Brook trout unfiltered

Non-clone filtered (unfiltered) VCF file of brook trout genotype data. VCF files were generated using stacks 2.46 with minimal filters (STACKS flags = -r 0.3, --min_maf 0.05). Data was generated using the SbfI enzyme, methods outlined in Ali et al. (2016)and prepared in the Genomic Variation Lab at the University of California--Davis and sequenced on Illumina NextSeq 500 (PE 75 bp reads, 96 samples/lane) at the Cornell Institute of Biotechnolog

Walleye clone filtered

Clone filtered (filtered) VCF file of walleye genotype data. VCF files were generated using stacks 2.46 with minimal filters (STACKS flags = -r 0.3, --min_maf 0.05). Data generated using the SbfI enzyme, methods outlined in Ali et al. (2016) prepared in the Larson Laboratory at the University of Wisconsin-Stevens Point and sequenced on a HiSeq 4000 (PE 150bp reads, 192 samples/lane) at the Michigan State Genomics Core Facility

Cisco clone filtered

Clone filtered (filtered) VCF file of cisco genotype data. VCF files were generated using stacks 2.46 with minimal filters (STACKS flags = -r 0.3, --min_maf 0.05). Data generated using the SbfI enzyme, methods outlined in Ali et al. (2016) prepared in the Larson Laboratory at the University of Wisconsin-Stevens Point and sequenced on a HiSeq 4000 (PE 150bp reads, 96 samples/lane) at the Michigan State Genomics Core Facility

Cisco unfiltered

Non-clone filtered (unfiltered) VCF file of cisco genotype data. VCF files were generated using stacks 2.46 with minimal filters (STACKS flags = -r 0.3, --min_maf 0.05). Data generated using the SbfI enzyme, methods outlined in Ali et al. (2016) prepared in the Larson Laboratory at the University of Wisconsin-Stevens Point and sequenced on a HiSeq 4000 (PE 150bp reads, 96 samples/lane) at the Michigan State Genomics Core Facility

Genomics and 20 years of sampling reveal phenotypic differences between subpopulations of outmigrating Central Valley Chinook salmon

Abstract Intraspecific diversity plays a critical role in the resilience of Chinook salmon populations. California's Central Valley (CV) historically hosted one of the most diverse population complexes of Chinook salmon in the world. However, anthropogenic factors have dramatically decreased this diversity, with severe consequences for population resilience. Here we use next generation sequencing and an archive of thousands of tissue samples collected across two decades during the juvenile outmigration to evaluate phenotypic diversity between and within populations of CV Chinook salmon. To account for highly heterogeneous sample qualities in the archive dataset, we develop and test an approach for population and subpopulation assignments of CV Chinook salmon that allows inclusion of relatively low‐quality samples while controlling error rates. We find significantly distinct outmigration timing and body size distributions for each population and subpopulation. Within the archive dataset, spring run individuals that assigned to the Mill and Deer Creeks subpopulation exhibited an earlier and broader outmigration distribution as well as larger body sizes than individuals that assigned to the Butte Creek subpopulation. Within the fall run population, individuals that assigned to the late‐fall run subpopulation also exhibited an earlier and broader outmigration distribution and larger body sizes than other fall run fish in our dataset. These results highlight the importance of distinct subpopulations for maintaining remaining diversity in CV Chinook salmon, and demonstrates the power of genomics‐based population assignments to aid the study and management of intraspecific diversity

A systematic review of context bias in invasion biology

<div><p>The language that scientists use to frame biological invasions may reveal inherent bias—including how data are interpreted. A frequent critique of invasion biology is the use of value-laden language that may indicate context bias. Here we use a systematic study of language and interpretation in papers drawn from invasion biology to evaluate whether there is a link between the framing of papers and the interpretation of results. We also examine any trends in context bias in biological invasion research. We examined 651 peer-reviewed invasive species competition studies and implemented a rigorous systematic review to examine bias in the presentation and interpretation of native and invasive competition in invasion biology. We predicted that bias in the presentation of invasive species is increasing, as suggested by several authors, and that bias against invasive species would result in misinterpreting their competitive dominance in correlational observational studies compared to causative experimental studies. We indeed found evidence of bias in the presentation and interpretation of invasive species research; authors often introduced research with invasive species in a negative context and study results were interpreted against invasive species more in correlational studies. However, we also found a distinct decrease in those biases since the mid-2000s. Given that there have been several waves of criticism from scientists both inside and outside invasion biology, our evidence suggests that the subdiscipline has somewhat self-corrected apparent biases.</p></div

Papers that used a boilerplate introduction remained constant in reporting invasive species as better competitors than natives whereas those that using a theoretical introduction declined significantly in reporting invasive species as better competitors.

<p>Papers that used a boilerplate introduction remained constant in reporting invasive species as better competitors than natives whereas those that using a theoretical introduction declined significantly in reporting invasive species as better competitors.</p

The percentage of invasive species papers that used boilerplate introductions peaked in the mid-to-late 2000s.

<p>This patterning may reflect the influence of several papers published 2003–2005 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182502#pone.0182502.ref006" target="_blank">6</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182502#pone.0182502.ref008" target="_blank">8</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0182502#pone.0182502.ref010" target="_blank">10</a>] that criticized the use of negative and militaristic language in invasive species papers.</p

Flow diagram of the search and study selection.

<p>Flow diagram of the search and study selection.</p

A systematic review of context bias in invasion biology - Fig 2

<p>Published studies reported invasive species as better competitors than natives equally between those that began with a 'boilerplate' introduction placing invasive species in a negative light (a). Conversely, observational studies more often reported invasive species competitively superior than did experimental studies (b). Given that observational data are correlational and more subject to interpretation than experimental data, the discrepancy seemed to indicate interpretation bias against invasive species.</p