A multi-locus perspective reveals connections between island biogeography and evolutionary history of an endangered shrew (Sorex pribilofensis)

Master of ScienceDepartment of BiologyAndrew HopeAccelerating anthropogenic environmental change poses numerous threats to mammalian wildlife. Island endemics are among the most vulnerable species to rapid environmental change, and account for a disproportionate amount of all documented extinctions. The current vulnerability of island species to global change is a result of their unique evolutionary ecology. The evolutionary forces of natural selection, genetic drift, and reduced or non-existent gene flow lead to the high levels of endemism on islands, but can also leave these species vulnerable to change. It is therefore vital for island biodiversity conservation that we understand how past environmental change has influenced evolutionary dynamics. Islands in the Bering Sea represent a classic system of land-bridge insular evolution. Through Quaternary climate cycling, oscillating sea levels have alternately connected Alaska and Siberia through the Bering Isthmus, and today the Arctic is experiencing climate change at a more rapid pace than lower latitudes. St. Paul Island, home of the endemic Pribilof Island Shrew (Sorex pribilofensis), is located in the southern Bering Sea and has been isolated from the mainland for ~14,000 years. This shrew is part of a diverse sibling species-complex, which has a wide-ranging Holarctic distribution. The goals of my thesis are to (1) resolve the evolutionary relationship of S. pribilofensis to other related shrews, and (2) clarify the evolutionary processes leading to speciation among these enigmatic mammals. Using a tiered genomic dataset of microsatellites, a maternally inherited mtDNA gene, and ~11,000 nuclear SNPs, I tested predictions related to the evolutionary and demographic history of S. pribilofensis. Given small island size and extended isolation, my overarching prediction was that genetic drift has led to rapid speciation and loss of genetic diversity within this shrew. In my first chapter, I show that S. pribilofensis is highly differentiated from sibling taxa using Discriminate Analysis of Principle Components and Structure clustering analyses. With phylogenetic analysis I then show that S. pribilofensis is the first to have diverged from closely related sibling taxa, and use Bayes Factor Species Delimitation to support species-level differentiation. In my second chapter, I give evidence for substantially reduced genetic diversity and a smaller effective population size of S. pribilofensis compared to mainland species. Through multiple linear regressions, I then show that genetic differentiation is closely tied to reduced genetic diversity in this system of shrews. Finally, compared to mainland sibling shrews, S. pribilofensis is most strongly differentiated at its least variable loci and least differentiated at its most variable loci. These combined results are indicative of strong genetic drift driving the differentiation of S. pribilofensis. Put together, my findings indicate a scenario whereby S. pribilofensis speciated rapidly after island isolation through neutral divergence, but in the process has lost much of its genomic diversity. These results highlight the potential for genetic drift, as a consequence of dramatic environmental change, to rapidly reshape island biodiversity while as a result potentially leaving island species less able to respond to multiple additional environmental stressors in an anthropogenic world

Reconciling mantle attenuation-temperature relationships from seismology, petrology, and laboratory measurements

Seismic attenuation measurements provide a powerful tool for sampling mantle properties. Laboratory experiments provide calibrations at seismic frequencies and mantle temperatures for dry melt-free rocks, but require ∼10²−10³ extrapolations in grain size to mantle conditions; also, the effects of water and melt are not well understood. At the same time, body wave attenuation measured from dense broadband arrays provides reliable estimates of shear wave attenuation (Q_S⁻¹), affording an opportunity for calibration. We reanalyze seismic data sets that sample arc and back-arc mantle in Central America, the Marianas, and the Lau Basin, confirming very high attenuation (Q_S ∼ 25–80) at 1 Hz and depths of 50–100 km. At each of these sites, independent petrological studies constrain the temperature and water content where basaltic magmas last equilibrated with the mantle, 1300–1450°C. The Q_S measurements correlate inversely with the petrologically inferred temperatures, as expected. However, dry attenuation models predict Q_S too high by a factor of 1.5–5. Modifying models to include effects of H₂O and rheology-dependent grain size shows that the effects of water-enhanced dissipation and water-enhanced grain growth nearly cancel, so H₂O effects are modest. Therefore, high H₂O in the arc source region cannot explain the low Q_S, nor in the back arc where lavas show modest water content. Most likely, the high attenuation reflects the presence of melt, and some models of melt effects come close to reproducing observations. Overall, body wave Q_S can be reconciled with petrologic and laboratory inferences of mantle conditions if melt has a strong influence beneath arcs and back arcs

Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics

Next-gen sequencing technologies have revolutionized data collection in genetic studies and advanced genome biology to novel frontiers. However, to date, next-gen technologies have been used principally for whole genome sequencing and transcriptome sequencing. Yet many questions in population genetics and systematics rely on sequencing specific genes of known function or diversity levels. Here, we describe a targeted amplicon sequencing (TAS) approach capitalizing on next-gen capacity to sequence large numbers of targeted gene regions from a large number of samples. Our TAS approach is easily scalable, simple in execution, neither time-nor labor-intensive, relatively inexpensive, and can be applied to a broad diversity of organisms and/or genes. Our TAS approach includes a bioinformatic application, BarcodeCrucher, to take raw next-gen sequence reads and perform quality control checks and convert the data into FASTA format organized by gene and sample, ready for phylogenetic analyses. We demonstrate our approach by sequencing targeted genes of known phylogenetic utility to estimate a phylogeny for the Pancrustacea. We generated data from 44 taxa using 68 different 10-bp multiplexing identifiers. The overall quality of data produced was robust and was informative for phylogeny estimation. The potential for this method to produce copious amounts of data from a single 454 plate (e.g., 325 taxa for 24 loci) significantly reduces sequencing expenses incurred from traditional Sanger sequencing. We further discuss the advantages and disadvantages of this method, while offering suggestions to enhance the approach

Increased diversification rates follow shifts to bisexuality in liverworts

Shifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts. We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests. We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present. Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism

Insect herbivores should follow plants escaping their relatives

Neighboring plants within a local community may be separated by many millions of years of evolutionary history, potentially reducing enemy pressure by insect herbivores. However, it is not known how the evolutionary isolation of a plant affects the fitness of an insect herbivore living on such a plant, especially the herbivore's enemy pressure. Here, we suggest that evolutionary isolation of host plants may operate similarly as spatial isolation and reduce the enemy pressure per insect herbivore. We investigated the effect of the phylogenetic isolation of host trees on the pressure exerted by specialist and generalist enemies (parasitoids and birds) on ectophagous Lepidoptera and galling Hymenoptera. We found that the phylogenetic isolation of host trees decreases pressure by specialist enemies on these insect herbivores. In Lepidoptera, decreasing enemy pressure resulted from the density dependence of enemy attack, a mechanism often observed in herbivores. In contrast, in galling Hymenoptera, enemy pressure declined with the phylogenetic isolation of host trees per se, as well as with the parallel decline in leaf damage by non-galling insects. Our results suggest that plants that leave their phylogenetic ancestral neighborhood can trigger, partly through simple density-dependency, an enemy release and fitness increase of the few insect herbivores that succeed in tracking these plants

The taming of an impossible child: a standardized all-in approach to the phylogeny of Hymenoptera using public database sequences

<p>Abstract</p> <p>Background</p> <p>Enormous molecular sequence data have been accumulated over the past several years and are still exponentially growing with the use of faster and cheaper sequencing techniques. There is high and widespread interest in using these data for phylogenetic analyses. However, the amount of data that one can retrieve from public sequence repositories is virtually impossible to tame without dedicated software that automates processes. Here we present a novel bioinformatics pipeline for downloading, formatting, filtering and analyzing public sequence data deposited in GenBank. It combines some well-established programs with numerous newly developed software tools (available at <url>http://software.zfmk.de/</url>).</p> <p>Results</p> <p>We used the bioinformatics pipeline to investigate the phylogeny of the megadiverse insect order Hymenoptera (sawflies, bees, wasps and ants) by retrieving and processing more than 120,000 sequences and by selecting subsets under the criteria of compositional homogeneity and defined levels of density and overlap. Tree reconstruction was done with a partitioned maximum likelihood analysis from a supermatrix with more than 80,000 sites and more than 1,100 species. In the inferred tree, consistent with previous studies, "Symphyta" is paraphyletic. Within Apocrita, our analysis suggests a topology of Stephanoidea + (Ichneumonoidea + (Proctotrupomorpha + (Evanioidea + Aculeata))). Despite the huge amount of data, we identified several persistent problems in the Hymenoptera tree. Data coverage is still extremely low, and additional data have to be collected to reliably infer the phylogeny of Hymenoptera.</p> <p>Conclusions</p> <p>While we applied our bioinformatics pipeline to Hymenoptera, we designed the approach to be as general as possible. With this pipeline, it is possible to produce phylogenetic trees for any taxonomic group and to monitor new data and tree robustness in a taxon of interest. It therefore has great potential to meet the challenges of the phylogenomic era and to deepen our understanding of the tree of life.</p

An extreme case of plant-insect co-diversification: figs and fig-pollinating wasps

It is thought that speciation in phytophagous insects is often due to colonization of novel host plants, because radiations of plant and insect lineages are typically asynchronous. Recent phylogenetic comparisons have supported this model of diversification for both insect herbivores and specialized pollinators. An exceptional case where contemporaneous plant insect diversification might be expected is the obligate mutualism between fig trees (Ficus species, Moraceae) and their pollinating wasps (Agaonidae, Hymenoptera). The ubiquity and ecological significance of this mutualism in tropical and subtropical ecosystems has long intrigued biologists, but the systematic challenge posed by >750 interacting species pairs has hindered progress toward understanding its evolutionary history. In particular, taxon sampling and analytical tools have been insufficient for large-scale co-phylogenetic analyses. Here, we sampled nearly 200 interacting pairs of fig and wasp species from across the globe. Two supermatrices were assembled: on average, wasps had sequences from 77% of six genes (5.6kb), figs had sequences from 60% of five genes (5.5 kb), and overall 850 new DNA sequences were generated for this study. We also developed a new analytical tool, Jane 2, for event-based phylogenetic reconciliation analysis of very large data sets. Separate Bayesian phylogenetic analyses for figs and fig wasps under relaxed molecular clock assumptions indicate Cretaceous diversification of crown groups and contemporaneous divergence for nearly half of all fig and pollinator lineages. Event-based co-phylogenetic analyses further support the co-diversification hypothesis. Biogeographic analyses indicate that the presentday distribution of fig and pollinator lineages is consistent with an Eurasian origin and subsequent dispersal, rather than with Gondwanan vicariance. Overall, our findings indicate that the fig-pollinator mutualism represents an extreme case among plant-insect interactions of coordinated dispersal and long-term co-diversification

The SuperCam Instrument Suite on the Mars 2020 Rover: Science Objectives and Mast-Unit Description

On the NASA 2020 rover mission to Jezero crater, the remote determination of the texture, mineralogy and chemistry of rocks is essential to quickly and thoroughly characterize an area and to optimize the selection of samples for return to Earth. As part of the Perseverance payload, SuperCam is a suite of five techniques that provide critical and complementary observations via Laser-Induced Breakdown Spectroscopy (LIBS), Time-Resolved Raman and Luminescence (TRR/L), visible and near-infrared spectroscopy (VISIR), high-resolution color imaging (RMI), and acoustic recording (MIC). SuperCam operates at remote distances, primarily 2-7 m, while providing data at sub-mm to mm scales. We report on SuperCam's science objectives in the context of the Mars 2020 mission goals and ways the different techniques can address these questions. The instrument is made up of three separate subsystems: the Mast Unit is designed and built in France; the Body Unit is provided by the United States; the calibration target holder is contributed by Spain, and the targets themselves by the entire science team. This publication focuses on the design, development, and tests of the Mast Unit; companion papers describe the other units. The goal of this work is to provide an understanding of the technical choices made, the constraints that were imposed, and ultimately the validated performance of the flight model as it leaves Earth, and it will serve as the foundation for Mars operations and future processing of the data.In France was provided by the Centre National d'Etudes Spatiales (CNES). Human resources were provided in part by the Centre National de la Recherche Scientifique (CNRS) and universities. Funding was provided in the US by NASA's Mars Exploration Program. Some funding of data analyses at Los Alamos National Laboratory (LANL) was provided by laboratory-directed research and development funds