Life Sciences Commons^™

Evolutionary Relationships Among Duiker Antelope (Bovidae: Cephalophinae), Anne Johnston

University of New Orleans Theses and Dissertations

Duikers are a species rich subfamily of threatened African antelope whose recent origin poses a challenge to the molecular identification of taxa and estimation of their phylogeny. I test the ability of DNA barcodes to identify all taxa within this group. I then use mitochondrial and nuclear genes to estimate a multi-locus species tree and to date divergence times. DNA barcodes are unable to distinguish many sister taxa, calling into question the utility of barcodes for the regulation of duiker trade or in identification of field-collected feces. The multi-locus phylogeny provides support for the relationships among major duiker lineages and …

A New Genus Of Miniaturized And Pug-Nosed Gecko From South America (Sphaerodactylidae: Gekkota), Tony Gamble, Juan D. Daza, Guarino R. Colli, Laurie J. Vitt, Aaron M. Bauer

Biological Sciences Faculty Research and Publications

Sphaerodactyl geckos comprise five genera distributed across Central and South America and the Caribbean. We estimated phylogenetic relationships among sphaerodactyl genera using both separate and combined analyses of seven nuclear genes. Relationships among genera were incongruent at different loci and phylogenies were characterized by short, in some cases zero-length, internal branches and poor phylogenetic support at most nodes. We recovered a polyphyletic Coleodactylus, with Coleodactylus amazonicus being deeply divergent from the remaining Coleodactylus species sampled. The C. amazonicus lineage possessed unique codon deletions in the genes PTPN₁₂ and RBMX while the remaining Coleodactylus species had unique codon …

The Evolution Of Lateralized Foot Use In Parrots: A Phylogenetic Approach, Culum Brown, Maria Magat

Sentience Collection

Cerebral lateralization refers to the division of cognitive function in either brain hemisphere and may be overtly expressed as behavioral asymmetries, such as handedness. The evolutionary history of laterality is of considerable interest due to its close link with the development of human language. Although considerable research effort has aimed at the proximate explanations of cerebral lateralization, considerably less attention has been paid to ultimate explanations. The extent to which laterality is constrained by phylogeny or shaped by ecological forces through natural selection has received little attention. Here, the foot preference of 23 species of Australian parrots was examined to …

Widespread Horizontal Gene Transfer From Circular Single-Stranded Dna Viruses To Eukaryotic Genomes, Huiquan Liu, Yanping Fu, Bo Li, Xiao Yu, Jiatao Xie, Jiasen Cheng, Said A. Ghabrial, Guoqing Li, Xianhong Yi, Daohong Jiang

Plant Pathology Faculty Publications

BACKGROUND: In addition to vertical transmission, organisms can also acquire genes from other distantly related species or from their extra-chromosomal elements (plasmids and viruses) via horizontal gene transfer (HGT). It has been suggested that phages represent substantial forces in prokaryotic evolution. In eukaryotes, retroviruses, which can integrate into host genome as an obligate step in their replication strategy, comprise approximately 8% of the human genome. Unlike retroviruses, few members of other virus families are known to transfer genes to host genomes.

RESULTS: Here we performed a systematic search for sequences related to circular single-stranded DNA (ssDNA) viruses in publicly available …

Relationships Among Rubus (Rosaceae) Species Used In Traditional Chinese Medicine, Yinu Wang

Masters Theses & Specialist Projects

Traditional Chinese medicine has a long history of using plants therapeutically including multiple species of the genus Rubus (Rosaceae). Fruits and other parts of Rubus plants have had a significant effect on human health and nutrition in both ancient and modern times. The pharmacological effects of Rubus include anti-inflammatory, antibacterial, anti-stress, anti-cancer and anti-aging properties. One of the current challenges limiting further development of Rubus resources in traditional Chinese medicine is a poor understanding of phylogenetic relationships among Rubus species in general and especially among Asian species, and also the need for additional studies of phytochemicals. Several confounding factors are …

Lafora Disease E3-Ubiquitin Ligase Malin Is Related To Trim32 At Both The Phylogenetic And Functional Level, Carlos Romá-Mateo, Daniel Moreno, Santiago Vernia, Teresa Rubio, Travis M. Bridges, Matthew S. Gentry, Pascual Sanz

Molecular and Cellular Biochemistry Faculty Publications

BACKGROUND: Malin is an E3-ubiquitin ligase that is mutated in Lafora disease, a fatal form of progressive myoclonus epilepsy. In order to perform its function, malin forms a functional complex with laforin, a glucan phosphatase that facilitates targeting of malin to its corresponding substrates. While laforin phylogeny has been studied, there are no data on the evolutionary lineage of malin.

RESULTS: After an extensive search for malin orthologs, we found that malin is present in all vertebrate species and a cephalochordate, in contrast with the broader species distribution previously reported for laforin. These data suggest that in addition to forming …

Multilocus And Parametric Analyses Of The Evolutionary History Of The Amazonian Peacock Cichlids, The Genus Cichla (Teleostei: Cichlidae), Stuart Willis

School of Biological Sciences: Dissertations, Theses, and Student Research

Accurate knowledge of species boundaries and species phylogeny are fundamental to testing hypotheses of recent evolutionary processes, but the estimation of these partitions is challenging due both to inherent confusion about what is being estimated as well as the data available to estimate them. Using multilocus data from mtDNA, microsatellites, and nuclear locus sequences of over 1100 individuals, we delimited eight separately evolving species of Cichla rather than the 15 described. Among species we found evidence of rare but widespread introgressive hybridization, while within these species we observed evidence of long-term gene exchange and constrained evolutionary trajectories. In most cases …

Episodic Radiations In The Fly Tree Of Life, Brian M. Wiegmann, Michelle D. Trautwein, Isaac S. Winkler, Norman B. Barr, Jung-Wook Kim, Christine Lambkin, Matthew Bertone, Brian Cassel, Keith Bayless, Alysha Heimberg

Dartmouth Scholarship

Flies are one of four superradiations of insects (along with beetles, wasps, and moths) that account for the majority of animal life on Earth. Diptera includes species known for their ubiquity (Musca domestica house fly), their role as pests (Anopheles gambiae malaria mosquito), and their value as model organisms across the biological sciences (Drosophila melanogaster). A resolved phylogeny for flies provides a framework for genomic, developmental, and evolutionary studies by facilitating comparisons across model organisms, yet recent research has suggested that fly relationships have been obscured by multiple episodes of rapid diversification. We provide a phylogenomic …

Genome-Wide Discovery Of Missing Genes In Biological Pathways Of Prokaryotes., Yong Chen, Fenglou Mao, Guojun Li, Ying Xu

Faculty Scholarship for the College of Science & Mathematics

BACKGROUND: Reconstruction of biological pathways is typically done through mapping well-characterized pathways of model organisms to a target genome, through orthologous gene mapping. A limitation of such pathway-mapping approaches is that the mapped pathway models are constrained by the composition of the template pathways, e.g., some genes in a target pathway may not have corresponding genes in the template pathways, the so-called "missing gene" problem.

METHODS: We present a novel pathway-expansion method for identifying additional genes that are possibly involved in a target pathway after pathway mapping, to fill holes caused by missing genes as well as to expand the …

Cellulose- And Xylan-Degrading Thermophilic Anaerobic Bacteria From Biocompost, M. V. Sizova, J. A. Izquierdo, N. S. Panikov, L. R. Lynd

Dartmouth Scholarship

Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S …

Coming To America: Multiple Origins Of New World Geckos, Tony Gamble, A. M. Bauer, G. R. Colli, E. Greenbaum, T. R. Jackman, Laurie J. Vitt, Andrew M. Simons

Biological Sciences Faculty Research and Publications

Geckos in the Western Hemisphere provide an excellent model to study faunal assembly at a continental scale. We generated a time-calibrated phylogeny, including exemplars of all New World gecko genera, to produce a biogeographic scenario for the New World geckos. Patterns of New World gecko origins are consistent with almost every biogeographic scenario utilized by a terrestrial vertebrate with different New World lineages showing evidence of vicariance, dispersal via temporary land bridge, overseas dispersal, or anthropogenic introductions. We also recovered a strong relationship between clade age and species diversity, with older New World lineages having more species than more recently …

Motus, Morphology, And Biodiversity Estimation: A Case Study Using Nematodes Of The Suborder Criconematina And A Conserved 18s Dna Barcode, Thomas O. Powers, Timothy Harris, Rebecca Higgins, Peter Mullin, Lisa Sutton, Kirsten Powers

Department of Plant Pathology: Faculty Publications

DNA barcodes are increasingly used to provide an estimate of biodiversity for small, cryptic organisms like nematodes. Nucleotide sequences generated by the barcoding process are often grouped, based on similarity, into molecular operational taxonomic units (MOTUs). In order to get a better understanding of the taxonomic resolution of a 3’ 592-bp 18S rDNA barcode, we have analyzed 100 MOTUs generated from 214 specimens in the nematode suborder Criconematina. Previous research has demonstrated that the primer set for this barcode reliably amplifies all nematodes in the Phylum Nematoda. Included among the Criconematina specimens were 25 morphologically described species representing 12 genera. …

Description Of Scottnema Lindsayae Timm, 1971 (Rhabditida: Cephalobidae) From Taylor Valley, Antarctica And Its Phylogenetic Relationship, Sven Boström, Oleksandr Holovachov, Steven A. Nadler

Harold W. Manter Laboratory of Parasitology: Faculty and Staff Publications

The endemic Antarctic nematode Scottnema lindsayae is described from specimens collected in Taylor Valley, McMurdo Dry Valleys, Victoria Land. The recently collected material is compared with the original description and other subsequent descriptions of the species. A more complete scanning electron microscopy (SEM) study of the species is presented. The phylogenetic position of S. lindsayae is inferred using a secondary structure-based alignment of a partial sequence of nuclear Large Subunit (LSU) ribosomal DNA. Phylogenetic trees were inferred using base-paired substitution models implemented in PHASE 2 software and Bayesian inference, and show S. lindsayae as the sister group to Stegelletina taxa.

Allotetraploid Origin And Divergence In Eleusine (Chloridoideae, Poaceae): Evidence From Low-Copy Nuclear Gene Phylogenies And A Plastid Gene Chronogram, Qing Liu, Jimmy K. Triplett, Jun Wen, Paul M. Peterson

Research, Publications & Creative Work

Background and Aims: Eleusine (Poaceae) is a small genus of the subfamily Chloridoideae exhibiting considerable morphological and ecological diversity in East Africa and the Americas. The interspecific phylogenetic relationships of Eleusine are investigated in order to identify its allotetraploid origin, and a chronogram is estimated to infer temporal relationships between palaeoenvironment changes and divergence of Eleusine in East Africa.

Methods: Two low-copy nuclear (LCN) markers, Pepc4 and EF-1a, were analysed using parsimony, likelihood and Bayesian approaches. A chronogram of Eleusine was inferred from a combined data set of six plastid DNA markers (ndhA intron, ndhF, rps16-trnK, rps16 intron, rps3, and …

Evolutionary Relationships Among Staphylococci And The Prevention Of Staphylococcus Aureus Nasal Colonization, Ryan Paul Lamers

Electronic Theses and Dissertations

Staphylococcus is a significant cause of human infection and mortality, worldwide. Currently, there are greater than 60 taxa within Staphylococcus, and nearly all are pathogenic. The collective potential for virulence among species of Staphylococcus heightens the overall clinical significance of this genus and argues for a thorough understanding of the evolutionary relationships among species. Within Staphylococcus, aureus is the most common cause of human infection, where nasal carriage of this bacterium is a known risk factor for autoinfection. The predisposition to infection by nasal carriers of S. aureus, and the ease with which strains are transferred between individuals, suggests that …

Phylogenetic Relationships Between Malcolmia, Strigosella, Zuvanda, And Some Closely Related Genera (Brassicaceae) From Turkey Revealed By Inter-Simple Sequence Repeat Amplification, Beki̇r Doğan, Murat Ünal, Fevzi̇ Özgökçe, Esra Marti̇n, Ayla Kaya

Turkish Journal of Botany

The genus Malcolmia W.T.Aiton is taxonomically problematic, and some of its species have recently been transferred to the genera Strigosella Boiss. and Zuvanda Dvorák. Three species of this genus are native to Turkey. The revision studies based on molecular data, which were collected in the past few years, display the phylogenetic relations and the systematic positions of the taxa more reliably and apparently. Thus taxonomic problems of species are resolved through DNA-based molecular analyses, which are not affected by environmental factors compared to phenotypic studies. In the present study, the amplifications of the DNA fragments were carried out using ISSR …

The Conservation And Ecology Of Carnivorous Plants, David Jennings

USF Tampa Graduate Theses and Dissertations

As discussed in Chapter 1, although our understanding of the ecology and evolution of carnivorous plants has greatly improved in recent years, many fundamental questions remain unanswered. Unfortunately, at the present time, many carnivorous plants are increasingly threatened by anthropogenic activities. Indeed, over half of the carnivorous plant species assessed by the International Union for the Conservation of Nature (IUCN) are listed as `threatened', but the threats to carnivorous plants have not previously been quantified. In Chapter 2, I quantified the conservation threats to carnivorous plant taxa worldwide by searching peer-reviewed literature, and found data on the threats to 48 …

Molecular Phylogeny And Divergence Times Estimates Of Lilium Section Liriotypus (Liliaceae) Based On Plastid And Nuclear Ribosomal Its Dna Sequence Data, Nursel İki̇nci̇

Turkish Journal of Botany

In the present study the phylogeny and the biogeography of the genus Lilium L. section Liriotypus Asch. et Graebn. were investigated and divergence times for the section Liriotypus were calculated. The study group covers Lilium species from Europe, the Italian and Balkan peninsulas, Anatolia, and the Caucasus. Plastid DNA sequence data (the trnC-petN intergenic spacer and petN gene) and nuclear DNA ITS sequence data were used to infer the phylogenetic history of the section Liriotypus. Molecular phylogenetic dating using the molecular clock hypothesis with sequences of nrDNA ITS region was used to calculate the time of diversification within the section …

Expanding Character Sampling For Ciliate Phylogenetic Inference Using Mitochondrial Ssu-Rdna As A Molecular Marker, Micah Dunthorn, Wilhelm Foissner, Laura A. Katz

Biological Sciences: Faculty Publications

Molecular systematics of ciliates, particularly at deep nodes, has largely focused on increasing taxon sampling using the nuclear small subunit rDNA (nSSU-rDNA) locus. These previous analyses have generally been congruent with morphologically-based classifications, although there is extensive non-monophyly at many levels. However, caution is needed in interpreting these results as nSSU-rDNA is just a single molecular marker. Here the mitochondrial small subunit rDNA (mtSSU-rDNA) is evaluated for deep ciliate nodes using the Colpodea as an example. Overall, well-supported nodes in the mtSSU-rDNA and concatenated topologies are well supported in the nSSU-rDNA topology; e.g., the non-monophyly of the Cyrtolophosidida. The two …