Intrapopulation Genetic Diversity Research Articles

Evolutionary history and genetic connectivity across highly fragmented populations of an endangered daisy

Conservation management can be aided by knowledge of genetic diversity and evolutionary history, so that ecological and evolutionary processes can be preserved. The Button Wrinklewort daisy (Rutidosis leptorrhynchoides) was a common component of grassy ecosystems in south-eastern Australia. It is now endangered due to extensive habitat loss and the impacts of livestock grazing, and is currently restricted to a few small populations in two regions >500 km apart, one in Victoria, the other in the Australian Capital Territory and nearby New South Wales (ACT/NSW). Using a genome-wide SNP dataset, we assessed patterns of genetic structure and genetic differentiation of 12 natural diploid populations. We estimated intrapopulation genetic diversity to scope sources for genetic management. Bayesian clustering and principal coordinate analyses showed strong population genetic differentiation between the two regions, and substantial substructure within ACT/NSW. A coalescent tree-building approach implemented in SNAPP indicated evolutionary divergence between the two distant regions. Among the populations screened, the last two known remaining Victorian populations had the highest genetic diversity, despite having among the lowest recent census sizes. A maximum likelihood population tree method implemented in TreeMix suggested little or no recent gene flow except potentially between very close neighbours. Populations that were more genetically distinctive had lower genetic diversity, suggesting that drift in isolation is likely driving population differentiation though loss of diversity, hence re-establishing gene flow among them is desirable. These results provide background knowledge for evidence-based conservation and support genetic rescue within and between regions to elevate genetic diversity and alleviate inbreeding.

InStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains.

Coexisting microbial cells of the same species often exhibit genetic variation that can affect phenotypes ranging from nutrient preference to pathogenicity. Here we present inStrain, a program that uses metagenomic paired reads to profile intra-population genetic diversity (microdiversity) across whole genomes and compares microbial populations in a microdiversity-aware manner, greatly increasing the accuracy of genomic comparisons when benchmarked against existing methods. We use inStrain to profile >1,000 fecal metagenomes from newborn premature infants and find that siblings share significantly more strains than unrelated infants, although identical twins share no more strains than fraternal siblings. Infants born by cesarean section harbor Klebsiella with significantly higher nucleotide diversity than infants delivered vaginally, potentially reflecting acquisition from hospital rather than maternal microbiomes. Genomic loci that show diversity in individual infants include variants found between other infants, possibly reflecting inoculation from diverse hospital-associated sources. inStrain can be applied to any metagenomic dataset for microdiversity analysis and rigorous strain comparison.

DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai.

Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan’s Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversity was observed in the populations of the Leninororsk ecogeographic group. Distinctions between these populations were also identified depending on the areas of their distribution. Low-land and mid-mountain living environments are characterized by a great variety of shapes and plasticity. This work allowed us to obtain new genetic data on the structure of A. altaicum populations on the territory of the Kazakhstan Altai for the subsequent development of preservation and reproduction strategies for this relict species.

Assessing the genetic diversity of Myrsine umbellata (Primulaceae) in Brazilian Atlantic Forest remnants - an important step towards reforestation efforts

Abstract The investigation of genetic diversity in natural populations of species that show potential for use in reforestation programs is a key step in making management decisions. However, reforestation programs with native species in Brazil are still rarely based on a genetic understanding of the seed matrices used for seedling production. This is also the case for Myrsine umbellata, a dioecious shrub within the family Primulaceae that has been used in reforestation programs in Brazil, mainly due to its high production capacity of fruits attractive to the avifauna. The goal of this study was to measure intra- and interpopulational genetic diversity in natural populations of M. umbellata in six forest remnants of the Atlantic Forest using ISSR markers. The results revealed that the intrapopulational genetic diversity was greater than the genetic diversity among the studied populations. For this reason, the cultivation of seedlings from seeds obtained in more than one population seems the most appropriate strategy for reforestation purposes. Even though the most isolated populations are also the ones with highest genetic structure, all populations of M. umbellata included in this study revealed to be an important germplasm bank conserved in situ.

Detection of 16S Mitochondrial Gene Polymorphism on Barb Fish (Barbodes binotatus Valenciennes, 1842) from Lake Lebo Taliwang, West Nusa Tenggara

The spotted barb fish (Barbodes binotatus), a tropical cyprinid fish, is one of the abundant fishes in Lake Lebo Taliwang commonly consumed due to high nutrition and utilized as an aquarium trade due to their exotic colour. However, no genetic information related to the intra-population genetic variation of the fish species in Lake Lebo Taliwang. Genetic information of the spotted barb fish can play an important role for the fish conservation. Therefore, the objective of this study was to detect 16S mitochondrial gene polymorphism of the spotted barb fish which can be used to detect their genetic variation. The method used in this study was a PCR method with primers 16Sar and 16Sbr. The data was then analysed using MESQUITE, MEGA, DnaSP and PopART to identify 16S mitochondrial gene polymorphism. This study obtained 610 base pairs after alignment of 16S sequences of all samples. Five haplotypes were detected with 9 variable sites and 2 parsimony informative sites. Haplotype diversity and nucleotide diversity of the spotted barb fish were 1.00 and 0.0066 respectively. In addition, genetic distance among the samples was 0.66. This finding exhibited polymorphism on 16S gene sequence among the fish samples and this data indicated genetic variation of the spotted barb from Lake Lebo Taliwang.

Human population genetics of Comoros islanders: Alu polymorphisms and the peopling of the three major islands

BackgroundThe Comoros archipelago is located in the Indian Ocean between Madagascar and the East African coast. Their geographic localization yielded an admixed population of sub-Saharan African, Middle Eastern, and Austronesian influences. AimTo evaluate the genetic diversity whithin and between the three major islands (Grande Comore, Anjouan, and Moheli) using Alu polymorphisms, and to assess their genetic relationships with Africans, Middle Easterns and South Eastern Asians. - To investigate the peopling of these islands. Subjects & methods18 polymorphic Alu insertions have been typed in 295 unrelated individuals from Comoros archipelago: Grande Comore (122), Anjouan (95), and Moheli (78). The data were analyzed for intra and inter-population genetic variations. ResultsThe Comoros archipelago showed a high level of intra-population genetic diversity and a strong genetic homogeneity between the three islands (FST = 0.0037). The MDS analyses showed higher affinity between the Comorians and nerby sub-Saharans. Admixture estimates highlight a high sub-Saharan component in the genetic background of the current Comorians with some Middle Eastern and Southeast Asian contributions. ConclusionThe Alu polymorphisms used in the present study provided interesting results about the peopling of the Comoros. They showed a high level of genetic diversity probably shaped by successive migratory waves from the three historically related regions and underlined also a high genetic homogeneity among the three islands, probably originated by their common demographic history and/or the geographic proximity.

تنوع ژنتیکی در میان جوامع گونههای گز با استفاده از نشانگر مولکولی CDDP

سرده Tamarix به دلیل عدم قطعیت تعداد گونه‌ها، پراکنش و اهمیت اکولوژیکی در ایران، یکی از مهم‌ترین موضوعات در رده‌بندی تیره گز است. در این مطالعه، تنوع ژنتیکی و روابط خانوادگی 34 فرد از 8 جمعیت از 3 گونه Tamarix در استان اصفهان مورد بررسی قرار گرفت. ده آغازگر از نشانگر مولکولی CDDP برای بررسی تنوع ژنتیکی این سرده استفاده شد. 125 باند از ده آغازگر ایجاد شد، که از این تعداد 102 (16/80 درصد) چند شکلی بودند. آنالیز خوشه‌ای جمعیت‌ها را به سه گروه مجزا دسته‌بندی کرد. جریان بالای ژنی در میان گونه‌های Tamarix با استفاده از تجزیه و تحلیل PCoA تنوع زیادی در بین سه گونه Tamarix نشان داد، به طوری که نمونه‌های گونه‌های مختلف با هم گروه‌بندی شدند. تجزیه واریانس مولکولی نشان داد که تنوع ژنتیکی بین جمعیت (90٪) بیشتر از تنوع ژنتیکی درون جمعیت (10٪) است. بالاترین میانگین تنوع ژنتیکی نای (H) و شاخص تنوع شانون (I) در جمعیت حبیب‌آباد مشاهده شد. تجزیه و تحلیل داده‌ها نشان داد که صفات ریخت‌شناختی و داده‌های توالی DNA در سرده Tamarix کاملا با هم ارتباط ندارند، که می‌تواند با وجود تعداد زیاد دورگه‌ بین گونه‌ها و عدم تمایز ژنتیکی بین گونه‌های مورد مطالعه توجیه شود.

The de novo genome assembly of Tapiscia sinensis and the transcriptomic and developmental bases of androdioecy

Tapiscia sinensis (Tapisciaceae) possesses an unusual androdioecious breeding system that has attracted considerable interest from evolutionary biologists. Key aspects of T. sinensis biology, including its biogeography, genomics, and sex-linked genes, are unknown. Here, we report the first de novo assembly of the genome of T. sinensis. The genome size was 410 Mb, with 22,251 predicted genes. Based on whole-genome resequencing of 55 trees from 10 locations, an analysis of population genetic structure indicated that T. sinensis has fragmented into five lineages, with low intrapopulation genetic diversity and little gene flow among populations. By comparing whole-genome scans of male versus hermaphroditic pools, we identified 303 candidate sex-linked genes, 79 of which (25.9%) were located on scaffold 25. A 24-kb region was absent in hermaphroditic individuals, and five genes in that region, TsF-box4, TsF-box10, TsF-box13, TsSUT1, and TsSUT4, showed expression differences between mature male and hermaphroditic flowers. The results of this study shed light on the breeding system evolution and conservation genetics of the Tapisciaceae.

Intrapopulation genetic variation in the level and rhythm of daily activity in Drosophila immigrans.

Genetic diversity within a population, such as polymorphisms and personality, is considered to improve population performance because such intraspecific variations have the potential to alleviate the competition for a limited resource or the risk of predation and sexual harassment at a population level. Variation in the level and rhythm of daily activity in a population could also affect population performance by directly altering ecological, social, and sexual interactions among individuals. However, it remains to be elucidated whether such intra‐population variation in the level and rhythms of daily activity exists in a natural population. Here, we investigated the genetic variation in daily activity within a single natural population of Drosophila immigrans. We established 21 isofemale lines from a single natural population and measured larval activity level and the level and daily pattern of adult activity over a 24 hr period. Larval activity level significantly varied among isofemale lines. Likewise, the activity level in the adult stage significantly varied among lines. The significant variation was also found in the daily pattern of adult activity; some lines showed greater activity level in the daytime, and others showed greater activity level in the night. Our results consistently suggest that there is a genetic variation in behavioral activity in a natural population, probably contributing to shaping the population performance.

Analysis of genetic diversity of Colletotrichum population causing anthracnose in fruit crops using ISSR markers

Colletotrichum spp. cause anthracnose disease in several plant species in tropical and temperate regions. In this study, a total of 30 isolates of Colletotrichum spp. were isolated from nine different fruit crops showing anthracnose symptoms. Phylogenetic analysis based on the GAPDH gene divided the population into four primary clades. All C. gloeosporioides species complex grouped together and separated from C. karstii and two different monophyletic lineages i.e. C. brevisporum, C. cliviae. C. gloeosporioides species complex was found dominant within the population containing 7 cryptic species. To study the population diversity of Colletotrichum species, the isolates were grouped into 4 geographical clusters based on their collection site i.e. Delhi, Maharashtra, West Bengal (WB), and North East (NE) states (Assam and Meghalaya). Out of 12 ISSR primers used 11 primers generated scorable polymorphic band of 100-1300 bp having average PIC value of 0.27. The intrapopulation genetic diversity was high in NE population with 78.75% polymorphism. The inter-population genetic distance was high (0.129) between Maharashtra and WB populations. The degree of genetic differentiation was 0.09 and gene flow was estimated at 2.45 within Colletotrichum population. Population stratification using UPGMA dendrogram divided the population into two main groups. Group 1 consisted of isolates from all over the four geographical region and population from NE region formed group 2. The overall result indicates admixture between isolates and homogeneous population structures from different geographical regions.

Genetic diversity and genetic structure of Acer monspessulanum L. across Zagros forests of Iran using molecular markers

Acer monspessulanum L. is an important tree species found in the temperate Zagros forests of Iran. Despite its importance, the long-term persistence of its small and fragmented populations is jeopardised by genetic erosion and hence, monitoring its genetic resource and variability is practically required for providing conservation measures of the species germplasm in Zagros woodland ecosystem. The present study aimed to provide the first data on genetic diversity and genetic differentiation pattern of 19 natural populations comprising 240 individuals of A. monspessulanum across its growing area in Zagros forests using three molecular tools including inter-simple sequence repeats (ISSR), start codon targeted (SCoT), and simple sequence repeat (SSR). In total, ISSR and SCoT primers generated a total of 141 and 121 clear and scorable bands for analysis with the polymorphism rate of 90.50 and 90.02% and a mean of 10.85 and 11 fragments per marker, respectively. In addition, 73 alleles were achieved using 10 polymorphic SSR loci from the studied accessions with 100% polymorphism, ranging between 5 and 10 alleles per locus. Average percentage of polymorphic alleles per population for ISSR, SCoT, and SSR data was 84.02%, 83%, and 100%, respectively, and generally, Nei's gene diversity (H) and Shannon's index of diversity (I) values for all populations demonstrated moderate to high levels of genetic diversity (H=0.267-0.707; I=0.38-1.38). The AMOVA results of the three marker systems attributed higher genetic variation to individuals within in each population than among populations. Furthermore, overall GST value for all populations detected the moderate to high levels of genetic differentiation, indicating a limited gene flow occurrence among the populations. STRUCTURE analysis (K=5) clustered the populations into four to five distinct groups, in accordance with geographical distances. These results could represent an important contribution for effective germplasm characterization and could be eventually used in in situ or ex situ conservation of A. monspessulanum genetic resources.

The genetic variation in response to drought in Tunisian populations of Brachypodium hybridum (Poaceae): an interplay between natural selection and phenotypic plasticity

With the ongoing climate change, widespread changes could be noticed in both the extent of the geographical distribution as well the patterns of phenotypic variation of plant species in response to environmental heterogeneity. Whether these changes are a direct consequence of global climate change, and whether they result from phenotypic plasticity or evolutionary forces, are currently main areas of interest. In the present study, 130 lines belonging to ten Tunisian Brachypodium hybridum populations differing greatly in climatic conditions were exposed to water stress and the pattern of their genetic variation was analyzed using sixteen functional traits in order to unravel the main drivers of their response to drought. Our results showed that B. hybridum populations exhibited an extensive intra-population genetic variation in control and water stress, whereas principal component analysis did not show any clear populations grouping pattern. In addition, ANOVA showed that most of analyzed traits revealed a significant population and line effects, indicating that their response to drought was, in part, controlled at the genetic level. These results suggest that the natural selection on standing intra-population genetic variation plays a major role in dealing with drought in B. hybridum. On the other hand, we found that many traits exhibited phenotypic plasticity in response to water stress. The plasticity index showed that the populations responded differently to water stress, with Ain Drahem and Djerba populations showed the highest and the lowest plasticity levels, respectively. However, plasticity of most analyzed traits seems to be unrelated to climatic factors, except for the precipitation of wettest month, which showed significant correlation with five traits related to biomass production and the mean plasticity index. In summary, the present study revealed that the genetic variation in response to drought in the natural populations of B. hybridum was most likely governed by an interplay between two major evolutionary and ecological processes: natural selection and phenotypic plasticity.

Genetic diversity of Euterpe edulis martius based on fruit traits

Juçara (Euterpe edulis Martius) is a palm species from the Atlantic Forest whose fruits are important as a source of food to several individuals from the fauna of the region. Despite its ecological importance, juçara is found in the list of endangered species, due to the fragmentation of the forests and the illegal extraction of the heart of palm. We aimed to evaluate the inter- and intra-populational genetic diversity of E. edulis based on fruit and seed traits in forest fragments of the Espírito Santo State in Brazil. The aim was to generate information to be used in E. edulis breeding programs, or in the delineation of more efficient management and reforestation strategies. The study was carried out in 20 forest fragments and 198 fruit plants were sampled. Positive genetic association was observed between the evaluated traits, with the longitudinal diameter of the fruit (LDF) and the seed mass (SM) greatly affecting fruit mass (FM). The existence of inter- and intra-populational genetic divergence was proved. The genetic divergence found in E. edulis suggests that there is genetic material that can be explored in breeding programs and this information may also contribute to management strategies that can increase the species genetic diversity.

An assessment on the intrapopulational and intraindividual genetic diversity in LSU rDNA in the harmful algal blooms-forming dinoflagellate Margalefidinium (= Cochlodinium) fulvescens based on clonal cultures and bloom samples from Jiaozhou Bay, China

Large subunit ribosomal DNA (LSU rDNA) sequences have been increasingly used to infer the phylogeny and species identity of organisms, a few previous studies, however, have observed high intraspecific and even intraindividual variability in LSU rDNA in some dinoflagellate species due to, assumably, large copy numbers of rDNA in dinoflagellates. Since the copy number of LSU rDNA varies tremendously among dinoflagellate species, the intraspecific and intraindividual diversity for a species of particular interest thus needs to be investigated individually. As a toxic and HABs-forming dinoflagellate, Margalefidinium (= Cochlodinium) fulvescens has been observed to approach blooming density in Jiaozhou Bay, China since 2015 after numerous blooms having been reported from other countries. In trying to identify the source of this newly observed HABs-forming species in China by sequencing the LSU rDNA for both field samples and clonal cultures, we noticed and thus further investigated high intrapopulational and intraindividual genetic diversities of the dinoflagellate. The D1–D6 region of the LSU rDNA (1,435 bases) was amplified from 7 field samples (pooled cells) and 11 clonal cultures, cloned, sequenced, and analyzed phylogenetically for 2,341 sequences obtained. All the numbers of sequences obtained from each clonal culture were far less than the estimated rDNA copy number in M. fulvescens. In the clone library, only one unique sequence was contained in all samples as the most dominant sequence. We found high intrapopulational and intraindividual genetic diversity in M. fulvescens as reflected in the number of polymorphic sites and unique sequences in the clone library for different field samples and clonal cultures in comparison to other species. The mean number of nucleotide differences of each sequence from different field samples and clonal cultures were 6.43 and 4.42 bases, respectively, with the highest being 132 bases, nearly 10%. The sequences with highest variability may be easily annotated as different species if they were obtained from environmental genomic studies because sequence-based species identification in meta-barcoding studies often use "97% identity" threshold. Based on that the mean and overall intrapopulational genetic diversity calculated for 7 field samples was equivalent to the mean and overall intraindividual variability for 11 clonal cultures in indices of genetic diversity, together with the result of AMOVA analysis, we infer that the variability within individual cells (i.e. variability among LSU rDNA polymorphic copies) caused both the intraindividual and intrapopulational genetic diversities observed in the M. fulvescens population, and a higher interpopulational diversity may exist among different geographic populations. The results provide an insightful basis for such a comprehensive interpopulational comparison and important implications for identifying species and establishing new taxa based on the similarity comparison to reference sequences deposited in databases.

Spatial genetic structuring in a widespread wetland plant on a plateau: Effects of elevation‐driven geographic isolation and environmental heterogeneity

Abstract Highlands are ideal research areas for improving our understanding of the influence of ecological factors on the diversity and spatial patterns of natural species. Elevation‐driven physical and environmental isolation greatly affect the evolution of plants. The mechanisms and essential drivers underlying these processes may differ among research scales, habitats and landscapes. Wetlands are important elements of the Qinghai–Tibetan Plateau, which is the highest plateau in the world, and these habitats harbour high aquatic organismal diversity. However, how the environments shape the genetic variation and structure of hydrophilous plants is poorly understood. Using microsatellite markers and a chloroplast fragment, we quantified the genetic diversity and spatial genetic pattern of Stuckenia filiformis, one of the most widespread aquatic plants on the plateau. The relative contributions of geography, climate and local conditions to intra‐ and interpopulation variation were estimated. The results showed that intrapopulation genetic variation of the plant is moderate to high and not constrained by high‐altitude environments. Topographical isolation mainly contributes to the genetic structure of S. filiformis, as inferred by simple sequence repeats and chloroplast DNA data. Significant effects of environmental variables on the spatial genetic patterns of this freshwater species were also suggested by landscape genetic analysis. Infrequent long‐distance dispersal, sexual recruitment and annual growth are probably important for the maintenance and distribution of this variation. Our findings imply a combined effect of geography and elevation‐driven environmental heterogeneity on the evolution of aquatic organisms in highlands.

DIVERSIDAD GENÉTICA EN POBLACIONES DE RAZAS MEXICANAS DE MAÍZ

El maíz (Zea mays L.) de México presenta amplia diversidad debido a que este país es considerado como centro de origen, domesticación y diversificación de esta especie, y si bien existen estudios al respecto, la gran abundancia de tipos hace pertinente profundizar en su análisis. El presente estudio tuvo como objetivo evaluar la diversidad genética inter e intra-poblacional de 25 poblaciones de razas de maíz con 10 marcadores SSR. La primera coordenada principal explicó 42.11 % y la segunda 18.18 % de la variación total. Se encontró un promedio de 2.6 alelos por locus y un valor de diversidad génica de 0.44. El estadístico FST (0.427) indicó una alta diferenciación genética entre las razas de maíz (Zea mays L.). Las razas Serrano de Jalisco y Tabloncillo mostraron los índices más altos de diversidad génica (0.53). La variación inter-poblacional fue del 43 %. Las razas destinadas para usos especiales y con distribución geográfica limitada, como Comiteco (0.33) y Chalqueño (0.30), presentaron los niveles más bajos de diversidad y a su vez exhibieron graves procesos de endogamia (FIT = 0.618) y deriva genética.

Seed Adaptive Traits of Fagus sylvatica Populations in Northeastern Greece

Abstract Fagus sylvatica in Europe is expected to be severely affected by the ongoing climate change. In this article, seed adaptive traits, in terms of morphology and germination, of F. sylvatica populations of different postglacial lineage and intrapopulation genetic diversity were evaluated. Eight plots from two geographical provenances, Evros and Drama, were selected. Provenance shaped both morphology and germination patterns, but the effect was more pronounced on germination. Seeds from Drama were larger and heavier than those from Evros but exhibited a higher degree of dormancy and slower germination. High among-plots variability on morphology and germination was also observed, especially in Evros. This higher variability was consistent with the higher level of genetic diversity observed at genomic and chloroplast DNA markers at small or larger spatial scales from previous published studies on the same plots. Results suggested the existence of different seed adaptation strategies, mainly between provenances, as a result of possible adaptation to different environmental conditions, whereas a possible influence of a generally complex pattern of admixture between different beech subspecies and postglacial lineages could not be excluded.

Genetic diversity and structure of Buxus hyrcana (Pojark) populations in the Caspian forests of northern Iran revealed by ISSR markers

The Caspian boxwood (Buxus hyrcana) is an endangered, evergreen species in the Hyrcanian forests. The prevalence of pests and boxwood blight disease are bound to reduce the genetic diversity of this species in the near future. Accordingly, the current study considered habitat conservation and restoration by evaluating the genetic diversity of different Caspian boxwood populations. Ninety-seven accessions from seven geographic regions of Hyrcanian forests in Iran were investigated to determine genetic diversity and differentiation among and between populations using 10 ISSR primers. Results showed that the inter-population genetic diversity in B. hyrcana was estimated to be higher than intra-population genetic diversity. Principal coordinates analysis was performed on the populations, along with cluster (based on the Nei distance) and Bayesian structure analysis which classified the populations based on their distance from the sea and their altitude above sea level. Our findings suggest that geographic and environmental factors have an essential role in shaping regional gene flow and influence the genetic structure of B. hyrcana populations in the Hyrcanian forests.

Rejection of the genetic implications of the \u201cAbundant Centre Hypothesis\u201d in marine mussels

The ‘Abundant-Centre Hypothesis’ is a well-established but controversial hypothesis stating that the abundance of a species is highest at the centre of its range and decreases towards the edges, where conditions are unfavourable. As genetic diversity depends on population size, edge populations are expected to show lower intra-population genetic diversity than core populations, while showing high inter-population genetic divergence. Here, the genetic implications of the Abundant-Centre Hypothesis were tested on two coastal mussels from South Africa that disperse by means of planktonic larvae, the native Perna perna and the invasive Mytilus galloprovincialis. Genetic structure was found within P. perna, which, together with evidence from Lagrangian particle simulations, points to significant reductions in gene flow between sites. Despite this, the expected diversity pattern between centre and edge populations was not found for either species. We conclude that the genetic predictions of the Abundant-Centre Hypothesis are unlikely to be met by high-dispersal species with large population sizes, and may only become evident in species with much lower levels of connectivity.

Detection of 16S mitochondrial sequence polymorphism and haplotype network of Ophiocara porocephala (Valenciennes, 1837) from Tekolok Estuary (NTB, Indonesia) using DnaSP and NETWORK

The two genetic software, DnaSP and NETWORK, is commonly used to analyse gene polymorphism and haplotype network which is useful for the understanding pattern of genetic variation and genetic relationship. In this study, the two software were applied to detect polymorphism of 16S sequence gene of Ophiocara paracephala from Tekolok Estuary (NTB, Indonesia) which has not been investigated. This study used a PCR method with 16Sar and 16Sbr primers. The results revealed two haplotypes and two variable sites with one parsimony informative within O.paracephala from Tekolok Estuary population. Next, if the 16S sequence data of O.paracephala from Tekolok Estuary was combined with the 16S gene data of O.paracephala from GenBank, three haplotypes were detected with five variables sites and one parsimony informative. This finding showed intra-population and intraspecific genetic variation of O.paracephala. In addition, haplotype network using NETWORK and a phylogenetic tree using Neighbor Joining and Maximum Likelihood methods exhibited that O.paracephala from Tekolok Estuary has a close genetic relationship with O.paracephala from Japan.