Fine-scale genetic structure and parentage in Urocitellus beldingi

Urocitellus beldingi (Belding\u27s ground squirrel), previously known as Spermophilus beldingi, is a social, montane rodent that occupies alpine and subalpine meadows in the Sierra Nevadas (Helgen et al. 2009). The Tioga Pass meadow (Mono Co. CA) population has been studied behaviorally and demographically for several decades. Microsatellites were developed for this species and conditions for polymerase chain reaction (PCR) were defined. Nine microsatellite loci amplified adequately and were in Hardy-Weinberg equilibrium, displaying an average heterozygosity of 0.67±0.19. These nine microsatellite loci were analyzed via PCR to elucidate the fine scale genetic structure, offering insight into population health, stochastic events, and dispersal. Two populations were identified, corresponding to the elevation differences between the sites (FST = 0.054605 pm) of 8.66. These populations appear to maintain a stable size and are not adversely affected by inbreeding. Urocitellus beldingi maternity can be deduced by observing female burrows usage during gestation and which offspring first emerge from the burrow associated with that particular female. Paternity, however, can only be posited by observation of mating because the species exhibits multiple mating in both sexes, though not all matings necessarily result in offspring. Multiple paternity has been previously verified through allozyme analysis. Microsatellites were used to verify maternity and determine paternity. Analysis of ten litters demonstrated an average of 1 father per 1.35 pups in a litter. Sibship deduced from maternity and paternity analysis was then compared with previously collected behavioral data. While previous observations indicate preference of fullsib play partners in juveniles, our findings do not corroborate this, though the results were not significant

The impact of one-decade ecological disturbance on genetic changes : a study on the brine shrimp Artemia urmiana from Urmia Lake, Iran

Urmia Lake, the largest natural habitat of the brine shrimp Artemia urmiana, has progressively desiccated over the last two decades, resulting in a loss of 80% of its surface area and producing thousands of hectares of arid salty land. This ecological crisis has seriously affected the lake's native biodiversity. Artemia urmiana has lost more than 90% of its population during the decade from 1994 (rainy period) to 2004 (drought period) due to salinity increasing to saturation levels (similar to 300 g/l). We studied the influence of this ecological crisis on the genetic diversity of A. urmiana in Urmia Lake, based on one cyst collections in 1994 and 2004. AMOVA analysis on ISSR data demonstrated a 21% genetic variation and there was a 5.5% reduction of polymorphic loci between samples. PCoA showed that 77.42% and 68.75% of specimens clustered separately in 1994 and 2004, respectively. Our analyses of four marker genes revealed different genetic diversity patterns with a decrease of diversity at ITS1 and an increase for Na+/K+ ATPase. There was no notable difference in genetic variation detected for CO/ and 16S genes between the two periods. However, they represented distinctly different haplotypes. ITS1 and COI followed a population expansion model, whereas Na+/K+ ATPase and 16S were under demographic equilibrium without selective pressure in the 1994 samples. Neutrality tests confirmed the excess of rare historical and recent mutations present in COI and ITS1 in both samples. It is evident that a short-term ecological disturbance has impacted the genetic diversity and structure of A. urmiana

Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure.

© The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bors, E. K., Herrera, S., Morris, J. A., Jr., & Shank, T. M. Population genomics of rapidly invading lionfish in the Caribbean reveals signals of range expansion in the absence of spatial population structure. Ecology and Evolution, 9(6), (2019):3306-3320, doi:10.1002/ece3.4952.Range expansions driven by global change and species invasions may have significant genomic, evolutionary, and ecological implications. During range expansions, strong genetic drift characterized by repeated founder events can result in decreased genetic diversity with increased distance from the center of the historic range, or the point of invasion. The invasion of the Indo‐Pacific lionfish, Pterois volitans, into waters off the US East Coast, Gulf of Mexico, and Caribbean Sea provides a natural system to study rapid range expansion in an invasive marine fish with high dispersal capabilities. We report results from 12,759 single nucleotide polymorphism loci sequenced by restriction enzyme‐associated DNA sequencing for nine P. volitans sampling areas in the invaded range, including Florida and other sites throughout the Caribbean, as well as mitochondrial control region D‐loop data. Analyses revealed low to no spatially explicit metapopulation genetic structure, which is partly consistent with previous finding of little structure within ocean basins, but partly divergent from initial reports of between‐basin structure. Genetic diversity, however, was not homogeneous across all sampled sites. Patterns of genetic diversity correlate with invasion pathway. Observed heterozygosity, averaged across all loci within a population, decreases with distance from Florida while expected heterozygosity is mostly constant in sampled populations, indicating population genetic disequilibrium correlated with distance from the point of invasion. Using an FST outlier analysis and a Bayesian environmental correlation analysis, we identified 256 and 616 loci, respectively, that could be experiencing selection or genetic drift. Of these, 24 loci were shared between the two methods.We thank the many participants of the Gulf and Caribbean Fisheries Institute for providing lionfish samples from around the Caribbean region, as well as Dr. Bernard Castillo at the University of the Virgin Islands and Kristian Rogers at the Biscayne Bay National Park. We would like to acknowledge Alex Bogdanoff at NOAA, Beaufort NC, for assistance with sample acquisition; Camrin Braun at WHOI, for assistance with the calculation of oceanic distances between sites; Dr. Tom Schultz at Duke Marine Lab and Dr. Margaret Hunter at USGS for discussions concerning ongoing population genetic projects; and Jack Cook at the WHOI Graphics department for his assistance in generating maps of the study area. We would like to extend a special thank you to Dr. John Wakeley of Harvard University for assistance in the interpretation of data. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 1122374. Sequencing funding was provided in part by the PADI Foundation Grant No. 14904. Additional research support was provided by the Woods Hole Oceanographic Institution (WHOI) Ocean Ventures Fund, the Coastal Ocean Institute at WHOI, the National Science Foundation (OCE‐1131620 to TMS), and the James Education Fund for Ocean Exploration within the Ocean Exploration Institute at WHOI. Publication of this paper was supported, in part, by the Henry Mastin Graduate Student Fund administered by the Oregon State University Department of Fisheries and Wildlife. Finally, we sincerely thank the reviewers and editors who helped to strengthen this manuscript

Modeling and Optimization of Dynamical Systems in Epidemiology using Sparse Grid Interpolation

Infectious diseases pose a perpetual threat across the globe, devastating communities, and straining public health resources to their limit. The ease and speed of modern communications and transportation networks means policy makers are often playing catch-up to nascent epidemics, formulating critical, yet hasty, responses with insufficient, possibly inaccurate, information. In light of these difficulties, it is crucial to first understand the causes of a disease, then to predict its course, and finally to develop ways of controlling it. Mathematical modeling provides a methodical, in silico solution to all of these challenges, as we explore in this work. We accomplish these tasks with the aid of a surrogate modeling technique known as sparse grid interpolation, which approximates dynamical systems using a compact polynomial representation. Our contributions to the disease modeling community are encapsulated in the following endeavors. We first explore transmission and recovery mechanisms for disease eradication, identifying a relationship between the reproductive potential of a disease and the maximum allowable disease burden. We then conduct a comparative computational study to improve simulation fits to existing case data by exploiting the approximation properties of sparse grid interpolants both on the global and local levels. Finally, we solve a joint optimization problem of periodically selecting field sensors and deploying public health interventions to progressively enhance the understanding of a metapopulation-based infectious disease system using a robust model predictive control scheme

Context‐dependent dispersal determines relatedness and genetic structure in a patchy amphibian population

Dispersal is a central process in ecology and evolution with far reaching consequences for the dynamics and genetics of spatially structured populations (SSPs). Individuals can adjust their decisions to disperse according to local fitness prospects, resulting in context-dependent dispersal. By determining dispersal rate, distance, and direction, these individual-level decisions further modulate the demography, relatedness, and genetic structure of SSPs. Here, we examined how context-dependent dispersal influences the dynamics and genetics of a Great Crested Newt (Triturus cristatus) SSP. We collected capture-recapture data of 5564 individuals and genetic data of 950 individuals across a SSP in northern Germany. We added genetic data from six sites outside this SSP to assess genetic structure and gene flow at a regional level. Dispersal rates within the SSP were high but dispersal distances were short. Dispersal was context-dependent: individuals preferentially immigrated into high-quality ponds where breeding probabilities were higher. The studied SSP behaved like a patchy population, where subpopulations at each pond were demographically interdependent. High context-dependent dispersal led to weak but significant spatial genetic structure and relatedness within the SSP. At the regional level, a strong hierarchical genetic structure with very few first-generation migrants as well as low effective dispersal rates suggest the presence of independent demographic units. Overall, our study highlights the importance of habitat quality for driving context-dependent dispersal and therefore demography and genetic structure in SSPs. Limited capacity for long-distance dispersal seems to increase genetic structure within a population and leads to demographic isolation in anthropogenic landscapes.Microsatellite Genotypes: Missing values are coded "-9". Presence/Absence Data: Missing values are coded "-". Funding provided by: Deutsche ForschungsgemeinschaftCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100001659Award Number: STE 1130/7-1Demographic Data (CMR and Presence/Absence Data): We surveyed 33 water bodies using mark-recapture methods for the presence, demography and reproduction of crested newts between 2012 and 2014. Newts were captured during two capture sessions (cs) per year, one early (April/May) and one late (June/July) in the breeding season. Every capture session thereby consisted of three consecutive capture events in intervals of two days. Within the context of a presence/absence analysis, all sites were surveyed for one more day in late July/early August in order to detect larvae. If a pond dried out and was therefore not surveyed during a capture session, such an event was treated as a missing observation. Newts were captured using Ortmann's funnel traps which were evenly distributed along the shoreline of a pond. The number of traps deployed per capture event varied according to pond perimeter (one trap per 10m shoreline), ranging from one to 27 traps. For individual recognition of newts during the CMR study, we used photographs of the ventral side of an individual which provides a natural marking in form of a highly variable but individually unique and stable color pattern through the time. Recaptured individuals were identified automatically by the software AmphIdent. Microsatellite Genotypes: Tissue samples were taken from seven sampling sites by puncturing the tails of captured great crested newts (Triturus cristatus) using micro haematocrit capillary tubes (Carl Roth, Ø 1.6 mm) and were then stored in 80% ethanol. Total genomic DNA was extracted using the sodium dodecyl sulfate (SDS)-proteinase K/ Phenol-Chloroform extraction method. Genomic DNA was stored in Tris-EDTA buffer (10 mM Tris-HCl, 0.1 mM EDTA, pH 8.0) and used for all subsequent reactions. Each individual sample was mugenotyped for 17 microsatellite loci. Primers were combined in three multiplex mixes (Drechsler et al., 2013). 10 µl Type-it Multiplex PCRs (Qiagen) containing 1 µl of genomic DNA were performed. The PCR profile was as follows: (1) 5 min at 95°C, (2) 30 s at 94°C, (3) 90 s at an annealing temperature of 60°C, (4) 60 s at 72°C, (5) return to step 2 for 30 times, (6) 30 min at 60°C. Obtained PCR products were diluted with 50-200 μl water depending on the strength of obtained PCR products. 1 µl of each diluted multiplex reaction was added to 20 μl of Genescan 500-LIZ size standard (Applied Biosystem) and then run on an ABI 3730 96-capillary or an ABI 3130 16-capillary automated DNA-sequencer. Allele scoring of microsatellite loci was performed using Genemarker software (SoftGenetics version 1.95)

Population ecology of the American pika (Ochotona princeps) in an extreme environment

Alteration of native habitat through human disturbance is generally implicated as the predominant cause of decline in terrestrial biodiversity. Anthropogenic forces destablilize critical processes such as reproductive success and dispersal of individuals; how species will respond depends to a large extent on the plasticity of habitat use. In this vein, habitat specialists may provide valuable opportunities to understand how colonization succeeds (or fails) in novel environments. The American pika (Ochotona princeps) is such a habitat specialist, occupying montane regions in western North America. This species is recognized as vulnerable to anthropogenic impacts (e.g. climate change) due to intrinsic characteristics (e.g. low thermal tolerance, low dispersal capability) that make it susceptible to local extirpations. In the southern interior of British Columbia, in a region that features extreme temperature shifts, I compared a population of pikas inhabiting a partially reclaimed mine site, with those found close by in natural habitat. All told, I monitored a total of 174 pikas from 2012-2014 to compare survival, physical characteristics, dispersal and den site attributes. Through mark-recapture and radio-telemetry, I found comparable survival and dispersal rates of pikas and almost no detectable physical differences. Investigation of undertalus temperatures of den sites revealed that microhabitats within the rocks largely were decoupled from the regional macroclimate, providing evidence of microrefugia as a functional buffer against macroscale climate impacts. Rock size of 1m3 and cryptogamic cover on talus near den entrances were positively influential to pika survival, whereas winter temperatures < -10°C under the talus negatively impacted survival. This study provides a relatively parsimonious explanation of pika persistence in atypical environments; within an extreme thermal environment such as in my study region, pikas appear capable of utilizing portions of anthropogenic habitat via microrefugia, although future longevity in a changing climate remains unknown.climate-sensitive speciesAmerican pikaOchotona princepsmicrorefugiaanthropogenic impactstalusmicrohabitatBritish Columbi