Jacob M. Daane
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View article: Establishment, conservation, and innovation of dorsal determination mechanisms during the evolution of vertebrate paired appendages
Establishment, conservation, and innovation of dorsal determination mechanisms during the evolution of vertebrate paired appendages Open
Limb function requires polarized anatomy across the dorsal-ventral (DV) axis, but it is unclear when the capacity for DV differentiation of paired appendages arose in evolution. Here we define ancestral DV patterning programs in the fins o…
View article: Projected warming disrupts embryonic development and hatch timing in Antarctic fish
Projected warming disrupts embryonic development and hatch timing in Antarctic fish Open
Rising ocean temperatures pose significant threats to marine ectotherms. Sensitivity to temperature change varies across life stages, with embryos often being less tolerant to thermal perturbation than adults. Antarctic notothenioid fishes…
View article: Convergent latitudinal erosion of circadian systems in a rapidly diversifying order of fishes
Convergent latitudinal erosion of circadian systems in a rapidly diversifying order of fishes Open
Biological clocks enable organisms to anticipate cyclical environmental changes. Some habitats, such as those at high latitudes or deep sea, experience seasonally diminished or absent diel cues upon which species entrain their circadian rh…
View article: Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation
Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation Open
Recent adaptive radiations provide experimental opportunities to parse the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genus Salvelinus) present a trove for phyl…
View article: Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation
Phylogenomic analysis of the Lake Kronotskoe species flock of Dolly Varden charr reveals genetic and developmental signatures of sympatric radiation Open
Recent adaptive radiations provide evolutionary case studies, which provide the context to parse the relationship between genomic variation and the origins of distinct phenotypes. Sympatric radiations of the charr complex (genus Salvelinus…
View article: Convergent genomics of longevity in rockfishes highlights the genetics of human life span variation
Convergent genomics of longevity in rockfishes highlights the genetics of human life span variation Open
Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, which range in longevity from 11 to over 205 years. Multiple…
View article: Genomics of exceptional longevity in rockfishes refines genetic foundations of human lifespan variation
Genomics of exceptional longevity in rockfishes refines genetic foundations of human lifespan variation Open
Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, ranging in longevity from 11 to over 205 years. Multiple shi…
View article: Convergent genomics of longevity in Rockfishes highlights the genetics of human lifespan variation
Convergent genomics of longevity in Rockfishes highlights the genetics of human lifespan variation Open
Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, which range in longevity from 11 to over 205 years. Multiple…
View article: Speciation genomics and the role of depth in the divergence of rockfishes ( <i>Sebastes</i> ) revealed through Pool‐seq analysis of enriched sequences
Speciation genomics and the role of depth in the divergence of rockfishes ( <i>Sebastes</i> ) revealed through Pool‐seq analysis of enriched sequences Open
Speciation in the marine environment is challenged by the wide geographic distribution of many taxa and potential for high rates of gene flow through larval dispersal mechanisms. Depth has recently been proposed as a potential driver of ec…
View article: Speciation genomics and the role of depth in the divergence of rockfishes (<i>Sebastes</i>) revealed through Pool-seq analysis of enriched sequences
Speciation genomics and the role of depth in the divergence of rockfishes (<i>Sebastes</i>) revealed through Pool-seq analysis of enriched sequences Open
Speciation in the marine environment is challenged by the wide geographic distribution of many taxa and potential for high rates of gene flow through larval dispersal mechanisms. Depth has recently been proposed as a potential driver of ec…
View article: The genomics of exceptional longevity in rockfishes refine genetic foundations of human lifespan variation
The genomics of exceptional longevity in rockfishes refine genetic foundations of human lifespan variation Open
Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, ranging in longevity from 11 to over 205 years. Shifts in ro…
View article: Refining Convergent Rate Analysis with Topology in Mammalian Longevity and Marine Transitions
Refining Convergent Rate Analysis with Topology in Mammalian Longevity and Marine Transitions Open
The quest to map the genetic foundations of phenotypes has been empowered by the modern diversity, quality, and availability of genomic resources. Despite these expanding resources, the abundance of variation within lineages makes it chall…
View article: Modulation of bioelectric cues in the evolution of flying fishes [Data set]
Modulation of bioelectric cues in the evolution of flying fishes [Data set] Open
Assembled reference contigs for protein-coding exons and conserved non-coding regions from targeted sequence enrichment of beloniform fishes. Current citation: Daane JM, Blum N, Lanni J, Boldt H, Iovine MK, Johnson SL, Lovejoy NR, and MP H…
View article: Modulation of bioelectric cues in the evolution of flying fishes [Data set]
Modulation of bioelectric cues in the evolution of flying fishes [Data set] Open
Assembled reference contigs for protein-coding exons and conserved non-coding regions from targeted sequence enrichment of beloniform fishes. Current citation: Daane JM, Blum N, Lanni J, Boldt H, Iovine MK, Johnson SL, Lovejoy NR, and MP H…
View article: Refining Convergent Rate Analysis with Topology in Mammalian Longevity and Marine Transitions
Refining Convergent Rate Analysis with Topology in Mammalian Longevity and Marine Transitions Open
The quest to map the genetic foundations of phenotypes has been empowered by the modern diversity, quality, and availability of genomic resources. Despite these expanding resources, the abundance of variation within lineages makes the asso…
View article: Novel regulators of growth identified in the evolution of fin proportion in flying fish
Novel regulators of growth identified in the evolution of fin proportion in flying fish Open
Identifying the genetic foundations of trait variation and evolution is challenging as it is often difficult to parse meaningful signals from confounding signatures such as drift and epistasis. However, identification of the genetic loci u…
View article: Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change
Developmental constraint shaped genome evolution and erythrocyte loss in Antarctic fishes following paleoclimate change Open
In the frigid, oxygen-rich Southern Ocean (SO), Antarctic icefishes (Channichthyidae; Notothenioidei) evolved the ability to survive without producing erythrocytes and hemoglobin, the oxygen-transport system of virtually all vertebrates. H…
View article: Historical contingency shapes adaptive radiation in Antarctic fishes [Data set]
Historical contingency shapes adaptive radiation in Antarctic fishes [Data set] Open
Assembled reference contigs for protein-coding exons and conserved non-coding regions from targeted sequence enrichment of notothenioid fishes and outgroups. Published in : Daane, JM, Dornburg, A, Smits, P, MacGuigan, D, Hawkins, B, Near, …
View article: Historical contingency shapes adaptive radiation in Antarctic fishes [Data set]
Historical contingency shapes adaptive radiation in Antarctic fishes [Data set] Open
Assembled reference contigs for protein-coding exons and conserved non-coding regions from targeted sequence enrichment of notothenioid fishes and outgroups. Published in : Daane, JM, Dornburg, A, Smits, P, MacGuigan, D, Hawkins, B, Near, …
View article: Historical contingency shapes adaptive radiation in Antarctic fishes
Historical contingency shapes adaptive radiation in Antarctic fishes Open
Adaptive radiation illustrates the links between ecological opportunity, natural selection, and the generation of biodiversity (1). Central to adaptive radiation is the association between a diversifying lineage and the evolution of key tr…
View article: Bioelectric-calcineurin signaling module regulates allometric growth and size of the zebrafish fin
Bioelectric-calcineurin signaling module regulates allometric growth and size of the zebrafish fin Open
The establishment of relative size of organs and structures is paramount for attaining final form and function of an organism. Importantly, variation in the proportions of structures frequently underlies adaptive change in morphology in ev…
View article: Genetic Screen for Postembryonic Development in the Zebrafish (<i>Danio rerio</i>): Dominant Mutations Affecting Adult Form
Genetic Screen for Postembryonic Development in the Zebrafish (<i>Danio rerio</i>): Dominant Mutations Affecting Adult Form Open
Large-scale forward genetic screens have been instrumental for identifying genes that regulate development, homeostasis, and regeneration, as well as the mechanisms of disease. The zebrafish, Danio rerio, is an established genetic and deve…
View article: Genetic and genomic approaches to understand size and proportion
Genetic and genomic approaches to understand size and proportion Open
The establishment of proper proportions during development is essential for the final form and function of an organism. While much is known concerning the regulation of proliferation and differentiation, how the relative sizes of structure…
View article: Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies
Parallelism and Epistasis in Skeletal Evolution Identified through Use of Phylogenomic Mapping Strategies Open
The identification of genetic mechanisms underlying evolutionary change is critical to our understanding of natural diversity, but is presently limited by the lack of genetic and genomic resources for most species. Here, we present a new c…
View article: Exome Data: Phoxinellus Alepidotus And Telestes Ukliva
Exome Data: Phoxinellus Alepidotus And Telestes Ukliva Open
Reference exome and variant files for Phoxinellus alepidotus and Telestes ukliva Published in : Daane, J.M., Rohner, N., Konstantinidis, P., Djuranovic, S. and Harris M.P. (2016). Parallelism and epistasis in skeletal evolution identified …