Rapid environmental change makes adaptive potential—the capacity of populations to evolve genetically based changes in response to selection—more important than ever for long-term persistence of ...at-risk species. At the same time, advances in genomics provide unprecedented power to test for and quantify adaptive potential, enabling consideration of adaptive potential in estimates of extinction risk and laws protecting endangered species. The U.S. Endangered Species Act (ESA) is one of the most powerful environmental laws in the world, but so far, the full potential of genomics in ESA listing and recovery decisions has not been realized by the federal agencies responsible for implementing the ESA or by conservation geneticists. The goal of our paper is to chart a path forward for integrating genomics into ESA decision making to facilitate full consideration of adaptive potential in evaluating long-term risk of extinction. For policy makers, managers, and other conservation practitioners, we outline why adaptive potential is important for population persistence and what genomic tools are available for quantifying it. For conservation geneticists, we discuss how federal agencies can integrate information on the effect of adaptive potential on extinction risk—and the related uncertainty—into decisions, and suggest next steps for advancing understanding of the effect of adaptive potential on extinction risk. The mechanisms and consequences of adaptation are incredibly complex, and we may never have a complete understanding of adaptive potential for any organism. Nevertheless, we argue that the best available evidence regarding adaptive potential can now be incorporated by federal agencies into modeling and decision making processes, while at the same time conserving genome-wide variation and striving for a deeper understanding of adaptive potential and its effects on population persistence to improve decision making into the future.
A
bstract
We present results of the Relic Axion Dark-Matter Exploratory Setup (RADES), a detector which is part of the CERN Axion Solar Telescope (CAST), searching for axion dark matter in the 34.67
...μ
eV mass range. A radio frequency cavity consisting of 5 sub-cavities coupled by inductive irises took physics data inside the CAST dipole magnet for the first time using this filter-like haloscope geometry. An exclusion limit with a 95% credibility level on the axion-photon coupling constant of g
aγ
≳ 4 × 10
−
13
GeV
−
1
over a mass range of 34
.
6738
μ
eV
< m
a
<
34
.
6771
μ
eV is set. This constitutes a significant improvement over the current strongest limit set by CAST at this mass and is at the same time one of the most sensitive direct searches for an axion dark matter candidate above the mass of 25
μ
eV. The results also demonstrate the feasibility of exploring a wider mass range around the value probed by CAST-RADES in this work using similar coherent resonant cavities.
Recently, Lowry et al. addressed the ability of RADseq approaches to detect loci under selection in genome scans. While the authors raise important considerations, such as accounting for the extent ...of linkage disequilibrium in a study system, we strongly disagree with their overall view of the ability of RADseq to inform our understanding of the genetic basis of adaptation. The family of RADseq protocols has radically improved the field of population genomics, expanding by several orders of magnitude the number of markers available while substantially reducing the cost per marker. Researchers whose goal is to identify regions of the genome under selection must consider the LD of the experimental system; however, there is no magical LD cutoff below which researchers should refuse to use RADseq. Lowry et al. further made two major arguments: a theoretical argument that modeled the likelihood of detecting selective sweeps with RAD markers, and gross summaries based on an anecdotal collection of RAD studies. Unfortunately, their simulations were off by two orders of magnitude in the worst case, while their anecdotes merely showed that it is possible to get widely divergent densities of RAD tags for any particular experiment, either by design or due to experimental efficacy. We strongly argue that RADseq remains a powerful and efficient approach that provides sufficient marker density for studying selection in many natural populations. Given limited resources, we argue that researchers should consider a wide range of trade‐offs among genomic techniques, in light of their study question and the power of different techniques to answer it.
Longevity is rightly considered one of the greatest achievements of modern society, not only as a function of lifespan, but, more importantly, as a function of healthspan. There are Longevity Blue ...Zones (LBZs), regions around the world, such as in Okinawa, Japan; the Nicoya Peninsula, Costa Rica; Loma Linda, California; Icaria, Greece; and Ogliastra, Sardinia, that are characterized by a significant percentage of residents who live exceptionally long lives, often avoiding age-related disability to a significantly higher degree than in the Western way of life. Longevity is not a universal phenomenon, so if there are places in the world with characteristics similar to the LBZs, it is important to identify them in order to better understand what other factors, in addition to the known ones, might contribute to a long and healthy life. This narrative review aims to identify common factors between Cilento and the five LBZs, taking into account environmental, nutritional, and lifestyle factors. Articles from 2004 to the present, limited to studies published in English, German, and Italian, were searched in PubMed/Medline, Scopus, and Google Scholar. The co-authors agreed on 18 final reference texts. In order to evaluate the similarities between Cilento and the LBZs, a descriptive comparative approach was used. Cilento and the LBZs share several common factors, including a hilly altitude ranging from 355 to 600 m; a mild climate throughout the year, with temperatures between 17.4 and 23.5 degrees Celsius; traditional professions, such as agriculture and animal husbandry; and a predominantly Mediterranean or plant-based diet, with typical recipes based on legumes, tubers, vegetables, and extra virgin olive oil. Additionally, maintenance of strong intergenerational family relationships, religious devotion, and social relationships within the community are also prevalent. Given the similarities to Cilento, one might wonder if this is an LBZ waiting to be discovered. The lessons learned from this discovery could be applied to the general population to protect them from non-communicable chronic diseases and help slow the aging process.
Phenotypic and genetic divergence are shaped by the homogenizing effects of gene flow and the differentiating processes of genetic drift and local adaptation. Herein, we examined the mechanisms that ...underlie phenotypic (size and color) and genetic divergence in 35 populations (535 individuals) of the poison frog Epipedobates anthonyi along four elevational gradients (0-1800 m asl) in the Ecuadorian Andes. We found phenotypic divergence in size and color despite relatively low genetic divergence at neutral microsatellite loci. Genetic and phenotypic divergence were both explained by landscape resistance between sites (isolation-by-resistance, IBR), likely due to a cold and dry mountain ridge between the northern and southern elevational transects that limits dispersal and separates two color morphs. Moreover, environmental differences among sites also explained genetic and phenotypic divergence, suggesting isolation-by-environment (IBE). When northern and southern transects were analyzed separately, genetic divergence was predicted either by distance (isolation-by-distance, IBD; northern) or environmental resistance between sites (IBR; southern). In contrast, phenotypic divergence was primarily explained by environmental differences among sites, supporting the IBE hypothesis. These results indicate that although distance and geographic barriers are important drivers of population divergence, environmental variation has a two-fold effect on population divergence. On the one hand, landscape resistance between sites reduces gene flow (IBR), while on the other hand, environmental differences among sites exert divergent selective pressures on phenotypic traits (IBE). Our work highlights the importance of studying both genetic and phenotypic divergence to better understand the processes of population divergence and speciation along ecological gradients.
Testing for intraspecific variation for host tolerance or resistance in wild populations is important for informing conservation decisions about captive breeding, translocation, and disease ...treatment. Here, we test the importance of tolerance and resistance in multiple populations of boreal toads (Anaxyrus boreas boreas) against Batrachochytrium dendrobatidis (Bd), the amphibian fungal pathogen responsible for the greatest host biodiversity loss due to disease. Boreal toads have severely declined in Colorado (CO) due to Bd, but toad populations challenged with Bd in western Wyoming (WY) appear to be less affected. We used a common garden infection experiment to expose post-metamorphic toads sourced from four populations (2 in CO and 2 in WY) to Bd and monitored changes in mass, pathogen burden and survival for 8 weeks. We used a multi-state modelling approach to estimate weekly survival and transition probabilities between infected and cleared states, reflecting a dynamic infection process that traditional approaches fail to capture. We found that WY boreal toads are more tolerant to Bd infection with higher survival probabilities than those in CO when infected with identical pathogen burdens. WY toads also appeared more resistant to Bd with a higher probability of infection clearance and an average of 5 days longer to reach peak infection burdens. Our results demonstrate strong intraspecific differences in tolerance and resistance that likely contribute to why population declines vary regionally across this species. Our multi-state framework allowed us to gain inference on typically hidden disease processes when testing for host tolerance or resistance. Our findings demonstrate that describing an entire host species as 'tolerant' or 'resistant' (or lack thereof) is unwise without testing for intraspecific variation.
Fibroblast growth factors (Fgf) are secreted signaling molecules that have mitogenic, patterning, neurotrophic and angiogenic properties. Their importance during embryonic development in patterning ...and morphogenesis of the vertebrate eye is well known, but less is known about the role of Fgfs in the adult vertebrate retina. To address Fgf function in adult retina, we determined the spatial distribution of components of the Fgf signaling pathway in the adult zebrafish retina. We detected differential expression of Fgf receptors, ligands and downstream Fgf targets within specific retinal layers. Furthermore, we blocked Fgf signaling in the retina, by expressing a dominant negative variant of Fgf receptor 1 conditionally in transgenic animals. After blocking Fgf signaling we observe a fast and progressive photoreceptor degeneration and disorganization of retinal tissue, coupled with cell death in the outer nuclear layer. Following the degeneration of photoreceptors, a profound regeneration response is triggered that starts with proliferation in the inner nuclear layer. Ultimately, rod and cone photoreceptors are regenerated completely. Our study reveals the requirement of Fgf signaling to maintain photoreceptors and for proliferation during regeneration in the adult zebrafish retina.
Abstract
Conservation units (CUs) are an essential tool for maximizing evolutionary potential and prioritizing areas across a species’ range for protection when implementing conservation and ...management measures. However, current workflows for identifying CUs on the basis of neutral and adaptive genomic variation largely ignore information contained in patterns of isolation by distance (IBD), frequently the primary signal of population structure in highly mobile taxa, such as birds, bats, and marine organisms with pelagic larval stages. While individuals located on either end of a species’ distribution may exhibit clear genetic, phenotypic, and ecological differences, IBD produces subtle changes in allele frequencies across space, making it difficult to draw clear boundaries for conservation purposes in the absence of discrete population structure. Here, we highlight potential pitfalls that arise when applying common methods for delineating CUs to continuously distributed organisms and review existing methods for detecting subtle breakpoints in patterns of IBD that can indicate barriers to gene flow in highly mobile taxa. In addition, we propose a new framework for identifying CUs in all organisms, including those characterized by continuous genomic differentiation, and suggest several possible ways to harness the information contained in patterns of IBD to guide conservation and management decisions.
Disentangling the effects of neutral and adaptive processes in maintaining phenotypic variation across environmental gradients is challenging in natural populations. Song sparrows (Melospiza melodia) ...on the California Channel Islands occupy a pronounced east‐west climate gradient within a small spatial scale, providing a unique opportunity to examine the interaction of genetic isolation (reduced gene flow) and the environment (selection) in driving variation. We used reduced representation genomic libraries to infer the role of neutral processes (drift and restricted gene flow) and divergent selection in driving variation in thermoregulatory traits with an emphasis on the mechanisms that maintain bill divergence among islands. Analyses of 22,029 neutral SNPs confirm distinct population structure by island with restricted gene flow and relatively large effective population sizes, suggesting bill differences are probably not a product of genetic drift. Instead, we found strong support for local adaptation using 3294 SNPs in differentiation‐based and environmental association analyses coupled with genome‐wide association tests. Specifically, we identified several putatively adaptive and candidate loci in or near genes involved in bill development pathways (e.g., BMP, CaM, Wnt), confirming the highly complex and polygenic architecture underlying bill morphology. Furthermore, we found divergence in genes associated with other thermoregulatory traits (i.e., feather structure, plumage colour, and physiology). Collectively, these results suggest strong divergent selection across an island archipelago results in genomic changes in a suite of traits associated with climate adaptation over small spatial scales. Future research should move beyond studying univariate traits to better understand multidimensional responses to complex environmental conditions.
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