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Texas A&M University
1.
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
2.
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
3.
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
4.
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
5.
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
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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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