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1.
Menard, Katrina Louise.
Population genetic structure of Conophthorus ponderosae Hopkins (Coleoptera: Scolytidae) inferred from mitochondrial DNA haplotypes.
Degree: MS, Entomology, 2006, Texas A&M University
URL: http://hdl.handle.net/1969.1/4210 
► Pine cone beetles (Conophthorus sp.) are serious pests of many forest ecosystems since they burrow into pine cone tissues for egg deposition, causing the death…
(more)
▼ Pine cone beetles (Conophthorus sp.) are serious pests of many forest ecosystems
since they burrow into pine cone tissues for egg deposition, causing the death of the
seeds. Management of these beetles in natural and commercial stands of pines has been
problematic due to lack of understanding about species limits and distribution. This study
was conducted to investigate the phylogeography and phylogenetics of the genus. Several
species represented by disjunct populations appear to be monophyletic including
Conophthorus edulis, C. mexicanus, C. coniperda, and C. conicollens, whereas C.
ponderosae is polyphyletic with many distinct clades isolated by geography. This study
explored whether host use or geography has played a greater role in the diversification of
this genus, focusing on the polyphyletic C. ponderosae and the monophyletic C. edulis.
In the first study, 751bp of the mtDNA CO1 gene were sequenced to reconstruct a
phylogeny of the genus, and the distribution and host use were compared to investigate
whether these factors were significantly associated. The second study addressed
population structure and possible historical influences on the C. edulis and C. ponderosae
populations using a nested clade analysis of the mtDNA haplotypes. Despite potential
limitations due to sampling, several conclusions could be drawn. Three separate
haplotype networks were found for the C. ponderosae haplotypes, indicating that there have been at least three lineages that have associated with P. ponderosa. Geography was
significantly associated with the phylogeny at greater distances (>900km), but host use
was not significant. At the species level, association with geography is variable.
Population structure for C. ponderosae at the species level is minimal, and suggests that
there has not been much time for lineage sorting of the haplotypes based on the nested
clade analysis as compared to C. edulis.
Advisors/Committee Members: Cognato, Anthony (advisor), Honeycutt, Rodney (committee member), Wharton, Robert (committee member), Woolley, Jim (committee member).
Subjects/Keywords: Conophthorus; population genetics; nested clade analysis; host use; geography
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APA (6th Edition):
Menard, K. L. (2006). Population genetic structure of Conophthorus ponderosae Hopkins (Coleoptera: Scolytidae) inferred from mitochondrial DNA haplotypes. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/4210
Chicago Manual of Style (16th Edition):
Menard, Katrina Louise. “Population genetic structure of Conophthorus ponderosae Hopkins (Coleoptera: Scolytidae) inferred from mitochondrial DNA haplotypes.” 2006. Masters Thesis, Texas A&M University. Accessed March 07, 2021.
http://hdl.handle.net/1969.1/4210.
MLA Handbook (7th Edition):
Menard, Katrina Louise. “Population genetic structure of Conophthorus ponderosae Hopkins (Coleoptera: Scolytidae) inferred from mitochondrial DNA haplotypes.” 2006. Web. 07 Mar 2021.
Vancouver:
Menard KL. Population genetic structure of Conophthorus ponderosae Hopkins (Coleoptera: Scolytidae) inferred from mitochondrial DNA haplotypes. [Internet] [Masters thesis]. Texas A&M University; 2006. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1969.1/4210.
Council of Science Editors:
Menard KL. Population genetic structure of Conophthorus ponderosae Hopkins (Coleoptera: Scolytidae) inferred from mitochondrial DNA haplotypes. [Masters Thesis]. Texas A&M University; 2006. Available from: http://hdl.handle.net/1969.1/4210
Texas A&M University
2.
Montoya Ceballos, Jose Vicente.
Influence of hydrological seasonality on sandbank benthos: algal biomass and shrimp abundance in a large neotropical river.
Degree: PhD, Wildlife and Fisheries Sciences, 2009, Texas A&M University
URL: http://hdl.handle.net/1969.1/ETD-TAMU-3262
► In this study, I examined the influence of hydrological seasonality on spatiotemporal variation of algal biomass and shrimp abundance on sandbanks of the Cinaruco River…
(more)
▼ In this study, I examined the influence of hydrological seasonality on
spatiotemporal variation of algal biomass and shrimp abundance on sandbanks of the
Cinaruco River in southwestern Venezuela. Seasonal variations of abiotic and biotic
variables in the Cinaruco were driven by the hydrological regime. During the highwater
periods, river sites in the main channel and lagoon sites were similar in water
physicochemical variables and algal biomass. In contrast, physicochemical variables
and algal biomass differed between river and lagoon sites during the low-water period.
The absence of flow in lagoons and consistently low algal biomass on river sandbanks
were the most important features of the spatial variability between main-channel and
lagoon sandbanks during low-water phases. Benthic algal biomass was highly uniform
at small spatial scales and significantly heterogeneous at large spatial scales. In the
second major part of this dissertation, I found a relatively species-rich shrimp
assemblage with seven species inhabiting the sandbanks of the Cinaruco. I also
observed clear patterns of temporal and spatial variation in shrimp abundance on the
Cinaruco sandbanks. Abundance of shrimp on the sandbanks presented remarkable diel variation, showing almost exclusive use of this habitat at nights. Seasonally, shrimp
were more abundant during rising- and falling-water periods, when rapid changes of
environmental conditions occur. Shrimp abundance was high on those sandbanks with
absence of troughs and presence of submerged vegetation. These environmental features
presumably promote colonization/establishment and survival/persistence of shrimp in
the sandbanks. In a patch-dynamic view of communities, a mobility control model
seems to apply to shrimp of the sandbanks in the Cinaruco during the period of rapid
changes in hydrology and habitat structure. During low-water periods, when habitat
structure of sandbanks is relatively constant, low shrimp abundance appears to be
heavily controlled by high fish predation. The annual flood regime of the Cinaruco,
which drives the concentrations of dissolved materials, affects material interchanges
between aquatic and terrestrial systems, and modifies aquatic habitat structural
complexity, is responsible for creating strong patterns of seasonal and spatial variation in
benthic algal crops and shrimp abundance on the sandbanks of this large floodplain
river.
Advisors/Committee Members: Roelke, Daniel (advisor), Winemiller, Kirk (advisor), Cognato, Anthony (committee member), Davis, Stephen (committee member).
Subjects/Keywords: Hydrological Seasonality; Large Rivers; Algal Biomass; Benthos; Freshwater Shrimps; Sandbanks
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APA (6th Edition):
Montoya Ceballos, J. V. (2009). Influence of hydrological seasonality on sandbank benthos: algal biomass and shrimp abundance in a large neotropical river. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-3262
Chicago Manual of Style (16th Edition):
Montoya Ceballos, Jose Vicente. “Influence of hydrological seasonality on sandbank benthos: algal biomass and shrimp abundance in a large neotropical river.” 2009. Doctoral Dissertation, Texas A&M University. Accessed March 07, 2021.
http://hdl.handle.net/1969.1/ETD-TAMU-3262.
MLA Handbook (7th Edition):
Montoya Ceballos, Jose Vicente. “Influence of hydrological seasonality on sandbank benthos: algal biomass and shrimp abundance in a large neotropical river.” 2009. Web. 07 Mar 2021.
Vancouver:
Montoya Ceballos JV. Influence of hydrological seasonality on sandbank benthos: algal biomass and shrimp abundance in a large neotropical river. [Internet] [Doctoral dissertation]. Texas A&M University; 2009. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1969.1/ETD-TAMU-3262.
Council of Science Editors:
Montoya Ceballos JV. Influence of hydrological seasonality on sandbank benthos: algal biomass and shrimp abundance in a large neotropical river. [Doctoral Dissertation]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-3262
Texas A&M University
3.
Yoder, Matthew Jon.
Advances in diapriid (Hymenoptera: diapriidae) systematics, with contributions to cybertaxonomy and the analysis of rRNA sequence data.
Degree: PhD, Entomology, 2009, Texas A&M University
URL: http://hdl.handle.net/1969.1/ETD-TAMU-1301
► Diapriids (Hymenoptera: Diapriidae) are small parasitic wasps. Though found throughout the world they are relatively unknown. A framework for advancing diapriid systematics is developed by…
(more)
▼ Diapriids (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.
Advisors/Committee Members: Wharton, Robert (advisor), Cognato, Anthony (committee member), Honeycutt, Rodney (committee member), Woolley, James B. (committee member).
Subjects/Keywords: Systematics; Diapriidae; rRNA; secondary structure; phylogeny; database; cybertaxonomy
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APA (6th Edition):
Yoder, M. J. (2009). Advances in diapriid (Hymenoptera: diapriidae) systematics, with contributions to cybertaxonomy and the analysis of rRNA sequence data. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/ETD-TAMU-1301
Chicago Manual of Style (16th Edition):
Yoder, Matthew Jon. “Advances in diapriid (Hymenoptera: diapriidae) systematics, with contributions to cybertaxonomy and the analysis of rRNA sequence data.” 2009. Doctoral Dissertation, Texas A&M University. Accessed March 07, 2021.
http://hdl.handle.net/1969.1/ETD-TAMU-1301.
MLA Handbook (7th Edition):
Yoder, Matthew Jon. “Advances in diapriid (Hymenoptera: diapriidae) systematics, with contributions to cybertaxonomy and the analysis of rRNA sequence data.” 2009. Web. 07 Mar 2021.
Vancouver:
Yoder MJ. Advances in diapriid (Hymenoptera: diapriidae) systematics, with contributions to cybertaxonomy and the analysis of rRNA sequence data. [Internet] [Doctoral dissertation]. Texas A&M University; 2009. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1301.
Council of Science Editors:
Yoder MJ. Advances in diapriid (Hymenoptera: diapriidae) systematics, with contributions to cybertaxonomy and the analysis of rRNA sequence data. [Doctoral Dissertation]. Texas A&M University; 2009. Available from: http://hdl.handle.net/1969.1/ETD-TAMU-1301
Texas A&M University
4.
Usener, Jessica LeAnn.
Phylogenetic revision of desert fireflies (Coleoptera: Lampyridae: microphotus).
Degree: MS, Entomology, 2006, Texas A&M University
URL: http://hdl.handle.net/1969.1/3063
► Morphological, mtCOI DNA, and luciferase DNA data are analyzed individually and simultaneously for phylogenetic signal. Analysis of 16 characters traditionally used in species identification for…
(more)
▼ Morphological, mtCOI DNA, and luciferase DNA data are analyzed individually
and simultaneously for phylogenetic signal. Analysis of 16 characters traditionally used
in species identification for 317 individual Microphotus specimens yields 5000 trees
with poor resolution. Although mtCOI and luciferase data conflict in basal clades, both
contribute to the phylogeny of Microphotus. Based on lack of morphological variation
and geographic and temporal proximity of collection localities,
M. decarthrus Fall 1912
and
M. fragilis Oliver 1912 are synonomized.
Microphotus octarthrus Fall occurs throughout the southwestern United States in
discontinuous pinyon-juniper and juniper-oak habitats. Wide geographic distribution,
discontinuous habitat and limited dispersal capabilities of females makes this species
ideal for the study of genetic variation. MantelÂs approximate t test indicates that
populations are both geographically and genetically isolated. Twenty-six haplotypes are
found among 28 individuals; haplotypes are unique for the populations studied. When
subjected to a 2.3% sequence divergence rate, mean branch lengths suggest segregation
of populations began in the Holocene, before Pleistocene glaciation. Although these
data suggest greater species diversity, more data, including mating behavior and more
genes are required to further elucidate species limits.
Advisors/Committee Members: Cognato, Anthony I. (advisor), Woolley, James (committee member), Honeycutt, Rodney (committee member).
Subjects/Keywords: Phlogenetics; Lampyridae; Microphotus
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APA (6th Edition):
Usener, J. L. (2006). Phylogenetic revision of desert fireflies (Coleoptera: Lampyridae: microphotus). (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/3063
Chicago Manual of Style (16th Edition):
Usener, Jessica LeAnn. “Phylogenetic revision of desert fireflies (Coleoptera: Lampyridae: microphotus).” 2006. Masters Thesis, Texas A&M University. Accessed March 07, 2021.
http://hdl.handle.net/1969.1/3063.
MLA Handbook (7th Edition):
Usener, Jessica LeAnn. “Phylogenetic revision of desert fireflies (Coleoptera: Lampyridae: microphotus).” 2006. Web. 07 Mar 2021.
Vancouver:
Usener JL. Phylogenetic revision of desert fireflies (Coleoptera: Lampyridae: microphotus). [Internet] [Masters thesis]. Texas A&M University; 2006. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1969.1/3063.
Council of Science Editors:
Usener JL. Phylogenetic revision of desert fireflies (Coleoptera: Lampyridae: microphotus). [Masters Thesis]. Texas A&M University; 2006. Available from: http://hdl.handle.net/1969.1/3063
Texas A&M University
5.
Benavides, Lucille H.
Genetic variation in the eastern subterranean termite Reticulitermes flavipes (Isoptera: Rhinotermitidae).
Degree: MS, Entomology, 2006, Texas A&M University
URL: http://hdl.handle.net/1969.1/3319
► The eastern subterranean termite, Reticulitermes flavipes, is the most widely dispersed termite in North America. The genus Reticulitermes spp. is responsible for 80% of total…
(more)
▼ The eastern subterranean termite, Reticulitermes flavipes, is the most widely dispersed termite in North America. The genus Reticulitermes spp. is responsible for 80% of total termite damage caused to urban structures each year. Little is known about the genetic structure of termites, particularly at the colony level. Evidence for what genetically defines a termite colony is a hotly debated topic in current literature due to the implications such findings would have regarding current lawsuits against pest control operations. Information on termite genetic structure is sparse.
In this study, the genetic variation and gene flow among
Texas populations of R. flavipes at the statewide level and city level was examined. A 324-337 base pairs segment of the mtDNA, AT-rich region was a polymerase chain reaction amplified from 104 different termite specimens from 12
Texas cities. The DNA extracts were then subjected to PCR amplification using specific primers and it was then sequenced. Using the sequence data and appropriate statistical measures it was found that, at the statewide level, nucleotide and haplotypic diversity is low. Gene flow was found to be low on a statewide basis. At the city level nucleotide and haplotypic diversity was high. The findings of this study provide insights into termite genetic structure.
Advisors/Committee Members: Cognato, Anthony (advisor), Gold, Roger (advisor), Cruz-Reyes, Jorge (committee member).
Subjects/Keywords: genetic variation
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APA (6th Edition):
Benavides, L. H. (2006). Genetic variation in the eastern subterranean termite Reticulitermes flavipes (Isoptera: Rhinotermitidae). (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/3319
Chicago Manual of Style (16th Edition):
Benavides, Lucille H. “Genetic variation in the eastern subterranean termite Reticulitermes flavipes (Isoptera: Rhinotermitidae).” 2006. Masters Thesis, Texas A&M University. Accessed March 07, 2021.
http://hdl.handle.net/1969.1/3319.
MLA Handbook (7th Edition):
Benavides, Lucille H. “Genetic variation in the eastern subterranean termite Reticulitermes flavipes (Isoptera: Rhinotermitidae).” 2006. Web. 07 Mar 2021.
Vancouver:
Benavides LH. Genetic variation in the eastern subterranean termite Reticulitermes flavipes (Isoptera: Rhinotermitidae). [Internet] [Masters thesis]. Texas A&M University; 2006. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1969.1/3319.
Council of Science Editors:
Benavides LH. Genetic variation in the eastern subterranean termite Reticulitermes flavipes (Isoptera: Rhinotermitidae). [Masters Thesis]. Texas A&M University; 2006. Available from: http://hdl.handle.net/1969.1/3319
Texas A&M University
6.
Mynhardt, Glene.
Population genetics of the pecan weevil, Curculio caryae Horn (Coleoptera: Curculionidae), inferred from mitochondrial nucleotide data.
Degree: MS, Entomology, 2006, Texas A&M University
URL: http://hdl.handle.net/1969.1/4388
► The pecan weevil, Curculio caryae Horn, is an obligate nut feeder of all North American hickory (Carya) and a key pest of the pecan, C.…
(more)
▼ The pecan weevil, Curculio caryae Horn, is an obligate nut feeder of all North American hickory
(Carya) and a key pest of the pecan, C. illinoinensis Koch. This study investigated population
structure of the pecan weevil. Gene flow and genetic variation was estimated for 90 pecan
weevil specimens sampled from the entire Carya range. Cladistic and nested clade analyses, as
well as an analysis of molecular variance (AMOVA) of mitochondrial DNA cytochrome oxidase
I (mtDNA COI) were performed. The data indicate C. caryae diverged from its sister species, C.
nasicus approximately 4.3 million years before present (mybp). Six-hundred and forty equally
parsimonious trees of 31 haplotypes demonstrated high genetic diversity across all pecan weevil
samples, and significant regional subdivision. Three clades recovered in the parsimony and
nested clade analyses were strongly associated with western, eastern and central localities
sampled within C. caryae's range. The current distribution of C. caryae and population structure
were explained by past glaciation events. Lineage divergence between the western and eastern
populations occurred during the Pleistocene (approx. 1.1 million years ago), and a more recent
divergence occurred between C. caryae populations east and west of the Appalachian mountain
range (870,000 yrs. ago). Haplotypes were segregated by region, but further sampling is
necessary to test for gene flow among these regions.
Advisors/Committee Members: Cognato, Anthony I. (advisor), Harris, Marvin K. (advisor), Bickham, John W. (committee member).
Subjects/Keywords: COI; Nested Clade Analysis
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APA (6th Edition):
Mynhardt, G. (2006). Population genetics of the pecan weevil, Curculio caryae Horn (Coleoptera: Curculionidae), inferred from mitochondrial nucleotide data. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/4388
Chicago Manual of Style (16th Edition):
Mynhardt, Glene. “Population genetics of the pecan weevil, Curculio caryae Horn (Coleoptera: Curculionidae), inferred from mitochondrial nucleotide data.” 2006. Masters Thesis, Texas A&M University. Accessed March 07, 2021.
http://hdl.handle.net/1969.1/4388.
MLA Handbook (7th Edition):
Mynhardt, Glene. “Population genetics of the pecan weevil, Curculio caryae Horn (Coleoptera: Curculionidae), inferred from mitochondrial nucleotide data.” 2006. Web. 07 Mar 2021.
Vancouver:
Mynhardt G. Population genetics of the pecan weevil, Curculio caryae Horn (Coleoptera: Curculionidae), inferred from mitochondrial nucleotide data. [Internet] [Masters thesis]. Texas A&M University; 2006. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1969.1/4388.
Council of Science Editors:
Mynhardt G. Population genetics of the pecan weevil, Curculio caryae Horn (Coleoptera: Curculionidae), inferred from mitochondrial nucleotide data. [Masters Thesis]. Texas A&M University; 2006. Available from: http://hdl.handle.net/1969.1/4388
Texas A&M University
7.
Caesar, Ryan Matthew.
Population structure of Acrotrichis xanthocera (Matthews) (Coleoptera: Ptiliidae) in the Klamath Ecoregion of northwestern California, inferred from mitochondrial DNA sequence variation.
Degree: MS, Entomology, 2004, Texas A&M University
URL: http://hdl.handle.net/1969.1/459
► The Klamath-Siskiyou Ecoregion of northern California and southern Oregon has extremely high biodiversity, but conservation centers on the protection of habitat for the northern spotted…
(more)
▼ The Klamath-Siskiyou Ecoregion of northern California and southern Oregon has extremely high biodiversity, but conservation centers on the protection of habitat for the northern spotted owl. A network of late successional reserves has been established without consideration of potential for protecting overall biodiversity, including genetic diversity. Mitochondrial DNA sequences are used to examine the population structure of Acrotrichis xanthocera (Coleoptera: Ptiliidae) sampled from five late successional reserves within the Klamath-Siskiyou Ecoregion and five comparison sites from northern California. Measures of gene flow, phylogenetic analysis, and nested clade analysis are employed to infer historical demographic and phylogeographic processes. Results show that A. xanthocera populations have undergone past range expansion, but gene flow is currently limited. Individual late successional reserves do not adequately protect the genetic variation in this species. Although further research is needed, these results are likely to be congruent for other edaphic arthropod species. Improvement of the late successional reserve system is warranted for maximum protection of the genetic diversity of soil arthropod populations.
Advisors/Committee Members: Cognato, Anthony I. (advisor), Woolley, James B. (committee member), Johnston, J. Spencer (committee member), Honeycutt, Rodney (committee member).
Subjects/Keywords: Coleoptera; phylogeography; nested clade analysis; population structure
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APA (6th Edition):
Caesar, R. M. (2004). Population structure of Acrotrichis xanthocera (Matthews) (Coleoptera: Ptiliidae) in the Klamath Ecoregion of northwestern California, inferred from mitochondrial DNA sequence variation. (Masters Thesis). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/459
Chicago Manual of Style (16th Edition):
Caesar, Ryan Matthew. “Population structure of Acrotrichis xanthocera (Matthews) (Coleoptera: Ptiliidae) in the Klamath Ecoregion of northwestern California, inferred from mitochondrial DNA sequence variation.” 2004. Masters Thesis, Texas A&M University. Accessed March 07, 2021.
http://hdl.handle.net/1969.1/459.
MLA Handbook (7th Edition):
Caesar, Ryan Matthew. “Population structure of Acrotrichis xanthocera (Matthews) (Coleoptera: Ptiliidae) in the Klamath Ecoregion of northwestern California, inferred from mitochondrial DNA sequence variation.” 2004. Web. 07 Mar 2021.
Vancouver:
Caesar RM. Population structure of Acrotrichis xanthocera (Matthews) (Coleoptera: Ptiliidae) in the Klamath Ecoregion of northwestern California, inferred from mitochondrial DNA sequence variation. [Internet] [Masters thesis]. Texas A&M University; 2004. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1969.1/459.
Council of Science Editors:
Caesar RM. Population structure of Acrotrichis xanthocera (Matthews) (Coleoptera: Ptiliidae) in the Klamath Ecoregion of northwestern California, inferred from mitochondrial DNA sequence variation. [Masters Thesis]. Texas A&M University; 2004. Available from: http://hdl.handle.net/1969.1/459
Texas A&M University
8.
Gillespie, Joseph James.
Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules.
Degree: PhD, Entomology, 2005, Texas A&M University
URL: http://hdl.handle.net/1969.1/2580
► Ribosomal 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.…
(more)
▼ Ribosomal 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.
Advisors/Committee Members: Cognato, Anthony I. (advisor), Honeycutt, Rodney L. (committee member), Woolley, James B. (committee member), Zhu-Salzman, Keyan (committee member).
Subjects/Keywords: ribosomal RNA; phylogeny; secondary structure; molecular evolution
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APA (6th Edition):
Gillespie, J. J. (2005). Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/2580
Chicago Manual of Style (16th Edition):
Gillespie, Joseph James. “Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules.” 2005. Doctoral Dissertation, Texas A&M University. Accessed March 07, 2021.
http://hdl.handle.net/1969.1/2580.
MLA Handbook (7th Edition):
Gillespie, Joseph James. “Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules.” 2005. Web. 07 Mar 2021.
Vancouver:
Gillespie JJ. Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules. [Internet] [Doctoral dissertation]. Texas A&M University; 2005. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1969.1/2580.
Council of Science Editors:
Gillespie JJ. Structure-based methods for the phylogenetic analysis of ribosomal RNA molecules. [Doctoral Dissertation]. Texas A&M University; 2005. Available from: http://hdl.handle.net/1969.1/2580
Texas A&M University
9.
Walker, Mindy Lynn.
Mitochondrial-DNA variation and the evolutionary affinities of the Peromyscus maniculatus complex from western North America.
Degree: PhD, Biology, 2006, Texas A&M University
URL: http://hdl.handle.net/1969.1/3216
► Intraspecific phylogeography and the phylogenetic relationships of recently-diverged taxa are best assessed with the use of a genetic marker that coalesces rapidly and thus provides…
(more)
▼ Intraspecific phylogeography and the phylogenetic relationships of recently-diverged taxa are best assessed with the use of a genetic marker that coalesces rapidly and thus provides phylogenetically informative characters for closely-related taxa. Mitochondrial DNA (mtDNA) fits these criteria and was thereby ideal for analyzing genetic variation within and among the youngest taxonomic members of the Peromyscus maniculatus species group, P. sejugis (restricted to two islands in the Sea of CortÃÂés), P. maniculatus (distributed throughout North and Central America) and P. keeni (a coastal species restricted to the Pacific Northwest of North America). The approach utilized in this research involved sequencing a 1439 base-pair (bp) region of mtDNA for a total of 581 specimens representing 45 different geographic localities from along the west coast of North America. The sequences obtained were used to assess the partitioning of genetic diversity within and among these taxa, address phylogenetic and taxonomic concerns about the western representatives of the P. maniculatus species group and discuss the post-Pleistocene biogeography of the west coast of North America. Analysis of mtDNA sequence variation, considered within the framework of a phylogenetic species concept, revealed the existence of two evolutionarily significant units of P. sejugis as well as a previously unrecognized sibling species nested within the Pacific coastal range of P. maniculatus. Moreover, analysis of intraspecific sequence divergence allowed for the identification of the ice-free refugium thought to harbor P. keeni throughout glaciation during the Pleistocene epoch. This work will establish the foundation for additional examination of cryptic genetic variation in different morphotypes of P. maniculatus and continue the precedent for recognizing P. maniculatus-group taxa that reflect true evolutionary entities.
Advisors/Committee Members: Greenbaum, Ira F. (advisor), Bickham, John W. (committee member), Cognato, Anthony I. (committee member), Honeycutt, Rodney L. (committee member).
Subjects/Keywords: Peromyscus maniculatus; Peromyscus keeni; Peromyscus sejugis; California; Baja; Hecate
Record Details
Similar Records
Cite
Share »
Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Walker, M. L. (2006). Mitochondrial-DNA variation and the evolutionary affinities of the Peromyscus maniculatus complex from western North America. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/3216
Chicago Manual of Style (16th Edition):
Walker, Mindy Lynn. “Mitochondrial-DNA variation and the evolutionary affinities of the Peromyscus maniculatus complex from western North America.” 2006. Doctoral Dissertation, Texas A&M University. Accessed March 07, 2021.
http://hdl.handle.net/1969.1/3216.
MLA Handbook (7th Edition):
Walker, Mindy Lynn. “Mitochondrial-DNA variation and the evolutionary affinities of the Peromyscus maniculatus complex from western North America.” 2006. Web. 07 Mar 2021.
Vancouver:
Walker ML. Mitochondrial-DNA variation and the evolutionary affinities of the Peromyscus maniculatus complex from western North America. [Internet] [Doctoral dissertation]. Texas A&M University; 2006. [cited 2021 Mar 07].
Available from: http://hdl.handle.net/1969.1/3216.
Council of Science Editors:
Walker ML. Mitochondrial-DNA variation and the evolutionary affinities of the Peromyscus maniculatus complex from western North America. [Doctoral Dissertation]. Texas A&M University; 2006. Available from: http://hdl.handle.net/1969.1/3216
. 
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