Biology subjects

Baker, J. P.

Publications and source records attributed to Baker, J. P..

3 recordsLinked to original sources

bioRxiv2024

Evidence of genetic isolation and differentiation among historically fragmented British populations of common juniper, Juniperus communis L.

Habitat fragmentation and populations isolation pose a threat to the genetic diversity and adaptability of many species. The common juniper, Juniperus communis L., a keystone species for juniper scrub habitat and one of only three conifers that are native to the UK, has been in decline for more than a century in the UK and across its European range. Remnant UK juniper populations are now highly fragmented and often small, which has raised concerns for their resilience, especially in the face of climate change and the introduction of novel pathogens, such as Phytophthora austrocedri. This work presents a baseline genetic survey of native UK juniper populations and compares patterns of diversity between populations and among three population centres in southern England, the Lake District, and Scotland using both Single Nucleotide Polymorphism (SNP) and Simple Sequence Repeat (SSR) genetic markers. The aim was to evaluate the standing genetic diversity of native juniper stands, the impacts of habitat fragmentation, and to determine whether juniper populations are genetically isolated from one another. We found that juniper populations, while not completely isolated from one another, face substantial barriers to gene flow, especially between the three population centres. These centres also show different patterns of genetic diversity, indicating varying levels of internal gene flow and inbreeding. Our findings can form a baseline from which to monitor the effectiveness of conservation activities, prioritize populations of concern, and guide genetic rescue efforts.

genetics↗

bioRxiv2024

Not like other conifers: evaluation of phenotypic diversity in British common juniper, Juniperus communis, indicates genetic isolation and local adaptations among remnant populations

Habitat fragmentation and genetic isolation pose threats to the genetic diversity and resilience of natural populations. Protecting the genetic diversity of populations, and the processes that sustain it, optimises their ability to adapt to changing conditions and new threats: conservation efforts with this specific goal are known as "dynamic conservation." The common juniper, Juniperus communis, is a keystone species that provides habitat and resources for many plants and animals. It is a highly polymorphic species, and across its natural range it grows in a variety of habitats and growth forms. Juniper populations have been shrinking and becoming increasingly fragmented for over a century in the UK and elsewhere in Europe, raising concerns about the genetic diversity present in juniper populations and their ability to adapt to changing conditions, or their adaptive potential. This paper presents an analysis of the partitioning of phenotypic diversity among regions, populations and families from 16 UK populations assessed in a common garden trial. Our findings suggest high phenotypic variation among populations compared to the variation among families within populations, indicating barriers to gene flow between juniper populations, relatively homogenous populations and, consequently, potentially reduced adaptive potential. This information is a useful baseline for conservation managers and can also help to infer the genetic diversity and adaptive potential of populations.

genetics↗

bioRxiv2024

PRRSV-2 variant classification: a dynamic nomenclature for enhanced monitoring and surveillance

Existing genetic classification systems for porcine reproductive and respiratory syndrome virus 2 (PRRSV-2), such as restriction fragment length polymorphisms (RFLPs) and sub-lineages, are unreliable indicators of genetic relatedness or lack sufficient resolution for epidemiological monitoring routinely conducted by veterinarians. Here, we outline a fine-scale classification system for PRRSV-2 genetic variants in the U.S. Based on >25,000 U.S. open-reading-frame 5 (ORF5) sequences, sub-lineages were divided into genetic variants using a clustering algorithm. Through classifying new sequences every three months and systematically identifying new variants across eight years, we demonstrated that prospective implementation of the variant classification system produced robust, reproducible results across time and can dynamically accommodate new genetic diversity arising from virus evolution. From 2015 and 2023, 118 variants were identified, with [~]48 active variants per year, of which 26 were common (detected >50 times). Mean within-variant genetic distance was 2.4% (max: 4.8%). The mean distance to the closest related variant was 4.9%. A routinely updated webtool (https://stemma.shinyapps.io/PRRSLoom-variants/) was developed and is publicly available for end-users to assign newly generated sequences to a variant ID. This classification system relies on U.S. sequences from 2015 onwards; further efforts are required to extend this system to older or international sequences. Finally, we demonstrate how variant classification can better discriminate between previous and new strains on a farm, determine possible sources of new introductions into a farm/system, and track emerging variants regionally. Adoption of this classification system will enhance PRRSV-2 epidemiological monitoring, research, and communication, and improve industry responses to emerging genetic variants. ImportanceThe development and implementation of a fine-scale classification system for PRRSV-2 genetic variants represents a significant advancement for monitoring PRRSV-2 occurrence in the swine industry. Based on systematically-applied criteria for variant identification using national-scale sequence data, this system addresses the shortcomings of existing classification methods by offering higher resolution and adaptability to capture emerging variants. This system provides a stable and reproducible method for classifying PRRSV-2 variants, facilitated by a freely available and regularly updated webtool for use by veterinarians and diagnostic labs. Although currently based on U.S. PRRSV-2 ORF5 sequences, this system can be expanded to include sequences from other countries, paving the way for a standardized global classification system. By enabling accurate and improved discrimination of PRRSV-2 genetic variants, this classification system significantly enhances the ability to monitor, research, and respond to PRRSV-2 outbreaks, ultimately supporting better management and control strategies in the swine industry.

microbiology↗