Angiosperm Phylogeny: 17 Genes, 640 Taxa

• Premise of the study : Recent analyses employing up to fi ve genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. • Methods : We conducted two primary analyses based on 640 species representing 330 families. The fi rst included 25 260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19 846 aligned bp from 13 genes (representing only the nucleus and plastid). • Key results : Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms ( Mesangiospermae ), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae ]. Eudicotyledoneae contains a basal grade subtending Gunneridae . Within Gunneridae , Gunnerales are sister to the remainder ( Pentapetalae ), which comprises (1) Superrosidae , consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae , comprising Berberidopsidales, Santalales, Caryophyllales , Asteridae , and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae , most deep-level relationships are resolved with strong support. • Conclusions : Our analyses confi rm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics

Angiosperm phylogeny: 17 genes, 640 taxa

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/1/ajb20704-sup-0010.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/2/ajb20704.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/3/ajb20704-sup-0001.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/4/ajb20704-sup-0016.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/5/ajb20704-sup-0017.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/6/ajb20704-sup-0021.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/7/ajb20704-sup-0003.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/8/ajb20704-sup-0002.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/9/ajb20704-sup-0011.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/10/ajb20704-sup-0019.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/11/ajb20704-sup-0015.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/12/ajb20704-sup-0006.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/13/ajb20704-sup-0020.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/14/ajb20704-sup-0013.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/15/ajb20704-sup-0004.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/16/ajb20704-sup-0012.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/17/ajb20704-sup-0005.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/18/ajb20704-sup-0018.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/19/ajb20704-sup-0009.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/20/ajb20704-sup-0014.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/21/ajb20704-sup-0007.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/142064/22/ajb20704-sup-0008.pd

TOLKIN – Tree of Life Knowledge and Information Network: Filling a Gap for Collaborative Research in Biological Systematics

The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users. The TOLKIN project (Tree of Life Knowledge and Information Network) addresses this need by supporting capabilities to manage, integrate, and provide public access to molecular, morphological, and biocollections data and research outcomes through a collaborative, web application. This data management framework allows aggregation and import of sequences, underlying documentation about their source, including vouchers, tissues, and DNA extraction. It combines features of LIMS and workflow environments by supporting management at the level of individual observations, sequences, and specimens, as well as assembly and versioning of data sets used in phylogenetic inference. As a web application, the system provides multi-user support that obviates current practices of sharing data sets as files or spreadsheets via email

Succession in hummock-hollow complexes in Gates Bog.

http://deepblue.lib.umich.edu/bitstream/2027.42/53482/1/1917.pdfDescription of 1917.pdf : Access restricted to on-site users at the U-M Biological Station

Library Module.

<p>Citation information is stored, view, and linked to data across all modules.</p

The TOLKIN architecture is built upon open source platforms and software, including Linux, Ruby on Rails and support for libraries, formats, and services such as BioRuby, NeXML, and GenBank.

<p>The diagram shows the relationship between TOLKIN modules and core data classes within each.</p

In a typical phylogenetic analysis workflow, common practice has been to manage data inside spreadsheets and in collaborative teams, to share them via email, as represented by Alternative a).

<p>While easy and effective for small data sets, spreadsheets can get out of sync and provenance is not well maintained. TOLKIN provides an Alternative b) to provide collaboration through a web portal, bulk data import and export of common formats, metadata and versioning support.</p

Molecular module.

<p>Data can be entered in each tab or through the matrix view. Each cell is interactive and linked to GenBank if a number is provided or when sequences are directly imported from GenBank. Data is exported into fasta files. Alignments and primer information can be stored for sharing and future repurposing.</p

Image Gallery.

<p>A list of stored images is displayed. These can be searched based on different parameters and are linked across all modules.</p