Phylogenetic Relationships in Tribe Cariceae (Cyperaceae) Based on Nested Analyses of Four Molecular Data Sets

Phylogenetic reconstruction for Carex and relatives in tribe Cariceae is complicated by species richness and nearly cosmopolitan distribution. In this investigation, our main objective was to estimate evolutionary relationships in tribe Cariceae using DNA sequence data from two spacer regions in nuclear ribosomal genes (ITS and ETS-1f) combined with noncoding chloroplast DNA (trnL intron, trnL–trnF intergenic spacer, and trnE–trnD intergenic spacers). Parsimony analyses of separate and combined data and Bayesian analysis of the combined data matrix revealed strong support for monophyly of tribe Cariceae and for monophyly of two major lineages, one comprising principally Carex subgen. Carex and Vigneastra, and the other representing subgen. Vignea. A third clade with representatives from Kobresia and Uncinia, along with Cymophyllus fraserianus, Carex curvula, and several unispicate Carex received weak-to-moderate support. A small clade comprising Schoenoxiphium and two unispicate carices was placed as sister to the clades comprising multispicate Carex species in the parsimony analysis, but sister to the clade of Kobresia, Uncinia, and unispicate Carex in the Bayesian analysis. Two large widespread groups within subgen. Carex, sect. Hymenochlaenae and sect. Physocarpae s.l. (‘‘bladder sedges ), were highly polyphyletic, while ten clades that grouped species from two or more sections were each strongly supported as monophyletic. Within subgen. Vignea, three sections were strongly supported as monophyletic while sects. Phaestoglochin and Vulpinae were polyphyletic. Adding the variable ETS-1f region improved resolution and bootstrap support values over previous studies, but many of the characters supporting major branches came from the trnL region

Phylogenetic Implications of a Unique 5.8S nrDNA Insertion in Cyperaceae

The purpose of this study was to assess the phylogenetic utility of a large insertion (3 bp) in the 5.8S gene of nuclear ribosomal DNA (nrDNA) in Cyperaceae and selected Juncaceae. This was done by reconstructing the character evolution of the insertion on a phylogeny derived from rbcL sequences. Results suggest that the insertion was gained once at the base of Cyperaceae followed by multiple losses in its most-derived taxa. Despite several homoplastic losses (CI = 0.20), the pattern of insertion loss (RI = 0.88), and base pair variation within the insertion were useful for defining sedge clades at various taxonomic levels. For example, whereas a loss of the insertion appeared to characterize a major terminal clade within Cyperaceae, both an insertion loss and sequence variation were consistent with infrageneric clades previously discovered in an ITS phylogeny of Eleocharis. The presence/absence of the insertion also supported previous conclusions based on morphological and molecular data that tribe Scirpeae and Scirpus s.l. are polyphyletic. In the context of our current understanding of Cyperaceae relationships, evolutionary patterns related to this insertion provide additional support for groups defined in prior phylogenetic analyses. The present analysis also suggests that the controversial position of Oxychloe andina (Juncaceae) in previous rbcL analyses, as sister to Cyperaceae (Y12978) or as nested within Cyperaceae (U49222), is due to the fact that Y12978 is a Juncaceae/Cyperaceae chimera, whereas U49222 is the sequence of a Cyperaceae contaminant. When U49222 is excluded from analyses and the Cyperaceae portion of Y12978 is removed, Juncaceae and Cyperaceae are monophyletic with Oxychloe positioned within a Juncaceae clade of single-flowered genera

A new classification of Cyperaceae (Poales) supported by phylogenomic data

Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology due to their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including multiple origins of C4 photosynthesis and holocentric chromosomes. Goetghebeur′s seminal work on Cyperaceae published in 1998 provided the most recent complete classification at tribal and generic level, based on a morphological study of Cyperaceae inflorescence, spikelet, flower, and embryo characters, plus anatomical and other information. Since then, several family-level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after the last comprehensive classification of the family, we present the first family-wide phylogenomic study of Cyperaceae based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. In addition, 62 accessions available from GenBank were mined for overlapping reads and included in the phylogenomic analyses. Informed by this backbone phylogeny, a new classification for the family at the tribal, subtribal, and generic levels is proposed. The majority of previously recognized suprageneric groups are supported, and for the first time, we establish support for tribe Cryptangieae as a clade including the genus Koyamaea. We provide a taxonomic treatment including identification keys and diagnoses for the 2 subfamilies, 24 tribes, and 10 subtribes, and basic information on the 95 genera. The classification includes five new subtribes in tribe Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae, and Oreobolinae

Targeted sequencing supports morphology and embryo features in resolving the classification of Cyperaceae tribe Fuireneae s.l.

Molecular phylogenetic studies based on Sanger sequences have shown that Cyperaceae tribe Fuireneae s.l. is paraphyletic. However, taxonomic sampling in these studies has been poor, topologies have been inconsistent, and support for the backbone of trees has been weak. Moreover, uncertainty still surrounds the morphological limits of Schoenoplectiella, a genus of mainly small, amphicarpic annuals that was recently segregated from Schoenoplectus. Consequently, despite ample evidence from molecular analyses that Fuireneae s.l. might consist of two to four tribal lineages, no taxonomic changes have yet been made. Here, we use the Angiosperms353 enrichment panel for targeted sequencing in order to: (1) clarify the relationships of Fuireneae s.l. with the related tribes Abildgaardieae, Eleocharideae and Cypereae; (2) define the limits of Fuireneae s.s., and (3) test the monophyly of Fuireneae s.l. genera with emphasis on Schoenoplectus and Schoenoplectiella. Using more than a third of Fuireneae s.l. diversity, our phylogenomic analyses strongly support six genera and four major Fuireneae s.l. clades that we recognise as tribes: Bolboschoeneae stat.nov., Fuireneae s.s., Schoenoplecteae, and Pseudoschoeneae tr.nov. These results are consistent with morphological, micromorphological (nutlet epidermal cell shape), and embryo differences detected for each tribe. At the generic level, most sub‐Saharan African perennials currently treated in Schoenoplectus are transferred to Schoenoplectiella. Our targeted sequencing results show that these species are nested in Schoenoplectiella, and their treatment here is consistent with micromorphological and embryo characters shared by all Schoenoplectiella species. Keys to recognised tribes and genera are provided

Phylogeny of Cyperaceae Based on DNA Sequence Data–a New rbcL Analysis

Since the Monocots II meeting in 1998, significant new data have been published that enhance our systematic knowledge of Cyperaceae. Phylogenetic studies in the family have also progressed steadily. For this study, a parsimony analysis was carried out using all rbcL sequences currently available for Cyperaceae, including data for two new genera. One of the four subfamilies (Caricoideae) and seven of the 14 tribes (Bisboeckelereae, Cariceae, Cryptangieae, Dulichieae, Eleocharideae, Sclerieae, Trilepideae) are monophyletic. Subfamily Mapanioideae and tribe Chrysitricheae are monophyletic if, as the evidence suggests, Hellmuthia is considered a member of Cypereae. Some other features of our analysis include: well-supported Trilepideae and Sclerieae–Bisboeckelereae clades; a possible close relationship between Cryptangieae and Schoeneae; polyphyletic tribes Schoeneae and Scirpeae; the occurrence of Cariceae within the Dulichieae–Scirpeae clade, and a strongly supported clade, representing Cyperus and allied genera in Cypereae, sister to a poorly supported Ficinia–Hellmuthia– Isolepis–Scirpoides clade. Such patterns are consistent with other studies based on DNA sequence data. One outcome may be that only two subfamilies, Mapanioideae and Cyperoideae, are recognized. Much further work is needed, with efforts carefully coordinated among researchers. The work should focus on obtaining morphological and molecular data for all genera in the family

The sensitivity of ECG contamination to surgical implantation site in brain computer interfaces.

BACKGROUND Brain sensing devices are approved today for Parkinson's, essential tremor, and epilepsy therapies. Clinical decisions for implants are often influenced by the premise that patients will benefit from using sensing technology. However, artifacts, such as ECG contamination, can render such treatments unreliable. Therefore, clinicians need to understand how surgical decisions may affect artifact probability. OBJECTIVES Investigate neural signal contamination with ECG activity in sensing enabled neurostimulation systems, and in particular clinical choices such as implant location that impact signal fidelity. METHODS Electric field modeling and empirical signals from 85 patients were used to investigate the relationship between implant location and ECG contamination. RESULTS The impact on neural recordings depends on the difference between ECG signal and noise floor of the electrophysiological recording. Empirically, we demonstrate that severe ECG contamination was more than 3.2x higher in left-sided subclavicular implants (48.3%), when compared to right-sided implants (15.3%). Cranial implants did not show ECG contamination. CONCLUSIONS Given the relative frequency of corrupted neural signals, we conclude that implant location will impact the ability of brain sensing devices to be used for "closed-loop" algorithms. Clinical adjustments such as implant location can significantly affect signal integrity and need consideration

A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis

The microtubule (MT) cytoskeleton is required for many aspects of cell function, including the transport of intracellular materials, the maintenance of cell polarity, and the regulation of mitosis. These functions are coordinated by MT-associated proteins (MAPs), which work in concert with each other, binding MTs and altering their properties. We have used a MT cosedimentation assay, combined with 1D and 2D PAGE and mass spectrometry, to identify over 250 MAPs from early Drosophila embryos. We have taken two complementary approaches to analyse the cellular function of novel MAPs isolated using this approach. First, we have carried out an RNA interference (RNAi) screen, identifying 21 previously uncharacterised genes involved in MT organisation. Second, we have undertaken a bioinformatics analysis based on binary protein interaction data to produce putative interaction networks of MAPs. By combining both approaches, we have identified and validated MAP complexes with potentially important roles in cell cycle regulation and mitosis. This study therefore demonstrates that biologically relevant data can be harvested using such a multidisciplinary approach, and identifies new MAPs, many of which appear to be important in cell division

A new classification of Cyperaceae (Poales) supported by phylogenomic data

Cyperaceae (sedges) are the third largest monocot family and are of considerable economic and ecological importance. Sedges represent an ideal model family to study evolutionary biology because of their species richness, global distribution, large discrepancies in lineage diversity, broad range of ecological preferences, and adaptations including multiple origins of C4 photosynthesis and holocentric chromosomes. Goetghebeur’s seminal work on Cyperaceae published in 1998 provided the most recent complete classification at tribal and generic level, based on a morphological study of Cyperaceae inflorescence, spikelet, flower and embryo characters plus anatomical and other information. Since then, several family‐level molecular phylogenetic studies using Sanger sequence data have been published. Here, more than 20 years after the last comprehensive classification of the family, we present the first family‐wide phylogenomic study of Cyperaceae based on targeted sequencing using the Angiosperms353 probe kit sampling 311 accessions. Additionally, 62 accessions available from GenBank were mined for overlapping reads and included in the phylogenomic analyses. Informed by this backbone phylogeny, a new classification for the family at the tribal, subtribal and generic levels is proposed. The majority of previously recognized suprageneric groups are supported, and for the first time we establish support for tribe Cryptangieae as a clade including the genus Koyamaea. We provide a taxonomic treatment including identification keys and diagnoses for the 2 subfamilies, 24 tribes and 10 subtribes and basic information on the 95 genera. The classification includes five new subtribes in tribe Schoeneae: Anthelepidinae, Caustiinae, Gymnoschoeninae, Lepidospermatinae and Oreobolinae. This article is protected by copyright. All rights reserved

Genome-wide meta-analyses reveal novel loci for verbal short-term memory and learning

Understanding the genomic basis of memory processes may help in combating neurodegenerative disorders. Hence, we examined the associations of common genetic variants with verbal short-term memory and verbal learning in adults without dementia or stroke (N = 53,637). We identified novel loci in the intronic region of CDH18, and at 13q21 and 3p21.1, as well as an expected signal in the APOE/APOC1/TOMM40 region. These results replicated in an independent sample. Functional and bioinformatic analyses supported many of these loci and further implicated POC1. We showed that polygenic score for verbal learning associated with brain activation in right parieto-occipital region during working memory task. Finally, we showed genetic correlations of these memory traits with several neurocognitive and health outcomes. Our findings suggest a role of several genomic loci in verbal memory processes.Peer reviewe

A Continuous Measure of Gross Primary Production for the Conterminous U.S. Derived from MODIS and AmeriFlux Data

The quantification of carbon fluxes between the terrestrial biosphere and the atmosphere is of scientific importance and also relevant to climate-policy making. Eddy covariance flux towers provide continuous measurements of ecosystem-level exchange of carbon dioxide spanning diurnal, synoptic, seasonal, and interannual time scales. However, these measurements only represent the fluxes at the scale of the tower footprint. Here we used remotely-sensed data from the Moderate Resolution Imaging Spectroradiometer (MODIS) to upscale gross primary productivity (GPP) data from eddy covariance flux towers to the continental scale. We first combined GPP and MODIS data for 42 AmeriFlux towers encompassing a wide range of ecosystem and climate types to develop a predictive GPP model using a regression tree approach. The predictive model was trained using observed GPP over the period 2000-2004, and was validated using observed GPP over the period 2005-2006 and leave-one-out cross-validation. Our model predicted GPP fairly well at the site level. We then used the model to estimate GPP for each 1 km x 1 km cell across the U.S. for each 8-day interval over the period from February 2000 to December 2006 using MODIS data. Our GPP estimates provide a spatially and temporally continuous measure of gross primary production for the U.S. that is a highly constrained by eddy covariance flux data. Our study demonstrated that our empirical approach is effective for upscaling eddy flux GPP data to the continental scale and producing continuous GPP estimates across multiple biomes. With these estimates, we then examined the patterns, magnitude, and interannual variability of GPP. We estimated a gross carbon uptake between 6.91 and 7.33 Pg C yr{sup -1} for the conterminous U.S. Drought, fires, and hurricanes reduced annual GPP at regional scales and could have a significant impact on the U.S. net ecosystem carbon exchange. The sources of the interannual variability of U.S. GPP were dominated by these extreme climate events and disturbances