Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons
Paul D Blischak, Maribeth Latvis, Diego F Morales-Briones, Jens C Johnson, Verónica S Di Stilio, Andrea D Wolfe, David C Tank. 2018. bioRxiv 242677; doi: https://doi.org/10.1101/242677
Premise of the study: Targeted enrichment strategies for phylogenomic inference are a time- and cost-efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies. Methods and Results: We present Fluidigm2PURC, an open source Python utility for processing paired-end Illumina data from double-barcoded PCR amplicons. In combination with the program PURC (Pipeline for Untangling Reticulate Complexes), our scripts process raw FASTQ files for analysis with PURC and use its output to infer haplotypes for diploids, polyploids, and samples with unknown ploidy. We demonstrate the use of the pipeline with an example data set from the genus Thalictrum L. (Ranunculaceae). Conclusions: Fluidigm2PURC is freely available for Unix-like operating systems on GitHub [https://github.com/pblischak/fluidigm2purc] and for all operating systems through Docker [https://hub.docker.com/r/pblischak/fluidigm2purc].
Moderate Disturbance Has Similar Effects on Production Regardless of Site Quality and Composition
Benjamin T. Sagara, Robert T. Fahey, Christoph S. Vogel, Alexander T. Fotis, Peter S. Curtis, and Christopher M. Gough. Forests 2018, 9(2), 70; doi:10.3390/f9020070
Moderate severity disturbances, which only kill a subset of canopy trees (e.g., via insects, pathogens, and windthrow), are increasingly widespread in North America, and can alter forest structure and production. Whether the net primary production (NPP) of forest stands differing in pre-disturbance site quality and composition respond similarly to moderate severity disturbance, however, is unknown, but critical to understanding the disturbance response dynamics of patchy landscapes. We experimentally disturbed three, 2-ha stands varying in pre-disturbance primary production and community composition, temporarily reducing live stand basal area by 38% to 66% through the stem girdling of all mature early successional aspen (Populus tremuloides Michx. and Populus grandidentata Michx.) and birch (Betula papyrifera Marshall). Disturbance significantly altered stand-scale physical and biological structure and prompted a similar decade-long pattern of wood NPP decline and recovery. All stands exhibited an initial reduction in wood NPP, followed by a recovery period and eventual return to pre-disturbance levels within eight years, with the most productive stand exhibiting an increase in primary production following recovery. Following wood NPP recovery, more biologically diverse forest canopies with higher leaf area indexes intercepted more light, and, consequently, had higher rates of wood NPP. We conclude that, despite substantial pre-disturbance differences in productivity and community composition, relative wood NPP recovery patterns can be similar, though long-term post-recovery primary production may trend higher in more productive and compositionally diverse stands. We suggest that improved mechanistic understanding of different forest ecosystems’ responses to disturbances remains critical to informing management decisions across diverse landscape mosaics.
A new species of Opilioacaridae (Parasitiformes: Opilioacarida) from Belize with some observations on life history and behavior
Maria Magdalena Vázquez, Daniel May, Elvia Alamilla, Hans Klompen. Systematic and Applied Acarology, [S.l.], p. 132–144, jan. 2018. ISSN 1362-1971. DOI: http://dx.doi.org/10.11158/saa.23.1.11
A new species of opilioacarid mite, Neocarus belizensis sp. nov., is described from mid-level elevations in Belize’s Maya Mountains. Laboratory observations confirmed that females nearly always deposit only one egg at a time, and that eggs are coated before deposition. Females guard both eggs and larvae. The larvae are non-feeding and molt quickly to protonymphs. Adults appear to facilitate feeding by protonymphs. Actual mating could not be observed, but pre-mating behavior is documented.
The importance of species: Pygmy rattlesnake venom toxicity differs between native prey and related non-native species
Sarah A.Smiley-Walters, Terence M.Farrell, H. Lisle Gibbs. Toxicon. Volume 144, 15 March 2018, Pages 42-47. https://doi.org/10.1016/j.toxicon.2018.01.022
Venom toxicity assessments are often based upon non-native surrogate prey species that are not consumed in the wild by the venomous predator. This raises questions about the relevance of toxicity results on these “model” prey in addressing ecological or evolutionary questions about venom effects on native prey. We explore this issue by comparing the toxicity of venom from pygmy rattlesnakes (Sistrurus miliarius) on taxonomically-diverse sets of model (non-native) and native prey. Specifically, we compared rattlesnake venom toxicity for nine species from three broad taxonomic groups of prey (reptiles, mammals, and amphibians) to determine whether estimates of venom toxicity for the non-native model species of each group was representative of species which were native prey. In all three groups, model species (Anolis sagrei, Mus musculus, and Lithobates pipiens) had a significantly different mortality response from one or more of the native prey species (Anolis carolinensis, Peromyscus gossypinus, Lithobates sphenocephalus, Hyla cinerea, and Hyla squirella) that the models were meant to represent. Two features of our results suggest an importance of evolutionary history in understanding these differences. First, there was a phylogenetic component to prey responses to venom in that in each group, non-native models and congeneric native prey showed more similar responses than prey from other genera suggesting that venom may act on common prey targets that result from common ancestry. Second, native prey generally showed higher LD50 values than their non-native counterparts, suggesting greater resistance to venom from a predator with which they interact in nature. Our results suggest that researchers should use native prey to generate measures of venom toxicity that are ecologically and evolutionarily relevant. If this is not possible using “model” prey species that are close taxonomic relatives to natural prey may be a reasonable alternative.
Cladogenesis and Genomic Streamlining in Extracellular Endosymbionts of Tropical Stink Bugs
Alejandro Otero-Bravo, Shana Goffredi, and Zakee L. Sabree. 2018. Genome Biol. Evol. 10(2):680–693. doi:10.1093/gbe/evy033
Phytophagous stink bugs are globally distributed and many harbor vertically inherited bacterial symbionts that are extracellular, yet little is known about how the symbiont’s genomes have evolved under this transmission strategy. Genome reduction is common in insect intracellular symbionts but limited genome sampling of the extracellular symbionts of distantly related stink bugs has precluded inferring patterns of extracellular symbiont genome evolution. To address this knowledge gap, we completely sequenced the genomes of the uncultivable bacterial symbionts of four neotropical stink bugs of the Edessa genus. Phylogenetic and comparative analyses indicated that the symbionts form a clade within the Pantoea genus and their genomes are highly reduced ( 0.8 Mb). Furthermore, genome synteny analysis and a jackknife approach for phylogenetic reconstruction, which corrected for long branch attraction artifacts, indicated that the Edessa symbionts were the result of a single symbiotic event that was distinct from the symbiosis event giving rise to Candidatus “Pantoea carbekii,” the extracellular symbiont of the invasive pentatomid stink bug, Halyomorpha halys. Metabolic functions inferred from the Edessa symbiont genomes suggests a shift in genomic composition characteristic of its lifestyle in that they retained many host-supportive functions while undergoing dramatic gene loss and establish- ing a stable relationship with their host insects. Given the undersampled nature of extracellular insect symbionts, this study is the first comparative analysis of these symbiont genomes from four distinct Edessa stink bug species. Finally, we propose the candidate name “Candidatus Pantoea edessiphila” for the species of these symbionts with strain designations according to their host species.
Recent lineage diversification in a venomous snake through dispersal across the Amazon River
H Lisle Gibbs, Michael Sovic, Diana Amazonas, Hippocrates Chalkidis, David Salazar-Valenzuela, Ana M Moura-Da-Silva. Biological Journal of the Linnean Society, , blx158, https://doi.org/10.1093/biolinnean/blx158
Identifying the evolutionary and ecological mechanisms that drive lineage diversification in the species-rich tropics is of broad interest to evolutionary biologists. Here, we use phylogeographical and demographic analyses of genome-scale RADseq data to assess the impact of a large geographical feature, the Amazon River, on lineage formation in a venomous pitviper, Bothrops atrox. We compared genetic differentiation in samples from four sites near Santarem, Brazil, that spanned the Amazon and represented major habitat types. A species delimitation analysis identified each population as a distinct evolutionary lineage while a species tree analysis with populations as taxa revealed a phylogenetic tree consistent with dispersal across the Amazon from north to south. Phylogenetic analyses of mitochondrial DNA variation confirmed this pattern and suggest that all lineages originated during the mid- to late Pleistocene. Historical demographic analyses support a population model of lineage formation through isolation between lineages with low ongoing migration between large populations and reject a model of differentiation through isolation by distance alone. The results provide a rare example of a phylogeographical pattern demonstrating dispersal over evolutionary timescales across a large tropical river and suggest a role for the Amazon River as a driver of in situ divergence both by impeding (but not preventing) gene flow and through parapatric differentiation along an ecological gradient.
Total duplication of the small single copy region in the angiosperm plastome: Rearrangement and inverted repeat instability in Asarum
Sinn, B. T., D. D. Sedmak, L. M. Kelly, and J. V. Freudenstein. 2018. American Journal of Botany 0(0): 1–14. DOI: 10.1002/ajb2.1001
As more plastomes are assembled, it is evident that rearrangements, losses, intergenic spacer expansion and contraction, and syntenic breaks within otherwise functioning plastids are more common than was thought previously, and such changes have developed independently in disparate lineages. However, to date, the magnoliids remain characterized by their highly conserved plastid genomes (plastomes).
Illumina HiSeq and MiSeq platforms were used to sequence the plastomes of Saruma henryi and those of representative species from each of the six taxonomic sections of Asarum. Sequenced plastomes were compared in a phylogenetic context provided by maximum likelihood and parsimony inferences made using an additional 18 publicly available plastomes from early-diverging angiosperm lineages.
In contrast to previously published magnoliid plastomes and the newly sequenced Saruma henryi plastome published here, Asarum plastomes have undergone extensive disruption and contain extremely lengthy AT-repeat regions. The entirety of the small single copy region (SSC) of A. canadense and A. sieboldii var. sieboldii has been incorporated into the inverted repeat regions (IR), and the SSC of A. delavayi is only 14 bp long. All sampled Asarum plastomes share an inversion of a large portion of the large single copy region (LSC) such that trnE-UUC is adjacent to the LSC-IR boundary.
Plastome divergence in Asarum appears to be consistent with trends seen in highly rearranged plastomes of the monocots and eudicots. We propose that plastome instability in Asarum is due to repetitive motifs that serve as recombinatory substrates and reduce genome stability.
Evidence that Myotis lucifugus ‘subspecies’ are five non-sister species, despite gene flow
Ariadna E Morales, Bryan C Carstens. 2018. Systematic Biology, syy010, https://doi.org/10.1093/sysbio/syy010
While genetic exchange between non-sister species was traditionally considered to be rare in mammals, analyses of molecular data in multiple systems suggest that it may be common. Interspecific gene flow, if present, is problematic for phylogenetic inference, particularly for analyses near the species level. Here, we explore how to detect and account for gene flow during phylogeny estimation using data from a clade of North American Myotis bats where previous results have led researchers to suspect that gene flow among lineages is present. Initial estimates of phylogenetic networks and species trees indicate that subspecies described within M. lucifugus are paraphyletic. In order to explore the extent to which gene flow is likely to interfere with phylogeny estimation, we use posterior predictive simulation and a novel ABC approach based on gene tree distances. The former indicates that the species tree model is a poor fit to the data, and the latter provides evidence that a species tree with gene flow is a better fit. Taken together, we present evidence that the currently recognized M. lucifugus subspecies are paraphyletic, exchange alleles with other Myotis species in regions of secondary contact, and should be considered independent evolutionary lineages despite their morphological similarity.
A mosaic of phenotypic variation in giant ragweed (Ambrosia trifida): local and continental scale patterns in a range-expanding agricultural weed
Stephen M. Hovick, Andrea McArdle, S. Kent Harrison, Emilie E. Regnier. 2018. doi: 10.1111/eva.12614
Spatial patterns of trait variation across a species’ range have implications for population success and evolutionary change potential, particularly in range-expanding and weedy species that encounter distinct selective pressures at large and small spatial scales simultaneously. We investigated intraspecific trait variation in a common garden experiment with giant ragweed (Ambrosia trifida), a highly variable agricultural weed with an expanding geographic range and broad ecological amplitude. Our study included paired populations from agricultural and natural riparian habitats in each of seven regions ranging east to west from the core of the species’ distribution in central Ohio to southeastern Minnesota, which is nearer the current invasion front. We observed trait variation across both large- and small-scale putative selective gradients. At large scales, giant ragweed populations from the westernmost locations were nearly four times more fecund and had a nearly 50% increase in reproductive allocation compared to populations from the core. The degree of surface texture on fruits also declined from east to west. Greater fecundity in the west represents a putative tradeoff between fruit size and fruit number across the study region, although no such tradeoff was found across individual plants. This pattern may effectively result in greater propagule pressure closer to the invasion front. At smaller spatial scales, plants from agricultural populations emerged later and were smaller than plants from riparian populations. However, because plants from agricultural populations allocated more biomass to reproduction, total fecundity did not differ across habitats. Our emergence data are consistent with previous observations showing delayed emergence in agricultural compared to natural populations; thus evolutionary change may be predictable as giant ragweed continues spreading into agricultural fields throughout North America. These shifts in life-history strategy apparently bear no fecundity cost, suggesting that giant ragweed’s success can be attributed at least in part to its substantial adaptive potential.
The importance of historical land use in the maintenance of early successional habitat for a threatened rattlesnake
Eric M. McCluskey, Stephen N. Matthews, Isaac Y. Ligocki, Matthew L. Holding, Gregory J. Lipps Jr., Thomas E. Hetherington. 2018. Global Ecology and Conservation. Available online 17 February 2018, Article e00370 https://doi.org/10.1016/j.gecco.2017.e00370