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Aim: Biotic interchanges between Africa, India, and Eurasia are central to explaining the present‐day distribution and diversity of freshwater organisms across these landmasses. Synbranchiformes is a diverse and species‐rich clade of freshwater acanthomorph fishes found on all southern continents except Antarctica, and include eel‐ and perch‐like, air‐breathing and non‐air‐breathing fishes. Lacking a comprehensive and resolved phylogeny of the entire clade, contemporary interpretations of synbranchiform biogeography invoke scenarios as disparate as Gondwanan vicariance and pan‐global rafting to explain their modern‐day distribution. Here, we study their biogeographic history of continental dispersal events and test whether these are associated with increases in lineage diversification. Location: Asia, India, Africa freshwater habitats. Taxon: Synbranchiformes (gouramis, snakeheads, swamp eels, and relatives). Methods: We used nearly 1000 ultra‐conserved elements (UCEs) and Sanger‐sequenced genes to infer a phylogeny with representatives of all major synbranchiform lineages and nearly two‐thirds of its known species diversity. Incorporating fossil calibrations, we inferred a time‐calibrated phylogeny to which we apply Bayesian methods of ancestral area reconstruction and test for diversification rate shifts. Results: Analyses of UCE data provide a resolved phylogeny for major synbranchiform lineages. Divergence times support a most recent common ancestor of the entire clade approximately 79.2 million years ago. We infer significant increases in lineage diversification in both the spiny eels (Mastacembelidae) and the genus Betta (Osphronemidae). Main Conclusions: Our results reject the hypothesis of Gondwanan vicariance explaining synbranchiform biogeography. Instead, our analyses reconstruct a southeast Asian origin of the entire clade and independent dispersal events to other continents by snakeheads, anabantids, and spiny eels, with no signal of elevated lineage diversification occurring after these invasions. Higher lineage diversification rates in spiny eels pre‐date their arrival to Africa, while the high diversification rates observed in Betta were initiated prior to the flooding of insular Sundaland in southeast Asia. [ABSTRACT FROM AUTHOR]

Birds display a rainbow of eye colours, but this trait has been little studied compared with plumage coloration. Avian eye colour variation occurs at all phylogenetic scales: it can be conserved throughout whole families or vary within one species, yet the evolutionary importance of this eye colour variation is under‐studied. Here, we summarize knowledge of the causes of eye colour variation at three primary levels: mechanistic, genetic and evolutionary. Mechanistically, we show that avian iris pigments include melanin and carotenoids, which also play major roles in plumage colour, as well as purines and pteridines, which are often found as pigments in non‐avian taxa. Genetically, we survey classical breeding studies and recent genomic work on domestic birds that have identified potential 'eye colour genes', including one associated with pteridine pigmentation in pigeons. Finally, from an evolutionary standpoint, we present and discuss several hypotheses explaining the adaptive significance of eye colour variation. Many of these hypotheses suggest that bird eye colour plays an important role in intraspecific signalling, particularly as an indicator of age or mate quality, although the importance of eye colour may differ between species and few evolutionary hypotheses have been directly tested. We suggest that future studies of avian eye colour should consider all three levels, including broad‐scale iris pigment analyses across bird species, genome sequencing studies to identify loci associated with eye colour variation, and behavioural experiments and comparative phylogenetic analyses to test adaptive hypotheses. By examining these proximate and ultimate causes of eye colour variation in birds, we hope that our review will encourage future research to understand the ecological and evolutionary significance of this striking avian trait. [ABSTRACT FROM AUTHOR]

Humans have profoundly impacted the distribution of plant and animal species over thousands of years. The most direct example of these effects is human‐mediated movement of individuals, either through translocation of individuals within their range or through the introduction of species to new habitats. While human involvement may be suspected in species with obvious range disjunctions, it can be difficult to detect natural versus human‐mediated dispersal events for populations at the edge of a species' range, and this uncertainty muddles how we understand the evolutionary history of populations and broad biogeographical patterns. Studies combining genetic data with archaeological, linguistic and historical evidence have confirmed prehistoric examples of human‐mediated dispersal; however, it is unclear whether these methods can disentangle recent dispersal events, such as species translocated by European colonizers during the past 500 years. We use genomic DNA from historical museum specimens and historical records to evaluate three hypotheses regarding the timing and origin of Northern Bobwhites (Colinus virginianus) in Cuba, whose status as an endemic or introduced population has long been debated. We discovered that bobwhites from southern Mexico arrived in Cuba between the 12th and 16th centuries, followed by the subsequent introduction of bobwhites from the southeastern USA to Cuba between the 18th and 20th centuries. These dates suggest the introduction of bobwhites to Cuba was human‐mediated and concomitant with Spanish colonial shipping routes between Veracruz, Mexico and Havana, Cuba during this period. Our results identify endemic Cuban bobwhites as a genetically distinct population born of hybridization between divergent, introduced lineages. see also the Perspective by Silu Wang [ABSTRACT FROM AUTHOR]

Aim: Continental evolutionary radiations provide opportunities to understand how landscape evolution and biotic factors interact to generate species diversity. Additionally, understanding whether diversification dynamics differ between montane and lowland environments is a long‐standing question with few comparative analyses in the Neotropics. To address these questions, we investigated the biogeographical patterns and the evolutionary processes underlying the diversification of a songbird genus, and compared diversification dynamics of clades occurring in lowland and montane Neotropical habitats. Location: Neotropical montane and lowland forests. Taxon: Arremon(Aves: Passerellidae). Methods: We sequenced genomic data (ultra‐conserved elements, UCEs) of 92 individuals (including historical skin specimens) comprising 47 of 50 currently recognized subspecies in the genus and collected habitat association data to (1) build the most complete phylogenetic hypothesis for the genus to date using maximum likelihood and Bayesian methods with a concatenated matrix, and a multi‐species coalescent method based on quartets; and (2) reconstruct the evolution of their ancestral ranges, habitat association and diversification rates. Results: All phylogenetic methods recovered essentially the same topology with strong support values for most interspecific nodes revealing relationships among species. We found evidence for a montane and humid ancestral range in Central America in the late Miocene and a later expansion into the lowlands of Central America, as well as into the lowlands and mountains of South America. Despite some temporal variation in diversification rate, we found overall similar diversification dynamics between montane and lowland clades. Main conclusion: Species diversity within the genus is likely underestimated by the current taxonomic arrangement. The colonization of lowlands and dry forests, and expansion across South America, may have provided new geographical and ecological opportunities for speciation resulting in high species diversification. Overall diversification dynamics were comparable between montane and lowland clades, contrasting with previous studies focused on such comparisons for Neotropical birds. [ABSTRACT FROM AUTHOR]

During the Last Glacial Maximum (LGM), global sea levels were 120–130 m lower than today, resulting in the emergence of most continental shelves and extirpation of subtidal organisms from these areas. During the interglacial periods, rapid inundation of shelf regions created a dynamic environment for coastal organisms, such as the charismatic leafy seadragon (Phycodurus eques, Syngnathidae), a brooder with low dispersal ability inhabiting kelp beds in temperate Australia. Reconstructions of the palaeoshoreline revealed that the increase of shallow areas since the LGM was not uniform across the species' range and we investigated the effects of these asymmetries on genetic diversity and structuring. Using targeted capture of 857 variable ultraconserved elements (UCEs, 2,845 single nucleotide polymorphisms) in 68 individuals, we found that the regionally different shelf topographies were paralleled by contrasting population genetic patterns. In the west, populations may not have persisted through sea‐level lows because shallow seabed was very limited. Shallow genetic structure, weak expansion signals and a westward cline in genetic diversity indicate a postglacial recolonization of the western part of the range from a more eastern location following sea‐level rise. In the east, shallow seabed persisted during the LGM and increased considerably after the flooding of large bays, which resulted in strong demographic expansions, deeper genetic structure and higher genetic diversity. This study suggests that postglacial flooding with rising sea levels produced locally variable signatures in colonizing populations. see also the Perspective by by Greer A. Dolby. [ABSTRACT FROM AUTHOR]

Determining how genetic diversity is structured between populations that span the divergence continuum from populations to biological species is key to understanding the generation and maintenance of biodiversity. We investigated genetic divergence and gene flow in eight lineages of birds with a trans‐Beringian distribution, where Asian and North American populations have likely been split and reunited through multiple Pleistocene glacial cycles. Our study transects the speciation process, including eight pairwise comparisons in three orders (ducks, shorebirds and passerines) at population, subspecies and species levels. Using ultraconserved elements (UCEs), we found that these lineages represent conditions from slightly differentiated populations to full biological species. Although allopatric speciation is considered the predominant mode of divergence in birds, all of our best divergence models included gene flow, supporting speciation with gene flow as the predominant mode in Beringia. In our eight lineages, three were best described by a split‐migration model (divergence with gene flow), three best fit a secondary contact scenario (isolation followed by gene flow), and two showed support for both models. The lineages were not evenly distributed across a divergence space defined by gene flow (M) and differentiation (FST), instead forming two discontinuous groups: one with relatively shallow divergence, no fixed single nucleotide polymorphisms (SNPs), and high rates of gene flow between populations; and the second with relatively deeply divergent lineages, multiple fixed SNPs, and low gene flow. Our results highlight the important role that gene flow plays in avian divergence in Beringia. [ABSTRACT FROM AUTHOR]

The formation of independent evolutionary lineages involves neutral and selective factors, and understanding their relative roles in population divergence is a fundamental goal of speciation research. Correlations between allele frequencies and environmental variability can reveal the role of selection, yet the relative contribution of drift can be difficult to establish. Recently diversified taxa like the Oregon junco (Aves, Passerellidae, Junco hyemalis oreganus) of western North America provide ideal scenarios to apply genetic‐environment association analyses (GEA) while controlling for population structure. Analysis of genome‐wide SNP loci revealed marked genetic structure consisting of differentiated populations in isolated, dry southern mountain ranges, and less divergent, recently expanded populations in humid northern latitudes. We used correlations between genomic and environmental variance to test for three specific modes of evolutionary divergence: (a) drift in geographic isolation, (b) differentiation along continuous selective gradients and (c) isolation‐by‐adaptation. We found evidence of strong drift in southern mountains, but also signals of local adaptation driven by temperature, precipitation, elevation and vegetation, especially when controlling for population history. We identified numerous variants under selection scattered across the genome, suggesting that local adaptation can promote rapid differentiation when acting over multiple independent loci. [ABSTRACT FROM AUTHOR]

Abstract: Anthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ~7,500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,306 RNA baits to capture 720 ultraconserved element loci and 1,071 exon loci. Library preparation and target enrichment were performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 ± 222, with more loci recovered from octocorals (783 ± 138 loci) than hexacorals (475 ± 187 loci). Parsimony informative sites ranged from 26 to 49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The per cent of variable sites within each of three genera (Acropora, Alcyonium, and Sinularia) for which multiple species were sequenced ranged from 4.7% to 30%. Maximum‐likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target‐enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Redesigning the baits with improved affinities to capture loci within each subclass will provide a valuable toolset to address systematic questions, further our understanding of the timing of diversifications and help resolve long‐standing controversial relationships in the class Anthozoa. [ABSTRACT FROM AUTHOR]

A prominent hypothesis for polyandry says that male-male competitive drivers induce males to coerce already-mated females to copulate, suggesting that females are more likely to be harassed in the presence of multiple males. This early sociobiological idea of male competitive drive seemed to explain why sperm-storing females mate multiply. Here, we describe an experiment eliminating all opportunities for male-male behavioral competition, while varying females' opportunities to mate or not with the same male many times, or with many other males only one time each. We limited each female subject's exposure to no more than one male per day over her entire lifespan starting at the age at which copulations usually commence. We tested a priori predictions about relative lifespan and daily components of RS of female Drosophila melanogaster in experimental social situations producing lifelong virgins, once-mated females, lifelong monogamous, and lifelong polyandrous females, using a matched-treatments design. Results included that (1) a single copulation enhanced female survival compared to survival of lifelong virgins, (2) multiple copulations enhanced the number of offspring for both monogamous and polyandrous females, (3) compared to females in lifelong monogamy, polyandrous females paired daily with a novel, age-matched experienced male produced offspring of enhanced viability, and (4) female survival was unchallenged when monogamous and polyandrous females could re-mate with age- and experienced-matched males. (5) Polyandrous females daily paired with novel virgin males had significantly reduced lifespans compared to polyandrous females with novel, age-matched, and experienced males. (6) Polyandrous mating enhanced offspring viability and thereby weakened support for the random mating hypothesis for female multiple mating. Analyzes of nonequivalence of variances revealed opportunities for within-sex selection among females. Results support the idea that females able to avoid constraints on their behavior from simultaneous exposure to multiple males can affect both RS and survival of females and offspring. [ABSTRACT FROM AUTHOR]

Targeted enrichment of conserved genomic regions is a popular method for collecting large amounts of sequence data from non-model taxa for phylogenetic, phylogeographic and population genetic studies. For example, two available bait sets each allow enrichment of thousands of orthologous loci from >20 000 species (Faircloth et al. Systematic Biology, 61, 717-726, 2012; Molecular Ecology Resources, 15, 489-501, 2015). Unfortunately, few open-source workflows are available to identify conserved genomic elements shared among divergent taxa and to design enrichment baits targeting these regions. Those that do exist require extensive bioinformatics expertise and significant amounts of time to use. These shortcomings limit the application of targeted enrichment methods to additional organismal groups., Here, I describe a universal workflow for identifying conserved genomic regions in available genomic data and for designing targeted enrichment baits to collect data from these conserved regions. These methods require less expertise, less time and better use commonly available information to identify conserved loci and design baits to capture them., I apply this computational approach to the understudied arthropod groups Arachnida, Coleoptera, Diptera, Hemiptera or Lepidoptera to identify thousands of conserved loci in each group and design target enrichment baits to capture these loci. I then use in silico analyses to demonstrate that targeted enrichment of the conserved loci can be used to reconstruct the accepted relationships among genome sequences from the focal arthropod orders., The software workflow I created allowed me to identify thousands of conserved loci in five diverse arthropod groups and design sequence capture baits to target them. This suite of capture bait designs should enable collection of phylogenomic data from >900 000 arthropod species. Although the examples in this manuscript focus on understudied arthropod groups, the approach I describe is applicable to all organismal groups having some form of pre-existing genomic information (e.g. other invertebrates, plants, fungi and microbes). Finally, the documentation, design steps, software code and bait sets developed here are available under an open-source license for restriction-free testing, use, and additional modification by any research group. [ABSTRACT FROM AUTHOR]

Arachnida is an ancient, diverse and ecologically important animal group that contains a number of species of interest for medical, agricultural and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress. Here, we present a genomic toolkit for arachnids featuring hundreds of conserved DNA regions (ultraconserved elements or UCEs) that allow targeted sequencing of any species in the arachnid tree of life. We used recently developed capture probes designed from conserved regions of available arachnid genomes to enrich a sample of loci from 32 diverse arachnids. Sequence capture returned an average of 487 UCE loci for all species, with a range from 170 to 722. Phylogenetic analysis of these UCEs produced a highly resolved arachnid tree with relationships largely consistent with recent transcriptome-based phylogenies. We also tested the phylogenetic informativeness of UCE probes within the spider, scorpion and harvestman orders, demonstrating the utility of these markers at shallower taxonomic scales and suggesting that these loci will be useful for species-level differences. This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery and conservation of these diverse arthropods. [ABSTRACT FROM AUTHOR]

Targeted enrichment of conserved genomic regions (e.g. ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them., We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The new strategy augments a previous bait design for Hymenoptera by (i) changing the parameters by which conserved genomic regions are identified and retained, and (ii) increasing the number of genomes used for locus identification and bait design. We perform in vitro validation of the approach in ants by synthesizing an ant-specific bait set that targets UCE loci and a set of 'legacy' phylogenetic markers. Using this bait set, we generate new data for 84 taxa (16/17 ant subfamilies) and extract loci from an additional 17 genome-enabled taxa. We then use these data to examine UCE capture success and phylogenetic performance across ants. We also test the workability of extracting legacy markers from enriched samples and combining the data with published datasets., The updated bait design (hym-v2) contained a total of 2590-targeted UCE loci for Hymenoptera, significantly increasing the number of loci relative to the original bait set (hym-v1; 1510 loci). Across 38 genome-enabled Hymenoptera and 84 enriched samples, experiments demonstrated a high and unbiased capture success rate, with the mean locus enrichment rate being 2214 loci per sample. Phylogenomic analyses of ants produced a robust tree that included strong support for previously uncertain relationships. Complementing the UCE results, we successfully enriched legacy markers, combined the data with published Sanger datasets and generated a comprehensive ant phylogeny containing 1060 terminals., Overall, the new UCE bait design strategy resulted in an enhanced bait set for genome-scale phylogenetics in ants and other Hymenoptera. Our in vitro tests demonstrate the utility of the updated design workflow, providing evidence that this approach could be applied to any organismal group with available genomic information. [ABSTRACT FROM AUTHOR]

Genomic studies are revealing that divergence and speciation are marked by gene flow, but it is not clear whether gene flow has played a prominent role during the generation of biodiversity in species-rich regions of the world where vicariance is assumed to be the principal mode by which new species form. We revisit a well-studied organismal system in the Mexican Highlands, Aphelocoma jays, to test for gene flow among Mexican sierras. Prior results from mitochondrial DNA (mt DNA) largely conformed to the standard model of allopatric divergence, although there was also evidence for more obscure histories of gene flow in a small sample of nuclear markers. We tested for these 'hidden histories' using genomic markers known as ultraconserved elements ( UCEs) in concert with phylogenies, clustering algorithms and newer introgression tests specifically designed to detect ancient gene flow (e.g. ABBA/ BABA tests). Results based on 4303 UCE loci and 2500 informative SNPs are consistent with varying degrees of gene flow among highland areas. In some cases, gene flow has been extensive and recent (although perhaps not ongoing today), whereas in other cases there is only a trace signature of ancient gene flow among species that diverged as long as 5 million years ago. These results show how a species complex thought to be a model for vicariance can reveal a more reticulate history when a broader portion of the genome is queried. As more organisms are studied with genomic data, we predict that speciation-with-bouts-of-gene-flow will turn out to be a common mode of speciation. [ABSTRACT FROM AUTHOR]

Evolutionary biologists from Darwin forward have dreamed of having data that would elucidate our understanding of evolutionary history and the diversity of life. Sequence capture is a relatively old DNA technology, but its use is growing rapidly due to advances in (i) massively parallel DNA sequencing approaches and instruments, (ii) massively parallel bait construction, (iii) methods to identify target regions and (iv) sample preparation. We give a little historical context to these developments, summarize some of the important advances reported in this special issue and point to further advances that can be made to help fulfill Darwin's dream. [ABSTRACT FROM AUTHOR]

New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5060 UCE loci in 27 western scrub-jays ( Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources. [ABSTRACT FROM AUTHOR]

Molecular ecologists seek to genotype hundreds to thousands of loci from hundreds to thousands of individuals at minimal cost per sample. Current methods, such as restriction-site-associated DNA sequencing ( RADseq) and sequence capture, are constrained by costs associated with inefficient use of sequencing data and sample preparation. Here, we introduce RADcap, an approach that combines the major benefits of RADseq (low cost with specific start positions) with those of sequence capture (repeatable sequencing of specific loci) to significantly increase efficiency and reduce costs relative to current approaches. RADcap uses a new version of dual-digest RADseq (3 RAD) to identify candidate SNP loci for capture bait design and subsequently uses custom sequence capture baits to consistently enrich candidate SNP loci across many individuals. We combined this approach with a new library preparation method for identifying and removing PCR duplicates from 3 RAD libraries, which allows researchers to process RADseq data using traditional pipelines, and we tested the RADcap method by genotyping sets of 96-384 Wisteria plants. Our results demonstrate that our RADcap method: (i) methodologically reduces (to <5%) and allows computational removal of PCR duplicate reads from data, (ii) achieves 80-90% reads on target in 11 of 12 enrichments, (iii) returns consistent coverage (≥4×) across >90% of individuals at up to 99.8% of the targeted loci, (iv) produces consistently high occupancy matrices of genotypes across hundreds of individuals and (v) costs significantly less than current approaches. [ABSTRACT FROM AUTHOR]

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities. [ABSTRACT FROM AUTHOR]

Gaining a genomic perspective on phylogeny requires the collection of data from many putatively independent loci across the genome. Among insects, an increasingly common approach to collecting this class of data involves transcriptome sequencing, because few insects have high-quality genome sequences available; assembling new genomes remains a limiting factor; the transcribed portion of the genome is a reasonable, reduced subset of the genome to target; and the data collected from transcribed portions of the genome are similar in composition to the types of data with which biologists have traditionally worked (e.g. exons). However, molecular techniques requiring RNA as a template, including transcriptome sequencing, are limited to using very high-quality source materials, which are often unavailable from a large proportion of biologically important insect samples. Recent research suggests that DNA-based target enrichment of conserved genomic elements offers another path to collecting phylogenomic data across insect taxa, provided that conserved elements are present in and can be collected from insect genomes. Here, we identify a large set ( n = 1510) of ultraconserved elements ( UCEs) shared among the insect order Hymenoptera. We used in silico analyses to show that these loci accurately reconstruct relationships among genome-enabled hymenoptera, and we designed a set of RNA baits ( n = 2749) for enriching these loci that researchers can use with DNA templates extracted from a variety of sources. We used our UCE bait set to enrich an average of 721 UCE loci from 30 hymenopteran taxa, and we used these UCE loci to reconstruct phylogenetic relationships spanning very old (≥220 Ma) to very young (≤1 Ma) divergences among hymenopteran lineages. In contrast to a recent study addressing hymenopteran phylogeny using transcriptome data, we found ants to be sister to all remaining aculeate lineages with complete support, although this result could be explained by factors such as taxon sampling. We discuss this approach and our results in the context of elucidating the evolutionary history of one of the most diverse and speciose animal orders. [ABSTRACT FROM AUTHOR]

The article focuses on the evaluation of translocation efficacy and the survival rates, home range, and site fidelity of resident and translocated bobwhites in fragmented site in Marion County near Tazewell, Georgia. It collected and classified bobwhites during 2003 and 2004 wherein the known-fate and strata models were used. Moreover, it proposes that conservation strategies should focus on habitat restoration and improvement using translocation as a means to complement the strategy.

We assessed effects of tissue collection methods (i.e., patagial microbiopsy and down feathers) and chick age at sampling on morphometrics and 21-day survival of 600 captive neonatal northern bobwhite (Colinus virginianus). We observed minimal effects on morphometrics and no difference in survival among patagial microbiopsy (x¯ = 0.96 ± 0.03), down feathers (x¯ = 0.92 ± 0.04), and control (x¯ = 0.86 ± 0.05) methods. DNA analysis from patagial microbiopsy, down feather, and egg tooth samples showed greater concentrations of DNA from patagial microbiopsy (x¯ = 10.28 ± 1.74 μg/ml) than either down feather (x¯ = 4.10 ± 1.74 μg/ml) or egg teeth (x¯ = 2.35 ± 1.74 μg/ml). [ABSTRACT FROM AUTHOR]

We describe primers and polymerase chain reaction conditions to amplify 21 tetranucleotide microsatellite DNA loci in black bears ( Ursus americanus). We tested primers using individuals from two populations, one each in Georgia and Florida. Among individuals from Georgia ( n = 29), primer pairs yielded an average of 2.9 alleles (range, one to four) and an average observed heterozygosity ( HO) of 0.50 (range, 0.00 to 0.79). Among individuals from Florida ( n = 19), primer pairs yielded an average of 5.7 alleles (range, one to 14) and an HO of 0.55 (range, 0.00 to 1.00). A comparison of previously developed markers with individuals from Georgia suggests that bear populations in Georgia and Florida have reduced allelic diversity relative to other populations. [ABSTRACT FROM AUTHOR]

We describe primers and polymerase chain reaction conditions to amplify 15 tetranucleotide microsatellite loci from the loggerhead sea turtle ( Caretta caretta). The primers were tested on 30 individuals that nested along the Georgia, USA coast. The primer pairs developed in this study yielded an average of 13.9 alleles per locus (range of 10–21), an average observed heterozygosity of 0.91 (range 0.79–1.00), and an average polymorphic information content of 0.88 (range 0.84–0.92). [ABSTRACT FROM AUTHOR]

We describe primers and polymerase chain reaction (PCR) conditions to amplify 18 tetranucleotide microsatellite DNA loci in eastern bluebirds ( Sialia sialis). The primers were tested using individuals from two study sites in Georgia and South Carolina. Among individuals from the Georgia population ( n = 23), the primer pairs developed in this study yielded an average of 6.6 alleles per locus (range 2–12), an average observed heterozygosity of 0.56 (range 0.24–0.96) and an average polymorphic information content of 0.65 (range 0.3–0.86). Among individuals from the South Carolina population ( n = 19), the primer pairs yielded an average of 5.8 alleles per locus (range 2–9), an average observed heterozygosity of 0.56 (range 0.05–0.86) and an average polymorphic information content of 0.63 (range 0.29–0.83). [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]

It has been a tumultuous 5 years in phylogeography and phylogenetics during which both fields have struggled to harness the power of next-generation sequencing ( NGS) (Ekblom & Galindo ; McCormack et al. ). Fortunately, several methodological approaches appear to be taking root. In this issue of Molecular Ecology, O'Neill et al. ) employ one such method - parallel tagged sequencing ( PTS) - to elucidate the phylogeography of a tiger salamander ( Ambystoma tigrinum) species complex. This study demonstrates a practical application of NGS on a scale appropriate (and not overkill) for most biologists interested in phylogeography (~100 loci for ~100 individuals), and their results highlight several analytical challenges that lie ahead for researchers employing NGS techniques. [ABSTRACT FROM AUTHOR]

We describe polymerase chain reaction primer pairs and reaction conditions for amplification of 15 microsatellite loci from eastern hemlock ( Tsuga canadensis). The primers were tested on 23 individuals from a natural population in southwestern North Carolina, USA. These primers yielded an average of 5.9 alleles per locus (range of 2–14), an average observed heterozygosity of 0.45 (range 0.14–0.73), and an average polymorphic information content of 0.54 (range 0.28–0.86). In addition, eight of the primer pairs were found to amplify microsatellite loci in one or more additional species of Tsuga. [ABSTRACT FROM AUTHOR]

msatcommander is a platform-independent program designed to search for microsatellite arrays, design primers, and tag primers using an automated routine.msatcommander accepts as input DNA sequence data in single-sequence or concatenated,fasta-formatted files. Search data and locus-specific primers are written to comma-separated value files for subsequent use in spreadsheet or database programs. Binary versions of the graphical interface formsatcommander are available for Apple OS X and Windows XP. Users of other operating systems may run the graphical interface version using the available source code, provided their environment supports at least Python 2.4, Biopython 1.43, and wxPython 2.8.msatcommander is available from . [ABSTRACT FROM AUTHOR]

gmconvert is a platform-independent program provided in GUI (for Apple OS X and Windows XP) and command-line versions (for other platforms).gmconvert allows rapid reformatting of microsatellite data from output files produced by Applied Biosystemsgenemapper software (version 3.x). The program will re-array data into three formats commonly used in downstream analysis:genepop,cervus, andgerud.gmconvert will greatly increase the speed of data preparation prior to analysis and aid in reducing transpositional errors associated with manual re-arraying and reformatting steps.gmconvert is available from . [ABSTRACT FROM AUTHOR]

We describe primers and polymerase chain reaction (PCR) conditions to amplify four dinucleotide, one trinucleotide, and three tetranucleotide microsatellite DNA loci from the bobcat (Lynx rufus). The primers were tested on 22 individuals collected from a population located within southwestern Georgia (USA). The primer pairs developed in this study yielded an average of 7.4 alleles per locus (range four to 10), an average observed heterozygosity of 0.60 (range 0.40 to 0.76), and an average polymorphic information content of 0.70 (range 0.51 to 0.78). [ABSTRACT FROM AUTHOR]