309 research outputs found
First person - Sonal
No full textFirst Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside their papers. Sonal is the first author on ‘Myosin-II activity generates a dynamic steady state with continuous actin turnover in a minimal actin cortex’, published in Journal of Cell Science. Sonal conducted the research in this article while a PhD student in the lab of Petra Schwille at the Max Planck Institute of Biochemistry, Martinsried, Germany, studying biological pattern formation using a bottom-up reconstitution approach
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No full textFirst published: 17 July 2023Genomic-scale datasets, sophisticated analytical techniques, and conceptual advances have disproportionately failed to resolve species boundaries in some groups relative to others. To understand the processes that underlie taxonomic intractability, we dissect the speciation history of an Australian lizard clade that arguably represents a “worst-case” scenario for species delimitation within vertebrates: the Ctenotus inornatus species group, a clade beset with decoupled genetic and phenotypic breaks, uncertain geographic ranges, and parallelism in purportedly diagnostic morphological characters. We sampled hundreds of localities to generate a genomic perspective on population divergence, structure, and admixture. Our results revealed rampant paraphyly of nominate taxa in the group, with lineages that are either morphologically cryptic or polytypic. Isolation-by-distance patterns reflect spatially continuous differentiation among certain pairs of putative species, yet genetic and geographic distances are decoupled in other pairs. Comparisons of mitochondrial and nuclear gene trees, tests of nuclear introgression, and historical demographic modelling identified gene flow between divergent candidate species. Levels of admixture are decoupled from phylogenetic relatedness; gene flow is often higher between sympatric species than between parapatric populations of the same species. Such idiosyncratic patterns of introgression contribute to species boundaries that are fuzzy while also varying in fuzziness. Our results suggest that “taxonomic disaster zones” like the C. inornatus species group result from spatial variation in the porosity of species boundaries and the resulting patterns of genetic and phenotypic variation. This study raises questions about the origin and persistence of hybridizing species and highlights the unique insights provided by taxa that have long eluded straightforward taxonomic categorization.Ivan Prates, Mark N. Hutchinson, Sonal Singhal, Craig Moritz, Daniel L. Rabosk
Data from: De novo transcriptomic analyses for non-model organisms: an evaluation of methods across a multi-species data set
No full textHigh-throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still poses notable challenges, especially for those working with organisms without a high-quality reference genome. For every stage of analysis – from assembly to annotation to variant discovery – researchers have to distinguish technical artefacts from the biological realities of their data before they can make inference. In this work, I explore these challenges by generating a large de novo comparative transcriptomic data set data for a clade of lizards and constructing a pipeline to analyse these data. Then, using a combination of novel metrics and an externally validated variant data set, I test the efficacy of my approach, identify areas of improvement, and propose ways to minimize these errors. I find that with careful data curation, HTS can be a powerful tool for generating genomic data for non-model organisms
transcriptomic analyses for non‐model organisms: an evaluation of methods across a multi‐species data set
No full textdataset for Bio 440 Mod 2 - featureCounts
No full textdata from Wu et al 2019: https://www.pnas.org/content/117/45/2833
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A Fine Scale Analysis of a Tropical Suture Zone
No full textIn my dissertation, I use a comparative approach to exploit an outstanding natural experiment, a suture zone in the rainforest of northeast Australia, to answer questions about speciation and hybridization. The suture zone consists of twenty identified contacts between phylogeographic lineages, mostly within morphologically defined species. Although the contacts in the zone likely formed concurrently in response to Holocene expansion from glacial refugia, the lineage-pairs meeting in the contacts exhibit a wide range of genetic divergences. This natural variation enables analysis of the outcomes of secondary contact at different stages of the divergence process. Importantly, although most studies of speciation focus on lineages that show marked phenotypic divergence, I focus on morphologically cryptic lineages, which, though common in nature, have been understudied in this regard. Through my dissertation, I consider contact zones between six lineage-pairs within four morphologically-defined skink species, Carlia rubrigularis, Lampropholis coggeri, Saproscincus basiliscus, and S. lewisi.Through this work, I find support for the reality of cryptic species and argue that the presence of cryptic species can suggest a wider plurality of speciation models than we typically consider (Chapter 1). Indeed, by combining multilocus methods and dense sampling, I find that reproductive isolation between phylogeographic lineages scales tightly with divergence (Chapter 2). These results support the widespread, yet previously unsubstantiated, notion that phylogeographic structure of increasing depth represents a continuum towards complete speciation, even in the absence of overt ecologically-driven divergent selection. I extend these results by looking at introgression across the genome, finding that genome-wide selection, driven by selection against hybrids, structures introgression patterns much more strongly than locus-specific selection histories (Chapter 3). By analyzing the sole lineage-pair in this system that exhibits genealogical discordance, I suggest that geographic stability across time is key to driving divergence (Chapter 4). Further, through combining a fine-scale investigation of a single contact zone with simulations and a meta-analysis, I argue that selection against hybrids, in the form of intrinsic genetic incompatibilities, maintains species boundaries at these contact zones (Chapter 5). Finally, as my work is enabled by emerging genomic technologies for non-model organisms, I summarize my genomics approach, and its associated benefits and challenges, as applied to transcriptome data from these lineages (Chapter 6)
RNAseq data for Module 4
No full text<p>RNAseq data from here: https://www.ncbi.nlm.nih.gov/sra/SRR1171978</p>
DNAseq data for Module 4
No full text<p>Data from <a href="https://zenodo.org/api/files/689f4a2c-4659-4fda-af5f-8b7752c07129/DNA_SRR1171886_1.fastq.gz">SRR1171886</a> (downfiltered)</p>
Mechanical behavior of unsaturated compacted Iowa loess
No full textThe collapsible soils possess a high apparent strength at their low natural moisture content but undergo large reduction in volume upon wetting. The volume change and shear strength behavior of a laboratory compacted loess soil was studied and presented. Collapse tests and partial collapse tests were conducted using conventional oedometer. Undrained shear strength was measured from Torvane shear tester. Penetration tests were also performed on collapsible soil specimens. Undrained cohesion, c[Subscript u], was obtained from the measured values of penetration resistance using Sanglerat's equation. Correlations were proposed to relate collapse potential with the penetration resistance. Tests were conducted to determine the variation of water content with suction for loess. The unsaturated soil behavior was investigated for nine conditions produced by varying initial water contents and compactive efforts. The initial water content was replaced with suction and the effect of initial suction on the collapse potential was studied. The collapse potential of loess was found to be dependent on the initial water content, initial dry unit weight and flooding stress (vertical stress at inundation). The amount of partial collapse increased with increase in degree of saturation. The effect of variation in initial water content was more significant as compared to the effect of compactive effort on soil water characteristic curves. Undrained cohesion obtained from Torvane shear tests and penetration tests were found to tally and to give a good correlation. The collapse potential increased with increase in initial suction. However, the percentage increase in collapse on increasing suction reduced as the compactive effort increased.</p
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