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Sequence capture and restriction site associated DNA sequencing (RAD-Seq) are two genomic enrichment strategies for applying next-generation sequencing technologies to systematics studies.At shallowtimescales, such as within species, RAD-Seq has been widely adopted among researchers, although there has been little discussion of the potential limitations and benefits of RAD-Seq and sequence capture. We discuss a series of issues that may impact the utility of sequence capture and RAD-Seq data for shallow systematics in non-model species.We review prior studies that used both methods, and investigate differences between the methods by re-analyzing existing RAD-Seq and sequence capture data sets from a Neotropical bird (Xenops minutus). We suggest that the strengths of RAD-Seq data sets for shallow systematics are the wide dispersion of markers across the genome, the relative ease and cost of laboratory work, the deep coverage and read overlap at recovered loci, and the high overall information that results. Sequence capture's benefits include flexibility and repeatability in the genomic regions targeted, success using low-quality samples, more straightforward read orthology assessment, and higher per-locus information content. The utility of a method in systematics, however, rests not only on its performance within a study, but on the comparability of data sets and inferences with those of prior work. In RADSeq data sets, comparability is compromised by low overlap of orthologous markers across species and the sensitivity of genetic diversity in a data set to an interaction between the level of natural heterozygosity in the samples examined and the parameters used for orthology assessment. In contrast, sequence capture of conserved genomic regions permits interrogation of the same loci across divergent species, which is preferable for maintaining comparability among data sets and studies for the purpose of drawing general conclusions about the impact of historical processes across biotas.We argue that sequence capture should be given greater attention as a method of obtaining data for studies in shallow systematics and comparative phylogeography. [ABSTRACT FROM AUTHOR]

Comparative genetic studies of non-model organisms are transforming rapidly due to major advances in sequencing technology. A limiting factor in these studies has been the identification and screening of orthologous loci across an evolutionarily distant set of taxa. Here, we evaluate the efficacy of genomic markers targeting ultraconserved DNA elements (UCEs) for analyses at shallow evolutionary timescales. Using sequence capture and massively parallel sequencing to generate UCE data for five co-distributed Neotropical rainforest bird species, we recovered 776–1516 UCE loci across the five species. Across species, 53–77% of the loci were polymorphic, containing between 2.0 and 3.2 variable sites per polymorphic locus, on average. We performed species tree construction, coalescent modeling, and species delimitation, and we found that the five co-distributed species exhibited discordant phylogeographic histories. We also found that species trees and divergence times estimated from UCEs were similar to the parameters obtained from mtDNA. The species that inhabit the understory had older divergence times across barriers, contained a higher number of cryptic species, and exhibited larger effective population sizes relative to the species inhabiting the canopy. Because orthologous UCEs can be obtained from a wide array of taxa, are polymorphic at shallow evolutionary timescales, and can be generated rapidly at low cost, they are an effective genetic marker for studies investigating evolutionary patterns and processes at shallow timescales. [Birds; coalescent theory; isolation-with-migration; massively parallel sequencing; Neotropics; next-generation sequencing; phylogeography; SNPs.] [ABSTRACT FROM PUBLISHER]

Background Urogenital schistosomiasis caused by Schistosoma haematobium is widely distributed across Africa and is increasingly being targeted for control. Genome sequences and population genetic parameters can give insight into the potential for population- or species-level drug resistance. Microsatellite DNA loci are genetic markers in wide use by Schistosoma researchers, but there are few primers available for S. haematobium. Methods We sequenced 1,058,114 random DNA fragments from clonal cercariae collected from a snail infected with a single Schistosoma haematobium miracidium. We assembled and aligned the S. haematobium sequences to the genomes of S. mansoni and S. japonicum, identifying microsatellite DNA loci across all three species and designing primers to amplify the loci in S. haematobium. To validate our primers, we screened 32 randomly selected primer pairs with population samples of S. haematobium. Results We designed >13,790 primer pairs to amplify unique microsatellite loci in S. haematobium, (available at http://www.cebio.org/projetos/schistosoma-haematobium-genome). The three Schistosoma genomes contained similar overall frequencies of microsatellites, but the frequency and length distributions of specific motifs differed among species. We identified 15 primer pairs that amplified consistently and were easily scored. We genotyped these 15 loci in S. haematobium individuals from six locations: Zanzibar had the highest levels of diversity; Malawi, Mauritius, Nigeria, and Senegal were nearly as diverse; but the sample from South Africa was much less diverse. Conclusions About half of the primers in the database of Schistosoma haematobium microsatellite DNA loci should yield amplifiable and easily scored polymorphic markers, thus providing thousands of potential markers. Sequence conservation among S. haematobium, S. japonicum, and S. mansoni is relatively high, thus it should now be possible to identify markers that are universal among Schistosoma species (i.e., using DNA sequences conserved among species), as well as other markers that are specific to species or species-groups (i.e., using DNA sequences that differ among species). Full genome-sequencing of additional species and specimens of S. haematobium, S. japonicum, and S. mansoni is desirable to better characterize differences within and among these species, to develop additional genetic markers, and to examine genes as well as conserved non-coding elements associated with drug resistance. [ABSTRACT FROM AUTHOR]

Although massively parallel sequencing has facilitated large-scale DNA sequencing, comparisons among distantly related species rely upon small portions of the genome that are easily aligned. Methods are needed to efficiently obtain comparable DNA fragments prior to massively parallel sequencing, particularly for biologists working with non-model organisms. We introduce a new class of molecular marker, anchored by ultraconserved genomic elements (UCEs), that universally enable target enrichment and sequencing of thousands of orthologous loci across species separated by hundreds of millions of years of evolution. Our analyses here focus on use of UCE markers in Amniota because UCEs and phylogenetic relationships are well-known in some amniotes. We perform an in silico experiment to demonstrate that sequence flanking 2030 UCEs contains information sufficient to enable unambiguous recovery of the established primate phylogeny. We extend this experiment by performing an in vitro enrichment of 2386 UCE-anchored loci from nine, nonmodel avian species. We then use alignments of 854 of these loci to unambiguously recover the established evolutionary relationships within and among three ancient bird lineages. Because many organismal lineages have UCEs, this type of genetic marker and the analytical framework we outline can be applied across the tree of life, potentially reshaping our understanding of phylogeny at many taxonomic levels. [ABSTRACT FROM AUTHOR]

The diversity of available 2nd and 3rd generation DNA sequencing platforms is increasing rapidly. Costs for these systems range from <$100 000 to more than $1 000 000, with instrument run times ranging from minutes to weeks. Extensive trade-offs exist among these platforms. I summarize the major characteristics of each commercially available platform to enable direct comparisons. In terms of cost per megabase (Mb) of sequence, the Illumina and SOLiD platforms are clearly superior (≤$0.10/Mb vs. >$10/Mb for 454 and some Ion Torrent chips). In terms of cost per nonmultiplexed sample and instrument run time, the Pacific Biosciences and Ion Torrent platforms excel, with the 454 GS Junior and Illumina MiSeq also notable in this regard. All platforms allow multiplexing of samples, but details of library preparation, experimental design and data analysis can constrain the options. The wide range of characteristics among available platforms provides opportunities both to conduct groundbreaking studies and to waste money on scales that were previously infeasible. Thus, careful thought about the desired characteristics of these systems is warranted before purchasing or using any of them. Updated information from this guide will be maintained at: and . [ABSTRACT FROM AUTHOR]

Research on populations from radioactively contaminated areas around Chornobyl has produced ambiguous results for the presence of radiation effects. More studies are needed to provide information on whether radiation exposure at Chornobyl significantly affected genetic diversity in natural populations of various taxa. Eleven and nine variable microsatellite loci were used to test for differences in genetic diversity between reference and Chornobyl populations of two cattail species ( Typha angustifolia and Typha latifolia, respectively) from Ukraine. Our purpose was to determine whether radiation had a significant impact on genetic diversities of the Chornobyl Typha populations, or if their genetic composition might be better explained by species demography and/or changes in population dynamics, mainly in sexual and asexual reproduction. Populations closest to the reactor had increased genetic diversities and high number of genets, which likely were due to factors other than radiation including increased gene flow among Chornobyl populations, enhanced sexual reproduction within populations, and/or origin of the genets from seed bank. Both Typha species also demonstrated small but significant effects associated with latitude, geographical regions, and watersheds. Typha's demography in Ukraine possibly varies with these three factors, and the small difference between Chornobyl and reference populations of T. latifolia detected after partitioning the total genetic variance between them is probably due primarily to these factors. However, the positive correlations of several genetic characteristics with radionuclide concentrations suggest that radiation may have also affected genetics of Chornobyl Typha populations but much less than was expected considering massive contamination of the Chornobyl area. [ABSTRACT FROM AUTHOR]

We describe polymerase chain reaction (PCR) primers and conditions to amplify eight dinucleotide, one trinucleotide and 14 tetranucleotide microsatellite DNA loci isolated from the northern bobwhite ( Colinus virginianus). The PCR primers were tested on 16 individuals collected from a population located within the Red Hills region of south Georgia and north Florida. The 23 primer pairs developed in this study yielded an average of 6.5 alleles per locus (range 2–11), an average observed heterozygosity of 0.47 (range 0.06–0.94) and average polymorphic information content of 0.60 (range 0.06–0.85). [ABSTRACT FROM AUTHOR]

Presents a study that investigated the genetic variation of Gulf Coast sandhill cranes using mitochondrial DNA sequencing. DNA isolation and amplification; Discussion of the restriction enzyme survey; Information on the morphological measurements to classify sandhill cranes from the Gulf Coast of Texas.

We isolated nine microsatellite loci from the Guanacaste tree ( Enterolobium cyclocarpum) and optimized them for future research on breeding populations of this species. Loci were screened across 53 individuals from one population and were shown to be variable with the number of alleles per locus ranging from five to 15. Polymorphic information content ranged from 0.420 to 0.900 and observed heterozygosity ranged from 0.547 to 0.906. [ABSTRACT FROM AUTHOR]

Thirteen microsatellite loci were isolated from the coqui frog ( Eleutherodactylus coqui) and optimized for future research. The loci were screened across 37 individuals from two Puerto Rican populations. Loci were variable with the number of alleles per locus ranging from three to 38. Polymorphic information content ranged from 0.453 to 0.963 and observed heterozygosity for each population ranged from 0.320 to 0.920. [ABSTRACT FROM AUTHOR]

Twelve polymorphic microsatellite loci were isolated from polyploid alpine wood-sorrel, Oxalis alpina (Oxalidaceae), and optimized for future studies of its breeding system. The loci were screened for variability among 72 individuals from Pinos Altos, New Mexico. The primers amplified loci with allele number ranging from two to 17 per locus and with estimates of Nei's genetic diversity varying from 0.10 to 0.99. These primers provide an opportunity to use polymorphic DNA markers to study the causes of breeding system variability in this species. [ABSTRACT FROM AUTHOR]

We isolated and characterized 16 microsatellite loci in the eastern chipmunk, Tamias striatus. The loci were screened across 25 individuals from one population and shown to be polymorphic with the number of alleles per locus ranging from two to 17. Polymorphic information content ranged from 0.212 to 0.887 and observed heterozygosity ranged from 0.200 to 0.960. Only two loci (Chip 10 and Chip 25) deviated from Hardy–Weinberg equilibrium. [ABSTRACT FROM AUTHOR]

Twelve polymorphic microsatellite DNA loci were isolated from saltgrass ( Distichlis spicata) and optimized for future studies of its breeding system. The loci were screened for variability among 24 individuals from two populations. The primers amplified loci with numbers of alleles ranging from four to 14 per locus and polymorphic information content from 0.481 to 0.951. Observed heterozygosity varied from 0.227 to 0.958. [ABSTRACT FROM AUTHOR]

Our previous study showed heritable reproductive toxicity in the nematode Caenorhabditis elegans after multigenerational exposure to AgNO 3 and silver nanoparticles (Ag-NPs). The aim of this study was to determine whether such inheritable effects are correlated with induced germline mutations in C. elegans. Individual C. elegans lineages were exposed for 10 generations to equitoxic concentrations at EC 30 of AgNO 3 , Ag-NPs, and sulfidized Ag-NPs (sAg-NPs), a predominant environmentally transformed product of pristine Ag-NPs. The mutations were detected via whole genome DNA sequencing approach by comparing F 0 and F 10 generations. An increase in the total number of variants, though not statistically significant, was observed for all Ag treatments and the variants were mainly contributed by single nucleotide polymorphisms (SNPs). This potentially contributed towards reproductive as well as growth toxicity shown previously after ten generations of exposure in every Ag treatment. However, despite Ag-NPs and AgNO 3 inducing stronger reproductive toxicity than sAg-NPs, exposure to sAg-NPs resulted in higher mutation accumulation with significant increase in the number of transversions. Thus our results suggest that other mechanisms of inheritance, such as epigenetics, may be at play in Ag-NP- and AgNO 3 -induced multigenerational and transgenerational reproductive toxicity. Image 1 • Multigenerational exposure to pristine and sulfidized Ag-NPs increase mutations. • Mutations are mainly contributed by single nucleotide polymorphisms. • Mutations alone cannot not explain multigenerational reproductive toxicity. • Epigenetic mechanisms might be involved in multigenerational toxicity of Ag-NPs. Multigenerational exposure to pristine and sulfidized Ag nanoparticles is characterized with overall increases in germline mutations. [ABSTRACT FROM AUTHOR]

We have developed primer pairs for 24 microsatellite loci isolated from Acacia brevispica, which is widespread in woodland savannas of East Africa. The loci were screened for levels of variation using 16-52 individuals from Mpala Research Centre, Kenya. Number of alleles per locus ranged from two to 17, and polymorphic information content ranged from 0.248 to 0.864. Several loci showed the presence null alleles, but many loci will be useful in ongoing studies of genetic structure, gene flow, breeding systems, and natural selection. [ABSTRACT FROM AUTHOR]

We developed 22 microsatellite loci for boreal owls ( Aegolius funereus). We genotyped 275 unrelated boreal owls ( Aegolius f. richardsoni) and 36 unrelated Tengmalm's owls ( Aegolius f. funereus) using seven loci that were polymorphic and did not have detectable null alleles. Among North American and Scandinavian boreal owls, respectively, allelic diversity ranged from three to 11 alleles and from one to 11 alleles, observed heterozygosity ranged from 0.31 to 0.80 and from 0.00 to 0.81, and expected heterozygosity ranged from 0.28 to 0.81 and from 0.00 to 0.81. These markers appeared to amplify DNA in six other Strigidae species. [ABSTRACT FROM AUTHOR]

We describe polymerase chain reaction (PCR) primers and conditions to amplify one dinucleotide and five tetranucleotide microsatellite DNA loci isolated from the grey fox ( Urocyon cinereoargenteus). The PCR primers were tested on nine to 12 individuals collected from the Department of Energy's Savannah River site (Aiken, SC, USA). The grey fox microsatellite primers developed had three to 10 alleles per locus that yielded observed heterozygosities ranging from 0.222 to 0.889. [ABSTRACT FROM AUTHOR]

In recent articles published in Molecular Phylogenetics and Evolution, Mark Springer and John Gatesy (S&G) present numerous criticisms of recent implementations and testing of the multispecies coalescent model in phylogenomics, popularly known as ''species tree" methods. After pointing out errors in alignments and gene tree rooting in recent phylogenomic data sets, in particular in Song et al. (2012) on mammals and Xi et al. (2014) on plants, they suggest that these errors seriously compromise the conclusions of these studies. Additionally, S&G enumerate numerous violated assumptions and deficiencies in the application of the multispecies coalescent model (MSC) in phylogenomics, such as its assumption of neutrality and in particular the use of transcriptomes, which are deemed inappropriate for the MSC because the constituent exons often subtend large regions of chromosomes within which recombination is substantial. We acknowledge these previously reported errors in recent phylogenomic data sets, but disapprove of S&G's excessively combative and taunting tone. We show that these errors, as well as two nucleotide-sorting methods used in the analysis of Amborella, have little impact on the conclusions of those papers. Moreover, several concepts introduced by S&G and an appeal to ''first principles" of phylogenetics in an attempt to discredit MSC models are invalid and reveal numerous misunderstandings of the MSC. Contrary to the claims of S&G we show that recent computer simulations used to test the robustness of MSC models are not circular and do not unfairly favorMSC models over concatenation. In fact, although both concatenation and MSC models clearly perform well in regions of tree space with long branches and little incomplete lineage sorting (ILS), simulations reveal the erratic behavior of concatenation when subjected to data subsampling and its tendency to produce spuriously confident yet conflicting results in regions of parameter space where MSC models still perform well. S&G's claims that MSC models explain little or none (0-15%) of the observed gene tree heterogeneity observed in a mammal data set and that MSC models assume ILS as the only source of gene tree variation are flawed. Overall many of their criticisms of MSC models are invalidated when concatenation is appropriately viewed as a special case of the MSC, which in turn is a special case of emerging network models in phylogenomics. We reiterate that there is enormous promise and value in recent implementations and tests of the MSC and look forward to its increased use and refinement in phylogenomics. [ABSTRACT FROM AUTHOR]

Molecular analyses of turtle relationships have overturned prevailing morphological hypotheses and prompted the development of a new taxonomy. Here we provide the first genome-scale analysis of turtle phylogeny. We sequenced 2381 ultraconserved element (UCE) loci representing a total of 1,718,154 bp of aligned sequence. Our sampling includes 32 turtle taxa representing all 14 recognized turtle families and an additional six outgroups. Maximum likelihood, Bayesian, and species tree methods produce a single resolved phylogeny. This robust phylogeny shows that proposed phylogenetic names correspond to well-supported clades, and this topology is more consistent with the temporal appearance of clades and paleobiogeography. Future studies of turtle phylogeny using fossil turtles should use this topology as a scaffold for their morphological phylogenetic analyses. [ABSTRACT FROM AUTHOR]