Isolation by distance, local adaptation, and fortuitous coincidence of geo-political boundaries with spatial-genetic clusters in southern Bog Turtles

Conservation strategies are often implemented within the jurisdiction of an administrative unit, such as a state or federal agency; however, boundaries between these units may or may not reflect biologically meaningful distinctions. Population genomic data provide a useful way to objectively assess whether boundaries of administrative units coincide with natural population structure, as well as compare future management scenarios within and among said units. Here we used 2658 SNPs generated by a triple-digest reduced representation library preparation method from 171 individuals to determine if genetic population structure of Bog Turtles corresponds with political boundaries. We also estimated gentetic diversity within populations pertinent to setting management priorities and tested for genetic signatures consistent with local adaptation as a preliminary step to assess translocation risk. We found that genetic differentiation among populations was strongly predicted by geographic distance. Fortuitously, the patchy distribution of remaining Bog Turtle sites results in spatial-genetic clusters that do correspond with state boundaries. We observed low genetic diversity within populations and several instances where the census size exceeded our estimates of effective population size. Lastly, we detected 20 outlier loci consistent with signatures of local adaptation, suggesting that outbreeding depression may be a risk in some translocation options. Our approach allowed us to improve population parameter estimates for the federally threatened Bog Turtle to address key recovery plan objectives, some of which had not been addressed previously

Life History and Habitat of the Rare Patch-nosed Salamander (Urspelerpes brucei)

We examined the life history and habitat characteristics for the Patch-nosed Salamander, Urspelerpes brucei. Body-size measurements of individuals captured using litter bags and by hand from 2008 to 2010 indicated that the larval period lasts at least 2 y, salamanders attain reproductive maturity at or shortly after metamorphosis, and adults have very little variation in body size. Occupied streams are characterized by small size, little water, and narrow, steep-walled ravines. Within occupied streams, larval capture rate was significantly and negatively related to mean water depth, underscoring the importance of protecting headwaters. We hypothesize that the only known population of U. brucei east of the Tugaloo River was isolated from the west-bank populations by the tremendous increase in w

Sex ratios and the city: Secondary offspring sex ratios, parental corticosterone, and parental body condition in an urban-adapted bird

The Trivers–Willard hypothesis states that mothers should adjust their offspring sex ratio according to their own condition and the environment they face during breeding. Past tests of this hypothesis have focused on how natural variation in weather, food availability, or predation pressure shapes sex allocation trade-offs. However, anthropogenic activities, such as urbanization, can alter all of the above characteristics presenting animals with novel challenges in optimizing their brood sex ratio. Previous research has examined how urban living influences individual body condition in several bird taxa, but few have explored subsequent impacts on secondary offspring sex ratio. One likely mediator of the link between environmental conditions, parental condition, and sex ratios is corticosterone (CORT), the primary glucocorticoid in birds. Research on CORT’s influence on sex ratios has focused solely on maternal CORT. However, for species with biparental care, paternal CORT or the similarity of maternal and paternal phenotypes may also help ensure that offspring demand matches parental care quality. To test these hypotheses, we explore offspring secondary sex ratios in European starlings (Sturnus vulgaris). We did not find an effect of site or parental body condition on the production of the more costly sex (males). Instead, we found preliminary evidence suggesting that the similarity of maternal and paternal CORT levels within a breeding pair may increase the likelihood of successfully fledging sons. Maternal and paternal CORT were not significant predictors of secondary sex ratio, suggesting that parental similarity, rather than parental CORT alone, could play a role in shaping secondary offspring sex ratios, but additional work is needed to support this pattern. Starlings are considered an urban-adapted species, making them a compelling model for future studies of the relationship between urbanization, parental body condition, and sex ratios

Extensive Cryptic Diversity Within the Physalaemus cuvieri - Physalaemus ephippifer Species Complex (Amphibia, Anura) Revealed by Cytogenetic, Mitochondrial, and Genomic Markers

Previous cytogenetic and phylogenetic analyses showed a high variability in the frog taxa Physalaemus cuvieri and Physalaemus ephippifer and suggested the presence of undescribed diversity in this species complex. Here, by 1) adding specimens from the Brazilian Amazon region, 2) employing sequence-based species delimitation approaches, and 3) including RADseq-style markers, we demonstrate that the diversity in the P. cuvieri–P. ephippifer species complex is even greater than previously suspected. Specimens from Viruá and Western Pará, located at the Guiana Amazonian area of endemism, were recovered as distinct from all previously identified lineages by the phylogenetic analyses based on mitochondrial DNA and RAD markers, a PCA from RAD data, and cytogenetic analysis. The sequence-based species delimitation analyses supported the recognition of one or two undescribed species among these Amazonian specimens and also supported the recognition of at least three other species in the P. cuvieri–P. ephippifer species complex. These new results reinforce the need for a comprehensive taxonomic revision.Fil: Nascimento, Juliana. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Lima, Jucivaldo D.. Instituto de Pesquisas Científicas e Tecnológicas do Estado do Amapá; BrasilFil: Suarez, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Baldo, Juan Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Posadas; ArgentinaFil: Andrade, Gilda V.. Universidade Federal Do Maranhao.; BrasilFil: Pierson, Todd W.. University of Tennessee; Estados UnidosFil: Fitzpatrick, Benjamin M.. University of Tennessee; Estados UnidosFil: Baptista Haddad, Célio Fernando. Universidade Estadual Paulista Julio de Mesquita Filho; BrasilFil: Recco Pimentel, Shirlei M.. Universidade Estadual de Campinas. Instituto de Biología; BrasilFil: Lourenço, Luciana B.. Universidade Estadual de Campinas. Instituto de Biología; Brasi

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge

There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. RESULTS: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. CONCLUSIONS: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups

The James Webb Space Telescope Mission

Twenty-six years ago a small committee report, building on earlier studies, expounded a compelling and poetic vision for the future of astronomy, calling for an infrared-optimized space telescope with an aperture of at least $4m$. With the support of their governments in the US, Europe, and Canada, 20,000 people realized that vision as the $6.5m$ James Webb Space Telescope. A generation of astronomers will celebrate their accomplishments for the life of the mission, potentially as long as 20 years, and beyond. This report and the scientific discoveries that follow are extended thank-you notes to the 20,000 team members. The telescope is working perfectly, with much better image quality than expected. In this and accompanying papers, we give a brief history, describe the observatory, outline its objectives and current observing program, and discuss the inventions and people who made it possible. We cite detailed reports on the design and the measured performance on orbit.Comment: Accepted by PASP for the special issue on The James Webb Space Telescope Overview, 29 pages, 4 figure

Investigating Potential Toxin Resistance in an Insectivorous Snake

The Rough Greensnake (Opheodrys aestivus) is a non-venomous colubrid native to North America. They are a harmless species with a diet consisting primarily of insects and other arthropods. Recently, a citizen scientist observed the first record of a wild Rough Greensnake consuming an adult Monarch Butterfly. This is remarkable because these butterflies are chemically defended by cardiac glycosides, toxins that they sequester from milkweed in their diet and that are lethal when ingested by organisms lacking the proper resistance. Cardiac glycoside resistance has evolved through convergent evolution in several animals (e.g., some snakes, including those that are dietary specialists upon toads that produce bufadienolide toxins) and occurs through a series of well-characterized amino acid substitutions in the genes that code for Na+/K+-ATPase. However, potential resistance has never been characterized in the Rough Greensnake. Since the toad and monarch toxins are similar, and because some snakes have a resistance to the toad toxins, there stands a possibility that some may also be capable of consuming Monarch Butterflies. To evaluate if the Monarch Butterfly is toxic to the Rough Greensnake, we conducted a polymerase chain reaction to amplify copies of ATP1A1 and ATP1A3 from a Rough Greensnake collected near the citizen science record. We then sequenced these amplicons and screened them for common amino acid substitutions known to confer resistance to cardiac glycosides. Our results contribute to a broader understanding of the evolution of toxin resistance among diverse vertebrate groups

A review and case study on the use of environmental DNA (eDNA) to detect species in urban streams

As urbanization increases, it is becoming increasingly important to understand its impacts on biological communities. Degraded systems often see a loss in native biodiversity due to changes in habitat availability and quality. Monitoring changes to the community composition of urban landscapes allows researchers to better understand and mitigate the effects of urban development on natural systems. One relatively new method of species detection uses DNA shed into the environment (environmental DNA [eDNA]), to determine species presence. eDNA offers a less disruptive, often faster method of determining species presence compared to traditional surveys. However, some characteristics of urban systems potentially undermine the accuracy and validity of eDNA-based species detection. We review the use of eDNA in urban streams, with emphasis on potential detection problems. We also describe a case study in which we collected eDNA from 25 streams in Atlanta, GA to characterize plethodontid salamander communities. eDNA did not detect plethodontid salamanders at multiple sites with visually confirmed salamander presence, suggesting potential environmental or methodological problems with our use of eDNA in an urban setting