ORCID Profile
0000-0002-1145-9226
Current Organisations
Uppsala University
,
The University of Auckland
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Publisher: Wiley
Date: 07-02-2013
DOI: 10.1002/ECE3.484
Abstract: Characterization of the genetic basis of fitness traits in natural populations is important for understanding how organisms adapt to the changing environment and to novel events, such as epizootics. However, candidate fitness‐influencing loci, such as regulatory regions, are usually unavailable in nonmodel species. Here, we analyze sequence data from targeted resequencing of the cis‐regulatory regions of three candidate genes for disease resistance ( CD 74 , HSP 90α , and LCP 1 ) in populations of the house finch ( Carpodacus mexicanus ) historically exposed (Alabama) and naïve (Arizona) to Mycoplasma gallisepticum . Our study, the first to quantify variation in regulatory regions in wild birds, reveals that the upstream regions of CD 74 and HSP 90α are GC ‐rich, with the former exhibiting unusually low sequence variation for this species. We identified two SNP s, located in a GC ‐rich region immediately upstream of an inferred promoter site in the gene HSP 90α , that were significantly associated with Mycoplasma pathogen load in the two populations. The SNP s are closely linked and situated in potential regulatory sequences: one in a binding site for the transcription factor nuclear NFY α and the other in a dinucleotide microsatellite (( GC ) 6 ). The genotype associated with pathogen load in the putative NFY α binding site was significantly overrepresented in the Alabama birds. However, we did not see strong effects of selection at this SNP , perhaps because selection has acted on standing genetic variation over an extremely short time in a highly recombining region. Our study is a useful starting point to explore functional relationships between sequence polymorphisms, gene expression, and phenotypic traits, such as pathogen resistance that affect fitness in the wild.
Publisher: Oxford University Press (OUP)
Date: 06-2023
Abstract: The ornate spiny rock lobster, Panulirus ornatus, is an attractive candidate for aquaculture. The larval stages of spiny lobsters, known as phyllosoma, are complex with many developmental stages. Very little is known about the inorganic element composition of phyllosoma. In this study, a novel method using synchrotron X-ray fluorescence microscopy (XFM) was applied to investigate the distributions of metals potassium (K), calcium (Ca), copper (Cu), zinc (Zn), the metalloid arsenic (As), and nonmetal bromine (Br) within in idual phyllosoma at stages 3, 4, and 8 of their development. For the first time, 1 µm resolution synchrotron XFM images of whole phyllosoma as well as closer examinations of their eyes, mouths, setae, and tails were obtained. Elements accumulated in certain locations within phyllosoma, providing insight into their likely biological role for these organisms. This information may be useful for the application of dietary supplementation in the future to closed larval cycle lobster aquaculture operations.
Publisher: Cold Spring Harbor Laboratory
Date: 13-02-2023
DOI: 10.1101/2023.02.13.528213
Abstract: Key innovations are fundamental to biological ersification, but their genetic architecture is poorly understood. A recent transition from egg-laying to live-bearing in Littorina snails provides the opportunity to study the architecture of an innovation that has evolved repeatedly in animals. S les do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous genomic regions where all live-bearers carry the same core haplotype. Associated regions show evidence for live-bearer-specific positive selection, and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest live-bearing alleles accumulated gradually, involving selection at different times in the past. Our results suggest that innovation can have a polygenic basis, and that novel functions can evolve gradually, rather than in a single step.
Publisher: Wiley
Date: 15-12-2022
DOI: 10.1111/MEC.16793
Abstract: The term “haplotype block” is commonly used in the developing field of haplotype‐based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a s le. We use simulated ex les to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked‐read sequencing technologies.
No related grants have been discovered for Daria Shipilina.