Recent fieldwork in southern Tanintharyi revealed the presence of a small Green Crested Lizard in... more Recent fieldwork in southern Tanintharyi revealed the presence of a small Green Crested Lizard in the wet evergreen forest. We generated mtDNA sequence data (ND2) that demonstrates that this population's nearest relative is Bronchocela rayaensis Grismer et al., 2015 of Pulau Langkawi, northwestern Peninsular Malaysia and Phuket Island. Morphologically the Burmese Bronchocela shares many features with B. ray-aensis, which potentially would make this recently described Thai-Malay species a synonym of Bronchocela burmana Blanford, 1878; however, we interpret the genetic and morphological differences to reflect evolutionary divergence and recommend the recognition of both species.
Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA s... more Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall " genome-quality " DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA " greater than X kb " as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards (" DNA Threshold " and " Percent above Threshold ") introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increa... more Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phyloge-ny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological , and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have becomeincreas... more Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have becomeincreasingly controversial. Squamates include >9000 species, making them the secondlargest group of terrestrial vertebrates. They are important medicinally and as modelsystems for ecological and evolutionary research. However, studies of squamate biologyare hindered by uncertainty over their relationships, and some consider squamate phylogenyunresolved, given recent conflicts between molecular and morphological results. To resolvethese conflicts, we expand existing morphological and molecular datasets forsquamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa,including a new set of 81 morphological characters and adding two genes from publishedstudies) and perform integrated analyses. Our results resolve higher-level relationships asindicated by molecular analyses, and reveal hidden morphological support for the molecularhypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades(Mosasauria and Polyglyphanodontia). These results further demonstrate the importance ofcombining fossil and molecular information, and the potential problems of estimating theplacement of fossil taxa from morphological data alone. Thus, our results caution againstestimating fossil relationships without considering relevant molecular data, and againstplacing fossils into molecular trees (e.g. for dating analyses) without considering the possibleimpact of molecular data on their placement.
Recent fieldwork in southern Tanintharyi revealed the presence of a small Green Crested Lizard in... more Recent fieldwork in southern Tanintharyi revealed the presence of a small Green Crested Lizard in the wet evergreen forest. We generated mtDNA sequence data (ND2) that demonstrates that this population's nearest relative is Bronchocela rayaensis Grismer et al., 2015 of Pulau Langkawi, northwestern Peninsular Malaysia and Phuket Island. Morphologically the Burmese Bronchocela shares many features with B. ray-aensis, which potentially would make this recently described Thai-Malay species a synonym of Bronchocela burmana Blanford, 1878; however, we interpret the genetic and morphological differences to reflect evolutionary divergence and recommend the recognition of both species.
Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA s... more Advances in biodiversity genomic sequencing will increasingly depend on the availability of DNA samples—and their quantifiable metadata—preserved in large institutional biorepositories that are discoverable to the scientific community. Improvements in sequencing technology constantly provide longer reads, such that longer fragment length, higher molecular weight, and overall " genome-quality " DNA (gDNA) will be desirable. Ideally, biorepositories should publish numerical scale measurements of DNA quality useful to the user community. However, the most widely used technique to evaluate DNA quality, the classic agarose gel, has yet to be quantified. Here we propose a simple and economical method using open source image analysis software to make gDNA gel images quantifiable, and propose percentage of gDNA " greater than X kb " as a standard of comparison, where X is a band from any widely used DNA ladder with desirably large band sizes. We employ two metadata standards (" DNA Threshold " and " Percent above Threshold ") introduced as part of the Global Genome Biodiversity Network (GGBN) Darwin Core extension. We illustrate the method using the traditionally used HindIII ladder and the 9,416 base-pair (bp) band as a standard. We also present data, for two taxa, a vertebrate (fish) and an invertebrate (crab), on how gDNA quality varies with seven tissue preservation methods, time since death, preservation method (i.e. buffers vs. cold temperatures), and storage temperature of various buffers over time. Our results suggest that putting tissue into a buffer prior to freezing may be better than directly into ultra-cold conditions.
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increa... more Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have become increasingly controversial. Squamates include >9000 species, making them the second largest group of terrestrial vertebrates. They are important medicinally and as model systems for ecological and evolutionary research. However, studies of squamate biology are hindered by uncertainty over their relationships, and some consider squamate phyloge-ny unresolved, given recent conflicts between molecular and morphological results. To resolve these conflicts, we expand existing morphological and molecular datasets for squamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa, including a new set of 81 morphological characters and adding two genes from published studies) and perform integrated analyses. Our results resolve higher-level relationships as indicated by molecular analyses, and reveal hidden morphological support for the molecular hypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological , and paleontological data leads to surprising placements for two major fossil clades (Mosasauria and Polyglyphanodontia). These results further demonstrate the importance of combining fossil and molecular information, and the potential problems of estimating the placement of fossil taxa from morphological data alone. Thus, our results caution against estimating fossil relationships without considering relevant molecular data, and against placing fossils into molecular trees (e.g. for dating analyses) without considering the possible impact of molecular data on their placement.
Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have becomeincreas... more Squamate reptiles (lizards and snakes) are a pivotal group whose relationships have becomeincreasingly controversial. Squamates include >9000 species, making them the secondlargest group of terrestrial vertebrates. They are important medicinally and as modelsystems for ecological and evolutionary research. However, studies of squamate biologyare hindered by uncertainty over their relationships, and some consider squamate phylogenyunresolved, given recent conflicts between molecular and morphological results. To resolvethese conflicts, we expand existing morphological and molecular datasets forsquamates (691 morphological characters and 46 genes, for 161 living and 49 fossil taxa,including a new set of 81 morphological characters and adding two genes from publishedstudies) and perform integrated analyses. Our results resolve higher-level relationships asindicated by molecular analyses, and reveal hidden morphological support for the molecularhypothesis (but not vice-versa). Furthermore, we find that integrating molecular, morphological, and paleontological data leads to surprising placements for two major fossil clades(Mosasauria and Polyglyphanodontia). These results further demonstrate the importance ofcombining fossil and molecular information, and the potential problems of estimating theplacement of fossil taxa from morphological data alone. Thus, our results caution againstestimating fossil relationships without considering relevant molecular data, and againstplacing fossils into molecular trees (e.g. for dating analyses) without considering the possibleimpact of molecular data on their placement.
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Papers by Dan Mulcahy