The connection between fighting a threat to one of California\u2019s favorite fruits and recently published research by a Harvey Mudd College computer science professor and his colleagues isn\u2019t immediately evident. On the way to connect one dot with the other, there\u2019s a story about the mutualistic pairing of a beetle and a fungus, extensive biological fieldwork and a nod to Darwin\u2019s prescient writings on co-evolution. But, as two recently published papers demonstrate, the solution to an increasingly serious problem and others like it may depend on the ability and speed of a computer program.<\/p>\n
Ran Libeskind-Hadas, R. Michael Shanahan Professor of Computer Science and an expert who studies algorithmic issues in computational biology\u2014in particular, the problem of reconciling pairs of evolutionary trees\u2014co-authored \u201cInvasive Asian Fusarium\u2013Euwallacea<\/em> ambrosia beetle mutualists pose a serious threat to forests, urban landscapes and the avocado industry,\u201d which was accepted to the journal Phytoparacitica<\/em>. A second paper, \u201cDTL Reconciliation Repair,\u201d co-authored by Libeskind-Hadas, Harvey Mudd student Anna Ma \u201917 and Pomona College student Dima Smirnov \u201917, has been accepted to the 2017 Asia Pacific Bioinformatics Conference (APBC) and will be published in BMC Systems Biology<\/em>.<\/p>\n The first paper deals with testing the hypothesis of co-evolution between pairs of species, in this case the Euwallacea<\/em> ambrosia beetle and the fungus Fusarium.<\/em> The researchers used a Harvey Mudd-developed software package called Jane to compare evolutionary trees of the two systems. The algorithm posits the most likely scenario by which the beetle and her best pal fungus developed their 21-million-year-old mutualistic relationship, which helps researchers to better understand the pair\u2019s co-evolutionary histories.<\/p>\n While Libeskind-Hadas\u2019s interest and involvement in this research is focused on the computational step of the process, the self-proclaimed \u201cavocado guy,\u201d acknowledges that the research may be used in the future to solve serious problems created by these notorious BFFs, namely the mass destruction of several species of tree in California, including the avocado. \u201cUltimately, that\u2019s what\u2019s driving this,\u201d he says. \u201cI love seeing this work being used in practice, but fundamentally, the problems I\u2019m working on have nothing to do with beetles. At the moment, I would say this is still in the realm of pure science.\u201d<\/p>\n Guacamole lovers eager for a quick solution to the beetle-fungus problem are probably out of luck, but the second paper, \u201cDTL Reconciliation Repair,\u201d may provide some hope. In their current research, the team looked at ways of improving Jane to perform phylogenetic tree alignment more quickly. \u201cAs the data sets get larger, it takes more time to get results,\u201d says Libeskind-Hadas. \u201cWe found that in about 15 percent of the data we tried, we were able to slightly outperform the best algorithm we have. If you\u2019re going to spend years doing fieldwork, even a small amount of extra accuracy in the computational step is meaningful.\u201d Ma will present the paper at APBC in Shenzhen, China, in January.<\/p>\n","protected":false},"excerpt":{"rendered":" The connection between fighting a threat to one of California\u2019s favorite fruits and recently published research by a Harvey Mudd […]<\/p>\n","protected":false},"author":145,"featured_media":5136,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[4,11,212,14,26,30],"class_list":["post-5130","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-biology","category-computer-science","category-experiential-learning","category-faculty","category-research","category-students"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/posts\/5130","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/users\/145"}],"replies":[{"embeddable":true,"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/comments?post=5130"}],"version-history":[{"count":0,"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/posts\/5130\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/media\/5136"}],"wp:attachment":[{"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/media?parent=5130"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.hmc.edu\/about\/wp-json\/wp\/v2\/categories?post=5130"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}