Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For one species, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for the other species. Missing data filters tend to suggest higher ex situ representation, while the impact of different SNP calling approaches depends on the species and analysis. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.
Acclimation through phenotypic plasticity represents a more rapid response to environmental change than adaptation and is vital to optimize organisms’ performance in different conditions. Generally, animals are less phenotypically plastic than plants, but reef-building corals exhibit plant properties. They are light-dependent with a sessile and modular construction that facilitates rapid morphological changes within their lifetime. We induced phenotypic changes by altering light exposure in a reciprocal transplant experiment and found that coral plasticity is a colony trait emerging from comprehensive morphological and physiological changes at the local level. Plasticity in skeletal features optimized coral light harvesting and utilization and paralleled with significant methylome and transcriptome modifications. Network-associated responses resulted in the identification of hub genes and clusters associated to the change in phenotype: inter-partner recognition and phagocytosis, soft tissue growth and biomineralization. Furthermore, we identified hub genes putatively involved in animal photoreception-phototransduction. These findings fundamentally alter our understanding of how cnidarian invertebrates repattern the methylome and adjust a phenotype, revealing an important role of light sensing by the coral animal to optimize photosynthetic performance of the symbionts.
Telomeres are chromosome protectors that shorten during cell replication and in stressful conditions. Developing individuals are susceptible to telomere erosion when their growth is fast and resources limited. This is critical because the rate of telomere attrition in early life is linked to health and life span of adults. The metabolic telomere attrition hypothesis (MeTA) suggests that telomere dynamics can respond to biochemical signals conveying information about the organism’s energetic state. Among these signals are glucocorticoids (hormones that promote catabolic processes, potentially impairing costly telomere maintenance) and nucleotides, which activate anabolic pathways though the cellular enzyme target of rapamycin (TOR) preventing telomere attrition. During the energetically demanding growth phase, the regulation of telomeres in response to two contrasting signals—one promoting telomere maintenance and the other inducing attrition—provides an ideal experimental setting to test MeTa. We studied nestlings of a rapidly developing free-living passerine, the great tit (Parus major), that either received glucocorticoids (Cort-chicks), nucleotides (Nuc-chicks), or a combination of both (NucCort-chicks) all compared with controls (Cnt-chicks). Contrary to Cort-chicks, which showed telomere attrition, NucCort-chicks, did not. NucCort-chicks was the only group showing increased gene expression of telo2 (proxy for TOR activation), of mitochondrial enzymes linked to ATP production (atp5f1a-atp5f1b-cox6a1-cox4) and a higher efficiency in aerobically producing ATP. NucCort-chicks had also a higher expression of telomere maintenance genes (trf2) and of enzymatic antioxidant genes (gpx4-sod1). The findings show that nucleotides availability is crucial for preventing telomere erosion during fast growth in stressful environments.
Local adaptation is often facilitated by loci clustered in relatively few regions of the genome, termed genomic islands of divergence. However, the mechanisms that create, mold, and maintain these islands are poorly understood. Here, we use sockeye salmon as a model species to investigate the mechanisms responsible for creating islands of divergence linked to adaptive variation. Previous research suggests that multiple islands are involved in adaptive radiation of sockeye salmon. However, these studies were based on low-density genomic methods that genotyped tens to thousands of loci, making it difficult to elucidate the mechanisms responsible for islands. We used whole genome resequencing to genotype millions of loci to investigate these mechanisms. We discovered 64 islands, 16 of which were shared between two isolated populations; these 16 islands were clustered in four genomic regions. Characterization of the shared regions suggested that three of four were likely created by chromosomal inversions, while the other was created by processes not involving structural variation. Additionally, all four regions were relatively small (< 600 kb), suggesting inversions and other low recombination regions do not have to span megabases to be important for adaptive divergence. In sum, our study demonstrates that heterogeneous selection can lead to a mosaic of islands created by different mechanisms within the same genome. Future studies should continue to investigate how gene flow, selection, and the architecture of genetic traits interact to influence the genomic landscape of adaptive divergence.
The Inyo County population of California towhee, now recognized as Melozone crissalis, was officially listed as Threatened under the U.S. Endangered Species Act in 1987. This isolated population in the Argus Mountains was then estimated to consist of less than 175 individuals. Its major threats were habitat destruction caused by grazing, mining, water exporting, and human recreational activities but stakeholders eventually developed a recovery plan to mitigate habitat damage. Due to the demographic success of the recovery plan, the U.S. Fish and Wildlife Service (USFWS) proposed to remove the California towhee from their formal list of threatened and endangered species in 2013. Herein, we generated a high-quality reference genome assembly for a typical representative of the California towhee (N50 = 22 Mb among 627 contigs, max contig size 89.1Mb), then conducted whole genome resequencing on birds sampled from geographic sites across much of the species’ range. Our findings indicate that the California towhee gene pool is relatively deep (i.e., diverse; mean individual heterozygosity = 0.0021, range = 0.0013-0.0026) and that moderately low levels of autozygosity in isolated populations are due to a combination of historic and contemporary inbreeding. Our population, landscape, and phylogeographic analyses indicate that the shallower (less diverse) regions of the gene pool are likely due to a combination of natural geography, anthropogenic impacts, and demographic histories associated with isolated habitats. None of our findings are inconsistent with the 2013 USFWS proposal and we see no reason to protest the delisting petition based exclusively on genetic/genomic data.
Global climate change is threatening aquatic organisms with rapid changes in habitat salinity and temperature. In response to such changing conditions, adaptation could rescue populations from extinction. Gene flow is a key factor that could either promote or hinder local adaptation, with either beneficial or maladapted alleles immigrating from elsewhere. This interplay between local adaptation and gene flow has not been fully explored in passive dispersers, such as plankton. Thus, we investigated patterns of gene flow and genomic signatures of local adaptation in populations of the copepod Eurytemora affinis spanning natural salinity and temperature gradients in the Baltic and North Seas. Based on whole-genome sequencing of 11 populations, we found population genomic signatures of selection associated with salinity and temperature gradients in both seas, indicating local adaptation, with ‘ion transmembrane transport’ as the most enriched gene ontology category under selection. Interestingly, the single nucleotide polymorphisms (SNPs) associated with responses to salinity and temperature were uncorrelated. We found clear population structure between the Baltic and North Seas, along with signals of admixture between populations, consistent with the presence of gene flow both within and between the seas. Our results suggest that gene flow of beneficial alleles from across the environmental gradients could provide the genetic substrate for populations to adapt to future climate change.
The homing behavior of salmon is a remarkable natural phenomenon, critical for shaping the ecology and evolution of populations, yet the spatial scale at which it occurs is poorly understood. This study investigated the spatial scale and mechanisms driving homing and spawning site-choice behavior in pink salmon in Prince William Sound, Alaska. Molecular pedigree analyses of nearly 15,000 adult spawners in five streams revealed that pink salmon can exhibit fine-scale site fidelity within a stream, returning to the same few meters of streams as their parents. Homing behaviors were driven in part by a salinity gradient between intertidal and freshwater environments, with individuals incubated in freshwater environments more than twice as likely to spawn upstream of the high tide line than those incubated in the intertidal. Our findings challenge the traditional view still held by some that pink salmon populations are genetically and phenotypically homogenous due to their short freshwater residency as juveniles and high rates of dispersal as returning adults (i.e., straying). This study has important implications for rates of inbreeding, local adaptation, and gene flow within populations, and is particularly relevant to the management of salmon hatcheries, given the high incidence of hatchery-origin pink salmon, reared in freshwater hatchery environments, that stray into wild populations in Prince William Sound.
The origin of new genes has long been a central interest of evolutionary biologists. However, novelty evades reconstruction by the classical tools of evolutionary modeling. This evasion of insight from deep ancestral investigation necessitates intensive study of model species within well-sampled, recently diversified clades. The model Neurospora species—which lack recent gene duplications yet harbor clusters of lineage-specific genes (LSGs) adjacent to the telomeres—constitute comprehensively characterized organisms apt for studying the evolution of LSGs. Using gene syntenies, we documented that 78% of Neurospora LSGs clusters accompany large non-coding regions, frequent gene duplications and relocation, or regional rearrangements. Ancestral status of the LSG mas-1 and its neighbors was investigated in detail, and we identified sequence conservation among syntenic non-coding regions that suggests that it arose from an ancient copy of a lysophospholipase precursor that is ubiquitous in lineages of the Sordariomycetes. High resistance to polyoxin D of the mas-1 mutant demonstrates that the gene exhibits a role in cell-wall integrity and cellular sensitivity to antifungal toxins. To perform a broader investigation of the function of LSGs, we assembled transcriptomics data from 68 experimental data points and identified co-regulatory modules using Weighted Gene Correlation Network Analysis. This analysis revealed no essential roles for LSGs in known regulatory machinery. Our discoveries illuminate a “rummage region” in the N. crassa genome that enables some novel elements and new functions to arise via gene duplication and relocation or invasion of genetic materials, followed by fast mutation and recombination facilitated by tandem repeats and unconstrained non-coding sequences.
Hybrid zones with multiple independent contact regions between the same species allow to determine the relative importance of intrinsic and extrinsic factors in the evolution of hybrid zones and thus, parallelism in hybridization outcomes. In this study, we take advantage of two hybrid regions between the damselfly species Ischnura elegans and I. graellsii in Spain to measure: i) the extent of parallelism across geographic hybridization replicates, and what factors (intrinsic and extrinsic) drive that variation; and ii) if hybridization has an impact on the ability of species to expand their ranges. RAD sequencing was used to generate 5,702 SNPs to quantify population diversity and population differentiation, and a subset of 381 species-specific SNPs to analyze genotypic composition (individual ancestry and the proportion of individuals in different hybrid classes Our individual ancestry results showed on-going hybridization and introgression with different admixture-class distributions between hybrid regions and between populations explained by i) species proportions, ii) time elapsed since colonization, and iii) asymmetric and reinforced prezygotic barriers and Batson Dobzhansky and Müller (BDM) hybrid incompatibilities, and indicated a role of hybridization as a facilitator of species range expansions. Our study highlights the value of studying complex hybrid zones to gain insights into microevolutionary processes.
Fish often spawn eggs with ovarian fluids that have been hypothesized to support sperm of some males over others (cryptic female choice). Alternatively, sperm reactions to ovarian fluids could reveal male strategies. We used wild-caught lake char (Salvelinus umbla) to experimentally test whether sperm react differently to the presence of ovarian fluid, depending on male breeding coloration, male inbreeding coefficients (based of 4,150 SNPs), or the kinship coefficients between males and females. Male coloration was positively linked to body size and current health (based on lymphocytosis and thrombocytosis) but was a poor predictor of inbreeding or kinship coefficients. We found that sperm of more colorful males were faster in diluted ovarian fluids than in water only, while sperm of paler males were faster in water than in ovarian fluids. We then let equal numbers of sperm compete for fertilizations in the presence or absence of ovarian fluids and genetically assigned 1,464 embryos (from 70 experimental trials) to their fathers. The presence of ovarian fluids significantly increased the success of the more colorful competitors. Sperm of less inbred competitors were more successful when tested in water only than in diluted ovarian fluids. The kinship coefficients had no significant effects on sperm traits or fertilization success in the presence of ovarian fluids, although parallel stress tests on embryos had revealed that females would profit more from mating with least related males rather than most colored ones. We conclude that sperm of more colorful males are best adapted to ovarian fluids, and that the observed reaction norms suggest male strategies rather than cryptic female choice.
Circadian regulation is linked to local environmental adaptation. Accordingly, many species with broad geographic and climatic niches display variation in circadian clock genes. Here we hypothesize that lichen-forming fungi, which occupy different climate zones along elevation gradients, tune their metabolism to local environmental conditions with the help of their circadian systems. We study two species of the genus Umbilicaria, which occupy similar climatic niches along elevation in different continents. Using homology to known functional genes from Neurospora crassa, we identify gene sets associated with circadian rhythms (11 core, 39 peripheral genes) and temperature response (37 genes). Population genomics approaches indicate that nucleotide diversity of these genes is significantly correlated with mean annual temperature, minimum temperature of the coldest month, and mean temperature of the coldest quarter. Altitudinal clines in allele frequencies pertain to several non-synonymous substitutions in core clock components, e.g. white collar-like, frh-like and various ccg-like genes. A dN/dS approach revealed a small number of significant peripheral clock- and temperature-associated genes (e.g. ras-1-like, gna-1-like) that may play a role in fine-tuning the circadian clock and temperature-response machinery. These results highlight the likely relevance of the circadian clock in environmental adaptation, particularly frost tolerance, of lichenized fungi. Whether or not the fungal clock modulates the symbiotic interaction within the lichen consortium remains to be investigated. We corroborate the finding of significant genetic variation in clock components along altitude – not only latitude – as has been reported in a variety of species.
Chemoreception is critical for the survival and reproduction of animals. Except for a reduced group of insects and spiders, the molecular identity of chemosensory proteins is poorly understood in invertebrates. Gastropoda is the extant mollusk class with the greatest species richness, including marine, freshwater, and terrestrial lineages, and likely, highly diverse chemoreception systems. Here, we performed a comprehensive comparative genome analysis taking advantage of the chromosome-level information of two Gastropoda species, one of which belongs to a lineage that underwent a whole genome duplication event. We identified thousands of previously uncharacterized chemosensory-related genes, the majority of them encoding G protein-coupled receptors (GPCR), mostly organized into clusters distributed across all chromosomes. We also detected gene families encoding degenerin epithelial sodium channels (DEG-ENaC), ionotropic receptors (IR), sensory neuron membrane proteins (SNMP), Niemann–Pick type C2 (NPC2) proteins, and lipocalins, although much smaller in size. Our phylogenetic analysis of the GPCR gene family across protostomes revealed: (i) large gene family expansions in Gastropoda; (ii) clades including members from all protostomes; and (iii) species-specific clades with a huge number of receptors. For the first time, we provide new and valuable knowledge into the evolution of the chemosensory gene families in invertebrates other than arthropods.
Tropical freshwater lakes are well-known for their high biodiversity, and the East African Great Lakes in particular are renowned for their endemic cichlid fish adaptive radiations. While comparative phylogenetic analyses of extant species flocks have revealed patterns and processes of their diversification, evolutionary trajectories within lineages, impacts of environmental drivers, or the scope and nature of now-extinct diversity remain largely unknown. Time-structured paleodata from geologically young fossil records, such as fossil counts and particularly ancient DNA data, would help fill this large knowledge gap. High ambient temperatures can be detrimental to the preservation of DNA, but refined methodology now allows data generation even from very poorly preserved samples. Here, we show for the first time that fish fossils from tropical lake sediments yield endogenous ancient DNA (aDNA). Despite generally low endogenous content and high sample drop-out, high-throughput sequencing and in some cases sequence capture allowed for taxonomic assignment to family or tribe level and phylogenetic placement of individuals. Even skeletal remains weighing less than 1 mg and up to 2700 years of age could be phylogenetically placed. We find that the relationship of degradation of aDNA with the thermal age of samples is similar to that described for terrestrial samples from cold environments adjusted for elevated temperatures. Success rates and aDNA preservation differed between the investigated lakes Chala, Kivu and Victoria, possibly caused by differences in water oxygenation at deposition. Our study demonstrates that sediments of tropical lakes preserve genetic information on rapidly diversifying taxa over time scales of millennia.
Partner specificity is a well-known phenomenon in biotic interactions, but little is known about biotic and abiotic factors that determine specificity in plant-fungal associations. Using PacBio sequencing of soils from monospecific and mixed forest stands, we determined the predictors driving partner specificity in both ectomycorrhizal plants and fungi. Fungal guilds differed strongly in the patterns of partner preference and avoidance, and specificity to particular tree genera. Specialist ectomycorrhizal fungi dominated in belowground communities, and most species preferred one of their partner trees - mostly at the plant genus level. Furthermore, all tree genera (sometimes species) displayed preference towards certain fungal groups. Partner specificity was unrelated to rarity of fungi or plants or environmental conditions except soil pH. Depending on partner taxon, specificity in fungi tended to increase with dominance and optimal pH of the partner tree genus and stand age. Partner tree richness and increased evenness of ectomycorrhizal fungi in multi-host communities promotes species richness. However, mainly partner-generalist fungi contribute to the high diversity in mixed forests. Our results further suggest that reforestation with mixed tree species promotes soil biodiversity, and that besides conserving mixed forests, protection of old pure stands may be particularly important for conserving partner-specific ectomycorrhizal fungi.
Epigenetic modifications, like DNA methylation, generate phenotypic diversity in fish and ultimately lead to adaptive evolutionary processes. Euryhaline marine species that migrate between salinity contrasted habitats have received little attention regarding the role of salinity on whole-genome DNA methylation. Investigation of salinity-induced DNA methylation in fish will help to better understand the potential role of this process in salinity acclimation. Using whole genome bisulfite sequencing, we compared DNA methylation patterns in European sea bass (Dicentrarchus labrax) juveniles in seawater and after freshwater transfer. We targeted the gill as a crucial organ involved in plastic responses to environmental changes. To investigate the function of DNA methylation in gills, we performed RNAseq and assessed DNA methylome-transcriptome correlations. We showed a negative correlation between gene expression levels and DNA methylation levels in promoters, first introns and exons. A significant effect of salinity on DNA methylation dynamics with an overall DNA hypomethylation in freshwater-transferred fish compared to seawater controls was demonstrated. This suggests a role of DNA methylation changes in salinity acclimation. Genes involved in key functions as metabolism, ion transport and transepithelial permeability (junctional complexes) were differentially methylated and expressed between salinity conditions. Expression of genes involved in mitochondrial metabolism was increased as well as the expression of DNA methyltransferases 3a. This study reveals novel aspects on the link of DNA methylation and gene expression patterns.
Phytoplankton have short generation times, flexible reproduction strategies, large population sizes, and high standing genetic diversity, traits that should facilitate rapid evolution under directional selection. We quantified local adaptation of copper tolerance in a population of the diatom Skeletonema marinoi from a mining exposed inlet in the Baltic Sea and in a non-exposed population 100 km away. We hypothesized that mining pollution has driven evolution of elevated copper tolerance in the impacted population of S. marinoi. Assays of 58 strains originating from sediment resting stages revealed no difference in the average tolerance to copper between the two populations. However, variation within populations was greater at the mining site, with three strains displaying hyper-tolerant phenotypes. In an artificial evolution experiment, we used a novel intraspecific metabarcoding locus to track selection and quantify fitness of all 58 strains during co-cultivation in one control and one toxic copper treatment. As expected, the hyper-tolerant strains enabled rapid evolution of copper tolerance in the mining exposed population through selection on available strain diversity. Within 42 days, in each experimental replicate a single strain dominated (30-99% abundance) but different strains dominated the different treatments. The reference population developed tolerance beyond expectations primarily due to slowly developing plastic response in one strain, suggesting that different modes of copper tolerance are present in the two populations. Our findings provide novel empirical evidence that standing genetic diversity of phytoplankton resting stage allows populations to evolve rapidly (20-50 generations) and flexibly on timescales relevant for seasonal bloom progressions.
Acquisition of new genes often results in the emergence of novel functions and is a key step in lineage-specific adaptation. As the only group of sessile crustaceans, barnacles establish permanent attachment through initial cement secretion at the larval phase followed by continuous cement secretion in juveniles and adults. However, the origins and evolution of barnacle larval and adult cement proteins remain poorly understood. By performing microdissection of larval cement glands, transcriptome and shotgun proteomics and immunohistochemistry validation, we identified 30 larval and 27 adult cement proteins of the epibiotic turtle barnacle Chelonibia testudinaria, of which the majority are stage- and barnacle-specific. While only two proteins, SIPC and CP100K, were expressed in both larvae and adults, detection of protease inhibitors and the cross-linking enzyme lysyl oxidase paralogs in larvae and adult cement suggested functional convergence. Other barnacle specific cement proteins such as CP100k and CP52k likely share a common origin dating back at least to the divergent of Rhizocephala and Thoracica. Different CP52k paralogs could be detected in larval and adult cement, suggesting stage-specific cement proteins may arise from duplication followed by changes in expression timing of the duplicates. Interestingly, the biochemical properties of larval- and adult-specific CP52k paralogs exhibited remarkable differences, reflecting the composition of cement in different life stages of turtle barnacle might be chemically different. We conclude that de novo gene formation and duplicate neofunctionalization are pivotal to the evolution of lineage-specific cement toolkits in barnacles, which may explain how barnacles can inhabit diverse marine substrata.
Mesozooplankton is a key component of the ocean, regulating global processes such as the carbon pump, and ensuring energy transfer from lower to higher trophic levels. Yet, despite the importance of understanding mesozooplankton diversity, distribution and connectivity at global scale to predict the impact of climate change in marine ecosystems, there is still fragmented knowledge. To fill this gap, we applied DNA metabarcoding to mesozooplankton samples collected during the Malaspina-2010 circumnavigation expedition across temperate and tropical oceans from the surface to bathypelagic depths. By conducting a hidden diversity analysis, we highlight the still scarce knowledge on global mesozooplankton diversity and identify the Indian Ocean and the deep sea as the most understudied areas. By analysing mesozooplankton community spatial distribution, we confirm global biogeographical patterns across the temperate to tropical oceans both in the vertical and horizontal gradients. Additionally, we reveal a consistent increase in mesozooplankton beta-diversity with depth, indicating reduced connectivity at deeper layers, and identify a water mass type-mediated structuring of bathypelagic communities, instead of an oceanic basin-mediated as observed at upper layers. This suggests limited dispersal at deep ocean layers, most likely due to weaker currents and lower mixing of water mass types. Overall, our work supports the neutral theory of biodiversity and thus the importance of oceanic currents and barriers in dispersal in shaping global plankton communities, and provides key knowledge for predicting the impact of climate change in the deep-sea.