Matthew P. Simmons

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In the analysis of sequence-based data matrices, the use of different methods of treating gaps has been demonstrated to influence the resulting phylogenetic hypotheses (e.g., Eernisse and Kluge, 1993; Vogler and DeSalle, 1994; Simons and May den, 1997). Despite this influence, a well-justified, uniformly applied method of treating gaps is lacking in(More)
In this work, we study the use of Twitter by House, Senate and gubernatorial candidates during the midterm (2010) elections in the U.S. Our data includes almost 700 candidates and over 690k documents that they produced and cited in the 3.5 years leading to the elections. We utilize graph and text mining techniques to analyze differences between Democrats,(More)
Social media is playing an increasingly vital role in information dissemination. But with dissemination being more distributed, content often makes multiple hops, and consequently has opportunity to change. In this paper we focus on content that should be changing the least, namely quoted text. We find changes to be frequent, with their likelihood depending(More)
We examined three parallel data sets with respect to qualities relevant to phylogenetic analysis of 20 exemplar monocotyledons and related dicotyledons. The three data sets represent restriction-site variation in the inverted repeat region of the chloroplast genome, and nucleotide sequence variation in the chloroplast-encoded gene rbcL and in the(More)
Phylogenetic relationships within Celastraceae (spindle-tree family) were inferred from nucleotide sequence characters from the 5' end of 26S nuclear ribosomal DNA (including expansion segments D1-D3; 84 species sampled), phytochrome B (58 species), rbcL (31 species), atpB (23 species), and morphology (94 species). Among taxa of questionable affinity,(More)
Phylogenetic relationships within Celastraceae were inferred using a simultaneous analysis of 61 morphological characters and 1123 base pairs of phytochrome B exon 1 from the nuclear genome. No gaps were inferred, and the gene tree topology suggests that the primers were specific to a single locus that did not duplicate among the lineages sampled. This(More)
In this paper, we propose a new method (uninode coding) for coding duplicate (paralogous) genes to infer species trees. Uninode coding incorporates data from duplicated and unduplicated gene copies in phylogenetic analyses of taxa. Uninode coding utilizes global parsimony through the inclusion of both duplicated and unduplicated gene copies, allows one to(More)
Virtual goods continue to emerge in online communities, offering scholars an opportunity to understand how social networks can facilitate the diffusion of innovations. We examine the social ties for over one million user-to-user virtual goods transfers in Second Life, a popular 3D virtual world, and the unique role that groups play in the diffusion of(More)
This paper examines social structures underlying economic activity in Second Life (SL), a massively multiplayer virtual world that allows users to create and trade virtual objects and commodities. We find that users conduct many of their transactions both within their social networks and within groups. Using frequency of chat as a proxy of tie strength, we(More)