Biology subjects

McFarlane, S. E.

Publications and source records attributed to McFarlane, S. E..

10 recordsLinked to original sources

bioRxiv2025

Anthropogenic factors explain wing colour variation in Colias (Lepidoptera: Pieridae) across the Toronto urbanization gradient

Hybridization, or interbreeding between two previously diverged populations, is increasing due to human influences on the environment. Rates of hybridization might be increasing particularly quickly among urban species, especially those that are known to be sensitive to environmental disturbances. Butterflies are one such taxa, as some species are commonly found in urban areas, despite being sensitive indicators. For example, Colias philodice and C. eurytheme (Lepidoptera: Pieridae) hybridize when their ranges are in contact or overlap and are commonly found in large cities throughout North America. However, it is an open question how variation in urbanization might affect variation in hybridization. Using wild Colias across a gradient of urbanization in Toronto, Ontario, we tested how the variation in Colias colour, as an indicator of hybridization, relates to human disturbance and urbanization. We created an objective numeric classification for both C. eurytheme and C. philodice, against which we categorized Colias samples. We found that some of the urbanization metrics, including distance to road, Julian date, and number of pedestrians affect the variation in Colias colour, suggesting that urbanization affects Colias colouration, and potentially rates of hybridization, in Toronto. This means that human disturbance of the environment could be affecting Colias rates of hybridization.

evolutionary biology↗

bioRxiv2025

Extensive multi-species hybridization between Leuciscidae minnow species

Anthropogenic disturbances can disrupt ecosystems and alter species population dynamics. Interspecific hybridization is common between genetically related organisms, especially once reproductive barriers such as spatial isolation have been removed. We used genotyping- by-sequencing data to assess outcomes of hybridization between several Leuciscidae minnow species and to identify to what extent land use type and environmental variables influence the frequency of hybridization. We found that both two-species and multi-species hybridization was widespread; hybrids were sampled at all 25 sampling sites and made up almost 30% of all individuals sampled. While most species hybridized with at least one other sampled species, the amount of hybridization was variable. We used logistic regression to estimate the influence of anthropogenic disturbance on hybridization, and found significant but weak relationships between hybridization and environmental factors. This research improves our understanding of hybridization dynamics in species-rich clades like the Leuciscidae with low reproductive isolation, and points to the need for additional work to better understand predictors of hybridization in multi-species hybrid zones.

evolutionary biology↗

bioRxiv2025

Temporal dynamics of color polymorphism and hybridization in Colias butterflies

Investigations into the genetic basis of color polymorphism have played a key role in our understanding of genetic architecture and the evolution of mating systems. Sulphur butterflies (Colias) have been models in this field, but also contain unsolved puzzles with respect to species boundaries and hybridization. We surveyed genomic variation across five years in a location where phenotypic intermediates between Colias eurytheme and C. eriphyle are observed, but ancestry variation of potential hybrids has not been quantified. Our results reveal individuals with hybrid ancestry roughly in proportion to the frequency of individuals of intermediate phenotype recorded in the wild. Individuals with hybrid ancestry were predominantly those with intermediate morphologies, but morphologically intermediate individuals were not always of hybrid origin, which raises alternative possibilities for the origin and maintenance of color variation in the system. Genomic regions differentiated between species are largely located on the Z chromosome, and we find more candidates on autosomes than in another Colias contact zone. The dynamics of hybridization in this system are highly variable through time, suggesting fertile avenues for future study into the maintenance of species boundaries in the face of temporally-variable, climatically influenced, and pervasive hybridization.

evolutionary biology↗

bioRxiv2025

Reappraisal of the Dilution and Amplification Effect Framework: A Case Study in Lyme Disease

The role of biodiversity in regulating zoonotic disease in ecological communities has been broadly referred to as the biodiversity-disease relationship in disease ecology. Whether biodiversity decreases or increases disease risk, known as a dilution or amplification effect respectively, remains unclear. The literature has focused on the strength, generality, nature, and context dependencies that could explain contradictory evidence. We suggest that a continued focus on this approach to resolving the biodiversity-disease debate detracts from a more foundational problem with testing these dilution and amplification hypotheses, in that these hypotheses are not falsifiable as proposed. When tested and interpreted as net effects in a system, these hypotheses do not possess a true null outcome and they are vulnerable to ad hoc explanations. To remedy this problem, we propose that biodiversity and disease risk can be modelled as latent variables in multivariate causal models to test specific mechanistic pathways. We present a case study on Lyme disease through a systematic review and meta-analysis, concluding that there is little evidence for a net dilution or amplification effect. We demonstrate how testing these net effect hypotheses falls short of providing robust evidence for its underlying mechanisms. While these hypotheses have previously been helpful in conceptualizing this idea of biodiversity as a potentially protective factor for human health, they need further specificity and clarity to move forwards with greater unity.

ecology↗

bioRxiv2024

Interpretable and predictive models to harness the life science data revolution

The proliferation of high-dimensional data in ecology and evolutionary biology raises the promise of statistical and machine learning models that are highly predictive and interpretable. However, high-dimensional data are commonly burdened with an inherent trade-off: in-sample prediction of outcomes will improve as additional variables are included in the model, but this may come at the cost of poor predictive accuracy and limited generalizability for future or unsampled observations (out-of-sample prediction). To confront this problem of overfitting, sparse models can focus on key variables by correctly placing low weight on unimportant variables. We competed nine methods to quantify their performance in variable selection and prediction using simulated data with different sample sizes, numbers of variables, and strengths of effects. Overfitting was typical for many methods and simulation scenarios. Despite this, in-sample and out-of-sample prediction converged on the true predictive target for simulations with more observations, larger causal effects, and fewer variables. Accurate variable selection to support process-based understanding will be unattainable for many realistic sampling schemes in ecology and evolution. We use our analyses to characterize data attributes for which statistical learning is possible, and illustrate how some sparse methods can achieve predictive accuracy while mitigating and learning the extent of overfitting.

genomics↗

bioRxiv2022

Selection leads to remarkable variability in the outcomes of hybridization across replicate hybrid zones

Hybrid zones have been viewed as an opportunity to see speciation in action. When hybrid zones are replicated, it is assumed that if the same genetic incompatibilities are maintaining reproductive isolation across all instances of secondary contact, those incompatibilities should be identifiable by consistent patterns in the genome. In contrast, changes in allele frequencies due to genetic drift should be idiosyncratic for each hybrid zone. To test this assumption, we simulated 20 replicates of each of 12 hybrid zone scenarios with varied genetic incompatibilities, rates of migration, selection and different starting population size ratios of parental species. We found remarkable variability in the outcomes of hybridization in replicate hybrid zones, particularly with Bateson-Dobzhansky-Muller incompatibilities and strong selection. We found substantial differences among replicates in the overall genomic composition of individuals, including admixture proportions, inter-specific ancestry complement, and number of ancestry junctions. Additionally, we found substantial variation in genomic clines among replicates at focal loci, regardless of locus-specific selection. We conclude that processes other than selection are responsible for some consistent outcomes of hybridization, whereas selection on incompatibilities can lead to genomically widespread and highly variable outcomes. We highlight the challenge of mapping between pattern and process in hybrid zones and call attention to how selection against incompatibilities will commonly lead to variable outcomes. We hope that this study informs future research on replicate hybrid zones and encourages further development of statistical techniques, theoretical models, and exploration of additional axes of variation to understand reproductive isolation.

evolutionary biology↗

bioRxiv2022

Identification of sex-determining loci in hybridizing Catostomus fish species

1Despite the near-universality of gonochorism (separate sexes) in eukaryotic organisms, the underlying mechanisms of sex determination are poorly understood and highly variable in some taxa. Sex determination mechanisms may promote or impede reproductive isolation depending on whether mechanisms are similar between related species, so identifying genomic regions associated with sex determination is especially relevant for understanding evolutionary diversification and hybridization between closely related species. In Catostomus fishes, contemporary hybridization is variable and extensive, but factors influencing hybridization dynamics are not fully understood. In the present study, we aim to describe the genetic basis of sex determination in bluehead (Catostomus discobolus) and white suckers (Catostomus commersonii ) to understand the potential impact of sex determination on reproductive isolation. We used genotyping-by-sequencing data from Catostomus species and their hybrids to identify regions of the genome associated with sex using a genome-wide association study and the identification of sex-specific loci. We identified a genetic basis of sex determination in Catostomus fishes, with a region of the genome significantly associating with sex in bluehead suckers. This region is suggestive of a master sex-determining region in bluehead suckers but is not significant in white suckers, implying that either the sex-determining region of the genome differs in these two species that hybridize, or that sample size was insufficient to identify this genomic region in white suckers. By describing and comparing sex-determination systems across Catostomus fish species, we highlight the relationship between sex determining systems and hybridization in closely related fish species.

evolutionary biology↗

bioRxiv2021

Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland

We deployed admixture mapping on a sample of 386 deer from a hybrid swarm between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon) sampled in Kintyre, Scotland to search for Quantitative Trait Loci (QTL) underpinning phenotypic differences between the species. These two species are highly diverged genetically (Fst between pure species, based on 50K SNPs, = 0.532) and phenotypically: pure red have on average twice the carcass mass of pure sika in our sample (38.7kg vs 19.1 kg). After controlling for sex, age and population genetic structure we found ten autosomal genomic locations with QTL for carcass mass. Effect sizes ranged from 0.191 to 1.839 Kg and as expected, in all cases the allele derived from sika conferred lower carcass mass. The sika population was fixed for all small carcass mass alleles, whereas the red deer population was typically polymorphic. GO term analysis of genes lying in the QTL regions are associated with oxygen transport. Although body mass is a likely target of selection, none of the SNPs marking QTL are introgressing faster or slower than expected in either direction.

evolutionary biology↗

bioRxiv2020

Locus-specific introgression in young hybrid swarms: drift dominates selection

Closely related species that have previously inhabited geographically separated ranges are hybridizing at an increasing rate due to human disruptions. These anthropogenic hybrid zones can be used to study reproductive isolation between species at secondary contact, including examining locus-specific rates of introgression. Introgression is expected to be heterogenous across the genome, reflecting variation in selection. Those loci that introgress especially slowly are good candidates for being involved in reproductive isolation, while those loci that introgress quickly may be involved in adaptive introgression. In the context of conservation, policy makers are especially concerned about introduced alleles moving quickly into the background of a native or endemic species, as these alleles could replace the native alleles in the population, leading to extinction via hybridization. We applied genomic cline analyses to 44997 SNPs to identify loci introgressing at excessive rates when compared to the genome wide expectation in an anthropogenic hybridizing population of red deer and sika in Kintyre Scotland. We found 11.4% of SNPs had cline centers that were significantly different from the genome wide expectation, and 17.6% had excessive rates of introgression. Based on simulations, we believe that many of these markers have diverged from average due to drift, rather than because of selection. Future work could determine the policy implications of allelic-replacement due to drift rather than selection, and could use replicate, geographically distinct hybrid zones to narrow down those loci that are indeed responding to selection in anthropogenic hybrid zones.

evolutionary biology↗

bioRxiv2019

Increased genetic marker density reveals high levels of admixture between red deer and introduced sika in Kintyre, Scotland

Hybridization is a natural process at species range boundaries, but increasing numbers of species are hybridizing due to direct or indirect human activities. In such cases of anthropogenic hybridization, subsequent introgression can threaten the survival of native species. To date many such systems have been studied with too few genetic markers to assess the level of threat resulting from advanced backcrossing. Here we use 44,999 single nucleotide polymorphisms and the ADMIXTURE program to study two areas of Scotland where a panel of 22 diagnostic microsatellites previously identified introgression between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon). In Kintyre we reclassify 26% of deer from the pure species categories to the hybrid category whereas in the NW Highlands we only reclassify 2%. As expected, the reclassified individuals are mostly advanced backcrosses. We also investigate the ability of marker panels selected on different posterior allele frequency criteria to find hybrids assigned by the full marker set, and show that in our data, ancestry informative markers (i.e. those that are highly differentiated between the species, but not fixed) are better than diagnostic markers (those markers that are fixed between the species) because they are more evenly distributed in the genome. Diagnostic loci are concentrated on the X chromosome to the detriment of autosomal coverage.

evolutionary biology↗