Biology subjects

Hodgins, K. A.

Publications and source records attributed to Hodgins, K. A..

16 recordsLinked to original sources

bioRxiv2026

Topographic complexity shapes adaptive genomic variation in co-occurring plant species

Co-occurring species often face similar selective environments, although adaptive responses to these environments are generally assumed to be species-specific, particularly in complex landscapes where selective pressures are likely to be multi-dimensional. We test this assumption by contrasting genotype-environment associations (GEAs) among a range of co-occurring but unrelated plants with different life histories from an isolated, mountainous national park in south-eastern Australia. Analyses were performed using single nucleotide polymorphism (SNP) loci derived from reduced genome representation sequencing to investigate genomic associations with spatial and environmental drivers across unrelated plant species within the same heterogeneous landscape. Several species showed GEAs that aligned with similar environmental gradients, particularly edaphic features, suggesting that similar selective pressures can shape genomic responses across taxa. Other species exhibited distinct spatial and environmental associations, highlighting idiosyncratic outcomes. Notably, GEAs were detected at fine spatial scales despite generally low levels of genome-wide divergence, suggesting adaptive variants can persist in the face of gene flow under strong selective pressure. This study highlights how community-level genomic diversity is shaped by common environmental processes, with implications for biodiversity management in rapidly changing environments, where diverse ecosystem-level responses to selection may underpin resilience.

evolutionary biology↗

bioRxiv2026

Selection shapes the evolution of genome size in a globally invasive plant

O_LIBiological invasions provide powerful natural experiments for understanding how genome architecture responds to novel climatic environments. Transposable elements (TEs) can rapidly restructure genomes, yet their role in adaptive genome size evolution during invasion remains poorly understood. C_LIO_LIHere, we examined genome size and TE abundance in 439 individuals of globally invasive common ragweed (Ambrosia artemisiifolia L.) across native (North American) and invasive (European, Australian) ranges. By integrating whole-genome resequencing, flow cytometry, and trait versus genetic differentiation comparison (QST-FST), we tested whether genome size evolution is shaped by selection, climate, and life-history traits. C_LIO_LIGenome size was significantly larger in Australian genotypes, driven by increased TE and rRNA (ribosomal RNA) abundance. Crucially, trait versus genetic differentiation comparison provided evidence of divergent selection on genome size in North American and European populations, but not in Australia. Genome size was correlated with mean annual temperature (MAT) across all ranges, linking genomic traits to environmental variables. C_LIO_LIGenome size evolution during invasion can be rapid, adaptive, and range-specific, with TE-driven genome expansion emerging as a potential genomic response to the demographic and environmental pressures accompanying colonization of novel environments. C_LI

evolutionary biology↗

bioRxiv2025

Meta-analysis reveals the tempo of evolutionary parallelism of local adaptation between native and introduced ranges of plant species

Invasive species are valuable systems for evaluating evolutionary predictability, as populations in native and introduced ranges evolve separately, yet often encounter similar environmental challenges that select for parallel patterns of local adaptation across each range. However, it remains unclear how pervasive and strong such parallelism is and how rapidly it evolves. To address these questions, we first extended cline theory to predict evolutionary patterns of trait cline parallelism between ranges. We then carried out a meta-analysis of clinal divergence in native and introduced populations of the same plant species and evaluated the tempo of trait cline parallelism between ranges. We found that clines in introduced ranges were somewhat shallower than native range clines, and directions of clinal divergence were, on average, partially aligned between ranges, with extensive variation in parallelism among traits and species, including counter-clines between native and introduced ranges. The degree of evolutionary parallelism of clinal divergence strongly increased, and the prevalence of counter-clines decreased, with the time since introduction, where greater parallelism in older introductions was primarily caused by increased alignment in the direction of clinal divergence between ranges rather than changes in their relative magnitudes of divergence. We argue that these observations are consistent with a two-phased process of cline evolution across introduced ranges. In the first phase, misaligned clines between introduced and native ranges can arise during range expansions, often owing to demographic and genetic constraints that initially hinder the evolution of local adaptation within the new range. During the second phase, the evolution of local adaptation eventually resolves early instances of maladaptation across introduced ranges, leading to strong trait cline parallelism between native and introduced ranges.

evolutionary biology↗

bioRxiv2024

Copy number variation contributes to parallel local adaptation in an invasive plant

Adaptation is a critical determinant of the diversification, persistence, and geographic range limits of species. Yet the genetic basis of adaptation is often unknown and potentially underpinned by a wide range of mutational types - from single nucleotide changes to large-scale alterations of chromosome structure. Copy number variation (CNV) is thought to be an important source of adaptive genetic variation, as indicated by decades of candidate gene studies that point to CNVs underlying rapid adaptation to strong selective pressures. Nevertheless, population- genomic studies of CNVs face unique logistical challenges not encountered by other forms of genetic variation. Consequently, few studies have systematically investigated the contributions of CNVs to adaptation at a genome-wide scale. We present a genome-wide analysis of CNV contributing to the adaptation of an invasive weed, Ambrosia artemisiifolia - the first such study in an invasive pest. CNVs show clear signatures of parallel local adaptation between North American (native) and European (invaded) ranges, implying widespread reuse of CNVs during adaptation to shared heterogeneous patterns of selection. We used a local principal component analysis to genotype CNV regions in whole-genome sequences of samples collected over the last two centuries. We identified 16 large CNV regions of up to 11.85 megabases in length, six of which show signals of rapid evolutionary change, with pronounced frequency shifts between historic and modern populations. Our results provide compelling genome-wide evidence that copy number variation underlies rapid adaptation over contemporary timescales of natural populations. Significance StatementUsing a population-genomic approach, we identified copy number variants - stretches of DNA that can be either present, absent, or in multiple copies - displaying parallel signatures of local adaptation across the native and introduced ranges of the invasive weed Ambrosia artemisiifolia. We further identified 16 large copy number variants, some associated with ecologically important traits including sex allocation and height, that show strong signatures of selection over space, along with dramatic temporal changes over the past several decades. These results highlight the importance of an often-overlooked form of genomic variation in both local adaptation and rapid adaptation of invasive species.

evolutionary biology↗

bioRxiv2023

Does urbanization lead to parallel demographic shifts across the world in a cosmopolitan plant?

Urbanization is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the "urban facilitation model" suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the Global Urban Evolution project (GLUE), to study the effects of urbanization on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of a reduction in Ne linked to urbanization. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides one of the largest comprehensive tests of demographic effects of urbanization and our results contrast the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.

evolutionary biology↗

bioRxiv2023

Temperature and sex shape reproductive barriers in a climate change hotspot

Climate change is shifting species ranges and altering reproductive interactions within those ranges, offering closely-related species new scope to mate and potentially hybridize. Predicting hybridization and its outcomes requires assessing the interplay of biological and climatic factors that mediate reproductive barriers across life stages. However, few studies have done so across the range of environments that parents and offspring potentially encounter in nature, as is crucial to understand the environmental sensitivity of reproductive isolation and its fate under climate change. We set out to assess prezygotic and postzygotic reproductive barriers, and their dependence on temperature and sex, in sister species of a marine tubeworm (Galeolaria) from a sentinel region for climate change impacts in southern Australia. We performed reciprocal crosses within- and between-species using replicate populations, and assessed fertility of crosses, survival of embryos, and survival of larvae, at five temperatures spanning the thermal ranges of populations in nature. We found that barriers were weak and independent of temperature at fertilization, but stronger and more temperature-sensitive at larval development, as species diverged in thermal tolerance. Barriers were asymmetric between reciprocal hybrids, moreover, suggesting a complex interplay between thermal adaptation in parental lineages and maternal inheritance of factors (e.g., mitochondria, endosymbionts) that influence hybrid viability across temperatures. Together, our findings provide new insights into the roles of temperature and sex in reproductive barriers across early life stages, and point to shifting strengths of reproductive isolation in future climates.

ecology↗

bioRxiv2023

Predicting the evolution of adaptation and plasticity from temporal environmental change

Environmental change drives evolutionary adaptation, which determines geographic patterns of biodiversity. At a time of rapid environmental change, however, our ability to predict its evolutionary impacts is far from complete. Temporal environmental change, in particular, often involves joint changes in major components such as mean, trend, cyclic change, and noise. While theoretical predictions exist for adaptation to temporal change in isolated components, knowledge gaps remain. To identify those gaps, we review the relevant theoretical literature, finding that studies rarely assess the relative effects of components changing simultaneously, or attempt to translate theoretical predictions to field conditions. To address those gaps, we draw on classic evolutionary theory to develop a model for the evolution of environmental tolerance, determined by an evolving phenotypically plastic trait, in response to major components of temporal environmental change. We assess the effects of different components on the evolution of tolerance, including rates of adaptation towards new environmental optima, and the evolution of plasticity. We retrieve and synthesize earlier predictions of responses to components changing in isolation, while also generating new predictions of responses to components changing simultaneously. Notably, we show how different forms of environmental predictability emerging from the interplay of cyclic change, stochastic change (noise), and generation time shape predicted outcomes. We then parameterise our model using temperature time series from global marine hotspot in southern Australia, illustrating its utility for predicting testable geographic patterns in evolved thermal tolerance. Our framework provides new insights into the evolution of adaptation and plasticity under temporal environmental change, while offering a path to improving predictions of biological responses to climate change.

evolutionary biology↗

bioRxiv2022

Climate adaptation and vulnerability of foundation species in a global change hotspot

Climate change is altering species ranges, and abundances within ranges, as populations become differentially adapted and vulnerable to the climates they face. Hence, characterising current ranges, whether species harbour and exchange adaptive genetic variants, and how variants are distributed across landscapes undergoing rapid change, is crucial to predicting responses to future climates and informing conservation strategies. Such insights are nonetheless lacking for most species of conservation concern. We characterise genomic patterns of neutral variation, climate adaptation, and climate vulnerability (the amount of genomic change needed to track climate change by adaptation) in sister foundation species, the endemic marine tubeworms Galeolaria caespitosa and Galeolaria gemineoa, across a sentinel region for climate change impacts. First, species are shown to be partly sympatric despite previous support for non-overlapping ranges, and genetically isolated despite known capacity for hybrid crosses to yield viable early offspring. Second, species show signals of polygenic adaptation, but to differing components of temperature and involving mostly different loci. Last, species are predicted to be differentially vulnerable to climate change, with G. gemineoa -- the less genetically diverse species -- needing double the adaptation to track projected changes in temperature compared to its sister species. Together, our findings provide new insights into climate adaptation and its potential disruption by climate change for foundation species that enhance local biodiversity, with implications for evolutionarily-enlightened management of coastal ecosystems.

evolutionary biology↗

bioRxiv2022

Large haploblocks underlie rapid adaptation in an invasive weed

Adaptation is the central feature and leading explanation for the evolutionary diversification of life. Adaptation is also notoriously difficult to study in nature, owing to its complexity and logistically prohibitive timescale. We leverage extensive contemporary and historical collections of Ambrosia artemisiifolia--an aggressively invasive weed and primary cause of pollen-induced hayfever--to track the phenotypic and genetic causes of recent local adaptation across its native and invasive ranges in North America and Europe, respectively. Large haploblocks-- indicative of chromosomal inversions--contain a disproportionate share (26%) of genomic regions conferring parallel adaptation to local climates between ranges, are associated with rapidly adapting traits, and exhibit dramatic frequency shifts over space and time. These results highlight the importance of large-effect standing variants in rapid adaptation, which have been critical to A. artemisiifolias global spread across vast climatic gradients.

evolutionary biology↗

bioRxiv2022

QTL analysis reveals an oligogenic architecture of a rapidly adapting trait during the European invasion of common ragweed

Biological invasions offer a unique opportunity to investigate evolution over contemporary time-scales. Rapid adaptation to local climates during range expansion can be a major determinant of invasion success, yet fundamental questions remain about its genetic basis. This study sought to investigate the genetic basis of climate adaptation in invasive common ragweed (Ambrosia artemisiifolia). Flowering time adaptation is key to this annual species invasion success, so much so that it has evolved repeated latitudinal clines in size and phenology across its native and introduced ranges despite high gene flow among populations. Here, we produced a high-density linkage map (4,493 SNPs) and paired this with phenotypic data from an F2 mapping population (n=336) to identify one major and two minor quantitative trait loci (QTL) underlying flowering time and height differentiation in this species. Within each QTL interval, several candidate flowering time genes were also identified. Notably, the major flowering time QTL detected in this study was found to overlap with a previously identified haploblock (putative inversion). Multiple genetic maps of this region identified evidence of suppressed recombination in specific genotypes, consistent with inversions. These discoveries support the expectation that a concentrated genetic architecture with fewer, larger and more tightly-linked alleles should underlie rapid local adaptation during invasion, particularly when divergently-adapting populations experience high-levels of gene flow.

evolutionary biology↗

bioRxiv2022

Uncovering the hologenomic basis of an extraordinary plant invasion

While invasive species are a key driver of the global biodiversity crisis, the drivers of invasiveness remain debated. To investigate the genomic basis of invasiveness in plants, we use the invasive weed Ambrosia artemisiifolia, introduced to Europe in the late 19th century, resequencing 655 ragweed genomes, including 308 herbarium specimens collected up to 190 years ago. In introduced European populations, we report selection signatures in defense genes and lower prevalence of particular plant pathogens in the invasive range. Together with temporal changes in population structure associated with introgression from closely related Ambrosia species, escape from microbial enemies likely favoured the plants remarkable success as an invasive species. One-Sentence SummaryThe invasive success of European ragweed was facilitated by release from enemy microbes and inter-species hybridization.

genomics↗

bioRxiv2021

Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands

The nematode Caenorhabditis elegans is among the most widely studied organisms, but relatively little is known about its natural ecology. Wild C. elegans have been isolated from both temperate and tropical climates, where they feed on bacteria associated with decomposing plant material. Genetic diversity is low across much of the globe but high in the Hawaiian Islands and across the Pacific Rim. The high genetic diversity found there suggests that: (1) the origin of the species lies in Hawaii or the surrounding Pacific Rim; and (2) the ancestral niche of the species is likely similar to the Hawaiian niche. A recent study of the Hawaiian niche found that genetically distinct groups appeared to correlate with elevation and temperature, but the study had a limited sample size. To better characterize the niche and genetic diversity of C. elegans on the Hawaiian Islands and to explore how genetic diversity might be influenced by local adaptation, we repeatedly sampled nematodes over a three-year period, measured various environmental parameters at each sampling site, and whole-genome sequenced the C. elegans isolates that we identified. We found that the typical Hawaiian C. elegans niche is moderately moist native forests at high elevations (500 to 1500 meters) where temperatures are cool (15 to 20{degrees}C). We measured levels of genetic diversity and differentiation among Hawaiian strains and found evidence of seven genetically distinct groups distributed across the islands. Then, we scanned these genomes for signatures of local adaptation and identified 18 distinct regions that overlap with hyperdivergent regions, which are likely maintained by balancing selection and enriched for genes related to environmental sensing, xenobiotic detoxification, and pathogen resistance. These results provide strong evidence of local adaptation among Hawaiian C. elegans and a possible genetic basis for this adaptation.

ecology↗

bioRxiv2019

Parallel clines in native and introduced ragweed populations are likely due to adaptation

As introduced species expand their ranges, they often encounter differences in climate which are often correlated with geography. For introduced species, encountering a geographically variable climate sometimes leads to the re-establishment of clines seen in the native range. However, clines can also be caused by neutral processes, and so it is important to gather additional evidence that population differentiation is the result of selection as opposed to non-adaptive processes. Here, we examine phenotypic and genetic differences in ragweed from the native (North America) and introduced (European) ranges. We used a common garden to assess phenotypic differentiation in size and flowering time in ragweed populations. We found significant parallel clines in flowering time in both North America and Europe. Height and branch number had significant clines in North America and, while not statistically significant, the patterns in Europe were the same. We used SNP data to assess population structure in both ranges and to compare phenotypic differentiation to neutral genetic variation. We failed to detect significant patterns of isolation by distance, geographic patterns in population structure, or correlations between the major axes of SNP variation and phenotypes or latitude of origin. We conclude that the clines seen for flowering time and size are most likely the result of adaptation.

evolutionary biology↗

bioRxiv2018

EICA Fails As An Explanation Of Growth And Defence Evolution Following Multiple Introductions

O_LIRapid adaptation can aid invasive populations in their competitive success. Resource-allocation trade-off hypotheses predict higher resource availability or the lack of natural enemies in introduced ranges allow for increased growth and reproduction, thus contributing to invasive success. Evidence for such hypotheses are however equivocal and tests among multiple ranges over productivity gradients are required to provide a better understanding of the general applicability of these theories.\nC_LIO_LIUsing common gardens, we investigated the adaptive divergence of various constitutive and inducible defence-related traits between the native North American and introduced European and Australian ranges, whilst controlling for divergence due to latitudinal trait clines, individual resource budgets and population differentiation, using >11,000 SNPs.\nC_LIO_LIRapid, repeated clinal adaptation in defence-related traits was apparent despite distinct demographic histories. We also identified divergence among ranges in some defence-related traits, although differences in energy budgets among ranges may explain some, but not all, defence-related trait divergence. We do not identify a general reduction in defence in concert with an increase in growth among the multiple introduced ranges as predicted trade-off hypotheses.\nC_LIO_LISynthesis: The rapid spread of invasive species is affected by a multitude of factors, likely including adaptation to climate and escape from natural enemies. Unravelling the mechanisms underlying invasives success enhances understanding of eco-evolutionary theory and is essential to inform management strategies in the face of ongoing climate change.\nC_LI

evolutionary biology↗

bioRxiv2018

Rapid And Repeated Local Adaptation To Climate In An Invasive Plant

O_LIBiological invasions provide opportunities to study evolutionary processes occurring over contemporary timescales. To explore the speed and repeatability of adaptation, we examined the divergence of life-history traits to climate, using latitude as a proxy, in the native North American and introduced European and Australian ranges of the annual plant Ambrosia artemisiifolia.\nC_LIO_LIWe explored niche changes following introductions using climate niche dynamic models. In a common garden, we examined trait divergence by growing seeds collected across three ranges with highly distinct demographic histories. Heterozygosity-fitness associations were used to explore the effect of invasion history on potential success. We accounted for non-adaptive population differentiation using 11,598 SNPs.\nC_LIO_LIWe revealed a centroid shift to warmer, wetter climates in the introduced ranges. We identified repeated latitudinal divergence in life-history traits, with European and Australian populations positioned at either end of the native clines.\nC_LIO_LIOur data indicate rapid and repeated adaptation to local climates despite the recent introductions and a bottleneck limiting genetic variation in Australia. Centroid shifts in the introduced ranges suggest adaptation to more productive environments, potentially contributing to trait divergence between the ranges.\nC_LI

evolutionary biology↗

bioRxiv2018

Quantifying how constraints limit the diversity of viable routes to adaptation

Convergent adaptation can occur at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel metric to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This metric is explicitly based on the probability of observing a given amount of repeatability by chance under an arbitrary null hypothesis, and is readily compared among different species and types of trait. We also formulate a metric to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these metrics can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to antibiotics in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.

evolutionary biology↗