Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies

info:eu-repo/semantics/publishe

Oyster NanoDrop DNA data

NanoDrop A260/280, A260/230, and yield estimates for genomic DNA of 24 adductor muscle samples extracted with 4 different methods

Data from: Modified low-salt CTAB extraction of high-quality DNA from contaminant rich tissues

The increasing use of high-throughput sequencing platforms has made the isolation of pure, high molecular weight DNA a primary concern for studies of a diverse range of organisms. Purification of DNA remains a significant challenge in many tissue and sample types due to various organic and inorganic molecules that co-precipitate with nucleic acids. Molluscs, for example, contain high concentrations of polysaccharides which often co-precipitate with DNA and can inhibit downstream enzymatic reactions. We modified a low-salt CTAB (MoLSC) extraction protocol to accommodate contaminant rich animal tissues and compared this method to a standard CTAB extraction protocol and two commercially available animal tissue DNA extraction kits using oyster adductor muscle. Comparisons of purity and molecular integrity showed that our in-house protocol yielded genomic DNA generally free of contaminants and shearing, whereas the traditional CTAB method and some of the commercial kits yielded DNA unsuitable for some applications of massively parallel sequencing (MPS). Our open-source MoLSC protocol provides a cost-effective, scalable, alternative DNA extraction method that can be easily optimized and adapted for sequencing applications in other contaminant rich samples

DNARatioData

Ratio of Native and Non-Native Plant DNA Instances Detected in the Small Mammal Scat Samples by Replicate and Mont

RodentPopSugarMapleRemovalWeaselPop

Comparison of Percent Total Sugar Maple Removed by Small Mammal Population Size and Weasel Populatio

Data from: Selective plant foraging and the top-down suppression of native diversity in a restored prairie

Clarifying what species are being consumed at what times can improve our understanding of how anthropogenic change affects food web dynamics, with implications for community assembly including restoration. This includes human-based changes to plant communities via species introductions, which can interact with consumer feeding preferences to indirectly alter assembly outcomes including reduced restoration success if planted species are preferentially targeted. We used DNA barcoding of plant material in rodent scat, combined with field-based feeding trials, rodent trapping, and rodent exclosures to test for dietary preferences and assembly impacts of native rodents on a restored and regionally rare tallgrass prairie of central North America. We examined whether native rodents preferred non-targeted and mostly non-native oldfield plants that are more locally abundant, thus protecting the rarer native planted species from consumption, or if rodents preferred native plants regardless of abundance. Our results supported the latter outcome. Barcoding revealed that native rodents consumed mostly non-planted oldfield species for ten months of the year (92% of the diet). The exceptions were August–September, when planted prairie species accounted for 87% of plants consumed and coincided with their peak seed production. Cafeteria trials suggested diet seasonality to be explained by food limitation – native prairie seeds were consumed year-round when made available. Non-targeted oldfield species thus appeared to be of sufficient quality to support rodent populations (peaking at 23 individuals ha−1 in summer), but without rescuing rarer prairie species from targeted granivory and resulting in reduced prairie diversity outside of experimental exclosures. Synthesis and applications. Our work illustrates how anthropogenic-based changes to producer communities may affect feeding pathways in grassland food webs, potentially facilitating establishment by non-target species via indirect consumer effects that can be difficult to detect. These findings suggest that rodents may reduce the restoration success of tallgrass prairie in our region, with some planted species likely to suffer future recruitment difficulties due to granivory. Managers may need to consider multiple trophic levels with restoration, not just the commonly planted producer communities but also the consumers and predators associated with them

ExclosureAbundanceRichnessData

Data for the Full Factorial Design of Mowed, Seeded, and Exclosed Considering Plant Abundance and Richness

CaptiveTrialSeedlingDamage

Seeding Damage (Rated Out of 5) Considering Seven Tallgrass Prairie Species Caused by Small Mammals Within an Enclosed Environment After 7 Day

12MonthSeedRemoval

Recorded Seed Removal (Out of 5) for Seven Tallgrass Prairie Species by Small Mammals Over 12 Months from the Tallgrass Prairie Environmen

CaptiveTrialSeedRemoval

Seed Removal (Out of 5) for 7 Tallgrass Prairie Species Caused by Small Mammals Within an Enclosed Environment Over 7 Day