Conservation evo-devo: preserving biodiversity by understanding its origins

Unprecedented rates of species extinction increase the urgency for effective conservation biology management practices. Thus, any improvements in practice are vital and we suggest that conservation can be enhanced through recent advances in evolutionary biology, specifically advances put forward by evolutionary developmental biology (i.e., evo-devo). There are strong overlapping conceptual links between conservation and evo-devo whereby both fields focus on evolutionary potential. In particular, benefits to conservation can be derived from some of the main areas of evo-devo research, namely phenotypic plasticity, modularity and integration, and mechanistic investigations of the precise developmental and genetic processes that determine phenotypes. Using examples we outline how evo-devo can expand into conservation biology, an opportunity which holds great promise for advancing both fields

The Scottish invasion of pink salmon in 2017

No abstract available

RADseq and mate choice assays reveal unidirectional gene flow among three lamprey ecotypes despite weak assortative mating: Insights into the formation and stability of multiple ecotypes in sympatry

Adaptive divergence with gene flow often results in complex patterns of variation within taxa exhibiting substantial ecological differences among populations. One example where this may have occurred is the parallel evolution of freshwater‐resident nonparasitic lampreys from anadromous‐parasitic ancestors. Previous studies have focused on transitions between these two phenotypic extremes, but here, we considered more complex evolutionary scenarios where an intermediate freshwater form that remains parasitic is found sympatrically with the other two ecotypes. Using population genomic analysis (restriction‐associated DNA sequencing), we found that a freshwater‐parasitic ecotype was highly distinct from an anadromous‐parasitic form (Qlake‐P = 96.8%, Fst = 0.154), but that a freshwater‐nonparasitic form was almost completely admixed in Loch Lomond, Scotland. Demographic reconstructions indicated that both freshwater populations likely derived from a common freshwater ancestor. However, while the nonparasitic ecotype has experienced high levels of introgression from the anadromous‐parasitic ecotype (Qanad‐P = 37.7%), there is no evidence of introgression into the freshwater‐parasitic ecotype. Paradoxically, mate choice experiments predicted high potential for gene flow: Males from all ecotypes were stimulated to spawn with freshwater‐parasitic females, which released gametes in response to all ecotypes. Differentially fixed single nucleotide polymorphisms identified genes associated with growth and development, which could possibly influence the timing of metamorphosis, resulting in significant ecological differences between forms. This suggests that multiple lamprey ecotypes can persist in sympatry following shifts in adaptive peaks, due to environmental change during their repeated colonization of post‐glacial regions, followed by periods of extensive gene flow among such diverging populations

Searching for a signal: Environmental DNA (eDNA) for the detection of invasive signal crayfish, Pacifastacus leniusculus (Dana, 1852)

Environmental DNA (eDNA) is a rapid, non-invasive method for species detection and distribution using DNA deposited in the environment by target organisms. eDNA has become a recognised and powerful tool for detecting invasive species in a broad range of aquatic ecosystems. We examined the use of eDNA as a tool for detecting the invasive American signal crayfish Pacifastacus leniusculus in Scotland. Species-specific TaqMan probe and primers were designed for P. leniusculus and a robust quantitative PCR (qPCR) assay and DNA extraction protocol were developed. We investigated the detection capability for P. leniusculus from water samples in a controlled laboratory experiment and determined whether crayfish density (low = 1 crayfish 5.5 L-1 or high = 3 crayfish 5.5 L-1) or length of time in tanks (samples taken at 1, 3 and 7 days) influenced DNA detectability. Additionally, the persistence of DNA was investigated after P. leniusculus removal (samples taken at 1, 3 and 7 days post removal). P. leniusculus DNA was consistently detected during the entire 7-day period and higher density tanks yielded stronger positive results with lower Ct values. After removal of P. leniusculus, there was a rapid and continuous decrease in the detectability of DNA. P. leniusculus DNA could only be detected in high density tanks by the end of the 7-day period, while DNA was no longer detectable in low density tanks after 72 hours. Preliminary field experiments sampled water from three sites in winter and five sites in summer. P. leniusculus was known to be present at two of these sites. P. leniusculus was not detected at any site in winter. However, in summer, positive signals were observed at sites with known P. leniusculus, and at sites where P. leniusculus was believed to be present anecdotally, but not confirmed. All sites where crayfish were believed to be absent were negative for eDNA. Therefore, eDNA represents a promising technique to detect and monitor invasive P. leniusculus, although the presence of detectable amounts of eDNA may be season and location dependent, even where invasive crayfish are known to be present

Evolvability under climate change: bone development and shape plasticity are heritable and correspond with performance in Arctic charr (Salvelinus alpinus)

Environmental conditions can impact the development of phenotypes and in turn the performance of individuals. Climate change, therefore, provides a pressing need to extend our understanding of how temperature will influence phenotypic variation. To address this, we assessed the impact of increased temperatures on ecologically significant phenotypic traits in Arctic charr (Salvelinus alpinus). We raised Arctic charr at 5°C and 9°C to simulate a predicted climate change scenario and examined temperature-induced variation in ossification, bone metabolism, skeletal morphology, and escape response. Fish reared at 9°C exhibited less cartilage and bone development at the same developmental stage, but also higher bone metabolism in localized regions. The higher temperature treatment also resulted in significant differences in craniofacial morphology, changes in the degree of variation, and fewer vertebrae. Both temperature regime and vertebral number affected escape response performance, with higher temperature leading to decreased latency. These findings demonstrate that climate change has the potential to impact development through multiple routes with the potential for plasticity and the release of cryptic genetic variation to have strong impacts on function through ecological performance and survival

Read counts from environmental DNA (eDNA) metabarcoding reflect fish abundance and biomass in drained ponds.

The sampling of environmental DNA (eDNA) coupled with cost-efficient and ever-advancing sequencing technology is propelling changes in biodiversity monitoring within aquatic ecosystems. Despite the increasing number of eDNA metabarcoding approaches, the ability to quantify species biomass and abundance in natural systems is still not fully understood. Previous studies have shown positive but sometimes weak correlations between abundance estimates from eDNA metabarcoding data and from conventional capture methods. As both methods have independent biases a lack of concordance is difficult to interpret. Here we tested whether read counts from eDNA metabarcoding provide accurate quantitative estimates of the absolute abundance of fish in holding ponds with known fish biomass and number of individuals. Environmental DNA samples were collected from two fishery ponds with high fish density and broad species diversity. In one pond, two different DNA capture strategies (on-site filtration with enclosed filters and three different preservation buffers versus lab filtration using open filters) were used to evaluate their performance in relation to fish community composition and biomass/abundance estimates. Fish species read counts were significantly correlated with both biomass and abundance, and this result, together with information on fish diversity, was repeatable when open or enclosed filters with different preservation buffers were used. This research demonstrates that eDNA metabarcoding provides accurate qualitative and quantitative information on fish communities in small ponds, and results are consistent between different methods of DNA capture. This method flexibility will be beneficial for future eDNA-based fish monitoring and their integration into fisheries management

The response of a brown trout (Salmo trutta) population to reintroduced Eurasian beaver (Castor fiber) habitat modification

Globally, freshwaters are the most degraded and threatened of all ecosystems. In northern temperate regions, beaver (Castor spp.) reintroductions are increasingly used as a low-cost and self-sustaining means to restore river corridors. River modifications by beavers can increase availability of suitable habitat for fish, including salmonids. This study investigated the response of a population of brown trout (Salmo trutta) to reintroduced Eurasian beaver (Castor fiber) habitat modifications in northern Scotland. The field site comprised two streams entering a common loch; one modified by beavers, the other unaltered. Electrofishing and PIT telemetry surveys indicated abundance of post-young-of-the-year (post-YOY) trout was higher in the modified stream. Considering juvenile year groups (YOY and post-YOY) combined, abundance and density varied with year and season. In the modified stream, fork length and mass were greater, there was a greater variety of age classes, and mean growth was positive during all seasons. Beavers had profound effects on the local brown trout population that promoted higher abundances of larger size classes. This study provides important insight into the possible future effect of beavers on freshwater ecosystems

Complex and divergent histories gave rise to genome‐wide divergence patterns amongst European whitefish (Coregonus lavaretus)

Pleistocene glaciations dramatically affected species distribution in regions that were impacted by ice cover and subsequent postglacial range expansion impacted contemporary biodiversity in complex ways. The European whitefish, Coregonus lavaretus, is a widely distributed salmonid fish species on mainland Europe, but in Britain it has only seven native populations, all of which are found on the western extremes of the island. The origins and colonization routes of the species into Britain are unknown but likely contributed to contemporary genetic patterns and regional uniqueness. Here, we used up to 25,751 genome-wide polymorphic loci to reconstruct the history and to discern the demographic and evolutionary forces underpinning divergence between British populations. Overall, we found lower genetic diversity in Scottish populations but high differentiation (FST = 0.433–0.712) from the English/Welsh and other European populations. Differentiation was elevated genome-wide rather than in particular genomic regions. Demographic modelling supported a postglacial colonization into western Scotland from northern refugia and a separate colonization route for the English/Welsh populations from southern refugia, with these two groups having been separated for more than ca. 50 Ky. We found cyto-nuclear discordance at a European scale, with the Scottish populations clustering closely with Baltic population in the mtDNA analysis but not in the nuclear data, and with the Norwegian and Alpine populations displaying the same mtDNA haplotype but being distantly related in the nuclear tree. These findings suggest that neutral processes, primarily drift and regionally distinct pre-glacial evolutionary histories, are important drivers of genomic divergence in British populations of European whitefish. This sheds new light on the establishment of the native British freshwater fauna after the last glacial maximum

High resolution sequencing of hepatitis C virus reveals limited intra-hepatic compartmentalization in end-stage liver disease

Background & Aims The high replication and mutation rate of hepatitis C virus (HCV) results in a heterogeneous population of viral sequences in vivo. HCV replicates in the liver and infected hepatocytes occur as foci surrounded by uninfected cells that may promote compartmentalization of viral variants. Given recent reports showing interferon stimulated gene (ISG) expression in chronic hepatitis C, we hypothesized that local interferon responses may limit HCV replication and evolution. Methods To investigate the spatial influence of liver architecture on viral replication we measured HCV RNA and ISG mRNA from each of the 8 Couinaud segments of the liver from 21 patients undergoing liver transplant. Results HCV RNA and ISG mRNA levels were comparable across all sites from an individual liver but showed up to 500-fold difference between patients. Importantly, there was no association between ISG and HCV RNA expression across all sites in the liver or plasma. Deep sequencing of HCV RNA isolated from the 8 hepatic sites from two subjects showed a similar distribution of viral quasispecies across the liver and uniform sequence diversity. Single genome amplification of HCV E1E2-envelope clones from 6 selected patients at 2 hepatic sites supported these data and showed no evidence for HCV compartmentalization. Conclusions We found no differences between the hepatic and plasma viral quasispecies in all patients sampled. We conclude that in end-stage liver disease HCV RNA levels and the genetic pool of HCV envelope sequences are indistinguishable between distant sites in the liver and plasma, arguing against viral compartmentalization

Spatio-temporal monitoring of lake fish spawning activity using environmental DNA metabarcoding

Determining the timing and location of fish reproductive events is crucial for the implementation of correct management and conservation schemes. Conventional methods used to monitor these events are often unable to assess the spawning activity directly or can be invasive and therefore problematic. This is especially the case when threatened fish populations are the study subject, such as the Arctic charr (Salvelinus alpinus L.) populations in Windermere (Cumbria, UK). Arctic charr populations have been studied in this lake since the 1940s, and the locations and characteristics of spawning grounds have been described in detail using techniques such as hydroacoustics, as well as physical and visual surveys of the lake bottom. Here, in conjunction with established netting surveys, we added an environmental DNA (eDNA) metabarcoding approach to assess the spatial distribution of Arctic charr in the lake throughout the year to test whether this tool could allow us to identify spawning locations and activity. Sampling was carried out between October 2017 and July 2018 at three locations in the lake, covering putative and known spawning sites. eDNA metabarcoding provided accurate spatial and temporal characterization of Arctic charr spawning events. Peaks of Arctic charr relative read counts from eDNA metabarcoding were observed during the spawning season and at specific locations of both putative and known spawning sites. Net catches of mature Arctic charr individuals confirmed the association between the Arctic charr spawning activity and the peaks of eDNA metabarcoding relative read counts. This study demonstrates the ability of eDNA metabarcoding to effectively and efficiently characterize the spatial and temporal nature of fish spawning in lentic systems