Todd Oakley | University of California, Santa Barbara (original) (raw)
Papers by Todd Oakley
Background The marine environment is comprised of numerous divergent organisms living under simil... more Background The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagic squids, fishes, and some marine mammals. However, little is known about the frequency of, and circumstances leading to, convergent evolution in the open ocean.
Background Duplication and divergence of genes and genetic networks is hypothesized to be a major... more Background Duplication and divergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in the context of eye evolution by using new approaches to understand patterns of gene duplication during the evolution of metazoan genomes.
Abstract–The primary goal of the field of experimental phylogenetics is to generate branching his... more Abstract–The primary goal of the field of experimental phylogenetics is to generate branching histories of biological entities in the laboratory for use in testing methods of phylogenetic reconstruction. Here, I explore possible reasons why this field has remained small, despite hints of a bright future 15 years ago. Specifically, I examine three primary arguments that researchers have used to motivate the field of experimental evolution.
Background Cnidocytes, the eponymous cell type of the Cnidaria, facilitate both sensory and secre... more Background Cnidocytes, the eponymous cell type of the Cnidaria, facilitate both sensory and secretory functions and are among the most complex animal cell types known. In addition to their structural complexity, cnidocytes display complex sensory attributes, integrating both chemical and mechanical cues from the environment into their discharge behavior. Despite more than a century of work aimed at understanding the sensory biology of cnidocytes, the specific sensory receptor genes that regulate their function remain unknown.
SUMMARY Many larval sponges possess pigment ring eyes that apparently mediate phototactic swimmin... more SUMMARY Many larval sponges possess pigment ring eyes that apparently mediate phototactic swimming. Yet sponges are not known to possess nervous systems or opsin genes, so the unknown molecular components of sponge phototaxis must differ fundamentally from those in other animals, inspiring questions about how this sensory system functions. Here we present molecular and biochemical data on cryptochrome, a candidate gene for functional involvement in sponge pigment ring eyes.
Abstract PDZ domains are protein–protein interaction modules widely used to assemble membranous s... more Abstract PDZ domains are protein–protein interaction modules widely used to assemble membranous signaling complexes including those found in the neuronal synapse. PDZ-containing genes encoded in metazoan genomes vastly outnumber those in prokaryotes, plants, and fungi. By comparing 40 proteomes to track the evolutionary history of the PDZ domain, we observed that the variety of associations between PDZ and other domains expands greatly along the stem leading to metazoans and choanoflagellates.
The stereotypical scientist is focused: intensely focused. Imagine an aging white man with wild, ... more The stereotypical scientist is focused: intensely focused. Imagine an aging white man with wild, graying hair and wide eyes behind thick, dark-rimmed glasses. He is so focused that nothing matters but science. A social life? Superfluous. Hobbies? Unnecessary. Fashion?“My neon pocket protector fits squarely in my lab coat.” Stereotypes often have some basis in reality, but they over-simplify, ignoring the complexities of life. True, scientists are usually focused and driven.
Abstract The evolutionary histories of complex traits are complicated because such traits are com... more Abstract The evolutionary histories of complex traits are complicated because such traits are comprised of multiple integrated and interacting components, which may have different individual histories. Phylogenetic studies of complex trait evolution often do not take this into account, instead focusing only on the history of whole, integrated traits; for example, mapping eyes as simply present or absent through history.
We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases an... more We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia’s genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.
Sponges are an ancient group of animals that diverged from other metazoans over 600 million years... more Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes. This diverse ‘toolkit’ of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic- and germ-cell specification, cell adhesion, innate immunity and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.
Trends in Ecology & Evolution, Jan 1, 1998
Proceedings of the …, Jan 1, 2002
Molecular Phylogenetics and Evolution, Jan 1, 1999
Molecular biology and …, Jan 1, 2004
Molecular biology and …, Jan 1, 2005
Background The marine environment is comprised of numerous divergent organisms living under simil... more Background The marine environment is comprised of numerous divergent organisms living under similar selective pressures, often resulting in the evolution of convergent structures such as the fusiform body shape of pelagic squids, fishes, and some marine mammals. However, little is known about the frequency of, and circumstances leading to, convergent evolution in the open ocean.
Background Duplication and divergence of genes and genetic networks is hypothesized to be a major... more Background Duplication and divergence of genes and genetic networks is hypothesized to be a major driver of the evolution of complexity and novel features. Here, we examine the history of genes and genetic networks in the context of eye evolution by using new approaches to understand patterns of gene duplication during the evolution of metazoan genomes.
Abstract–The primary goal of the field of experimental phylogenetics is to generate branching his... more Abstract–The primary goal of the field of experimental phylogenetics is to generate branching histories of biological entities in the laboratory for use in testing methods of phylogenetic reconstruction. Here, I explore possible reasons why this field has remained small, despite hints of a bright future 15 years ago. Specifically, I examine three primary arguments that researchers have used to motivate the field of experimental evolution.
Background Cnidocytes, the eponymous cell type of the Cnidaria, facilitate both sensory and secre... more Background Cnidocytes, the eponymous cell type of the Cnidaria, facilitate both sensory and secretory functions and are among the most complex animal cell types known. In addition to their structural complexity, cnidocytes display complex sensory attributes, integrating both chemical and mechanical cues from the environment into their discharge behavior. Despite more than a century of work aimed at understanding the sensory biology of cnidocytes, the specific sensory receptor genes that regulate their function remain unknown.
SUMMARY Many larval sponges possess pigment ring eyes that apparently mediate phototactic swimmin... more SUMMARY Many larval sponges possess pigment ring eyes that apparently mediate phototactic swimming. Yet sponges are not known to possess nervous systems or opsin genes, so the unknown molecular components of sponge phototaxis must differ fundamentally from those in other animals, inspiring questions about how this sensory system functions. Here we present molecular and biochemical data on cryptochrome, a candidate gene for functional involvement in sponge pigment ring eyes.
Abstract PDZ domains are protein–protein interaction modules widely used to assemble membranous s... more Abstract PDZ domains are protein–protein interaction modules widely used to assemble membranous signaling complexes including those found in the neuronal synapse. PDZ-containing genes encoded in metazoan genomes vastly outnumber those in prokaryotes, plants, and fungi. By comparing 40 proteomes to track the evolutionary history of the PDZ domain, we observed that the variety of associations between PDZ and other domains expands greatly along the stem leading to metazoans and choanoflagellates.
The stereotypical scientist is focused: intensely focused. Imagine an aging white man with wild, ... more The stereotypical scientist is focused: intensely focused. Imagine an aging white man with wild, graying hair and wide eyes behind thick, dark-rimmed glasses. He is so focused that nothing matters but science. A social life? Superfluous. Hobbies? Unnecessary. Fashion?“My neon pocket protector fits squarely in my lab coat.” Stereotypes often have some basis in reality, but they over-simplify, ignoring the complexities of life. True, scientists are usually focused and driven.
Abstract The evolutionary histories of complex traits are complicated because such traits are com... more Abstract The evolutionary histories of complex traits are complicated because such traits are comprised of multiple integrated and interacting components, which may have different individual histories. Phylogenetic studies of complex trait evolution often do not take this into account, instead focusing only on the history of whole, integrated traits; for example, mapping eyes as simply present or absent through history.
We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases an... more We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia’s genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.
Sponges are an ancient group of animals that diverged from other metazoans over 600 million years... more Sponges are an ancient group of animals that diverged from other metazoans over 600 million years ago. Here we present the draft genome sequence of Amphimedon queenslandica, a demosponge from the Great Barrier Reef, and show that it is remarkably similar to other animal genomes in content, structure and organization. Comparative analysis enabled by the sequencing of the sponge genome reveals genomic events linked to the origin and early evolution of animals, including the appearance, expansion and diversification of pan-metazoan transcription factor, signalling pathway and structural genes. This diverse ‘toolkit’ of genes correlates with critical aspects of all metazoan body plans, and comprises cell cycle control and growth, development, somatic- and germ-cell specification, cell adhesion, innate immunity and allorecognition. Notably, many of the genes associated with the emergence of animals are also implicated in cancer, which arises from defects in basic processes associated with metazoan multicellularity.
Trends in Ecology & Evolution, Jan 1, 1998
Proceedings of the …, Jan 1, 2002
Molecular Phylogenetics and Evolution, Jan 1, 1999
Molecular biology and …, Jan 1, 2004
Molecular biology and …, Jan 1, 2005