Browsing by Subject "phylogeny"
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Item A review of Salsuginus seculus (Platyhelminthes: Monogenean) in the western mosquitofish (Gambusia affinis) from TexasVasquez, Gizell; Negovetich, Nicholas J.; Strenth, Ned E.; Ammerman, Loren K.Western mosquitofish (Gambusia affinis) are cosmopolitan in warmer climates and can serve as a host for a number of parasites. The gill monogeneans from this host are especially interesting because of the very low species diversity that has been reported in the literature. In the United States alone, only a single species, Salsuginus seculus, is reported from the gills of fish collected across the country. To assess the validity of a single species on the gills of G. affinis, fish were collected from 11 geographically-distant aquatic systems in Texas and surveyed for monogenean infections. The gill monogeneans were then subjected to morphological and molecular analyses. Preliminary analyses suggested that more than one species of monogenean may be infecting the gills of G. affinis in Texas. Morphologically, most of the monogeneans resemble S. seculus, but parasites from a few locations exhibited anatomical differences that did not conform to the description of S. seculus. They are smaller in overall size and differ in their opisthaptor, including the size of the hamuli and the length of the haptoral bars. Sequence analysis on these parasites was performed to determine if consistent patterns of genetic differences exist between specimens collected from the various locations. Based on analysis of a partial 28S rRNA gene region, sufficient support is lacking to distinguish these parasites as different species.Item Advances in diapriid (Hymenoptera: diapriidae) systematics, with contributions to cybertaxonomy and the analysis of rRNA sequence data(2009-05-15) Yoder, Matthew JonDiapriids (Hymenoptera: Diapriidae) are small parasitic wasps. Though found throughout the world they are relatively unknown. A framework for advancing diapriid systematics is developed by introducing a new web-based application/database capable of storing a broad range of systematic data, and the first molecular phylogeny specifically focused at examining intrafamilial relationships. In addition to these efforts, a description of a new taxon is provided. Several advantages of digital description, including linking descriptions to an ontology of morphological terms, are highlighted. The functionality of the database is further illustrated in the production of a catalog of diapriid host associations. The hosts database currently holds over 450 association records, for over 500 named taxa (parasitoids and hosts), and over 180 references. Diapriids are found to be primarily endoparasitoids of Diptera emerging from the host pupa. Phylogenetic inference for a molecular dataset of 28S and 18S rRNA sequence data, derived from a diverse selection of diapriids, is accomplished with a new suite of tools developed for handling complex rRNA datasets. Several parsimony-based methodologies, including an alignment-free method of analyzing multiple sequences, are reviewed and applied using the new software tools. Diapriid phylogenetic relationships are shown to be broadly congruent with existing morphology-based classifications. Methods for analyzing typically excluded sequence data are shown to recover phylogenetic signal that would otherwise be lost and the alignment-free method performed remarkably well in this regard. Empirically, phylogenetic approaches that incorporate structural data were not notably different than those that did not.Item Efficient Algorithms for Comparing, Storing, and Sharing Large Collections of Phylogenetic Trees(2012-07-16) Matthews, SuzanneEvolutionary relationships between a group of organisms are commonly summarized in a phylogenetic (or evolutionary) tree. The goal of phylogenetic inference is to infer the best tree structure that represents the relationships between a group of organisms, given a set of observations (e.g. molecular sequences). However, popular heuristics for inferring phylogenies output tens to hundreds of thousands of equally weighted candidate trees. Biologists summarize these trees into a single structure called the consensus tree. The central assumption is that the information discarded has less value than the information retained. But, what if this assumption is not true? In this dissertation, we demonstrate the value of retaining and studying tree collections. We also conduct an extensive literature search that highlights the rapid growth of trees produced by phylogenetic analysis. Thus, high performance algorithms are needed to accommodate this increasing production of data. We created several efficient algorithms that allow biologists to easily compare, store and share tree collections over tens to hundreds of thousands of phylogenetic trees. Universal hashing is central to all these approaches, allowing us to quickly identify the shared evolutionary relationships contained in tree collections. Our algorithms MrsRF and Phlash are the fastest in the field for comparing large collections of trees. Our algorithm TreeZip is the most efficient way to store large tree collections. Lastly, we developed Noria, a novel version control system that allows biologists to seamlessly manage and share their phylogenetic analyses. Our work has far-reaching implications for both the biological and computer science communities. We tested our algorithms on four large biological datasets, each consisting of 20; 000 to 150; 000 trees over 150 to 525 taxa. Our experimental results on these datasets indicate the long-term applicability of our algorithms to modern phylogenetic analysis, and underscore their ability to help scientists easily exchange and analyze their large tree collections. In addition to contributing to the reproducibility of phylogenetic analysis, our work enables the creation of test beds for improving phylogenetic heuristics and applications. Lastly, our data structures and algorithms can be applied to managing other tree-like data (e.g. XML).Item Molecular systematics of bonneted bats (Molossidae: Eumops) based on mitochondrial and nuclear DNA sequences(2012-05-12) Bartlett, Sarah; Bartlett,Sarah Nichole; Ammerman, Loren K.; Maxwell, Terry; Strenth, Ned; Pierce, Jason; Angelo State University. Department of Biology.Previous understanding of the relationships among the species of bats in the genus Eumops has been based on phenetic and cladistic analyses of morphological data. The objective of this study was to construct a phylogeny of the bats within the genus Eumops using DNA sequence data from 2 mitochondrial genes (cytochrome b and nicotinamide adenine dinucleotide dehydrogenase subunit 1) and 1 nuclear locus (β-fibrinogen intron 7) for members of Eumops and outgroups from the family Molossidae. Data for each locus were analyzed separately using maximum-likelihood and Bayesian methods then were combined for complete data analyses using Bayesian Inference and Bayesian concordance analysis on a total of 2715 base pairs. Our results conflicted with some of the relationships proposed in previous morphological studies. Minor disagreements existed between the individual mitochondrial and nuclear data sets. However, the monophyly of the genus was significantly supported in all of the analyses.Item Phylogeny of Geophagine cichlids from South America (Perciformes: Labroidei)(Texas A&M University, 2004-11-15) Hernan, Lopez FernandezThree new species of cichlid fishes of the genus Geophagus, part of the Neotropical subfamily Geophaginae, are described from the Orinoco and Casiquiare drainages in Venezuela. Phylogenetic relationships among 16 genera and 30 species of Geophaginae are investigated using 136 morphological characters combined with DNA sequences coding for the mitochondrial gene NADH dehydrogenase subunit 4 (ND4) and the nuclear Recombination Activating Gene 2 (RAG2). Data from previous studies are integrated with the new dataset by incorporating published DNA sequences from the mitochondrial genes cytochrome b and 16S and the microsatellite flanking regions Tmo-M27 and Tmo-4C4. Total-evidence analysis revealed that Geophaginae is monophyletic and includes eighteen genera grouped into two major clades. In the first clade, the tribe Acarichthyini (genera Acarichthys and Guianacara) is sister-group to a clade in which Gymnogeophagus, 'Geophagus' steindachneri, and Geophagus sensu stricto are sister to 'Geophagus' brasiliensis and Mikrogeophagus; all these are in turn sister-group to Biotodoma, Dicrossus and Crenicara. In the second clade, Satanoperca, Apistogramma (including Apistogrammoides), and Taeniacara are sister to Crenicichla and Biotoecus. Monophyly and significantly short branches at the base of the phylogeny indicate that genera within Geophaginae differentiated rapidly within a relatively short period. High morphological, ecological, and behavioral diversity within the subfamily suggest that geophagine divergence may be the result of adaptive radiation.Item Resolution of Phylogenetic Relationships and Characterization of Y-Linked Microsatellites within the Big Cats, Panthera(2010-10-12) Davis, Brian W.The pantherine lineage of cats diverged from the remainder of modern Felidae less than 11 million years ago. This clade consists of the five big cats of the genus Panthera, the lion, tiger, jaguar, leopard, and snow leopard, as well as the closely related clouded leopard, which diverged from Panthera approximately 6 million years ago. A significant problem exists with respect to the precise phylogeny of these highly threatened great cats. Within the past four years, despite multiple publications on the subject, no two studies have reconstructed the phylogeny of Panthera with the same topology, showing particular discordance with respect to sister-taxa relationships to the lion and the position of the enigmatic snow leopard. The evolutionary relationship among these cats remains unresolved partially due to their recent and rapid radiation 3-5 million years ago, individual speciation events occurring within less than 1 million years, and probable introgression between lineages following their divergence. We assembled a 47.6 kb dataset using novel and published DNA sequence data from the autosomes, both sex chromosomes and the mitochondrial genome. This dataset was analyzed both as a supermatrix and with respect to individual partitions using maximum likelihood and Bayesian phylogeny inference. Since discord may exist among gene segments in a multilocus dataset due to their unique evolutionary histories, inference was also performed using Bayesian estimation of species trees (BEST) to form a robust consensus topology. Incongruent topologies for autosomal loci indicated phylogenetic signal conflict within the corresponding segments. We resequenced four mitochondrial and three nuclear gene segments used in recent attempts to reconstruct felid phylogeny. The newly generated data was combined with available GenBank sequence data from all published studies to highlight phylogenetic disparities stemming either from the amplification of a mitochondrial to nuclear translocation event, or errors in species identification. We provide an alternative, highly supported interpretation of the evolutionary history of the pantherine lineage using 39 single-copy regions of the felid Y chromosome and supportive phylogenetic evidence from a revised mitochondrial partition. These efforts result in a highly corroborated set of species relationships that open up new avenues for the study of speciation genomics and understanding the historical events surrounding the origin of the members of this lineage.Item Revision and Phylogenetic Analysis of the North American Antlion Genus Paranthaclisis Banks (Neuroptera: Myrmeleontidae)(2012-10-19) Diehl, BenjaminThe North American antlion genus Paranthaclisis is comprehensively revised for the first time. Four species are recognized: P. congener (Hagen), P. floridensis Stange & Miller, P. hageni (Banks) and P. nevadensis Banks. Redescriptions, distribution maps and figures of diagnostic morphological characters are provided for adults of each species. A key to adults of Paranthaclisis is also included. Paranthaclisis californica Navas (1922) is recognized as a new synonym of P. hageni Banks. The monophyly of, and interspecific relationships within, the antlion genus Paranthaclisis, and its relationships to other genera within the tribe Acanthaclisini, are investigated using multiple datasets. Fifteen datasets were produced and analyzed to explore the effects of inference method, alignment strategy and data partitioning on phylogenetic estimates using morphological, molecular and mixed data inputs. Eighteen unordered and unweighted morphological characters were coded from across adult body regions. Molecular sequence data generated for this study consisted of two ribosomal genes, 16S and 18S. Paranthaclisis was recovered as monophyletic in analyses using 14 of 15 datasets, with low to moderate support in maximum parsimony and maximum likelihood analyses and high support from Bayesian inference methods. A sister-group relationship between Paranthaclisis and Vella, the only other New World acanthaclisine genus, was also recovered in analysis of 13 of 15 datasets, with low to moderate support in all phylogenetic inference methods tested. Choice of phylogenetic inference method and partitioning of gene datasets had the most influence on resulting topologies and support values. Choice of alignment strategy resulted in few topological differences, but Clustal datasets generally had higher clade support values, compared to MAFFT-aligned sequences.Item Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules(Texas A&M University, 2005-11-01) Gillespie, Joseph JamesRibosomal RNA (rRNA) molecules form highly conserved secondary and tertiary structures via rRNA-rRNA and rRNA-protein interactions that collectively comprise the macromolecule that is the ribosome. Because of their cellular universality, rRNA molecules are commonly used for phylogeny estimations spanning all divergences of life. In this dissertation, I elucidate the structure of several rRNAs by analyzing multiply aligned sequences for basepair covariation and conserved higher order structural motifs. Specifically, I predict novel structures for expansion segments D2 and D3 of the nuclear large subunit rRNA (28S) and variable regions V4-V9 of the nuclear small subunit rRNA (18S) from from 249 galerucine leaf beetles (Coleoptera: Chrysomelidae). I describe a novel means for characterizing regions of alignment ambiguity that improves methods for retaining phylogenetic information without violating nucleotide positional homology. In the program PHASE, I explore a variety of RNA maximum likelihood models using the 28S rRNA dataset and discuss the utitilty of these models in light of their performance under Bayesian analysis. I conclude that seven-state models are likely the best models to use for phylogenetic estimation, although I cannot determine with confidence which of the two seven-state models (7A or 7D) is better. Evaluation of the unpaired sites within both rRNAs in Modeltest provided a similar model of evolution for these non-pairing regions (TrN+ I+G). In addition, a sequenced region of the mitochondrial cytochrome oxidase I gene (COI) from the galerucines was evaluated in Modeltest, with each codon position modeled separately (GTR+I+G for positions 1 and 2, GTR+G for position 3). The combined galerucine dataset (28S+18S rRNA helices, 28S+18S rRNA unpaired sites, COI 1st, 2nd and 3rd positions) provided for two mixedmodel Bayesian analysis of five discretely-modeled partitions (using 7A and 7D). The results of these analyses are compared with those obtained from equally weighted parsimony to provide a robust phylogenetic estimate of the Galerucinae and related leaf beetle taxa. Finally, the odd characteristics of strepsipteran 18S rRNA are evaluated through comparison of 12 strepsipterans with 163 structurally-aligned arthropod sequences. Among other interesting results, I identify errors in previously published strepsipteran sequences and predict structures not previously known from metazoan rRNA.Item The use of CEN38 in assessing evolutionary relationships in the genus Sorghum(Texas A&M University, 2005-11-01) Anderson, Jason CorrenthA DNA sequence-based phylogenetic tree (Dillon et al., 2004) places the species of the genus Sorghum into two sister lineages, one with x = 5 and the other with x = 10 as a basic chromosome number. It has not been resolved whether or not these lineages are monophyletic or polyphyletic. A repetitive sequence, CEN38, found only in Sorghum and sugarcane, was used to assess evolutionary relationships among Sorghum species. The objectives of this research were to determine the taxonomic distribution of CEN38, its chromosomal position(s), and its organization in DNA. CEN38 was detected by filter hybridization to be present in the DNA of 16 of 21 Sorghum species analyzed, ranging from 15 to ~21,000 copies. It was detected by fluorescence in situ hybridization (FISH) only in chromosomes of species of the section Eu-sorghum, where it had a pericentromeric distribution. The low copy number and/or chromosomal distribution of CEN38 in other Sorghum species apparently does not allow for its detection by FISH. Analysis of restriction enzyme digested DNA with homology to CEN38 and of fragments amplified by PCR using primers selected to amplify S. bicolor CEN38 sequences showed that S. laxiflorum and S. macrospermum have tandemly arranged CEN38 sequences as is found in S. bicolor. This supports the close evolutionary affinity of the species in the x = 10 lineage. In the x = 5 lineage, DNA of 11 of 16 species analyzed hybridized with CEN38 by filter hybridization. In S. versicolor, large DNA fragments (4.36 kb to 23 kb) generated by digestion with restriction enzymes hybridized to CEN38. Since a ladder of smaller fragments was not detected, CEN38 may have been inserted into a transposable element in this species and dispersed throughout the genome. Among species of the x = 5 lineage, PCR using primers for S. bicolor CEN38 amplified only DNA fragments from S. timorense and these formed a ladder based on a ~125 bp repeat. Since hybridization of the CEN38 sequence to DNA of S. timorense was not detected by filter hybridizations, these sequences apparently are not similar to CEN38. Cloning and sequencing of DNA from species of the x = 5 lineage that hybridizes to CEN38 are needed to determine whether or not they are in the CEN38 family. A monophyletic or polyphyletic origin of the x = 5 and x = 10 lineages was not resolved.