The genomics revolution continues to change how ecologists and evolutionary biologists study the evolution and maintenance of biodiversity. It is now easier than ever to generate large molecular data sets consisting of hundreds to thousands of independently evolving nuclear loci to estimate a suite of evolutionary and demographic parameters. However, any inferences will be incomplete or inaccurate if incorrect taxonomic identities and perpetuated throughout the analytical pipeline. Due to decades of research and comprehensive online databases, sequencing of mitochondrial DNA (mtDNA), chloroplast DNA (cpDNA) and select nuclear genes can provide researchers with a cost effective and simple means to verify the species identity of samples prior to subsequent phylogeographic and population genomic analysis. The addition of these sequences to genomic studies can also shed light on other important evolutionary questions such as explanations for gene tree-species tree discordance, species limits, sex-biased dispersal patterns, and mtDNA introgression. Although the mtDNA and cpDNA genomes often should not be used exclusively to make historical inferences given their well-known limitations, the addition of these data to modern genomic studies adds little cost and effort while simultaneously providing a wealth of useful data that can have significant implications for both basic and applied research.
Telomerase activity and telomere maintenance in certain somatic cells of human adults support the proliferative capacity of these cells and thus contribute to their regenerative potential, and telomerase activity and telomere length are commonly considered lifespan predictors. Eusocial insects provide excellent models for aging research based on their extraordinary caste-related lifespan differences that contradict the typical mammalian fecundity/lifespan trade-off. Telomerase activity is upregulated in the reproductive, long-lived individuals of eusocial insects such as queens and kings, and telomerase activity may act as a key factor in their extended longevity. But, as documented by the presence of telomerase in somatic tissues of numerous invertebrate and vertebrate species, the connection between telomerase activity and the predicted lifespan is not clear. Here, I ask whether somatic telomerase activity in eusocial reproductives may serve its non-canonical function to protect its individuals against the metabolic stress due to reproduction and reflect a more common phenomenon among species. Here, I propose a hypothesis that the presence of telomerase activity in somatic cells reflects a different reproduction strategy of species.
Divergence in the face of high dispersal capabilities is a documented but poorly understood phenomenon. The white-tailed eagle (Haliaeetus albicilla) has a large geographic dispersal capability and should theoretically be able to maintain genetic homogeneity across its dispersal range. However, following analysis of the genomic variation of white-tailed eagles, from both historical and contemporary samples, clear signatures of ancient biogeographic substructure across Europe and the North-East Atlantic is observed. The greatest genomic differentiation was observed between island (Greenland and Iceland) and mainland (Denmark, Norway and Estonia) populations. The two island populations share a common ancestry from a single mainland population, distinct from the other sampled mainland populations, and despite the potential for high connectivity between Iceland and Greenland they are well separated from each other and are characterized by inbreeding and little variation. Temporal differences also highlight a pattern of regional populations persisting despite the potential for admixture. All sampled populations generally showed a decline in effective population size over time, which may have been shaped by four historical events: I) isolation of refugia during the last glacial period 110-115,000 years ago, II) population divergence following the colonization of the deglaciated areas ~10,000 years ago, III) human population expansion, which led to the settlement in Iceland ~1,100 years ago, and IV) human persecution and exposure to toxic pollutants during the last two centuries.
Indirect genetic effects describe phenotypic variation that results from differences in the genotypic composition of social partners. Such effects represent heritable sources of environmental variation in eusocial organisms because individuals are typically reared by their siblings. In the fire ant Solenopsis invicta, a social supergene exhibits striking indirect genetic effects on worker regulation of colony queen number, such that the genotypic composition of workers at the supergene determines whether colonies contain a single or multiple queens. We assessed the direct and indirect genetic effects of this supergene on gene expression in brains and abdominal tissues from lab-reared workers and compared these with previously published data from field-collected pre-reproductive queens. We found that direct genetic effects caused larger gene expression changes and were more consistent across tissue types and castes than indirect genetic effects. Indirect genetic effects influenced the expression of many loci but were generally restricted to the abdominal tissues. Further, indirect genetic effects were only detected when the genotypic composition of social partners differed throughout the development and adult life of focal workers, and were often only significant with relatively lenient statistical cutoffs. Our study provides insight into direct and indirect genetic effects of a social supergene on gene regulatory dynamics across tissues and castes in a complex society.
Linear infrastructure stands as one of the main culprits of anthropogenically caused biodiversity decline. As it fragments landscapes, it ultimately results in a myriad of direct and indirect ecological consequences for wildlife. As transportation networks will continue to grow under increasing human population growth, biodiversity will continue to decline making the need to understand and mitigate their impact on species an urgent need for conservation worldwide. The implementation of mitigation measures to alleviate the barrier effect produced by linear transport infrastructure on local fauna is not new, and research has shown that their effectiveness has been shown to be influenced by their design, their placement and the biology of the impacted species. Our understanding of their effectiveness in preventing the longer-term impacts of linear transport infrastructure on habitat connectivity via gene flow, however, remains poorly understood. Here, we used a pre- and post-habitat fragmentation genetic dataset collected as part of an extensive Koala Management Program to ask questions about the immediate and predicted longer-term genetic consequences of linear transport infrastructure on the impacted species. Importantly, using forward migration simulations, we show that to preserve connectivity would need to result in around 20% of the population mixing to avoid long-term genetic drift. These results have important consequences for the management of species at the forefront of linear infrastructure. In particular, the study shows the importance of considering gene flow in our assessment of the effectiveness of fauna crossings.
By evaluating genetic variation across the entire genome, one can address existing questions in a novel way while new can be asked. Such questions include how different local environments influence both adaptive and neutral genomic variation within and among populations, providing insights not only into local adaptation of natural populations, but also into their responses to global change and the exploitation-induced evolution. Here, under a seascape genomic approach, ddRAD genomic data were used along with environmental information to uncover the underlying processes (migration, selection) shaping European sardines (Sardina pilchardus) of the Western Mediterranean and adjacent Atlantic waters. This information can be relevant to the (re)definition of fishery stocks, and their short-term adaptive potential. We found that studied sardine samples form two clusters, detected using both neutral and adaptive (outlier) loci suggesting that natural selection and local adaptation play a key role in driving genetic change among the Atlantic and the Mediterranean sardines. Temperature and especially the trend in the number of days with sea surface temperature (SST) above 19oC was crucial at all levels of population structuring with implications on species’ key biological processes, especially reproduction. Our findings provide evidence for a dynamic equilibrium where population structure is maintained by physical and biological factors under the opposing influences of migration and selection. Given its dynamic nature, such a system postulates a continuous monitoring under a seascape genomic approach that can benefit by incorporating a temporal as well as a more detailed spatial dimension.
Anthropogenic biological invasions represent major concerns but enable us to investigate rapid evolutionary changes and adaptation to novel environments. The goldfish Carassius auratus with sexual diploids and asexual triploids coexisting in natural waters, is one of the most widespread invasive fishes in Tibet, providing an ideal model to study evolutionary processes during invasion in different reproductive forms from the same vertebrate. Here, using whole-genome resequencing data of 151 C. auratus individuals from invasive and native ranges, we found different patterns of genomic responses between diploid and triploid populations during their invasion to Tibet. For diploids, although invasive individuals derived from two different genetically distinct sources and had a relative higher diversity (π) at the population level, their individual genetic diversity (genome-wide observed heterozygosity) was significantly lower (21.4%) than that of source individuals. Population structure analysis revealed that the invasive individuals formed a specific genetic cluster distinct from the source populations. Runs of homozygosity analysis showed low inbreeding only in invasive individuals, and only the invasive population experienced a recent decline in effective population size reflecting founder events. For triploids, however, invasive populations showed no loss of individual genetic diversity and no genetic differentiation relative to source populations. Regions of putative selective sweeps between invasive and source populations of diploids mainly involved genes associated with mannosidase activity and embryo development. Our results suggest invasive diploids deriving from distinct sources still lost individual genetic diversity resulting from recent inbreeding and founder events and selective sweeps, and invasive triploids experienced no genetic change owing to their reproduction mode of gynogenesis that precludes inbreeding and founder effects and may make them more powerful invaders.
Pregnancy, the post-fertilization period when embryos are incubated within the body, is a dynamic multistage process that has convergently evolved in many vertebrates. To increase independence from environmental fluctuations and protect offspring from predation, challenges had to be initially overcome. The most obvious, when considering such an intimate relation between the parent and its semi-allogenic offspring, was the pressing need to dodge immunity-associated embryo rejection. In mammals, immunological tolerance was found to be dependent on the active modulation of the immune system. Even though supporting much of the current knowledge on vertebrate pregnancy, mammals lack extant transitional stages that could help reconstruct the evolutionary pathway of this fascinatingly complex reproduction mode. In this issue of Molecular Ecology, Parker et al. (2022) selected an untraditional model - the seahorse and pipefish family, whose species evolved male pregnancy across an almost continuous gradient of complexity, from external oviparity to internal gestation. By contrasting gene expression profiles of syngnathids with distinct brooding architectures, this study allowed for the observation of subtle evolutionary adaptations, while confirming the existence of remarkable similarities to ‘female’ pregnancy (e.g., the evolution of male pregnancy in pouched species occurred alongside immune downregulation, and inflammation seems vital during early pregnancy stages). In a world where the debate on sex-roles takes centre stage, Parker et al. (2022) appeasing results hint at the fact that the strongly convergent evolution of vertebrate pregnancy was seemingly unaffected by which sex carries the burden of gestation.
Processes governing genetic diversity and adaptive potential in reef-building corals are of interest both for fundamental evolutionary biology and for reef conservation. Here, we investigated the possibility of “sweepstakes reproductive success” (SRS) in a broadcast spawning coral Acropora hyacinthus at Yap Island, Micronesia. SRS is an extreme yearly variation in the number of surviving offspring among parents. It is predicted to generate genetically differentiated, low genetic diversity recruit cohorts, containing close kin individuals. We have tested these predictions by comparing genetic composition of size classes (adults and juveniles) at several sites on the island of Yap, Micronesia. We did see the genome-wide dip in genetic diversity in juveniles compared to adults at two of the four sites; however, both adults and juveniles varied in genetic diversity across sites, and there was no detectable genetic structure among juveniles, which does not conform to the classical SRS scenario. Yet, we have identified a pair of juvenile siblings at the site where juveniles had the lowest genetic diversity compared to adults, an observation that is hard to explain without invoking SRS. While further support for SRS is needed to fully settle the issue, we show that incorporating SRS into the Indo-West Pacific coral metapopulation adaptation model had surprisingly little effect on mean rates of coral cover decline during warming. Still, SRS notably increases year-to-year variation in coral cover throughout the simulation.
Community-level traits as a way to partly circumvent the culturing problem in mycorrhizal trait-based ecology?Chagnon, P.-L.Data availability statement: No new data has been generated in this manuscript.Traits are the intermediate by which species respond to environmental filters and influence ecosystem functions. With the myriad of biogeochemical processes controlled by fungi, the past decade has witnessed a rising interest in applying trait-based approaches, core to the toolkit of plant and animal ecophysiologists, to fungi. One of the first challenges to tackle when working on fungal ecophysiology is to circumscribe the very definition of what we consider a fungal trait. Traits are characteristics/features possessed by an individualthat can influence how it interacts with its environment. Here the individual scale is both important, and problematic. Important because the very goal of comparative ecology is to measure traits on individuals belonging to known species. This allows to populate trait databases, and syntheses of such databases can reveal key trade-offs and trait syndromes that govern species’ life-histories. The scale of the individual is problematic, however, because it is hard to define for soil fungi, and because a rare minority of fungi can be sampled at the individual scale in the environment (e.g., macroscopic sporocarps, ectomycorrhizal root tips, lichen thalli). Beyond this minority, the individual organisms can only be accessed/sampled through establishing fungal cultures, which probably represents one of the main bottlenecks in the development of fungal trait databases. In this issue, Zhang et al. (2022) show how interesting insights in fungal trait-based ecology can be gained by working at the community level.In their study, Zhang et al. (2022) adapted a protocol developed by Neumann & George (2005) to capture mycorrhizal fungal hyphae using ingrowth bags. If we assume that most hyphae recovered through this technique are mycorrhizal, the washed hyphae can be characterized through various chemical/morphological downstream analyses. Measuring such traits for biomass recovered from whole communities is akin to estimating community-weighted mean (CWM) traits, which are central to many aspects of ecophysiology. Various paradigms/theories in community ecology assume some form of equilibrium between species and their environment (Leibold et al., 2004). If we assume (1) a heterogeneous environment, (2) species as reproductively isolated units competing for space/resources and (3) traits as determinants of their reproductive success, correlations between species traits and environmental parameters are naturally expected to arise (Shipley et al., 2011). Under specific stable environmental conditions, a species bearing certain traits should have a higher probability to (1) occur and (2) become abundant in such environment. At the community level, we thus expect a correlation between CWM traits (the sum of species mean traits weighted by their relative abundances), and environmental parameters (box 1). With mycorrhizal fungi, we can have a reasonable access to species’ relative abundances through sequence-based profiles of communities, but the species × traits matrix remains inaccessible. The shortcut taken by Zhang et al. (2022) is to take measurements of traits (here, hyphal C:N:P stoichiometry) at the community level directly.Does the species × traits become dispensable in mycorrhizal ecology? Certainly not. Bringing mycorrhizal fungi into cultures, identifying traits likely to represent important trade-offs in fungal resource management strategies (Chagnon et al., 2013), ensuring reproducible measurement of such traits and establishing common resources to share such traits (Kattge et al., 2020; Zanne et al., 2020) remains a priority of mycorrhizal ecophysiology. Opinions (Chagnon et al., 2013) and definitions (Chaudhary et al., 2020) will only be useful if followed by actual work to populate databases currently storing the very fragmentary data on fungal traits. We cannot leave aside this important work at the species and individual scales, because evolutionary trade-offs defining resource management and life history strategies emerge at those very scales, not at the community level (Grime & Pierce, 2012).Trait-environment relationships, however, can inform us on the way environmental pressures may select for particular species characteristics, and in this regard, progress can be made over much shorter timescales than the work expected to rely on permanent culture banks and individual-level trait measurements. Zhang et al. (2022), for example, identified an increase in hyphal P concentrations in response to warming and drought treatments, illustrating hyphal stoichiometry as a potentially important “response trait” for mycorrhizal fungi. The upcoming challenge with stoichiometry is now to link form and function. What is the purpose of enhanced mycelial P for the fungus? Luxury uptake and storage as polyphosphates, which may confer bargaining power to the fungus? Increased cellular concentration of “growth-related molecules” (sensu Zhang et al., 2022) such as RNA? This remains to be elucidated. The same is true for nitrogen, which can be present in both growth- and function-related proteins, or in cell wall components slowing down necromass decomposition (Fernandez et al., 2019). This will influence how likely are fungal hyphae to contribute to soil organic pools of different turnover times (See et al., 2022; Klink et al., 2022).We can probably identify many other traits that we expect to be (1) measurable at the community level and (2) associated with environmental filters. Spore size and wall ornamentations could be linked to dispersal dynamics (e.g., Chaudhary et al., 2020). Cell wall thickness could be linked with susceptibility to fungivory (as a constitutive structural defense), and could be expected to be associated with predation risk, but also community-level productivity. Generally, structural defenses are expected to be maximal under harsh conditions promoting conservative species with long-lived, constitutively defended tissues (Coley, 1988). Hyphal allocation allometry to the root vs. the soil habitats already has received considerable attention (e.g., Maherali & Klironomos, 2007), although the assumption that extensive soil foraging is associated with more efficient P return to host can be questioned (Jakobsen et al., 1992). Community-level allometric measurements could be coupled with soil nutrient availability along natural or experimental gradients could clarify this issue. Relative mycelial investments in the soil, however, is a multifaceted trait that bears implication for other aspects of fungal growth and dispersal, namely the colonization of new patches (emerging roots), the exposition to parasites/predators, and the interactions with non-mycorrhizal microorganisms potentially including hyphosphere mutualists. In other words, soil hyphae are not strictly foraging units, but may also serve dispersal, chemical warfare and interkingdom cooperation. This may decrease the probability of finding clear univariate linkages between hyphal allometry and single environmental filters such as nutrient availability. Other traits requiring our attention are biomass growth and turnover rates. Tissue maximal growth rate and lifespan are central to the definition of ecological strategies (e.g., Westoby et al., 2002; Darling et al., 2012). In principle, this can be measured at the community level for mycorrhizal fungi, although the experimental approach should be selected wisely. Traditional approaches to measuring biomass accumulation in mycorrhizal studies typically rely either on microcosms inoculated with fungal propagules, or on ingrowth bags. Both these approaches will select for colonists that can rapidly invade this new empty niche (a bulk sterile pot/ingrowth bag), thus biasing our estimates of growth rates in favor of those displayed by ruderal colonists (i.e., community-level trait not matching the community composition/structure). However, regarding biomass turnover rates, it could be envisaged to derive such estimate using stable isotope probing targeting a specific biomarker (e.g., NLFA 16:1ω5). The only drawback is that evaluating dilution rate of heavy carbon in such a biomarker rapidly makes the cost per sample prohibitive, hampering measurements of biomass turnover rates along environmental gradients, or in response to an experimental treatment.Despite the technical difficulties associated with measuring community-level traits, or the challenges to linking form and function, the approach put forth by Zhang et al. (2022) with hyphal stoichiometry are part of the equation to advance mycorrhizal ecophysiology, and should be extended to other traits. Meanwhile, the long-term objective for mycorrhizal ecophysiologists should still be to isolate and culture strains, and make these permanent resources for them and other research groups to measure traits in future studies. Intraspecific trait variation appears so important, at least for arbuscular mycorrhizal fungi (e.g., Munkvold et al., 2004; Antunes et al., 2011), that strain identity will be just as important as species identity in building trait databases. And as mycorrhizal ecophysiology matures, new traits will gain interest and have to be measured on those strains for which we have already measured a number of other traits. Plant and animal ecophysiologists have a permanent resource they can sample individuals from: it is called nature. Mycorrhizal ecologists are in need for such analogous resource: permanent culture banks. Thus, it seems that challenges lying ahead in mycorrhizal ecophysiology are multifaceted, encompassing the need for conceptual development, standard laboratory methods, but also creativity in getting long-term funding to maintain biological material.
Genomes retain evidence of the demographic history and evolutionary forces that have shaped populations. Across island systems, contemporary patterns of genetic diversity reflect complex population demography, including colonisation events, bottlenecks, gene flow and genetic drift. Here, we investigate whether island founder events have prolonged effects on genome-wide diversity and runs of homozygosity (ROH) distributions, using whole genome resequencing from six populations across three archipelagos of Berthelot’s pipit (Anthus berthelotii) - a passerine which has undergone island speciation relatively recently. Pairwise sequential Markovian coalescent (PSMC) analyses estimated divergence from its sister species approximately two million years ago. Results indicate that all Berthelot’s pipit populations had shared ancestry until approximately 50,000 years ago, when the Madeiran archipelago populations were founded, while the Selvagens were colonised within the last 8,000 years. We identify extensive long ROH (>1 Mb) in genomes in the most recently colonised populations of Madeira and Selvagens which have experienced sequential island founder events and population crashes. Population expansion within the last 100 years may have eroded long ROH in the Madeiran archipelago, resulting in a prevalence of short ROH (<1 Mb). Extensive long and short ROH in the Selvagens reflects strong recent inbreeding, small contemporary effective population size and past bottleneck effects, with as much as 37.7% of the autosomes comprised of ROH >250 kb in length. These findings highlight the importance of demographic history, as well as selection and genetic drift, in shaping contemporary patterns of genomic diversity across diverging populations.
Many long-term genetic monitoring programs began before next-generation sequencing became widely available. Older programs can now transition to new marker systems usually consisting of 1000s of SNP loci, but there are still important questions about comparability, precision, and accuracy of key metrics estimated using SNPs. Ideally, transitioned programs should capitalize on new information without sacrificing continuity of inference across the time series. We combined existing microsatellite-based genetic monitoring information with SNP-based microhaplotypes obtained from archived samples of Rio Grande silvery minnow (Hybognathus amarus) across a 20-year time series to evaluate point estimates and trajectories of key genetic metrics. Demographic and genetic monitoring bracketed multiple collapses of the wild population, and included cases where captive-born repatriates comprised the majority of spawners in the wild. Even with smaller sample sizes, microhaplotypes yielded comparable and in some cases more precise estimates of variance genetic effective population size, multilocus heterozygosity and inbreeding compared to microsatellites because many more microhaplotype loci were available. Microhaplotypes also recorded shifts in allele frequencies associated with population bottlenecks. Trends in microhaplotype-based inbreeding metrics were associated with the fraction of hatchery-reared repatriates to the wild, and should be incorporated into future genomic monitoring. Although differences in accuracy and precision of some metrics were observed between marker types, biological inferences and management recommendations were consistent.
Wolbachia are among the most prevalent and widespread endosymbiotic bacteria on earth. Wolbachia’s success in infecting an enormous number of arthropod species is attributed to two features: the range of phenotypes they induce in their hosts, and their ability to switch between host species. Whilst much progress has been made in elucidating their induced phenotypes, our understanding of Wolbachia host shifting is still very limited: we lack answers to even fundamental questions concerning Wolbachia’s routes of transfer and the importance of factors influencing host shifts. Here, we investigate the diversity and host-shift patterns of Wolbachia in scale insects, a group of arthropods with intimate associations with other insects that make them well-suited to studying host shifts. Using Illumina multi-target amplicon sequencing of Wolbachia-infected scale insects and their direct associates we determined the identity of all Wolbachia strains. We then fitted a Generalised Additive Mixed Model (GAMM) to our data to estimate the influence of host phylogeny and the geographic distribution on Wolbachia strain sharing among scale insect species. The model predicts no significant contribution of host geography but strong effects of host phylogeny, with high rates of Wolbachia sharing among closely related species and a sudden drop-off in sharing with increasing phylogenetic distance. We also detected the same Wolbachia strain in scale insects and several intimately associated species (ants, wasps, beetles, and flies). This indicates putative host shifts and potential routes of transfers via these associates and highlights the importance of ecological connectivity in Wolbachia host-shifting.
This study employs landscape genetics to investigate the environmental drivers of a deadly vector-borne disease, malaria caused by Plasmodium falciparum, in a more spatially comprehensive manner than any previous work. With 1,804 samples from 44 sites collected in western Kenya in 2012 and 2013, we performed resistance surface analysis to show that Lake Victoria acts as a barrier to transmission between areas north and south of the Winam Gulf. In addition, Mantel correlograms clearly showed significant correlations between genetic and geographic distance over short distances (< 70 km). In both cases, we used an identity-by-state measure of relatedness tailored to highly-related individuals in order to focus on recent gene flow that is more relevant to transmission. To supplement these results, we also performed conventional population genetics analyses, including Bayesian clustering methods and spatial ordination techniques. These revealed some differentiation on the basis of geography and elevation and a cluster of genetic similarity in the lowlands north of the Winam Gulf of Lake Victoria. Taken as a whole, these results indicate low overall genetic differentiation in the Lake Victoria region, but with some separation of populations north and south of the Winam Gulf that is explained by the presence of the lake as a geographic barrier to gene flow. We recommend similar landscape genetics analyses in future molecular epidemiology studies of vector-borne diseases to extend and contextualize the results of traditional population genetics.
Studies of natural hybrid zones can provide documentation of range shifts in response to climate change and identify loci important to reproductive isolation. Using a deep temporal (36-38 years) comparison of the black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadee hybrid zone, we investigated movement of the western portion of the zone (western Missouri) and assessed whether loci and pathways underpinning reproductive isolation were similar to those in the eastern portion of the hybrid zone. Using 92 birds sampled along the hybrid zone transect in 2016 and 68 birds sampled between 1978 and 1980, we generated 11,669 SNPs via ddRADseq. These SNPs were used to assess movement of the hybrid zone through time and to evaluate variation in introgression among loci. We demonstrate that the interface has moved ~5 km to the northwest over the last 36-38 years, i.e., at only one-fifth the rate at which the eastern portion (e.g., Pennsylvania, Ohio) of the hybrid zone has moved. Temperature trends over the last 38 years reveal that eastern areas have warmed 50% more than western areas in terms of annual mean temperature, possibly providing an explanation for the slower movement of the hybrid zone in Missouri. Our results suggest hybrid zone movement in broadly distributed species, such as chickadees, will vary between areas in response to local differences in the impacts of climate change.
Foraging behaviours encompass strategies to locate resources and to exploit them. In many taxa these behaviours are controlled by a major gene called for, but mechanisms vary between species. In the parasitoid wasp Venturia canescens, sexual and asexual populations coexist in sympatry but differ in their foraging behaviours. Here we explored the molecular bases underpinning this divergence in foraging behaviours by testing two mutually non-exclusive hypotheses: firstly the divergence in the for gene results in difference in foraging strategies, and second this latter is due to a divergence in whole-genome expression. Using comparative genomics, we showed that the for gene was conserved across insects considering both sequence as well as gene model complexity. Polymorphism analysis did not support the occurrence of two allelic variants diverging across the two populations, yet asexual population exhibited less polymorphism compared to the sexual one. Sexual and asexual transcriptomes sharply split up, with 10.9% of differentially expressed genes, but these were not enriched in behavioural related genes. We showed that the for gene was more expressed in asexual female heads than in sexual ones, and that asexuals were the ones that explored more the environment and exploited more host patches. Overall, these results suggested that a fine tuning in the for gene expression between populations may have led to distinct foraging behaviours. We hypothesized that reproductive polymorphism and coexistence in sympatry of sexual and asexual populations specialized to different ecological niches via divergent optima on phenotypic traits, could imply adaptation through different expression patterns of the for gene and at many other loci throughout the genome.
Trade-offs between traits arise and reflect constraints imposed by the environment and physicochemical laws. Trade-off situations are expected to be highly relevant for sessile plants, which have to respond to changes in the environment to ensure survival. Despite increasing interest in determining the genetic and molecular basis of plant trade-offs, there are still gaps and differences with respect to how trade-offs are defined, how they are measured, and how their genetic architecture is dissected. The first step to fill these gaps is to establish what is meant by trade-offs. In this review we provide a classification of the existing definitions of trade-offs according to: (1) the measures used for their quantification, (2) the dependence of trade-offs on environment, and (3) whether data based on which they are inferred are from a single individual across different environments or a population of individuals in single or multiple environments. We then compare the approaches for quantification of trade-offs based on phenotypic, between-individual, and genetic correlations, and stress the need for developing further quantification indices particularly for trade-offs between multiple traits. Lastly, we highlight the genetic mechanisms underpinning trade-offs and experimental designs that facilitate their discovery in plants, with focus on usage of natural variability. This review also offers a perspective for future research aimed at identification of plant trade-offs, dissection of their genetic architecture, and development of strategies to overcome trade-offs, with applications in crop breeding.
Environmental pollution can result in poor sperm quality either directly or indirectly. However, adaptive and compensatory sperm morphology change and motility improvement rapidly evolved in tree sparrow (Passer montanus) inhabited the polluted area within the past 65 years. To identify the genetic underpinnings of the rapidly evolved sperm phenotype, both the population genomic and transcriptomic methods were used in our study. We identified a gene encoding serine/threonine protein kinase PIM1 which may drive the rapid phenotypic evolution of sperm. An unprecedent and remarkably expansion of PIM gene family caused by tandem and segmental duplication of PIM1 was subsequently noticed in tree sparrow genome. Most of the PIM1 duplicates showed a testis-specific expression pattern, suggesting their functions related to male reproduction. Furthermore, the elevated expression level of PIM1 was consistent with our earlier findings of longer and faster swimming sperm in polluted site, indicating an important role of duplicated PIM1 in facilitating rapid evolution of sperm. Our results suggested that the duplicated PIM1 provide sources of genetic variation that enable rapid evolution of sperm under environmental heavy metal pollution. The findings in this study verified the duplicated genes can be targets of selection and predominant sources for rapid adaptation to environmental change and shed lights on the sperm evolution under environmental stress.