Unifying Parsimonious Tree Reconciliation

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of multiple species, their genes, and the environment they live in. A common approach to address this research problem is to describe each individual evolution as a phylogenetic tree and construct a tree reconciliation which is parsimonious with respect to a given event model. Unfortunately, most of the previous approaches are designed only either for host-parasite systems, for gene tree/species tree reconciliation, or biogeography. Hence, a method is desirable, which addresses the general problem of mapping phylogenetic trees and covering all varieties of coevolving systems, including e.g., predator-prey and symbiotic relationships. To overcome this gap, we introduce a generalized cophylogenetic event model considering the combinatorial complete set of local coevolutionary events. We give a dynamic programming based heuristic for solving the maximum parsimony reconciliation problem in time O(n^2), for two phylogenies each with at most n leaves. Furthermore, we present an exact branch-and-bound algorithm which uses the results from the dynamic programming heuristic for discarding partial reconciliations. The approach has been implemented as a Java application which is freely available from http://pacosy.informatik.uni-leipzig.de/coresym.Comment: Peer-reviewed and presented as part of the 13th Workshop on Algorithms in Bioinformatics (WABI2013

The compositional and evolutionary logic of metabolism

Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which layers of that system emerged. Metabolism also serves as the foundation in other hierarchies, at least up to cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, suggests metabolism as a source of causation or constraint on many forms of organization in the biosphere. We identify as modules widely reused subsets of chemicals, reactions, or functions, each with a conserved internal structure. At the small molecule substrate level, module boundaries are generally associated with the most complex reaction mechanisms and the most conserved enzymes. Cofactors form a structurally and functionally distinctive control layer over the small-molecule substrate. Complex cofactors are often used at module boundaries of the substrate level, while simpler ones participate in widely used reactions. Cofactor functions thus act as "keys" that incorporate classes of organic reactions within biochemistry. The same modules that organize the compositional diversity of metabolism are argued to have governed long-term evolution. Early evolution of core metabolism, especially carbon-fixation, appears to have required few innovations among a small number of conserved modules, to produce adaptations to simple biogeochemical changes of environment. We demonstrate these features of metabolism at several levels of hierarchy, beginning with the small-molecule substrate and network architecture, continuing with cofactors and key conserved reactions, and culminating in the aggregation of multiple diverse physical and biochemical processes in cells.Comment: 56 pages, 28 figure

Using Nuclear DNA to Investigate the Phylogenetics of Californian Threespine Stickleback Populations

The threespine stickleback, Gasterosteus aculeatus, is a diverse superspecies that exists mainly in coastal temperate zones of the Northern hemisphere with a variety of life history modes. Past phylogenetic analyses of the populations of threespine stickleback have been completed using mitochondrial DNA (mtDNA) data. However, mitochondrial introgression has been observed in many fish species, including threespine stickleback, which causes phylogenetic studies using mtDNA to be false. Here, mitochondrial introgression refers to the movement of mitochondrial genes from one population to another population. Nuclear DNA (nDNA) was analyzed in this study to assess the validity of the mtDNA phylogenetic studies of Californian populations. Up to three nuclear loci containing a total of 41 single nucleotide polymorphisms (SNPs) were analyzed from five Californian populations of threespine stickleback and compared to stickleback from Pacific North America. Neighbor-joining trees were constructed and showed different relationships than found in the mtDNA-based study. Californian populations were found to be distinct from a British Columbian population and two different clades of Californian populations were found, including a Lost Lake/Shay Creek/Fillmore clade and a Holcomb Creek/williamsoni clade. These results, however, are inconclusive due to a large amount of intrapopulation variation at the sites assayed. Lost Lake seems to contain an unusually large amount of variation that makes it unique. Further study, though, must be completed to determine the validity of the these results and those from the previous mtDNA-based studies. Specifically, Shay Creek Stickleback may be confirmed as being closely related to Gasterosteus aculeatus williamsoni, which is already on the endangered species list or Lost Lake may be found to be another unique population. Conservation efforts may then be made to protect Shay Creek and/or Lost Lake Stickleback

Evolution of genomes, host shifts and the geographic spread of SARS-CoV and related coronaviruses

Severe acute respiratory syndrome (SARS) is a novel human illness caused by a previously unrecognized coronavirus (CoV) termed SARS-CoV. There are conflicting reports on the animal reservoir of SARS-CoV. Many of the groups that argue carnivores are the original reservoir of SARS-CoV use a phylogeny to support their argument. However, the phylogenies in these studies often lack outgroup and rooting criteria necessary to determine the origins of SARS-CoV. Recently, SARS-CoV has been isolated from various species of Chiroptera from China (e.g., Rhinolophus sinicus) thus leading to reconsideration of the original reservoir of SARS-CoV. We evaluated the hypothesis that SARS-CoV isolated from Chiroptera are the original zoonotic source for SARS-CoV by sampling SARS-CoV and non-SARS-CoV from diverse hosts including Chiroptera, carnivores, artiodactyls and humans. Regardless of alignment parameters, optimality criteria, or isolate sampling, the resulting phylogenies clearly show that the SARS-CoV was transmitted to small carnivores well after the epidemic of SARS in humans that began in late 2002. The SARS-CoV isolates from small carnivores in Shenzhen markets form a terminal clade that emerged recently from within the radiation of human SARS-CoV. There is evidence of subsequent exchange of SARS-CoV between humans and carnivores. In addition SARS-CoV was transmitted independently from humans to farmed pigs (Sus scrofa). The position of SARS-CoV isolates from Chiroptera are basal to the SARS-CoV clade isolated from humans and carnivores. Although sequence data indicate that Chiroptera are a good candidate for the original reservoir of SARS-CoV, the structural biology of the spike protein of SARS-CoV isolated from Chiroptera suggests that these viruses are not able to interact with the human variant of the receptor of SARS-CoV, angiotensin-converting enzyme 2 (ACE2). In SARS-CoV study, both visually and statistically, labile genomic fragments and, putative key mutations of the spike protein that may be associated with host shifts. We display host shifts and candidate mutations on trees projected in virtual globes depicting the spread of SARS-CoV. These results suggest that more sampling of coronaviruses from diverse hosts, especially Chiroptera, carnivores and primates, will be required to understand the genomic and biochemical evolution of coronaviruses, including SARS-CoV.Fil: Janies, Daniel. Ohio State University; Estados UnidosFil: Habib, Farhat. Ohio State University; Estados UnidosFil: Alexandrov, Boyan. Ohio State University; Estados UnidosFil: Hill, Andrew. University of Colorado; Estados UnidosFil: Pol, Diego. Museo Paleontológico Egidio Feruglio; Argentina. Ohio State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

A remarkable diversity of bone-eating worms (Osedax; Siboglinidae; Annelida)

<p>Abstract</p> <p>Background</p> <p>Bone-eating <it>Osedax </it>worms have proved to be surprisingly diverse and widespread. Including the initial description of this genus in 2004, five species that live at depths between 25 and 3,000 m in the eastern and western Pacific and in the north Atlantic have been named to date. Here, we provide molecular and morphological evidence for 12 additional evolutionary lineages from Monterey Bay, California. To assess their phylogenetic relationships and possible status as new undescribed species, we examined DNA sequences from two mitochondrial (<it>COI </it>and <it>16S </it>rRNA) and three nuclear genes (<it>H3</it>, <it>18S </it>and <it>28S </it>rRNA).</p> <p>Results</p> <p>Phylogenetic analyses identified 17 distinct evolutionary lineages. Levels of sequence divergence among the undescribed lineages were similar to those found among the named species. The 17 lineages clustered into five well-supported clades that also differed for a number of key morphological traits. Attempts to determine the evolutionary age of <it>Osedax </it>depended on prior assumptions about nucleotide substitution rates. According to one scenario involving a molecular clock calibrated for shallow marine invertebrates, <it>Osedax </it>split from its siboglinid relatives about 45 million years ago when archeocete cetaceans first appeared and then diversified during the late Oligocene and early Miocene when toothed and baleen whales appeared. Alternatively, the use of a slower clock calibrated for deep-sea annelids suggested that <it>Osedax </it>split from its siboglinid relatives during the Cretaceous and began to diversify during the Early Paleocene, at least 20 million years before the origin of large marine mammals.</p> <p>Conclusion</p> <p>To help resolve uncertainties about the evolutionary age of <it>Osedax</it>, we suggest that the fossilized bones from Cretaceous marine reptiles and late Oligocene cetaceans be examined for possible trace fossils left by <it>Osedax </it>roots. Regardless of the outcome, the present molecular evidence for strong phylogenetic concordance across five separate genes suggests that the undescribed <it>Osedax </it>lineages comprise evolutionarily significant units that have been separate from one another for many millions of years. These data coupled with ongoing morphological analyses provide a solid foundation for their future descriptions as new species.</p

Cophylogenetic analysis of dated trees

Parasites and the associations they form with their hosts is an important area of research due to the associated health risks which parasites pose to the human population. The associations parasites form with their hosts are responsible for a number of the worst emerging diseases impacting global health today, including Ebola, HIV, and malaria. Macro-scale coevolutionary research aims to analyse these associations to provide further insights into these deadly diseases. This approach, first considered by Fahrenholz in 1913, has been applied to hundreds of coevolutionary systems and remains the most robust means to infer the underlying relationships which form between coevolving species. While reconciling the coevolutionary relationships between a pair of evolutionary systems is NP-Hard, it has been shown that if dating information exists there is a polynomial solution. These solutions however are computationally expensive, and are quickly becoming infeasible due to the rapid growth of phylogenetic data. If the rate of growth continues in line with the last three decades, the current means for analysing dated systems will become computationally infeasible. Within this thesis a collection of algorithms are introduced which aim to address this problem. This includes the introduction of the most efficient solution for analysing dated coevolutionary systems optimally, along with two linear time heuristics which may be applied where traditional algorithms are no longer feasible, while still offering a high degree of accuracy 91%. Finally, this work integrates these incremental results into a single model which is able to handle widespread parasitism, the case where parasites infect multiple hosts. This proposed model reconciles two competing theories of widespread parasitism, while also providing an accuracy improvement of 21%, one of the largest single improvements provided in this field to date. As such, the set of algorithms introduced within this thesis offers another step toward a unified coevolutionary analysis framework, consistent with Fahrenholz original coevolutionary analysis model

Sperm ultrastructure of an oviparous and an ovoviviparous onychophoran species (Peripatopsidae) with some phylogenetic considerations

The spermatozoa of the Australian oviparous Ooperipatellus insignis and the South African ovoviviparous Opisthopatus cinctipes (both: Onychophora, Peripatopsidae) were studied and compared with the spermatozoal patterns already described in the taxon. The spermatozoa of both species conform with the general plan described for the Onychophora: they are filiform cells formed, in sequence, by an elongated, fully condensed nucleus capped by an acrosome and surrounded by several spiral ridges; by a mitochondrial midpiece characteristically interpolated between the nucleus and a characteristic flagellum. Major differences between the spermatozoa of both species concern their acrosome organization. The correlation between the acrosomal pattern and the size and structure of the ovarial eggs (oocytes) in onychophorans has been investigated. A parsimony analysis was performed on 21 spermatozoal characters of the species considered. Its results are congruent with those of the traditional systematics. A new set of autapomorphies characterising onychophoran sperm is suggested and some of the spermatological homologies proposed between Onychophora and Euclitellata spermatozoa are critically discussed. Our analysis suggests that spermatozoal characters are good phylogenetic markers among onychophorans, also at low taxonomic level. Zusammenfassung Die Ultrastruktur der Spermien zweier Onychophoren-Arten (Peripatopsidae) wird vergleichend untersucht. Erstmals wird ein oviparer Vertreter berucksichtigt; namlich Ooperipatellus insignis vom Locus typicus; Mt. Macedon, Victoria, Australien. Seine Spermatozoen werden mit denen der ovoviviparen sudafrikanischen Art Opisthopatus cinctipes verglichen. Die Ergebnisse dieser Untersuchung werden mit verfugbaren Literaturdaten abgeglichen und ein Grundmuster fur Onychophoren-Spermien entwickelt. Die Spermien der beiden hier untersuchten Arten stimmen in ihrer Morphologie und Ultrastruktur im Wesentlichen mit dem bereits fur Onychophoren bekannten Muster uberein. Es sind fadige Zellen, die recht einheitlich aufgebaut sind. Sie weisen einen langlichen, kompakten Kern mit Akrosom-Kappe auf und sind spiralig von Furchen umgeben. Der mitochondriale Mittelbereich der Spermien liegt zwischen dem Nukleus und einem fur Onychophoren typischen Flagellum. Unterschiede betreffen dagegen die Organisation des Onychophoren-Akrosoms. Die mogliche Korrelation zwischen Akrosom-Ausbildung und Grose und Struktur der Ovarialeier wird untersucht. Basierend auf 21 Spermatozoen-Charakteren wird eine Parsimonie-Analyse durchgefuhrt. Die so gewonnenen Daten decken sich mit denjenigen der traditionellen Systematik. Die Spermien der Onychophoren weisen Merkmale auf, welche Autapomorphien des Taxon Onychophora sein konnen. Daruber hinaus werden mutmasliche Spermien-Homologien, die von verschiedenen Autoren fur die Taxa Onychophora und Euclitellata vorgeschlagen wurden, kritisch bewertet. Unsere Analyse zeigt, dass Spermien-Merkmale fur Onychophoren gute phylogenetische Marker darstellen, sogar auf Art-Niveau