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Papers by Tom Titus

Research paper thumbnail of The Northern Red-legged Frog (Rana aurora) on the Proposed Green Valley Glen Development Site

Research paper thumbnail of Genetic Variation in Two Subspecies of Ambystoma gracile (Caudata: Ambystomatidae)

Journal of Herpetology, 1990

... Interpreting breeding patterns from census data: a solution to the Husting dilemma. ... Genet... more ... Interpreting breeding patterns from census data: a solution to the Husting dilemma. ... Genetic Variation in Two Subspecies of Ambystoma gracile (Caudata: Ambystomatidae) TOM A. TITUS, Museum of Natural History and Depart-ment of Systematics and Ecology, University of ...

Research paper thumbnail of Color polymorphism in neotropical treefrogs: an allozymic investigation of the taxonomic status of Hyla favosa Cope

Herpetologica, Mar 1, 1989

Hyla favosa, Hyla leucophyllata, and phenotypic intermediates between these species were discover... more Hyla favosa, Hyla leucophyllata, and phenotypic intermediates between these species were discovered in microsympatry in southeastern Peru. The genetic composition of individuals of all three phenotypes was analyzed using starch-gel protein electrophoresis to test the validity of species level status for H. favosa and H. leucophyllata. Twenty-two presumptive gene loci were scored. No alleles diagnostic of the two pure phenotypes were found. Phenotypic intermediates were genetically indistinguishable from the two pure forms and ...

Research paper thumbnail of Molecular Phylogenetics of Desmognathine Salamanders (Caudata: Plethodontidae): A Reevaluation of Evolution in Ecology, Life History, and Morphology

Systematic Biology, 1996

Phylogenetic relationships were reconstructed for salamanders of the plethodontid subfamily Desmo... more Phylogenetic relationships were reconstructed for salamanders of the plethodontid subfamily Desmognathinae to examine evolution of morphology, ecology, and life history. Mitochondrial DNA sequences encoding 12S and 16S ribosomal RNA and the valine transfer RNA provided 259 phylogenetically informative sites from approximately 1,200 nucleotide positions for 21 specimens representing 15 species and subspecies. These data were analyzed in conjunction with 13 morphological and reproductive characters to generate phylogenetic hypotheses. The directly developing terrestrial desmognathines Phaeognathus hubrichti and Desmognathus wrighti represent, respectively, the first and second phylogenetic branching events within the subfamily, and the remaining terrestrial lineage, D. aeneus, also branches near the base of the phylogenetic tree. These results challenge earlier hypotheses that within Desmognathus the small nonmetamorphosing species, D. aeneus and D. wrighti, represent the end of a graded phylogenetic decrease in size and decrease in use of aquatic habitats. In contrast to previous hypotheses, our results suggest that desmognathine evolution includes transformations in the direction of larger body sizes, lengthened larval periods, and greater use of aquatic habitats.

Research paper thumbnail of Phylogenetics of the Lizard Genus Tropidurus (Squamata: Tropiduridae: Tropidurinae): Direct Optimization, Descriptive Efficiency, and Sensitivity Analysis of Congruence Between Molecular Data and Morphology

Molecular Phylogenetics and Evolution, 2001

By use of the technique of direct optimization the phylogenetics of the cis-Andean lizard genus T... more By use of the technique of direct optimization the phylogenetics of the cis-Andean lizard genus Tropidurus were examined on the basis of both molecular (ca. 1.04 kb of sequences from 12S rDNA, valine tDNA, and 16S rDNA) and morphological (93 characters) data. Although equal weighting of all parsimony cost functions logically must maximize descriptive efficiency and explanatory power of all evidence, a sensitivity analysis demonstrated that equal weighting of indels, transitions, transversions, and morphological change provided the most congruent solution between the molecular and the morphological data partitions. The position of Uranoscodon is resolved as the sister taxon of the remaining members of the Tropidurinae. Plica, Uracentron, and Strobilurus, previously considered synonyms of Tropidurus, are resurrected; the group of these three genera form the sister taxon of the former Tropidurus nanuzae group (herein named Eurolophosaurus) plus Tropidurus sensu stricto (composed of the T. bogerti, T. semitaeniatus, T. spinulosus, and T. torquatus groups, herein diagnosed).

Research paper thumbnail of Molecular Homology Assessment and Phylogeny in the Lizard Family Opluridae (Squamata: Iguania)

Molecular Phylogenetics and Evolution, 1996

The effect of utilizing secondary structure on multiple alignment and phylogeny reconstruction wa... more The effect of utilizing secondary structure on multiple alignment and phylogeny reconstruction was examined for the mitochondrial 12S ribosomal RNA and valine transfer RNA genes in the lizard family Opluridae. Computer-generated multiple alignments were performed under parsimony using gap costs of 1-10 both with and without reference to secondary structure. Alignments performed without secondary structure resulted in disruption of positional homology in some stems at all gap costs. Number of misaligned stem positions increased with gap cost. Phylogenetic analyses of multiple alignments without secondary structure recovered a well-supported morphological tree for five gap costs, and this was the single most parsimonious tree only for a gap cost of 1. Computer-generated multiple alignments using secondary structure to maintain positional homologs in stems recovered the morphological tree over all gap costs, and this was the single most parsimonious tree for 8 of 10 gap costs. The combined morphological and molecular data produced a single most parsimonious oplurid tree that was congruent with the morphological tree over all gap costs. Chalaradon madagascariensis is the sister taxon of Oplurus, which itself contains two clades: one with the arboreal Oplurus cuvieri and Oplurus cyclurus and the other with the saxicolous Oplurus grandidieri, Oplurus fierinensis, Oplurus quadrimaculatus, and Oplurus saxicola.

Research paper thumbnail of Tissue-specific gene expression in the smallmouth salamander, Ambystoma texanum (Caudata: Ambystomatidae)

Biochemical Systematics and Ecology, 1994

Relative staining activity, heteropolymer assembly, and secondary isozymes are described for gene... more Relative staining activity, heteropolymer assembly, and secondary isozymes are described for gene products of 22 loci examined for expression in eight tissues of Ambystoma texanum. Locus homologies based on tissue specificity and staining patterns in mitochondria-enriched liver fractions are proposed. Quaternary structure was inferred from polymorphisms resolved at seven loci. Gene expression was undetectable in 17 of the 176 tissue/locus comparisons. The phylogenetic pattern of changes in gene number and the extensive variation in tissue-specific expression among tetrapods suggest that these attributes will be useful as phylogenetic characters in groups less inclusive than tetrapods.

Research paper thumbnail of A Molecular Perspective on the Phylogeny of the Girdled Lizards (Cordylidae, Squamata)

American Museum Novitates, 2001

Mitochondrial DNA sequences were obtained for 16 species representing all nominal genera of Cordy... more Mitochondrial DNA sequences were obtained for 16 species representing all nominal genera of Cordylidae (Platysaurus, Chamaesaura, Cordylus, and Pseudocordylus). Gerrhosauridae and Teiidae were used as first and second outgroups. Results indicate that the oviparous Platysaurus is the sister taxon of the remaining cordylids (all of which are ovoviviparous). Within the ovoviviparous group Cordylus is paraphyletic with respect to Chamaesaura and Pseudocordylus. No evidence of Pseudocordylus monophyly was discovered. The three species of Chamaesaura and the seven species of Pseudocordylus are transferred to Cordylus to render a monophyletic taxonomy. 2 NO. 3310 AMERICAN MUSEUM NOVITATES

Research paper thumbnail of A molecular phylogenetic perspective on the evolutionary history of Alosa spp. (Clupeidae)

Molecular Phylogenetics and Evolution, 2006

... to A. alosa. However, the bootstrap support for this clade is inconsistent among reconstruc-t... more ... to A. alosa. However, the bootstrap support for this clade is inconsistent among reconstruc-tion approaches and there is a lack of reciprocal mono-phyly between A. fallax and the Black Sea/Lake Volvi clades (Fig. 1), due to the one highly divergent haplotype from Turkey (A ...

Research paper thumbnail of Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus Cavefish

Molecular Biology and Evolution, 2013

In adaptating to perpetual darkness, cave species gradually lose eyes and body pigmentation and e... more In adaptating to perpetual darkness, cave species gradually lose eyes and body pigmentation and evolve alternatives for exploring their environments. Although troglodyte features evolved independently many times in cavefish, we do not yet know whether independent evolution of these characters involves common genetic mechanisms. Surface-dwelling and many cave-dwelling species make the freshwater teleost genus Sinocyclocheilus an excellent model for studying the evolution of adaptations to life in constant darkness. We compared the mature retinal histology of surface and cave species in Sinocyclocheilus and found that adult cavefish showed a reduction in the number and length of photoreceptor cells. To identify genes and genetic pathways that evolved in constant darkness, we used RNA-seq to compare eyes of surface and cave species. De novo transcriptome assemblies were developed for both species, and contigs were annotated with gene ontology. Results from cave-dwelling Sinocyclocheilus revealed reduced transcription of phototransduction and other genes important for retinal function. In contrast to the blind Mexican tetra cavefish Astyanax mexicanus, our results on morphologies and gene expression suggest that evolved retinal reduction in cave-dwelling Sinocyclocheilus occurs in a lens-independent fashion by the reduced proliferation and downregulation of transcriptional factors shown to have direct roles in retinal development and maintenance, including cone-rod homeobox (crx) and Wnt pathway members. These results show that the independent evolution of retinal degeneration in cavefish can occur by different developmental genetic mechanisms.

Research paper thumbnail of Two additional midline barriers function with midline lefty1 expression to maintain asymmetric Nodal signaling during left-right axis specification in zebrafish

Development, 2011

Left-right (L/R) patterning is crucial for the proper development of all vertebrates and requires... more Left-right (L/R) patterning is crucial for the proper development of all vertebrates and requires asymmetric expression of nodal in the lateral plate mesoderm (LPM). The mechanisms governing asymmetric initiation of nodal have been studied extensively, but because Nodal is a potent activator of its own transcription, it is also crucial to understand the regulation required to maintain this asymmetry once it is established. The 'midline barrier', consisting of lefty1 expression, is a conserved mechanism for restricting Nodal activity to the left. However, the anterior and posterior extremes of the LPM are competent to respond to Nodal signals yet are not adjacent to this barrier, suggesting that lefty1 is not the only mechanism preventing ectopic Nodal activation. Here, we demonstrate the existence of two additional midline barriers. The first is a 'posterior barrier' mediated by Bmp signaling that prevents nodal propagation through the posterior LPM. In contrast to previous reports, we find that Bmp represses Nodal signaling independently of lefty1 expression and through the activity of a ligand other than Bmp4. The 'anterior barrier' is mediated by lefty2 expression in the left cardiac field and prevents Nodal activation from traveling across the anterior limit of the notochord and propagating down the right LPM. Both barriers appear to be conserved across model systems and are thus likely to be present in all vertebrates.

Research paper thumbnail of Geographic Variation, Species Recognition, and Molecular Evolution of Cytochrome Oxidase I in the Tropidurus spinulosus Complex (Iguania: Tropiduridae)

Copeia, 1998

... 4 rio Paraguay, y su distribucion extende al este y noreste en Mato Grosso do Sul y Goias, Br... more ... 4 rio Paraguay, y su distribucion extende al este y noreste en Mato Grosso do Sul y Goias, Brasil. Aunque las diagnoses son discutibles, predecimos que datos adicion-ales revelaran que T. guarani esta compuesto de dos lineas que denotamos T. guarani "Paraguari" y T ...

Research paper thumbnail of The Fanconi anemia gene network is conserved from zebrafish to human

Gene, Apr 26, 2006

Fanconi anemia (FA) is a complex disease involving nine identified and two unidentified loci that... more Fanconi anemia (FA) is a complex disease involving nine identified and two unidentified loci that define a network essential for maintaining genomic stability. To test the hypothesis that the FA network is conserved in vertebrate genomes, we cloned and sequenced zebrafish (Danio rerio) cDNAs and/or genomic BAC clones orthologous to all nine cloned FA genes (FANCA, FANCB, FANCC, FANCD1, FANCD2, FANCE, FANCF, FANCG, and FANCL), and identified orthologs in the genome database for the pufferfish Tetraodon nigroviridis. Genomic organization of exons and introns was nearly identical between zebrafish and human for all genes examined. Hydrophobicity plots revealed conservation of FA protein structure. Evolutionarily conserved regions identified functionally important domains, since many amino acid residues mutated in human disease alleles or shown to be critical in targeted mutagenesis studies are identical in zebrafish and human. Comparative genomic analysis demonstrated conserved syntenies for all FA genes. We conclude that the FA gene network has remained intact since the last common ancestor of zebrafish and human lineages. The application of powerful genetic, cellular, and embryological methodologies make zebrafish a useful model for discovering FA gene functions, identifying new genes in the network, and identifying therapeutic compounds.

Research paper thumbnail of The Fanconi anemia/BRCA gene network in zebrafish: Embryonic expression and comparative genomics

Mutation Research Fundamental and Molecular Mechanisms of Mutagenesis, Jul 1, 2009

Fanconi anemia (FA) is a genic disease resulting in bone marrow failure, high cancer risks, and i... more Fanconi anemia (FA) is a genic disease resulting in bone marrow failure, high cancer risks, and infertility, and developmental anomalies including microphthalmia, microcephaly, hypoplastic radius and thumb. Here we present cDNA sequences, genetic mapping, and genomic analyses for the four previously undescribed zebrafish FA genes (fanci, fancj, fancm, and fancn, and show that they reverted to single copy after the teleost genome duplication. We tested the hypothesis that FA genes are expressed during embryonic development in tissues that are disrupted in human patients by investigating fanc gene expression patterns. We found fanc gene maternal message, which can provide Fanc proteins to repair DNA damage encountered in rapid cleavage divisions. Zygotic expression was broad but especially strong in eyes, central nervous system and hematopoietic tissues. In the pectoral fin bud at hatching, fanc genes were expressed specifically in the apical ectodermal ridge, a signaling center for fin/limb development that may be relevant to the radius/thumb anomaly of FA patients. Hatching embryos expressed fanc genes strongly in the oral epithelium, a site of squamous cell carcinomas in FA patients. Larval and adult zebrafish expressed fanc genes in proliferative regions of the brain, which may be related to microcephaly in FA. Mature ovaries and testes expressed fanc genes in specific stages of oocyte and spermatocyte development, which may be related to DNA repair during homologous recombination in meiosis and to infertility in human patients. The intestine strongly expressed some fanc genes specifically in proliferative zones. Our results show that zebrafish has a complete complement of fanc genes in single copy and that these genes are expressed in zebrafish embryos and adults in proliferative tissues that are often affected in FA patients. These results support the notion that zebrafish offers an attractive experimental system to help unravel mechanisms relevant not only to FA, but also to breast cancer, given the involvement of fancj (brip1), fancn (palb2) and fancd1 (brca2) in both conditions.

Research paper thumbnail of Albertson'10SkeletalEvolutionInAntarcticFishes

Research paper thumbnail of The Fanconi anemia/BRCA gene network in zebrafish: Embryonic expression and comparative genomics

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 2009

Fanconi anemia (FA) is a genic disease resulting in bone marrow failure, high cancer risks, and i... more Fanconi anemia (FA) is a genic disease resulting in bone marrow failure, high cancer risks, and infertility, and developmental anomalies including microphthalmia, microcephaly, hypoplastic radius and thumb. Here we present cDNA sequences, genetic mapping, and genomic analyses for the four previously undescribed zebrafish FA genes (fanci, fancj, fancm, and fancn, and show that they reverted to single copy after the teleost genome duplication. We tested the hypothesis that FA genes are expressed during embryonic development in tissues that are disrupted in human patients by investigating fanc gene expression patterns. We found fanc gene maternal message, which can provide Fanc proteins to repair DNA damage encountered in rapid cleavage divisions. Zygotic expression was broad but especially strong in eyes, central nervous system and hematopoietic tissues. In the pectoral fin bud at hatching, fanc genes were expressed specifically in the apical ectodermal ridge, a signaling center for fin/limb development that may be relevant to the radius/thumb anomaly of FA patients. Hatching embryos expressed fanc genes strongly in the oral epithelium, a site of squamous cell carcinomas in FA patients. Larval and adult zebrafish expressed fanc genes in proliferative regions of the brain, which may be related to microcephaly in FA. Mature ovaries and testes expressed fanc genes in specific stages of oocyte and spermatocyte development, which may be related to DNA repair during homologous recombination in meiosis and to infertility in human patients. The intestine strongly expressed some fanc genes specifically in proliferative zones. Our results show that zebrafish has a complete complement of fanc genes in single copy and that these genes are expressed in zebrafish embryos and adults in proliferative tissues that are often affected in FA patients. These results support the notion that zebrafish offers an attractive experimental system to help unravel mechanisms relevant not only to FA, but also to breast cancer, given the involvement of fancj (brip1), fancn (palb2) and fancd1 (brca2) in both conditions.

Research paper thumbnail of Persistent pulmonary artery hypertension in patients undergoing balloon mitral valvotomy

Pulmonary Circulation, 2013

Pulmonary artery pressure (PAP) is known to regress after successful balloon mitral valvotomy (BM... more Pulmonary artery pressure (PAP) is known to regress after successful balloon mitral valvotomy (BMV). Data of persistent pulmonary artery hypertension (PPAH) following BMV is scarce. We analyzed the clinical, echocardiographic, and hemodynamic data of 701 consecutive patients who have undergone successful BMV in our institute from 1997 to 2003. Data of 287 patients who had PPAH (defined by pulmonary artery systolic pressure [PASP] of ≥ 40 mmHg at one year following BMV) were compared to the data of 414 patients who did not have PPAH. Patients who had PPAH were older (39.9 ± 9.9 years vs. 29.4 ± 10.1; P < 0.001). They had higher prevalence of atrial fibrillation (AF; 21.9 vs. 12.1%, P < 0.05), moderate or severe pulmonary artery hypertension (PAH) defined as PASP more than 50 mmHg (43.5 vs. 33.8%, P = 0.00), anatomically advanced mitral valve disease as assessed by Wilkin's echocardiographic score > 8 (33.7 vs. 23.2%, P < 0.001), and coexistent aortic valve disease (45.6 vs. 37.9%, P < 0.001) at the baseline. Those patients with PPAH had comparatively lower immediate postprocedural mitral valve area (MVA). On follow-up of more than five years, the occurrence of restenosis (39.3 vs. 10.1%, P = 0.000), new onset heart failure (14% vs. 4%, P < 0.05) and need for reinterventions (9.5% vs. 2.8%, P < 0.05) were higher in the PPAH group. Patients with PPAH were older, sicker, and had advanced rheumatic mitral valve disease. They had higher incidence of restenosis, new onset heart failure, and need for reinterventions on long term follow-up. PPAH represents an advanced stage of rheumatic valve disease and indicates chronicity of the disease, which may be the reason for the poorer prognosis of these patients. Patients with PPAH requires intense and more frequent follow-up.

Research paper thumbnail of Harmonin (Ush1c) is required in zebrafish Müller glial cells for photoreceptor synaptic development and function

Disease models & mechanisms, 2011

Usher syndrome is the most prevalent cause of hereditary deaf-blindness, characterized by congeni... more Usher syndrome is the most prevalent cause of hereditary deaf-blindness, characterized by congenital sensorineural hearing impairment and progressive photoreceptor degeneration beginning in childhood or adolescence. Diagnosis and management of this disease are complex, and the molecular changes underlying sensory cell impairment remain poorly understood. Here we characterize two zebrafish models for a severe form of Usher syndrome, Usher syndrome type 1C (USH1C): one model is a mutant with a newly identified ush1c nonsense mutation, and the other is a morpholino knockdown of ush1c. Both have defects in hearing, balance and visual function from the first week of life. Histological analyses reveal specific defects in sensory cell structure that are consistent with these behavioral phenotypes and could implicate Müller glia in the retinal pathology of Usher syndrome. This study shows that visual defects associated with loss of ush1c function in zebrafish can be detected from the onset ...

Research paper thumbnail of Wild sex in zebrafish: loss of the natural sex determinant in domesticated strains

Genetics, 2014

Sex determination can be robustly genetic, strongly environmental, or genetic subject to environm... more Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this "RAD-sex" method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, "male genotypes" became males and some…

Research paper thumbnail of Adverse outcome of human islet-allogeneic blood interaction1,2

Transplantation, 2003

A report of inflammatory damage when islets come into contact with allogeneic blood prompted us t... more A report of inflammatory damage when islets come into contact with allogeneic blood prompted us to confirm the finding. Fresh handpicked human islets were incubated in blood group matched, nonsensitized allogeneic blood. Destruction was quantified by assaying the supernatants for proinsulin release and by blood clot histology. The effect on global hemostasis was assessed by thromboelastography (TEG), and heparin-bonded tubing was used to assess the effect on blood cellular counts. In separate experiments, islets were incubated in allogeneic blood with heparin or Reopro (monoclonal anti-GpIIbIIIa). Islets were also incubated in serum, and cryosections were stained for C1q, C4, C3, C5b-9, immunoglobulin (Ig)M, and IgG binding using immunohistochemistry. Histologic assessment showed severe destruction in 37% of islets in contact with allogeneic blood versus none in controls and a sevenfold increase in proinsulin release from controls (n = 6)(P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.005). TEG (n = 11) showed accelerated coagulation in the presence of islets (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001). Analysis of blood cellular counts (n = 3) showed consumption of platelets, neutrophils, and monocytes in the presence of islets (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001). Inhibition of coagulation with heparin (n = 3) or inhibition of platelet aggregation with Reopro (n = 3), separately or together (n = 3), did not make a substantial improvement in the destruction in terms of histology or proinsulin release. Immunohistochemical staining (n = 4) revealed C1q, C4, C3, and C5b-9 deposition along with IgG binding. IgM binding was weak if anything. This study confirms and extends the finding that human islet-allogeneic blood interaction results in significant destruction of islet tissue with activation of the coagulation cascade and platelet, neutrophil, and monocyte consumption. There was evidence for activation of complement by the classical pathway along with IgG binding.

Research paper thumbnail of The Northern Red-legged Frog (Rana aurora) on the Proposed Green Valley Glen Development Site

Research paper thumbnail of Genetic Variation in Two Subspecies of Ambystoma gracile (Caudata: Ambystomatidae)

Journal of Herpetology, 1990

... Interpreting breeding patterns from census data: a solution to the Husting dilemma. ... Genet... more ... Interpreting breeding patterns from census data: a solution to the Husting dilemma. ... Genetic Variation in Two Subspecies of Ambystoma gracile (Caudata: Ambystomatidae) TOM A. TITUS, Museum of Natural History and Depart-ment of Systematics and Ecology, University of ...

Research paper thumbnail of Color polymorphism in neotropical treefrogs: an allozymic investigation of the taxonomic status of Hyla favosa Cope

Herpetologica, Mar 1, 1989

Hyla favosa, Hyla leucophyllata, and phenotypic intermediates between these species were discover... more Hyla favosa, Hyla leucophyllata, and phenotypic intermediates between these species were discovered in microsympatry in southeastern Peru. The genetic composition of individuals of all three phenotypes was analyzed using starch-gel protein electrophoresis to test the validity of species level status for H. favosa and H. leucophyllata. Twenty-two presumptive gene loci were scored. No alleles diagnostic of the two pure phenotypes were found. Phenotypic intermediates were genetically indistinguishable from the two pure forms and ...

Research paper thumbnail of Molecular Phylogenetics of Desmognathine Salamanders (Caudata: Plethodontidae): A Reevaluation of Evolution in Ecology, Life History, and Morphology

Systematic Biology, 1996

Phylogenetic relationships were reconstructed for salamanders of the plethodontid subfamily Desmo... more Phylogenetic relationships were reconstructed for salamanders of the plethodontid subfamily Desmognathinae to examine evolution of morphology, ecology, and life history. Mitochondrial DNA sequences encoding 12S and 16S ribosomal RNA and the valine transfer RNA provided 259 phylogenetically informative sites from approximately 1,200 nucleotide positions for 21 specimens representing 15 species and subspecies. These data were analyzed in conjunction with 13 morphological and reproductive characters to generate phylogenetic hypotheses. The directly developing terrestrial desmognathines Phaeognathus hubrichti and Desmognathus wrighti represent, respectively, the first and second phylogenetic branching events within the subfamily, and the remaining terrestrial lineage, D. aeneus, also branches near the base of the phylogenetic tree. These results challenge earlier hypotheses that within Desmognathus the small nonmetamorphosing species, D. aeneus and D. wrighti, represent the end of a graded phylogenetic decrease in size and decrease in use of aquatic habitats. In contrast to previous hypotheses, our results suggest that desmognathine evolution includes transformations in the direction of larger body sizes, lengthened larval periods, and greater use of aquatic habitats.

Research paper thumbnail of Phylogenetics of the Lizard Genus Tropidurus (Squamata: Tropiduridae: Tropidurinae): Direct Optimization, Descriptive Efficiency, and Sensitivity Analysis of Congruence Between Molecular Data and Morphology

Molecular Phylogenetics and Evolution, 2001

By use of the technique of direct optimization the phylogenetics of the cis-Andean lizard genus T... more By use of the technique of direct optimization the phylogenetics of the cis-Andean lizard genus Tropidurus were examined on the basis of both molecular (ca. 1.04 kb of sequences from 12S rDNA, valine tDNA, and 16S rDNA) and morphological (93 characters) data. Although equal weighting of all parsimony cost functions logically must maximize descriptive efficiency and explanatory power of all evidence, a sensitivity analysis demonstrated that equal weighting of indels, transitions, transversions, and morphological change provided the most congruent solution between the molecular and the morphological data partitions. The position of Uranoscodon is resolved as the sister taxon of the remaining members of the Tropidurinae. Plica, Uracentron, and Strobilurus, previously considered synonyms of Tropidurus, are resurrected; the group of these three genera form the sister taxon of the former Tropidurus nanuzae group (herein named Eurolophosaurus) plus Tropidurus sensu stricto (composed of the T. bogerti, T. semitaeniatus, T. spinulosus, and T. torquatus groups, herein diagnosed).

Research paper thumbnail of Molecular Homology Assessment and Phylogeny in the Lizard Family Opluridae (Squamata: Iguania)

Molecular Phylogenetics and Evolution, 1996

The effect of utilizing secondary structure on multiple alignment and phylogeny reconstruction wa... more The effect of utilizing secondary structure on multiple alignment and phylogeny reconstruction was examined for the mitochondrial 12S ribosomal RNA and valine transfer RNA genes in the lizard family Opluridae. Computer-generated multiple alignments were performed under parsimony using gap costs of 1-10 both with and without reference to secondary structure. Alignments performed without secondary structure resulted in disruption of positional homology in some stems at all gap costs. Number of misaligned stem positions increased with gap cost. Phylogenetic analyses of multiple alignments without secondary structure recovered a well-supported morphological tree for five gap costs, and this was the single most parsimonious tree only for a gap cost of 1. Computer-generated multiple alignments using secondary structure to maintain positional homologs in stems recovered the morphological tree over all gap costs, and this was the single most parsimonious tree for 8 of 10 gap costs. The combined morphological and molecular data produced a single most parsimonious oplurid tree that was congruent with the morphological tree over all gap costs. Chalaradon madagascariensis is the sister taxon of Oplurus, which itself contains two clades: one with the arboreal Oplurus cuvieri and Oplurus cyclurus and the other with the saxicolous Oplurus grandidieri, Oplurus fierinensis, Oplurus quadrimaculatus, and Oplurus saxicola.

Research paper thumbnail of Tissue-specific gene expression in the smallmouth salamander, Ambystoma texanum (Caudata: Ambystomatidae)

Biochemical Systematics and Ecology, 1994

Relative staining activity, heteropolymer assembly, and secondary isozymes are described for gene... more Relative staining activity, heteropolymer assembly, and secondary isozymes are described for gene products of 22 loci examined for expression in eight tissues of Ambystoma texanum. Locus homologies based on tissue specificity and staining patterns in mitochondria-enriched liver fractions are proposed. Quaternary structure was inferred from polymorphisms resolved at seven loci. Gene expression was undetectable in 17 of the 176 tissue/locus comparisons. The phylogenetic pattern of changes in gene number and the extensive variation in tissue-specific expression among tetrapods suggest that these attributes will be useful as phylogenetic characters in groups less inclusive than tetrapods.

Research paper thumbnail of A Molecular Perspective on the Phylogeny of the Girdled Lizards (Cordylidae, Squamata)

American Museum Novitates, 2001

Mitochondrial DNA sequences were obtained for 16 species representing all nominal genera of Cordy... more Mitochondrial DNA sequences were obtained for 16 species representing all nominal genera of Cordylidae (Platysaurus, Chamaesaura, Cordylus, and Pseudocordylus). Gerrhosauridae and Teiidae were used as first and second outgroups. Results indicate that the oviparous Platysaurus is the sister taxon of the remaining cordylids (all of which are ovoviviparous). Within the ovoviviparous group Cordylus is paraphyletic with respect to Chamaesaura and Pseudocordylus. No evidence of Pseudocordylus monophyly was discovered. The three species of Chamaesaura and the seven species of Pseudocordylus are transferred to Cordylus to render a monophyletic taxonomy. 2 NO. 3310 AMERICAN MUSEUM NOVITATES

Research paper thumbnail of A molecular phylogenetic perspective on the evolutionary history of Alosa spp. (Clupeidae)

Molecular Phylogenetics and Evolution, 2006

... to A. alosa. However, the bootstrap support for this clade is inconsistent among reconstruc-t... more ... to A. alosa. However, the bootstrap support for this clade is inconsistent among reconstruc-tion approaches and there is a lack of reciprocal mono-phyly between A. fallax and the Black Sea/Lake Volvi clades (Fig. 1), due to the one highly divergent haplotype from Turkey (A ...

Research paper thumbnail of Evolution of the Eye Transcriptome under Constant Darkness in Sinocyclocheilus Cavefish

Molecular Biology and Evolution, 2013

In adaptating to perpetual darkness, cave species gradually lose eyes and body pigmentation and e... more In adaptating to perpetual darkness, cave species gradually lose eyes and body pigmentation and evolve alternatives for exploring their environments. Although troglodyte features evolved independently many times in cavefish, we do not yet know whether independent evolution of these characters involves common genetic mechanisms. Surface-dwelling and many cave-dwelling species make the freshwater teleost genus Sinocyclocheilus an excellent model for studying the evolution of adaptations to life in constant darkness. We compared the mature retinal histology of surface and cave species in Sinocyclocheilus and found that adult cavefish showed a reduction in the number and length of photoreceptor cells. To identify genes and genetic pathways that evolved in constant darkness, we used RNA-seq to compare eyes of surface and cave species. De novo transcriptome assemblies were developed for both species, and contigs were annotated with gene ontology. Results from cave-dwelling Sinocyclocheilus revealed reduced transcription of phototransduction and other genes important for retinal function. In contrast to the blind Mexican tetra cavefish Astyanax mexicanus, our results on morphologies and gene expression suggest that evolved retinal reduction in cave-dwelling Sinocyclocheilus occurs in a lens-independent fashion by the reduced proliferation and downregulation of transcriptional factors shown to have direct roles in retinal development and maintenance, including cone-rod homeobox (crx) and Wnt pathway members. These results show that the independent evolution of retinal degeneration in cavefish can occur by different developmental genetic mechanisms.

Research paper thumbnail of Two additional midline barriers function with midline lefty1 expression to maintain asymmetric Nodal signaling during left-right axis specification in zebrafish

Development, 2011

Left-right (L/R) patterning is crucial for the proper development of all vertebrates and requires... more Left-right (L/R) patterning is crucial for the proper development of all vertebrates and requires asymmetric expression of nodal in the lateral plate mesoderm (LPM). The mechanisms governing asymmetric initiation of nodal have been studied extensively, but because Nodal is a potent activator of its own transcription, it is also crucial to understand the regulation required to maintain this asymmetry once it is established. The 'midline barrier', consisting of lefty1 expression, is a conserved mechanism for restricting Nodal activity to the left. However, the anterior and posterior extremes of the LPM are competent to respond to Nodal signals yet are not adjacent to this barrier, suggesting that lefty1 is not the only mechanism preventing ectopic Nodal activation. Here, we demonstrate the existence of two additional midline barriers. The first is a 'posterior barrier' mediated by Bmp signaling that prevents nodal propagation through the posterior LPM. In contrast to previous reports, we find that Bmp represses Nodal signaling independently of lefty1 expression and through the activity of a ligand other than Bmp4. The 'anterior barrier' is mediated by lefty2 expression in the left cardiac field and prevents Nodal activation from traveling across the anterior limit of the notochord and propagating down the right LPM. Both barriers appear to be conserved across model systems and are thus likely to be present in all vertebrates.

Research paper thumbnail of Geographic Variation, Species Recognition, and Molecular Evolution of Cytochrome Oxidase I in the Tropidurus spinulosus Complex (Iguania: Tropiduridae)

Copeia, 1998

... 4 rio Paraguay, y su distribucion extende al este y noreste en Mato Grosso do Sul y Goias, Br... more ... 4 rio Paraguay, y su distribucion extende al este y noreste en Mato Grosso do Sul y Goias, Brasil. Aunque las diagnoses son discutibles, predecimos que datos adicion-ales revelaran que T. guarani esta compuesto de dos lineas que denotamos T. guarani "Paraguari" y T ...

Research paper thumbnail of The Fanconi anemia gene network is conserved from zebrafish to human

Gene, Apr 26, 2006

Fanconi anemia (FA) is a complex disease involving nine identified and two unidentified loci that... more Fanconi anemia (FA) is a complex disease involving nine identified and two unidentified loci that define a network essential for maintaining genomic stability. To test the hypothesis that the FA network is conserved in vertebrate genomes, we cloned and sequenced zebrafish (Danio rerio) cDNAs and/or genomic BAC clones orthologous to all nine cloned FA genes (FANCA, FANCB, FANCC, FANCD1, FANCD2, FANCE, FANCF, FANCG, and FANCL), and identified orthologs in the genome database for the pufferfish Tetraodon nigroviridis. Genomic organization of exons and introns was nearly identical between zebrafish and human for all genes examined. Hydrophobicity plots revealed conservation of FA protein structure. Evolutionarily conserved regions identified functionally important domains, since many amino acid residues mutated in human disease alleles or shown to be critical in targeted mutagenesis studies are identical in zebrafish and human. Comparative genomic analysis demonstrated conserved syntenies for all FA genes. We conclude that the FA gene network has remained intact since the last common ancestor of zebrafish and human lineages. The application of powerful genetic, cellular, and embryological methodologies make zebrafish a useful model for discovering FA gene functions, identifying new genes in the network, and identifying therapeutic compounds.

Research paper thumbnail of The Fanconi anemia/BRCA gene network in zebrafish: Embryonic expression and comparative genomics

Mutation Research Fundamental and Molecular Mechanisms of Mutagenesis, Jul 1, 2009

Fanconi anemia (FA) is a genic disease resulting in bone marrow failure, high cancer risks, and i... more Fanconi anemia (FA) is a genic disease resulting in bone marrow failure, high cancer risks, and infertility, and developmental anomalies including microphthalmia, microcephaly, hypoplastic radius and thumb. Here we present cDNA sequences, genetic mapping, and genomic analyses for the four previously undescribed zebrafish FA genes (fanci, fancj, fancm, and fancn, and show that they reverted to single copy after the teleost genome duplication. We tested the hypothesis that FA genes are expressed during embryonic development in tissues that are disrupted in human patients by investigating fanc gene expression patterns. We found fanc gene maternal message, which can provide Fanc proteins to repair DNA damage encountered in rapid cleavage divisions. Zygotic expression was broad but especially strong in eyes, central nervous system and hematopoietic tissues. In the pectoral fin bud at hatching, fanc genes were expressed specifically in the apical ectodermal ridge, a signaling center for fin/limb development that may be relevant to the radius/thumb anomaly of FA patients. Hatching embryos expressed fanc genes strongly in the oral epithelium, a site of squamous cell carcinomas in FA patients. Larval and adult zebrafish expressed fanc genes in proliferative regions of the brain, which may be related to microcephaly in FA. Mature ovaries and testes expressed fanc genes in specific stages of oocyte and spermatocyte development, which may be related to DNA repair during homologous recombination in meiosis and to infertility in human patients. The intestine strongly expressed some fanc genes specifically in proliferative zones. Our results show that zebrafish has a complete complement of fanc genes in single copy and that these genes are expressed in zebrafish embryos and adults in proliferative tissues that are often affected in FA patients. These results support the notion that zebrafish offers an attractive experimental system to help unravel mechanisms relevant not only to FA, but also to breast cancer, given the involvement of fancj (brip1), fancn (palb2) and fancd1 (brca2) in both conditions.

Research paper thumbnail of Albertson'10SkeletalEvolutionInAntarcticFishes

Research paper thumbnail of The Fanconi anemia/BRCA gene network in zebrafish: Embryonic expression and comparative genomics

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, 2009

Fanconi anemia (FA) is a genic disease resulting in bone marrow failure, high cancer risks, and i... more Fanconi anemia (FA) is a genic disease resulting in bone marrow failure, high cancer risks, and infertility, and developmental anomalies including microphthalmia, microcephaly, hypoplastic radius and thumb. Here we present cDNA sequences, genetic mapping, and genomic analyses for the four previously undescribed zebrafish FA genes (fanci, fancj, fancm, and fancn, and show that they reverted to single copy after the teleost genome duplication. We tested the hypothesis that FA genes are expressed during embryonic development in tissues that are disrupted in human patients by investigating fanc gene expression patterns. We found fanc gene maternal message, which can provide Fanc proteins to repair DNA damage encountered in rapid cleavage divisions. Zygotic expression was broad but especially strong in eyes, central nervous system and hematopoietic tissues. In the pectoral fin bud at hatching, fanc genes were expressed specifically in the apical ectodermal ridge, a signaling center for fin/limb development that may be relevant to the radius/thumb anomaly of FA patients. Hatching embryos expressed fanc genes strongly in the oral epithelium, a site of squamous cell carcinomas in FA patients. Larval and adult zebrafish expressed fanc genes in proliferative regions of the brain, which may be related to microcephaly in FA. Mature ovaries and testes expressed fanc genes in specific stages of oocyte and spermatocyte development, which may be related to DNA repair during homologous recombination in meiosis and to infertility in human patients. The intestine strongly expressed some fanc genes specifically in proliferative zones. Our results show that zebrafish has a complete complement of fanc genes in single copy and that these genes are expressed in zebrafish embryos and adults in proliferative tissues that are often affected in FA patients. These results support the notion that zebrafish offers an attractive experimental system to help unravel mechanisms relevant not only to FA, but also to breast cancer, given the involvement of fancj (brip1), fancn (palb2) and fancd1 (brca2) in both conditions.

Research paper thumbnail of Persistent pulmonary artery hypertension in patients undergoing balloon mitral valvotomy

Pulmonary Circulation, 2013

Pulmonary artery pressure (PAP) is known to regress after successful balloon mitral valvotomy (BM... more Pulmonary artery pressure (PAP) is known to regress after successful balloon mitral valvotomy (BMV). Data of persistent pulmonary artery hypertension (PPAH) following BMV is scarce. We analyzed the clinical, echocardiographic, and hemodynamic data of 701 consecutive patients who have undergone successful BMV in our institute from 1997 to 2003. Data of 287 patients who had PPAH (defined by pulmonary artery systolic pressure [PASP] of ≥ 40 mmHg at one year following BMV) were compared to the data of 414 patients who did not have PPAH. Patients who had PPAH were older (39.9 ± 9.9 years vs. 29.4 ± 10.1; P < 0.001). They had higher prevalence of atrial fibrillation (AF; 21.9 vs. 12.1%, P < 0.05), moderate or severe pulmonary artery hypertension (PAH) defined as PASP more than 50 mmHg (43.5 vs. 33.8%, P = 0.00), anatomically advanced mitral valve disease as assessed by Wilkin's echocardiographic score > 8 (33.7 vs. 23.2%, P < 0.001), and coexistent aortic valve disease (45.6 vs. 37.9%, P < 0.001) at the baseline. Those patients with PPAH had comparatively lower immediate postprocedural mitral valve area (MVA). On follow-up of more than five years, the occurrence of restenosis (39.3 vs. 10.1%, P = 0.000), new onset heart failure (14% vs. 4%, P < 0.05) and need for reinterventions (9.5% vs. 2.8%, P < 0.05) were higher in the PPAH group. Patients with PPAH were older, sicker, and had advanced rheumatic mitral valve disease. They had higher incidence of restenosis, new onset heart failure, and need for reinterventions on long term follow-up. PPAH represents an advanced stage of rheumatic valve disease and indicates chronicity of the disease, which may be the reason for the poorer prognosis of these patients. Patients with PPAH requires intense and more frequent follow-up.

Research paper thumbnail of Harmonin (Ush1c) is required in zebrafish Müller glial cells for photoreceptor synaptic development and function

Disease models & mechanisms, 2011

Usher syndrome is the most prevalent cause of hereditary deaf-blindness, characterized by congeni... more Usher syndrome is the most prevalent cause of hereditary deaf-blindness, characterized by congenital sensorineural hearing impairment and progressive photoreceptor degeneration beginning in childhood or adolescence. Diagnosis and management of this disease are complex, and the molecular changes underlying sensory cell impairment remain poorly understood. Here we characterize two zebrafish models for a severe form of Usher syndrome, Usher syndrome type 1C (USH1C): one model is a mutant with a newly identified ush1c nonsense mutation, and the other is a morpholino knockdown of ush1c. Both have defects in hearing, balance and visual function from the first week of life. Histological analyses reveal specific defects in sensory cell structure that are consistent with these behavioral phenotypes and could implicate Müller glia in the retinal pathology of Usher syndrome. This study shows that visual defects associated with loss of ush1c function in zebrafish can be detected from the onset ...

Research paper thumbnail of Wild sex in zebrafish: loss of the natural sex determinant in domesticated strains

Genetics, 2014

Sex determination can be robustly genetic, strongly environmental, or genetic subject to environm... more Sex determination can be robustly genetic, strongly environmental, or genetic subject to environmental perturbation. The genetic basis of sex determination is unknown for zebrafish (Danio rerio), a model for development and human health. We used RAD-tag population genomics to identify sex-linked polymorphisms. After verifying this "RAD-sex" method on medaka (Oryzias latipes), we studied two domesticated zebrafish strains (AB and TU), two natural laboratory strains (WIK and EKW), and two recent isolates from nature (NA and CB). All four natural strains had a single sex-linked region at the right tip of chromosome 4, enabling sex genotyping by PCR. Genotypes for the single nucleotide polymorphism (SNP) with the strongest statistical association to sex suggested that wild zebrafish have WZ/ZZ sex chromosomes. In natural strains, "male genotypes" became males and some…

Research paper thumbnail of Adverse outcome of human islet-allogeneic blood interaction1,2

Transplantation, 2003

A report of inflammatory damage when islets come into contact with allogeneic blood prompted us t... more A report of inflammatory damage when islets come into contact with allogeneic blood prompted us to confirm the finding. Fresh handpicked human islets were incubated in blood group matched, nonsensitized allogeneic blood. Destruction was quantified by assaying the supernatants for proinsulin release and by blood clot histology. The effect on global hemostasis was assessed by thromboelastography (TEG), and heparin-bonded tubing was used to assess the effect on blood cellular counts. In separate experiments, islets were incubated in allogeneic blood with heparin or Reopro (monoclonal anti-GpIIbIIIa). Islets were also incubated in serum, and cryosections were stained for C1q, C4, C3, C5b-9, immunoglobulin (Ig)M, and IgG binding using immunohistochemistry. Histologic assessment showed severe destruction in 37% of islets in contact with allogeneic blood versus none in controls and a sevenfold increase in proinsulin release from controls (n = 6)(P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.005). TEG (n = 11) showed accelerated coagulation in the presence of islets (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001). Analysis of blood cellular counts (n = 3) showed consumption of platelets, neutrophils, and monocytes in the presence of islets (P &amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt; 0.001). Inhibition of coagulation with heparin (n = 3) or inhibition of platelet aggregation with Reopro (n = 3), separately or together (n = 3), did not make a substantial improvement in the destruction in terms of histology or proinsulin release. Immunohistochemical staining (n = 4) revealed C1q, C4, C3, and C5b-9 deposition along with IgG binding. IgM binding was weak if anything. This study confirms and extends the finding that human islet-allogeneic blood interaction results in significant destruction of islet tissue with activation of the coagulation cascade and platelet, neutrophil, and monocyte consumption. There was evidence for activation of complement by the classical pathway along with IgG binding.