Organization of genetic and reproductive behavioral diversity in the two-lined salamander (\u3ci\u3eEurycea bislineata\u3c/i\u3e) species complex

Describing the mechanisms that generate and maintain genetic and phenotypic diversity is a central goal of evolutionary biology. This is dependent upon accurate reconstructions of evolutionary histories, which have traditionally been inferred as simple, bifurcating phylogenies. However, speciation is often neither instantaneous nor permanent, and genomic data have revealed the ubiquity of reticulate evolutionary histories across diverse organisms. This revelation has underscored the importance of understanding the causes and outcomes of ancient and modern hybridization. Here, I examine these themes by studying the distribution of genetic and reproductive behavioral diversity in the two-lined salamander (Eurycea bislineata) species complex—a group of plethodontid salamanders. First, I use a phylogenomic methods with dataset of \u3e 2 million SNPs from \u3e 120 individuals to demonstrate the importance of river drainage reorganization in the reticulate evolutionary history of the group. Next, I use population genomic methods and a dataset of \u3e 9,000 SNPs from 330 individuals in replicate contact zones to demonstrate reproductive isolation and fine-scale ecological segregation between two sympatric species. Finally, I use a genomic, behavioral, and field observational data to demonstrate the existence of alternative reproductive tactics within three putative species in the group and comment more broadly on variation in reproductive behavior. Together, these results demonstrate previously unrecognized genetic and behavioral variation in the E. bislineata species complex and describe the mechanisms—from large-scale geologic change to fine-scale ecological gradients—responsible for its organization

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

An evaluation of sexual dimorphism in head size and shape of Red Salamanders (Pseudotriton ruber)

For many secretive species of amphibians and reptiles, observations of reproductive behavior are limited to sparse anecdotes from the field or to animals held in captivity. However, a careful examination of morphological differences between the sexes can help shape hypotheses about behaviors with which they may be correlated. For example, sexual dimorphism in head size and shape are correlated with courtship, territoriality, and mate-defense behaviors in some salamanders. One widespread species with a poorly described reproductive natural history is the Red Salamander (Pseudotriton ruber). Here, we measure head size and employ geometric morphometric methods to evaluate head shape in P. ruber, with the goals of: 1) quantifying and visualizing sexual variation; 2) forming hypotheses about reproductive behavior. We found preliminary evidence for differences in head size and shape that are consistent with mate-guarding behavior, and we remark upon directions for future research

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

Diversity and structure of Bettongia tropica: using population genetics to guide reintroduction and help prevent the extinction of an endangered Australian marsupial

Conservation translocations can restore populations and prevent extinction of threatened species. Sourcing adequate genetic diversity is an essential consideration when planning reintroductions, because it influences individual fitness and long-term persistence of populations, yet available populations of threatened species may lack diversity. We estimated population genetic parameters for one of Australia’s most threatened mammals, the northern bettong, Bettongia tropica, to select source populations for reintroduction. Individuals from sites across the species’ extant range in the Wet Tropics of north Queensland were genotyped, using 6,133 informative SNPs. We found that samples clustered into four populations: an isolated northern population at Mt Spurgeon and three connected southern populations in the Lamb Range. Most of the species’ genetic diversity was dispersed across the Lamb Range populations in approximately equal proportions. Populations showed an isolation-by-distance effect, even over short distances within continuous habitat. Admixture of populations was high at distances 11 km, and there was asymmetrical gene flow between the two closest neighboring populations. All populations had small effective sizes and experienced drift, but connectivity appears to have mitigated drift and stabilized population sizes within the Lamb Range. The Mt Spurgeon population had a very small effective population size and low genetic diversity. We use our findings to weigh up the risks and benefits of mixing sources for reintroduction, and we recommend a mixed source approach. We do not currently recommend sourcing individuals from Mt Spurgeon and conservation efforts to preserve this population are urgently required

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

Placental Growth Factor Levels in Populations with High Versus Low Risk for Cardiovascular Disease and Stressful Physiological Environments such as Microgravity: A Pilot Study

This pilot study compared placental growth factor (PIGF) levels in populations with high versus low risk for cardiovascular disease. Previous experiments from our laboratory (Sundaresan et al. 2005, 2009) revealed that the angiogenic factor PIGF was up regulated in modeled microgravity conditions in human lymphocytes leading to possible atherogenesis and pathogenesis in microgravity. Since the findings came from microgravity analog experiments, there is a strong link to its usefulness in the microgravity field as a biomarker. It is important to understand, that these findings came from both studies on expression levels of this cardiovascular marker in human lymphocytes in microgravity (in vitro microgravity analog), and a follow up gene expression study in hind limb suspended mice (in vivo microgravity analog). The relevance is enhanced because in life on earth, PIGF is an inflammatory biomarker for cardiovascular disease. Studies on the levels of PIGF would help to reduce the risk and prevention of heart failures in astronauts. If we can use this marker to predict and reduce the risk of cardiac events in astronauts and pilots, it would significantly help aerospace medicine operations. The investigations here confirmed that in a cardiovascular stressed population such as coronary artery disease (CAD) and acute coronary syndrome (ACS) patients, PIGF could be overexpressed. We desired to re-evaluate this marker in patients with cardiovascular disease in our own study. PIGF is a marker of inflammation and a predictor of short-term and long-term adverse outcome in ACS. In addition, elevated PIGF levels may be associated with increased risk for CAD.PIGF levels were determined in thirty-one patients undergoing cardiovascular catheterization for reasons other than ACS and in thirty-three low-risk asymptomatic subjects. Additional data on traditional cardiovascular risk factors for both populations were also compiled and compared. We found that PIGF levels were significantly higher in the high-risk population as compared to low-risk population. Also we were able to ascertain that PIGF levels were inversely correlated with HDL-cholesterol but directly correlated with the triglyceride levels. With further validation, PIGF may prove a useful addition to the armamentarium of noninvasive biomarkers for cardiovascular disease including a new area of stressful physiological conditions such as microgravity

Report from the conference, ‘identifying obstacles to applying big data in agriculture’

Data-centric technology has not undergone widespread adoption in production agriculture but could address global needs for food security and farm profitability. Participants in the U.S. Department of Agriculture (USDA) National Institute for Food and Agriculture (NIFA) funded conference, “Identifying Obstacles to Applying Big Data in Agriculture,” held in Houston, TX, in August 2018, defined detailed scenarios in which on-farm decisions could benefit from the application of Big Data. The participants came from multiple academic fields, agricultural industries and government organizations and, in addition to defining the scenarios, they identified obstacles to implementing Big Data in these scenarios as well as potential solutions. This communication is a report on the conference and its outcomes. Two scenarios are included to represent the overall key findings in commonly identified obstacles and solutions: “In-season yield prediction for real-time decision-making”, and “Sow lameness.” Common obstacles identified at the conference included error in the data, inaccessibility of the data, unusability of the data, incompatibility of data generation and processing systems, the inconvenience of handling the data, the lack of a clear return on investment (ROI) and unclear ownership. Less common but valuable solutions to common obstacles are also noted