Scott Hotaling

Species discovery and validation in a cryptic radiation of endangered primates: coalescent‐based species delimitation in Madagascar's mouse lemurs

Implementation of the coalescent model in a Bayesian framework is an emerging strength in genetically based species delimitation studies. By providing an objective measure of species diagnosis, these methods represent a quantitative enhancement to the analysis of multilocus data, and complement more traditional methods based on phenotypic and ecological characteristics. Recognized as two species 20 years ago, mouse lemurs (genus Microcebus) now comprise more than 20 species, largely diagnosed from mtDNA sequence data. With each new species description, enthusiasm has been tempered with scientific scepticism. Here, we present a statistically justified and unbiased Bayesian approach towards mouse lemur species delimitation. We perform validation tests using multilocus sequence data and two methodologies: (i) reverse‐jump Markov chain Monte Carlo sampling to assess the likelihood of different models defined a priori by a guide tree, and (ii) a Bayes factor delimitation test that compares different species‐tree models without a guide tree. We assess the sensitivity of these methods using randomized individual assignments, which has been used in bpp studies, but not with Bayes factor delimitation tests. Our results validate previously diagnosed taxa, as well as new species hypotheses, resulting in support for three new mouse lemur species. As the challenge of multiple researchers using differing criteria to describe diversity is not unique to Microcebus, the methods used here have significant potential for clarifying diversity in other taxonomic groups. We echo previous studies in advocating that multiple lines of evidence, including use of the coalescent model, should be trusted to delimit new species.

The influence of locus number and information content on species delimitation: an empirical test case in an endangered Mexican salamander

Perhaps the most important recent advance in species delimitation has been the development of model‐based approaches to objectively diagnose species diversity from genetic data. Additionally, the growing accessibility of next‐generation sequence data sets provides powerful insights into genome‐wide patterns of divergence during speciation. However, applying complex models to large data sets is time‐consuming and computationally costly, requiring careful consideration of the influence of both individual and population sampling, as well as the number and informativeness of loci on species delimitation conclusions. Here, we investigated how locus number and information content affect species delimitation results for an endangered Mexican salamander species, Ambystoma ordinarium. We compared results for an eight‐locus, 137‐individual data set and an 89‐locus, seven‐individual data set. For both data sets, we used species discovery methods to define delimitation models and species validation methods to rigorously test these hypotheses. We also used integrated demographic model selection tools to choose among delimitation models, while accounting for gene flow. Our results indicate that while cryptic lineages may be delimited with relatively few loci, sampling larger numbers of loci may be required to ensure that enough informative loci are available to accurately identify and validate shallow‐scale divergences. These analyses highlight the importance of striking a balance between dense sampling of loci and individuals, particularly in shallowly diverged lineages. They also suggest the presence of a currently unrecognized, endangered species in the western part of A. ordinariums range.

Climate change and alpine stream biology: progress, challenges, and opportunities for the future

In alpine regions worldwide, climate change is dramatically altering ecosystems and affecting biodiversity in many ways. For streams, receding alpine glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, basal resources, and threatening the very existence of some habitats and biota. Alpine streams harbour substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity. Climate change is expected to affect alpine stream biodiversity across many levels of biological resolution from micro‐ to macroscopic organisms and genes to communities. Herein, we describe the current state of alpine stream biology from an organism‐focused perspective. We begin by reviewing seven standard and emerging approaches that combine to form the current state of the discipline. We follow with a call for increased synthesis across existing approaches to improve understanding of how these imperiled ecosystems are responding to rapid environmental change. We then take a forward‐looking viewpoint on how alpine stream biologists can make better use of existing data sets through temporal comparisons, integrate remote sensing and geographic information system (GIS) technologies, and apply genomic tools to refine knowledge of underlying evolutionary processes. We conclude with comments about the future of biodiversity conservation in alpine streams to confront the daunting challenge of mitigating the effects of rapid environmental change in these sentinel ecosystems.

Longitudinal changes in stream invertebrate assemblages of Grand Teton National Park, Wyoming

High elevation ecosystems are predicted to be strongly impacted by climate change; however, little is known of extant biodiversity in mountain streams. For this study, five streams in Grand Teton National Park, Wyoming were sampled along a longitudinal gradient to establish a baseline of invertebrate assemblages and environmental conditions. Five Surber samples were collected from low, middle and high elevation sites along each stream. Nearly 10 000 ind m−2 lived in these streams on average, but the density (mixed effects model, P = 0.54) and richness (P = 0.18) of invertebrates did not vary significantly by elevation. Total density of invertebrates was positively related to the amount of visible biofilm (anova, P = 0.03) and oxidation‐reduction potential (P = 0.05) and taxa richness was negatively related to specific conductivity (P = 0.009). Invertebrate assemblages and environmental conditions were more similar at low versus high sites when compared using non‐metric multidimensional scaling and tests of multivariate dispersion indicating that higher elevation sites harboured more environmental and species diversity. These results can help target which aquatic invertebrates to monitor as stream temperatures rise, and highlight the biotic and abiotic factors that structure aquatic ecosystems in the Teton Range of Grand Teton National Park.

Surmounting the Large-Genome “Problem” for Genomic Data Generation in Salamanders

Salamanders have some of the largest genomes among all extant organisms, due in large part to the proliferation of repetitive elements and the expansion of intron size. This increased complexity and size has limited the application of genomic tools to the population genetic and phylogenetic study of salamanders, even as these methods have become common for most other organisms. However, the generation of genomic data in salamanders is not out of reach for most researchers. High-quality and informative data sets can be acquired for salamander-centric research projects with careful consideration of the genomic tool(s) most appropriate for the question at hand and how best to apply these to a salamander genome. Here, we review a range of genomic tools representing the current best options for use in the study of genome-wide variation within and between salamander species. This includes the use of transcriptomics (RNAseq), restriction site-associated DNA sequencing (RADseq), sequence capture enrichment methods, and PCR-based parallel tagged amplicon sequencing. Each of these methods has a particular set of benefits, as well as limitations in the study of salamander genomics. We highlight their trade-offs and the factors that should be considered when choosing among them, and we provide descriptions of exemplar studies that illustrate their empirical applications. By making informed decisions about the choice and implementation of these subgenomic methods, we believe that they can be broadly and effectively applied as important resources for the study of salamander evolution and conservation.

Next-generation teaching: a template for bringing genomic and bioinformatic tools into the classroom

Abstract The recent increase in accessibility and scale of genetic data available through next-generation sequencing (NGS) technology has transformed biological inquiry. As a direct result, the application and analysis of NGS data has quickly become an important skill for future scientists. However, the steep learning curve for applying NGS technology to biological questions, including the complexity of sample preparation for sequencing and the analysis of large data sets, are deterrents to the integration of NGS into undergraduate education. Here, we present a course-based undergraduate research experience (CURE) designed to aid in overcoming these limitations through NGS investigations of prokaryotic diversity. Specifically, we use 16S rRNA sequencing to explore patterns of diversity stemming from student-directed hypothesis development. This CURE addresses three learning objectives: (1) it provides a forum for experimental design hypothesis generation, (2) it introduces modern genomic tools through a hands-on experience generating an NGS data-set, and (3) it provides students with an introductory experience in bioinformatics.

Macroinvertebrate richness is lower in high-elevation lakes vs nearby streams: evidence from Grand Teton National Park, Wyoming

ABSTRACT Mountain ecosystems will be strongly impacted by climate change, yet little is known of extant biodiversity in high-elevation lakes, particularly in North America. In this study, we sampled the littoral zone of six alpine and subalpine lakes in Grand Teton National Park (GRTE), Wyoming, to characterise invertebrate diversity and environmental variation in these climate change-threatened ecosystems. Overall, we collected 19 aquatic invertebrate taxa, and found that each lake harboured a unique assemblage of invertebrates despite close geographic proximity in some instances (e.g. less than 5 km). The results of this study complement previous efforts focused on macroinvertebrate diversity of streams in the Teton Range, highlighting much lower diversity in montane lakes vs nearby streams. Taken together, the two studies establish an important baseline understanding of mountain freshwater biodiversity in GRTE. With rapidly changing hydrologic inputs to mountain lakes driven primarily by the recession of alpine glaciers, these results may help target aquatic invertebrates to monitor as climate change affects the region. Moreover, these data clarify habitat factors, both biotic and abiotic, that influence high-elevation lake assemblages of the Teton Range.