Biology subjects

Richardson, M. F.

Publications and source records attributed to Richardson, M. F..

11 recordsLinked to original sources

bioRxiv2023

Is developmental plasticity triggered by DNA methylation changes in the invasive cane toad (Rhinella marina)?

Many organisms can adjust their development according to environmental conditions, including the presence of conspecifics. Although this developmental plasticity is common in amphibians, its underlying molecular mechanisms remain largely unknown. Exposure during development to either cannibal cues from older conspecifics, or alarm cues from injured conspecifics, causes reduced growth and survival in cane toad (Rhinella marina) tadpoles. Epigenetic modifications, such as changes in DNA methylation patterns, are a plausible mechanism underlying these developmental plastic responses. Here we tested this hypothesis, and asked whether cannibal cues and alarm cues trigger the same DNA methylation changes in developing cane toads. We found that exposure to both cannibal cues and alarm cues induced local changes in DNA methylation patterns. These DNA methylation changes affected genes putatively involved in developmental processes, but in different genomic regions for different conspecific-derived cues. Genetic background explained most of the epigenetic variation among individuals. Overall, the molecular mechanisms triggered by exposure to cannibal cues seem to differ from those triggered by alarm cues. Studies linking epigenetic modifications to transcriptional activity are needed to clarify the proximate mechanisms that regulate developmental plasticity in cane toads.

molecular biology↗

bioRxiv2021

Brain transcriptome analysis reveals gene expression differences associated with dispersal behaviour between range-front and range-core populations of invasive cane toads in Australia

Understanding the mechanisms underlying rapid adaptation of invasive species in novel environments is key to improving our ability to manage these species. Many invaders demonstrate rapid evolution of behavioural traits involved in range expansion such as locomotor activity, exploration and risk-taking. However, the molecular mechanisms that underpin these changes are poorly understood. In 86 years, invasive cane toads (Rhinella marina) in Australia have drastically expanded their geographic range westward from coastal Queensland to Western Australia. During their range expansion, toads have undergone extensive phenotypic changes, particularly in behaviours that enhance the toads dispersal ability. Common-garden experiments have shown that some changes in behavioural traits related to dispersal are heritable. However, genetic diversity is greatly reduced across the invasive range due to a strong founder effect, and the genetic basis underlying dispersal-related behavioural changes remains unknown. Here we used RNA-seq to compare the brain transcriptomes of toads from the Hawaiian source population, as well as three distinct populations from across the Australian invasive range. We found markedly different gene expression profiles between the source population and Australian toads. By contrast, cane toads from across the Australian invasive range had very similar transcriptomic profiles. Yet, key genes with functions putatively related to dispersal behaviour showed differential expression between range-core and range-front populations. These genes could play an important role in the behavioural changes characteristic of range expansion in Australian cane toads.

genomics↗

bioRxiv2020

Inherent population structure determines the importance of filtering parameters for reduced representation sequencing analyses

As technological advancements enhance our ability to study population genetics, we must understand how the intrinsic properties of our datasets influence the decisions we make when designing experiments. Filtering parameter thresholds, such as call rate and minimum minor allele frequency (MAF), are known to affect inferences of population structure in reduced representation sequencing (RRS) studies. However, it is unclear to what extent the impacts of these parameter choices vary across datasets. Here, we reviewed literature on filtering choices and levels of genetic differentiation across RRS studies on wild populations to highlight the diverse approaches that have been used. Next, we hypothesized that choices in filtering thresholds would have the greatest impact when analyzing datasets with low levels of genetic differentiation between populations. To test this hypothesis, we produced seven simulated RRS datasets with varying levels of population structure, and analyzed them using four different combinations of call rate and MAF. We performed the same analysis on two empirical RRS datasets (low or high population structure). Our simulated and empirical results suggest that the effects of filtering choices indeed vary based on inherent levels of differentiation: specifically, choosing stringent filtering choices was important to detect distinct populations that were slightly differentiated, but not those that were highly differentiated. As a result, experimental design and analysis choices need to consider attributes of each specific dataset. Based on our literature review and analyses, we recommend testing a range of filtering parameter choices, and presenting all results with clear justification for ultimate filtering decisions used in downstream analyses.

bioinformatics↗

bioRxiv2020

Supervising the PhD: identifying common mismatches in expectations between candidate and supervisor to improve research training outcomes

The relationship between a PhD candidate and their supervisor is influential in not only successful candidate completion, but maintaining candidate satisfaction and mental health. We quantified potential mismatches between the PhD candidates and supervisors expectations as a potential mechanism that facilitates poor candidate experiences and research training outcomes. 114 PhD candidates and 52 supervisors ranked the importance of student attributes and outcomes at the beginning and end of candidature. In relation to specific attributes, supervisors indicated the level of guidance they expected to give the candidate and candidates indicated the level of guidance they expected to receive. Candidates also report on whether different aspects of candidature influenced their mental well-being. We identified differences between candidates and supervisors perceived supervisor teaching responsibility and influences on mental well-being. Our results indicate that the majority of candidates were satisfied overall with their supervision, and find alignment of many expectations between both parties. Yet, we find that candidates have much higher expectations of achieving quantitative outcomes than supervisors. Supervisors believed they give more guidance to candidates than candidates perceive they received, and supervisors often only provided guidance when the candidate explicitly asked. Personal expectations and research progress significantly and negatively influenced over 50% of candidates mental well-being. Our results highlight the importance of candidates and supervisors explicitly communicating the responsibilities and expectations of the roles they play in helping candidates develop research skills. We provide four suggestions to supervisors that may be particularly effective at increasing communication, avoiding potential conflict and promoting candidate success and wellbeing.

scientific communication and education↗

bioRxiv2019

Local signatures of founding populations confound examination of adaptive divergence in invasive populations

A detailed understanding of population genetics in invasive populations helps us to identify drivers of successful introductions. Here, we investigate putative signals of selection in Australian populations of invasive common starlings, Sturnus vulgaris, and seek to understand how these have been influenced by introduction history. We use reduced representation sequencing to determine population structure, and identity Single Nucleotide Polymorphisms (SNPs) that are putatively under selection. We found that since their introduction into Australia, starling populations have become genetically differentiated despite the potential for high levels of dispersal, and that selection has facilitated their adaptation to the wide range of environmental conditions across their geographic range. Isolation by distance appears to have played a strong role in determining genetic substructure across the starlings Australian range. Analyses of candidate SNPs that are putatively under selection indicate that aridity, precipitation, and temperature may be important factors driving adaptive variation across the starlings invasive range in Australia. However, we also note that the historic introduction regime may leave footprints on sites flagged as being under adaptive selection, and encourage critical interpretation of selection analyses.

evolutionary biology↗

bioRxiv2019

Immune and environment-driven gene expression during invasion: An eco-immunological application of RNA-Seq

Host-pathogen dynamics change rapidly during a biological invasion and are predicted to impose strong selection on immune function. The invader may experience an abrupt reduction in pathogen-mediated selection ( enemy release), thereby favoring decreased investment into costly immune responses, and the extent of this reduction may depend on factors such as propagule size. Across plants and animals, there is mixed support for this prediction. Pathogens are not the only form of selection imposed on invaders; differences in abiotic environmental conditions between native and introduced ranges are also expected to drive rapid evolution. Here, we assess the expression patterns of immune and environmentally-associated genes in the cane toad (Rhinella marina) across its invasive Australian range. Transcripts encoding mediators of costly immune responses (inflammation, cytotoxicity) showed a curvilinear relationship with invasion history, with highest expression in toads from oldest and newest colonized areas. This pattern is surprising given theoretical expectations of density dynamics in invasive species, and may be because density influences both intraspecific competition and parasite transmission, generating conflicting effects on the strength of immune responses. Alternatively, this expression pattern may be the result of other evolutionary forces, such as spatial sorting and genetic drift, working simultaneously with natural selection. Our findings do not support predictions about immune function based on the enemy release hypothesis, and suggest instead that the effects of enemy release are difficult to isolate in wild populations. Additionally, expression patterns of genes underlying putatively environmentally-associated traits are consistent with previous genetic studies, providing further support that Australian cane toads have adapted to novel abiotic challenges.

ecology↗

bioRxiv2019

Invaders weather the weather: rapid adaptation to a novel environment occurs despite reduced genetic diversity

Invasive species often exhibit rapid evolution in their introduced ranges despite the genetic bottlenecks that are thought to accompany the translocation of small numbers of founders; however, some invasions may not fit this "genetic paradox." The invasive cane toad (Rhinella marina) displays high phenotypic variation across its environmentally heterogeneous introduced Australian range. Here, we used three genome-wide datasets to characterize population structure and genetic diversity in invasive toads: RNA-Seq data generated from spleens sampled from the toads native range in French Guiana, the introduced population in Hawaii that was the source of Australian founders, and Australia; RNA-Seq data generated from brains sampled more extensively in Hawaii and Australia; and previously published RADSeq data from transects across Australia. We found that toads form three genetic clusters: (1) native range toads, (2) toads from the source population in Hawaii and long-established areas near introduction sites in Australia, and (3) toads from more recently established northern Australian sites. In addition to strong divergence between native and invasive populations, we find evidence for a reduction in genetic diversity after introduction. However, we do not see this reduction in loci putatively under selection, suggesting that genetic diversity may have been maintained at ecologically relevant traits, or that mutation rates were high enough to maintain adaptive potential. Nonetheless, cane toads encounter novel environmental challenges in Australia and appear to respond to selection across environmental breaks; the transition between genetic clusters occurs at a point along the invasion transect where temperature rises and rainfall decreases. We identify loci known to be involved in resistance to heat and dehydration that show evidence of selection in Australian toads. Despite well-known predictions regarding genetic drift and spatial sorting during invasion, this study highlights that natural selection occurs rapidly and plays a vital role in shaping the structure of invasive populations. Author SummaryDespite longstanding evidence for the link between genetic diversity and population viability, the "genetic paradox" concept reflects the observation that invasive populations are successful in novel environments despite a putative reduction in genetic diversity. However, some recent studies have suggested that successful invasions may often occur due to an absence of obstacles such as genetic diversity loss or novel adaptive challenges. The recent emergence of genome-wide technologies provides us with the tools to study this question comprehensively by assessing both overall genetic diversity, and diversity of loci that underlie ecologically relevant traits. The invasive cane toad is a useful model because there is abundant phenotypic evidence of rapid adaptation during invasion. Our results suggest strong genetic divergence between native and invasive populations, and a reduction in overall genetic diversity; however, we do not see this reduction when solely assessing ecologically relevant loci. This could be for reasons that support or refute the genetic paradox. Further studies may provide perspectives from other systems, allowing us to explore how variables such as propagule size affect the fit of an invasion to the model of the paradox. Studying invasive species remains important due to their largely negative impacts on the environment and economy.

evolutionary biology↗

bioRxiv2018

A field guide for the compositional analysis of any-omics data

Next-generation sequencing (NGS) has made it possible to determine the sequence and relative abundance of all nucleotides in a biological or environmental sample. Today, NGS is routinely used to understand many important topics in biology from human disease to microorganism diversity. A cornerstone of NGS is the quantification of RNA or DNA presence as counts. However, these counts are not counts per se: the magnitude of the counts are determined arbitrarily by the sequencing depth, not by the input material. Consequently, counts must undergo normalization prior to use. Conventional normalization methods require a set of assumptions: they assume that the majority of features are unchanged, and that all environments under study have the same carrying capacity for nucleotide synthesis. These assumptions are often untestable and may not hold when comparing heterogeneous samples (e.g., samples collected across distinct cancers or tissues). Instead, methods developed within the field of compositional data analysis offer a general solution that is assumption-free and valid for all data. In this manuscript, we synthesize the extant literature to provide a concise guide on how to apply compositional data analysis to NGS count data. In doing so, we review zero replacement, differential abundance analysis, and within-group and between-group coordination analysis. We then discuss how this pipeline can accommodate complex study design, facilitate the analysis of vertically and horizontally integrated data, including multiomics data, and further extend to single-cell sequencing data. In highlighting the limitations of total library size, effective library size, and spike-in normalizations, we propose the log-ratio transformation as a general solution to answer the question, \"Relative to some important activity of the cell, what is changing?\". Taken together, this manuscript establishes the first fully comprehensive analysis protocol that is suitable for any and all -omics data.

bioinformatics↗

bioRxiv2017

Understanding sequencing data as compositions: anoutlook and review

MotivationAlthough seldom acknowledged explicitly, count data generated by sequencing platforms exist as compositions for which the abundance of each component (e.g., gene or transcript) is only coherently interpretable relative to other components within that sample. This property arises from the assay technology itself, whereby the number of counts recorded for each sample is constrained by an arbitrary total sum (i.e., library size). Consequently, sequencing data, as compositional data, exist in a non-Euclidean space that renders invalid many conventional analyses, including distance measures, correlation coefficients, and multivariate statistical models.\n\nResultsThe purpose of this review is to summarize the principles of compositional data analysis (CoDA), provide evidence for why sequencing data are compositional, discuss compositionally valid methods available for analyzing sequencing data, and highlight future directions with regard to this field of study.

bioinformatics↗

bioRxiv2017

Best Practice Data Life Cycle Approaches for the Life Sciences

Throughout history, the life sciences have been revolutionised by technological advances; in our era this is manifested by advances in instrumentation for data generation, and consequently researchers now routinely handle large amounts of heterogeneous data in digital formats. The simultaneous transitions towards biology as a data science and towards a life cycle view of research data pose new challenges. Researchers face a bewildering landscape of data management requirements, recommendations and regulations, without necessarily being able to access data management training or possessing a clear understanding of practical approaches that can assist in data management in their particular research domain.\n\nHere we provide an overview of best practice data life cycle approaches for researchers in the life sciences/bioinformatics space with a particular focus on omics datasets and computer-based data processing and analysis. We discuss the different stages of the data life cycle and provide practical suggestions for useful tools and resources to improve data management practices.

bioinformatics↗

bioRxiv2017

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

In the life sciences, many assays measure only the relative abundances of components for each sample. These data, called compositional data, require special handling in order to avoid misleading conclusions. For example, in the case of correlation, treating relative data like absolute data can lead to the discovery of falsely positive associations. Recently, researchers have proposed proportionality as a valid alternative to correlation for calculating pairwise association in relative data. Although the question of how to best measure proportionality remains open, we present here a computationally efficient R package that implements two proposed measures of proportionality. In an effort to advance the understanding and application of proportionality analysis, we review the mathematics behind proportionality, demonstrate its application to genomic data, and discuss some ongoing challenges in the analysis of relative abundance data.

bioinformatics↗