An Integrative Approach to Phylogeography: Investigating the Effects of Ancient Seaways, Climate, and Historical Geology on Multi-Locus Phylogeographic Boundaries of the Arboreal Salamander (Aneides Lugubris)

Background: Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus data to reconstruct the evolutionary history of A. lugubris and to discover the geographic location of major genetic breaks within the species. We also used species distribution modeling and comparative phylogeography to better understand the environmental factors that have shaped the genetic history of A. lugubris. Results: We found six major mitochondrial clades in A. lugubris. Nuclear loci supported the existence of at least three genetically distinct groups, corresponding to populations north of the San Francisco Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the central coast and southern California. All of the genetic breaks in mitochondrial and nuclear loci corresponded to regions where historical barriers to dispersal have been observed in other species. Geologic or water barriers likely were the most important factors restricting gene flow among clades. Climatic unsuitability during glacial maximum may have contributed to the isolation of the mitochondrial clades in the central coast and southern California. A projection of our species distribution model to a future scenario with a moderate amount of climate change suggests that most of the range of A. lugubris will remain climatically suitable, but climatic conditions in the Sierra Nevada and low elevation areas in Southern California are likely to deteriorate. Conclusions: Aneides lugubris contains substantial cryptic genetic diversity as a result of historical isolation of populations. At least two (and perhaps three) evolutionarily significant units in A. lugubris merit protection; all six mitochondrial clades should be considered as management units within the species

Spatially Extended Low Ionization Emission Regions (LIERs) at z∼0.9z\sim0.9

We present spatially resolved emission diagnostics for eight $z\sim0.9$ galaxies that demonstrate extended low ionization emission-line regions (LIERs) over kpc scales. Eight candidates are selected based on their spatial extent and emission line fluxes from slitless spectroscopic observations with the HST/WFC3 G141 and G800L grisms in the well-studied GOODS survey fields. Five of the candidates (62.5%) are matched to X-ray counterparts in the \textit{Chandra X-Ray Observatory} Deep Fields. We modify the traditional Baldwin-Philips-Terlevich (BPT) emission line diagnostic diagram to use [SII]/(H$\alpha$+[NII]) instead of [NII]/H$\alpha$ to overcome the blending of [NII] and H$\alpha$+[NII] in the low resolution slitless grism spectra. We construct emission line ratio maps and place the individual pixels in the modified BPT. The extended LINER-like emission present in all of our candidates, coupled with X-Ray properties consistent with star-forming galaxies and weak [OIII]$\lambda$5007\AA\ detections, is inconsistent with purely nuclear sources (LINERs) driven by active galactic nuclei. While recent ground-based integral field unit spectroscopic surveys have revealed significant evidence for diffuse LINER-like emission in galaxies within the local universe $(z\sim0.04)$, this work provides the first evidence for the non-AGN origin of LINER-like emission out to high redshifts.Comment: 11 pages, 1 table, 6 figures, accepted for publication in the Astrophysics Journal (ApJ

Divergence of thermal physiological traits in terrestrial breeding frogs along a tropical elevational gradient

Critical thermal limits are thought to be correlated with the elevational distribution of species living in tropical montane regions, but with upper limits being relatively invariant compared to lower limits. To test this hypothesis, we examined the variation of thermal physiological traits in a group of terrestrial breeding frogs (Craugastoridae) distributed along a tropical elevational gradient. We measured the critical thermal maximum (CTmax; n = 22 species) and critical thermal minimum (CTmin; n = 14 species) of frogs captured between the Amazon floodplain (250 m asl) and the high Andes (3,800 m asl). After inferring a multilocus species tree, we conducted a phylogenetically informed test of whether body size, body mass, and elevation contributed to the observed variation in CTmax and CTmin along the gradient. We also tested whether CTmax and CTmin exhibit different rates of change given that critical thermal limits (and their plasticity) may have evolved differently in response to different temperature constraints along the gradient. Variation of critical thermal traits was significantly correlated with speciesâ elevational midpoint, their maximum and minimum elevations, as well as the maximum air temperature and the maximum operative temperature as measured across this gradient. Both thermal limits showed substantial variation, but CTmin exhibited relatively faster rates of change than CTmax, as observed in other taxa. Nonetheless, our findings call for caution in assuming inflexibility of upper thermal limits and underscore the value of collecting additional empirical data on speciesâ thermal physiology across elevational gradients.A widely held assumption is that climatic niches have not changed along the history of species, both within and among closely related species. Using a phylogenetic framework, this study documents high variability in both elevational distribution and tolerance to heat among closely related species. Our findings suggest that thermal traits in ectotherms can adjust rapidly and so cannot be simply extrapolated from relatives.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136724/1/ece32929_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136724/2/ece32929.pd

Dark energy constraints from cosmic shear power spectra: impact of intrinsic alignments on photometric redshift requirements

Cosmic shear constrains cosmology by exploiting the apparent alignments of pairs of galaxies due to gravitational lensing by intervening mass clumps. However galaxies may become (intrinsically) aligned with each other, and with nearby mass clumps, during their formation. This effect needs to be disentangled from the cosmic shear signal to place constraints on cosmology. We use the linear intrinsic alignment model as a base and compare it to an alternative model and data. If intrinsic alignments are ignored then the dark energy equation of state is biased by ~50 per cent. We examine how the number of tomographic redshift bins affects uncertainties on cosmological parameters and find that when intrinsic alignments are included two or more times as many bins are required to obtain 80 per cent of the available information. We investigate how the degradation in the dark energy figure of merit depends on the photometric redshift scatter. Previous studies have shown that lensing does not place stringent requirements on the photometric redshift uncertainty, so long as the uncertainty is well known. However, if intrinsic alignments are included the requirements become a factor of three tighter. These results are quite insensitive to the fraction of catastrophic outliers, assuming that this fraction is well known. We show the effect of uncertainties in photometric redshift bias and scatter. Finally we quantify how priors on the intrinsic alignment model would improve dark energy constraints.Comment: 14 pages and 9 figures. Replaced with final version accepted in "Gravitational Lensing" Focus Issue of the New Journal of Physics at http://www.iop.org/EJ/abstract/1367-2630/9/12/E0

Ring distributions leading to species formation: a global topographic analysis of geographic barriers associated with ring species

<p>Abstract</p> <p>Background</p> <p>In the mid 20^thcentury, Ernst Mayr and Theodosius Dobzhansky championed the significance of circular overlaps or ring species as the perfect demonstration of speciation, yet in the over 50 years since, only a handful of such taxa are known. We developed a topographic model to evaluate whether the geographic barriers that favor processes leading to ring species are common or rare, and to predict where other candidate ring barriers might be found.</p> <p>Results</p> <p>Of the 952,147 geographic barriers identified on the planet, only about 1% are topographically similar to barriers associated with known ring taxa, with most of the likely candidates occurring in under-studied parts of the world (for example, marine environments, tropical latitudes). Predicted barriers separate into two distinct categories: (i) single cohesive barriers (< 50,000 km²), associated with taxa that differentiate at smaller spatial scales (salamander: <it>Ensatina eschscholtzii</it>; tree: <it>Acacia karroo</it>); and (ii) composite barriers - formed by groups of barriers (each 184,000 to 1.7 million km²) in close geographic proximity (totaling 1.9 to 2.3 million km²) - associated with taxa that differentiate at larger spatial scales (birds: <it>Phylloscopus trochiloide</it>s and <it>Larus </it>(sp. <it>argentatus </it>and <it>fuscus</it>)). When evaluated globally, we find a large number of cohesive barriers that are topographically similar to those associated with known ring taxa. Yet, compared to cohesive barriers, an order of magnitude fewer composite barriers are similar to those that favor ring divergence in species with higher dispersal.</p> <p>Conclusions</p> <p>While these findings confirm that the topographic conditions that favor evolutionary processes leading to ring speciation are, in fact, rare, they also suggest that many understudied natural systems could provide valuable demonstrations of continuous divergence towards the formation of new species. Distinct advantages of the model are that it (i) requires no <it>a priori </it>information on the relative importance of features that define barriers, (ii) can be replicated using any kind of continuously distributed environmental variable, and (iii) generates spatially explicit hypotheses of geographic species formation. The methods developed here - combined with study of the geographical ecology and genetics of taxa in their environments - should enable recognition of ring species phenomena throughout the world.</p

Tomographic Magnification of Lyman Break Galaxies in The Deep Lens Survey

Using about 450,000 galaxies in the Deep Lens Survey, we present a detection of the gravitational magnification of z > 4 Lyman Break Galaxies by massive foreground galaxies with 0.4 < z < 1.0, grouped by redshift. The magnification signal is detected at S/N greater than 20, and rigorous checks confirm that it is not contaminated by any galaxy sample overlap in redshift. The inferred galaxy mass profiles are consistent with earlier lensing analyses at lower redshift. We then explore the tomographic lens magnification signal by splitting our foreground galaxy sample into 7 redshift bins. Combining galaxy-magnification cross-correlations and galaxy angular auto-correlations, we develop a bias-independent estimator of the tomographic signal. As a diagnostic of magnification tomography, the measurement of this estimator rejects a flat dark matter dominated Universe at > 7.5{\sigma} with a fixed \sigma_8 and is found to be consistent with the expected redshift-dependence of the WMAP7 {\Lambda}CDM cosmology.Comment: 12 pages, 9 figures, Accepted to MNRA

The clustering of massive galaxies at z~0.5 from the first semester of BOSS data

We calculate the real- and redshift-space clustering of massive galaxies at z~0.5 using the first semester of data by the Baryon Oscillation Spectroscopic Survey (BOSS). We study the correlation functions of a sample of 44,000 massive galaxies in the redshift range 0.4<z<0.7. We present a halo-occupation distribution modeling of the clustering results and discuss the implications for the manner in which massive galaxies at z~0.5 occupy dark matter halos. The majority of our galaxies are central galaxies living in halos of mass 10^{13}Msun/h, but 10% are satellites living in halos 10 times more massive. These results are broadly in agreement with earlier investigations of massive galaxies at z~0.5. The inferred large-scale bias (b~2) and relatively high number density (nbar=3e-4 h^3 Mpc^{-3}) imply that BOSS galaxies are excellent tracers of large-scale structure, suggesting BOSS will enable a wide range of investigations on the distance scale, the growth of large-scale structure, massive galaxy evolution and other topics.Comment: 11 pages, 12 figures, matches version accepted by Ap

A novel method to quantify fibrin-fibrin and fibrin-α2AP cross-links in thrombi formed from human trauma patient plasma.

The widespread use of the anti-fibrinolytic agent, tranexamic acid (TXA), interferes with the quantification of fibrinolysis by dynamic laboratory assays such as clot lysis, making it difficult to measure fibrinolysis in many trauma patients. At the final stage of coagulation, Factor XIIIa (FXIIIa) catalyses the formation of fibrin-fibrin and fibrin-α2-antiplasmin (α2AP) cross-links which increases clot mechanical strength and resistance to fibrinolysis. Here, we develop a method to quantify fibrin-fibrin and fibrin-α2AP cross-links that avoids the challenges posed by TXA in determining fibrinolytic resistance in conventional assays. Fibrinogen alpha chain (FGA-FGA), fibrinogen gamma chain (FGG-FGG) and FGA-α2AP cross-links were quantified using liquid-chromatography-mass spectrometry (LC-MS) and parallel reaction monitoring (PRM) in paired plasma samples from trauma patients pre- and post-fibrinogen replacement. Differences in the abundance of cross-links in trauma patients receiving cryoprecipitate (cryo) or fibrinogen concentrate (Fg-C) were analysed. The study found that the abundance of cross-links was significantly increased in trauma patients post-cryo, but not Fg-C, transfusion (p < 0.0001). The abundance of cross-links was positively correlated with the toughness of individual fibrin fibres, the peak thrombin concentration and FXIII antigen (p < 0.05). We have developed a novel method that allows us to quantify fibrin cross-links in trauma patients who have received TXA, providing an indirect measure of fibrinolytic resistance. Using this novel approach we have avoided the effect of TXA and shown that cryo increases fibrin-fibrin and fibrin-α2AP cross-linking when compared to Fg-C, highlighting the importance of FXIII in clot formation and stability in trauma patients