Genetic population structure and low genetic diversity in the over-exploited sea cucumber <Emphasis Type="Italic">Holothuria edulis</Emphasis> Lesson, 1830 (Echinodermata: Holothuroidea) in Okinawa Island

Understanding genetic connectivity is fundamental for ecosystem-based management of marine resources. Here we investigate the metapopulation structure of the edible sea cucumber Holothuria edulis Lesson, 1830 across Okinawa Island, Japan. This species is of economic and ecological importance and is distributed from the Red Sea to Hawai‘i. We examined sequence variation in fragments of mitochondrial cytochrome oxidase subunit I (COI) and 16S ribosomal RNA (16S), and nuclear histone (H3) at six locations across Okinawa Island. We found higher haplotype diversity for mtDNA (COI: Hd = 0.69 and 16S: Hd = 0.67) and higher heterozygosity of nDNA (H3: H _E = 0.39) in populations from the west coast of Okinawa compared to individuals from populations on the east coast (COI: Hd = 0.40; 16S: Hd = 0.21; H3: H _E = 0.14). Overall population structure was significant (AMOVA results for COI: Φ _ST = 0.49, P < 0.0001; 16S: Φ _ST = 0.34, P < 0.0001; H3: Φ _ST = 0.12, P < 0.0001). One population in the east, Uruma, showed elevated pairwise Φ _ST values in comparisons with all other sites and a marked reduction of genetic diversity (COI: Hd = 0.25 and 16S: Hd = 0.24), possibly as a consequence of a shift to a more dominant asexual reproduction mode. Recent reports have indicated that coastal development in this area influences many marine organisms, and ecosystem degradation in this location could cause the observed decrease of genetic diversity and isolation of H. edulis in Uruma. Our study should provide valuable data to help with the urgently needed management of sea cucumber populations in Okinawa, and indicates particular attention needs to be paid to vulnerable locations.     

Demographic history and population genetic structure of <Emphasis Type="Italic">Hagenia abyssinica</Emphasis> (Rosaceae), a tropical tree endemic to the Ethiopian highlands and eastern African mountains

The distribution of genetic diversity among natural populations is significantly shaped by geographical and environmental heterogeneity. The key objectives of this study were to outline the population genetic structure and to investigate the effects of historical and current factors in shaping the population structure of an endemic tropical tree, Hagenia abyssinica. We used 11 polymorphic microsatellites to estimate genetic variability and evaluate gene flow among natural populations of H. abyssinica. Further, we employed ecological niche modeling approaches, to analyze the demographic history and map potential distributions of H. abyssinica during the Last Glacial Maximum and the present. Significant levels of genetic diversity (H _O = 0.477, H _E = 0.439) were observed among the sampled locations. High coefficient of genetic differentiation (F _ST = 0.32) and considerable genetic variation within the sampled locations (68.01%) were detected. Our results indicated the existence of three genetic groups with limited gene exchange and revealed positive correlations (r = 0.425, P < 0.05) between genetic diversity and geo-graphic distance. The ecological niche modeling (ENM) results support the existence of three distribution zones during the Last Glacial Maximum (LGM), with high probability of occurrence (0.8–1.0), and indicated slight distribution disturbances during and after the LGM. The fundamental patterns of genetic diversity and population structuring of H. abyssinica result from a combination of both environmental and geographical factors, including long-term isolation by distance and characteristic life history of this species. Our ENM results identified three zones that could have served as glacial refugia for this species and lay a foundation for further studies, outlining demographic histories and population structures of Afromontane species.     

Spatial patterns and intraspecific diversity of the glacial relict legume species <Emphasis Type="Italic">Vavilovia formosa</Emphasis> (Stev.) Fed. in Eurasia

Vavilovia formosa is one of five genera in tribe Fabeae, (Fabaceae, Leguminosae) with close phylogenetic relationships to Pisum. It grows in subalpine and alpine levels in Armenia, Azerbaijan, Georgia, Iran, Iraq, Lebanon, Russia and Turkey and is recognized as an endangered and protected plant. This study was conducted to reveal its intraspecific variability, as well as to predict the past, extant and future species distribution range. We analysed 51 accessions with common phylogenetic markers (trnF-trnL, trnS-trnG, matK, rbcL, psbA-trnH and ITS). These represent in total up to 2551 bp of chloroplast and 664 bp of nuclear sequences per sample. Two populations from Turkey and Armenia were analysed for genetic diversity by AFLP. Leaf morphometry was conducted on 1457 leaflets from 43 specimens. Extracted bioclimatic parameters were used for niche-modelling approach. Analysis of cpDNA revealed two haplotypes, 12 samples from Armenia, Daghestan, Nakhichevan and Iran belonged to H1 group, while 39 samples of all Turkish and part of Armenian were in H2 group. The mean intrapopulation diversity based on AFLP was low (H _E = 0.088) indicating limited outcrossing rate. A significantly positive correlation between geographical latitude and leaf area (\(\rho\) = 0.527, p < 0.05) was found. Niche modelling has shown temporal variation of predicted occurrence across the projected time periods. Vavilovia formosa has suffered a range reduction following climate warming after last glacial maximum, which classify this species as cold-adapted among the Fabeae species as well as a glacial relict.     

Genetic analysis of forest species <Emphasis Type="Italic">Eugenia uniflora</Emphasis> L. through of newly developed SSR markers

Nine microsatellite loci for genetic analysis of three populations of the tropical tree Eugenia uniflora L. (pitanga or Brazilian cherry) from fragments of semideciduous forest were developed. We used the technique of building a (GA) _n and (CA) _n microsatellite-enriched library by capture with streptavidin-coated magnetic beads. We assessed the polymorphism of seven microsatellites in 84 mature trees found in three areas (Ribeirão Preto, Tambaú and São José do Rio Pardo), highly impacted by the agricultural practices, in a large region among Pardo river and Mogi-Guaçu river basins, in state of São Paulo, Brazil. All loci were polymorphic, and the number of alleles was high, ranging from 6 to 24, with a mean of 14.4. All stands showed the same high level of genetic diversity (mean H _E  = 0.83) and a low genetic differentiation (mean F _ST = 0.031), indicating that genetic diversity was higher within rather than among populations. Seven of the nine loci were highly variable, and sufficiently informative for E. uniflora. It was concluded that these new SSR markers can be efficiently used for gene flow studies.     

Fine-scale spatial genetic structure in the frankincense tree <Emphasis Type="Italic">Boswellia papyrifera</Emphasis> (Del.) Hochst. and implications for conservation

The fine-scale genetic structure and how it varies between generations depends on the spatial scale of gene dispersal and other fundamental aspects of species’ biology, such as the mating system. Such knowledge is crucial for the design of genetic conservation strategies. This is particularly relevant for species that are increasingly fragmented such as Boswellia papyrifera. This species occurs in dry tropical forests from Ethiopia, Eritrea and Sudan and is an important source of frankincense, a highly valued aromatic resin obtained from the bark of the tree. This study assessed the genetic diversity and fine-scale spatial genetic structure (FSGS) of two cohorts (adults and seedlings) from two populations (Guba-Arenja and Kurmuk) in Western Ethiopia and inferred intra-population gene dispersal in the species, using microsatellite markers. The expected heterozygosity (H _E) was 0.664–0.724. The spatial analyses based on kinship coefficient (F _ij) revealed a significant positive genetic correlation up to a distance of 130 m. Spatial genetic structure was relatively weak (Sp = 0.002–0.014) indicating that gene dispersal is extensive within the populations. Based on the FSGS patterns found, we estimate indirectly gene dispersal distances of 103 and 124 m for the two populations studied. The high heterozygosity, the low fixation index and the low Sp values found in this study are consistent with outcrossing as the (predominant) mating system in B. papyrifera. We suggest that seed collection for ex situ conservation and reforestation programmes of B. papyrifera should use trees separated by distances of at least 100 m but preferably 150 m to limit genetic relatedness among seeds from different trees.     

A mountain range is a strong genetic barrier between populations of <Emphasis Type="Italic">Afzelia quanzensis</Emphasis> (pod mahogany) with low genetic diversity

Understanding patterns of genetic diversity of plants is important in guiding conservation programs. The aim of our study was to characterize genetic diversity in Afzelia quanzensis, an economically important African tree species. We genotyped 192 individuals at 10 nuclear microsatellite loci. Samples were collected from nine sites in Zimbabwe, five in the north and four in the south, separated by a mountain range, the Kalahari-Zimbabwe axis. Overall, genetic diversity was relatively low across all sites (expected heterozygosity (H _E)?=?0.452, mean number of alleles (A)?=?4.367, allelic richness (A _R)?=?2.917, effective number of alleles (A _E)?=?2.208, and private allelic richness (PA_R)?=?0.197). Genetic diversity estimates, H _E, A, A _R, and PA_R, were not significantly different between northern and southern sites. Allelic richness was significantly higher in southern sites. Significant population differentiation was observed among all sites (F _ST ?=?0.0936, G′ _ST ?=?0.1982, G _ST ?=?0.1001, D _JOST?=?0.0598). STRUCTURE analysis and principal components analysis identified two gene pools, one predominantly made up of southern individuals, and the other of northern individuals. A Monmonier’s function detected a genetic barrier that coincided with the Kalahari-Zimbabwe axis. The relatively low level of genetic diversity in A. quanzensis may reduce adaptability and limit future evolutionary responses. All sites should be monitored for deleterious effects of low genetic diversity, and genetic resource management should take into consideration the existence of the distinct gene pools to capture the entire extant genetic variation.     

A novel set of EST-InDel markers in <Emphasis Type="Italic">Eucalyptus</Emphasis> L’Hérit.: polymorphisms,cross-species amplification,physical positions and genetic mapping

Insertion/deletion (InDel) markers are valuable for genetic applications in plant species, and the public databases of expressed sequence tags (ESTs) have facilitated the development of genic InDel markers. In this study, we developed a novel set of 144 InDel markers in an important tree genus Eucalyptus L’Hérit. using the ESTs of GenBank. Amplicon sequencing against two parents of a mapping population (Eucalyptus urophylla S. T. Blake × E. tereticornis Smith) revealed that the InDel size ranged from 2 to 44 bases, and the dinucleotide type was the most abundant (37.3 %). The cross-species/subgenus amplification rate ranged from 62.5 % in E. tessellaris F. Muell. (subgenus Blakella) to 99.3 % in E. grandis Hill ex Maiden (subgenus Symphyomyrtus) with an average of 85.4 %. There were 121 EST-InDels (84.0 %) polymorphic among 12 individuals of E. grandis, and the mean number of alleles per polymorphic locus (N _a), observed heterozygosity (H _o), expected heterozygosity (H _e) and polymorphic information content (PIC) were 4.0, 0.278, 0.538 and 0.465, respectively. Physical positions of 143 EST-InDels were predicted on the E. grandis genome sequence. A total of 81 EST-InDels were incorporated into prior dense genetic maps of E. urophylla and E. tereticonis, and extensive synteny and colinearity were observed between E. grandis genome sequence and the mapped EST-InDel markers. These EST-InDels will provide a valuable resource of functional markers for genetic diversity evaluation, genome comparison, QTL mapping and marker-assisted breeding in Eucalyptus.     

Population genetics of the naturally rare tree <Emphasis Type="Italic">Dimorphandra wilsonii</Emphasis> (Caesalpinioideae) of the Brazilian Cerrado

Naturally rare species have a higher probability of stochastic extinction due to genetic, demographic, or environmental hazards; human disturbance may intensify these threats. Rare species may therefore be in need of short-term intervention to survive. The ecosystem with the second highest biodiversity in Brazil, the Cerrado, is suffering from fragmentation and threats to its flora. Dimorphandra wilsonii, a 30-m tall endemic tree of the Brazilian Cerrado, is listed as critically endangered; only 21 adult trees have been identified. We carried out mating system and pollen flow analyses to understand the current gene flow and limitations in the reproduction of D. wilsonii. With seven fluorescently labelled microsatellite primers, we genotyped 20 adult trees and 269 progeny from 13 mother trees. D. wilsonii displayed low levels of genetic diversity; bottleneck events are likely to have occurred (H _e ?=?0.60 and 0.29; H _o ?=?0.71 and 0.33, for adults and progeny, respectively). This species is predominantly outcrossing (t _m ?=?0.88), with some selfing (1-t _m ?=?0.12), as well as crossing between related individuals (t _m -t _s ?=?0.11). None of the studied trees was reproductively isolated; a high proportion of pollen (55 %) came from trees yet to be discovered. Two genetic clusters (Northern and Southern) were identified, with high values of genetic divergence among the Southern sites. Planting of seedlings and monitoring of seed dispersion in order to maintain the genetic diversity and genetic structure of D. wilsonii are strategies that may ensure the continuation of D. wilsonii, but this species does not seem to require reproductive intervention to remain viable.     

Comparison of molecular genetic utilities of TD,AFLP, and MSAP among the accessions of <Emphasis Type="Italic">japonica,indica</Emphasis>, and <Emphasis Type="Italic">Tongil</Emphasis> of <Emphasis Type="Italic">Oryza sativa</Emphasis> L.

Rice is one of the most important food crops in the world. Genetic diversity is essential for cultivar improvement programs. We compared genetic diversity derived from insertion–deletion (in–del) or base substitutions by amplified fragment length polymorphism (AFLP), from transposon transposition mutations by transposon display (TD), and from cytosine methylation by methylation-sensitive amplified polymorphism (MSAP) in japonica, indica, and Tongil type varieties of Oryza sativa L. Polymorphic profiles from the three marker systems allowed us to clearly distinguish the three types of varieties. The indica type varieties showed the highest genetic diversity followed by the Tongil and japonica type varieties. Of the three marker systems, TD produced the highest marker indices, and AFLP and MSAP produced similar marker indices. Pair-wise comparisons of the three marker systems showed that the correlation between the two genetic markers systems (AFLP and TD, r = 0.959) was higher than the correlations between the genetic and epigenetic marker systems (AFLP and MSAP, r = 0.52; TD and MSAP, r = 0.505). Both genetic marker systems had similar levels of gene differentiation (G _ST ) and gene flow (N _m ), which differed in the epigenetic marker system. Although the G _ST of the epigenetic marker system was lower than the genetic marker systems, the N _m of the epigenetic marker system was higher than in the genetic marker systems, indicating that epigenetic variations have a greater influence than genetic variations among the O. sativa L. types.     

Conserving the small milkwort, <Emphasis Type="Italic">Comesperma polygaloides</Emphasis>, a vulnerable subshrub in a fragmented landscape

The conservation of remnant grassland vegetation on the Victorian volcanic plain (VVP) is crucial for the persistence of local biodiversity. Recent habitat loss has restricted the grassland to only a small percentage of its former range. Along with grassland habitats, species that occur on the VVP are in decline and many are legally protected. Comesperma polygaloides is a grassland species of the VVP that also occurs outside of the region in woodland habitats. We use 12 neutral microsatellite loci and two chloroplast regions to understand genotypic patterns of C. polygaloides in southeastern Australia. We found separate genetic clusters but they do not follow geographic boundaries. There are fewer alleles (2.96) and effective alleles (2.01) than expected from 12 microsatellite markers compared to other species. Even with the low number of alleles per locus there was a moderate level of genetic diversity detected (I = 0.69; H_o = 0.43; H_e = 0.40). Populations of the VVP could not be differentiated from populations elsewhere using neutral markers or chloroplast analyses. The genetic structure discovered was not consistent with the level of fragmentation observed. There may be several reasons for the observed lack of genetic structure: the species is more common than perceived, plants are long-lived and can reproduce clonally, and the bioregion is relatively young, geologically. Results indicate that restoration projects and long-term viability of C. polygaloides will be improved by composite seed sourcing, alleviating the risk of insufficient genetic diversity posed by an over-emphasis on local provenancing.     

Development of microsatellite markers and their use in genetic diversity and population structure analysis in <Emphasis Type="Italic">Casuarina</Emphasis>

Casuarina is a widely cultivated plantation tree species in coastal India, primarily due to its fast growth, high productivity and suitable for pulp and paper production. However, genetic studies of Casuarina have been hindered by lack of genomic resources and genetic markers. Knowledge of the genetic diversity and population structure of Casuarina germplasms will provide the basis for utilizing and improving resource in the breeding program. Keeping this in view, in the present study, we have identified a total of 11,503 simple sequence repeat (SSR) makers from 86,415 expressed sequence tags (ESTs) of Casuarina equisetifolia and C. junghuhniana after redundancy elimination. Dinucleotide repeats were the most abundant accounting for 72.5 % of all microsatellites, followed by trimer (23.4 %), hexamer (1.7 %), tetramer (1.5 %), and very few pentamer (0.6 %) repeats. Of these, 50 markers were used to estimate genetic diversity and population structure among 96 accessions of C. cunninghamiana and C. junghuhniana. EST-SSR markers revealed high level of polymorphism, detecting a total of 829 alleles with an average of 17 alleles per locus. Polymorphic information content (PIC) values ranged from 0.32 to 0.93, with an average of 0.78 per locus. The average observed (H _o ) and expected heterozygosity (H _e ) obtained was high and fairly similar in C. cunninghamiana and C. junghuhniana, thereby suggesting highly heterogeneous nature of Casuarina. Population structure using a Bayesian model-based clustering approach identified clear delineation between C. cunninghamiana and C junghuhniana. Further, these markers were also evaluated in four species of Casuarina confirming high rate of cross-species transferability. The results of this study can provide valuable insights for genetic and genomic research in Casuarina.     

Elucidating the multiple genetic lineages and population genetic structure of the brooding coral <Emphasis Type="Italic">Seriatopora</Emphasis> (Scleractinia: Pocilloporidae) in the Ryukyu Archipelago

The elucidation of species diversity and connectivity is essential for conserving coral reef communities and for understanding the characteristics of coral populations. To assess the species diversity, intraspecific genetic diversity, and genetic differentiation among populations of the brooding coral Seriatopora spp., we conducted phylogenetic and population genetic analyses using a mitochondrial DNA control region and microsatellites at ten sites in the Ryukyu Archipelago, Japan. At least three genetic lineages of Seriatopora (Seriatopora-A, -B, and -C) were detected in our specimens. We collected colonies morphologically similar to Seriatopora hystrix, but these may have included multiple, genetically distinct species. Although sexual reproduction maintains the populations of all the genetic lineages, Seriatopora-A and Seriatopora-C had lower genetic diversity than Seriatopora-B. We detected significant genetic differentiation in Seriatopora-B among the three populations as follows: pairwise F _ST = 0.064–0.116 (all P = 0.001), pairwise G′′_ST = 0.107–0.209 (all P = 0.001). Additionally, only one migrant from an unsampled population was genetically identified within Seriatopora-B. Because the peak of the settlement of Seriatopora larvae is within 1 d and almost all larvae are settled within 5 d of spawning, our observations may be related to low dispersal ability. Populations of Seriatopora in the Ryukyu Archipelago will probably not recover unless there is substantial new recruitment from distant populations.     

Assessing genetic structure in a rare clonal eucalypt as a basis for augmentation and introduction translocations

Genetics can provide information that is critical for planning translocations for conservation, such as levels of diversity and divergence of target and source populations. For clonal plants, assessing population characteristics (size, diversity, mortality, gene flow) that influence conservation values also requires identification of different genetic individuals. We used 12 microsatellite markers to guide germplasm source recommendations for augmentation and introduction translocations to conserve the critically endangered Eucalyptus cuprea that occurs in fragmented populations in the semi-arid shrublands of Western Australia. Ramet clumps with identical multilocus genotypes were identified in all populations but clonal richness (R = 0 ? 0.86) and heterogeneity (D = 0 ? 0.98) varied among populations. Genetic diversity was low to moderate in all populations (mean H _o = 0.61, mean A = 3.78) and did not differ significantly between localities. There was evidence of inbreeding in some populations but outcrossing (t _m = 0.495) in the small number of families available for study (N = 4) and genotypic diversity of the larger extant populations suggest the generation of novel genotypes is a component of the reproductive strategy. Most diversity was within populations and differentiation among populations was moderate (F _ST = 0.100) suggesting mixing of source population for translocation is unlikely to lead to outbreeding depression. Principal Co-ordinate and Bayesian analyses indicated the Northern population is distinct from Central/Southern populations. We recommend use of mixed germplasm to conserve the moderate diversity characterising larger remnant populations and to enable the production of recombinants through sexual reproduction. But given seed availability and the distinction of the Northern population, an initial precautionary approach to a translocation proposed for south of the geographical range may be to source germplasm from the Central/Southern locality.     

Hybrid peony (<Emphasis Type="Italic">Paeonia hybrida</Emphasis> Pall.), a rare endangered plant of Bashkir Trans-Uralian region: Autocorrelation analysis of the spatial genotype distribution under different environmental conditions

Hybrid peony (Paeonia hybrida Pall.) is listed as endangered in Russian Federation (since 1988) and in several regions of Russia. The structure of the isolated population from Bashkir Trans-Uralian region, separated by 1500 km from the main geographic range of this species, has been studied using isoenzyme markers from 11 loci. The population is split between two geographical locations, both characterized by a relatively high genetic diversity (mean allele number A = 1.9±0.3, percentage of polymorphic loci P = 0.54, observed heterozigosity H _O = 0.223±0.068, expected heterozigosity H _E = 0.229±0.067) and a quite low intergroup genetic differentiation (fixation index F _ST = 0.008, Nei’s genetic distance D = 0.011). In a subpopulation located near a swampy lake in dense cereal grass and steppe shrubby vegetation, autocorrelation analysis has revealed spatial structuring of genetic variability. In the other location, a stipa-forb steppe on a flat hill slope, a uniform spatial structure of the genotypes has been observed. The results are discussed with respect to the ecological characteristics of the species and the conservation of the genetic pool of the population in situ and ex situ.     

High genetic diversity in an endangered medicinal plant, <Emphasis Type="Italic">Saussurea involucrata</Emphasis> (<Emphasis Type="Italic">Saussurea</Emphasis>, Asteraceae), in western Tianshan Mountains,China

Saussurea involucrata (Asteraceae) is a medicinal and second-degree national priority endangered plant that is mainly distributed in the high latitude region of the western Tianshan Mountains. The population is fragmented and isolated, and extensive human impact merits a suitable and specific conservation strategy, which can be compiled based on the genetic diversity, population structure, and demographic history. Phylogeographic studies were conducted on a total of five natural populations and 150 individuals were sampled. Data from three cpDNA intergenic spacer regions (trnL-F, matK, and ndhF-rpl32) and nrDNA ITS sequences showed that twelve haplotypes in cpDNA and five haplotypes in nrDNA indicated high genetic diversity among populations sampled (H _T?=?0.820 and 0.756) and within populations sampled (H _S?=?0.792 and 0.721). Additionally, the high genetic diversity did not mirror genetic structure in either cpDNA (F _ST?=?0.03153, G _ST?>?N _ST, p?<?0.05) or nrDNA (F _ST?=?0.03666, meaningless G _ST and N _ST). Two groups (north and south) were determined for a SAMOVA analysis. Based on this analysis, the demographic history was conducted with a Bayesian Skyline Plot and Isolation with Migration analysis, which showed sustainable and stable extension without a marked bottleneck. Divergence time was indicated at c. 6.25 Mya (90%HPD: 15.30–0.22 Mya) in the Miocene, which is consistent with the formation of the Kelasu section of Tianshan. The southern populations in the Bayanbulak and Gonglu regions require additional attention and transplanting would be an effective way to restore rare cpDNA haplotypes, increase effective population size, and migration rate. Our results suggested that in situ conservation of S. involucrata in western Tianshan should be the main strategy for protection and recovery of the species.     

Negligence in the Atlantic forest,northern Brazil: a case study of an endangered orchid

Currently, many Brazilian orchids are threatened with extinction resulting from habitat loss and intense harvesting pressure stemming from their value as ornamental plants. Therefore, the genetic diversity in remaining populations is fundamental to the survival of these species in natural environments. In order to inform conservation strategies, this study evaluated the genetic diversity and structure of Cattleya granulosa populations. The sample consisted of 151 individuals from 12 populations in the Atlantic Forest, northeastern Brazil, evaluated using 91 ISSR markers. Genetic variability was assessed through molecular variance, diversity indexes, clusters of genotypes through Bayesian analysis, and tests for genetic bottlenecks. From all polymorphic loci, genetic diversity (H_E) varied between 0.210 and 0.321 and the Shannon index ranged from 0.323 and 0.472. Significant genetic differentiation between populations (Φ_ST = 0.391; P < 0.0001) resulted in the division of the populations into five groups based on the log-likelihood Bayesian analysis. We found significant positive correlation between geographical and genetic distances between populations (r = 0.794; P = 0.017), indicating isolation by distance. Patterns of allelic diversity within populations suggest the occurrence of bottlenecks in most C. granulosa populations (n = 8). Therefore, in order to maintain the genetic diversity of the species, the conservation of spatially distant groups is necessary.     

Unspecific histological and hematological alterations in anadromous and resident <Emphasis Type="Italic">Salvelinus malma</Emphasis> induced by volcanogenic pollution

Knowledge of larval dispersal and connectivity in coral reef species is crucial for understanding population dynamics, resilience, and evolution of species. Here, we use ten microsatellites and one mitochondrial marker (cytochrome b) to investigate the genetic population structure, genetic diversity, and historical demography of the powder-blue tang Acanthurus leucosternon across more than 1000 km of the scarcely studied Eastern African region. The global AMOVA results based on microsatellites reveal a low but significant F _ST value (F _ST = 0.00252 P < 0.001; D _EST = 0.025 P = 0.0018) for the 336 specimens sampled at ten sample sites, while no significant differentiation could be found in the mitochondrial cytochrome b dataset. On the other hand, pairwise F _ST, PCOA, and hierarchical analysis failed to identify any genetic breaks among the Eastern African populations, supporting the hypothesis of genetic homogeneity. The observed genetic homogeneity among Eastern African sample sites can be explained by the lengthy post-larval stage of A. leucosternon, which can potentiate long-distance dispersal. Tests of neutrality and mismatch distribution signal a population expansion during the mid-Pleistocene period.     

Genetic diversity of <Emphasis Type="Italic">Phytophthora capsici</Emphasis> recovered from Massachusetts between 1997 and 2014

Phytophthora blight caused by Phytophthora capsici limits the production of cucurbits and peppers in the United States and is a growing threat to sustainable vegetable production in New England. Little is known about the genetic diversity of P. capsici in New England, and a total of 210 P. capsici isolates from 18 sites were genotyped using 46 single nucleotide polymorphism markers, revealing 85 unique and 34 repeated multi-locus genotypes. Both mating types were recovered from 7 of the 18 locations. Isolates with identical genotypes (clonal lineages) ranged from 2 to 16. Three clonal lineages were recovered from multiple sites within the same year, although none were recovered across multiple years. Bayesian clustering revealed individuals with a complex genetic cluster composition. This, coupled with a high outcrossing rate (mean t = 0.87) and no clear clustering in principal coordinates analysis, suggests outcrossing among the populations. Phylogenetic and genetic distance analysis indicate differentiation based on farm location and movement among farms may be infrequent. There was no obvious differentiation based on cucurbit, tomato or pepper hosts.