Origin of functional de novo genes in humans from "hopeful monsters"

For a long time, it was believed that new genes arise only from modifications of preexisting genes, but the discovery of de novo protein-coding genes that originated from noncoding DNA regions demonstrates the existence of a "motherless" origination process for new genes. However, the features, distributions, expression profiles, and origin modes of these genes in humans seem to support the notion that their origin is not a purely "motherless" process; rather, these genes arise preferentially from genomic regions encoding preexisting precursors with gene-like features. In such a case, the gene loci are typically not brand new. In this short review, we will summarize the definition and features of human de novo genes and clarify their process of origination from ancestral non-coding genomic regions. In addition, we define the favored precursors, or "hopeful monsters," for the origin of de novo genes and present a discussion of the functional significance of these young genes in brain development and tumorigenesis in humans. This article is categorized under: RNA Evolution and Genomics > RNA and Ribonucleoprotein Evolution.

Multidrug resistance of Botrytis cinerea associated with its adaptation to plant secondary metabolites

Fungicides are an effective way to control gray mold of grapes, but the pathogen Botrytis cinerea can develop resistance, overcoming the effectiveness of a fungicide that is repeatedly applied. More importantly, the emergence of multidrug resistance (MDR) in the field, where multiple fungicides with different modes of action simultaneously lose their efficacies, is a significant concern. MDR is associated with ATP-binding cassette (ABC) transporters of the pathogen, and certain plant secondary metabolites (PSMs) stimulate the upregulation of ABC transporters, we hypothesized that the pathogen's preadaptation to PSMs might contribute to MDR development. To test this in B. cinerea, ten PSMs, namely, resveratrol, reserpine, chalcone, flavanone, eugenol, farnesol, anethene, camptothecin, salicylic acid, and psoralen, were selected based on their association with ABC transporters involved in fungicide resistance. B. cinerea strain B05.10 was continuously transferred for 15 generations on potato dextrose agar amended with a PSM (PDAP), and sensitivities to PSMs and fungicides were examined on the 5th, 10th, and 15th generations. RNA was extracted from B. cinerea from the selected generations. After 15 generations of culture transfers, an up-regulation was observed in the expression of ABC transporter-encoding genes BcatrB, BcatrD, and BcatrK using quantitative polymerase chain reaction (qPCR). This upregulation was found to contribute to MDR of B. cinerea against two or more fungicides, among azoxystrobin, boscalid, fludioxonil, difenoconazole, prochloraz, and pyrimethanil. This finding was confirmed through genetic transformation. The decreased sensitivity of B. cinerea to fungicides was confirmed as a subsequent MDR phenotype after exposure to camptothecin, flavanone, and resveratrol. Besides, transcriptome analysis also revealed the upregulation of transcription factors related to ABC expression following resveratrol exposure. This suggests that PSMs contributed to inducing preadaptation of B. cinerea, leading to subsequent MDR.IMPORTANCEThe emergence of MDR in plant pathogens is a threat to plant disease management and leads to the use of excessive fungicides. Botrytis cinerea is of particular concern because its MDR has widely emerged in the field. Understanding its genesis is the first step for controlling MDR. In this study, the contribution of PSMs to MDR has been examined. Effective management of this pathogen in agroecosystems relies on a better understanding of how it copes with phytochemicals or fungicides.

Ergot Alkaloids Contribute to the Pathogenic Potential of the Fungus Aspergillus leporis

Opportunistically pathogenic fungi have varying potential to cause disease in animals. Factors contributing to their virulence include specialized metabolites, which in some cases evolved in contexts unrelated to pathogenesis. Specialized metabolites that increase fungal virulence in the model insect Galleria mellonella include the ergot alkaloids fumigaclavine C in Aspergillus fumigatus (syn. Neosartorya fumigata) and lysergic acid α-hydroxyethylamide (LAH) in the entomopathogen Metarhizium brunneum. Three species of Aspergillus recently found to accumulate high concentrations of LAH were investigated for their pathogenic potential in G. mellonella. Aspergillus leporis was most virulent, A. hancockii was intermediate, and A. homomorphus had very little pathogenic potential. Aspergillus leporis and A. hancockii emerged from and sporulated on dead insects, thus completing their asexual life cycles. Inoculation by injection resulted in more lethal infections than did topical inoculation, indicating that A. leporis and A. hancockii were preadapted for insect pathogenesis but lacked an effective means to breach the insect's cuticle. All three species accumulated LAH in infected insects, with A. leporis accumulating the most. Concentrations of LAH in A. leporis were similar to those observed in the entomopathogen M. brunneum. LAH was eliminated from A. leporis through a CRISPR/Cas9-based gene knockout, and the resulting strain had reduced virulence to G. mellonella. The data indicate that A. leporis and A. hancockii have considerable pathogenic potential and that LAH increases the virulence of A. leporis. IMPORTANCE Certain environmental fungi infect animals occasionally or conditionally, whereas others do not. Factors that affect the virulence of these opportunistically pathogenic fungi may have originally evolved to fill some other role for the fungus in its primary environmental niche. Among the factors that may improve the virulence of opportunistic fungi are specialized metabolites--chemicals that are not essential for basic life functions but provide producers with an advantage in particular environments or under specific conditions. Ergot alkaloids are a large family of fungal specialized metabolites that contaminate crops in agriculture and serve as the foundations of numerous pharmaceuticals. Our results show that two ergot alkaloid-producing fungi that were not previously known to be opportunistic pathogens can infect a model insect and that, in at least one of the species, an ergot alkaloid increases the virulence of the fungus.

Assessment of phenotypic heterogeneity in Salmonella Typhimurium preadapted to ciprofloxacin and tetracycline

Bacterial population exposed to stressful antibiotic conditions consists of various subpopulations such as tolerant, persister, and resistant cells. The aim of this study was to evaluate the phenotypic heterogeneity of Salmonella Typhimurium preadapted to sublethal concentrations of antibiotics. Salmonella Typhimurium cells were treated with 1/2 × MIC of antibiotics for the first 48 h and successively 1 × MIC for the second 24 h at 37°C, including untreated control (CON), no antibiotic and 1 × MIC ciprofloxacin (NON-CIP), 1/2 × MIC ciprofloxacin and 1 × MIC ciprofloxacin (CIP-CIP), 1/2 × MIC tetracycline and 1 × MIC ciprofloxacin (TET-CIP), no antibiotic and 1 × MIC tetracycline (NON-TET), 1/2 × MIC ciprofloxacin and 1 × MIC tetracycline (CIP-TET), and 1/2 × MIC tetracycline and 1 × MIC tetracycline (TET-TET). All treatments were evaluated by antibiotic susceptibility, ATP level, relative fitness, cross-resistance, and persistence. S. Typhimurium cells were more susceptible to non-adapted NON-CIP and NON-TET (>3-log reduction) than pre-adapted CIP-CIP, TET-CIP, CIP-TET, and TET-TET. CON exhibited the highest ATP level, corresponding to the viable cell number. The relative fitness levels were more than 0.95 for all treatments, except for NON-CIP (0.78). The resistance to ciprofloxacin and tetracycline was increased at all treatments with the exception of NON-TET. The persister cells were noticeably induced at CIP-TET treatment, showing more than 5 log CFU mL-1. The results suggest that the antibiotic preadaptation led to heterogeneous populations including persisters that can develop to resistance. This study provides new insight in the bacterial persistence associated with their potential risk and paves the way to design antibiotic therapy targeting dormant bacteria.

Random peptides rich in small and disorder-promoting amino acids are less likely to be harmful

Proteins are the workhorses of the cell, yet they carry great potential for harm via misfolding and aggregation. Despite the dangers, proteins are sometimes born de novo from non-coding DNA. Proteins are more likely to be born from non-coding regions that produce peptides that do little to no harm when translated than from regions that produce harmful peptides. To investigate which newborn proteins are most likely to "first, do no harm", we estimate fitnesses from an experiment that competed Escherichia coli lineages that each expressed a unique random peptide. A variety of peptide metrics significantly predict lineage fitness, but this predictive power stems from simple amino acid frequencies rather than the ordering of amino acids. Amino acids that are smaller and that promote intrinsic structural disorder have more benign fitness effects. We validate that the amino acids that indicate benign effects in random peptides expressed in E. coli also do so in an independent dataset of random N-terminal tags in which it is possible to control for expression level. The same amino acids are also enriched in young animal proteins.

Digitized collections elucidate invasion history and patterns of awn polymorphism in Microstegium vimineum

PREMISE

Digitized collections can help illuminate the mechanisms behind the establishment and spread of invasive plants. These databases provide a record of traits in space and time that allows for investigation of abiotic and biotic factors that influence invasive species.

METHODS

Over 1100 digitized herbarium records were examined to investigate the invasion history and trait variation of Microstegium vimineum. Presence-absence of awns was investigated to quantify geographic patterns of this polymorphic trait, which serves several functions in grasses, including diaspore burial and dispersal to germination sites. Floret traits were further quantified, and genomic analyses of contemporary samples were conducted to investigate the history of M. vimineum's introduction and spread into North America.

RESULTS

Herbarium records revealed similar patterns of awn polymorphism in native and invaded ranges of M. vimineum, with awned forms predominating at higher latitudes and awnless forms at lower latitudes. Herbarium records and genomic data suggested initial introduction and spread of the awnless form in the southeastern United States, followed by a putative secondary invasion and spread of the awned form from eastern Pennsylvania. Awned forms have longer florets, and floret size varies significantly with latitude. There is evidence of a transition zone with short-awned specimens at mid-latitudes. Genomic analyses revealed two distinct clusters corresponding to awnless and awned forms, with evidence of admixture.

CONCLUSIONS

Our results demonstrate the power of herbarium data to elucidate the invasion history of a problematic weed in North America and, together with genomic data, reveal a possible key trait in introduction success: presence or absence of an awn.

The persistence and evolutionary consequences of vestigial behaviours

Behavioural traits are often noted to persist after relaxation or removal of associated selection pressure, whereas it has been observed that morphological traits under similar conditions appear to decay more rapidly. Despite this, persistent non‐adaptive, ‘vestigial’ behavioural variation has received little research scrutiny. Here we review published examples of vestigial behavioural traits, highlighting their surprising prevalence, and argue that their further study can reveal insights about the widely debated role of behaviour in evolution. Some vestigial behaviours incur fitness costs, so may act as a drag on adaptive evolution when that adaptation occurs via trait loss or reversal. In other cases, vestigial behaviours can contribute to future evolutionary trajectories, for example by preserving genetic and phenotypic variation which is later co‐opted by selection during adaptive evolution or diversification, or through re‐emergence after ancestral selection pressures are restored. We explore why vestigial behaviours appear prone to persistence. Behavioural lag may be a general phenomenon arising from relatively high levels of non‐genetic variation in behavioural expression, and pleiotropic constraint. Long‐term persistence of non‐adaptive behavioural traits could also result when their expression is associated with morphological features which might be more rapidly lost or reduced. We propose that vestigial behaviours could provide a substrate for co‐option by novel selective forces, and advocate further study of the fate of behavioural traits following relaxed and reversed selection. Vestigial behaviours have been relatively well studied in the context of antipredator behaviours, but they are far from restricted to this ecological context, and so deserve broader consideration. They also have practical importance, with mixed evidence, for example, as to whether predator/parasite‐avoidance behaviours are rapidly lost in wildlife refuges and captivity. We identify important areas for future research to help determine whether vestigial behaviours essentially represent a form of evolutionary lag, or whether they have more meaningful evolutionary consequences distinct from those of other vestigial and behavioural traits.

Selective ancestral sorting and de novo evolution in the agricultural invasion of Amaranthus tuberculatus

The relative role of hybridization, de novo evolution, and standing variation in weed adaptation to agricultural environments is largely unknown. In Amaranthus tuberculatus, a widespread North American agricultural weed, adaptation is likely influenced by recent secondary contact and admixture of two previously isolated lineages. We characterized the extent of adaptation and phenotypic differentiation accompanying the spread of A. tuberculatus into agricultural environments and the contribution of ancestral divergence. We generated phenotypic and whole-genome sequence data from a manipulative common garden experiment, using paired samples from natural and agricultural populations. We found strong latitudinal, longitudinal, and sex differentiation in phenotypes, and subtle differences among agricultural and natural environments that were further resolved with ancestry inference. The transition into agricultural environments has favored southwestern var. rudis ancestry that leads to higher biomass and treatment-specific phenotypes: increased biomass and earlier flowering under reduced water availability, and reduced plasticity in fitness-related traits. We also detected de novo adaptation in individuals from agricultural habitats independent of ancestry effects, including marginally higher biomass, later flowering, and treatment-dependent divergence in time to germination. Therefore, the invasion of A. tuberculatus into agricultural environments has drawn on adaptive variation across multiple timescales-through both preadaptation via the preferential sorting of var. rudis ancestry and de novo local adaptation.

Evolutionary mismatch along salinity gradients in a Neotropical water strider

The evolution of local adaptation is crucial for the in situ persistence of populations in changing environments. However, selection along broad environmental gradients could render local adaptation difficult, and might even result in maladaptation. We address this issue by quantifying fitness trade-offs (via common garden experiments) along a salinity gradient in two populations of the Neotropical water strider Telmatometra withei-a species found in both fresh (FW) and brackish (BW) water environments across Panama. We found evidence for local adaptation in the FW population in its home FW environment. However, the BW population showed only partial adaptation to the BW environment, with a high magnitude of maladaptation along naturally occurring salinity gradients. Indeed, its overall fitness was ~60% lower than that of the ancestral FW population in its home environment, highlighting the role of phenotypic plasticity, rather than local adaptation, in high salinity environments. This suggests that populations seemingly persisting in high salinity environments might in fact be maladapted, following drastic changes in salinity. Thus, variable selection imposed by salinization could result in evolutionary mismatch, where the fitness of a population is displaced from its optimal environment. Understanding the fitness consequences of persisting in fluctuating salinity environments is crucial to predict the persistence of populations facing increasing salinization. It will also help develop evolutionarily informed management strategies in the context of global change.

Readthrough Errors Purge Deleterious Cryptic Sequences, Facilitating the Birth of Coding Sequences

De novo protein-coding innovations sometimes emerge from ancestrally noncoding DNA, despite the expectation that translating random sequences is overwhelmingly likely to be deleterious. The "preadapting selection" hypothesis claims that emergence is facilitated by prior, low-level translation of noncoding sequences via molecular errors. It predicts that selection on polypeptides translated only in error is strong enough to matter and is strongest when erroneous expression is high. To test this hypothesis, we examined noncoding sequences located downstream of stop codons (i.e., those potentially translated by readthrough errors) in Saccharomyces cerevisiae genes. We identified a class of "fragile" proteins under strong selection to reduce readthrough, which are unlikely substrates for co-option. Among the remainder, sequences showing evidence of readthrough translation, as assessed by ribosome profiling, encoded C-terminal extensions with higher intrinsic structural disorder, supporting the preadapting selection hypothesis. The cryptic sequences beyond the stop codon, rather than spillover effects from the regular C-termini, are primarily responsible for the higher disorder. Results are robust to controlling for the fact that stronger selection also reduces the length of C-terminal extensions. These findings indicate that selection acts on 3' UTRs in Saccharomyces cerevisiae to purge potentially deleterious variants of cryptic polypeptides, acting more strongly in genes that experience more readthrough errors.

Morphological malleability of the lateral line allows for surface fish (Astyanax mexicanus) adaptation to cave environments

The lateral line is the primary modality fish use to create a hydrodynamic image of their environment. These images contribute to a variety of behaviors, from rheotaxis to escape responses. Here we discern the contributions of visual and lateral line modalities in hunting behavior of larvae that have developed under different photic conditions. In particular, cave animals have a hypertrophied sense of mechanosensation, and we studied the common animal model cavefish Astyanax mexicanus and its closest related surface relative. We raised larvae in a diurnal light-dark regimen and in complete darkness. We then examined the distribution of neuromasts in their lateral lines, and their hunting performance in light and dark conditions, with and without the contribution of the lateral line. We report that all larva depend on the lateral line for success in hunting and that surface fish raised in the dark have a greater dependency on the lateral line.

Mosaic evolution, preadaptation, and the evolution of evolvability in apes

A major goal in postsynthesis evolutionary biology has been to better understand how complex interactions between traits drive movement along and facilitate the formation of distinct evolutionary pathways. I present analyses of a character matrix sampled across the haplorrhine skeleton that revealed several modules of characters displaying distinct patterns in macroevolutionary disparity. Comparison of these patterns to those in neurological development showed that early ape evolution was characterized by an intense regime of evolutionary and developmental flexibility. Shifting and reduced constraint in apes was met with episodic bursts in phenotypic innovation that built a wide array of functional diversity over a foundation of shared developmental and anatomical structure. Shifts in modularity drove dramatic evolutionary changes across the ape body plan in two distinct ways: (1) an episode of relaxed integration early in hominoid evolution coincided with bursts in evolutionary rate across multiple character suites; (2) the formation of two new trait modules along the branch leading to chimps and humans preceded rapid and dramatic evolutionary shifts in the carpus and pelvis. Changes to the structure of evolutionary mosaicism may correspond to enhanced evolvability that has a "preadaptive" effect by catalyzing later episodes of dramatic morphological remodeling.

Newly Identified Nematodes from Mono Lake Exhibit Extreme Arsenic Resistance

Extremophiles have much to reveal about the biology of resilience, yet their study is limited by sampling and culturing difficulties [1-3]. The broad success and small size of nematodes make them advantageous for tackling these problems [4-6]. We investigated the arsenic-rich, alkaline, and hypersaline Mono Lake (CA, US) [7-9] for extremophile nematodes. Though Mono Lake has previously been described to contain only two animal species (brine shrimp and alkali flies) in its water and sediments [10], we report the discovery of eight nematode species from the lake, including microbe grazers, parasites, and predators. Thus, nematodes are the dominant animals of Mono Lake in species richness. Phylogenetic analysis suggests that the nematodes originated from multiple colonization events, which is striking, given the young history of extreme conditions at Mono Lake [7, 11]. One species, Auanema sp., is new, culturable, and survives 500 times the human lethal dose of arsenic. Comparisons to two non-extremophile sister species [12] reveal that arsenic resistance is a common feature of the genus and a preadaptive trait that likely allowed Auanema to inhabit Mono Lake. This preadaptation may be partly explained by a variant in the gene dbt-1 shared with some Caenorhabditis elegans natural populations and known to confer arsenic resistance [13]. Our findings expand Mono Lake's ecosystem from two known animal species to ten, and they provide a new system for studying arsenic resistance. The dominance of nematodes in Mono Lake and other extreme environments and our findings of preadaptation to arsenic raise the intriguing possibility that nematodes are widely pre-adapted to be extremophiles.

The Neolithic Plant Invasion Hypothesis: the role of preadaptation and disturbance in grassland invasion

A long-standing hypothesis is that many European plants invade temperate grasslands globally because they are introduced simultaneously with pastoralism and cultivation, to which they are 'preadapted' after millennia of exposure dating to the Neolithic era ('Neolithic Plant Invasion Hypothesis' (NPIH)). These 'preadaptations' are predicted to maximize their performance relative to native species lacking this adaptive history. Here, we discuss the explanatory relevance of the NPIH, clarifying the importance of evolutionary context vs other mechanisms driving invasion. The NPIH makes intuitive sense given established connections between invasion and agricultural-based perturbation. However, tests are often incomplete given the need for performance contrasts between home and away ranges, while controlling for other mechanisms. We emphasize six NPIH-based predictions, centring on trait similarity of invaders between home vs away populations, and differing perturbation responses by invading and native plants. Although no research has integrated all six predictions, we highlight studies suggesting preadaptation influences on invasion. Given that many European grasslands are creations of human activity from the past, current invasions by these flora may represent the continuation of processes dating to the Neolithic. Ironically, European Neolithic-derived grasslands are becoming rarer, reflecting changes in management and illustrating the importance of human influences on these species.

Differentiation in native as well as introduced ranges: germination reflects mean and variance in cover of surrounding vegetation

Germination, a crucial phase in the life cycle of a plant, can be significantly influenced by competition and facilitation. The aim of this study was to test whether differences in cover of surrounding vegetation can lead to population differentiation in germination behaviour of an annual grassland species, and if so, whether such a differentiation can be found in the native as well as in the introduced range. We used maternal progeny of Erodium cicutarium previously propagated under uniform conditions that had been collected in multiple populations in the native and two introduced ranges, in populations representing extremes in terms of mean and variability of the cover of surrounding vegetation. In the first experiment, we tested the effect of germination temperature and mean cover at the source site on germination, and found interlinked effects of these factors. In seeds from one of the introduced ranges (California), we found indication for a 2-fold dormancy, hindering germination at high temperatures even if physical dormancy was broken and water was available. This behaviour was less strong in high cover populations, indicating cross-generational facilitating effects of dense vegetation. In the second experiment, we tested whether spatial variation in cover of surrounding vegetation has an effect on the proportion of dormant seeds. Contrary to our expectations, we found that across source regions, high variance in cover was associated with higher proportions of seeds germinating directly after storage. In all three regions, germination seemed to match the local environment in terms of climate and vegetation cover. We suggest that this is due to a combined effect of introduction of preadapted genotypes and local evolutionary processes.

EVOLUTIONARY RESPONSE OF PREDATORS TO DANGEROUS PREY: PREADAPTATION AND THE EVOLUTION OF TETRODOTOXIN RESISTANCE IN GARTER SNAKES

Coevolutionary interactions typically involve only a few specialized taxa. The factors that cause some taxa and not others to respond evolutionarily to selection by another species are poorly understood. Preadaptation may render some species predisposed for evolutionary response to new pressures, whereas a lack of genetic variation may limit the evolutionary potential of other taxa. We evaluate these factors in the predator-prey interaction between toxic newts (Taricha granulosa) and their resistant garter snake predators (Thamnophis sirtalis). Using a bioassay of resistance to tetrodotoxin (TTX), the primary toxin in the prey, we examined phenotypic evolution in the genus Thamnophis. Reconstruction of ancestral character states suggests that the entire genus Thamnophis, and possibly natricine snakes in general, has slightly elevated TTX resistance compared to other lineages of snakes. While this suggests that T. sirtalis is indeed predisposed to evolving TTX resistance, it also indicates that the potential exists in sympatric congeners not expressing elevated levels of TTX resistance. We also detected significant family level variation for TTX resistance in a species of Thamnophis that does not exhibit elaborated levels of the trait. This finding suggests that evolutionary response in other taxa is not limited by genetic variability. In this predator-prey system, species and population differences in resistance appear to be largely determined by variation in the selective environment rather than preadaptation or constraint.

Persistence of Salmonella Typhimurium LT2 in Soil Enhanced after Growth in Lettuce Medium

The persistence of Salmonella in the environment is influenced by a multitude of biotic and abiotic factors. In addition, its persistence can be influenced by preadaptation before the introduction into the environment. In order to study how preadaptation changes the survival of Salmonella in soil and therefore its potential to colonize the phytosphere, we developed a new medium based on lettuce material [lettuce medium (LM)]. Salmonella enterica serovar Typhimurium strain LT2 was used as a model for Salmonella in this study. LT2 was inoculated into soil microcosms after pregrowth in Luria Bertani (LB) broth or in LM. Survival of LT2 in soil was monitored over 56 days by plate counts and quantification of the Typhimurium-specific gene STM4497 using qPCR in total community DNA for which primers and TaqMan probe were designed in this study. Significantly enhanced persistence was observed for LT2 pregrown in LM compared to LT2 pregrown in LB, indicating a preadaptation effect. Surprisingly, no improved survival could be observed for S. Typhimurium strain 14028s and S. enterica serovar Senftenberg after pregrowth on LM. This indicates a high strain specificity of preadaptation. Results from previous studies suggested that biofilm formation could enhance the survival of human pathogens in various environments and might contribute to enhanced survival on plants. In vitro biofilm assays with several Salmonella strains revealed a strain-specific effect of LM on the biofilm formation. While LM significantly improved the biofilm formation of S. Senftenberg, the biofilm formation of LT2 was better in LB. This indicates that the better survival of LM-pregrown LT2 in soil was not linked to an improved ability to form biofilms but was likely due to other factors. Most importantly, this study showed that the medium used to pregrow Salmonella can influence its survival in soil and its biofilm formation which might influence the fate of Salmonella in soil.

Potential preadaptation to anthropogenic pollution: evidence from a common quantitative trait locus for zinc and cadmium tolerance in metallicolous and nonmetallicolous accessions of Arabidopsis halleri

As a drastic environmental change, metal pollution may promote the rapid evolution of genetic adaptations contributing to metal tolerance. In Arabidopsis halleri, genetic bases of zinc (Zn) and cadmium (Cd) tolerance have been uncovered only in a metallicolous accession, although tolerance is species-wide. The genetic determinants of Zn and Cd tolerance in a nonmetallicolous accession were thus investigated for the first time. The genetic architecture of tolerance was investigated in a nonmetallicolous population (SK2) by using first backcross progeny obtained from crosses between SK2 and Arabidopsis lyrata petraea, a nonmetallophyte species. Only one significant and common quantitative trait locus (QTL) region was identified explaining 22.6% and 31.2% of the phenotypic variation for Zn and Cd tolerance, respectively. This QTL co-localized with HEAVY METAL ATPASE 4 (AhHMA4), which was previously validated as a determinant of Zn and Cd tolerance in a metallicolous accession. Triplication and high expression of HMA4 were confirmed in SK2. In contrast, gene duplication and high expression of METAL TOLERANT PROTEIN 1A (MTP1A), which was previously associated with Zn tolerance in a metallicolous accession, were not observed in SK2. Overall, the results support the role of HMA4 in tolerance capacities of A. halleri that may have pre-existed in nonmetallicolous populations before colonization of metal-polluted habitats. Preadaptation to metal-contaminated sites is thus discussed.

Sensitivity to dietary phosphorus limitation in native vs. invasive lineages of a New Zealand freshwater snail

Why some species and lineages are more likely to be invasive than others is one of the most important unanswered questions in basic and applied biology. In particular, the relative contributions to the invasion process of factors like pre-adaptation to invasiveness in the native range, evolution post-colonization, and random vs. non-random sampling of colonist lineages remain unclear. We use a powerful common garden approach to address the potential for a role for sensitivity to nutrient limitation in determining the invasiveness of particular lineages of Potamopyrgus antipodarum, a New Zealand freshwater snail that has become globally invasive. We quantified specific growth rate (SGR), an important fitness-related trait in this species, under high phosphorus (P) vs. low-P conditions for a diverse set of native and invasive P. antipodarum. This experiment revealed that native-range P. antipodarum experience a more severe decline in SGR in low-P conditions relative to SGR in high-P conditions than their invasive range counterparts. Although these results suggest resilience to P limitation in invasive lineages, the absence of significant absolute differences in SGR between native and invasive lineages indicates that a straightforward connection between response to P limitation and invasiveness in P. antipodarum is unlikely. Regardless, our data demonstrate that invasive vs. native lineages of P. antipodarum exhibit consistently different responses to an important environmental variable that is rarely studied in the context of invasion success. Further studies directed at exploring and disentangling the roles of sampling effects, selection on preexisting variation, and evolution after colonization will be required to provide a comprehensive picture of the role (or lack thereof) of nutrient limitation in the global invasion of P. antipodarum, as well for as other invasive taxa.

The ecology of sex explains patterns of helping in arthropod societies

Across arthropod societies, sib-rearing (e.g. nursing or nest defence) may be provided by females, by males or by both sexes. According to Hamilton's 'haplodiploidy hypothesis', this diversity reflects the relatedness consequences of diploid vs. haplodiploid inheritance. However, an alternative 'preadaptation hypothesis' instead emphasises an interplay of ecology and the co-option of ancestral, sexually dimorphic traits for sib-rearing. The preadaptation hypothesis has recently received empirical support, but remains to be formalised. Here, we mathematically model the coevolution of sex-specific helping and sex allocation, contrasting these hypotheses. We find that ploidy per se has little effect. Rather, the ecology of sex shapes patterns of helping: sex-specific preadaptation strongly influences who helps; a freely adjustable sex ratio magnifies sex biases and promotes helping; and sib-mating, promiscuity, and reproductive autonomy also modulate the sex and abundance of helpers. An empirical survey reveals that patterns of sex-specific helping in arthropod taxa are consistent with the preadaptation hypothesis.

Expression of venom gene homologs in diverse python tissues suggests a new model for the evolution of snake venom

Snake venom gene evolution has been studied intensively over the past several decades, yet most previous studies have lacked the context of complete snake genomes and the full context of gene expression across diverse snake tissues. We took a novel approach to studying snake venom evolution by leveraging the complete genome of the Burmese python, including information from tissue-specific patterns of gene expression. We identified the orthologs of snake venom genes in the python genome, and conducted detailed analysis of gene expression of these venom homologs to identify patterns that differ between snake venom gene families and all other genes. We found that venom gene homologs in the python are expressed in many different tissues outside of oral glands, which illustrates the pitfalls of using transcriptomic data alone to define "venom toxins." We hypothesize that the python may represent an ancestral state prior to major venom development, which is supported by our finding that the expansion of venom gene families is largely restricted to highly venomous caenophidian snakes. Therefore, the python provides insight into biases in which genes were recruited for snake venom systems. Python venom homologs are generally expressed at lower levels, have higher variance among tissues, and are expressed in fewer organs compared with all other python genes. We propose a model for the evolution of snake venoms in which venom genes are recruited preferentially from genes with particular expression profile characteristics, which facilitate a nearly neutral transition toward specialized venom system expression.

The origin of a mutualism: a morphological trait promoting the evolution of ant-aphid mutualisms

Mutualisms are mutually beneficial interactions between species and are fundamentally important at all levels of biological organization. It is not clear, however, why one species participates in a particular mutualism whereas another does not. Here we show that pre-existing traits can dispose particular species to evolve a mutualistic interaction. Combining morphological, ecological, and behavioral data in a comparative analysis, we show that resource use in Chaitophorus aphids (Hemiptera: Aphididae) modulates the origin of their mutualism with ants. We demonstrate that aphid species that feed on deeper phloem elements have longer mouthparts, that this inhibits their ability to withdraw their mouthparts and escape predators and that, consequently, this increases their need for protection by mutualist ants.