SSR marker development for Japanagromyza tokunagai (Agromyzidae, Diptera) using genome sequences obtained by nanopore sequencing.

Agricultural intensification is one of the major forces driving populations of many traditionally common native species into smaller, fragmented populations which are prone to isolation and loss of genetic diversity. Identifying the spatial extent and characteristics of rural systems that support gene flow and promote genetic diversity for these species is thus essential for their long-term conservation. Here we used asymmetric autosomal genetic structure between sexes to investigate current gene flow among four neighbouring suburban populations of hedgehogs (Erinaceus europaeus) in England, which are separated by agricultural land. Contrary to expectations, we found that individuals belonged to a single genetic population despite the populations being separated by unoccupied agricultural land. Spatial autocorrelation was significant in adult female hedgehogs, but non-significant in adult males, revealing male driven contemporary gene flow between local populations. The results suggest that male hedgehogs are capable of moving between population patches separated by at least 3 km across the agricultural matrix. This finding is crucial to aid the development of a conservation strategy for hedgehogs as, for the first time, it shows the extent that previously assumed isolated populations across a perceived inhospitable landscape are connected by current gene flow. Higher within patch relatedness, and lower allelic richness were found from smaller suburban patches, largely reflecting local population size, indicating an early stage of genetic diversity loss due to habitat loss and associated fragmentation. Our study illustrates that considering current gene flow and local genetic diversity together is important to better understand habitat effects on genetic variation and to inform future conservation management.

Many studies performed during the last years demonstrated the usefulness of neutral molecular markers in the field of conservation and population genetics of forest trees, in particular to understand the importance of migration patterns in shaping current genetic and geographic diversity and to measure important parameters such as effective population size, gene flow and past bottleneck. During the next years, a large amount of data at marker loci or at sequence level is expected to be collected, and to become excellent statistical power for the assessment of biological and evolutionary value.

Tracking population genetic signatures of local extinction with herbarium specimens.

Microsatellite Libraries Enriched for Several Microsatellite Sequences in Plants

Simple SummaryReindeer herding is the most important agricultural sector of the Russian Far North, representing the local genetic resources that compose original genetic wealth for the indigenous Arctic ethnic groups, which has maintained their life in harsh conditions of the area for many years. Conservation about and further rational use of such resources are very difficult without taking into account genetic diversity. Here, for the first time, the current genetic composition of the four officially recognized reindeer breeds and their ecotypes inhabiting the area from the Kola Peninsula in the west to the Chukotka region in the east are described using a single-nucleotide polymorphism (SNP) array. Our findings reveal the genetic uniqueness of each breed, formed by the consequences of ecological processes, internal gene flow, breeding practices, and geographical features. The obtained results will assist the ongoing breeding policy to develop accurate programs to preserve genetic resources of this essential element of Russia’s Far North ecosystem.To examine the genetic diversity and population structure of domestic reindeer, using the BovineHD BeadChip, we genotyped reindeer individuals belonging to the Nenets breed of the five main breeding regions, the Even breed of the Republic of Sakha, the Evenk breed of the Krasnoyarsk and Yakutia regions, and the Chukotka breed of the Chukotka region and its within-breed ecotype, namely, the Chukotka–Khargin, which is bred in Yakutia. The Chukotka reindeer was shown to have the lowest genetic diversity in terms of the allelic richness and heterozygosity indicators. The principal component analysis (PCA) results are consistent with the neighbor-net tree topology, dividing the reindeer into groups according to their habitat location and origin of the breed. Admixture analysis indicated a genetic structuring of two groups of Chukotka origin, the Even breed and most of the geographical groups of the Nenets breed, with the exception of the Murmansk reindeer, the gene pool of which was comprised of the Nenets and apparently the native Sami reindeer. The presence of a genetic component of the Nenets breed in some reindeer inhabiting the Krasnoyarsk region was detected. Our results provide a deeper insight into the current intra-breeding reindeer genetic diversity, which is an important requirement for future reindeer herding strategies and for animal adaptation to environmental changes.

Rai MK (2010) Review: Biotechnological strategies for conservation of rare and endangered medicinal plants. Biodiversitas 11: 157166. The use of medicinal plants is as old as human civilization. The biotechnological tools play a crucial role in conservation of rare and endangered medicinal plants. The rapid depletion of plant genetic diversity has made essential to develop new in situ and ex situ conservation methods. Advances in biotechnology offer new methods for conservation of rare and endangered medicinal plants. The present review is focused on biotechnological tools like in vitro culture, micropropagation, mycorrhization, genetic transformation and development of DNA banks. These are imperative and important alternatives for the conservation of rare and endangered medicinal plants.

Diversity and dispersal of aquatic invertebrate species from surface and groundwater: Development and application of microsatellite markers for the detection of hydrological exchange processes

This chapter explores linkages between studies of the biology of rare plants and strategies for their conservation. Because of their low numbers and consequent vulnerability to destruction, rare plant species provide an important test of the current state of the art in conservation, particularly important in an era of biological management. The primary threats and patterns of endangerment to the flora of the United States are summarized, with special reference to causes of decline beyond outright destruction of habitat. The chapter addresses the major biological considerations in rare plant conservation and management, including endemism and narrow distribution, and demographic or genetic effects in small populations. Finally, integrated strategies for rare plant conservation are discussed, emphasizing the interactions among land conservation, biological management, offsite research and propagation, and introduction and habitat restoration. A bibliography on rare plant biology and conservation is also provided.

BackgroundUntil recently the isolation of microsatellite markers from Lepidoptera has proved troublesome, expensive and time-consuming. Following on from a previous study of Edith's checkerspot butterfly, Euphydryas editha, we developed novel microsatellite markers for the vulnerable marsh fritillary butterfly, E. aurinia. Our goal was to optimize the process in order to reduce both time and cost relative to prevailing techniques. This was accomplished by using a combination of previously developed techniques: in silico mining of a de novo assembled transcriptome sequence, and genotyping the microsatellites found there using an economic method of fluorescently labelling primers.Principal FindingsIn total, we screened nine polymorphic microsatellite markers, two of which were previously published, and seven that were isolated de novo. These markers were able to amplify across geographically isolated populations throughout Continental Europe and the UK. Significant deviations from Hardy-Weinberg equilibrium were evident in some populations, most likely due to the presence of null alleles. However, we used an Fst outlier approach to show that these markers are likely selectively neutral. Furthermore, using a set of 128 individuals from 11 populations, we demonstrate consistency in population differentiation estimates with previously developed amplified fragment length polymorphism (AFLP) markers (r = 0.68, p<0.001).SignificanceRapid development of microsatellite markers for difficult taxa such as Lepidoptera, and concordant results with other putatively neutral molecular markers, demonstrate the potential of de novo transcriptional sequencing for future studies of population structure and gene flow that are desperately needed for declining species across fragmented landscapes.

Phyllanthus emblica and P. indofischeri, commonly known as the Indian gooseberry, are important nontimber forest product (NTFP) species widely distributed across the Indian subcontinent. The fruits of these species are rich in vitamin C and are used in the preparation of a number of herbal medicines for treating a wide range of disorders. Due to the increased demand, they have been harvested extensively and form a major source of income for the forest-dwelling communities living in southern India. There are limited studies to understand the impact of harvesting on the genetic structure of these species. In this study, 15 polymorphic microsatellite markers have been developed for P. emblica and were characterized by screening 20 individuals each of P. emblica and P. indofischeri. The number of alleles per locus ranged 2-9 for P. emblica and 2-11 for P. indofischeri. The observed and expected heterozygosity of P. emblica ranged 0-1 and 0.401-0.825, respectively. Similarly, the observed and expected heterozygosity of P. indofischeri ranged 0.5-1 and 0.366-0.842, respectively. Cross-amplification of the designed primers was assessed with seven related Phyllanthus species. The microsatellite markers developed can be used for studying the population genetic structure, gene flow and genetic diversity of P. emblica and P. indofischeri.

Anopheles flavirostris (Ludlow) belongs to the Oriental Myzomyia Series ofnAnopheles subgenus Cellia. Anopheles flavirostris is the most important malaria vector innthe Philippines and it transmits bancroftian filariasis in some regions of the country. AsnAn. flavirostris shows variation in biting behaviour, it may be composed of cryptic species.nnnnnnnn The objectives of this thesis are to determine whether An. flavirostris is a complexnof species and to gain an understanding of the evolutionary relationship among individualsnby studying the population structure and gene flow within this taxon. Genomic DNA wasnextracted from samples of An. flavirostris, amplified and the internal transcribed spacer -2n(ITS-2) and the third domain (D3) of the ribosomal DNA gene and a fragment ofnmitochondrial cytochrome oxidase subunit I gene (mt CO1) were sequenced and analysednfor variation. Polymorphic microsatellite markers for population study of An. flavirostrisnwere developed to determine gene flow. The relevance of the results to malaria control isndiscussed.nnnnnnnnn No evidence of intra-and inter-specific sequence variation among the populations ofnAn. flavirostris was found using two markers (ITS-2 and D3), strongly supporting thenhypothesis that An. flavirostris is a single species. However, the mitochondrialncytochrome oxidase subunit I gene (mtCOI) showed high gene diversity (0.867p0.015)nwith 15 haplotypes in the 102 An. flavirostris analysed from the Philippines. Thenmitochondrial DNA data were analysed using nested clade analysis to assess evolutionarynprocesses explaining the geographical distribution (among island regions of Luzon,nMindanao, Visayas and Palawan) of mtDNA diversity in An. flavirostris. Three divergentnhaplotype clades were revealed: clade 3-1 (haplotypes from Mindanao), clade 2-1 (includes haplotypes mostly present in Luzon) and clade 2-2 (haplotypes from Visayas, Mindanaonand Palawan). Genetic structure was associated with geography (Pl0.001). Allopatricnfragmentation was the most likely explanation for the geographical pattern and the threenmutations between clade 2-1 and 2-2 provided further evidence of allopatric fragmentation.nMitochondrial DNA data sequences strongly supported the specific status of An.nflavirostris. Microsatellite markers demonstrated more polymorphism and proved to benmore useful in studying the population structure and in determining gene flow. Significantndifferentiations were observed (FST ranged from 0.066-0.277, Pl0.05) between 14ncollection sites as well as between regional populations (FST ranged from 0.058 - 0.131,nPl0.01). Analysis of molecular variance indicated more extensive genetic differentiationnamong individuals within sites (85%, FST = 0.144, Pl0.001) than among populations withinnregions (2%, Frt = 0.018, Pl0.001). Based on Nei's unbiased genetic distances,npopulations of An. flavirostris can be grouped into three regional clusters: one includesnLuzon and Mindanao, Visayas and Palawan. This grouping accords with the geologicalnhistory of these regions. Results of the estimates of gene flow (Nm ranged from 4.10-1.66)nindicate that barriers to gene flow exist between populations of An. flavirostris, however,nexchange of genes occurs between populations that are 10 kilometres apart as evidenced byntheir low genetic differentiation (FST = 0.016, Nm = 15.38).nnnnnnnn This, the first study to investigate An. flavirostris populations in the Philippinesnthroughout its range using four genetic markers, revealed no evidence of cryptic speciesnwithin An. flavirostris. Sequence variations in the mtCO1 gene provided strong supportnthat An. flavirostris has specific status among the Oriental species of the Myzomyia Series.nData on gene flow from this study can be applied in the management of insecticidenresistance when the problem arises. For example, if resistance to permethrin (the insecticide commonly used for bed net impregnation) occurs in Palawan, it is likely tonspread within Palawan as exemplified by the high estimate of gene flow (Nm =15.38)nbetween populations that are 10 kilometres apart; resistance is unlikely to spread quickly tonother regions like Mindanao as indicated by the low estimate of gene flow (Nm = 1.66)nbetween these regions. Thus, management of the resistance problem can be confined tonaffected areas only. In the long term, the extent and pattern of the population variation andnlevel of gene flow between populations of An. flavirostris revealed by this study is useful innevaluating the potential success of genetic control of this vector.n

Precise empirical data on current gene flow by pollen, both with respect to distance and abundance, is crucial to understand whether habitat fragments are functionally connected. Based on a large-scale inventory ( approximately 100 km(2)) in which all individuals of a naturally scattered forest tree (Sorbus domestica) were mapped, we inferred current gene flow by pollen using genetic paternity analysis. We detected an extensive network of effective pollen transfer. Although short pollen flow distances were most abundant, 10% of the assigned pollen donors were more than 2 km away from their female mating partners, and 1.8% were even at a distance of 12-16 km. This latter pollen flow shows that current long-distance gene flow over a fragmented landscape clearly occurs. Pollen dispersal was well described by a fat-tailed inverse curve. Using parentage analysis of established trees, maternally inherited chloroplast markers and diameter at breast height measurements as an indicator of individual tree age, we were able to infer regular seed dispersal distances over several hundred metres up to more than 10 km. We conclude that in temperate, insect-pollinated and animal-dispersed tree species such as S. domestica, fragmented subpopulations are functionally connected by gene flow through both pollen and seed.

The patterns of hybridization and asymmetrical gene flow among species are important for understanding the processes that maintain distinct species. We examined the potential for asymmetrical gene flow in sympatric populations of Eucalyptus aggregata and Eucalyptus rubida, both long-lived trees of southern Australia. A total of 421 adults from three hybrid zones were genotyped with six microsatellite markers. We used genealogical assignments, admixture analysis and analyses of spatial genetic structure and spatial distribution of individuals, to assess patterns of interspecific gene flow within populations. A high number of admixed individuals were detected (13.9-40% of individuals), with hybrid populations consisting of F(1) and F(2) hybrids and backcrosses in both parental directions. Across the three sites, admixture proportions were skewed towards the E. aggregata genetic cluster (x=0.56-0.65), indicating that backcrossing towards E. aggregata is more frequent. Estimates of long-term migration rates also indicate asymmetric gene flow, with higher migration rates from E. aggregata to hybrids compared with E. rubida. Taken together, these results indicate a greater genetic input from E. aggregata into the hybrid populations. This asymmetry probably reflects differences in style lengths (E. rubida: ~7 mm, E. aggregata: ~4 mm), which can prevent pollen tubes of smaller-flowered species from fertilizing larger-flowered species. However, analyses of fine-scale genetic structure suggest that localized seed dispersal (<40 m) and greater clustering between hybrid and E. aggregata individuals may also contribute to directional gene flow. Our study highlights that floral traits and the spatial distributions of individuals can be useful predictors of the directionality of interspecific gene flow in plant populations.

Ancient and current gene flow between two distantly related Mediterranean oak species, Quercus suber and Q. ilex.

Urbanization has been linked to amphibian population declines globally. Habitat fragmentation can negatively impact gene flow among populations but what role artificially constructed wetlands have in maintaining gene flow in urban amphibian populations remains uncertain. We assessed gene flow in a population of wood frogs (Lithobates sylvaticus) inhabiting both constructed and natural wetlands located in Edmonton, Alberta, Canada. We genotyped 10 microsatellite loci in 182 frogs from eight wetlands and tested for genetic differentiation between wetlands. We tested if bottlenecks had occurred at constructed wetlands and if there were differences in allelic richness between natural wetlands and constructed wetlands. We found no evidence of bottlenecks, no differences in allelic richness among subpopulations, and no genetic structure within the population. Although significant differences in pair-wise comparisons of allele frequency distributions between wetlands were detected, all F ST values were low (0.003–0.053) and Bayesian clustering indicated the presence of a single genetic cluster. Despite extensive urbanization within our study area, genetic homogeneity has been preserved indicating that it may be possible to use constructed wetlands to maintain amphibian populations and preserve gene flow among subpopulations living within urbanized landscapes.