A scientific basis for restoring fish spawning habitat in the St. Clair and Detroit Rivers of the Laurentian Great Lakes

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/110848/1/rec12159.pd

Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency

As organisms adaptively evolve to a new environment, selection results in the improvement of certain traits, bringing about an increase in fitness. Trade-offs may result from this process if function in other traits is reduced in alternative environments either by the adaptive mutations themselves or by the accumulation of neutral mutations elsewhere in the genome. Though the cost of adaptation has long been a fundamental premise in evolutionary biology, the existence of and molecular basis for trade-offs in alternative environments are not well-established. Here, we show that yeast evolved under aerobic glucose limitation show surprisingly few trade-offs when cultured in other carbon-limited environments, under either aerobic or anaerobic conditions. However, while adaptive clones consistently outperform their common ancestor under carbon limiting conditions, in some cases they perform less well than their ancestor in aerobic, carbon-rich environments, indicating that trade-offs can appear when resources are non-limiting. To more deeply understand how adaptation to one condition affects performance in others, we determined steady-state transcript abundance of adaptive clones grown under diverse conditions and performed whole-genome sequencing to identify mutations that distinguish them from one another and from their common ancestor. We identified mutations in genes involved in glucose sensing, signaling, and transport, which, when considered in the context of the expression data, help explain their adaptation to carbon poor environments. However, different sets of mutations in each independently evolved clone indicate that multiple mutational paths lead to the adaptive phenotype. We conclude that yeasts that evolve high fitness under one resource-limiting condition also become more fit under other resource-limiting conditions, but may pay a fitness cost when those same resources are abundant

A community challenge to evaluate RNA-seq, fusion detection, and isoform quantification methods for cancer discovery

The accurate identification and quantitation of RNA isoforms present in the cancer transcriptome is key for analyses ranging from the inference of the impacts of somatic variants to pathway analysis to biomarker development and subtype discovery. The ICGC-TCGA DREAM Somatic Mutation Calling in RNA (SMC-RNA) challenge was a crowd-sourced effort to benchmark methods for RNA isoform quantification and fusion detection from bulk cancer RNA sequencing (RNA-seq) data. It concluded in 2018 with a comparison of 77 fusion detection entries and 65 isoform quantification entries on 51 synthetic tumors and 32 cell lines with spiked-in fusion constructs. We report the entries used to build this benchmark, the leaderboard results, and the experimental features associated with the accurate prediction of RNA species. This challenge required submissions to be in the form of containerized workflows, meaning each of the entries described is easily reusable through CWL and Docker containers at https://github.com/SMC-RNA-challenge. A record of this paper's transparent peer review process is included in the supplemental information

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

New light on the variability of hunting equipment in the Gravettian

Hunting is commonly believed to have been one of the central aspects in the lives of Palaeolithic groups and it is therefore an integral part of almost any attempt to explain the archaeological record. Different methods are used to understand prey selection (archaeozoology), to identify lithic or osseous armatures (use-wear analysis) and to reconstruct their production sequences (chaîne opératoire analysis). Despite these achievements, our current methods tell us little about the overall design of hunting weapons and their change through time, which would be a key aspect for a true reconstruction of Palaeolithic hunting practices. In this contribution, we argue that this methodological gap can be bridged and weapon design (projecting modes and hafting arrangements) reconstructed. As an example of exploiting the full potential of lithic armatures, we present the results of a collaborative project which aims at identifying possible changes in weapon design and use and at understanding their links with morphological variation of lithic armatures within Gravettian industries. Our approach represents a strong integration of morphological, technological and functional analyses supported by a multi-step experimental program. The archaeological material consists of tanged points from Maisières-Canal (Belgium, 28 000 BP) and microgravette points from Ormesson - les Bossats (France, 26 500 BP) and Abri Pataud (France, 24 000 BP). The results provide a more profound understanding of the weapon systems the tanged points and microgravette points were part of, including their mode of propulsion, and shed new light on the evolution of these systems during the Gravettian. We argue that detailed data on organisation and operation of hunting equipment can help us understand certain major technological changes observed in the Upper Palaeolithic

Lake sturgeon spawning habitat in the Big Manistee River, Michigan

Spawning sites of lake sturgeon Acipenser fulvescens were verified using egg collection mats in the Big Manistee River in northwestern lower Michigan. Photographs taken by a fixed-position underwater video camera were used to characterize the substrate at egg mat locations. A total of 3,913 lake sturgeon eggs were captured at two discrete spawning locations in 2003 and 2004. Spawning locations consisted of 34-44% cobble and 0.04-8% sand, and nonspawning locations consisted of 2-43% cobble and 0.16-7% sand. Shannon diversity indices describing substrate heterogeneity at spawning locations were statistically higher than those for nonspawning locations in 2003 (P = 0.002). Four spawning events (one in 2003 and three in 2004) were documented at water temperatures ranging from 11.1°C to 14.8°C and egg incubation periods ranging from 6 to 10 d. Depth at spawning sites was 1.5-3.0 m, average water velocity was 0.34-1.32 m/s, and near-substrate water velocity was 0.08-1.26 m/s. The topography of the Big Manistee River channel appears to have been altered by manipulated river flows, resulting in the development of barchans (ridges or shelves along the river bottom) in the region utilized for spawning. This study is the first to document lake sturgeon spawning success in the Big Manistee River and identify the specific characteristics of spawning bed material used as well as the presence of barchans that may produce eddies or turbulent irregular flows that affect egg dispersal and survival. © Copyright by the American Fisheries Society 2008

Chemical and biological recovery from acid deposition within the Honnedaga Lake watershed, New York, USA

Abstract Honnedaga Lake in the Adirondack region of New York has sustained a heritage brook trout population despite decades of atmospheric acid deposition. Detrimental impacts from acid deposition were observed from 1920 to 1960 with the sequential loss of acid-sensitive fishes, leaving only brook trout extant in the lake. Open-lake trap net catches of brook trout declined for two decades into the late 1970s, when brook trout were considered extirpated from the lake but persisted in tributary refuges. Amendments to the Clean Air Act in 1990 mandated reductions in sulfate and nitrogen oxide emissions. By 2000, brook trout had re-colonized the lake coincident with reductions in surface-water sulfate, nitrate, and inorganic monomeric aluminum. No changes have been observed in surfacewater acid-neutralizing capacity (ANC) or calcium concentration. Observed increases in chlorophyll a and decreases in water clarity reflect an increase in phytoplankton abundance. The zooplankton community exhibits low species richness, with a scarcity of acidsensitive Daphnia and dominance by acid-tolerant copepods. Trap net surveys indicate that relative abundance of adult brook trout population has significantly increased since the 1970s. Brook trout are absent in 65 % of tributaries that are chronically acidified with ANC of &lt;0 μeq/L and toxic aluminum levels (&gt;2 μmol/ L). Given the current conditions, a slow recovery of chemistry and biota is expected in Honnedaga Lake and its tributaries. We are exploring the potential to accelerate the recovery of brook trout abundance in Honnedaga Lake through lime applications to chronically and episodically acidified tributaries

A structured approach to remediation site assessment: lessons from 15 years of fish spawning habitat creation in the St. Clair‐Detroit River System

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/168267/1/rec13359.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/168267/2/rec13359_am.pd

Probability (mean±95% confidence interval) of navigation channel use by acoustic-tagged Lake Sturgeon in the lower Detroit and St. Clair rivers when analyses included and excluded the extrapolated Livingstone Channel passage data.

<p>Upstream and downstream passages were pooled because direction of sturgeon movement for the extrapolated sturgeon passage data was unknown. Expected probabilities of navigation channel use under the null model are shown as dashed horizontal lines.</p

Path use (% of observed passages) by acoustic-tagged Lake Sturgeon in the lower Detroit (left panel) and St. Clair (right panel) rivers.

<p>Total number of passages was 280 in the lower Detroit River and 404 in the lower St. Clair River. Movement pathways through navigation channels are shown in red. Lake Sturgeon moving upstream at Sugar Island in the lower Detroit River turned eastward and entered the Livingstone navigation channel (solid path) rather than continuing along the expected path (dashed extension) towards Stony Island.</p