Phylogenetic and morphometric analysis of speckled dace (Rhinichthys osculus) from Oregon's Great Basin

Speckled dace (Rhinichthys osculus) is a small cyprinid that is geographically widespread throughout western North America, and the most frequently occurring sh in Oregon. Because of the genetic and morphological variation in this species across its range, it has been referred to as a "species complex" and no revision to its taxonomy has occurred since 1984. We investigated the phylogenetics, population genetics, and morphometrics of speckled dace from Oregon's Great Basin region to describe the genetic and morphological variation of speckled dace, identify any unrecognized taxonomic diversity, and to test the validity of Foskett Spring speckled dace, an undescribed putative subspecies that occurs in a single spring within Warner Valley in Southeast Oregon. We collected morphometric and genetic data from Foskett Spring and the surrounding basins (Warner, Goose Lake, Lake Abert, Silver Lake, and Malheur), as well as Stinking Lake Spring (located within Malheur). We created Maximum Likelihood and Bayesian phylogenetic trees from mitochondrial ND2 and nuclear S7 sequence data and genotyped eight microsatellite loci. We identi fied three genetic clades within our samples area that warrant species-level status: Malheur stream dace, Stinking Lake Spring dace, and dace from the other four basins. Population structure was detected at the basin-level and separated Foskett Spring dace from other dace in Warner Valley. The geometric and linear morphometric data indicate that overall body shape did not di ffer among sh occupying streams in these basins, except for in Warner Valley dace, which had larger heads. The two populations of spring dace were distinct from stream dace by having more posterior dorsal fins, and were distinct from each other in head size. With this data we recommend species status for Malheur stream dace, Stinking Lake Spring dace, and dace from the other basins. Because of the strong morphological and slight genetic distinction of Foskett Spring speckled dace, ESU status is recommended, and this population will likely continue to be protected under the ESA

Cut and paste invariants of manifolds via algebraic K-theory

Recent work of Jonathan Campbell and Inna Zakharevich has focused on building machinery for studying scissors congruence problems via algebraic $K$-theory, and applying these tools to studying the Grothendieck ring of varieties. In this paper we give a new application of their framework: we construct a $K$-space that recovers the classical $\mathrm{SK}$ ("schneiden und kleben," German for "cut and paste") groups for manifolds on $\pi_0$, and we construct a derived version of the Euler characteristic

Attentional bias for negative, positive, and threat words in current and remitted depression

Background The aim of this study was to improve our understanding of the underlying mechanisms in the maintenance of depression. We examined attentional bias (AB) for negative and positive adjectives and general threat words in strictly-defined clinical groups of participants with pure Major Depressive Disorder (MDD) without a history of anxiety disorders (AD), mixed MDD and AD, and remitted participants. Method We investigated both stimulus specificity and time course of AB in these groups, adopting a cross-sectional design. Data were drawn from the large scale Netherlands Study of Depression and Anxiety (NESDA), from which we selected all participants with pure current MDD without a history of AD (n = 29), all participants with current MDD and co-morbid AD(s) (n = 86), all remitted MDD participants (n = 294), and a comparison group without (a history of) MDD or ADs (n = 474). AB was measured with an Exogenous Cueing Task covering short and long presentation times (500 and 1250 ms) and 4 stimulus types (negative, positive, threat, neutral). Results Both traditional and trial level (dynamic) AB scores failed to show an AB for negative adjectives in participants with MDD or mixed MDD/AD. Specifically for long duration trials (1250 ms), remitted participants showed a larger AB traditional score (albeit the actual score still being negative) than the comparison group. The mixed MDD/AD group showed a higher trial-level AB score away from positive adjectives (1250 ms) than the comparisons. In addition, the mixed MDD/AD group showed higher and more variable trial-level AB scores away from short and towards longer presented general threat words together with a non-significant tendency to show less negative traditional AB scores for threat trials (500 ms) than the comparison group. Conclusions All in all, the findings do not corroborate the view that an AB towards negative or away from positive adjectives is critically involved in currently depressed individuals. Yet, the relatively high (less negative) AB score for negative adjectives in remitted individuals points to the possibility that an AB for negative information may be involved as a risk factor in the recurrence of MDD

The Missing Luminous Blue Variables and the Bistability Jump

We discuss an interesting feature of the distribution of luminous blue variables on the H-R diagram, and we propose a connection with the bistability jump in the winds of early-type supergiants. There appears to be a deficiency of quiescent LBVs on the S Dor instability strip at luminosities between log L/Lsun = 5.6 and 5.8. The upper boundary, is also where the temperature-dependent S Dor instability strip intersects the bistability jump at about 21,000 K. Due to increased opacity, winds of early-type supergiants are slower and denser on the cool side of the bistability jump, and we postulate that this may trigger optically-thick winds that inhibit quiescent LBVs from residing there. We conduct numerical simulations of radiation-driven winds for a range of temperatures, masses, and velocity laws at log L/Lsun=5.7 to see what effect the bistability jump should have. We find that for relatively low stellar masses the increase in wind density at the bistability jump leads to the formation of a modest to strong pseudo photosphere -- enough to make an early B-type star appear as a yellow hypergiant. Thus, the proposed mechanism will be most relevant for LBVs that are post-red supergiants. Yellow hypergiants like IRC+10420 and rho Cas occupy the same luminosity range as the ``missing'' LBVs, and show apparent temperature variations at constant luminosity. If these yellow hypergiants do eventually become Wolf-Rayet stars, we speculate that they may skip the normal LBV phase, at least as far as their apparent positions on the HR diagram are concerned.Comment: 20 pages, 4 figs, accepted by Ap

A Target Enrichment Bait Set for Studying Relationships among Ostariophysan Fishes

© 2020 by the American Society of Ichthyologists and Herpetologists. Target enrichment of conserved nuclear loci has helped reconstruct evolutionary relationships among a wide variety of species. While there are preexisting bait sets to enrich a few hundred loci across all fishes or a thousand loci from acanthomorph fishes, no bait set exists to enrich large numbers (\u3e1,000 loci) of ultraconserved nuclear loci from ostariophysans, the second largest actinopterygian superorder. In this study, we describe how we designed a bait set to enrich 2,708 ultraconserved nuclear loci from ostariophysan fishes by combining an existing genome assembly with low coverage sequence data collected from two ostariophysan lineages. We perform a series of enrichment experiments using this bait set across the ostariophysan tree of life, from the deepest splits among the major groups (\u3e150 Ma) to more recent divergence events that have occurred during the last 50 million years. Our results demonstrate that the bait set we designed is useful for addressing phylogenetic questions from the origin of crown ostariophysans to more recent divergence events, and our in silico results suggest that this bait set may be useful for addressing evolutionary questions in closely related groups of fishes, like Clupeiformes

What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)?

The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long-lived species with few geographic barriers to dispersal. Worldwide mtDNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear whether this female philopatry is due to geographic regions or social groups, or how this might vary on a worldwide scale. To answer these questions, we combined mtDNA information for 1091 previously published samples with 542 newly obtained DNA profiles (394-bp mtDNA, sex, 13 microsatellites) including the previously unsampled Indian Ocean, and social group information for 541 individuals. We found low mtDNA diversity (π = 0.430%) reflecting an expansion event <80 000 years bp, but strong differentiation by ocean, among regions within some oceans, and among social groups. In comparison, microsatellite differentiation was low at all levels, presumably due to male-mediated gene flow. A hierarchical amova showed that regions were important for explaining mtDNA variance in the Indian Ocean, but not Pacific, with social group sampling in the Atlantic too limited to include in analyses. Social groups were important in partitioning mtDNA and microsatellite variance within both oceans. Therefore, both geographic philopatry and social philopatry influence genetic structure in the sperm whale, but their relative importance differs by sex and ocean, reflecting breeding behaviour, geographic features and perhaps a more recent origin of sperm whales in the Pacific. By investigating the interplay of evolutionary forces operating at different temporal and geographic scales, we show that sperm whales are perhaps a unique example of a worldwide population expansion followed by rapid assortment due to female social organization.Genetic samples from the 'Voyage of the Odyssey' were collected under permit #0751-1614 from the US National Marine Fisheries Service

A High-Quality Bonobo Genome Refines The Analysis Of Hominid Evolution

The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation(1,2). Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes(1,3-5) and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome

Scientific assessment of the quality of OSIRIS images

OSIRIS, the scientific imaging system onboard the ESA Rosetta spacecraft, has been imaging the nucleus of comet 67P/Churyumov-Gerasimenko and its dust and gas environment since March 2014. The images serve different scientific goals, from morphology and composition studies of the nucleus surface, to the motion and trajectories of dust grains, the general structure of the dust coma, the morphology and intensity of jets, gas distribution, mass loss, and dust and gas production rates. We present the calibration of the raw images taken by OSIRIS and address the accuracy that we can expect in our scientific results based on the accuracy of the calibration steps that we have performed. Methods. We describe the pipeline that has been developed to automatically calibrate the OSIRIS images. Through a series of steps, radiometrically calibrated and distortion corrected images are produced and can be used for scientific studies. Calibration campaigns were run on the ground before launch and throughout the years in flight to determine the parameters that are used to calibrate the images and to verify their evolution with time. We describe how these parameters were determined and we address their accuracy. Results. We provide a guideline to the level of trust that can be put into the various studies performed with OSIRIS images, based on the accuracy of the image calibration