A genetic perspective on rapid evolution in cane toads (Rhinella marina)

Infection by the Lungworm Rhabdias pseudosphaerocephala Affects the Expression of Immune-Related microRNAs by Its Co-Evolved Host, the Cane Toad Rhinella marina

Parasites may suppress the immune function of infected hosts using microRNAs (miRNAs) to prevent protein production. Nonetheless, little is known about the diversity of miRNAs and their mode(s) of action. In this study, we investigated the effects of infection by a parasitic lungworm (Rhabdias pseudosphaerocephala) on miRNA and mRNA expression of its host, the invasive cane toad (Rhinella marina). To investigate the cane toad's innate and adaptive immune response to this parasite, we compared miRNA and mRNA expression in naïve toads that had never been infected by lungworms to toads that were infected with lungworms for the first time in their lives, and toads that were infected the second time in their lives (i.e., had two consecutive infections). In total, we identified 101 known miRNAs and 86 potential novel miRNAs. Compared to uninfected and single-infection toads, multiple-infection animals drastically downregulated three miRNAs. These miRNAs were associated with gene pathways related to the immune response, potentially reflecting the immunosuppression of cane toads by their parasites. Infected hosts did not respond with substantially differential mRNA transcription; only one gene was differentially expressed between control and single-infection hosts. Our study suggests that miRNA may play an important role in mediating host-parasite interactions in a system in which an ongoing range expansion by the host has generated substantial divergence in host-parasite interactions.

Repeat-Rich Regions Cause False-Positive Detection of NUMTs: A Case Study in Amphibians Using an Improved Cane Toad Reference Genome

Mitochondrial DNA (mtDNA) has been widely used in genetics research for decades. Contamination from nuclear DNA of mitochondrial origin (NUMTs) can confound studies of phylogenetic relationships and mtDNA heteroplasmy. Homology searches with mtDNA are widely used to detect NUMTs in the nuclear genome. Nevertheless, false-positive detection of NUMTs is common when handling repeat-rich sequences, while fragmented genomes might result in missing true NUMTs. In this study, we investigated different NUMT detection methods and how the quality of the genome assembly affects them. We presented an improved nuclear genome assembly (aRhiMar1.3) of the invasive cane toad (Rhinella marina) with additional long-read Nanopore and 10× linked-read sequencing. The final assembly was 3.47 Gb in length with 91.3% of tetrapod universal single-copy orthologs (n = 5,310), indicating the gene-containing regions were well assembled. We used 3 complementary methods (NUMTFinder, dinumt, and PALMER) to study the NUMT landscape of the cane toad genome. All 3 methods yielded consistent results, showing very few NUMTs in the cane toad genome. Furthermore, we expanded NUMT detection analyses to other amphibians and confirmed a weak relationship between genome size and the number of NUMTs present in the nuclear genome. Amphibians are repeat-rich, and we show that the number of NUMTs found in highly repetitive genomes is prone to inflation when using homology-based detection without filters. Together, this study provides an exemplar of how to robustly identify NUMTs in complex genomes when confounding effects on mtDNA analyses are a concern.

Global invasion history with climate-related allele frequency shifts in the invasive Mediterranean fruit fly (Diptera, Tephritidae: Ceratitis capitata)

The Mediterranean fruit fly (Ceratitis capitata) is a globally invasive species and an economically significant pest of fruit crops. Understanding the evolutionary history and local climatic adaptation of this species is crucial for developing effective pest management strategies. We conducted a comprehensive investigation using whole genome sequencing to explore (i) the invasion history of C. capitata with an emphasis on historical admixture and (ii) local climatic adaptation across African, European, Central, and South American populations of C. capitata. Our results suggest a stepwise colonization of C. capitata in Europe and Latin America in which Mediterranean and Central American populations share an ancestral lineage. Conversely, South American invasion history is more complex, and our results partly suggest an old secondary invasion into South America from Europe or a colonization of South America directly from Africa, followed by admixture with an European lineage. Throughout its invasive range, C. capitata is challenged with diverse climatic regimes. A genome wide association study identified a relationship between allele frequency changes and specific bioclimatic variables. Notably, we observed a significant allele frequency shift related to adaptation to cold stress (BIO6), highlighting the species' ability to rapidly adapt to seasonal variations in colder climates.

Whole-mitogenome analysis unveils previously undescribed genetic diversity in cane toads across their invasion trajectory

Invasive species offer insights into rapid adaptation to novel environments. The iconic cane toad (Rhinella marina) is an excellent model for studying rapid adaptation during invasion. Previous research using the mitochondrial NADH dehydrogenase 3 (ND3) gene in Hawai'ian and Australian invasive populations found a single haplotype, indicating an extreme genetic bottleneck following introduction. Nuclear genetic diversity also exhibited reductions across the genome in these two populations. Here, we investigated the mitochondrial genomics of cane toads across this invasion trajectory. We created the first reference mitochondrial genome for this species using long-read sequence data. We combined whole-genome resequencing data of 15 toads with published transcriptomic data of 125 individuals to construct nearly complete mitochondrial genomes from the native (French Guiana) and introduced (Hawai'i and Australia) ranges for population genomic analyses. In agreement with previous investigations of these populations, we identified genetic bottlenecks in both Hawai'ian and Australian introduced populations, alongside evidence of population expansion in the invasive ranges. Although mitochondrial genetic diversity in introduced populations was reduced, our results revealed that it had been underestimated: we identified 45 mitochondrial haplotypes in Hawai'ian and Australian samples, none of which were found in the native range. Additionally, we identified two distinct groups of haplotypes from the native range, separated by a minimum of 110 base pairs (0.6%). These findings enhance our understanding of how invasion has shaped the genetic landscape of this species.

A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years

The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950s, opossum shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Mysis were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity, test for genetic divergence between populations, and for evidence of adaptive evolution within the introduced populations in Colorado. We found very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that at least one undocumented introduction from an unknown source population hybridized with the population in Gross Reservoir. Despite the overall low genetic diversity we observed, F ST outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments. From an applied perspective, the observed patterns of divergence between populations suggest that genetic analysis can be a useful forensic tool to determine likely sources of invasive species.

(Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions

Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (Ciona intestinalis) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of divergent selection. In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating the strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, Gene Ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.

A biological invasion reduces rates of cannibalism by Japanese toad tadpoles

Biological invasions can favour rapid changes in intraspecific competitive mechanisms such as cannibalism by imposing novel evolutionary pressures. For example, cane toad (Rhinella marina) tadpoles are highly cannibalistic on eggs and hatchlings in their invasive range in Australia, but not in their native range in South America. Whether such changes in cannibalism occur in invasive populations of other amphibian species is unknown. To explore this question, we collected wild-laid egg clutches of Japanese common toads (Bufo japonicus) from native and invasive populations in Japan, and conducted laboratory experiments to examine cannibalism responses. Contrary to the Australian system, we found that invasion has been accompanied by reduced cannibalistic tendency of B. japonicus tadpoles. This reduction has occurred despite invasive-range B. japonicus eggs/hatchlings being more vulnerable than native-range B. japonicus eggs/hatchlings to cannibalism by native-range conspecific tadpoles, and to predation by native-range frog tadpoles. Our findings thus support the idea that biological invasions can generate rapid changes in rates of cannibalism, but also show that decreases as well as increases can occur. Future work could investigate the proximate cues and selective forces responsible for this rapid decrease in rates of cannibalism by tadpoles in an invasive B. japonicus population.

Investigating the genetic basis of vertebrate dispersal combining RNA-seq, RAD-seq and quantitative genetics

Although animal dispersal is known to play key roles in ecological and evolutionary processes such as colonization, population extinction and local adaptation, little is known about its genetic basis, particularly in vertebrates. Untapping the genetic basis of dispersal should deepen our understanding of how dispersal behaviour evolves, the molecular mechanisms that regulate it and link it to other phenotypic aspects in order to form the so-called dispersal syndromes. Here, we comprehensively combined quantitative genetics, genome-wide sequencing and transcriptome sequencing to investigate the genetic basis of natal dispersal in a known ecological and evolutionary model of vertebrate dispersal: the common lizard, Zootoca vivipara. Our study supports the heritability of dispersal in semi-natural populations, with less variation attributable to maternal and natal environment effects. In addition, we found an association between natal dispersal and both variation in the carbonic anhydrase (CA10) gene, and in the expression of several genes (TGFB2, SLC6A4, NOS1) involved in central nervous system functioning. These findings suggest that neurotransmitters (serotonin and nitric oxide) are involved in the regulation of dispersal and shaping dispersal syndromes. Several genes from the circadian clock (CRY2, KCTD21) were also differentially expressed between disperser and resident lizards, supporting that the circadian rhythm, known to be involved in long-distance migration in other taxa, might affect dispersal as well. Since neuronal and circadian pathways are relatively well conserved across vertebrates, our results are likely to be generalisable, and we therefore encourage future studies to further investigate the role of these pathways in shaping dispersal in vertebrates.

Geographic variation in bacterial assemblages on cane toad skin is influenced more by local environments than by evolved changes in host traits

Bacterial assemblages on amphibian skin may play an important role in protecting hosts against infection. In hosts that occur over a range of environments, geographic variation in composition of bacterial assemblages might be due to direct effects of local factors and/or to evolved characteristics of the host. Invasive cane toads (Rhinella marina) are an ideal candidate to evaluate environmental and genetic mechanisms, because toads have evolved major shifts in physiology, morphology, and behavior during their brief history in Australia. We used samples from free-ranging toads to quantify site-level differences in bacterial assemblages and a common-garden experiment to see if those differences disappeared when toads were raised under standardised conditions at one site. The large differences in bacterial communities on toads from different regions were not seen in offspring raised in a common environment. Relaxing bacterial clustering to operational taxonomic units in place of amplicon sequence variants likewise revealed high similarity among bacterial assemblages on toads in the common-garden study, and with free-ranging toads captured nearby. Thus, the marked geographic divergence in bacterial assemblages on wild-caught cane toads across their Australian invasion appears to result primarily from local environmental effects rather than evolved shifts in the host.

Cryptic lineages and standing genetic variation across independent cane toad introductions

Widespread introduced species can be leveraged to investigate the genetic, ecological and adaptive processes underlying rapid evolution and range expansion, particularly the contributions of genetic diversity to adaptation. Rhinella marina, the cane toad, has been a focus of invasion biology for decades in Australia. However, their introduction history in North America is less clear. Here, we investigated the roles of introduction history and genetic diversity in establishment success of cane toads across their introduced range. We used reduced representation sequencing (ddRAD) to obtain 34,000 SNPs from 247 toads in native (French Guiana, Guyana, Ecuador, Panama, Texas) and introduced (Bermuda, southern Florida, northern Florida, Hawai'i, Puerto Rico) populations. Unlike all other cane toad introductions, we found that Florida populations were more closely related to native Central American lineages (R. horribilis), than to native Southern American lineages (R. marina). Furthermore, we found high levels of diversity and population structure in the native range, corroborating suggestions that R. marina is a species complex. We also found that introduced populations exhibit only slightly lower genetic diversity than native populations. Together with demographic analyses, this indicates founding populations of toads in Florida were larger than previously reported. Lastly, within R. marina, only one of 245 putatively adaptive SNPs showed fixed differences between native and introduced ranges, suggesting that putative selection in these introduced populations is based upon existing genetic variation. Our findings highlight the importance of genetic sequencing in understanding biological introductions and hint at the role of standing genetic variation in range expansion.

Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations

Understanding how genetic and ecological effects can interact to shape genetic loads within and across local populations is key to understanding ongoing persistence of systems that should otherwise be susceptible to extinction through mutational meltdown. Classic theory predicts short persistence times for metapopulations comprising small local populations with low connectivity, due to accumulation of deleterious mutations. Yet, some such systems have persisted over evolutionary time, implying the existence of mechanisms that allow metapopulations to avoid mutational meltdown. We first hypothesize a mechanism by which the combination of stochasticity in the numbers and types of mutations arising locally (genetic stochasticity), resulting local extinction, and recolonization through evolving dispersal facilitates metapopulation persistence. We then test this mechanism using a spatially and genetically explicit individual-based model. We show that genetic stochasticity in highly structured metapopulations can result in local extinctions, which can favor increased dispersal, thus allowing recolonization of empty habitat patches. This causes fluctuations in metapopulation size and transient gene flow, which reduces genetic load and increases metapopulation persistence over evolutionary time. Our suggested mechanism and simulation results provide an explanation for the conundrum presented by the continued persistence of highly structured populations with inbreeding mating systems that occur in diverse taxa.

A centenary tale: population genetic insights into the introduction history of the oriental fire-bellied toad (Bombina orientalis) in Beijing

Background

The successful establishment of a species population following a single introduction of a few individuals to a non-native area has been limited. Nevertheless, the oriental fire-bellied toad (Bombina orientalis) population in Beijing is purportedly descended from a single introduction of about 200 individuals translocated from Yantai, Shandong Province, China, in 1927.

Results

To resolve the introduction process and to understand the genetic consequences since that introduction approximately 90 years ago, we investigated the population’s genetic diversity and structure using 261 toads from Beijing and two native Shandong populations and inferred the species’ introduction history using simulation-based approaches. Analysis of mitochondrial DNA (mtDNA) sequences showed the two haplotypes found in Beijing nested within Yantai haplotypes, thus corroborating the historical record of the translocation source. The mtDNA and 11 nuclear microsatellite markers revealed both considerably lower genetic diversity in Beijing than in the source population and strong genetic differentiation between them. Although the current census population in Beijing may be in the range of a few thousand, the effective population size was estimated at only 20–57. Simulations also suggest that this population may have descended from 40–60 founders.

Conclusions

The Beijing population’s genetic patterns were consistent with the consequences of a severe bottleneck during introduction followed by genetic drift. The introduction trajectory constructed for this B. orientalis population reveals the genetic footprints of a small population sustained in isolation for nearly a century. Our results provide an intriguing example of establishment success from limited founders and may inform ex situ conservation efforts as well as the management of biological invasions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-022-02072-z.

Captivity induces large and population-dependent brain transcriptomic changes in wild-caught cane toads (Rhinella marina)

Gene expression levels are key molecular phenotypes at the interplay between genotype and environment. Mounting evidence suggests that short-term changes in environmental conditions, such as those encountered in captivity, can substantially affect gene expression levels. Yet, the exact magnitude of this effect, how general it is, and whether it results in parallel changes across populations are not well understood. Here, we take advantage of the well-studied cane toad, Rhinella marina, to examine the effect of short-term captivity on brain gene expression levels, and determine whether effects of captivity differ between long-colonized and vanguard populations of the cane toad's Australian invasion range. We compared the transcriptomes of wild-caught toads immediately assayed with those from toads captured from the same populations but maintained in captivity for seven months. We found large differences in gene expression levels between captive and wild-caught toads from the same population, with an over-representation of processes related to behaviour and the response to stress. Captivity had a much larger effect on both gene expression levels and gene expression variability in toads from vanguard populations compared to toads from long-colonized areas, potentially indicating an increased plasticity in toads at the leading edge of the invasion. Overall, our findings indicate that short-term captivity can induce large and population-specific transcriptomic changes, which has significant implications for studies comparing phenotypic traits of wild-caught organisms from different populations that have been held in captivity.

Invasive Widow Spiders Perform Differently At Low Temperatures than Conspecifics from the Native Range

Temperature challenges are one of the leading abiotic causes of success or failure of non-native species in a novel environment, and this is particularly true for low temperatures. Establishing and reproducing in a novel thermal environment can alter survival, behaviour, and traits related to fitness. It has been proposed that plasticity or adaptation of thermal tolerance may allow an introduced species to thrive, or that successful invaders may be those with a thermal breadth in their native habitat that encompasses their new environment. Here, we tested these hypotheses using native and invasive populations of Australian redback spiders (Latrodectus hasselti). We measured how exposure to temperatures (exposure to 15°C and 25°C, respectively) common to invasive and native range habitats affected behavioural and life-history traits and tradeoffs that may underlie fitness in an invasive population detected in 1995 in Japan and a native population from Australia. We found that the critical thermal minimum (CTmin) was higher in the invasive population from Japan than in the native population, but critical thermal maximum (CTmax) did not differ between populations. Compared to the invasive population, eggs from the native population had a longer development time and lower hatching success at 15°C. Both populations performed equally well at 25 °C, as measured by egg development time and hatching success. Invasive juveniles that developed at 15 °C were slower to explore a novel environment and less bold when tested at 25 °C vs. 15 °C. In comparison, the native population showed faster average exploration, with no differences in response at the two development or testing temperatures. Overall, L. hasselti from Japan maintained hatching success and development across a wider temperature range than the native population, indicating greater thermal breadth and higher behavioural plasticity. These results support the importance of plasticity in thermal tolerance and behaviour for a successful invasion under novel environmental temperatures.

Coexistence of two newt species in a transition zone of range overlap

Theory suggests that spatial segregation of similar, co-occurring species may be driven by alternative innate life history and dispersal strategies, and that it operates through catastrophic events. An inventory of the evolutionary closely related small-bodied newts Lissotriton helveticus and L. vulgaris in the northwest of France demonstrated the species’ spatial partitioning, with L. vulgaris dominating in two pond-rich and historically disturbed coastal areas and L. helveticus prevailing inland where ponds are sparser. Population numbers were followed over several decades (1975–2021) in a pond within the narrow (ca. 2000 m wide) species transition zone. Early in the temporal survey (1986) a massive die-off was observed of two-third of the L. helveticus breeding population from a late frost event. Yet, the contribution of L. helveticus to the newt assemblage was more or less stable around 60%, even though the total population size fluctuated by an order of magnitude. Lissotriton vulgaris and a third species, Ichthyosaura alpestris, made up ca. 30% and 10% of the total till 1993, after which date their relative contributions reversed. These data suggest that a state shift may have occurred among the latter two species and that the assumed two-species dynamics of Lissotriton underlying the study has been an oversimplification. The local decline of L. vulgaris is paralleled by the loss of well-vegetated ponds from the wider agricultural terrain that affects this species more than L. helveticus and I. alpestris.

In an arms race between host and parasite, a lungworm's ability to infect a toad is determined by host susceptibility not parasite preference

Evolutionary arms races can alter both parasite infectivity and host resistance, and it is difficult to separate the effects of these twin determinants of infection outcomes. We used a co-introduced, invasive host-parasite system (the lungworm Rhabdias pseudosphaerocephala and cane toads Rhinella marina), where rapid adaptation and dispersal have led to population differences in infection resistance. We quantified behavioural responses of parasite larvae to skin-chemical cues of toads from different invasive populations, and rates at which juvenile hosts became infected following standardized exposure to lungworms. Chemical cues from toad skin altered host-seeking behaviour by parasites, similarly among populations. The number of infection attempts (parasite larvae entering the host's body) also did not differ between populations, but rates of successful infection (establishment of adult worm in host lungs) were higher for range-edge toads than for range-core conspecifics. Thus, lower resistance to parasite infection in range-edge juvenile toads appears to be due to less effective immune defences of the host rather than differential behavioural responses of the parasite. In this ongoing host-parasite arms race, changing outcomes appear to be driven by shifts in host immunocompetence.

Natural History of Model Organisms: The big potential of the small frog Eleutherodactylus coqui

The Puerto Rican coquí frog Eleutherodactylus coqui is both a cultural icon and a species with an unusual natural history that has attracted attention from researchers in a number of different fields within biology. Unlike most frogs, the coquí frog skips the tadpole stage, which makes it of interest to developmental biologists. The frog is best known in Puerto Rico for its notoriously loud mating call, which has allowed researchers to study aspects of social behavior such as vocal communication and courtship, while the ability of coquí to colonize new habitats has been used to explore the biology of invasive species. This article reviews existing studies on the natural history of E. coqui and discusses opportunities for future research.

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 allowing invasive species to adapt to novel environments is a challenge in invasion biology. 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. At the molecular level, it is currently unknown whether these changes in dispersal‐related behaviour are underlain by small or large differences in gene expression, nor is known the biological function of genes showing differential expression. Here, we used RNA‐seq to gain a better understanding of the molecular mechanisms underlying dispersal‐related behavioural changes. We compared the brain transcriptomes of toads from the Hawai'ian 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, 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 populations located at each end of the invasive range. These genes could play an important role in the behavioural changes characteristic of range expansion in Australian cane toads.

Discovery of Novel Viruses Associated With the Invasive Cane Toad (Rhinella marina) in Its Native and Introduced Ranges

Cane toads (Rhinella marina) are notoriously successful invaders: from 101 individuals brought to Australia in 1935, poisonous toads now cover an area >1.2 million km² with adverse effects on native fauna. Despite extensive research on the role of macroparasites in cane toad invasion, viral research is lagging. We compared viral prevalence and diversity between toads in their native range (French Guiana, n=25) and two introduced ranges: Australia (n=151) and Hawai'i (n=10) with a metatranscriptomic and metagenomic approach combined with PCR screening. Australian toads almost exclusively harbor one of seven viruses detected globally. Rhimavirus-A (Picornaviridae) exhibited low genetic diversity and likely actively infected 9% of sampled Australian toads extending across ~2,000km of Northern Australia and up to the current invasion front. In native range cane toads, we identified multiple phylogenetically distinct viruses (Iridoviridae, Picornaviridae, Papillomaviridae, and Nackedna-like virus). None of the same viruses was detected in both ranges, suggesting that Australian cane toads have largely escaped the viral infection experienced by their native range counterparts. The novel native range viruses described here are potential biocontrol agents, as Australian toads likely lack prior immunological exposure to these viruses. Overall, our evidence suggests that there may be differences between viruses infecting cane toads in their native vs. introduced ranges, which lays the groundwork for further studies on how these viruses have influenced the toads' invasion history.

The Genomic Processes of Biological Invasions: From Invasive Species to Cancer Metastases and Back Again

The concept of invasion is useful across a broad range of contexts, spanning from the fine scale landscape of cancer tumors up to the broader landscape of ecosystems. Invasion biology provides extraordinary opportunities for studying the mechanistic basis of contemporary evolution at the molecular level. Although the field of invasion genetics was established in ecology and evolution more than 50 years ago, there is still a limited understanding of how genomic level processes translate into invasive phenotypes across different taxa in response to complex environmental conditions. This is largely because the study of most invasive species is limited by information about complex genome level processes. We lack good reference genomes for most species. Rigorous studies to examine genomic processes are generally too costly. On the contrary, cancer studies are fortified with extensive resources for studying genome level dynamics and the interactions among genetic and non-genetic mechanisms. Extensive analysis of primary tumors and metastatic samples have revealed the importance of several genomic mechanisms including higher mutation rates, specific types of mutations, aneuploidy or whole genome doubling and non-genetic effects. Metastatic sites can be directly compared to primary tumor cell counterparts. At the same time, clonal dynamics shape the genomics and evolution of metastatic cancers. Clonal diversity varies by cancer type, and the tumors’ donor and recipient tissues. Still, the cancer research community has been unable to identify any common events that provide a universal predictor of “metastatic potential” which parallels findings in evolutionary ecology. Instead, invasion in cancer studies depends strongly on context, including order of events and clonal composition. The detailed studies of the behavior of a variety of human cancers promises to inform our understanding of genome level dynamics in the diversity of invasive species and provide novel insights for management.

Transposable elements expression in Rhinella marina (cane toad) specimens submitted to immune and stress challenge

Transposable elements (TEs) are important components of eukaryotic genomes and compose around 30% of the genome of Rhinella marina, an invasive toad species. Considering the possible role of TEs in the adaptation of populations, we have analyzed the expression of TEs in publicly available spleen tissue transcriptomic data generated for this species after immune and stress challenge. By analyzing the transcriptome assembly, we detected a high number of TE segments. Moreover, some distinct TE families were differentially expressed in some conditions. Our result shows that several TEs are capable of being transcribed in R. marina and they could help to generate a rapid response of specimens to the environment. Also, we can suggest that these TEs could be activated in the germinative cells as well producing variability to be selected and shaped by the evolutionary processes behind the success of this invasive species. Thus, the TEs are important targets for investigation in the context of R. marina adaptation.

Evolutionary Dynamics of Treatment-Induced Resistance in Cancer Informs Understanding of Rapid Evolution in Natural Systems

Rapid evolution is ubiquitous in nature. We briefly review some of this quite broadly, particularly in the context of response to anthropogenic disturbances. Nowhere is this more evident, replicated and accessible to study than in cancer. Curiously cancer has been late - relative to fisheries, antibiotic resistance, pest management and evolution in human dominated landscapes - in recognizing the need for evolutionarily informed management strategies. The speed of evolution matters. Here, we employ game-theoretic modeling to compare time to progression with continuous maximum tolerable dose to that of adaptive therapy where treatment is discontinued when the population of cancer cells gets below half of its initial size and re-administered when the cancer cells recover, forming cycles with and without treatment. We show that the success of adaptive therapy relative to continuous maximum tolerable dose therapy is much higher if the population of cancer cells is defined by two cell types (sensitive vs. resistant in a polymorphic population). Additionally, the relative increase in time to progression increases with the speed of evolution. These results hold with and without a cost of resistance in cancer cells. On the other hand, treatment-induced resistance can be modeled as a quantitative trait in a monomorphic population of cancer cells. In that case, when evolution is rapid, there is no advantage to adaptive therapy. Initial responses to therapy are blunted by the cancer cells evolving too quickly. Our study emphasizes how cancer provides a unique system for studying rapid evolutionary changes within tumor ecosystems in response to human interventions; and allows us to contrast and compare this system to other human managed or dominated systems in nature.

Host defense or parasite cue: Skin secretions mediate interactions between amphibians and their parasites

Amphibian skin secretions (substances produced by the amphibian plus microbiota) plausibly act as a first line of defense against parasite/pathogen attack, but may also provide chemical cues for pathogens. To clarify the role of skin secretions in host-parasite interactions, we conducted experiments using cane toads (Rhinella marina) and their lungworms (Rhabdias pseudosphaerocephala) from the range-core and invasion-front of the introduced anurans' range in Australia. Depending on the geographical area, toad skin secretions can reduce the longevity and infection success of parasite larvae, or attract lungworm larvae and enhance their infection success. These striking differences between the two regions were due both to differential responses of the larvae, and differential effects of the skin secretions. Our data suggest that skin secretions play an important role in host-parasite interactions in anurans, and that the arms race between a host and parasite can rapidly generate spatial variation in critical features of that interaction.

The evolutionary ecology of fatty-acid variation: Implications for consumer adaptation and diversification

The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.

Epigenetics and the success of invasive plants

Biological invasions impose ecological and economic problems on a global scale, but also provide extraordinary opportunities for studying contemporary evolution. It is critical to understand the evolutionary processes that underly invasion success in order to successfully manage existing invaders, and to prevent future invasions. As successful invasive species sometimes are suspected to rapidly adjust to their new environments in spite of very low genetic diversity, we are obliged to re-evaluate genomic-level processes that translate into phenotypic diversity. In this paper, we review work that supports the idea that trait variation, within and among invasive populations, can be created through epigenetic or other non-genetic processes, particularly in clonal invaders where somatic changes can persist indefinitely. We consider several processes that have been implicated as adaptive in invasion success, focusing on various forms of 'genomic shock' resulting from exposure to environmental stress, hybridization and whole-genome duplication (polyploidy), and leading to various patterns of gene expression re-programming and epigenetic changes that contribute to phenotypic variation or even novelty. These mechanisms can contribute to transgressive phenotypes, including hybrid vigour and novel traits, and may thus help to understand the huge successes of some plant invaders, especially those that are genetically impoverished. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

The worldwide invasion of Drosophila suzukii is accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions

Transposable Elements (TEs) are ubiquitous and mobile repeated sequences. They are major determinants of host fitness. Here, we characterized the TE content of the spotted wing fly Drosophila suzukii. Using a recently improved genome assembly, we reconstructed TE sequences de novo, and found that TEs occupy 47% of the genome and are mostly located in gene poor regions. The majority of TE insertions segregate at low frequencies, indicating a recent and probably ongoing TE activity. To explore TE dynamics in the context of biological invasions, we studied variation of TE abundance in genomic data from 16 invasive and six native populations of D. suzukii. We found a large increase of the TE load in invasive populations correlated with a reduced Watterson estimate of genetic diversity θ̂w a proxy of effective population size. We did not find any correlation between TE contents and bioclimatic variables, indicating a minor effect of environmentally induced TE activity. A genome-wide association study revealed that ca. 2,000 genomic regions are associated with TE abundance. We did not find, however, any evidence in such regions of an enrichment for genes known to interact with TE activity (e.g. transcription factor encoding genes or genes of the piRNA pathway). Finally, the study of TE insertion frequencies revealed 15 putatively adaptive TE insertions, six of them being likely associated with the recent invasion history of the species.

Intergenerational effects of manipulating DNA methylation in the early life of an iconic invader

In response to novel environments, invasive populations often evolve rapidly. Standing genetic variation is an important predictor of evolutionary response but epigenetic variation may also play a role. Here, we use an iconic invader, the cane toad (Rhinella marina), to investigate how manipulating epigenetic status affects phenotypic traits. We collected wild toads from across Australia, bred them, and experimentally manipulated DNA methylation of the subsequent two generations (G1, G2) through exposure to the DNA methylation inhibitor zebularine and/or conspecific tadpole alarm cues. Direct exposure to alarm cues (an indicator of predation risk) increased the potency of G2 tadpole chemical cues, but this was accompanied by reductions in survival. Exposure to alarm cues during G1 also increased the potency of G2 tadpole cues, indicating intergenerational plasticity in this inducible defence. In addition, the negative effects of alarm cues on tadpole viability (i.e. the costs of producing the inducible defence) were minimized in the second generation. Exposure to zebularine during G1 induced similar intergenerational effects, suggesting a role for alteration in DNA methylation. Accordingly, we identified intergenerational shifts in DNA methylation at some loci in response to alarm cue exposure. Substantial demethylation occurred within the sodium channel epithelial 1 subunit gamma gene (SCNN1G) in alarm cue exposed individuals and their offspring. This gene is a key to the regulation of sodium in epithelial cells and may help to maintain the protective epidermal barrier. These data suggest that early life experiences of tadpoles induce intergenerational effects through epigenetic mechanisms, which enhance larval fitness. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'

Developmental assays using invasive cane toads, Rhinella marina, reveal safety concerns of a common formulation of the rice herbicide, butachlor

Identifying the adverse impacts of pesticide exposure is essential to guide regulations that are protective of wildlife and human health. Within rice ecosystems, amphibians are valuable indicators because pesticide applications coincide with sensitive reproductive and developmental life stages. We conducted two experiments using wild cane toads (Rhinella marina) to test 1) whether environmentally relevant exposure to a commercial formulation of butachlor, an acetanilide herbicide used extensively in rice, affects amphibian development and 2) whether cane toad tadpoles are capable of acclimatizing to sub-lethal exposure. First, we exposed wild cane toads to 0.002, 0.02, or 0.2 mg/L of butachlor (Machete EC), during distinct development stages (as eggs and hatchlings, as tadpoles, or continuously) for 12 days. Next, we exposed a subset of animals from the first experiment to a second, lethal concentration and examined survivorship. We found that cane toads exposed to butachlor developed slower and weighed less than controls, and that development of the thyroid gland was affected: exposed individuals had smaller thyroid glands and thyrocyte cells, and more individual follicles. Analyses of the transcriptome revealed that butachlor exposure resulted in downregulation of transcripts related to metabolic processes, anatomic structure development, immune system function, and response to stress. Last, we observed evidence of acclimatization, where animals exposed to butachlor early in life performed better than naïve animals during a second exposure. Our findings indicate that the commercial formulation of butachlor, Machete EC, causes thyroid endocrine disruption in vertebrates, and suggest that exposure in lowland irrigated rice fields presents a concern for wildlife and human health. Furthermore, we establish that developmental assays with cane toads can be used to screen for adverse effects of pesticides in rice fields.

Environmental correlates of genetic variation in the invasive European starling in North America

Populations of invasive species that colonize and spread in novel environments may differentiate both through demographic processes and local selection. European starlings (Sturnus vulgaris) were introduced to New York in 1890 and subsequently spread throughout North America, becoming one of the most widespread and numerous bird species on the continent. Genome-wide comparisons across starling individuals and populations can identify demographic and/or selective factors that facilitated this rapid and successful expansion. We investigated patterns of genomic diversity and differentiation using reduced-representation genome sequencing of 17 winter-season sampling sites. Consistent with this species' high dispersal rate and rapid expansion history, we found low geographical differentiation and few F_ST outliers even at a continental scale. Despite starting from a founding population of ~180 individuals, North American starlings show only a moderate genetic bottleneck, and models suggest a dramatic increase in effective population size since introduction. In genotype-environment associations we found that ~200 single-nucleotide polymorphisms are correlated with temperature and/or precipitation against a background of negligible genome- and range-wide divergence. Given this evidence, we suggest that local adaptation in North American starlings may have evolved rapidly even in this wide-ranging and evolutionarily young system. This survey of genomic signatures of expansion in North American starlings is the most comprehensive to date and complements ongoing studies of world-wide local adaptation in these highly dispersive and invasive birds.

Introduced ant species occupy empty climatic niches in Europe

Exploring shifts in the climatic niches of introduced species can provide significant insight into the mechanisms underlying the invasion process and the associated impacts on biodiversity. We aim to test the phylogenetic signal hypothesis in native and introduced species in Europe by examining climatic niche similarity. We examined data from 134 ant species commonly found in western Europe; 130 were native species, and 4 were introduced species. We characterized their distribution patterns using species records from different databases, determined their phylogenetic relatedness, and tested for a phylogenetic signal in their optimal climatic niches. We then compared the introduced species' climatic niches in Europe with their climatic niches in their native ranges and with the climatic niches of their closest relative species in Europe. We found a strong phylogenetic signal in the optimal climatic niches of the most common ant species in Europe; however, this signal was weak for the main climatic variables that affect the distributions of introduced versus native species. Also, introduced species occupied different climatic niches in Europe than in their native ranges; furthermore, their European climatic niches did not resemble those of their closest relative species in Europe. We further discovered that there was not much concordance between the climatic niches of introduced species in their native ranges and climatic conditions in Europe. Our findings suggest that phylogenetics do indeed constrain shifts in the climatic niches of native European ant species. However, introduced species would not face such constraints and seemed to occupy relatively empty climatic niches.

Rapid divergence of parasite infectivity and host resistance during a biological invasion

By perturbing co-evolved interactions, biological invasions provide an opportunity to study the evolution of interactions between hosts and their parasites on ecological timescales. We studied the interaction between the cane toad (Rhinella marina) and its direct-lifecycle lungworm (Rhabdias pseudosphaerocephala) that was brought from South America to Australia with the toads in 1935. Compared with infective parasite larvae from long-established (range-core) toad populations, parasite larvae from toads near the invasion front were larger, lived longer and were better able to resist exposure to toxin from the parotoid glands of toads. Experimentally, we infected the common-garden-reared progeny of toads from range-core and invasion-front populations within Australia with lungworms from both populations. Infective larvae from invasion-front (vs. range-core) populations of the parasite were more successful at entering toads (by skin penetration) and establishing infections in the lungs. Toads from invasion-front populations were less prone to infection by either type of larvae. Thus, within 84 years, parasites at an invasion front have increased infectivity, whereas hosts have increased resistance to parasite infection compared with range-core populations. Rapid evolution of traits might affect host–parasite interactions during biological invasions, generating unpredictable effects both on the invaders and on native ecosystems.

Biogeographic history moulds population differentiation in ageing of oxidative status in an amphibian

Regulation of oxidative status plays a substantial role in physiological ageing. However, we know little about age-related changes of oxidative status in wild animals, and even less about the role of population history in moulding ageing rates. We addressed these questions by means of a common garden experiment, using the Tyrrhenian tree frog Hyla sarda as the study species. This species underwent a range expansion from northern Sardinia (source) up to Corsica (newly founded) during the Late Pleistocene, and then the two populations became geographically isolated. We found that, at the beginning of the experiment, Sardinian and Corsican frogs had similar concentrations of all oxidative status markers analysed. One year later, Corsican frogs had higher oxidative stress and suffered higher mortality than Sardinian frogs. Our results suggest the intriguing scenario that population differentiation in rates of physiological ageing owing to oxidative stress might be an overlooked legacy of past biogeographic processes.

Differential immune gene expression associated with contemporary range expansion in two invasive rodents in Senegal

Biological invasions are major anthropogenic changes associated with threats to biodiversity and health. However, what determines the successful establishment and spread of introduced populations remains unclear. Here, we explore several hypotheses linking invasion success and immune phenotype traits, including those based on the evolution of increased competitive ability concept. We compared gene expression profiles between anciently and recently established populations of two major invading species, the house mouse Mus musculus domesticus and the black rat Rattus rattus, in Senegal (West Africa). Transcriptome analyses identified differential expression between anciently and recently established populations for 364 mouse genes and 83 rat genes. All immune-related genes displaying differential expression along the mouse invasion route were overexpressed at three of the four recently invaded sites studied. Complement activation pathway genes were overrepresented among these genes. By contrast, no particular immunological process was found to be overrepresented among the differentially expressed genes of black rat. Changes in transcriptome profiles were thus observed along invasion routes, but with different specific patterns between the two invasive species. These changes may be driven by increases in infection risks at sites recently invaded by the house mouse, and by stochastic events associated with colonization history for the black rat. These results constitute a first step toward the identification of immune eco-evolutionary processes potentially involved in the invasion success of these two rodent species.

Most invasive species largely conserve their climatic niche

The ecological niche is a key concept for elucidating patterns of species distributions and developing strategies for conserving biodiversity. However, recent times are seeing a widespread debate whether species niches are conserved across space and time (niche conservatism hypothesis). Biological invasions represent a unique opportunity to test this hypothesis in a short time frame at the global scale. We synthesized empirical findings for 434 invasive species from 86 studies to assess whether invasive species conserve their climatic niche between native and introduced ranges. Although the niche conservatism hypothesis was rejected in most studies, highly contrasting conclusions for the same species between and within studies suggest that the dichotomous conclusions of these studies were sensitive to techniques, assessment criteria, or author preferences. We performed a consistent quantitative analysis of the dynamics between native and introduced climatic niches reported by previous studies. Our results show there is very limited niche expansion between native and introduced ranges, and introduced niches occupy a position similar to native niches in the environmental space. These findings support the niche conservatism hypothesis overall. In particular, introduced niches were narrower for terrestrial animals, species introduced more recently, or species with more native occurrences. Niche similarity was lower for aquatic species, species introduced only intentionally or more recently, or species with fewer introduced occurrences. Climatic niche conservatism for invasive species not only increases our confidence in transferring ecological niche models to new ranges but also supports the use of niche models for forecasting species responses to changing climates.

Do Epigenetic Changes Drive Corticosterone Responses to Alarm Cues in Larvae of an Invasive Amphibian?

The developmental environment can exert powerful effects on animal phenotype. Recently, epigenetic modifications have emerged as one mechanism that can modulate developmentally plastic responses to environmental variability. For example, the DNA methylation profile at promoters of hormone receptor genes can affect their expression and patterns of hormone release. Across taxonomic groups, epigenetic alterations have been linked to changes in glucocorticoid (GC) physiology. GCs are metabolic hormones that influence growth, development, transitions between life-history stages, and thus fitness. To date, relatively few studies have examined epigenetic effects on phenotypic traits in wild animals, especially in amphibians. Here, we examined the effects of exposure to predation threat (alarm cues) and experimentally manipulated DNA methylation on corticosterone (CORT) levels in tadpoles and metamorphs of the invasive cane toad (Rhinella marina). We included offspring of toads sampled from populations across the species' Australian range. In these animals, exposure to chemical cues from injured conspecifics induces shifts in developmental trajectories, putatively as an adaptive response that lessens vulnerability to predation. We exposed tadpoles to these alarm cues, and measured changes in DNA methylation and CORT levels, both of which are mechanisms that have been implicated in the control of phenotypically plastic responses in tadpoles. To test the idea that DNA methylation drives shifts in GC physiology, we also experimentally manipulated methylation levels with the drug zebularine. We found differentially methylated regions (DMRs) between control tadpoles and their full-siblings exposed to alarm cues, zebularine, or both treatments. However, the effects of these manipulations on methylation patterns were weaker than clutch (e.g., genetic, maternal, etc.) effects. CORT levels were higher in larval cane toads exposed to alarm cues and zebularine. We found little evidence of changes in DNA methylation across the GC receptor gene (NR3C1) promoter region in response to alarm cue or zebularine exposure. In both alarm cue and zebularine-exposed individuals, we found differentially methylated DNA in the suppressor of cytokine signaling 3 gene (SOCS3), which may be involved in predator avoidance behavior. In total, our data reveal that alarm cues have significant impacts on tadpole physiology, but show only weak links between DNA methylation and CORT levels. We also identify genes containing DMRs in tadpoles exposed to alarm cues and zebularine, particularly in range-edge populations, that warrant further investigation.

Stress and immunity: Field comparisons among populations of invasive cane toads in Florida

Cane toads (Rhinella marina) were introduced worldwide and have become invasive in multiple locations, representing a major driver of biodiversity loss through competition (food, shelter, territory), predation, and the poisoning of native species. These toads have been used in Australia as a model for studies concerning invasion biology and ecoimmunology, as longer-established (core) and invasion front (edge) populations show altered stress and immune response profiles. Although cane toads were also introduced into the United States in the 1950s, these patterns have yet to be evaluated for the populations spanning Florida. Toads introduced into Florida have dispersed primarily northward along a latitudinal gradient, where they encounter cooler temperatures that may further impact stress and immune differences between core and edge populations. In this study, we sampled cane toads from nine different locations spanning their invasion in Florida. Cane toads from southern populations showed higher plasma bacterial killing ability and natural antibody titers than the toads from the northern populations, indicating they have a better immune surveillance system. Also, southern toads were more responsive to a novel stressor (1 hr restraint), showing a higher increase in corticosterone levels. These results indicate that possible trade-offs have occurred between immune and stress responses as these toads have become established in northern cooler areas in Florida.

Evolutionary principles guiding amphibian conservation

The Anthropocene has witnessed catastrophic amphibian declines across the globe. A multitude of new, primarily human-induced drivers of decline may lead to extinction, but can also push species onto novel evolutionary trajectories. If these are recognized by amphibian biologists, they can be engaged in conservation actions. Here, we summarize how principles stemming from evolutionary concepts have been applied for conservation purposes, and address emerging ideas at the vanguard of amphibian conservation science. In particular, we examine the consequences of increased drift and inbreeding in small populations and their implications for practical conservation. We then review studies of connectivity between populations at the landscape level, which have emphasized the limiting influence of anthropogenic structures and degraded habitat on genetic cohesion. The rapid pace of environmental changes leads to the central question of whether amphibian populations can cope either by adapting to new conditions or by shifting their ranges. We gloomily conclude that extinction seems far more likely than adaptation or range shifts for most species. That said, conservation strategies employing evolutionary principles, such as selective breeding, introduction of adaptive variants through translocations, ecosystem interventions aimed at decreasing phenotype-environment mismatch, or genetic engineering, may effectively counter amphibian decline in some areas or for some species. The spread of invasive species and infectious diseases has often had disastrous consequences, but has also provided some premier examples of rapid evolution with conservation implications. Much can be done in terms of setting aside valuable amphibian habitat that should encompass both natural and agricultural areas, as well as designing protected areas to maximize the phylogenetic and functional diversity of the amphibian community. We conclude that an explicit consideration and application of evolutionary principles, although certainly not a silver bullet, should increase effectiveness of amphibian conservation in both the short and long term.

A comparison of nonlethal sampling methods for amphibian gut microbiome analyses

Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.

Genomic footprints of a biological invasion: Introduction from Asia and dispersal in Europe of the topmouth gudgeon (Pseudorasbora parva)

Facilitated by the intensification of global trading, the introduction and dispersal of species to areas in which they are historically non-native is nowadays common. From an evolutionary standpoint, invasions are paradoxical: not only non-native environments could be different from native ones for which introduced individuals would be ill-adapted, but also small founding population size should be associated with reduced adaptive potential. As such, biological invasions are considered valuable real-time evolutionary experiments. Here, we investigated the population structure and adaptive potential of the highly invasive topmouth gudgeon (Pseudorasbora parva) across Europe and East Asia. We RAD-sequenced 301 specimens from sixteen populations and three distinct within-catchment invaded regions as well as two locations in the native range. With 13,785 single nucleotide polymorphisms, we provide conclusive evidence for a genome-wide signature of two distinct invasion events, in Slovakia and Turkey, each originating from a specific area in the native range. A third invaded area, in France, appears to be the result of dispersal within the invasive range. Few loci showed signs of selection, the vast majority of which being identified in the Slovakian region. Functional annotation suggests that faster early stage development, resistance to pollution and immunocompetence contribute to the invasion success of the local habitats. By showing that populations in the invasive range have different evolutionary histories, our study reinforces the idea that populations, rather than species, are the units to consider in invasion biology.

Increased Adaptive Variation Despite Reduced Overall Genetic Diversity in a Rapidly Adapting Invader

Invasive species often evolve rapidly following introduction despite genetic bottlenecks that may result from 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 introduced Australian range. Here, we used three genome-wide datasets to characterize their population structure and genetic diversity. 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. Although we find an overall reduction in genetic diversity following introduction, 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, toads encounter novel environmental challenges in Australia, and the transition between genetic clusters occurs at a point along the invasion transect where temperature rises and rainfall decreases. We identify environmentally associated loci known to be involved in resistance to heat and dehydration. This study highlights that natural selection occurs rapidly and plays a vital role in shaping the structure of invasive populations.

Rapid adaptation to cold in the invasive cane toad Rhinella marina

Understanding rapid adaptation to novel environments is essential as we face increasing climatic change. Invasive species are an ideal system for studying adaptation as they are typically introduced to novel environments where they must adapt if they are to persist. We used the invasive cane toad, Rhinella marina, to investigate the contribution of plasticity and evolution to rapid adaptation in a novel environment. Rhinella marina is a neotropical toad that has invaded areas with climates outside of its native environmental niche. The goal of this research was to understand how cane toads persist in northern Florida, the coldest region of their combined natural and invasive range, and originally thought to be beyond their thermal breadth. We measured Critical thermal minima in cane toads from the original, warm introduction location (Miami), and their northern range edge (Tampa) to determine whether northern toads were more cold-tolerant, and to examine the contribution of adaptive plasticity and evolution to any changes in tolerance. Our results show that following acclimation to cold temperatures, southern toads are less tolerant of cold than northern toads. This persistent population difference implies selection for cold-tolerance in northern populations. Differences in individual responses indicate that plasticity is also involved in this response. Our findings have implications for conservation because predatory cane toad invasions threaten local faunas, especially native amphibians. Characterizing specific adaptive mechanisms that allow R. marina to expand its range will identify evolutionary processes that shape a highly successful invasive species.