Co-phylogeographic structure in a disease-causing parasite and its oyster host.

With the increasing affordability of next-generation sequencing technologies, genotype-by-sequencing has become a cost-effective tool for ecologists and conservation biologists to describe a species' evolutionary history. For host–parasite interactions, genotype-by-sequencing can allow the simultaneous examination of host and parasite genomes and can yield insight into co-evolutionary processes. The eastern oyster, , is among the most important aquacultured species in the United States.

Engaging Undergraduates in Research Experiences at a Distance: Insights and Recommendations for Remote URE.

Undergraduates phenotyping knockouts (unPAK) is a biology research network that has provided undergraduate research experiences (URE) since 2010. In 2019, unPAK expanded to include a summer URE that engaged undergraduate researchers from across the network in an intensive collaborative program. In response to the COVID-19 pandemic in 2020, unPAK rapidly shifted to provide the summer URE program remotely.

Founder effects shape linkage disequilibrium and genomic diversity of a partially clonal invader.

The genomic variation of an invasive species may be affected by complex demographic histories and evolutionary changes during the invasion. Here, we describe the relative influence of bottlenecks, clonality, and population expansion in determining genomic variability of the widespread red macroalga Agarophyton vermiculophyllum. Its introduction from mainland Japan to the estuaries of North America and Europe coincided with shifts from predominantly sexual to partially clonal reproduction and rapid adaptive evolution.

Using RAD-seq to develop sex-linked markers in a haplodiplontic alga.

For many taxa, including isomorphic haplodiplontic macroalgae, determining sex and ploidy is challenging, thereby limiting the scope of some population demographic and genetic studies. Here, we used double-digest restriction site-associated DNA sequencing (ddRAD-seq) to identify sex-linked molecular markers in the widespread red alga Agarophyton vermiculophyllum. In the ddRAD-seq library, we included 10 female gametophytes, 10 male gametophytes, and 16 tetrasporophytes from one native and one non-native site (N = 40 gametophytes and N = 32 tetrasporophytes total).

Undergraduates Phenotyping Knockouts in a Course-Based Undergraduate Research Experience: Exploring Plant Fitness and Vigor Using Quantitative Phenotyping Methods.

We present a curriculum description, an initial student outcome investigation, and sample scientific results for a representative Course-Based Undergraduate Research Experience (CURE) that is part of the "Undergraduates Phenotyping Knockouts" (unPAK) network. CUREs in the unPAK network characterize quantitative phenotypes of the model plant from across environments to uncover connections between genotype and phenotype. Students in unPAK CUREs grow plants in a replicated block design and make quantitative measurements throughout the semester.

Distributed phenomics with the unPAK project reveals the effects of mutations.

Determining how genes are associated with traits in plants and other organisms is a major challenge in modern biology. The unPAK project - undergraduates phenotyping Arabidopsis knockouts - has generated phenotype data for thousands of non-lethal insertion mutation lines within a single Arabidopsis thaliana genomic background. The focal phenotypes examined by unPAK are complex macroscopic fitness-related traits, which have ecological, evolutionary and agricultural importance.

When and where plant-soil feedback may promote plant coexistence: a meta-analysis.

Plant-soil feedback (PSF) theory provides a powerful framework for understanding plant dynamics by integrating growth assays into predictions of whether soil communities stabilise plant-plant interactions. However, we lack a comprehensive view of the likelihood of feedback-driven coexistence, partly because of a failure to analyse pairwise PSF, the metric directly linked to plant species coexistence. Here, we determine the relative importance of plant evolutionary history, traits, and environmental factors for coexistence through PSF using a meta-analysis of 1038 pairwise PSF measures.

Frequency-dependent feedback constrains plant community coexistence.

Ecological theory suggests that coexistence of many species within communities requires negative frequency-dependent feedbacks to prevent exclusion of the least fit species. For plant communities, empirical evidence of negative frequency dependence driving species coexistence and diversity patterns is rapidly accumulating, but connecting these findings to theory has been difficult as corresponding theoretical frameworks only consider small numbers of species. Here, we show how frequency-dependent feedback constrains community coexistence, regardless of the number of species and inherent fitness inequalities between them.

Next-generation metrics for monitoring genetic erosion within populations of conservation concern.

Genetic erosion is a major threat to biodiversity because it can reduce fitness and ultimately contribute to the extinction of populations. Here, we explore the use of quantitative metrics to detect and monitor genetic erosion. Monitoring systems should not only characterize the mechanisms and drivers of genetic erosion (inbreeding, genetic drift, demographic instability, population fragmentation, introgressive hybridization, selection) but also its consequences (inbreeding and outbreeding depression, emergence of large-effect detrimental alleles, maladaptation and loss of adaptability).

Combining niche shift and population genetic analyses predicts rapid phenotypic evolution during invasion.

The rapid evolution of non-native species can facilitate invasion success, but recent reviews indicate that such microevolution rarely yields expansion of the climatic niche in the introduced habitats. However, because some invasions originate from a geographically restricted portion of the native species range and its climatic niche, it is possible that the frequency, direction, and magnitude of phenotypic evolution during invasion have been underestimated. We explored the utility of niche shift analyses in the red seaweed , which expanded its range from the northeastern coastline of Japan to North America, Europe, and northwestern Africa within the last 100 years.

Genetic identification of source and likely vector of a widespread marine invader.

The identification of native sources and vectors of introduced species informs their ecological and evolutionary history and may guide policies that seek to prevent future introductions. Population genetics provides a powerful set of tools to identify origins and vectors. However, these tools can mislead when the native range is poorly sampled or few molecular markers are used.

skelesim: an extensible, general framework for population genetic simulation in R.

Simulations are a key tool in molecular ecology for inference and forecasting, as well as for evaluating new methods. Due to growing computational power and a diversity of software with different capabilities, simulations are becoming increasingly powerful and useful. However, the widespread use of simulations by geneticists and ecologists is hindered by difficulties in understanding these softwares' complex capabilities, composing code and input files, a daunting bioinformatics barrier and a steep conceptual learning curve.

Invasion of novel habitats uncouples haplo-diplontic life cycles.

Baker's Law predicts uniparental reproduction will facilitate colonization success in novel habitats. While evidence supports this prediction among colonizing plants and animals, few studies have investigated shifts in reproductive mode in haplo-diplontic species in which both prolonged haploid and diploid stages separate meiosis and fertilization in time and space. Due to this separation, asexual reproduction can yield the dominance of one of the ploidy stages in colonizing populations.

Development and characterization of microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla.

Microsatellite loci are popular molecular markers due to their resolution in distinguishing individual genotypes. However, they have rarely been used to explore the population dynamics in species with biphasic life cycles in which both haploid and diploid stages develop into independent, functional organisms. We developed microsatellite loci for the haploid-diploid red seaweed Gracilaria vermiculophylla, a widespread non-native species in coastal estuaries of the Northern hemisphere.

Changes in root architecture under elevated concentrations of CO₂ and nitrogen reflect alternate soil exploration strategies.

Predicting the response of fine roots to increased atmospheric CO₂ concentration has important implications for carbon (C) and nutrient cycling in forest ecosystems. Root architecture is known to play an important role in how trees acquire soil resources in changing environments. However, the effects of elevated CO₂ on the fine-root architecture of trees remain unclear.

Root length, biomass, tissue chemistry and mycorrhizal colonization following 14 years of CO2 enrichment and 6 years of N fertilization in a warm temperate forest.

Root systems serve important roles in carbon (C) storage and resource acquisition required for the increased photosynthesis expected in CO2-enriched atmospheres. For these reasons, understanding the changes in size, distribution and tissue chemistry of roots is central to predicting the ability of forests to capture anthropogenic CO2. We sampled 8000 cm(3) soil monoliths in a pine forest exposed to 14 years of free-air-CO2-enrichment and 6 years of nitrogen (N) fertilization to determine changes in root length, biomass, tissue C : N and mycorrhizal colonization.

The Adaptive Cline at LDH (Lactate Dehydrogenase) in Killifish Fundulus heteroclitus Remains Stationary After 40 Years of Warming Estuaries.

Since the 1970s, water temperatures along the Atlantic seaboard of the United States have risen by an average of 0.5 °C in summer months and 2.2 °C in winter months.

Long-term dynamics of mycorrhizal root tips in a loblolly pine forest grown with free-air CO2 enrichment and soil N fertilization for 6 years.

Large-scale, long-term FACE (Free-Air CO2 enrichment) experiments indicate that increases in atmospheric CO2 concentrations will influence forest C cycling in unpredictable ways. It has been recently suggested that responses of mycorrhizal fungi could determine whether forest net primary productivity (NPP) is increased by elevated CO2 over long time periods and if forests soils will function as sources or sinks of C in the future. We studied the dynamic responses of ectomycorrhizae to N fertilization and atmospheric CO2 enrichment at the Duke FACE experiment using minirhizotrons over a 6 year period (2005-2010).

Sampling volume in root studies: the pitfalls of under-sampling exposed using accumulation curves.

Root systems are important for global models of below-ground carbon and nutrient cycling. Notoriously difficult sampling methods and the fractal distribution of root diameters in the soil make data being used in these models especially susceptible to error resulting from under-sampling. We applied the concept of species accumulation curves to root data to quantify the extent of under-sampling inherent to minirhizotron and soil coring sampling for both root uptake and carbon content studies.

Can diversifying selection be distinguished from history in geographic clines? A population genomic study of killifish (Fundulus heteroclitus).

A common geographical pattern of genetic variation is the one-dimensional cline. Clines may be maintained by diversifying selection across a geographical gradient but can also reflect historical processes such as allopatry followed by secondary contact. To identify loci that may be undergoing diversifying selection, we examined the distribution of geographical variation patterns across the range of the killifish (Fundulus heteroclitus) in 310 loci, including microsatellites, allozymes, and single nucleotide polymorphisms.

Effects of endosulfan exposure and Taura Syndrome Virus infection on the survival and molting of the marine penaeid shrimp, Litopenaeus vannamei.

Molting in crustaceans is an important endocrine-controlled biological process that plays a critical role in growth and reproduction. Many factors can affect this physiological cycle in crustaceans including environmental stressors and disease agents. For example the pathology of Taura Syndrome Virus (TSV) of shrimp is closely related to molting cycle.

Use of molecular tools in identification of philometrid larvae in fishes: technical limitations parallel our poor assessment of their biodiversity.

The usefulness of the polymerase chain reaction with restriction fragment length polymorphism (PCR-RFLP) and partial sequencing of the cytochrome oxidase I (COI) gene was tested regarding the utility of these techniques in unraveling philometrid life cycles and, in particular, to determine putative paratenic host species. Our focus was to study three species of philometrids commonly found in the estuaries of South Carolina: Philometroides paralichthydis and Philometra overstreeti from the southern flounder, Paralichthys lethostigma and Philometra carolinensis from the spotted seatrout, Cynoscion nebulosus. A total of 473 fish in 19 species known to be potential prey of the spotted seatrout and the southern flounder were dissected.

tossm: an R package for assessing performance of genetic analytical methods in a management context.

tossm (Testing of Spatial Structure Methods) is a package for testing the performance of genetic analytical methods in a management context. In the tossm package, any method developed to detect population genetic structure can be combined with a mechanism for creating management units (MUs) based on the genetic analysis. The resulting Boundary-Setting Algorithm (BSA) dictates harvest boundaries with a genetic basis.

Irreconcilable differences: fine-root life spans and soil carbon persistence.

The residence time of fine-root carbon in soil is one of the least understood aspects of the global carbon cycle, and fine-root dynamics are one of the least understood aspects of plant function. Most recent studies of these belowground dynamics have used one of two methodological strategies. In one approach, based on analysis of carbon isotopes, the persistence of carbon is inferred; in the other, based on direct observations of roots with cameras, the longevity of individual roots is measured.