Biology subjects

Kostic, A.

Publications and source records attributed to Kostic, A..

4 recordsLinked to original sources

bioRxiv2026

A tribal-scale phylogenomic perspective on ancestry and major lineages of the allotetraploid Hawaiian silversword alliance (Madieae, Compositae)

Premise of the studyDisentangling ancestry of insular plant lineages is important for resolving their evolutionary histories but often complicated by polyploidy, an overrepresented condition in remote island floras. A phylogenomic approach was used to study the origin of subgenomes of the tetraploid Hawaiian silversword alliance and advance understanding of this major example of adaptive radiation. MethodsSequences from 461 target-capture nuclear loci were phased to subgenomes of the tetraploid silversword alliance (Compositae) using assemblies from diploid North American tarweeds as clade references. Maximum-likelihood and multispecies- coalescent analyses of phased loci were conducted with and without representatives of diploid lineages throughout tribe Madieae. Key resultsAn allopolyploid origin of the silversword alliance was corroborated, with Subgenome-A phased consistently to Anisocarpus madioides and Subgenome-B phased to diploid representatives of each of three other sublineages of the "Madia" lineage. Phylogenomic analyses indicate Anisocarpus madioides is more closely related to Subgenome-A than to other tarweeds, including Anisocarpus scabridus. Subgenome trees for the silversword alliance are highly congruent with each other and with structural genomic differences between lineages. ConclusionsThese results indicate an even closer relationship of the silversword alliance to extant California tarweeds than previously understood. Anisocarpus madioides has chromosomal and ecological traits anticipated in an ancestor of the silversword alliance, with the widest geographic range among perennial tarweeds and sticky bracts completely enveloping fruits. Within the silversword alliance, robust support for four major clades reinforces the phylogenetic value of chromosomal interchanges and taxonomic insights by Asa Gray regarding the enigmatic liana Dubautia latifolia.

evolutionary biology↗

bioRxiv2024

The ReAct project: Analysis of data from 23 differentlaboratories to characterise DNA recovery given twosets of activity level propositions

The ReAct (Recovery, Activity) project is an ENFSI (European Network of Forensic Science Institutes) supported initiative comprising a large consortium of laboratories. Here, the results from more than 23 laboratories are presented. The primary purpose was to design experiments simulating typical casework circumstances; collect data and to implement Bayesian networks to assess the value (i.e., likelihood ratio) of DNA results given activity level propositions. Two different experimental designs were used to simulate a robbery, where a screwdriver was used to force a door or window. Propositions and case information were chosen following laboratory feedback listing typical casework circumstances (included in the paper). Whereas the proposition representing prosecutions view is applicable to many cases: the defendant forced the door/window with his screwdriver; the proposition representing defences view are more variable depending on what is alleged to have happened. In a direct transfer experiment, the defendant owned and used the screwdriver, but he did not force the door/window in question. An unknown person used the defendants stolen screwdriver. In an indirect transfer experiment, the defendant neither owned, saw, nor used the screwdriver, nor did they force the door or window. Instead, an unknown individual--someone with whom the defendant had interacted (e.g., by shaking hands or touching the same objects)--used the recovered tool to force entry. In the first experiment, if the defendant forced the door/window, then s/he is the last handler of the screw driver, whereas if the tool was stolen and used by an unknown person, the defendant is the first handler. For the second experiment, given the defence view, the defendant never held the screwdriver. We envisaged the situation where an object manipulated by the defendant (or the defendant himself/herself) would be touched by the unknown offender who would then force the window. The time delay between the touching of the object and the forcing of the window was 0, 1h, and 2h. This was accomplished by handshaking experiments, where the person forcing the door would shake a persons hand, and then use the screwdriver either immediately after hand-shake or after 1, 2 hours. It was found for the direct transfer experiment that unless a single contributor profile aligning with the known persons of interest profile was retrieved, the results did not allow to discriminate propositions. On the other hand, for the indirect transfer experiment, both single and major contributor profiles that aligned with the person of interest (POI) supported the proposition that the person used the tool rather than an unknown person who had touched an object, when indeed the former was true. There was considerable variation in median recoveries of DNA between laboratories (between 200pg - 5ng) for a given experiment if quantities are taken into account. These differences affect the likelihood ratios given activity level propositions. More than 2,700 samples were analysed in the course of this study. Two different Bayesian Networks are made available via an open source application written in Shiny R: Shiny_React(). For comparison, all datasets were analysed using a qualitative method categorised into absent, single, balanced or major given contributors. The need for standardisation of methods is highlighted, along with the need for new methods to assess probability of laboratory dependent DNA recovery. Open access databases that are made freely available are important adjuncts

genetics↗

bioRxiv2019

CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal sediments, from a range of archaeological contexts.

microbiology↗

bioRxiv2019

Mash Screen: High-throughput sequence containment estimation for genome discovery

The MinHash algorithm has proven effective for rapidly estimating the resemblance of two genomes or metagenomes. However, this method cannot reliably estimate the containment of a genome within a metagenome. Here we describe an online algorithm capable of measuring the containment of genomes and proteomes within either assembled or unassembled sequencing read sets. We describe several use cases, including contamination screening and retrospective analysis of metagenomes for novel genome discovery. Using this tool, we provide containment estimates for every NCBI RefSeq genome within every SRA metagenome, and demonstrate the identification of a novel polyomavirus species from a public metagenome.

bioinformatics↗