Corals show spatial acclimatisation to local environment conditions. However, the various cellular mechanisms involved in local acclimatisation and variable bleaching patterns in corals remain to be thoroughly understood. In this study, the modulation of a protein implicated in cellular heat stress tolerance, the Heat shock protein 70, was compared at both gene (hsp70) and protein (Hsp70) expression level in bleaching tolerant near-coast Acropora muricata colonies and bleaching susceptible reef colonies, in the lagoon of Belle Mare (Mauritius). The relative Hsp70 levels varied significantly between colonies from the two different locations, colonies having different health conditions and the year of collection. Before the bleaching event of 2016, near-coast colonies had higher basal levels of both Hsp70 gene and protein compared to reef colonies. During the bleaching event, the near-coast colonies did not bleach and had significantly higher relative levels of both Hsp70 gene and protein compared to bleached reef colonies. No significant genetic differentiation between the two studied coral populations was observed and all the colonies analysed were associated with Symbiodiniaceae of the genus Symbiodinium (Clade A) irrespective of location and sampling period. These findings provide further evidence of the involvement of Hsp70 in conferring bleaching tolerance to corals. Moreover, the consistent expression differences of Hsp70 gene and protein between the near-coast and reef coral populations in a natural setting indicate that the modulation of this Hsp is involved in local acclimatisation of corals to their environments.
We introduce a new pattern of population genetic structure in a host-parasite system that can arise after secondary contact of previously isolated populations. Due to different generation time and therefore different tempo of molecular evolution the host and parasite populations reach different degrees of genetic differentiation during their separation (e.g. in refugia). Consequently, during the secondary contact the host populations are able to re-establish a single panmictic population across the area of contact, while the parasite populations stop their dispersal at the secondary contact zone and create a narrow hybrid zone. From the host’s perspective, the parasite’s hybrid zone functions on a microevolutionary scale as a “parasite turnover zone”: while the hosts are passing from area A to area B, their parasites turn genetically from the area A genotypes to the area B genotypes. We demonstrate this novel pattern on a model composed of Apodemus mice and Polyplax lice by comparing maternally inherited markers (complete mitochondrial genomes, and complete genomes of vertically transmitted symbiont Legionella polyplacis) with SNPs derived from the louse genomic data. We discuss circumstances that may lead to this pattern and possible reasons why it has been overlooked in the studies on host-parasite population genetics.
Saline migrants into freshwater habitats constitute among the most destructive invaders in aquatic ecosystems throughout the globe. However, evolutionary and physiological mechanisms underlying such habitat transitions remain poorly understood. To explore mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, we examined genome-wide patterns of gene expression between ancestral saline and derived freshwater populations of the Eurytemora affinis species complex, reared under two different common-garden conditions (0 vs. 15 PSU). We found that evolutionary shifts in gene expression (between saline and freshwater inbred lines) showed far greater changes and were more widespread than acclimatory responses to salinity (0 vs. 15 PSU). Most notably, many genes showing evolutionary shifts in gene expression across the salinity boundary were associated with ion transport function, with inorganic cation transmembrane transport forming the largest Gene Ontology category. Of particular interest was the sodium transporter, the Na+/H+ antiporter (NHA) gene family, which was discovered in animals relatively recently. A few key ion regulatory genes, such as NHA paralog #7, demonstrated concordant evolutionary and plastic shifts in gene expression, suggesting the evolution of ion transporter plasticity and function during rapid invasions into novel salinities. Moreover, freshwater invasions were associated with the evolution of reduced plasticity in the freshwater population, again for the same key ion transporters, consistent with the predicted evolution of canalization following adaptation to stressful conditions. Our results have important implications for understanding invasion mechanisms by some of the most widespread invaders in aquatic habitats.
With the growing anthropogenic pressure on marine ecosystems, the need for efficient monitoring of biodiversity grows stronger. DNA metabarcoding of bulk samples is increasingly implemented in ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on morphology. However, before raw sequences are obtained from bulk samples, a profound number of methodological choices must be made. Here, we critically review the recent methods used for metabarcoding of marine bulk samples (including benthic, plankton and diet samples) and indicate how potential biases can be introduced throughout sampling, pre-processing, DNA extraction, marker and primer selection, PCR amplification and sequencing. From a total of 64 studies evaluated, our recommendations for best practices include to (a) consider DESS as a fixative instead of ethanol, (b) use the DNeasy PowerSoil kit for any samples containing traces of sediment, (c) not limit the marker selection to COI only, but preferably include multiple markers for higher taxonomic resolution, (d) avoid touchdown PCR profiles, (e) use a fixed annealing temperature for each primer pair when comparing across studies or institutes, (f) use a minimum of 3 PCR replicates and (g) include both negative and positive controls. Although the implementation of DNA metabarcoding still faces several technical complexities, we foresee wide-ranging advances in the near future, including improved bioinformatics for taxonomic assignment, sequencing of longer fragments, and the use of whole-genome information. Despite the bulk of biases involved in metabarcoding of bulk samples, it is clear that DNA metabarcoding provides a valuable tool in ecosystem assessments.
Morphological traits have served generations of biologists as a taxonomic indicator, and have been the main basis to delineate species for museum taxonomists for centuries. Widespread awareness of the importance of behavioural characters, such as vocalizations, has arisen much more recently, and the relative importance of these different traits in the speciation process remains poorly understood. To shed more light on the interplay between morphological and behavioral traits in the speciation process, we generated a draft genome of a cryptic Southeast Asian songbird, the Limestone Wren-babbler Napothera crispifrons, and re-sequenced whole genomes of multiple individuals of all three traditional subspecies and a distinct leucistic population that had previously been misinterpreted as a plumage polymorphism. We demonstrate strong genomic and mitochondrial divergence among all three taxa, pointing to the existence of three species-level lineages. Despite its great phenotypic distinctness, the leucistic population was characterized by shallow genomic differentiation from its neighbor, with only a few localized regions emerging as highly-diverged. Quantitative bioacoustic analysis across multiple traits revealed deep differences especially between the two taxa characterized by limited plumage differentiation. Our study demonstrates that speciation in these furtive songbirds is not governed by the evolution of marked color differences, but is regulated by an interplay between color and bioacoustic traits. Extreme color differences can be anchored in few genomic loci and may therefore arise and subside rapidly.
Over time, populations of species can expand, contract, and become isolated, creating subpopulations that can adapt to local conditions. Understanding how species adapt following these changes is of great interest, especially as the current climate crisis has caused range shifts for many species. Here, we characterize how Drosophila innubila came to inhabit and adapt to its current range: mountain forests in southwestern USA separated by large expanses of desert. Using population genomic data from more than 300 wild-caught individuals, we examine four distinct populations to determine their population history in these mountain-forests, looking for signatures of local adaptation to establish a genomic model for this spatially-distributed system with a well understood ecology. We find D. innubila spread northwards during the previous glaciation period (30-100 KYA), and has recently expanded even further (0.2-2 KYA). Surprisingly, D. innubila shows little evidence of population structure, though consistent with a recent migration, we find signatures of a population contraction following this migration, and signatures of recent local adaptation and selective sweeps in cuticle development and antifungal immunity. However, we find little support for recurrent selection in these genes suggesting recent local adaptation. In contrast, we find evidence of recurrent positive selection in the Toll-signaling system and the Toll-regulated antimicrobial peptides.
Long term environmental variation often drives local adaptation and leads to trait differentiation across populations. Additionally, when traits change in an environment-dependent way through phenotypic plasticity, the underlying genetic variation will also be under selection, but only in the inducing environment. Both of these processes will create a landscape of differentiation across populations in trait means as well as their plasticity. However, studies uncovering environmental drivers of this variation are scarce. With this work, we studied drought responses in seedlings of a shrub species from the Cape Floristic Region, the common sugarbush (Protea repens). We measured morphological and physiological traits as well as whole transcriptomes in 8 populations that represent both the climatic and the geographic distribution of this species. We found that there is substantial variation in how populations respond to drought, but we also observe common patterns such as reduced leaf size and thickness and upregulation of stress- and down-regulation of growth-related gene groups. Both environmental heterogeneity and milder source site climates were associated with higher plasticity in various traits and co-expression gene networks. By uncovering associations between traits, trait plasticity, co-expression gene networks with source site climate, we showed that temperature plays a bigger role in shaping these patterns when compared to precipitation, in line with recent changes in the region due to climate change. We also found that traits respond to climatic variation in a context dependent manner: some associations between traits and climate were apparent only under certain growing conditions.
Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of the major human malaria parasites, Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) populations following nationwide distribution of long-lasting insecticide treated nets (LLIN) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-6) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik: Pf=54.9-8.5%, Pv=35.7-5.6%, Madang: Pf=38.0-9.0%, Pv: 31.8-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, He = 0.77-0.71; Madang: Rs= 8.2-6.1, He = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs=11.4-9.3, He=0.83-0.80; Madang: Rs=12.2-14.5, He=0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium (mLD) post-LLIN was a positive indicator of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.
Theoretical and empirical studies have shown that species radiations are facilitated when a trait under divergent natural selection is also involved in sexual selection. It is yet unclear how quick and effective radiations are where sexual selection is unrelated to the ecological environment. We address this question using grasshopper species of the genus Chorthippus, which have evolved strong assortative mating while lacking noticeable eco-morphological divergence. Mitochondrial genomes suggest that the radiation is relatively recent, dating to the mid-Pleistocene, which leads to extensive incomplete lineage sorting throughout the mitochondrial and the nuclear genomes. Nuclear data show extremely low genomic differentiation among species, yet hybrids are absent in sympatric localities. Demographic analyses shed some light into these seemingly contradictory patterns. The estimated demographic model shows a long period of geographic isolation, followed by secondary contact and extensive introgression. This suggests that an initial period of geographic isolation might favor the coupling of male signaling and female preference, which currently maintains species boundaries in the face of long-term gene flow. More generally, these results suggest that sexual selection can lead to radiations without a primary role of divergent natural selection, resulting in cryptic species that are genetically, morphologically and ecologically similar, but otherwise behave mostly as good biological species.
Coral reefs are losing coral cover across the globe largely as a result of a rise in seawater temperatures that trigger coral bleaching and induce coral mortality. How coral reefs will respond to climate change will be a function of genetic variation and how it is partitioned among species. A critical initial step is to accurately delineate species and quantify their physiological potential to cope with heat stress. Cryptic species, morphologically indistinguishable but genetically different ones, typically harbor distinct physiological variation and respond differently to climatic changes. A dominant Caribbean reef builder severely affected by climate change is the mountainous star coral, Orbicella faveolata. Recently, Dziedzic et al. (2019) reported genetic variation in the physiological response to thermal stress in a single population of this species, suggesting that variation within populations will allow these corals to adapt to rising ocean temperatures. We reanalyzed their data and found multiple cryptic lineages rather than a single panmictic population, with only one of the lineages being heat-tolerant. Our finding of hidden lineages within a threatened species highlights the varying extinction risks faced by these independently evolving groups, especially when the prospects of survival under warmer oceans seem favorable for a few of them only.
Roe deer (Capreolus spp.) are a little odd. They are one of only a few placental mammals — and the only genus among even-toed ungulates — capable of putting embryonic development “on ice”, also known as embryonic diapause (Fig. 1). It would seem such an unusual trait is likely the product of natural selection, but a big question is, how does selection for important traits, such as diapause, interact with the historical demography of a species? In a ‘From the Cover’ article in this issue of Molecular Ecology, de Jong et al. (2020) demonstrate that selection is acting on genes associated with reproductive biology in roe deer, despite heightened genetic drift due to reduced effective population size through the Pleistocene.
Summer heat waves are the principal global driver of mortality in reef-building corals. Resilience-based genetic management may increase coral heat tolerance, but it is unclear how temperature responses are regulated at a genomic level and thus how corals may adapt to warming naturally or through selective breeding. Here we combine phenotypic, pedigree, and genomic marker data from colonies sourced from a warm reef on the Great Barrier Reef reproductively crossed with conspecific colonies from a cooler reef to produce combinations of warm and cool purebred and hybrid larvae and juveniles. Intra-population breeding created significantly greater genetic diversity across the coral genome and maintained diversity in key regions associated with heat tolerance and fitness. High-density genome-wide scans of single nucleotide polymorphisms (SNPs) identified alleles significantly associated with offspring reared at 27.5°C (87 – 2,224 loci), including loci putatively associated with proteins involved in responses to heat stress (cell membrane formation, metabolism, and immune responses). Underlying genetics explained 43% of PCoA variation in juvenile survival, growth, and bleaching responses at 27.5°C and 31°C between the multilocus genotypes. Genetic marker contribution to total variation in fitness traits (narrow-sense heritability) were high for survival but not for growth and bleaching in juveniles, with heritability of these traits influenced more at 31°C relative to 27.5°C. Using only a limited number of crosses, the mechanistic understanding presented here demonstrates that allele frequencies are affected by one generation of selective breeding, key information for the assessments of genetic intervention feasibility and modelling of reef futures.
The fire ant Solenopsis invicta exists in two alternate social forms: monogyne nests contain a single reproductive queen and polygyne nests contain multiple reproductive queens. This colony-level social polymorphism corresponds with individual differences in queen physiology, queen dispersal patterns, and worker discrimination behaviors, all evidently regulated by an inversion-based supergene that spans more than 13Mb of a “social chromosome,” contains over 400 protein-coding genes, and rarely undergoes recombination. The specific mechanisms by which this supergene influences expression of the many distinctive features that characterize the alternate forms remain almost wholly unknown. To advance our understanding of these mechanisms, we explore effects of social chromosome genotype and natal colony social form on gene expression in virgin queens sampled as they embarked on nuptial flights, using RNA-sequencing of two important tissues. We observe relatively minor effects of natal social form, that is, of the social/developmental environment, on gene expression profiles, but substantial effects of genotype, including i) supergene-associated gene upregulation, ii) allele-specific expression, and iii) pronounced extra-supergene trans-regulatory effects. These findings, along with observed spatial variation in differential and allele-specific expression within the supergene region, highlight the complex gene regulatory landscape that emerged following evolutionary divergence of the inversion-mediated Sb haplotype from its homolog that largely retained the ancestral gene order. The distinctive social chromosome-linked gene expression trajectories we document at the onset of a queen’s reproductive life expand the known record of relevant molecular correlates of a complex social polymorphism and point to putative genetic underpinnings of the alternate social syndromes.
It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. But evidence that CYP2J19 explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones between related species provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with forecrown colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 79 individuals, measuring spectral reflectance of forecrown feathers as well as scoring colours from photographs. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a Pogoniulus tinkerbird that we assembled. Admixture mapping using 104,933 SNPs identified a region of chromosome 8 that includes CYP2J19 as the only locus with more than two SNPs significantly associated with both crown hue and crown score. The hybrid zone was bimodal with asymmetric backcrossing, consistent with the hypothesis that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males may reinforce species divergence and is consistent with the hypothesis that converted carotenoids are an honest signal of quality.
Environmental DNA metabarcoding is becoming a key tool for biodiversity monitoring over large geographical or taxonomic scales and for elusive taxa like soil organisms. Increasing sample sizes and interest in remote or extreme areas often require the preservation of soil samples and thus deviations from optimal standardized protocols. However, we still ignore the impact of different methods of soil sample preservation on the results of metabarcoding studies and there is no guidelines for best practices so far. Here, we assessed the impact of four methods of soil sample preservation commonly used in metabarcoding studies (preservation at room temperature for 6h, preservation at 4°C for three days, desiccation immediately after sampling and preservation for 21 days, and desiccation after 6h at room temperature and preservation for 21 days). For each preservation method, we benchmarked resulting estimates of taxon diversity and community composition of three different taxonomic groups (bacteria, fungi and eukaryotes) in three different habitats (forest, river bank and grassland) against results obtained under optimal conditions (i.e. extraction of eDNA right after sampling). Overall, the different preservation methods only marginally impaired results and only under certain conditions. When rare taxa were considered, we detected small but significant changes in MOTU richness of bacteria, fungi and eukaryotes across treatments, while the exclusion of rare taxa led to robust results across preservation methods. The differences in community structure among habitats were evident for all treatments, and the communities retrieved using the different preservation conditions were extremely similar. We propose guidelines on the selection of the optimal soil sample preservation conditions for metabarcoding studies, depending on the practical constraints, costs and ultimate research goals.
Populations of ectothermic vertebrates are vulnerable to environmental pollution and climate change because certain chemicals and high temperature can cause sex reversal during their larval development (i.e. genetically female individuals develop male phenotype or vice versa), which may distort population sex ratios. However, we have troublingly little information on sex reversals in natural populations, due to unavailability of genetic sex markers. Here we developed a genetic sexing method based on sex-linked single nucleotide polymorphism loci to study the prevalence and fitness consequences of sex reversal in agile frogs (Rana dalmatina). Out of 125 juveniles raised in laboratory without exposure to sex-reversing stimuli, 6 showed male phenotype but female genotype according to our markers. These individuals exhibited several signs of poor physiological condition, suggesting stress-induced sex reversal and inferior fitness prospects. Among 162 adults from 11 wild populations in North-Central Hungary, 20% of phenotypic males had female genotype according to our markers. These individuals occurred more frequently in areas of anthropogenic land use; this association was attributable to agriculture and less strongly to urban land use. Female-to-male sex-reversed adults had similar body mass as normal males. We recorded no events of male-to-female sex reversal either in the lab or in the wild. These results support recent suspicions that sex reversal is widespread in nature, and suggest that human-induced environmental changes may contribute to its pervasiveness. Furthermore, our findings indicate that sex-reversal is associated with stress and poor health in early life, but sex-reversed individuals surviving to adulthood may participate in breeding.
Rapid shifts in environmental variables associated with elevational changes in montane ecosystems provide opportunities to test hypotheses regarding the effects of environmental heterogeneity on gene flow and genetic structure. In tropical mountains, spatial environmental heterogeneity combined with seasonal environmental stability is predicted to result in low dispersal across elevations. Few studies have investigated the genetic consequences of elevational environmental heterogeneity in tropical montane mammals. Here, we use a population genomics approach to test the hypothesis that mountain treeshrews (Tupaia montana) exhibit limited gene flow across elevational gradients and between two neighboring peaks within Kinabalu National Park (KNP) in Borneo. We sampled 83 individuals across elevations on Mt. Tambuyukon (MT) and Mt. Kinabalu (MK) and sequenced mitogenomes and 4,106 ultraconserved elements containing an average of 1.9 single nucleotide polymorphisms per locus. We detected high gene flow across elevations and between peaks. We found greater genetic differentiation on MT than MK despite its lower elevation and associated environmental variation. This implies that, contrary to our hypothesis, genetic structure in this system is not primarily shaped by elevation. We propose that this pattern may instead be the result of colonization history combined with restricted upslope gene flow on MT due to unique plant communities associated with its upper montane habitats. Our results serve as a foundation to identify and mitigate future effects of climate change on mountain treeshrews in KNP. Given predictions for 2100 CE, we predict that mountain treeshrews will maintain genetic connectivity in KNP, making it an important conservation stronghold.
Environmental DNA and metabarcoding have great potential for the biomonitoring of freshwater environments. However, successful application of metabarcoding to biodiversity monitoring requires universal primers with high taxonomic coverage that amplify highly-variable, short metabarcodes with high taxonomic resolution. Moreover, reliable and extensive reference databases are essential to match the outcome of metabarcoding analyses with the available taxonomy and biomonitoring indices. Benthic invertebrates, particularly insects, are key taxa for freshwater biomonitoring. Nevertheless, so far, no formal comparison has assessed primers for metabarcoding of freshwater macrobenthos. Here we combined in vitro and in silico analyses to test the performance of metabarcoding primers amplifying regions in the 18S rDNA (Euka02 metabarcode), 16S rDNA (Inse01), and COI (BF1_BR2-COI) genes, and developed an extensive database of benthic invertebrates of France and Europe, with a special focus on three key insect orders (Ephemeroptera, Plecoptera and Trichoptera). In vitro analyses on 1514 individuals, belonging to 578 different taxonomic units showed very different amplification rates across primer combinations. The Euka02 marker showed the highest universality, while the Inse01 marker showed excellent performance for the amplification of insects. The BF1_BR2-COI metabarcode showed the highest resolution, while the resolution of Euka02 was often limited. By combining in vitro data with GenBank information, we developed a curated database including sequences representing 822 genera. The heterogeneous performance of the different metabarcodes highlights the complexity of the identification of the best markers, and advocates for the integration of multiple metabarcodes for a more comprehensive and accurate understanding of ecological impacts on freshwater biodiversity.