Environmental DNA for biomonitoringJan Pawlowski1,2,3, Aurélie Bonin4, Frédéric Boyer5, Tristan Cordier1,6, Pierre Taberlet5,71 Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland2 Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland3 ID-Gene Ecodiagnostics, Geneva, Switzerland4 Department of Environmental Science and Policy, Università degli Studi di Milano, Milano, Italy5 Laboratoire d’Ecologie Alpine (LECA), CNRS, Université Grenoble Alpes, Grenoble, France6 NORCE Climate, NORCE Norwegian Research Centre AS, Bjerknes Centre for Climate Research, Jahnebakken 5, 5007 Bergen, Norway7 Tromsø Museum, UiT – The Arctic University of Norway, Tromsø, NorwayCorresponding authorJan.Pawlowski@unige.chIn 2012, Molecular Ecology published a special issue on environmental DNA, which provided an overview of the field of eDNA research and presented a selection of papers on eDNA studies (Taberlet, Coissac, Hajibabaei, & Rieseberg, 2012). This special issue also introduced the concept of Biomonitoring 2.0, advocating for the use of DNA-based identification of taxa in biodiversity surveys and ecosystem assessment (Baird & Hajibabaei, 2012). Since then, hundreds of papers have been published covering various aspects of eDNA-based biomonitoring from single-species detection to community studies and environmental impact assessments. Numerous reviews have summarized these studies for both freshwater and marine environments (e.g. Bohmann et al., 2014; Thomsen & Willerslev, 2015).The progress made in the eDNA field during these last ten years has been spectacular (Taberlet, Bonin, Zinger, & Coissac, 2018). Although the basic concepts and workflow of DNA barcoding and metabarcoding have not changed, the technological advances in high-throughput sequencing have greatly facilitated the access to eDNA data. It has become possible to monitor biodiversity with unprecedented precision and depth. Massive environmental genomic datasets have been rapidly generated at relatively low cost. The analysis of these datasets using machine learning and other taxonomy-free approaches opened wide the doors for using new groups of bioindicators to infer ecological status (Cordier et al., 2018; Cordier, Lanzén, Apothéloz-Perret-Gentil, Stoeck, & Pawlowski, 2019; Pawlowski et al., 2018). At the same time, constant efforts to fill gaps in barcoding reference databases considerably increased the effectiveness of taxonomic identification of eDNA data (Weigand et al., 2019).Astonishingly, these rapid advances in eDNA-based technologies are rather timidly implemented in routine biomonitoring (Hering et al., 2018; Shackleton et al., 2021). Although the concept of Biomonitoring 2.0 is widely endorsed, its acceptance in practice is hampered for various reasons. There is no consensus whether eDNA-based biomonitoring should only apply to conventional bioindicators (Renovate) or should also include new bioindicators (Rebuild) or new taxonomy-free approaches (Revolutionize) (see Fig. 1). Moreover, three main steps on the roadmap from eDNA to biomonitoring are not developed equally. The main attention is given to the development and optimization of eDNA data generation and analysis. The standardization of eDNA methods and their translation into legislatory framework remain at a very early stage. One of the main issues impeding the application of eDNA-based tools concerns the lack of congruence between the results of traditional and molecular analyses (Aylagas et al., 2020). It is expected that the new method is “safe to use” only if it provides the same or almost same results as the conventional one. However, obtaining such perfect congruence is often impossible because the character of data is very different (e.g., abundance of individuals vs abundance of eDNA reads). Moreover, the eDNA “ecology” can hardly be translated directly into species ecology. There are also numerous biological and technical biases that can affect the generation and processing of eDNA data, impacting their interpretation.This special issue addresses some of these challenges by presenting the latest advances in eDNA field and discussing their strengths and limitations when applied to routine biomonitoring. The issue comprises 29 papers grouped into four sections and covering different aspects of eDNA applications. It is accompanied by an opinion paper, which clarifies the eDNA terminology in relation to its use in biomonitoring (Pawlowski, Apothéloz-Perret-Gentil, & Altermatt, 2020). The first section comprises a series of studies using new analytical tools (e.g. machine learning), new types of bioindicators and genomic data (e.g. shotgun sequencing) for the assessment of ecological status. It is followed by a section dedicated to fish eDNA, whose application in biomonitoring is the most advanced. The third section comprises papers dealing with various methodological aspects and the comparison between conventional and molecular methods. The final section presents few examples of eDNA applications for biodiversity surveys and population genetics.Novel approaches to monitor ecosystemsThe development of environmental genomics enables monitoring of microbial and meiofaunal communities that were previously inaccessible when using conventional methods. However, our knowledge of the ecology of these communities is very limited and therefore new analytic approaches are necessary to integrate them into routine bioassessment. This section begins with a review of implementation strategies for the application of environmental genomics in ecological diagnostics (Cordier et al., 2021). The authors introduce four broad categories of possible strategies, including (1) DNA-based taxonomic identification of known bioindicators, (2) taxonomy-free discovery of new bioindicators, (3) structural community metrics, and (4) functional community metrics. Each of these strategies is adapted to a particular type of data (metabarcoding, metagenomics, metatranscriptomics) and rely on different computational analyses in order to provide an assessment of the ecological status.Among the different analytical tools, machine learning seems to be the most promising way to predict the ecological status (Cordier et al., 2018, 2019). In this issue, its performance is tested in the case of the benthic diatoms index widely used in the assessment of ecological quality of rivers and streams (Apothéloz-Perret-Gentil et al., 2021). This study shows that supervised machine learning performs better than the taxonomic assignment, but its predictions are similar to those obtained using a taxonomy-free molecular assignment approach. Moreover, the efficiency of a taxonomic assignment method strongly depends on the completeness of the reference database, highlighting the need to fill in the existing gaps, particularly in the case of bioindicator taxa.The ability of de novo prokaryotic bioindicators to predict multiple anthropogenic impacts on estuarine and coastal benthic communities is demonstrated by Lanzén, Mendibil, Borja, & Alonso-Sáez (2021). The authors compare their results to the traditional macrofauna-based indices and discuss various advantages of using microbial bioindicators as they are more sensitive to different abiotic pressures. Similar conclusions were reached in the case of environmental impact assessment of marine aquaculture (Frühe et al., 2021) and the oil and gas industry (Mauffrey et al., 2021). Both studies demonstrate the effectiveness of machine learning andde novo microbial bioindicators and promote their use for benthic monitoring in marine environments.The last two papers in this series explore new directions for the further development of ecogenomic diagnostics. Broman et al. (2021) use environmental RNA (eRNA) shotgun sequencing to analyse the impact of organic enrichment on benthic micro-eukaryotic communities. Compared to eDNA metabarcoding that is used in the majority of studies, eRNA shotgun data has the advantage to overcome the potential biases of PCR amplification and to better capture the organismic response to environmental pressures by targeting predominantly active cells. Ibrahim et al. (2021) use historical eDNA metabarcoding data to analyze the impact of eutrophication on lake phytoplankton in the 20thcentury. This study demonstrates the potential of paleo-metabarcoding to characterize past biodiversity and establish reference conditions for future monitoring.Refining fish eDNA surveysThe second series of papers concerns the use of eDNA to monitor fish diversity. We focus on fish because they are among the most important groups of bioindicators and also because their study from an eDNA perspective is the most advanced (Pont et al., 2021). The barcoding reference database of common fish species in some regions is close to completeness (Knebelsberger, Dunz, Neumann, & Geiger, 2015), fish-specific markers are well defined (M. Miya et al., 2015; Valentini et al., 2016; Zhang, Zhao, & Yao, 2020) and protocols for fish eDNA sampling and processing are well established (Masaki Miya, Gotoh, & Sado, 2020; Valentini et al., 2016). Currently, considerable efforts are directed to solve the most challenging issue, which is related to quantitative fish eDNA data and its application for inferring fish indices in routine biomonitoring.Two papers address this issue by proposing different approaches to estimate fish abundance from eDNA data. Fukaya et al. (2021) use numerical hydrodynamic models to simulate the spatial and temporal distribution of fish eDNA in aquatic environments. By integrating the models to the measures of eDNA concentration, the authors obtained estimates of fish population abundance comparable to those obtained by the quantitative echo sounder method. Yates et al. (2021) improve the correlation between eDNA concentration and fish abundance by integrating allometric scaling coefficients. Such coefficients can help adjust the values of eDNA production taking in consideration density, biomass and metabolic rates characteristic to a given taxon.A better understanding of the “ecology” of fish eDNA, and particularly how its temporal and spatial distribution is shaped by abiotic and biotic factors, is the subject of the following papers. Littlefair et al. (2021) tested how seasonal variations in thermal stratification influence the distribution of fish eDNA in lakes. The authors show that eDNA distribution follows lake stratification and the thermal niche of the species, which in turn may affect its detection in certain seasons. The distribution of fish and amphibian eDNA in a lentic system was investigated experimentally by Brys et al. (2021). This study indicates high eDNA decay rates and limited dispersal, reinforcing the accuracy of eDNA-based monitoring for retrieving the spatiotemporal occupancy patterns. The advantages of using eDNA for survey of fish populations were also demonstrated by other papers in this section. McColl-Gausden et al. (2021) showed that eDNA metabarcoding is generally more sensitive than electrofishing for conducting fish surveys in freshwater streams, while Aglieri et al. (2021) demonstrate strong complementarity of eDNA-based analysis with visual and capture-based methods in the survey of coastal fish communities.Methodology and comparison with conventional methodsGeneral acceptance of molecular methods in biomonitoring requires their benchmarking against conventional morphotaxonomy-based approaches. This is commonly achieved by processing the same samples in parallel using different methods and by assessing how the molecular data fit to the results of traditional approaches, considered as a ground truth. The papers of this section compare the results of eDNA metabarcoding vs bulk DNA metabarcoding vs different morphology-based approaches. They also present and discuss the biases of molecular methods and propose solutions to improve the outcomes of molecular data generation and processing.The section begins with the three comparative studies of marine biomonitoring. Suter et al. (2021) evaluate the performance of water eDNA and bulk DNA metabarcoding in assessing the biodiversity of zooplankton in open ocean, currently monitored by using continuous plankton recorders. The study shows that both methods recover more species than morphological analyses, however, their efficiency depends on the sampling method and selected marker. They conclude that eDNA metabarcoding is very promising, but it still requires some refinement and standardization before it can be routinely used for zooplankton biomonitoring. Similar conclusions are drawn from the comparison of sediment DNA metabarcoding and macrofauna surveys applied to monitor benthic impacts of salmon farms (He et al., 2021). Although the authors found a certain coherence in relative abundance of common macrofauna bioindicators inferred from morphological and eDNA data, they observed that the correlation with organic enrichment was much stronger for meiofauna, which is not usually included in biomonitoring studies. Significant differences were also found between water eDNA samples and bulk DNA extracts from adjacent benthic communities (Antich et al., 2021). The authors concluded that water eDNA is a poor proxy for the analysis of benthic communities, although they do not exclude that the use of taxon-specific markers could improve the congruence between eDNA and bulk DNA metabarcoding data.The importance of marker selection has also been emphasized in the case of freshwater macrobenthos metabarcoding. The performance of different markers, with focus on key insect orders (Ephemeroptera, Plecoptera and Trichoptera) was tested by Ficetola et al. (2021). The authors demonstrate the complexity of the marker selection process and advocate for the use of multiple markers to cover the widest range of taxa. Combining data from different markers was shown to considerably improve the match between macrobenthic indices inferred from bulk DNA and morphotaxonomic surveys (Meyer et al., 2021). A multimarker approach was also recommended for the assessment of macroinvertebrate communities from the bulk preservative (Martins et al., 2021). Despite the importance of using multiple markers, the authors also demonstrate that the presence of heavily sclerotized exoskeleton can act as a limiting factor for the detection of some taxa.The comparison of bulk DNA vs water eDNA metabarcoding has been reported by two papers. Gleason et al. (2021) show that bulk DNA metabarcoding more accurately represents the local stream macroinvertebrate community, with water eDNA data being overwhelmed by non-metazoan sequences. The same difference was observed when comparing bulk DNA to water eDNA and morphological inventories of pond macroinvertebrates (Harper et al., 2021). However, the authors consider both approaches as complementary and suggest that they should be combined for comprehensive assessment of the invertebrate community. The importance of bulk DNA metabarcoding as a tool for the assessment of marine ecosystems is also highlighted by van de Loos and Nijland (2021). The authors review various technical biases affecting bulk DNA metabarcoding workflow and discuss possible improvements that could help overcoming these biases in the future.The analysis of water samples from five sites in the Brazilian Atlantic forest and one adjacent site in Cerrado grasslands allowed Lopes et al. (2021) to demonstrate that eDNA metabarcoding significantly improves traditional monitoring methods, confirming the presence of frog species undetected by traditional methods. For a few years, invertebrate-derived DNA (iDNA) from leech blood-meal have been used to track mammalian species (Schnell et al., 2012). Here, Drinkwater et al. (2021) apply this approach to assess differences in mammalian diversity across a gradient of forest degradation in Borneo. For monitoring elusive mammals, the iDNA method complements the more traditional and widely used camera trapping.The last two papers in this section provide examples of metabarcoding optimizations aiming at improving its effectiveness in biomonitoring surveys. Guerrieri et al. (2021) show how soil preservation methods can affect estimates of taxonomic richness and community composition. The authors propose guidelines for optimizing soil preservation conditions in agreement with the objectives and practical constraints of the research project. On the other hand, Mächler et al. (2021) address the optimization of data analysis, by investigating how stringency filtering can affect eDNA diversity estimates. The authors conclude that the use of Hill numbers can help in comparisons of eDNA datasets that strongly differ in diversity.Other perspectives for eDNA-based biomonitoringThe last three articles in this special issue present ground-breaking approaches to monitoring biodiversity. Martel et al. (2021) clearly show that eDNA surveys paired with occupancy modelling can uncover metapopulation dynamics and their drivers. Such type of information is important for monitoring endangered species distributed in metapopulations and is quite difficult to obtain via traditional inventories. Shum and Palumbi (2021) reanalyzed a published marine metabarcoding dataset concerning cobble communities found within kelp forest ecosystems. They focussed on diversity data at the intraspecific level to infer population structure and demographic trends. This type of approach greatly increases the scope and value of metabarcoding studies, also opening the way towards metaphylogeography (Turon, Antich, Palacín, Praebel, & Wangensteen, 2020). Finally, Sigsgaard et al. (2021) successfully tracked insects from cow dungs from different environments, and showed that eDNA metabarcoding represents an efficient method for assessing insect diversity, with potential for biomonitoring in relation with the relatively easy standardization of such an approach.ConclusionAs shown by the collection of papers published in this issue, potential applications of eDNA in biomonitoring are highly diverse. Their scope ranges from tracking endangered species to surveying biodiversity or assessing environmental impact. Some papers focus on integrating eDNA into existing bioindication systems, whereas others use eDNA to expand the range of bioindicators and include inconspicuous, commonly overlooked microbial and meiofaunal taxa. All these papers attest to major efforts that have been done to improve eDNA methodology at every step of the workflow from sampling to data analysis. They also contribute to better understand the biological and technical factors impacting the eDNA analyses. Yet, despite this huge new knowledge and numerous practical advantages, the implementation of eDNA in routine biomonitoring still has not taken off.It is now high time to move on and to transform the eDNA field into a truly applied science. The biodiversity crisis and global environmental changes call for an urgent modernization of the tools to monitor biodiversity and assess the ecological status of our environment. As shown by the papers published here, the eDNA methodology achieved top levels of technical and scientific excellence in many areas. Certainly, there are some biases and limitations inherent to eDNA specificity, but there is no reason to consider that the technology is less “safe to use” than the conventional morpho-taxonomic approaches. There are also actions to be taken to ensure the quality and to build confidence in eDNA analyses through standardization of technical protocols and intercalibration tests. However, in view of the substantial efforts that have been made by the scientific community and illustrated by the content of this special issue, it is reasonable to expect that the implementation of eDNA-based tools in biomonitoring will not be long in coming
A fundamental aspect of evolutionary biology is natural selection on trait variation. Classically, selection has been estimated primarily on external morphological traits such as beak size and coloration, or on easily-assayable physiological traits such as heat-tolerance. As technologies and methods improved, evolutionary biologists began examining selection on molecular traits such as protein sequences and cellular processes. In a From the Cover manuscript in this issue of Molecular Ecology, Ahmad et al. (2021) continue this trend by estimating parasite driven selection on the molecular trait of transcript abundance in a wild population of brown trout (Salmo trutta) by uniquely combining a mark-recapture experimental design with non-invasive RNA sampling. Using transcript abundance to estimate selection allows for many different traits (each unique gene’s transcript counts) to be tested in a single experiment, providing the opportunity to examine trends in selection. Ahmad et al.(2021) find directional selection strength on transcript counts is generally low and normally distributed. Surprisingly, transcripts under non-linear selection showed a disruptive selection bias contradicting previous comparative studies and theoretical work. This highlights the importance of within-generation selection studies, where mechanisms may differ from longer time frames. Their manuscript also highlights the benefits of an improved 3’ RNA sequencing technique to measure gene expression.
Humans and non-human primates (NHPs) harbor complex gut microbial communities that affect phenotypes and fitness. The gut microbiotas of wild NHPs reflect their hosts’ phylogenetic histories and are compositionally distinct from those of humans, but in captivity the endogenous gut microbial lineages of NHPs can be lost or replaced by lineages found in humans. Despite its potential contributions to gastrointestinal dysfunction, this humanization of the gut microbiota has not been investigated systematically across captive NHP species. Here we show through comparisons of well-sampled wild and captive populations of apes and monkeys that the fraction of the gut microbiota humanized by captivity varies significantly between NHP species but is remarkably reproducible between captive populations of the same NHP species. Conspecific captive populations displayed significantly greater than expected overlap in the sets of bacterial 16S rRNA gene variants that were differentially abundant between captivity and the wild. This overlap was evident even between captive populations residing on different continents but was never observed between heterospecific captive populations. In addition, we developed an approach incorporating human gut microbiota data to rank NHPs’ gut microbial clades based on the propensity of their lineages to be lost or replaced by lineages found in humans in captivity. Relatively few microbial genera displayed reproducible degrees of humanization in different captive host species, but most microbial genera were reproducibly humanized or retained from the wild in conspecific pairs of captive populations. These results demonstrate that the gut microbiotas of captive NHPs display predictable, host-species specific responses to captivity.
The Green Odorous Frog (Odorrana margaretae) around the Sichuan Basin of western China displays a ring-shaped distributional pattern and possesses multiple replicate contact zones between lineages at various levels of differentiation. To understand its unique speciation history and mechanisms, we obtained 1,540 SNPs from 29 populations and 227 individuals using ddRAD sequencing. Population structure analysis revealed three groups within the species: The West, the North & South, and the East groups. These groups were initially isolated at ~2.03 million years ago, and subsequent post-glacial expansion produced the current ring-shaped distribution around Sichuan Basin with three contact zones. Hybridization in those zones involved lineages with different levels of divergence and produced greatly different outcomes. Both the hybrid zones at southwest (S-W) and southeast (E-NS) of the Basin have extensive admixture and less barrier effect. Consequently, the southern region has the highest genetic diversity and becomes an ‘evolutionary melting pot’. In contrast, the hybrid zone at northwestern corner (N-W), which resembles the overlap zone between two expansion terminals of a ring species, has limited admixture with a narrow geographic cline, suggesting partial reproductive isolation between the northern and western populations. The three hybrid zones likely resemble three time points along a speciation continuum; while both E-NS and S-W hybrid zones are merging, the N-W zone may have passed the ‘tipping point’ and is destined for a complete reproductive isolation over time.
During geographical expansion of a species individual colonizers have to confront different ecological challenges, and the capacity of the species to broaden its range may depend on the total amount of adaptive genetic variation supplied by evolution. We set out to test whether the distribution of loci under selection along a contrasting environmental gradient can be turned into a model that accurately predicts a species' range. If positive, this may shed light on the genetic source of adaptive limits that shape range boundaries. We sampled five populations of the western Mediterranean lizard Psammodromus algirus that inhabit a noticeable environmental gradient of temperature and precipitation. We used 21 SNPs putatively under selection to correlate the genotypes of 95 individuals with environmental variation among their populations, using 1x1 km2 grid cells as sampling units. By extrapolating the resulting model to all possible combinations of alleles, we inferred the locations that were theoretically suitable for the species. The inferred distribution range overlapped to a large extent with the realized range of the species, including an accurate prediction of internal gaps and range borders. Our results suggest an adaptability threshold determined by the amount of genetic variation available that would be required to warrant adaptation beyond a certain limit of environmental variation. These results support the idea that the expansion of a species' range may be ultimately linked to the arising of new variants under selection.
Seagrasses play a vital role in structuring coastal marine ecosystems, but their distributional range and genetic diversity have declined rapidly over the past decades. In order to improve conservation of seagrass species, it is important to predict how climate change may impact their ranges. Such predictions are typically made with correlative species distribution models (SDMs), which can estimate a species’ potential distribution under present and future climatic scenarios given species’ presence data and climatic predictor variables. However, these models are typically constructed with species-level data, and thus ignore intraspecific genetic variability of populations that potentially have adaptations to heterogeneous climatic conditions. Here, we explore the link between intraspecific adaptation and niche differentiation in Thalassia hemprichii, a seagrass broadly distributed in the tropical Indo-Pacific Ocean and a crucial provider of habitat for numerous marine species. Using microsatellite-based genotyping, we identified two distinct phylogeographical lineages within the nominal species and found an intermediate level of differentiation in their multidimensional environmental niches, suggesting the possibility for local adaptation. We then compared projections of the species’ habitat suitability under climate change scenarios using species-level and lineage-level SDMs. In the Central Tropical Indo-Pacific region, both models predicted considerable range contraction in the future, but the lineage-level model predicted more severe habitat loss. The two modelling approaches predicted opposite pattern in habitat change in the Western Tropical Indo-Pacific region. Our results highlight the necessity of conserving distinct populations and genetic pools under climate change and have important implications for guiding future management of seagrasses.
Several recent publications have stated that epistatic fitness interactions cause the fixation of inversions that suppress recombination among the loci involved. Under this model, however, the suppression of recombination in an inversion heterozygote creates a form of heterozygote advantage, which prevents the inversion from becoming fixed by selection. This process has been explicitly modelled by previous workers.
While hybridisation has long been recognised as an important natural phenomenon in evolution, the conservation of taxa subject to introgressive hybridisation from domesticated forms is a subject of intense debate. Hybridisation of the Scottish wildcat, the UK’s sole extant native felid, with the domestic cat is a good example in this regard. We develop a modelling framework to determine the timescale and mode of introgression using approximate Bayesian computation (ABC). Applying the model to ddRAD-seq data from 129 individuals, genotyped at 6,546 loci, we show that a population of wildcats genetically distant from domestic cats is still present in Scotland, though these individuals are found almost exclusively within the captive breeding program. Most wild-living cats sampled were introgressed to some extent. Additionally, we evaluate the effectiveness of current methods that are used to classify hybrids. We show that an optimised 35 SNP panel is a better predictor of the ddRAD-based hybrid score in comparison with a morphological method.
A recent Molecular Ecology editorial made a proactive statement of support for the “Nagoya Protocol” and the principle of benefit-sharing (Marden et al. 2020) by requiring authors to provide a “Data Accessibility and Benefit‐Sharing Statement” in their articles. Here, we encourage another step that enables Indigenous communities to provide their own definitions and aspirations for access and benefit-sharing alongside the author’s “Statement”. We invite the Molecular Ecology research community to use Biocultural-, Traditional Knowledge-, and Cultural Institution Notices to help Indigenous communities gain visibility within our research structures. Notices are one of the tools offered by the Biocultural Labels Initiative (part of the Local Contexts system) designed specifically for researchers and institutions. The Notices are highly visible, machine-readable icons that signal the Indigenous provenance of genetic resources, and rights of Indigenous communities to define the future use of genetic resources and derived benefits. The Notices invite collaboration with Indigenous communities and create spaces within our research systems for them to define the provenance, protocols, and permissions associated with genetic resources using Labels. Authors contributing to Molecular Ecology can apply Notices to their articles by providing the persistent unique identifier and an optional use-statement associated with the Notice in their “Data Accessibility and Benefit‐Sharing Statement”. In this way, our research community has an opportunity to accelerate support for the principles of the Nagoya Protocol, to alleviate concerns regarding Indigenous Data Sovereignty and equitable outcomes, and to build better relationships with Indigenous collaborators to enhance research, biodiversity, and conservation outcomes.
Telomeres have been advocated to be important markers of biological age in evolutionary and ecological studies. Telomeres usually shorten with age, and shortening is frequently associated with environmental stressors and increased subsequent mortality. Telomere lengthening – an apparent increase in telomere length between repeated samples from the same individual – also occurs. However, the exact circumstances, and consequences, of telomere lengthening are poorly understood. Using longitudinal data from the Seychelles warbler (Acrocephalus sechellensis), we tested whether telomere lengthening – which occurs in adults of this species – is associated with specific stressors (reproductive effort, food availability, malarial infection and cooperative breeding) and predicts subsequent survival. In females, telomere shortening was observed under greater stress (i.e. low food availability, malaria infection), while telomere lengthening was observed in females experiencing lower stress (i.e. high food availability, assisted by helpers, without malaria). The telomere dynamics of males were not associated with the key stressors tested. These results indicate that, at least for females, telomere lengthening occurs in circumstances more conducive to self-maintenance. Importantly, both females and males with lengthened telomeres had improved subsequent survival relative to individuals that displayed unchanged, or shortened, telomeres – indicating that telomere lengthening is associated with individual fitness. These results demonstrate that telomere dynamics are bidirectionally responsive to the level of stress that an individual faces, but may poorly reflect the accumulation of stress over the lifetime. This study challenges how we think of telomeres as a marker of biological age.
Globalization and international trade have impacted organisms around the world leading to a considerable number of species establishing in new geographic areas. Many organisms have taken advantage of human-made environments, including buildings. One such species is the dry rot fungus Serpula lacrymans, which is the most aggressive wood-decay fungus in indoor environments in temperate regions. By using population genomic analyses of 36 full genome sequenced isolates, we revealed that isolates from Europe and Japan are highly divergent and that these populations split 3,000 - 19,000 generations ago, probably predating human influence. Approximately 250 generations ago, the European population went through a tight bottleneck, likely corresponding to the time it colonized the built environment. Moreover, evidence of admixture between European and Japanese populations was shown in an isolate from New Zealand. Genomic analyses revealed that low differentiation appeared in genes with functions related to of growth and intracellular transport, possibly important to its ability to effectively decay large substrates. These functions may have enabled both populations to independently establish in the human-made environment. Further, selective sweep analyses identified rapid changes in genes possibly related to decay of various substrates in Japan and in genes involved DNA replication and protein modification in Europe. These two fungal populations were preadapted to the built environment, but have more recently and independently adapted to their local environment.
A key step in understanding the genetic basis of different evolutionary outcomes (e.g., adaptation) is to determine the roles played by different mutation types. To do this we must simultaneously consider different mutation types in an evolutionary framework. Here we propose a research framework that directly utilizes the most important characteristics of mutations, their population genetic effects, to determine their relative evolutionary significance. We review known population genetic effects of different mutation types and show how these may be connected to different evolutionary outcomes. We provide examples of how to implement this framework and pinpoint areas where more data, theory and synthesis are needed. Linking experimental and theoretical approaches to examine different mutation types simultaneously is a critical step towards understanding their evolutionary significance.
Germline mutations are the raw material for natural selection, driving species evolution and the creation of earth’s biodiversity. Life on earth would stagnate without this driver of genetic diversity. Yet, it is a double-edged sword. An excess of mutations can have devastating effects on fitness and population viability. It is therefore one of the great challenges of molecular ecology to determine the rate and spectrum by which these mutations accrue across the tree of life. Advances in high-throughput sequencing are providing new opportunities for characterizing these rates and patterns within species and populations, thus informing essential evolutionary parameters such as the timing of speciation events, the intricacies of historical demography, and the degree to which lineages are subject to the burdens of mutational load. Here, we will focus on the applications and limitations of whole-genome comparisons among closely related individuals in what are typically described as “trio” analyses for the detection of germline mutations as they arise in real time. By sequencing and comparing whole-genomes generated for individuals of known relatedness – typically, parent to offspring – investigators can ideally count and characterize mutations as they appear per generation. The promise for gaining insight into classic hypotheses of molecular evolution is high, though so too is the cost. Namely, the technical challenges are daunting given that pedigree-based studies are essentially searching for needles in a haystack. Even so, the opportunities are so enticing, and the field so young, we can say with confidence that fundamental insights have only just begun to emerge.
There is ample evidence that macroscopic animals form geographic clusters termed as zoogeographic realms (zones), whereas distributions of species of microscopic animals are still poorly understood. The common view has been that micrometazoans, thanks to their putatively excellent dispersal abilities, are subject to the ‘Everything is Everywhere but environment selects’ hypothesis (EiE). One of such groups, <1 mm in length, are limnoterrestrial water bears (Tardigrada), which can additionally enter cryptobiosis that should further enhance their potential for long distance dispersion (e.g. by wind). However, an increasing number of studies, including the most recent phylogeny of a eutardigrade genus Milnesium, seem to question the general applicability of the EiE hypothesis to tardigrade species. Nevertheless, all the Milnesium phylogenies published to date were based on a limited number of populations, which are likely to falsely suggest limited geographic ranges. Thus, in order to comprehensively test the EiE hypothesis, here, we considerably enlarged the Milnesium dataset both taxonomically and geographically, and we analysed it in tandem with climate type and reproductive mode. Additionally, we time-calibrated our phylogeny to align it with major geological events. Our results show that, although cases of long distance dispersal are present, they seem to be rare and mostly ancient. Overall, Milnesium species are restricted to single zoogeographic realms, which suggests that these tardigrades have limited dispersal abilities. Finally, our results also suggest that the breakdown of Gondwana may influenced the evolutionary history of Milnesium. In conclusion, phylogenetic relationships within the genus seem to be determined mainly by paleogeography.
Reconstructing the geographic origins of invasive species is critical for establishing effective management strategies. Frequently, molecular investigations are undertaken when the source population is not known, however; these analyses are constrained both by the amount of diversity present in the native region and by changes in the genetic background of the invading population following bottlenecks and/or hybridization events. Here we explore the geographical origins of the invasive winter moth (Operopthera brumata L.) that has caused widespread defoliation to forests, orchards, and crops in four discrete regions: Nova Scotia, British Columbia, Oregon, and the northeastern United States. It is not known whether these represent independent introductions to North America, or “stepping stone” spread among regions. Using a combination of Bayesian assignment and approximate Bayesian computation methods, we analyzed a population genetic dataset of 24 polymorphic microsatellite loci. We estimate that winter moth was introduced to North America on at least four occasions, with the Nova Scotian and British Columbian populations likely being introduced from France and Sweden, respectively; the Oregonian population likely being introduced from either the British Isles or northern Fennoscandia; and the population in the northeastern United States likely being introduced from somewhere in Central Europe. To our surprise, we found that hybridization has not played a large role in the establishment of winter moth populations even though previous reports have documented widespread hybridization between winter moth and a native congener. We discuss the impact of genetic bottlenecks on analyses meant to determine region of origin.
Understanding where and how genetic variation is maintained within populations is important from an evolutionary and conservation perspective. Signatures of past selection suggest that pathogen-mediated balancing selection is a key driver of immunogenetic variation, but studies tracking contemporary evolution are needed to help resolve the evolutionary forces and mechanism at play. Previous work in a bottlenecked population of Seychelles warblers (Acrocephalus sechellensis) show that functional variation has been maintained at the viral-sensing Toll-like receptor 3 (TLR3) gene. Here, we characterise evolution at this TLR3 locus over a 25-year period within the original remnant population of the Seychelles warbler, and in four other derived, contained populations. Results show a significant and consistent temporal decline in the frequency of the TLR3C allele in the original population, and that similar declines in the TLR3C allele frequency occurred in all the derived populations. Individuals (of both sexes) with the TLR3CC genotype had lower survival, and males - but not females - that carry the TLR3C allele had significantly lower lifetime reproductive success than those with only the TLR3A allele. These results indicate that positive selection, caused by an as yet unknown agent, is driving TLR3 evolution in the Seychelles warblers. No evidence of heterozygote advantage was detected. However, whether the positive selection observed is part of a longer-term pattern of balancing selection (through fluctuating selection or rare-allele advantage) cannot be resolved without tracking the TLR3C allele in the populations over an extended period of time.
Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune system and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.
By studying invasive species, evolutionary geneticists have been able to simultaneously inform management strategies and quantify rapid evolution in the wild. The role of genomics in invasion science is increasingly recognised, and the growing availability of reference genomes for invasive species is paving the way for whole-genome resequencing studies in a wide range of systems. Here, we survey the literature to assess the application of whole-genome resequencing data in invasion biology. For some applications, such as the reconstruction of invasion routes in time and space, sequencing the whole genome of many individuals simply increases the accuracy of existing methods. In other cases, population genomic approaches such as haplotype analysis can permit entirely new questions to be addressed and new technologies to be applied. To date whole-genome resequencing has only been applied to a handful of invasive systems, but these studies have highlighted important roles for processes such as balancing selection and hybridization that allow invasive species to reuse existing adaptations and rapidly overcome the challenges of a foreign ecosystem. The use of genomic data does not constitute a paradigm shift per se, but by leveraging new theory, tools, and technologies, population genomics can provide unprecedented insight into basic and applied aspects of invasion science.