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(LPWG), Legume Phylogeny Working Group; Bruneau, Anne; Azani, Nasim; Babineau, Marielle; Gagnon, Edeline; Sinou, Carole; Steeves, Royce; Zimmerman, Erin; Bailey, C. Donovan; Kovar, Lynsey; Nageswara-Rao, Madhugiri; Banks, Hannah; Clark, RuthP.; De La Estrella, Manuel; Gasson, Peter; Kite, GeoffreyC.; Klitgaard, BenteB.; Lewis, GwilymP.; Neves, Danilo; Prenner, Gerhard; Rico-Arce, María de Lourdes; Barbosa, ArianeR.; López-Roberts, Maria Cristina; de Queiroz, Luciano Paganucci; Ribeiro, PétalaG.; Snak, Cristiane; Cruz, Daiane Trabuco da; Pinto, Rafael Barbosa; Candido, Elisa; Azevedo Tozzi, Ana Maria Goulart de; Kochanovski, FábioJ.; Boatwright, JamesS.; Borges, LeonardoM.; Brown, GillianK.; Cardoso, Domingos; Ramos, Gustavo; Chung, Kuo-Fang; Conceição, Adilva deS.; Santos-Silva, Juliana; de Souza, ÉlviaR.; Crisp, Michael; Gunn, Bee; Delgado-Salinas, Alfonso; Dexter, KyleG.; Doyle, JeffJ.; Duminil, Jérôme; Ojeda, DarioI.; Egan, AshleyN.; Vatanparast, Mohammad; Falcão, MarcusJ.; de Lima, HaroldoC.; Mansano, VidalF.; Ranzato Filardi, FabianaL.; Filatov, DmitryA.; Nevado, Bruno; Fortuna-Perez, Ana Paula; Rando, Juliana Gastaldello; Harris, David; Haston, Elspeth; Mackinder, Barbara; Pennington, R. Toby; Hawkins, JulieA.; Mattapha, Sawai; Hughes, ColinE.; Koenen, ErikJ.M.; Iganci, JoãoR.V.; Javadi, Firouzeh; Kanu, Sheku Alfred; Kazempour-Osaloo, Shahrokh; Lavin, Matt; Roux, Marianne le; Maia, Vitor Hugo; Malécot, Valéry; Miller, JosephT.; Mitsuyuki, Chika; Tagane, Shuichiro; Toyama, Hironori; Yahara, Tetsukazu; Murphy, DanielJ.; Prado, DariénE.; Sanderson, MichaelJ.; São-Mateus, WallaceM.B.; Silva, MarcosJ.S.; Sprent, Janet; Steele, KellyP.; Steier, JuliaE.; Wojciechowski, MartinF.; Stirton, CharlesH.; Torke, BenjaminM.; Wieringa, JanJ.; Wink, Michael; Yi, Tingshuang — 2018-01-12 The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most widely sequenced across the legumes, and in most legume lineages, this gene region is sufficiently variable to yield well-supported clades. This analysis resolves the same major clades as in other phylogenies of whole plastid and nuclear gene sets (with much sparser taxon sampling). Our analysis improves upon previous studies that have used large phylogenies of the Leguminosae for addressing evolutionary questions, because it maximises generic sampling and provides a phylogenetic tree that is based on a fully curated set of sequences that are vouchered and taxonomically validated. The phylogenetic trees obtained and the underlying data are available to browse and download, facilitating subsequent analyses that require evolutionary trees. Here we propose a new community-endorsed classification of the family that reflects the phylogenetic structure that is consistently resolved and recognises six subfamilies in Leguminosae: a recircumscribed Caesalpinioideae DC., Cercidoideae Legume Phylogeny Working Group (stat. nov.), Detarioideae Burmeist., Dialioideae Legume Phylogeny Working Group (stat. nov.), Duparquetioideae Legume Phylogeny Working Group (stat. nov.), and Papilionoideae DC. The traditionally recognised subfamily Mimosoideae is a distinct clade nested within the recircum-scribed Caesalpinioideae and is referred to informally as the mimosoid clade pending a forthcoming formal tribal and/or clade-based classification of the new Caesalpinioideae. We provide a key for subfamily identification, descriptions with diagnostic charactertistics for the subfamilies, figures illustrating their floral and fruit diversity, and lists of genera by subfamily. This new classification of Leguminosae represents a consensus view of the international legume systematics community; it invokes both compromise and practicality of use.

Schneider, Stefan; Steeves, Royce; Newmaster, Steven; MacDougall, Andrew S.; Newmaster, Steve — 2018-01-20 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.

Bernatchez, Simon; Xuereb, Amanda; Laporte, Martin; Benestan, Laura; Steeves, Royce; Laflamme, Mark; Bernatchez, Louis; Mallet, Martin — 2018-11-20 Interactions between environmental factors and complex life-history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11 321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean FST= 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDA) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype–environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster.

Arseneau, Jean-Rene; Steeves, Royce; Laflamme, Mark — 2016-10-19 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.