Rise of the machines--recommendations for ecologists when using next generation sequencing for microsatellite development

Genome-wide characterization of microsatellites in cobia Rachycentron canadum (Linnaeus, 1766): Survey and analysis of their abundance and diversity

The cobia Rachycentron canadum, mainly distributed in the warm waters of tropical and subtropical regions around the world, remains a fish of considerable economic importance. Detailed diversity and the number of microsatellite sequences in the cobia genome are still unintelligible. The primary aim of this work was to identify and quantify the miscellaneous SSR sequences in the cobia genome. More than 280,000 sequences were sequenced and screened using next-generation sequencing technology and microsatellite identification. Perfect mononucleotide repeats, dinucleotide microsatellites, and trinucleotide microsatellites contain (A)10 /(T)10 , (AC)6 /(TG)6 , and (AAT)5-32 as the largest number of motifs in each type of microsatellite, respectively. The tetranucleotide and pentanucleotide microsatellites (TTM and PTM) consist of the largest number of motifs of both (ATCT)5-32 and (TCAT)5-31 in TTMs, and (CTCTC)5-9 in PTMs, whereas the hexanucleotide microsatellites are rarely observed in the cobia genome. All c. 38000 sequences of composite microsatellites are extremely diverse, including compound (11.71%), interrupted compound (71.77%), complex (0.45%), and interrupted complex (16.07%). In this study, we developed a convenient and useful recording system for writing down and categorizing diverse composite microsatellite types. This system will provide great support for exploring repeat origins, evolutionary mechanisms, and the application of polymorphic microsatellites.

Genome survey sequencing and mining of genome-wide microsatellite markers in yellow-billed babbler (Turdoides affinis)

Turdoides affinis is a species of group dwelling old world passerine of family Leiothrichidae. Unavailability of genome-wide sequence and species-specific molecular markers have hindered comprehensive understanding of cooperative breeding behaviour in T. affinis. Therefore, we generated genome-wide microsatellite markers through whole genome short read sequencing of T. affinis. A total of 68.8 gigabytes of paired-end raw data were sequenced containing 195,067,054 reads. Total sequenced reads spanned a coverage of 17X with genome size of 1.18 Gb. A large number of microsatellite markers (265,297) were mined in the T. affinis genome using Krait, and 50 most informative markers were identified and validated further. In-silico PCR results validated 47 markers. Of these 47 markers, five were randomly selected and validated in-vitro in twelve individuals of T. affinis. Genotyping data on these five loci estimated observed heterozygosity (H₀) and expected heterozygosity (H_e) ratios between 0.333 - 0.833 and 0.851-0.906, respectively. Effective allele size ranged from 6.698 to 10.667, inbreeding coefficient of the population ranged from 0.080 to 0.631 and null allele frequency was calculated at 0.055 to 0.303. Polymorphic information content of all the five loci varied between 0.850 and 0.906. Probabilities of exclusion and identity across 5 loci was estimated to be 0.95 and 0.0036, respectively. All the loci showed significant adherence to Hardy-Weinberg equilibrium. The microsatellite markers reported in this study will facilitate future population genetics studies on T. affinis and other congeneric species.

Limited phylogeographic and genetic connectivity in Acacia species of low stature in an arid landscape

Widespread plant species are expected to maintain genetic diversity and gene flow via pollen and seed dispersal. Stature is a key life history trait that affects seed and potentially pollen dispersal, with limited stature associated with limited dispersal and greater genetic differentiation. We sampled Hill's tabletop wattle (Acacia hilliana) and curry wattle (Acacia spondylophylla), two co-distributed, widespread, Acacia shrubs of low stature, across the arid Pilbara region of north-western Australia. Using chloroplast sequence and nuclear microsatellite data we evaluated patterns of population genetic and phylogeographic diversity and structure, demographic signals, ratios of pollen to seed dispersal, evidence for historical refugia, and association between elevation and diversity. Results showed strong phylogeographic (chloroplast, G ST = 0.831 and 0.898 for A. hilliana and A. spondylophylla, respectively) and contemporary (nuclear, F ST = 0.260 and 0.349 for A. hilliana and A. spondylophylla, respectively) genetic structure in both species. This indicates limited genetic connectivity via seed and pollen dispersal associated with Acacia species of small stature compared to taller tree and shrub acacias across the Pilbara bioregion. This effect of stature on genetic structure is superimposed on moderate levels of genetic diversity that were expected based on widespread ranges (haplotype diversity h = 25 and 12; nuclear diversity He = 0.60 and 0.47 for A. hilliana and A. spondylophylla, respectively). Contemporary genetic structure was congruent at the greater landscape scale, especially in terms of strong genetic differentiation among geographically disjunct populations in less elevated areas. Measures of diversity and connectivity were associated with traits of greater geographic population proximity, population density, population size, and greater individual longevity, and some evidence for range expansion in A. hilliana. Results illustrate that low stature is associated with limited dispersal and greater patterns of genetic differentiation for congenerics in a common landscape and highlight the complex influence of taxon-specific life history and ecological traits to seed and pollen dispersal.

SSR individual identification system construction and population genetics analysis for Chamaecyparis formosensis

Chamaecyparis formosensis is an endemic species of Taiwan, threatened from intensive use and illegal felling. An individual identification system for C. formosensis is required to provide scientific evidence for court use and deter illegal felling. In this study, 36 polymorphic simple sequence repeat markers were developed. By applying up to 28 non-linked of the developed markers, it is calculated that the cumulative random probability of identity (CP_I) is as low as 1.652 × 10^–12, and the identifiable population size is up to 60 million, which is greater than the known C. formosensis population size in Taiwan. Biogeographical analysis data show that C. formosensis from four geographic areas belong to the same genetic population, which can be further divided into three clusters: SY (Eastern Taiwan), HV and GW (Northwestern Taiwan), and MM (Southwestern Taiwan). The developed system was applied to assess the provenance of samples with 88.44% accuracy rate and therefore can serve as a prescreening tool to reduce the range required for comparison. The system developed in this study is a potential crime-fighting tool against illegal felling.

A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi-sample genomic data

Simple sequence repeats (SSRs) are widely used genetic markers in ecology, evolution, and conservation even in the genomics era, while a general limitation to their application is the difficulty of developing polymorphic SSR markers. Next-generation sequencing (NGS) offers the opportunity for the rapid development of SSRs; however, previous studies developing SSRs using genomic data from only one individual need redundant experiments to test the polymorphisms of SSRs. In this study, we designed a pipeline for the rapid development of polymorphic SSR markers from multi-sample genomic data. We used bioinformatic software to genotype multiple individuals using resequencing data, detected highly polymorphic SSRs prior to experimental validation, significantly improved the efficiency and reduced the experimental effort. The pipeline was successfully applied to a globally threatened species, the brown eared-pheasant (Crossoptilon mantchuricum), which showed very low genomic diversity. The 20 newly developed SSR markers were highly polymorphic, the average number of alleles was much higher than the genomic average. We also evaluated the effect of the number of individuals and sequencing depth on the SSR mining results, and we found that 10 individuals and ~10X sequencing data were enough to obtain a sufficient number of polymorphic SSRs, even for species with low genetic diversity. Furthermore, the genome assembly of NGS data from the optimal number of individuals and sequencing depth can be used as an alternative reference genome if a high-quality genome is not available. Our pipeline provided a paradigm for the application of NGS technology to mining and developing molecular markers for ecological and evolutionary studies.

Development of polymorphic microsatellites for genetic studies of white scar oyster (Crassostrea belcheri) using paired-end shotgun sequencing

White scar oyster Crassostrea belcheri is a commercially important bivalve species in Thailand. Appropriate genetic markers are needed for effective management to elevate its production efficiency. Type II microsatellites of C. belcheri were identified and characterized using an Illumina paired-end shotgun sequencing. A total of 14,743,710 reads were generated for which 198,849 reads containing microsatellites and 217,998 microsatellite loci were found. Twenty out of 60 microsatellite loci (33.33%) were polymorphic and these microsatellites were further tested against DNA bulks (N = 10 each) originating from 7 different geographic locations in Thai waters. Results indicated that newly developed microsatellites can be used for genetic diversity analysis of C. belcheri. Genotyping of C. belcheri collected from Surat Thani (Gulf of Thailand; N = 50) were performed. The number of alleles per locus ranged from 2 to 12 (average = 4.95). Observed and expected heterozygosities ranged from 0.0000 to 0.9400 (average = 0.3419) and 0.1139 to 0.8190 (average = 0.5844), respectively. Genome information and 20 newly isolated microsatellites will facilitate further studies in population genetics, stock management, and genetic improvement of C. belcheri in Thailand.

Mitochondrial Markers Identify a Genetic Boundary of the Green Tiger Prawn (Penaeus semisulcatus) in the Indo-Pacific Ocean

A population genetics study of the commercially important Green Tiger Prawn (Penaeus semisulcatus) was conducted in the Indo-Pacific Ocean with a focus on the Indo-Malay Archipelago waters of the South China Sea (SCS), Sulu Sea (SLS), Celebes Sea (CLS) and the Strait of Malacca (SOM), the latter being the main waterway that connects the Indian Ocean with the Pacific Ocean. A 548-base-pair region of mitochondrial COI and 571 base pairs of the control region (CR) were analysed in 284 specimens from 15 locations. Genetic divergences (Tamura 3-parameter) for COI ranged from 0.1% to 7.2% and CR 2.3% to 21.7%, with Bagan Pasir (BGP) in central SOM being the most genetically different from other populations (COI: 3.3-4.2%; CR: 7.1-16.5%). All populations were differentiated into two lineages with a genetic break in the vicinity of BGP; Lineage I comprised populations south of this site (SCS, SLS, CLS and part of SOM) and Lineage II comprised populations north of BGP (part of the SOM). Specifically, most individuals of Bagan Pasir (BGP) and another site just south of it, Batu Pahat (BPT), clustered in Lineage I, while all SOM populations to the north of these sites clustered in Lineage II. The BGP population is believed to be a mixed gene pool between the two lineages. The results could be attributed to the fluctuations of Pleistocene sea levels and a possible influence of the One Fathom Bank in SOM. High genetic diversity was recorded, π (Lineage I: COI: 3.4%; CR: 7.4%) (Lineage II: COI: 3.8%; CR: 12.6%) and, h (Lineage I: COI: 0.81; CR: 1.0) (Lineage II: COI: 0.57; CR: 0.99). Demographic statistics revealed that both lineages underwent a sudden expansion and consequent stabilisation in genetic variability. The findings of this study have wide implications for fisheries in the Indo-Pacific. The increased sampling effort within a narrower geographical scale by the current study permitted a precise locality of the genetic break for this species within the Indo-Pacific Ocean to be identified. The substantial genetic diversity within both lineages should be considered in fishery management and aquaculture development programs of this species in this region.

Extensive Genetic Connectivity and Historical Persistence Are Features of Two Widespread Tree Species in the Ancient Pilbara Region of Western Australia

Phylogeographic studies can be used as a tool to understand the evolutionary history of a landscape, including the major drivers of species distributions and diversity. Extensive research has been conducted on phylogeographic patterns of species found in northern hemisphere landscapes that were affected by glaciations, yet the body of literature for older, unaffected landscapes is still underrepresented. The Pilbara region of north-western Australia is an ancient and vast landscape that is topographically complex, consisting of plateaus, gorges, valleys, and ranges, and experiences extreme meteorological phenomena including seasonal cyclonic activity. These features are expected to influence patterns of genetic structuring throughout the landscape either by promoting or restricting the movement of pollen and seed. Whilst a growing body of literature exists for the fauna endemic to this region, less is known about the forces shaping the evolution of plant taxa. In this study we investigate the phylogeography of two iconic Pilbara tree species, the Hamersley Bloodwood (Corymbia hamersleyana) and Western Gidgee (Acacia pruinocarpa), by assessing patterns of variation and structure in several chloroplast DNA regions and nuclear microsatellite loci developed for each species. Gene flow was found to be extensive in both taxa and there was evidence of long-distance seed dispersal across the region (pollen to seed ratios of 6.67 and 2.96 for C. hamersleyana and A. pruinocarpa, respectively), which may result from flooding and strong wind gusts associated with extreme cyclonic activity. Both species possessed high levels of cpDNA genetic diversity in comparison to those from formerly glaciated landscapes (C. hamersleyana = 14 haplotypes, A. pruinocarpa = 37 haplotypes) and showed evidence of deep lineage diversification occurring from the late Miocene, a time of intensifying aridity in this landscape that appears to be a critical driver of evolution in Pilbara taxa. In contrast to another study, we did not find evidence for topographic features acting as refugia for the widely sampled C. hamersleyana.

Infestation Pattern and Population Dynamics of the Tropical Bed Bug, Cimex hemipterus (F.) (Hemiptera: Cimicidae) Based on Novel Microsatellites and mtDNA Markers

The tropical bed bug, Cimex hemipterus (F.), has now emerged as an important public health pest in the tropics. Despite its alarming infestation rate, the information on its population genetics remains scarce. Here, we described the infestation structure and population dynamics of C. hemipterus in the tropics, especially Malaysia and Singapore, based on eight novel microsatellites and two mtDNA markers, including cytochrome c oxidase I (COI) and 16S rRNA genes. Across populations, microsatellite data revealed high genetic diversity with significant genetic differentiation and restricted gene flow. Analysis within populations revealed evidence of a recent bottleneck. Nonetheless, elevated genetic diversity in nearly all populations suggests that the propagule in C. hemipterus populations were much diverse, distantly related (mean r = 0.373), and not significantly inbred (mean F_IS = 0.24) than that observed in Cimex lectularius from previous studies. We observed seven mtDNA haplotypes across the 18 populations studied (Hd = 0.593) and several populations displayed more than one matrilineal descent. The two markers were generally congruent in suggesting a common, genetically diverse (especially at the nuclear region) source population with possibilities of multiple introductions for the bed bug populations in the present study.

Development and characterization of microsatellite markers in Rosy-faced and other lovebirds (Agapornis spp.) using next-generation sequencing

Agapornis are a group of small African parrots that are heavily traded around the world. They are invasive species in many places, but some of them are listed as Vulnerable or Near Threatened. However, the genetic tools for assessing inter-individual relationships, population structure, and genetic diversity of these birds are very limited. Therefore, we developed polymorphic microsatellite markers in A. roseicollis and tested the transferability on 5 lovebird species including A. personatus, A. nigrigenis, A. fischeri, A. pullarius, and A. canus, and two closely related outgroups (i.e. Bolbopsittacus lunulatus and Loriculus galgulus). We first performed whole-genome re-sequencing on five individuals of A. roseicollis to identify potential polymorphic loci. Out of 37 loci tested in 11 A. roseicollis, 27 loci were demonstrated to be polymorphic, with the number of the alleles ranging from 2 to 7 (mean = 3.963). The observed heterozygosity ranged from 0 to 0.875 (mean = 0.481) and expected heterozygosity ranged from 0.233 to 0.842 (mean = 0.642). Five loci (Agro-A13, p < 0.01; Agro-A15, p < 0.05; Agro-A43, p < 0.05, Agro-A65, p < 0.05; Agro-A67, p < 0.05) were detected to deviate from Hardy-Weinberg equilibrium, with the presence of null alleles suggested in locus Agro-A13 and Agro-A77. The exclusion powers for PE1 and PE2 are 0.997 and 0.999, respectively. The 27 novel polymorphic markers developed here will be useful for parentage and kinship assignment and population genetics study in Agapornis, and provide a tool for scientific research, captive breeding industry, and invasion and conservation management of these species.

Characterisation and cross-amplification of 42 microsatellite markers in two Amphiprion species (Pomacentridae) and a natural hybrid anemonefish to inform genetic structure within a hybrid zone

The hybrid anemonefish, Amphiprion leucokranos, is known to be the product of ongoing, introgressive hybridization between parent taxa Amphiprion sandaracinos and Amphiprion chrysopterus. Hybridization is an important evolutionary phenomenon contributing to biodiversity within marine systems, where hybrid zones provide ideal systems in which to study hybridization events. Here, a suite of 42 Amphiprion microsatellite markers (including development of 8 novel markers) were cross-amplified in individuals from parent taxa and hybrid populations to facilitate investigation into the relatedness of hybridizing species across the A. leucokranos hybrid zone. Analysis revealed 15, 20 and 24 highly polymorphic loci (PIC > 0.5) in the two parent species and hybrid, respectively, for use in population genetic and parentage studies, with 305 unique alleles found overall (ranging from 1 to 13 alleles per locus) and 7 alleles per locus on average. Observed and expected heterozygosities ranged from 0.000 to 1.000 and 0.000 to 0.978, respectively. Significant deviations from Hardy-Weinberg equilibrium were found in eight loci, possibly due to relatedness among samples or the presence of null alleles. Use of the suite of markers tested here will provide valuable insights into the contemporary population structure and introgression among species and hybrids within the Amphiprion leucokranos hybrid zone, as well as inform future ecological and evolutionary studies of anemonefishes more broadly.

Genome-wide developed microsatellites reveal a weak population differentiation in the hoverfly Eupeodes corollae (Diptera: Syrphidae) across China

The hoverfly, Eupeodes corollae, is a worldwide natural enemy of aphids and a plant pollinator. To provide insights into the biology of this species, we examined its population genetic structure by obtaining 1.15-GB random genomic sequences using next-generation sequencing and developing genome-wide microsatellite markers. A total of 79,138 microsatellite loci were initially isolated from the genomic sequences; after strict selection and further testing of 40 primer pairs in eight individuals, 24 polymorphic microsatellites with high amplification rates were developed. These microsatellites were used to examine the population genetic structure of 96 individuals from four field populations collected across southern to northern China. The number of alleles per locus ranged from 5 to 13 with an average of 8.75; the observed and expected heterozygosity varied from 0.235 to 0.768 and from 0.333 to 0.785, respectively. Population genetic structure analysis showed weak genetic differentiation among the four geographical populations of E. corollae, suggesting a high rate of gene flow reflecting likely widespread migration of E. corollae in China.

Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome

Tianma (Gastrodia elata Blume) has unique biological characteristics and high medicinal value. The wild resource of G. elata is being overutilized and should be conserved as it is already included in the list of endangered species in China. The population size of cultivated G. elata is small because of domestication bottleneck. Therefore, it is of utmost importance to evolve high-quality varieties and conserve wild resources of G. elata. In this study, we sequenced tuber transcriptomes of three major cultivated sub-species of Gastrodia elata, namely G. elata BI. f. elata, G. elata Bl. f. glauca S. Chow, and G. elata Bl. f. Viridis, and obtained about 7.8G clean data. The assembled high-quality reads of three sub-species were clustered into 56,884 unigenes. Of these, 31,224 (54.89%), 25,733 (45.24%), 22,629 (39.78%), and 11,856 (20.84%) unigenes were annotated by Nr, Swiss-Port, Eukaryotic Ortholog Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Here, a total of 3766 EST-SSRs and 128,921 SNPs were identified from the unigenes. The results not only offer huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.

Polymorphic microsatellite loci and partial mitogenome for the Chestnut-bellied Seed-finch Sporophila angolensis (Aves, Passeriformes) using next generation sequencing

Brazil is one of the major contributors to international trade in wildlife and species of the bird genus Sporophila are currently under threat due to illegal trade. Microsatellite loci and mitochondrial DNA constitute important molecular markers for population genetics studies and parentage analyses, and hold great potential to help authorities manage illegal trafficking and control commercial breeders. We describe and characterize 19 polymorphic microsatellite loci and recover part of the mitochondrial genome for Sporophila angolensis using massive parallel sequencing with the Illumina platform. DNA sequencing resulted in a dataset with 2,379,295 paired reads, of which 392 were mapped to the mitogenome of S. maximiliani, resulting in a partial mitogenome of 16,785 bp for S. angolensis. The microsatellite search identified a total of 4737 loci, from which 27 primer pairs were tested on 24 individuals of unknown geographic origin. Nineteen of the 27 loci were successfully amplified and exhibited high levels of genetic variation, with a mean of 11.2 alleles per locus, a mean observed heterozygosity of 0.588 and a mean expected heterozygosity of 0.852. About half of the loci showed significant evidence for the presence of a null allele and significant deviation from Hardy-Weinberg equilibrium; the remaining eight loci had high paternity exclusion probabilities and low identity probabilities. The high levels of polymorphism for these loci, as well as their high paternity exclusion probability and low identity probability, indicate that they hold potential for parentage analyses and population genetics studies of S. angolensis.

Population Genetic Analyses Using 10 New Polymorphic Microsatellite Loci Confirms Genetic Subdivision within the Olm, Proteus anguinus

We provide a comparative population genetic study of the elusive amphibian, Proteus anguinus, by comparing the genetic diversity and divergence among 4 cave populations (96 individuals) sampled in the Dinaric Karst of Croatia. We developed 10 variable microsatellite markers using pyrosequencing and applied them to the 4 selected populations belonging to 4 different cave systems. The results showed strong genetic differentiation between the 4 caves corroborating with previous findings suggesting that Proteus might comprise several unrecognized taxa. Our results confirmed that gene flow should be high within the caves, whereas it is low between hydrographic systems since geological periods. Finally, we conclude that the high genetic subdivision suggests the necessity of treating the 4 studied Proteus populations as evolutionary significant units.

Microsatellite development from genome skimming and transcriptome sequencing: comparison of strategies and lessons from frog species

Background

Even though microsatellite loci frequently have been isolated using recently developed next-generation sequencing (NGS) techniques, this task is still difficult because of the subsequent polymorphism screening requires a substantial amount of time. Selecting appropriate polymorphic microsatellites is a critical issue for ecological and evolutionary studies. However, the extent to which assembly strategy, read length, sequencing depth, and library layout produce a measurable effect on microsatellite marker development remains unclear. Here, we use six frog species for genome skimming and two frog species for transcriptome sequencing to develop microsatellite markers, and investigate the effect of different isolation strategies on the yield of microsatellites.

Results

The results revealed that the number of isolated microsatellites increases with increased data quantity and read length. Assembly strategy could influence the yield and the polymorphism of microsatellite development. Larger k-mer sizes produced fewer total number of microsatellite loci, but these loci had a longer repeat length, suggesting greater polymorphism. However, the proportion of each type of nucleotide repeats was not affected; dinucleotide repeats were always the dominant type. Finally, the transcriptomic microsatellites displayed lower levels of polymorphisms and were less abundant than genomic microsatellites, but more likely to be functionally linked loci.

Conclusions

These observations provide deep insight into the evolution and distribution of microsatellites and how different isolation strategies affect microsatellite development using NGS.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5329-y) contains supplementary material, which is available to authorized users.

OzPythonPlex: An optimised forensic STR multiplex assay set for the Australasian carpet python (Morelia spilota)

Reptile species, and in particular snakes, are protected by national and international agreements yet are commonly handled illegally. To aid in the enforcement of such legislation, we report on the development of three 11-plex assays from the genome of the carpet python to type 24 loci of tetra-nucleotide and penta-nucleotide repeat motifs (pure, compound and complex included). The loci range in size between 70 and 550 bp. Seventeen of the loci are newly characterised with the inclusion of seven previously developed loci to facilitate cross-comparison with previous carpet python genotyping studies. Assays were optimised in accordance with human forensic profiling kits using one nanogram template DNA. Three loci are included in all three of the multiplex reactions as quality assurance markers, to ensure sample identity and genotyping accuracy is maintained across the three profiling assays. Allelic ladders have been developed for the three assays to ensure consistent and precise allele designation. A DNA reference database of allele frequencies is presented based on 249 samples collected from throughout the species native range. A small number of validation tests are conducted to demonstrate the utility of these multiplex assays. We suggest further appropriate validation tests that should be conducted prior to the application of the multiplex assays in criminal investigations involving carpet pythons.

Non-invasive genetic censusing and monitoring of primate populations

Knowing the density or abundance of primate populations is essential for their conservation management and contextualizing socio-demographic and behavioral observations. When direct counts of animals are not possible, genetic analysis of non-invasive samples collected from wildlife populations allows estimates of population size with higher accuracy and precision than is possible using indirect signs. Furthermore, in contrast to traditional indirect survey methods, prolonged or periodic genetic sampling across months or years enables inference of group membership, movement, dynamics, and some kin relationships. Data may also be used to estimate sex ratios, sex differences in dispersal distances, and detect gene flow among locations. Recent advances in capture-recapture models have further improved the precision of population estimates derived from non-invasive samples. Simulations using these methods have shown that the confidence interval of point estimates includes the true population size when assumptions of the models are met, and therefore this range of population size minima and maxima should be emphasized in population monitoring studies. Innovations such as the use of sniffer dogs or anti-poaching patrols for sample collection are important to ensure adequate sampling, and the expected development of efficient and cost-effective genotyping by sequencing methods for DNAs derived from non-invasive samples will automate and speed analyses.

Adding loci improves phylogeographic resolution in red mangroves despite increased missing data: comparing microsatellites and RAD-Seq and investigating loci filtering

The widespread adoption of RAD-Seq data in phylogeography means genealogical relationships previously evaluated using relatively few genetic markers can now be addressed with thousands of loci. One challenge, however, is that RAD-Seq generates complete genotypes for only a small subset of loci or individuals. Simulations indicate that loci with missing data can produce biased estimates of key population genetic parameters, although the influence of such biases in empirical studies is not well understood. Here we compare microsatellite data (8 loci) and RAD-Seq data (six datasets ranging from 239 to 25,198 loci) from red mangroves (Rhizophora mangle) in Florida to evaluate how different levels of data filtering influence phylogeographic inferences. For all datasets, we calculated population genetic statistics and evaluated population structure, and for RAD-Seq datasets, we additionally examined population structure using coalescence. We found higher F_ST using microsatellites, but that RAD-Seq-based estimates approached those based on microsatellites as more loci with more missing data were included. Analyses of RAD-Seq datasets resolved the classic Gulf-Atlantic coastal phylogeographic break, which was not significant in the microsatellite analyses. Applying multiple levels of filtering to RAD-Seq datasets can provide a more complete picture of potential biases in the data and elucidate subtle phylogeographic patterns.

Genetics and Hatchery Management: A Parentage-based Tagging Approach to Blueback Herring Conservation

Blueback Herring Alosa aestivalis populations throughout the East Coast have declined precipitously since the late 1980s and were listed as a Species of Concern in 2006 by the National Oceanic and Atmospheric Administration. Natural resource agencies are attempting to restore this species to viable and sustainable levels with fry stockings cultured in hatcheries. To evaluate the long-term contribution of stockings to populations, agencies need an accurate method to track these stocking efforts. Genetic parentage-based tagging is recognized as a feasible means of assessing hatchery contribution of stocked fish to rivers of interest. However, Blueback Herring lack a reliable set of genetic markers to conduct parentage-based tagging. To this end, we analyzed previously described microsatellites as well as new microsatellite markers identified through NextGeneration sequencing to create a suite of 14 Blueback Herring markers useful for parentage-based tagging. The markers were successful in parentage analysis for Blueback Herring collected from the Chowan River, North Carolina. An additional challenge in the management of Blueback Herring is the ability to phenotypically distinguish Blueback Herring from the closely related Alewife Alosa pseudoharengus. Furthermore, recent studies provide evidence that these two species, collectively referred to as river herring, may be hybridizing with one another in some systems. Microsatellite marker AsaC334 can be utilized to discriminate between the two species, as well as to identify their F1 hybrids, thereby providing another genetic tool for hatchery management.

Development and Validation of Polymorphic Microsatellite Loci for the NA2 Lineage of Phytophthora ramorum from Whole Genome Sequence Data

Phytophthora ramorum is the causal agent of sudden oak death and sudden larch death, and is also responsible for causing ramorum blight on woody ornamental plants. Many microsatellite markers are available to characterize the genetic diversity and population structure of P. ramorum. However, only two markers are polymorphic in the NA2 lineage, which is predominant in Canadian nurseries. Microsatellite motifs were mined from whole-genome sequence data of six P. ramorum NA2 isolates. Of the 43 microsatellite primer pairs selected, 13 loci displayed different allele sizes among the four P. ramorum lineages, 10 loci displayed intralineage variation in the EU1, EU2, and/or NA1 lineages, and 12 microsatellites displayed polymorphism in the NA2 lineage. Genotyping of 272 P. ramorum NA2 isolates collected in nurseries in British Columbia, Canada, from 2004 to 2013 revealed 12 multilocus genotypes (MLGs). One MLG was dominant when examined over time and across sampling locations, and only a few mutations separated the 12 MLGs. The NA2 population observed in Canadian nurseries also showed no signs of sexual recombination, similar to what has been observed in previous studies. The markers developed in this study can be used to assess P. ramorum inter- and intralineage genetic diversity and generate a better understanding of the population structure and migration patterns of this important plant pathogen, especially for the lesser-characterized NA2 lineage.

Isolation and characterisation of microsatellites for the endangered Slater’s skink, Liopholis slateri (Squamata : Scincidae), via next-generation sequencing

We characterised 14 new polymorphic microsatellite loci for the endangered lizard Liopholis slateri. Initially, 454 shotgun sequencing was used to identify 46 loci, which were trialled for amplification. Subsequently, 14 of these loci were screened for variation in 21 individuals from scat-derived DNA samples collected from Owen Springs Reserve in central Australia. All 14 loci were polymorphic, with observed heterozygosity ranging from 0.19 to 0.86 and the number of alleles per locus ranging from 2 to 10. These loci will be useful in understanding the genetic variation and connectivity within and among extant L. slateri populations.

Characterization of 11 Polymorphic Microsatellite Markers for Black Drummer (Girella elevata) Developed Using 454 Next-Generation Sequencing

Black Drummer (Girella elevata) is a long-lived fish species that experiences considerable recreational fishing pressure, although managers lack a clear understanding of stock structure and dispersal patterns that are essential for the design, implementation, and administration of fisheries stock management. We used 454 sequencing to identify and develop 11 microsatellite primer pairs from 31 G. elevata All loci were found to be polymorphic, with the number of alleles detected ranging from 4 to 8 and observed heterozygosity ranging from 0.19 to 0.87. These markers will be used to assess the genetic diversity and connectivity throughout the range of G. elevata, which can assist in the development of population management strategies.

Characterization, development and multiplexing of microsatellite markers in three commercially exploited reef fish and their application for stock identification

Thirty-four microsatellite loci were isolated from three reef fish species; golden snapper Lutjanus johnii, blackspotted croaker Protonibea diacanthus and grass emperor Lethrinus laticaudis using a next generation sequencing approach. Both IonTorrent single reads and Illumina MiSeq paired-end reads were used, with the latter demonstrating a higher quality of reads than the IonTorrent. From the 1–1.5 million raw reads per species, we successfully obtained 10–13 polymorphic loci for each species, which satisfied stringent design criteria. We developed multiplex panels for the amplification of the golden snapper and the blackspotted croaker loci, as well as post-amplification pooling panels for the grass emperor loci. The microsatellites characterized in this work were tested across three locations of northern Australia. The microsatellites we developed can detect population differentiation across northern Australia and may be used for genetic structure studies and stock identification.

Development and characterization of 24 polymorphic microsatellite loci for the freshwater fish Ichthyoelephas longirostris (Characiformes: Prochilodontidae)

The Neotropical freshwater fish Ichthyoelephas longirostris (Characiformes: prochilodontidae) is a short-distance migratory species endemic to Colombia. This study developed for the first time a set of 24 polymorphic microsatellite loci by using next-generation sequencing to explore the population genetics of this commercially exploited species. Nineteen of these loci were used to assess the genetic diversity and structure of 193 I. longirostris in three Colombian rivers of the Magdalena basin. Results showed that a single genetic stock circulates in the Cauca River, whereas other single different genetic stock is present in the rivers Samaná Norte and San Bartolomé-Magdalena. Additionally, I. longirostris was genetically different among and across rivers. This first insight about the population genetic structure of I. longirostris is crucial for monitoring the genetic diversity, the management and conservation of its populations, and complement the genetic studies in Prochilodontidae.

Investigation of population structure in Gulf of Mexico Seepiophila jonesi (Polychaeta, Siboglinidae) using cross-amplified microsatellite loci

BACKGROUND

Vestimentiferan tubeworms are some of the most recognizable fauna found at deep-sea cold seeps, isolated environments where hydrocarbon rich fluids fuel biological communities. Several studies have investigated tubeworm population structure; however, much is still unknown about larval dispersal patterns at Gulf of Mexico (GoM) seeps. As such, researchers have applied microsatellite markers as a measure for documenting the transport of vestimentiferan individuals. In the present study, we investigate the utility of microsatellites to be cross-amplified within the escarpiid clade of seep vestimentiferans, by determining if loci originally developed for Escarpia spp. could be amplified in the GoM seep tubeworm, Seepiophila jonesi. Additionally, we determine if cross-amplified loci can reliably uncover the same signatures of high gene flow seen in a previous investigation of S. jonesi.

METHODS

Seventy-seven S. jonesi individuals were collected from eight seep sites across the upper Louisiana slope (<1,000 m) in the GoM. Forty-eight microsatellite loci that were originally developed for Escarpia laminata (18 loci) and Escarpia southwardae (30 loci) were tested to determine if they were homologous and polymorphic in S. jonesi. Loci found to be both polymorphic and of high quality were used to test for significant population structuring in S. jonesi.

RESULTS

Microsatellite pre-screening identified 13 (27%) of the Escarpia loci were homologous and polymorphic in S. jonesi, revealing that microsatellites can be amplified within the escarpiid clade of vestimentiferans. Our findings uncovered low levels of heterozygosity and a lack of genetic differentiation amongst S. jonesi from various sites and regions, in line with previous investigations that employed species-specific polymorphic loci on S. jonesi individuals retrieved from both the same and different seep sites. The lack of genetic structure identified from these populations supports the presence of significant gene flow via larval dispersal in mixed oceanic currents.

DISCUSSION

The ability to develop "universal" microsatellites reduces the costs associated with these analyses and allows researchers to track and investigate a wider array of taxa, which is particularly useful for organisms living at inaccessible locations such as the deep sea. Our study highlights that non-species specific microsatellites can be amplified across large evolutionary distances and still yield similar findings as species-specific loci. Further, these results show that S. jonesi collected from various localities in the GoM represents a single panmictic population, suggesting that dispersal of lecithotrophic larvae by deep sea currents is sufficient to homogenize populations. These data are consistent with the high levels of gene flow seen in Escarpia spp., which advocates that differences in microhabitats of seep localities lead to variation in biogeography of separate species.

Microsatellite Length Scoring by Single Molecule Real Time Sequencing - Effects of Sequence Structure and PCR Regime

Microsatellites are DNA sequences consisting of repeated, short (1–6 bp) sequence motifs that are highly mutable by enzymatic slippage during replication. Due to their high intrinsic variability, microsatellites have important applications in population genetics, forensics, genome mapping, as well as cancer diagnostics and prognosis. The current analytical standard for microsatellites is based on length scoring by high precision electrophoresis, but due to increasing efficiency next-generation sequencing techniques may provide a viable alternative. Here, we evaluated single molecule real time (SMRT) sequencing, implemented in the PacBio series of sequencing apparatuses, as a means of microsatellite length scoring. To this end we carried out multiplexed SMRT sequencing of plasmid-carried artificial microsatellites of varying structure under different pre-sequencing PCR regimes. For each repeat structure, reads corresponding to the target length dominated. We found that pre-sequencing amplification had large effects on scoring accuracy and error distribution relative to controls, but that the effects of the number of amplification cycles were generally weak. In line with expectations enzymatic slippage decreased proportionally with microsatellite repeat unit length and increased with repetition number. Finally, we determined directional mutation trends, showing that PCR and SMRT sequencing introduced consistent but opposing error patterns in contraction and expansion of the microsatellites on the repeat motif and single nucleotide level.

The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century

Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers.

A new resource for the development of SSR markers: Millions of loci from a thousand plant transcriptomes

PREMISE OF THE STUDY

The One Thousand Plant Transcriptomes Project (1KP, 1000+ assembled plant transcriptomes) provides an enormous resource for developing microsatellite loci across the plant tree of life. We developed loci from these transcriptomes and tested their utility.

METHODS AND RESULTS

Using software packages and custom scripts, we identified microsatellite loci in 1KP transcriptomes. We assessed the potential for cross-amplification and whether loci were biased toward exons, as compared to markers derived from genomic DNA. We characterized over 5.7 million simple sequence repeat (SSR) loci from 1334 plant transcriptomes. Eighteen percent of loci substantially overlapped with open reading frames (ORFs), and electronic PCR revealed that over half the loci would amplify successfully in conspecific taxa. Transcriptomic SSRs were approximately three times more likely to map to translated regions than genomic SSRs.

CONCLUSIONS

We believe microsatellites still have a place in the genomic age-they remain effective and cost-efficient markers. The loci presented here are a valuable resource for researchers.

Understanding the Spatial Scale of Genetic Connectivity at Sea: Unique Insights from a Land Fish and a Meta-Analysis

Quantifying the spatial scale of population connectivity is important for understanding the evolutionary potential of ecologically divergent populations and for designing conservation strategies to preserve those populations. For marine organisms like fish, the spatial scale of connectivity is generally set by a pelagic larval phase. This has complicated past estimates of connectivity because detailed information on larval movements are difficult to obtain. Genetic approaches provide a tractable alternative and have the added benefit of estimating directly the reproductive isolation of populations. In this study, we leveraged empirical estimates of genetic differentiation among populations with simulations and a meta-analysis to provide a general estimate of the spatial scale of genetic connectivity in marine environments. We used neutral genetic markers to first quantify the genetic differentiation of ecologically-isolated adult populations of a land dwelling fish, the Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal is the only probable means of connectivity among populations. We then compared these estimates to simulations of a range of marine dispersal scenarios and to collated FST and distance data from the literature for marine fish across diverse spatial scales. We found genetic connectivity at sea was extensive among marine populations and in the case of A. arnoldorum, apparently little affected by the presence of ecological barriers. We estimated that ~5000 km (with broad confidence intervals ranging from 810-11,692 km) was the spatial scale at which evolutionarily meaningful barriers to gene flow start to occur at sea, although substantially shorter distances are also possible for some taxa. In general, however, such a large estimate of connectivity has important implications for the evolutionary and conservation potential of many marine fish communities.

Microsatellites for microbiologists

Microsatellites are repeating sequences of 2-6base pairs of DNA. Currently, they are used as molecular markers in many organisms, specifically in genetic studies analyzing kinship and population structure. In addition, they can be used to study gene duplication and/or deletion. Although they are used in studies on microorganisms including fungi, bacteria, protists, and archaea, it appears that these genetic markers are not being utilized to their full microbiological potential. Microsatellites have many advantages over other genetic markers currently in use as they are in general species specific, and therefore, cross-contamination by nontarget organisms is rare. Furthermore, microsatellites are suitable for use with fast and cheap DNA extraction methods, with ancient DNA or DNA from hair and fecal samples used in noninvasive sampling, making them widely available as a genetic marker. Microsatellites have already proven to be a useful tool for evolutionary studies of pathogenic microorganisms such as Candida albicans and Helicobacter pylori, and the onset of new sequencing techniques (such as 454, PACBIO, and mini-ion sequencing) means the ability to detect such markers will become less time consuming and cheaper, thus further expanding their potential to answer important microbial ecology questions.

Developing informative microsatellite markers for non-model species using reference mapping against a model species' genome

Microsatellites have a wide range of applications from behavioral biology, evolution, to agriculture-based breeding programs. The recent progress in the next-generation sequencing technologies and the rapidly increasing number of published genomes may greatly enhance the current applications of microsatellites by turning them from anonymous to informative markers. Here we developed an approach to anchor microsatellite markers of any target species in a genome of a related model species, through which the genomic locations of the markers, along with any functional genes potentially linked to them, can be revealed. We mapped the shotgun sequence reads of a non-model rodent species Apodemus semotus against the genome of a model species, Mus musculus, and presented 24 polymorphic microsatellite markers with detailed background information for A. semotus in this study. The developed markers can be used in other rodent species, especially those that are closely related to A. semotus or M. musculus. Compared to the traditional approaches based on DNA cloning, our approach is likely to yield more loci for the same cost. This study is a timely demonstration of how a research team can efficiently generate informative (neutral or function-associated) microsatellite markers for their study species and unique biological questions.

Characterisation of 12 microsatellite loci in the Vietnamese commercial clam Lutraria rhynchaena Jonas 1844 (Heterodonta: Bivalvia: Mactridae) through next-generation sequencing

The marine clam Lutraria rhynchaena is gaining popularity as an aquaculture species in Asia. Lutraria populations are present in the wild throughout Vietnam and several stocks have been established and translocated for breeding and aquaculture grow-out purposes. In this study, we demonstrate the feasibility of utilising Illumina next-generation sequencing technology to streamline the identification and genotyping of microsatellite loci from this clam species. Based on an initial partial genome scan, 48 microsatellite markers with similar melting temperatures were identified and characterised. The 12 most suitable polymorphic loci were then genotyped using 51 individuals from a population in Quang Ninh Province, North Vietnam. Genetic variation was low (mean number of alleles per locus = 2.6; mean expected heterozygosity = 0.41). Two loci showed significant deviation from Hardy-Weinberg equilibrium (HWE) and the presence of null alleles, but there was no evidence of linkage disequilibrium among loci. Three additional populations were screened (n = 7-36) to test the geographic utility of the 12 loci, which revealed 100 % successful genotyping in two populations from central Vietnam (Nha Trang). However, a second population from north Vietnam (Co To) could not be successfully genotyped and morphological evidence and mitochondrial variation suggests that this population represents a cryptic species of Lutraria. Comparisons of the Qang Ninh and Nha Trang populations, excluding the 2 loci out of HWE, revealed statistically significant allelic variation at 4 loci. We reported the first microsatellite loci set for the marine clam Lutraria rhynchaena and demonstrated its potential in differentiating clam populations. Additionally, a cryptic species population of Lutraria rhynchaena was identified during initial loci development, underscoring the overlooked diversity of marine clam species in Vietnam and the need to genetically characterise population representatives prior to microsatellite development. The rapid identification and validation of microsatellite loci using next-generation sequencing technology warrant its integration into future microsatellite loci development for key aquaculture species in Vietnam and more generally, aquaculture countries in the South East Asia region.

Isolation and characterisation of 12 polymorphic microsatellite loci for the threatened mound-building malleefowl, Leipoa ocellata (Aves : Megapodiidae)

Using 454 pyrosequencing and genomic enrichment techniques we developed 12 polymorphic markers for the endangered megapode, the malleefowl (Leipoa ocellata). Pyrosequencing on a 454 instrument resulted in 65 536 reads, with 3469 containing microsatellite repeats. Of these, 232 contained unique flanking sequences and had more than 8 repeat motifs. We chose 13 loci based on reliability of amplification and, from these, 12 unlinked loci were selected for genotyping. In a single population (n = 19), the 12 markers were moderately polymorphic (number of alleles per locus range = 3–7) and showed moderate to high levels of heterozygosity (0.285–0.882). Nine microsatellite primer pairs developed from the brush turkey (Alectura lathami), the closest living relative of the malleefowl in the family, Megapodiidae, failed to reliably amplify malleefowl DNA.

Characterisation of microsatellites for Litoria nannotis (Amphibia : Hylidae), an endangered waterfall frog endemic to the Australian Wet Tropics

Litoria nannotis is an endangered waterfall frog from the wet tropics region in north Queensland that has suffered significant population declines due to the emerging fungal disease known as chytridiomycosis. The species has two deeply divergent lineages, and we used 454 shotgun sequencing of DNA extracted from one individual of the northern lineage to identify and design PCR primers for 576 microsatellite loci. Thirty markers were tested for amplification success and variability in a population sample from each lineage. Of these, 17 were found to be polymorphic in the northern lineage and 10 loci were polymorphic in the southern lineage. Numbers of alleles per locus ranged from 2 to 14 (mean = 6.47, s.d. = 4.02) for the northern lineage (17 polymorphic loci), and from 2 to 8 (mean = 5.40, s.d. = 2.55) in the southern lineage (10 polymorphic loci). Levels of heterozygosity were high in both lineages (northern mean HE = 0.63, s.d. = 0.21, range = 0.27–0.89; southern mean HE = 0.57, s.d. = 0.25, range = 0.18–0.81). These loci will be useful in understanding the genetic variation and connectivity amongst populations of this species recovering from mass population declines due to disease.

Population genetics of the koala (Phascolarctos cinereus) in north-eastern New South Wales and south-eastern Queensland

Habitat loss and fragmentation are key threats to local koala (Phascolarctos cinereus) populations. Broad-scale management is suboptimal for koalas because distribution models are not easily generalised across regions. Therefore, it is imperative that data relevant to local management bodies are available. Genetic data provides important information on gene flow and potential habitat barriers, including anthropogenic disturbances. Little genetic data are available for nationally significant koala populations in north-eastern New South Wales, despite reported declines due to urbanisation and habitat loss. In this study, we develop 14 novel microsatellite loci to investigate koala populations in north-eastern New South Wales (Port Macquarie, Coffs Harbour, Tyagarah, Ballina) and south-eastern Queensland (Coomera). All locations were significantly differentiated (FST = 0.096–0.213; FʹST = 0.282–0.582), and this pattern was not consistent with isolation by distance (R2 = 0.228, P = 0.058). Population assignment clustered the more northern populations (Ballina, Tyagarah and Coomera), suggesting contemporary gene flow among these sites. For all locations, low molecular variation among (16%) rather than within (84%) sites suggests historical connectivity. These results suggest that koala populations in north-eastern New South Wales and south-eastern Queensland are experiencing contemporary impediments to gene flow, and highlight the importance of maintaining habitat connectivity across this region.

Characterization of the complete mitochondrial genome and a set of polymorphic microsatellite markers through next-generation sequencing for the brown brocket deer Mazama gouazoubira

The complete mitochondrial genome of the brown brocket deer Mazama gouazoubira and a set of polymorphic microsatellite markers were identified by 454-pyrosequencing. De novo genome assembly recovered 98% of the mitochondrial genome with a mean coverage of 9-fold. The mitogenome consisted of 16,356 base pairs that included 13 protein-coding genes, two ribosomal subunit genes, 22 transfer RNAs and the control region, as found in other deer. The genetic divergence between the mitogenome described here and a previously published report was ∼0.5%, with the control region and ND5 gene showing the highest intraspecific variation. Seven polymorphic loci were characterized using 15 unrelated individuals; there was moderate genetic variation across most loci (mean of 5.6 alleles/locus, mean expected heterozygosity = 0.70), with only one locus deviating significantly from Hardy-Weinberg equilibrium, probably because of null alleles. Marker independence was confirmed with tests for linkage disequilibrium. The genetic variation of the mitogenome and characterization of microsatellite markers will provide useful tools for assessing the phylogeography and population genetic patterns in M. gouazoubira, particularly in the context of habitat fragmentation in South America.