Molecular Ecology Resources

Published by Wiley
Online ISSN: 1755-0998
Print ISSN: 1755-098X
Publications
clonality V.0.4 is a program for testing heterozygosity-genet size relationships in clonal organisms using a randomization procedure. The software has been developed under the Borland Delphi developing environment and a Windows-executable version is freely downloadable from http://gemi.mpl.ird.fr/SiteSGASS/Prugnolle/ClonalityPage.html. The program compares the observed F(IS) of the population with the F(IS) expected if genets (multilocus genotypes present in multiple copies within the population) were chosen randomly from the set of different multilocus genotypes. The randomization procedure is performed with the same number of genets and the same number of repetitions per genet as what is observed in the original data set.
 
This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls.
 
Examples of inter-individual distance and population diversity interpolating surfaces in the case of Colletes hederae. These graphs are based on input files generated by spads. (a) graph generated with a matrix of average inter-individual distances based on allelic frequency (IID1). (b) graph generated with a matrix of average inter-individual distances based on allelic distances (IID2). (c) graph based on the allelic richness (AR) estimated for each sampled population. (d) graph based on the nucleotide diversity (π) estimated for each sampled population.
SPADS 1.0 (for "Spatial and Population Analysis of DNA Sequences") is a population genetic toolbox for characterizing genetic variability within and among populations from DNA sequences. In view of the drastic increase in genetic information available through sequencing methods, SPADS was specifically designed to deal with multi-locus datasets of DNA sequences. It computes several summary statistics from populations or groups of populations, performs input file conversions for other population genetic programs, and implements locus-by-locus and multi-locus versions of two clustering algorithms to study the genetic structure of populations. The toolbox also includes two Matlab and R functions, GDisPAL and GDivPAL, to display differentiation and diversity patterns across landscapes. These functions aim to generate interpolating surfaces based on multi-locus distance and diversity indices. In the case of multiple loci, such surfaces can represent a useful alternative to multiple pie charts maps traditionally used in phylogeography to represent the spatial distribution of genetic diversity. These coloured surfaces can also be used to compare different datasets or different diversity and/or distance measures estimated on the same dataset. This article is protected by copyright. All rights reserved.
 
Next-generation sequencing technologies are extensively used in the field of molecular microbial ecology to describe taxonomic composition and to infer functionality of microbial communities. In particular, the so-called barcode or metagenetic applications that are based on PCR amplicon library sequencing are very popular at present. One of the problems, related to the utilization of the data of these libraries, is the analysis of reads quality and removal (trimming) of low-quality segments, while retaining sufficient information for subsequent analyses (e.g., taxonomic assignment). Here, we present StreamingTrim, a DNA reads trimming software, written in Java, with which researchers are able to analyze the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way. This software has been developed with the aim to provide a tool capable of trimming amplicon library data, retaining as much as taxonomic information as possible. This software is equipped with a graphical user interface for a user-friendly usage. Moreover, from a computational point of view, StreamingTrim reads and analyzes sequences one by one from an input fastq file, without keeping anything in memory, permitting to run the computation on a normal desktop PC or even a laptop. Trimmed sequences are saved in an output file and a statistics summary is displayed that contains the mean and standard deviation of the length and quality of the whole sequence file. Compiled software, a manual, and example data sets are available under the BSD-2-Clauses License at the GitHub repository at https://github.com/GiBacci/StreamingTrim/. This article is protected by copyright. All rights reserved.
 
Creating a geophylogeny. 
Intraspecific COII mtDNA geophylogeny of the European Bushcricket Ephippiger ephippiger (Spooner & Ritchie 2006) created with geophylbuilder and visualized in arcscene . Geophylogeny tips are individuals and depicted as spheres. Geophylogeny ‘elevation’ is scaled to tree depth and four deep clades colour coded. Droplines connect small tertrahedra representing sample locations to the individuals at the geophylogeny tips. The geophlylogeny is located in south- eastern France and displayed over a digital elevation model; the viewer is looking north- east from the central Pyrenees towards the western Alps and Golfe du Lion. 
Path-enumerated node coding.
Evolution is inherently a spatiotemporal process; however, despite this, phylogenetic and geographical data and models remain largely isolated from one another. Geographical information systems provide a ready-made spatial modelling, analysis and dissemination environment within which phylogenetic models can be explicitly linked with their associated spatial data and subsequently integrated with other georeferenced data sets describing the biotic and abiotic environment. geophylobuilder 1.0 is an extension for the arcgis geographical information system that builds a 'geophylogenetic' data model from a phylogenetic tree and associated geographical data. Geophylogenetic database objects can subsequently be queried, spatially analysed and visualized in both 2D and 3D within a geographical information systems.
 
For evolutionary studies of polyploid species estimates of the genetic identity between species with different degrees of ploidy are particularly required because gene counting in samples of polyploid individuals often cannot be done, e.g., in triploids the phenotype AB can be genotypically either ABB or AAB. We recently suggested a genetic distance measure that is based on phenotype counting and made available the computer program POPDIST. The program provides maximum-likelihood estimates of the genetic identities and distances between polyploid populations, but this approach is not informative for populations within species that only differ in their allele frequencies. We now close this gap by applying the frequencies of shared 'bands' in both populations to Nei's identity measure. Our simulation study demonstrates the close correlation between the band-sharing identity and the genetic identity calculated on the basis of gene frequencies for any degree of ploidy. The new extended version of POPDIST (version 1.2.0) provides the option of choosing either the maximum-likelihood estimator or the band-sharing measure.
 
The barcode of life project has assembled a tremendous number of mitochondrial cytochrome c oxidase I (COI) sequences. Although these sequences were gathered to develop a DNA-based system for species identification, it has been suggested that further biological inferences may also be derived from this wealth of data. Recurrent selective sweeps have been invoked as an evolutionary mechanism to explain limited intraspecific COI diversity, particularly in birds, but this hypothesis has not been formally tested. In this study, I collated COI sequences from previous barcoding studies on birds and tested them for evidence of selection. Using this expanded data set, I re-examined the relationships between intraspecific diversity and interspecific divergence and sampling effort, respectively. I employed the McDonald-Kreitman test to test for neutrality in sequence evolution between closely related pairs of species. Because amino acid sequences were generally constrained between closely related pairs, I also included broader intra-order comparisons to quantify patterns of protein variation in avian COI sequences. Lastly, using 22 published whole mitochondrial genomes, I compared the evolutionary rate of COI against the other 12 protein-coding mitochondrial genes to assess intragenomic variability. I found no conclusive evidence of selective sweeps. Most evidence pointed to an overall trend of strong purifying selection and functional constraint. The COI protein did vary across the class Aves, but to a very limited extent. COI was the least variable gene in the mitochondrial genome, suggesting that other genes might be more informative for probing factors constraining mitochondrial variation within species.
 
We have characterized a set of 106 microsatellite markers in 26-127 individual blue tits (Cyanistes caeruleus), and assigned their location on the zebra finch (Taeniopygia guttata) and on the chicken (Gallus gallus) genome on the basis of sequence homology. Thirty-one markers are newly designed from zebra finch EST (expressed sequence tags) sequences, 22 markers were developed by others from EST sequences using different methods and the remaining 53 loci were previously designed or modified passerine markers. The 106 microsatellite markers are distributed over 26 and 24 chromosomes in the zebra finch and in the chicken genome respectively and the number of alleles varies between 2 and 49. Eight loci deviate significantly from Hardy-Weinberg equilibrium and show a high frequency of null alleles, and three pairs of markers located in the same chromosome appear to be in linkage disequilibrium. With the exception of these few loci, the polymorphic microsatellite markers presented here provide a useful genome-wide resource for population and evolutionary genetic studies of the blue tit, in addition to their potential utility in other passerine birds.
 
Eleven polymorphic microsatellite loci were isolated from the Western Australian millipede Antichiropus variabilis. The number of alleles observed ranged from 2 to 12, with observed heterozygosities ranging from 0.20 to 0.80. All loci were in Hardy-Weinberg equilibrium, and no pairs of loci were in linkage disequilibrium. Many of the loci amplified successfully in eight other Antichiropus species.
 
Crepidula convexa, a calyptreid gastropod with direct embryonic development, changes sex from male to female in the course of its lifetime (protandry). Under sex-allocation theory, male reproductive success should be independent from age and size (a proxy used for age). However, this may be counterbalanced by female cryptic choice or gregarious behaviour. Eleven polymorphic microsatellite loci were thus developed to examine paternity of embryos and larvae. This set of loci appears suitable to carry out paternity analyses due to the high exclusion probability of unrelated males given the maternal genotype.
 
The Chilean isopod Excirolana hirsuticauda is a marine benthic brooder with wide distributional range and low potential for long-distance dispersal. Eleven microsatellite markers were developed for E. hirsuticauda using enriched libraries. Characterization of those loci in 35 individuals from Playa Blanca beach showed high allelic diversity with a mean of 10.9 alleles per locus. The average expected and observed heterozygosities were 0.65 and 0.41. These microsatellite loci are the first published for any Excirolana species and should be useful to study the genetic structure of E. hirsuticauda.
 
Although F(ST) is widely used as a measure of population structure, it has been criticized recently because of its dependency on within-population diversity. This dependency can lead to difficulties in interpretation and in the comparison of estimates among species or among loci and has led to the development of two replacement statistics, F'(ST) and D. F'(ST) is the normal F(ST) standardized by the maximum value it can obtain, given the observed within-population diversity. D uses a multiplicative partitioning of diversity, based on the effective number of alleles rather than on the expected heterozygosity. In this study, we review the relationships between the three classes of statistics (F(ST), F'(ST) and D), their estimation and their properties. We illustrate the relationships between the statistics using a data set of estimates from 84 species taken from the last 4 years of Molecular Ecology. As with F(ST), unbiased estimators are available for the two new statistics D and F'(ST). Here, we develop a new unbiased F'(ST) estimator based on G(ST), which we call G''(ST). However, F'(ST) can be calculated using any F(ST) estimator for which the maximum value can be obtained. As all three statistics have their advantages and their drawbacks, we recommend continued use of F(ST) in combination with either F'(ST) or D. In most cases, F'(ST) would be the best choice among the latter two as it is most suited for inferences of the influence of demographic processes such as genetic drift and migration on genetic population structure.
 
Eleven polymorphic microsatellite markers were developed from a (CA)(n) -enrichment library of the whitegirdled goby (Pterogobius zonoleucus). Polymorphism at these loci ranged from 2 to 12 alleles, and observed and expected heterozygosities from 0.05 to 0.90 and from 0.05 and 0.86, respectively. All loci conformed to Hardy-Weinberg equilibrium, with no significant linkage disequilibrium between all locus pairs. Cross-species amplification tests were successful in P. elapoides, and most loci were polymorphic. These microsatellite markers will be useful in further population genetic studies of both species.
 
Eleven new microsatellite markers were isolated from taro, Colocasia esculenta (L.) Schott, a root crop widely distributed all over the world. Forty-eight primer pairs were designed from a microsatellite-enriched genomic library, of which 11 primer pairs have polymorphisms in 30 individuals tested from a population in China, which revealed two to six alleles per locus with the observed and expected heterozygosity levels ranging from 0 to 0.733 and from 0.381 to 0.731, respectively. These new genetic markers will be useful for the study of taro germplasm management and population evolution in the future.
 
We report on the isolation and evaluation of 11 microsatellites from a widespread eastern North American wetland sedge, Carex scoparia. Loci exhibit 3-9 alleles over five populations and significant F(IS) (0.204-0.717) in most populations. All primers cross-amplify in at least two other species, and 10 cross-amplify in the more distantly related C. stipata. These markers will be used to examine population genetics and patterns of chromosomal diversification in this ecologically important sedge species and its relatives.
 
We developed 11 microsatellite loci for Sagittaria latifolia, an aquatic plant common to wetlands of North America. From an (AG)-enriched library, we identified 66 unique microsatellite sequences for which primers could be designed. Twenty-two loci reliably amplified a clear single band of expected size, and 11 loci were scoreable and polymorphic. For these 11 loci, we genotyped a monoecious and a dioecious population, yielding four to 14 alleles per locus. Three loci exhibited significant linkage disequilibrium leaving eight independent variable loci. Eight loci also amplified in four other Sagittaria species. These microsatellite loci will be useful to compare genetic structure among monoecious and dioecious populations of S. latifolia.
 
We isolated and characterized 11 microsatellite loci in the Mona Island iguana (Cyclura cornuta stejnegeri). Eleven loci exhibit moderate to high allelic diversity (two to 12 alleles, mean = 4.5) and polymorphism (mean observed heterozygosity, 0.56; range, 0.26 to 0.78) in 41 adults. This marker set has low probability of identity and high parentage exclusion power and will be suitable for studies of paternity, social organization and relatedness in this species.
 
Simple sequence repeat (SSR) markers for Fusarium pseudograminearum with 2 to 3 bp repeat motifs were identified by screening the genome database of the related species Fusarium graminearum. Twelve SSRs amplified single loci in both F. graminearum and F. pseudograminearum. Forty F. pseudograminearum and six F. graminearum individual isolates were screened to determine levels of polymorphism, with all SSRs displaying three to 14 alleles across all isolates. Eleven SSRs were polymorphic across F. pseudograminearum isolates tested proving the usefulness of genome databases of closely related species in identifying genetic markers.
 
The flea (Oropsylla hirsuta) is an important vector of the plague bacterium, Yersinia pestis, in black-tailed prairie dog (Cynomys ludovicianus) colonies. We developed 11 anonymous microsatellite primers for O. hirsuta using a subtractive hybridization procedure. All primers were polymorphic exhibiting 4-12 alleles.
 
We report an accurate multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) assay, capable of reproducing gene expression profiles from 16 target genes [12 genes of interest (GOIs) and four reference genes (RGs)] in Acropora millepora, a common reef-building model coral species. The 12 GOIs have known or putative roles in the coral bleaching response, yet the method is not restricted to this particular assay and gene set. The procedure is based on the Beckman Coulter (Fullerton, CA, USA) GenomeLab™ GeXP Genetic Analysis System and bridges the gap between quantitative real-time PCR (qPCR) expression analysis of a single or a small number of genes and microarray gene expression surveys of thousands of genes. Despite large variation among biological replicates, the majority of GOIs were up-regulated (up to 4000%) in most colonies during a laboratory-based thermal stress experiment. Two genes, Nf-kβ2 and MnSod, were consistently up-regulated in all colonies tested, and we therefore propose these as candidate markers useful for population-level evaluations of thermal stress. Our assay provides an important new tool for coral bleaching studies; because of the lower cost, labour and amount of cDNA required compared with singleplex qPCR, population-level studies with large biological replication are feasible.
 
We report the isolation of 11 polymorphic tetranucleotide microsatellite loci in the Egyptian mongoose (Herpestes ichneumon). In a sample of 27 individuals, we observed between 4 and 7 alleles per locus and their observed and expected heterozygosities ranged from 0.37 to 0.85 and from 0.44 to 0.79, respectively. All genotypic frequencies conformed to Hardy-Weinberg equilibrium expectations and there were no instances of linkage disequilibrium detected between pairs of loci.
 
The increased numbers of genetic markers produced by genomic techniques have the potential to both identify hybrid individuals and localize chromosomal regions responding to selection and contributing to introgression. We used restriction-site-associated DNA sequencing to identify a dense set of candidate SNP loci with fixed allelic differences between introduced rainbow trout (Oncorhynchus mykiss) and native westslope cutthroat trout (Oncorhynchus clarkii lewisi). We distinguished candidate SNPs from homeologs (paralogs resulting from whole-genome duplication) by detecting excessively high observed heterozygosity and deviations from Hardy-Weinberg proportions. We identified 2923 candidate species-specific SNPs from a single Illumina sequencing lane containing 24 barcode-labelled individuals. Published sequence data and ongoing genome sequencing of rainbow trout will allow physical mapping of SNP loci for genome-wide scans and will also provide flanking sequence for design of qPCR-based TaqMan(®) assays for high-throughput, low-cost hybrid identification using a subset of 50-100 loci. This study demonstrates that it is now feasible to identify thousands of informative SNPs in nonmodel species quickly and at reasonable cost, even if no prior genomic information is available.
 
The social parasite ant Solenopsis daguerrei infests colonies of several mound-building fire ant species. Twenty-four microsatellite markers were isolated from a repeat-enriched genomic library of S. daguerrei. Eleven loci were polymorphic in this ant with two to six alleles per locus. Expected heterozygosity ranged from 0.0222 to 0.7940 among loci. Most microsatellites amplified successfully across the 11 Solenopsis species tested and will be useful for evolutionary genetic studies in this diverse ant group.
 
Fifteen highly polymorphic microsatellite loci were characterized in the reed bunting, Emberiza schoeniclus. Eleven loci were autosomal and four linked to the Z chromosome. All loci were characterized and tested in 45 unrelated reed buntings from a Swiss population. Autosomal loci displayed seven to 17 and sex-linked loci displayed four to 13 alleles with heterozygosities ranging from 0.756 to 0.933 and from 0.478 to 0.957, respectively. These loci will be used in population genetic and mating system studies of reed buntings.
 
Mean intra- and interspecific genetic distances of evaluated DNA regions based on (a) the number of base differences between sequences and (b) Kimura 2-parameter model of nucleotide substitution.
The taxa used in the study with the number of analy- sed specimens
Characteristics of the DNA barcodes evaluated in this study
The aim of this work was to evaluate the suitability of selected DNA regions in the barcoding of plants, based on the species belonging to the genus Lamium (Lamiaceae). For this purpose, nine chloroplast barcodes, i.e. accD, matK, rbcL, rpoA, rpoB, rpoC1, rpoC2, trnH-psbA, trnL-trnF, as well as ITS nuclear region, and intron of mitochondrial nad5 gene were tested. Among the single-locus barcodes, most effective in the identification of Lamium species was the trnH-psbA spacer and matK gene. The high level of variability and resolving power was also observed in the case of rpoA and rpoC2 genes. Despite the high interspecies variability of ITS region, it turned out to be inapplicable in Lamium identification. An important disadvantage of ITS as a barcode is a limitation of its use in polyploid plants, samples contaminated with fungal material or samples with partially degraded DNA. We have also evaluated five two-locus and two three-locus barcode regions created from a combination of most effective single loci. The best performing barcode combinations were matK+trnH-psbA and matK+rpoA. Both of them had equally high discriminative power to identify Lamium species. This article is protected by copyright. All rights reserved.
 
Eleven polymorphic microsatellite loci for Haliotis diversicolor were isolated and characterized from (CT)(n) - and (AC)(n) -enriched library. They were tested in 24 individuals from a natural population. All of them were polymorphic, with the number of alleles varying between three and 10. The observed heterozygosities and expected heterozygosities ranged from 0.083 to 0.913 and from 0.159 to 0.856, respectively. The 11 isolated microsatellite loci, except SA-JMU6 and SA-JMU12, followed Hardy-Weinberg expectations. Seven sets of primers also amplify in closely related species, H. ovina and H. asinine. These 11 polymorphic microsatellites will be useful for analysing the population structure and genetic diversity in H. diversicolor.
 
We provide primer sequences for 11 new polymorphic microsatellite markers developed in the tropical ant-plant genus Macaranga (Euphorbiaceae), after enrichment cloning of Macaranga tanarius and Macaranga hypoleuca. Allele numbers per locus ranged from two to 16 among 20 accessions of M. tanarius, and from three to 10 among 22 accessions of M. hypoleuca. Observed and expected heterozygosities ranged from 0.150 to 0.900 and from 0.375 to 0.894 in M. tanarius, and from 0.545 to 1.000 and from 0.434 to 0.870 in M. hypoleuca, respectively. Six of the 11 primer pairs successfully cross-amplified polymorphic polymerase chain reaction products in Macaranga winkleri.
 
Vallisneria americana Michaux (wild celery) is currently a target of submersed aquatic vegetation restoration efforts in the Chesapeake Bay watershed. To aid these efforts, we have developed 11 polymorphic microsatellite markers to assess the distribution and degree of genetic diversity in both restored and naturally occurring populations in the Chesapeake Bay. In 59 individuals from two populations, we detected two to 10 total alleles per locus. Observed heterozygosity ranged from 0.125 to 0.929, and two loci exhibited significant deviations from Hardy-Weinberg equilibrium in at least one of the populations assayed.
 
Venn diagram showing the number of pinniped microsatellite sequences aligned in the dog, cat and giant panda genomes.
Pinniped microsatellite flanking sequences that have at least 80% homologous sequence in each of dog (blue), cat (red) and giant panda (green) genomes are shown. Each vertical bar appertains to a specific pinniped microsatellite, and each coloured bar represents the percentage sequence homologous between that species and the pinniped sequence. The graph indicates which pinniped microsatellites are the most conserved between species and therefore those that should be most successful in cross-species amplification.
A schematic showing wider homology and conservation of chromosomal structure between the dog, cat, giant panda and pinniped genomes. A 9.4 Mb region of dog chromosomes 15 and 33 is shown, with pinniped microsatellites and genes of interest placed in their assigned location in the dog genome. ‘Start’ indicates the start of the region on the dog genome where the cat and giant panda sequence retrieved through alignment to pinniped microsatellites is homologous. ‘Stop’ indicates where this sequence similarity ends; however, this is because of the short length of cat and giant panda contigs, and similarity likely extends beyond these limits.
Understanding genetic variation responsible for phenotypic differences in natural populations is significantly hampered by a lack of genomic data for many species. Levels of variation can, however, be estimated using microsatellite markers, which may be useful for relating individual fitness to genetic diversity. Prior studies have demonstrated correlations between heterozygosity and individual fitness in some species. These correlations are sometimes driven by a subset of markers, and it is unclear whether this is because those markers best reflect genome-wide heterozygosity, or whether they are linked to fitness-related genes. Differentiating between these scenarios is hindered when the genomic location of markers is unknown. Here, we develop a predicted genomic map of pinniped microsatellite loci based on conservation of primary sequence and genomic location between dog, cat and giant panda. We mapped 210 of 260 (81%) microsatellites from pinnipeds to locations in dog, cat and giant panda genomes. Based on the demonstrable synteny between the genomes of closely related taxa within the Carnivora, we use these data to identify those microsatellites with the greatest chance of cross-species amplification success and demonstrate successful amplification of 21 of 26 loci for cat, dog and two seal species. We also demonstrate the potential to identify candidate genes that may underpin the functional relationship with individual fitness. Overall, we show that this approach provides a rapid and robust method to elucidate genome organisation for nonmodel organisms and have established a resource that facilitates further genetic research on pinnipeds that also has wider applicability to other carnivores.
 
Eleven microsatellites were characterized for Semicossyphus pulcher (California sheephead) using an enrichment protocol. The number of alleles varied from three to 14 for a sample of 40 individuals from two populations. Expected heterozygosities ranged from 0.311 to 0.891. All loci but one were in Hardy-Weinberg equilibrium. No evidence for linkage disequilibrium was observed. These polymorphic microsatellites will be useful for genetic diversity and connectivity analyses of S. pulcher.
 
We describe the isolation of 11 polymorphic trinucleotide microsatellite loci from the stonefly Arcynopteryx compacta. Loci were highly variable with 3 to 14 alleles (mean = 6.45). Observed heterozygosity ranged from 0 to 0.867. Seven loci showed significant deviation from Hardy-Weinberg equilibrium across both populations. There was no evidence for null alleles, and thus, Hardy-Weinberg departures could have resulted from genetic structure between populations or subpopulations. No linkage between loci was found. The 11 loci should prove highly informative for population genetic studies.
 
Eleven polymorphic microsatellite loci were isolated and developed from the black fly, Simulium negativum, a member of the Simulium arcticum sibling species complex. The observed heterozygosity of the 11 loci ranged from 0.03 to 0.83. The number of alleles per locus ranged from 8 to 19. Significant linkage disequilibria were encountered only for the primer pairs BF7-1 with BF7-5 and BF6-32 with BF7-16. Presumably, these microsatellite loci can be used to study genetic structure within the entire S. arcticum complex.
 
Eleven polymorphic microsatellite loci were described for the mangrove crab, Ucides cordatus, an important fishery resource on the Brazilian coast. The number of alleles observed at each locus varied between eight and 23. Observed and expected mean heterozygosities were 0.791 and 0.893 respectively. Amplification of all loci was highly successful, under the same polymerase chain reaction conditions. With the exception of P2D3, all loci adhered to the assumptions of the Hardy-Weinberg equilibrium and did not present deviations reflecting linkage disequilibrium. Given this, these markers will be extremely useful in future management programmes for U. cordatus stocks.
 
We have characterized 11 polymorphic microsatellite loci in the invasive ant Solenopsis invicta. Primer pairs were evaluated on fire ants collected from monogyne mounds in Lauderdale County, Mississippi. The observed and effective number of alleles ranged from two to six and from 1.31 to 2.64, respectively. The observed and expected heterozygosity values ranged from 0.1613 to 0.7826 and from 0.1491 to 0.6242, respectively. The polymorphism information content of the microsatellites ranged from 0.1482 to 0.6208. Probability tests indicated significant deviations from the Hardy-Weinberg equilibrium at three loci. Pairwise tests did not detect linkage disequilibrium between any pair of loci.
 
Caribbean reef-building corals in the genus Acropora have been declining dramatically since the 1980s and are now listed as threatened. The study of their complex reproductive system (mixed asexual and sexual) and their population structure requires highly polymorphic nuclear genetic markers. Of eight previously developed microsatellite loci for A. palmata, only five behaved in a Mendelian fashion and only four reliably amplified the sister species, A. cervicornis. Here, nine novel microsatellite markers are presented that dramatically increase the power to distinguish between asexual and sexual reproductive events and may help to refine population boundaries and gene flow across their ranges.
 
Thirteen newly developed tri- and tetranucleotide repeat microsatellite markers were developed for Lahontan cutthroat trout (Oncorhynchus clarki henshawi), a threatened subspecies endemic to the Lahontan hydrographic basin in the western USA. These loci are highly polymorphic with five to 30 alleles per locus and observed heterozygosities ranging from 0.4 to 0.7. Cross-species amplification of these markers was most successful in the closely related rainbow trout, Oncorhynchus mykiss, with only three loci amplifying in brown trout, Salmo trutta. Nonoverlapping allelic distributions for many of these loci among the six salmonid species screened suggest these markers may be useful for hybrid determination.
 
Thirteen polymorphic microsatellite loci are described for the South American freshwater fish Percichthys trucha. Number of alleles per locus ranged from two to 21 and observed heterozygosities ranged from 0.304 to 0.915 in a sample of 47 individuals from four different sampling locations.
 
Thirteen new microsatellite loci were isolated and tested on two land snail species, Trochulus villosus and T. sericeus (Pulmonata: Hygromiidae), resulting in a set of eight polymorphic markers for each species. The expected heterozygosity was high for all loci and species (between 0.616 and 0.944). Such levels of variability will allow detailed insights into the population genetic structure of some Trochulus species.
 
A suite of 13 polymorphic tri- and tetranucleotide microsatellite loci were isolated from the ahermatypic deep-sea coral, Lophelia pertusa. Among 51 individuals collected from three disjunct oceanic regions, allelic diversity ranged from six to 38 alleles and averaged 9.1 alleles per locus. Observed heterozygosity ranged from 9.1 to 96.8% and averaged 62.3% in the Gulf of Mexico population. For some loci, amplification success varied among collections, suggesting regional variation in priming site sequences. Four loci showed departures from Hardy-Weinberg equilibrium in certain collections which may reflect nonrandom mating.
 
Characteristics of 13 polymorphic microsatellite markers isolated from Neochamaelea pulverulenta (Cneoraceae) populations at Teno Bajo (TE) and Punta de Juan Centella (CE) (Tenerife, Canary Islands) 
We report 13 polymorphic nuclear microsatellite loci for Neochamaelea pulverulenta (Cneoraceae) using an enriched-library approach. Although this plant species is tetraploid, expected patterns for tetrasomic segregation were completely absent, and all loci analysed showed a diploid pattern of inheritance. We detected a total of 102 alleles in 57 individuals genotyped (mean number of alleles per locus was 7.85). The values of observed and expected heterozygosities ranged from 0.193 to 0.737 and 0.425 to 0.812 respectively. Disomic segregation, levels of polymorphism and the exclusionary power of the developed markers render them readily applicable for parentage assignment of dispersed seeds, and for analyses of spatial genetic structure and population connectivity.
 
Thirteen microsatellite loci were isolated from a size-selected genomic library of the surfperch (Ditrema temmincki Bleeker). All loci displayed a high degree of length polymorphism, as observed in the total number of alleles per locus (two to 23) and a high degree of estimated heterozygosity, ranging from 0.080 to 0.893. The primers developed for D. temmincki were also tested for their ability to amplify homologous sequences in D. viride and Neoditrema ransonetii. Distinct differences were observed among three species of surfperches, in both genetic variability and the frequency distribution of the alleles.
 
Probability of identity [P (ID) ] and mean expected heterozy- gosity (H E ) calculated for each focal species using the selected panel of nine microsatellite loci
We tested 47 tetranucleotide microsatellite loci developed for the domestic dog in four species of Neotropical canids, aiming to produce a standardized set that could be successfully used even in noninvasive samples across this group. We identified 13 suitable loci, nine of which constitute a standardized set for all species. Considering only the ideal panel of nine loci, the mean expected heterozygosity (averaged across species) per locus ranged from 0.58 to 0.92 (overall mean 0.76), and the maximum probability of identity value was 1.3 × 10(-9) . This set of loci has a great potential for application in evolutionary, ecological and conservation studies.
 
A set of 13 simple sequence repeat markers was developed from D. trimaculatus genomic DNA, tested for D. auripinnis and characterized using 40 individuals per species. All the loci were polymorphic with a number of alleles ranging from three to 30. Observed heterozygosities varied from 0.23 to 0.89 for D. trimaculatus and from 0.11 to 0.85 for D. auripinnis. Early results show that these will be powerful markers for the study of ecological and evolutionary mechanism in this coral reef fish species complex.
 
Comparison between mass proportion of three fish species fed to seals (triangles) vs. overall proportions of sequence reads recovered (box plots). Box plots were generated from the sequence read proportions from 39 individual scat samples (Run I – 100 bp) using combined forward and reverse reads.
Bar plots showing proportions of fish sequences recovered from 39 individual seal scats in sequenced in Run I (blue = capelin, red = herring, green = mackerel). Each bar represents an individual sample, and proportions of forward and reverse reads are shown separately. Data were filtered to retain either sequences >100 bp (top) or >90 bp (bottom). Proportions of three fish species by mass in the diet are shown as dotted lines on plots.
Mean sequence counts for fish in 39 individual seal scats for various levels of quality filtering (Run I – 100 bp; forward and reverse reads are shown separately).
Plots depicting the interacting effects of three different primer tags (A, B, C) and eight different quality filter cut-off values on proportions of fish sequences detected in 39 scats (Run I – 100 bp). Sequence proportions for each tag (represented by different shapes) at a given quality score cut-off (varies along the x-axis) and add up to 1. Results for forward and reverse read directions are displayed separately. Error bars represent standard error.
A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals' diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis.
 
Fifteen polymorphic microsatellites were developed for the Karoo scrub-robin, Cercotrichas coryphaeus. Here we describe and characterize microsatellite variation of 13 autosomal loci and two Z-linked loci in 42 individuals from two distinct South African populations. The number of alleles per locus varied from three to 13 and values of observed heterozygosity ranged from 0.318 to 0.900. These loci will be used to test hypotheses relating to fine-scale social structure and mating strategies in this cooperatively breeding species.
 
Thirteen polymorphic microsatellite loci were developed for the northern pine processionary moth (Thaumetopoea pinivora) and tested for cross-amplification in seven other species within the Thaumetopoea family. Number of alleles ranged from two to 10 when at least 28 individuals from one population were screened and one locus, Thapin06, appears to be sex linked. Expected heterozygosity ranged from 0.094 to 0.856 and observed heterozygosity ranged from 0.097 to 0.806. Amplification success varied between sister species, with two up to seven loci being successfully amplified. The described loci will be valuable for studying the population genetic structure and dispersal behaviour of this forest pest.
 
Genetic clustering algorithms require a certain amount of data to produce informative results. In the common situation that individuals are sampled at several locations, we show how sample group information can be used to achieve better results when the amount of data is limited. New models are developed for the structure program, both for the cases of admixture and no admixture. These models work by modifying the prior distribution for each individual's population assignment. The new prior distributions allow the proportion of individuals assigned to a particular cluster to vary by location. The models are tested on simulated data, and illustrated using microsatellite data from the CEPH Human Genome Diversity Panel. We demonstrate that the new models allow structure to be detected at lower levels of divergence, or with less data, than the original structure models or principal components methods, and that they are not biased towards detecting structure when it is not present. These models are implemented in a new version of structure which is freely available online at http://pritch.bsd.uchicago.edu/structure.html.
 
Key features of the user interface of NEESTIMATOR v2. 
Summary of results comparing performance of effective size estimators on simulated data with true N e = 100
Distribution of estimates of effective population size ( ^ N e ) from three single-sample estimators, based on 100 replicate, simulated data sets using 20 'microsatellite' loci (top panel, with up to 10 alleles each) or 200 'SNP' loci (bottom panel, with up to two alleles each). True N e was 100. The numbers above the vertical bars for ^ N e > 200 indicate the number of those estimates that were infinitely large. The microsatellite analyses used P Crit = 0.02; the SNP analyses used P Crit = 0. 
NeEstimator v2 is a completely revised and updated implementation of software that produces estimates of contemporary effective population size, using several different methods and a single input file. NeEstimator v2 includes three single-sample estimators (updated versions of the linkage disequilibrium and heterozygote-excess methods, and a new method based on molecular coancestry), as well as the two-sample (moment-based temporal) method. New features include the following: (i) an improved method for accounting for missing data; (ii) options for screening out rare alleles; (iii) confidence intervals for all methods; (iv) the ability to analyse data sets with large numbers of genetic markers (10 000 or more); (v) options for batch processing large numbers of different data sets, which will facilitate cross-method comparisons using simulated data; and (vi) correction for temporal estimates when individuals sampled are not removed from the population (Plan I sampling). The user is given considerable control over input data and composition, and format of output files. The freely available software has a new JAVA interface and runs under MacOS, Linux and Windows.
 
We screened the genome of Xanthomonas citri pv. citri strain 306 for tandem repeats. A multiplex polymerase chain reaction protocol was used to assess the genetic diversity of 239 strains of X. citri pv. citri from Asia. The total number of alleles per locus ranged from three to 20. Using pooled data sets, 223 different haplotypes were identified. Successful amplifications were obtained at most loci for seven other X. citri pathovars. This typing scheme is expected to be useful at different spatial scales for population studies of pathovars of X. citri, several of which cause plant diseases of economic importance.
 
Fourteen polymorphic microsatellite loci (di, tetra and di-tetra complexes) were developed for the argasid tick Ornithodoros coriaceus. Polymorphism was assessed for 56 individuals from two populations separated by ~95 km. All loci were polymorphic (X = 7, range 3-17 alleles). All loci were in Hardy-Weinberg equilibrium except for one locus (OrC 8) in a single population (P < 0.00119, after Bonferroni correction for multiple tests).
 
Top-cited authors
Laurent Excoffier
  • Universität Bern
Jinliang Wang
  • Zoological Society of London
Pierre Taberlet
  • Université Grenoble Alpes
Éric Coissac
  • University Grenoble-Alpes
Itay Mayrose
  • Tel Aviv University