propose establishment of an Asian elephant national park. However, planning is hampered by a lack of genetic information on the remaining populations in China. We collected DNA from 497 dung samples from all 5 populations encompassing the entire range of elephants in China and used mitochondrial and microsatellite markers to investigate their genetic and demographic structure. We identified 237 unique genotypes (153 females, 84 males), representing 81% of the known population. However, the effective population size was small (28, range 25-32). Historic demographic contraction appeared to account for low haplotype diversity (Hd = 0.235), but moderate nucleotide and nuclear diversity (π = 0.6%, He = 0.55) was attributable to post-bottleneck recovery involving recent population expansion plus historical gene exchange with elephants in Myanmar, Lao PDR, and Vietnam. The 5 populations fell into 3 clusters, with Nangunhe elephants differing consistently from the other 4 populations (FST = 0.23); elephants from Mengyang, Simao, and Jiangcheng belonged to a single population (henceforth, MSJ), and differed from the Shangyong population (FST = 0.11). Interpopulation genetic variation reflected isolation by distance and female-biased dispersal. Chinese elephants should be managed as 2 distinct units: Nangunhe and another combining Shangyong and MSJ; their long-term viability will require restoring gene flow between Shangyong and MSJ, and between elephants in China and neighboring countries. Our results have the potential to inform conservation planning for an iconic megafaunal species.

Intra- and Inter-Population Genetic Diversity of “Russello” and “Timilia” Landraces from Sicily: A Proxy towards the Identification of Favorable Alleles in Durum Wheat

Climate change and global population growth call for urgent recovery of genetic variation from underexploited or unexplored durum wheat (Triticum turgidum ssp. durum) landraces. Indeed, these untapped genetic resources can be a valuable source of favorable alleles for environmental adaptation and tolerance or resistance to (a)biotic stress. In southern Italy, in addition to the widespread modern and highly productive durum wheat cultivars, various landraces have been rediscovered and reused for their adaptation to sustainable and low-input cropping systems and for their peculiar qualitative characteristics. Sicily is a semiarid area rich in landraces, some of which are independently reproduced by many farmers. Among these, “Timilia” and “Russello” have been independently grown in various areas and are now cultivated, mostly under organic systems, for their hypothetical greater benefits and height, which give them a high level of competitiveness against weeds despite their low yield potential. So far, there is little information on the genetic variations of “Timilia” and “Russello” despite their putative origin from a common funder. This work aims to dissect the genetic variation patterns of two large germplasm collections of “Timilia” and “Russello” using SNP genotyping. The analysis of intra- and inter-population genetic variation and the identification of divergent loci between genetic groups showed that (i) there are two “Russello” genetic groups associated with different Sicilian geographical areas, which differ in important traits related to gluten quality and adaptation, and (ii) the individuals of “Timilia”, although presenting wide genetic variation, have undergone a conservative selection, likely associated with their distinctive traits. This work paves the way for a deeper exploration of the wide genetic diversity in Sicilian landraces, which could be conveniently exploited in future breeding programs, and points out that intra-population genetic diversity should be taken into account when ‘conservation varieties’ are to be registered in national registers of crops.

Genetic diversity, redundancy and population structure in flax (Linum usitatissimum L.) as revealed by dominant molecular marker system

In the present investigation, RAPD profiling was employed to estimate the genetic diversity, population structure and linkage disequilibrium in 232 flax germplasm which were divided into three population viz. CRIJAF population, NBPGR population and CSKHPKV population based on their source of collection. The RAPD markers generated total 122 allele out of which 72 showed polymorphism (61.83 %) with mean effective number of allele, PIC, MI, RP value as 1.14, 0.13, 21.39 and 1.59 respectively. The RAPD primers also exhibited the highest Nei’s gene diversity (h) and Shannon’s diversity index (I) in CRIJAF population (h = 00.116 and I = 0.206) followed by CSKHPKV and NBPGR population, with a low level of overall genetic variability (h = 0.107 and I = 0.187). AMOVA illustrated that 14% of the total genetic variability was originated due to inter population whereas the remaining 80% of the total variability arose within the populations. The overall relative magnitude of genetic differentiation among the populations was 0.15 and also high level of gene flow between the populations was observed. The results of population structure analysis proposed that total flax accessions were distributed into nine genetic groups. Phylogenetic tree also successfully identified the redundant genotypes from the total flax accession. LD analysis indicated narrow inter-population genetic variation and higher level of intra-population genetic variation in flax. The findings of the present investigation will be helpful for utilization of flax germplasm in future crop improvement programme and association mapping.

Genetic Structure and Gene Flow of Octopus maya (Mollusca: Cephalopoda) in the States of Yucatan and Campeche, Mexico / Estrutura genética e fluxo gênico do polvo maya (Mollusca: Cephalopoda) nos Estados de Yucatan e Campeche, México

It was determined the population genetic structure of the red octopus Octopus maya in the states of Campeche and Yucatan in Yucatan Peninsula, Mexico, through the expression of isozymes in polyacrylamide gels. Mantle samples from 25 octopuses, captured in nine sites of the Yucatan Peninsula, were used to characterize the genotypic expression revealed by the expression of 26 loci in thirty enzyme systems. Program TFPGA version 1.3 (Tools for Population Genetic Analyses), was used to process data of allozyme gene frequencies of the studied populations. The parameters determined were: descriptive statistics, F statistics, genetic distances, Hardy - Weinberg, UPGMA and the number of migrants as an indicator of gene flow. The average number of alleles per locus, percentage of polymorphic loci, average and direct and direct heterozygosity were: 1.08 ± 0.05 to 1.15 ± 0.04. P95 26.9231% to 34.6154, Have 0.1142 to 0.1390 and Hdir = 0.0354 to 0.0938 respectively. Heterozygosity values in a range of 0.3506 to 0.4793 and G6PDH for ARGK with an average heterozygosity value of 0.1824, Fisher average value of 0.5313 and 0.0140 Fst indicates a heterozygous deficiency but it is within the ranges reported for marine invertebrate species. The number of migrants derived from the Slatkin equation is 1824 per generation, globally indicates some degree of variability between sites and is consistent with the low values of Nei genetic distance found, particularly the node showing the separation of the population of Lagartos River and Dzilam Bravo from the other locations with an obtained value of 0.0004. From the results of this study, it is concluded that locations of Octopus maya have a certain level of interpopulation genetic variability that does not reflect its fragility.

Establishing the first DNA barcode reference library for freshwater decapod species (Crustacea: Decapoda) in Republic of North Macedonia

The freshwater ecosystems in the Republic of North Macedonia are considered as biodiversity hotspot on the European level since they provide diverse habitats that correspond with the complex of ecological preferences that many species require. This specially applies to the freshwater crustaceans that, unfortunately, have never been in the focus of a continuous research. In R. North Macedonia, freshwater crustaceans usually inhabit ecosystems exposed to negative anthropogenic impact. Thus, some species may become extinct presenting an irreversible loss for the Macedonian natural heritage. Although DNA barcoding, as a highly effective tool for fast species detection, is already a routine protocol in many taxonomical studies all over the world, there is still no official national DNA barcoding initiative in Republic of North Macedonia. This study employs DNA barcoding based on the ca. 650-bp long standard fragment of the mt COI gene of Astacus astacus, Austropotamobius torrentium, Potamon fluviatile and Potamon ibericum previously identified based on morphological characters, collected from different parts in R. North Macedonia. The ability of the DNA barcoding to rapidly identify all species has been proven. Our research presents the first comprehensive study that employs DNA barcoding as a molecular tool in decapod taxonomy in Republic of North Macedonia, giving the first attempt to establish DNA barcode reference library for freshwater decapod species in the country. We hope that further application of this approach will lead to the construction of DNA barcode reference library for different aquatic biota in the country. Such a library will find purpose in effective and modern bioassessment protocols as well as in phylogenetic research detecting interpopulation genetic variability.

Reproductive compatibility among populations and host-associated lineages of the common bed bug (Cimex lectularius L.).

As populations differentiate across geographic or host‐association barriers, interpopulation fertility is often a measure of the extent of incipient speciation. The bed bug, Cimex lectularius L., was recently found to form two host‐associated lineages within Europe: one found with humans (human‐associated, HA) and the other found with bats (bat‐associated, BA). No unequivocal evidence of contemporary gene flow between these lineages has been found; however, it is unclear whether this is due to an inability to produce viable “hybrid” offspring. To address this question and determine the extent of compatibility between host‐associated lineages, we set up mating crosses among populations of bed bugs based on both their host association (human—HA vs. bat—BA) and geographic origin (North America vs. Europe). Within‐population fecundity was significantly higher for all HA populations (>1.7 eggs/day) than for BA populations (<1 egg/day). However, all within‐population crosses, regardless of host association, had >92% egg hatch rates. Contrary to previous reports, in all interlineage crosses, successful matings occurred, fertile eggs were oviposited, and the F1 “hybrid” generation was found to be reproductively viable. In addition, we evaluated interpopulation genetic variation in Wolbachia among host‐associated lineages. We did not find any clear patterns related to host association, nor did we observe a homogenization of Wolbachia lineages across populations that might explain a breakdown of reproductive incompatibility. These results indicate that while the HA and BA populations of C. lectularius represent genetically differentiated host‐associated lineages, possibly undergoing sympatric speciation, this is in its incipient stage as they remain reproductively compatible. Other behavioral, physiological, and/or ecological factors likely maintain host‐associated differentiation.

Genetic structure and diversity in the freshwater gastropod Chilina dombeiana in the Biobío River, Chile

In river ecosystems, spatial complexity as well as anthropogenic factors operating at different temporal and spatial scales are shaping demography, connectivity and population genetic structure of species inhabiting these habitats. Chilina dombeiana is a freshwater gastropod with direct development (absence of a free larval phase) that inhabits the Biobio river basin in Chile (36°S). No studies have yet evaluated the spatial patterns of the genetic diversity of this species and the potential factors that influence these patterns. Consequently, in this study, we analyzed the population genetics of C. dombeiana based on 15 locations along the Biobio river. Eight microsatellite loci were genotyped. Also, at each sampling site, 40 environmental parameters were recorded to characterize them. Results showed that C. dombeiana has low genetic variability with high population structure. In addition, we detected signs of historical decreases in effective population sizes, unidirectional gene flow (upstream to downstream) and contemporary demographic bottleneck. Spatial subdivisions in populations showed a pattern of isolation by distance. The redundancy analysis and variance partitioning showed that spatial components and dissolved oxygen could explain 28% of the interpopulation genetic variation, while the Random Forest analysis identified significant effects of dissolved oxygen, nitrite and total coliforms on the genetic variability of populations (22%). Although C. dombeiana is widely distributed in Chilean rivers, its low dispersal and specific habitat requirements make this species very sensitive to the severe increase in anthropogenic disturbances affecting river ecosystems in recent decades. Long-term monitoring of genetic population conditions and environmental parameters are needed to implement robust management and conservation policies.

Diversidade genética de matrizes e progênies de &lt;i&gt;Euterpe edulis&lt;/i&gt; Mart. em área manejada e em populações naturais por marcadores microssatélites

Euterpe edulis, uma palmeira ameaçada de extinção da Mata Atlântica, tem importância ecológica e econômica pelo uso da polpa dos frutos. A identificação de matrizes geneticamente divergentes nas populações é útil para a conservação e o melhoramento da espécie. Neste trabalho, objetivou-se estimar a diversidade genética de plantas divergentes morfologicamente que possam ser utilizadas como matrizes, e de suas famílias de progênies em uma área manejada e em áreas de populações naturais da espécie no estado do Espírito Santo. Foram avaliadas 21 matrizes, das quais 13 obtidas em área manejada para a exploração sustentável dos frutos (anteriormente avaliadas quanto a caracteres de frutos) e oito oriundas de populações naturais no estado do Espírito Santo. Para cada matriz avaliou-se 10 progênies, constituindo 21 famílias. A partir de genotipagem por marcadores microssatélites, a caracterização das plantas matrizes e suas progênies foi realizada pelas heterozigosidades observada (Ho) e esperada (He) e o índice de endogamia (f), bem como a análise de variância molecular das plantas oriundas dos diferentes locais de coleta. As matrizes da área de cultivo manejada de Rio Novo do Sul apresentaram maiores Ho e He, e menor f, indicando maior diversidade. Menores Ho (0,36) e He (0,41) e maior f (0,15) foram observados para as matrizes de Pinheiros, indicando menor diversidade e maior endogamia. A análise da variância entre os locais de coleta das matrizes revelou maior variação genética intrapopulacional que interpopulacional. As matrizes coletadas em populações naturais, Linhares e, especialmente, de Pinheiros, apresentam menor diversidade genética. Na área manejada, os indivíduos apresentaram maior diversidade para as matrizes e suas progênies, indicando potencial para a conservação e uso sustentável do recurso genético nesta área. As matrizes indicadas para cruzamento, com possibilidade de gerar descendentes com maior desempenho morfológico para frutos e alta diversidade foram RNS_154 e RNS_76.

Neutral and Climate-Driven Adaptive Processes Contribute to Explain Population Variation in Resin Duct Traits in a Mediterranean Pine Species.

Resin ducts are important anatomical defensive traits related to biotic resistance in conifers. Previous studies have reported intraspecific genetic variation in resin duct characteristics. However, little is currently known about the micro-evolutionary patterns and adaptive value of these defensive structures. Here, we quantified inter-population genetic variation in resin duct features and their inducibility in Pinus pinaster and assessed whether such variation was associated with climate gradients. To that end, we characterized the resin duct system of 2-year-old saplings from 10 populations across the species’ distribution range. We measured axial resin duct features (density, mean size, and percentage conductive area of resin ducts) and their inducibility in response to methyl jasmonate. Genotyping of single nucleotide polymorphisms allowed to account for the population genetic structure in our models in order to avoid spurious correlations between resin duct characteristics and climate. We found large inter-population variation in resin duct density and conductive area, but not in their inducibility. Our results suggest that population variation in the percentage conductive area of resin ducts likely arise from adaptation to local climate conditions. This study highlights the adaptive relevance of resin ducts and helps to shed light on the micro-evolutionary patterns of resin-based defenses in conifers.

From metabarcoding to metaphylogeography: separating the wheat from the chaff.

Metabarcoding is by now a well‐established method for biodiversity assessment in terrestrial, freshwater, and marine environments. Metabarcoding data sets are usually used for α‐ and β‐diversity estimates, that is, interspecies (or inter‐MOTU [molecular operational taxonomic unit]) patterns. However, the use of hypervariable metabarcoding markers may provide an enormous amount of intraspecies (intra‐MOTU) information—mostly untapped so far. The use of cytochrome oxidase (COI) amplicons is gaining momentum in metabarcoding studies targeting eukaryote richness. COI has been for a long time the marker of choice in population genetics and phylogeographic studies. Therefore, COI metabarcoding data sets may be used to study intraspecies patterns and phylogeographic features for hundreds of species simultaneously, opening a new field that we suggest to name metaphylogeography. The main challenge for the implementation of this approach is the separation of erroneous sequences from true intra‐MOTU variation. Here, we develop a cleaning protocol based on changes in entropy of the different codon positions of the COI sequence, together with co‐occurrence patterns of sequences. Using a data set of community DNA from several benthic littoral communities in the Mediterranean and Atlantic seas, we first tested by simulation on a subset of sequences a two‐step cleaning approach consisting of a denoising step followed by a minimal abundance filtering. The procedure was then applied to the whole data set. We obtained a total of 563 MOTUs that were usable for phylogeographic inference. We used semiquantitative rank data instead of read abundances to perform AMOVAs and haplotype networks. Genetic variability was mainly concentrated within samples, but with an important between seas component as well. There were intergroup differences in the amount of variability between and within communities in each sea. For two species, the results could be compared with traditional Sanger sequence data available for the same zones, giving similar patterns. Our study shows that metabarcoding data can be used to infer intra‐ and interpopulation genetic variability of many species at a time, providing a new method with great potential for basic biogeography, connectivity and dispersal studies, and for the more applied fields of conservation genetics, invasion genetics, and design of protected areas.

Genetic diversity and population structure of the medicinal plant Achillea fragrantissima (Forssk.) Sch. Bip. in the mountains of South Sinai, Egypt

The genetic diversity of 50 plant accessions of Achillea fragrantissima, in eight populations in the mountainous area of south Sinai, Egypt was studied using variation in inter-simple sequence repeats (ISSR) fingerprinting with reference to variation in some morphological quantitative traits and soil physical texture. Two clustering methods were used to illustrate intra and inter-population genetic variation of the 50 examined plants. The plants of the same population were clustered together indicating close genetic affinity of plants in the same site. On the other hand plants in populations growing at high elevations, in rocky gravelly soils, were differentiated from populations at lower elevations and gravely sandy soils. Scatter plot constructed by Principal coordinates analysis (PCA) differentiated the populations. These results are supported by assessing population structure, which allocated the individuals to their population. The Nei's genetic diversity analysis showed total genetic diversity (HT) of 0.2623 among the populations, genetic diversity within populations (HS) of 0.1370, and overall estimated genetic diversity (GST) of 0.4779, indicating that 47.79% of the genetic diversity was distributed among populations. Low gene flow (NM = 0.5463) was recorded indicating a limited gene exchange between populations. The results indicate the existence of three local gene pools for A. fragrantissima plants growing in the mountainous area of south Sinai but gene flow in the study area is limited due to its mountainous topography. The data reported here provide important baseline information for conservation and collection strategies for this species. Selected populations may be sampled for ex-situation protection to retain as much genetic diversity as possible.

Correlations between genetic, epigenetic and phenotypic variation of an introduced clonal herb.

Heritable epigenetic modifications may occur in response to environmental variation, further altering phenotypes through gene regulation, without genome sequence changes. However, epigenetic variation in wild plant populations and their correlations with genetic and phenotypic variation remain largely unknown, especially for clonal plants. We investigated genetic, epigenetic and phenotypic variation of ten populations of an introduced clonal herb Hydrocotyle vulgaris in China. Populations of H. vulgaris exhibited extremely low genetic diversity with one genotype exclusively dominant, but significantly higher epigenetic diversity. Both intra- and inter-population epigenetic variation were related to genetic variation. But there was no correlation between intra-/inter-population genetic variation and phenotypic variation. When genetic variation was controlled, intra-population epigenetic diversity was related to petiole length, specific leaf area, and leaf area variation, while inter-population epigenetic distance was correlated with leaf area differentiation. Our study provides empirical evidence that even though epigenetic variation is partly under genetic control, it could also independently play a role in shaping plant phenotypes, possibly serving as a pathway to accelerate evolution of clonal plant populations.