Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology

Serb, Jeanne M.; Oakley, Todd H.

doi:10.1002/bies.20291

Cited by 47 publications

(43 citation statements)

References 61 publications

(77 reference statements)

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“…Such inferences rely on phylogenetics, a field that has developed highly sophisticated techniques for modeling evolution and for inferring the probabilities of past events based on common ancestry (Cunningham et al 1998;Pagel 1999). Although many people conceive of phylogenetics as applying to species relationships and to relationships among members of gene families, phylogenetic thinking can also be applied to other levels of biological organization (Arendt 2003;Geeta 2003;Oakley 2003;Oakley et al 2007;Serb and Oakley 2005). Each component of any animal eye has an evolutionary history that can be reconstructed by comparative techniques.…”

Section: Origins Of Variation In Eye Evolutionmentioning

confidence: 99%

Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution

Oakley

Pankey

2008

Evo Edu Outreach

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Eyes provide a rich narrative for understanding evolution, having attracted the attention of preeminent scientists and communicators alike. Until recently, this narrative has focused primarily on the evolution of eye structure and far less on biochemistry or genetics. Although eye biochemistry was once likened to an unknown "black box;" the flood of discoveries in biochemistry is now allowing an increasingly detailed understanding of the processes involved in vision. As a result, evolutionary comparative ("tree-thinking") analyses that use these data currently allow a new and still unfolding narrative, both richer in detail and more comprehensive in scope. Rather than toppling evolutionary theory by finding irreducibly complex molecular machines, eye evolution provides detailed accounts of how natural processes tinker with existing genetic components, duplicating and recombining them, to yield complex, intricate, and highly functional eyes. Understanding the new biochemical narrative is critical for researchers and teachers alike, in order to answer antievolutionist claims, and to provide an up-to-date account of the state of knowledge on the subject of eye evolution.Keywords Evolution . Phototransduction . Vision . Eyes . Phylogeny . Novelty . ComplexityThe evolutionary history of eyes is one of the most intriguing and often-told stories in biology. It is a topic researched and discussed by members of the pantheon of evolutionists, including Darwin (1859), Salvini-Plawen and Mayr (1977), Gould (1994), andDawkins (1996). The commonly told story is familiar and has not changed much since Darwin first proposed it: A light-sensitive nerve gradually changes over evolutionary time, adding complexity across the generations. To Darwin's sketch, Salvini-Plawen and Mayr (1977) added detail, and Nilsson and Pelger (1994) tested the temporal component. The ancient canon of gradual evolution is certainly valuable for demonstrating that some assumptions are met for the hypothesis that natural selection generates complexity, serving as a colorful and graphical example (Dawkins 1996). However, this account-if taken too far-can easily be criticized, as demonstrated, for example, by proponents of Intelligent Design (ID; Behe 1996) who point out that the Darwinian canon ignores complexity at the molecular level. The structure of this article is first to briefly present the "gradual morphological" account of the evolution of eye form and to describe how this account relates to understanding evolution by natural selection. Section II will point out two primary limitations of this "gradual morphological" model, including one highlighted by ID proponents. Third, the paper will present molecular and biochemical details describing how phototransduction (the cascade of signaling events that generate a nervous impulse in response to light) and complex lenses evolved. These two case studies provide specific details about how eyes evolved. The processes elucidated, such as duplication and co-option (the use of existing components ...

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Section: Origins Of Variation In Eye Evolutionmentioning

confidence: 99%

Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution

Oakley

Pankey

2008

Evo Edu Outreach

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“…The G-protein g subunit family consists of 12 mammalian members (Serb & Oakley 2005;Birnbaumer 2007) and many of these are expressed in the brain. Distinct g subunit genes are used in rods and cones: GNGT1 and GNGT2.…”

Section: Phototransduction Gene Familiesmentioning

confidence: 99%

Evolution of vertebrate rod and cone phototransduction genes

Larhammar

Nordström

Larsson

2009

Phil. Trans. R. Soc. B

115

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Vertebrate cones and rods in several cases use separate but related components for their signal transduction (opsins, G-proteins, ion channels, etc.). Some of these proteins are also used differentially in other cell types in the retina. Because cones, rods and other retinal cell types originated in early vertebrate evolution, it is of interest to see if their specific genes arose in the extensive gene duplications that took place in the ancestor of the jawed vertebrates (gnathostomes) by two tetraploidizations (genome doublings). The ancestor of teleost fishes subsequently underwent a third tetraploidization. Our previously reported analyses showed that several gene families in the vertebrate visual phototransduction cascade received new members in the basal tetraploidizations. We here expand these data with studies of additional gene families and vertebrate species. We conclude that no less than 10 of the 13 studied phototransduction gene families received additional members in the two basal vertebrate tetraploidizations. Also the remaining three families seem to have undergone duplications during the same time period but it is unclear if this happened as a result of the tetraploidizations. The implications of the many early vertebrate gene duplications for functional specialization of specific retinal cell types, particularly cones and rods, are discussed.

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“…(57) Here, we used this approach to determine if understanding the evolution of VNS-specific genes would help understand VNS evolution. Strictly from a morphological standpoint, the VNS exists only in tetrapods.…”

Section: Discussionmentioning

confidence: 99%

“…First, to establish the presence of a homologous physiological system (or a system precursor) by the presence of homologous genes, the gene must be system-specific. (56,57) Therefore, components of the VNS signal transduction pathway that are also found in other signal transduction pathways, such as PLC, DAG, IP 3 , G ai2 or G ao , are not suitable markers for studying the origin and evolution of the VNS. Additionally, genes that function in the VNS of a small number of evolutionary lineages are not useful because those genes are not part of the ancestral molecular definition of the system.…”

Section: Trpc2 Channel Protein Shows Vns-specific Functionmentioning

confidence: 99%

Origin and evolution of the vertebrate vomeronasal system viewed through system‐specific genes

Grus

Zhang

2006

BioEssays

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Tetrapods have two distinct nasal chemosensory systems, the main olfactory system and the vomeronasal system (VNS). Defined by certain morphological components, the main olfactory system is present in all groups of vertebrates, while the VNS is found only in tetrapods. Previous attempts to identify a VNS precursor in teleost fish were limited by functional and morphological characters that could not clearly distinguish between homologous and analogous systems. In the past decade, several genes that specifically function in the VNS have been discovered. Here we first describe recent evolutionary studies of mammalian VNS-specific genes. We then review evidence showing the presence and tissue-specific expression of the VNS-specific genes in teleosts, as well as co-expression patterns of these genes in specific regions of the teleost olfactory epithelium. We propose that a VNS precursor exists in teleosts and that its evolutionary origin predated the separation between teleosts and tetrapods.

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Hierarchical phylogenetics as a quantitative analytical framework for evolutionary developmental biology

Cited by 47 publications

References 61 publications

Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution

Opening the “Black Box”: The Genetic and Biochemical Basis of Eye Evolution

Evolution of vertebrate rod and cone phototransduction genes

Origin and evolution of the vertebrate vomeronasal system viewed through system‐specific genes

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