AmphibiaWeb tracks the paradox: New species discovery in an era of declines • Write species accou... more AmphibiaWeb tracks the paradox: New species discovery in an era of declines • Write species accounts, or have your herpetology students contribute • Share amphibian photos, sound recordings, and videos, which are linked to species accounts • Contact AmphibiaWeb with your ideas Record and share your observations with science and fellow citizen scientists on the Global Amphibian Bioblitz. Log onto iNaturalist.org to start contributing. How to Contribute: Where else can you find AmphibiaWeb accounts? Via webservice, original and dynamically updated AmphibiaWeb species accounts appear on both EOL and iNaturalist species pages. Content is shared with partners with full credits to the original author and AmphibiaWeb. Help Record Species! Become an AmphibiaWeb contributor! Got AWeb? We have an app for that! We used the latest published phylogeny based on DNA sequence data of nearly a third of amphibian species (Pyron & Wiens 2011) to illustrate the way in which taxonomy over the past three decades has contributed to our knowledge of relationships and phylogenetic diversity. In the tree above, we highlighted in green all species that do not appear in the summary provided by Frost in 1985. More than 900 of the nearly 2,900 species included in this phylogeny (approximately one-third of the tips) represent contributions from post-1985 taxonomy to understanding the Amphibian Tree of Life. Taxonomic effort appears distributed across amphibian diversity, including new discoveries from diverse lineages representing more than 250 million years of evolution. At right, we illustrate the family tree available on AmphibiaWeb.
The western diamondback rattlesnake (Crotalus atrox) is a prominent member of North American dese... more The western diamondback rattlesnake (Crotalus atrox) is a prominent member of North American desert and semi-arid ecosystems, and its importance extends from its impact on the region's ecology and imagery, to its medical relevance as a large deadly venomous snake. We used mtDNA sequences to identify population genetic structure and historical demographic patterns across the range of this species, and relate these to broader patterns of historical biogeography of desert and semi-arid regions of the southwestern USA and adjacent Mexico. We inferred a Late Pliocene divergence between peninsular and continental lineages of Crotalus, followed by an Early Mid Pleistocene divergence across the continental divide within C. atrox. Within desert regions (Sonoran and Chihuahuan Deserts, Southern Plains, and Tamaulipan Plain) we observed population structure indicating isolation of populations in multiple Pleistocene refugia on either side of the continental divide, which we attempt to identify. Evidence of post-glacial population growth and range expansion was inferred, particularly in populations east of the continental divide. We observed clear evidence of (probably recent) gene Xow across the continental divide and secondary contact of haplotype lineages. This recent gene Xow appears to be particularly strong in the West-to-East direction. Our results also suggest that Crotalus tortugensis (Tortuga Island rattlesnake) and a population of 'C. atrox' inhabiting Santa Cruz Island (in the Gulf of California) previously suggested to be an unnamed species, are in fact deeply phylogenetically nested within continental lineages of C. atrox. Accordingly, we suggest C. tortugensis and 'C. atrox' from Santa Cruz Island be placed in the synonymy of C. atrox.
The pale postocular stripes end before the rictus of the mouth. A darker stripe is present poster... more The pale postocular stripes end before the rictus of the mouth. A darker stripe is present posterior to the pale postocular stripe. Similar to C. atrox, the tail has a distinctive and contrasting color pattern of black and ash-white alternating stripes. The black caudal rings are as wide or wider than the white rings and the black rings are sometimes not continuous. • DIAGNOSIS. Crotalus tortugensis is most similar to C. atrox, with differences in the dorsal blotches (diamonds) being the most noticeable divergence. The blotches are less distinct than in C. atrox. In C. tortugensis, the margins of the blotches are much darker than the central portion and usually "include on each side [of the blotch] a group of lighter scales as pale as the general dorsal ground color" (Van Denburgh and Slevin 1921). These Catalogue of American Amphibians and Reptiles.
To address the limitations of manufacturing noodle products using rice, brown rice noodles were c... more To address the limitations of manufacturing noodle products using rice, brown rice noodles were created by the fermentation of brown rice containing several nutrients and the quality of these noodles were evaluated. White rice noodles, fermented white rice noodles, brown rice noodles, and fermented brown rice noodles were developed using white rice and brown rice, respectively. We found that the content of crude proteins present in the noodles during the fermentation process increased and the content of crude fat and carbohydrates in the noodles was reduced. In addition, the water content of brown rice noodles was twofold higher than that of white rice, although under fermentation conditions, the water content of brown rice noodles decreased slightly. A slight change of chromaticity was observed during the fermentation process. In cooking, the weight and volume of the noodles increased, with the change being lowest in noodles based on white rice. White rice-based noodles exhibited significantly higher turbidity in the cooked noodle soup, while other noodle products showed relatively constant turbidity. Most of the products showed a decreased texture, becoming soft with cooking; however, the elasticity of the cooked products increased. Our results suggest that the disadvantages of producing rice noodles can be overcome by the development of fermented brown rice noodles containing a variety of nutritional components. This would potentially develop a market for rice-based manufactured foods that appeal to modern preferences.
Molecular Phylogenetics and Evolution, Feb 1, 2015
We used mitochondrial DNA sequence data from 151 individuals to estimate population genetic struc... more We used mitochondrial DNA sequence data from 151 individuals to estimate population genetic structure across the range of the Western Diamondback Rattlesnake (Crotalus atrox), a widely distributed North American pitviper. We also tested hypotheses of population structure using double-digest restriction site associated DNA (ddRADseq) data, incorporating thousands of nuclear genome-wide SNPs from 42 individuals. We found strong mitochondrial support for a deep divergence between eastern and western C. atrox populations, and subsequent intermixing of these populations in the Inter-Pecos region of the United States and Mexico. Our nuclear RADseq data also identify these two distinct lineages of C. atrox, and provide evidence for nuclear admixture of eastern and western alleles across a broad geographic region. We identified contrasting patterns of mitochondrial and nuclear genetic variation across this genetic fusion zone that indicate partially restricted patterns of gene flow, which may be due to either pre-or post-zygotic isolating mechanisms. The failure of these two lineages to maintain complete genetic isolation, and evidence for partially-restricted gene flow, imply that these lineages were in the early stages of speciation prior to secondary contact.
Amphibians are a clade of over 8,400 species that provide unique research opportunities and chall... more Amphibians are a clade of over 8,400 species that provide unique research opportunities and challenges. With amphibians undergoing severe global declines, we posit that assessing our current understanding of amphibians is imperative. Focusing on the past five years (2016–2020), we examine trends in amphibian research, data, and systematics. New species of amphibians continue to be described at a pace of ~150 per year. Phylogenomic studies are increasing, fueling a growing consensus in the amphibian tree of life. Over 3,000 species of amphibians are now represented by expert-curated accounts or data in AmphibiaWeb, AmphibiaChina, BioWeb, or the Amphibian Disease Portal. Nevertheless, many species lack basic natural history data (e.g., diet records, morphological measurements, call recordings) and major gaps exist for entire amphibian clades. Genomic resources appear on the cusp of a rapid expansion, but large, repetitive amphibian genomes still pose significant challenges. Conservati...
AmphibiaWeb tracks the paradox: New species discovery in an era of declines • Write species accou... more AmphibiaWeb tracks the paradox: New species discovery in an era of declines • Write species accounts, or have your herpetology students contribute • Share amphibian photos, sound recordings, and videos, which are linked to species accounts • Contact AmphibiaWeb with your ideas Record and share your observations with science and fellow citizen scientists on the Global Amphibian Bioblitz. Log onto iNaturalist.org to start contributing. How to Contribute: Where else can you find AmphibiaWeb accounts? Via webservice, original and dynamically updated AmphibiaWeb species accounts appear on both EOL and iNaturalist species pages. Content is shared with partners with full credits to the original author and AmphibiaWeb. Help Record Species! Become an AmphibiaWeb contributor! Got AWeb? We have an app for that! We used the latest published phylogeny based on DNA sequence data of nearly a third of amphibian species (Pyron & Wiens 2011) to illustrate the way in which taxonomy over the past three decades has contributed to our knowledge of relationships and phylogenetic diversity. In the tree above, we highlighted in green all species that do not appear in the summary provided by Frost in 1985. More than 900 of the nearly 2,900 species included in this phylogeny (approximately one-third of the tips) represent contributions from post-1985 taxonomy to understanding the Amphibian Tree of Life. Taxonomic effort appears distributed across amphibian diversity, including new discoveries from diverse lineages representing more than 250 million years of evolution. At right, we illustrate the family tree available on AmphibiaWeb.
AmphibiaWeb Team Kellie Whittaker AmphibiaWeb Coordinator University of California at Berkeley Da... more AmphibiaWeb Team Kellie Whittaker AmphibiaWeb Coordinator University of California at Berkeley David B. Wake Director and Founder University of California at Berkeley Vance Vredenburg Associate Director, and Founder San Francisco State University Joyce Gross Database Programmer, and Founder University of California at Berkeley David C. Blackburn Senior Associate California Academy of Sciences (as of September 2011) David C. Cannatella Senior Associate University of Texas, Austin Michelle S. Koo Senior Associate University of California at Berkeley Carol L. Spencer Senior Associate University of California at Berkeley Arie van der Meijden Senior Associate CIBIO Institute, Portugal
The Mohave Rattlesnake (Crotalus scutulatus) is a highly venomous pitviper inhabiting the arid in... more The Mohave Rattlesnake (Crotalus scutulatus) is a highly venomous pitviper inhabiting the arid interior deserts, grasslands, and savannas of western North America. Currently two subspecies are recognized: the Northern Mohave Rattlesnake (C. s. scutulatus) ranging from southern California to the southern Central Mexican Plateau, and the Huamantla Rattlesnake (C. s. salvini) from the region of Tlaxcala, Veracruz, and Puebla in south-central Mexico. Although recent studies have demonstrated extensive geographic variation in venom composition and cryptic genetic diversity in this species, no modern studies have focused on geographic variation in morphology. Here we analyzed a series of qualitative, meristic, and morphometric traits from 347 specimens of C. scutulatus and show that this species is phenotypically cohesive without discrete subgroups, and that morphology follows a continuous cline in primarily color pattern and meristic traits across the major axis of its expansive distribu...
Snake venoms represent an enriched system for investigating the evolutionary processes that lead ... more Snake venoms represent an enriched system for investigating the evolutionary processes that lead to complex and dynamic trophic adaptations. It has long been hypothesized that natural selection may drive geographic variation in venom composition, yet previous studies have lacked the population genetic context to examine these patterns. We leverage range-wide sampling of Mojave Rattlesnakes (Crotalus scutulatus) and use a combination of venom, morphological, phylogenetic, population genetic, and environmental data to characterize the striking dichotomy of neurotoxic (Type A) and hemorrhagic (Type B) venoms throughout the range of this species. We find that three of the four previously identified major lineages within C. scutulatus possess a combination of Type A, Type B, and a 'mixed' Type A + B venom phenotypes, and that fixation of the two main venom phenotypes occurs on a more fine geographic scale than previously appreciated. We also find that Type A + B individuals occur in regions of inferred introgression, and that this mixed phenotype is comparatively rare. Our results support strong directional local selection leading to fixation of alternative venom phenotypes on a fine geographic scale, and are inconsistent with balancing selection to maintain both phenotypes within a single population. Our comparisons to biotic and abiotic factors further indicate that venom phenotype correlates with fang morphology and climatic variables. We hypothesize that links to fang morphology may be indicative of co-evolution of venom and other trophic adaptations, and that climatic variables may be linked to prey distributions and/or physiology, which in turn impose selection pressures on snake venoms.
AmphibiaWeb tracks the paradox: New species discovery in an era of declines • Write species accou... more AmphibiaWeb tracks the paradox: New species discovery in an era of declines • Write species accounts, or have your herpetology students contribute • Share amphibian photos, sound recordings, and videos, which are linked to species accounts • Contact AmphibiaWeb with your ideas Record and share your observations with science and fellow citizen scientists on the Global Amphibian Bioblitz. Log onto iNaturalist.org to start contributing. How to Contribute: Where else can you find AmphibiaWeb accounts? Via webservice, original and dynamically updated AmphibiaWeb species accounts appear on both EOL and iNaturalist species pages. Content is shared with partners with full credits to the original author and AmphibiaWeb. Help Record Species! Become an AmphibiaWeb contributor! Got AWeb? We have an app for that! We used the latest published phylogeny based on DNA sequence data of nearly a third of amphibian species (Pyron & Wiens 2011) to illustrate the way in which taxonomy over the past three decades has contributed to our knowledge of relationships and phylogenetic diversity. In the tree above, we highlighted in green all species that do not appear in the summary provided by Frost in 1985. More than 900 of the nearly 2,900 species included in this phylogeny (approximately one-third of the tips) represent contributions from post-1985 taxonomy to understanding the Amphibian Tree of Life. Taxonomic effort appears distributed across amphibian diversity, including new discoveries from diverse lineages representing more than 250 million years of evolution. At right, we illustrate the family tree available on AmphibiaWeb.
The western diamondback rattlesnake (Crotalus atrox) is a prominent member of North American dese... more The western diamondback rattlesnake (Crotalus atrox) is a prominent member of North American desert and semi-arid ecosystems, and its importance extends from its impact on the region's ecology and imagery, to its medical relevance as a large deadly venomous snake. We used mtDNA sequences to identify population genetic structure and historical demographic patterns across the range of this species, and relate these to broader patterns of historical biogeography of desert and semi-arid regions of the southwestern USA and adjacent Mexico. We inferred a Late Pliocene divergence between peninsular and continental lineages of Crotalus, followed by an Early Mid Pleistocene divergence across the continental divide within C. atrox. Within desert regions (Sonoran and Chihuahuan Deserts, Southern Plains, and Tamaulipan Plain) we observed population structure indicating isolation of populations in multiple Pleistocene refugia on either side of the continental divide, which we attempt to identify. Evidence of post-glacial population growth and range expansion was inferred, particularly in populations east of the continental divide. We observed clear evidence of (probably recent) gene Xow across the continental divide and secondary contact of haplotype lineages. This recent gene Xow appears to be particularly strong in the West-to-East direction. Our results also suggest that Crotalus tortugensis (Tortuga Island rattlesnake) and a population of 'C. atrox' inhabiting Santa Cruz Island (in the Gulf of California) previously suggested to be an unnamed species, are in fact deeply phylogenetically nested within continental lineages of C. atrox. Accordingly, we suggest C. tortugensis and 'C. atrox' from Santa Cruz Island be placed in the synonymy of C. atrox.
The pale postocular stripes end before the rictus of the mouth. A darker stripe is present poster... more The pale postocular stripes end before the rictus of the mouth. A darker stripe is present posterior to the pale postocular stripe. Similar to C. atrox, the tail has a distinctive and contrasting color pattern of black and ash-white alternating stripes. The black caudal rings are as wide or wider than the white rings and the black rings are sometimes not continuous. • DIAGNOSIS. Crotalus tortugensis is most similar to C. atrox, with differences in the dorsal blotches (diamonds) being the most noticeable divergence. The blotches are less distinct than in C. atrox. In C. tortugensis, the margins of the blotches are much darker than the central portion and usually "include on each side [of the blotch] a group of lighter scales as pale as the general dorsal ground color" (Van Denburgh and Slevin 1921). These Catalogue of American Amphibians and Reptiles.
To address the limitations of manufacturing noodle products using rice, brown rice noodles were c... more To address the limitations of manufacturing noodle products using rice, brown rice noodles were created by the fermentation of brown rice containing several nutrients and the quality of these noodles were evaluated. White rice noodles, fermented white rice noodles, brown rice noodles, and fermented brown rice noodles were developed using white rice and brown rice, respectively. We found that the content of crude proteins present in the noodles during the fermentation process increased and the content of crude fat and carbohydrates in the noodles was reduced. In addition, the water content of brown rice noodles was twofold higher than that of white rice, although under fermentation conditions, the water content of brown rice noodles decreased slightly. A slight change of chromaticity was observed during the fermentation process. In cooking, the weight and volume of the noodles increased, with the change being lowest in noodles based on white rice. White rice-based noodles exhibited significantly higher turbidity in the cooked noodle soup, while other noodle products showed relatively constant turbidity. Most of the products showed a decreased texture, becoming soft with cooking; however, the elasticity of the cooked products increased. Our results suggest that the disadvantages of producing rice noodles can be overcome by the development of fermented brown rice noodles containing a variety of nutritional components. This would potentially develop a market for rice-based manufactured foods that appeal to modern preferences.
Molecular Phylogenetics and Evolution, Feb 1, 2015
We used mitochondrial DNA sequence data from 151 individuals to estimate population genetic struc... more We used mitochondrial DNA sequence data from 151 individuals to estimate population genetic structure across the range of the Western Diamondback Rattlesnake (Crotalus atrox), a widely distributed North American pitviper. We also tested hypotheses of population structure using double-digest restriction site associated DNA (ddRADseq) data, incorporating thousands of nuclear genome-wide SNPs from 42 individuals. We found strong mitochondrial support for a deep divergence between eastern and western C. atrox populations, and subsequent intermixing of these populations in the Inter-Pecos region of the United States and Mexico. Our nuclear RADseq data also identify these two distinct lineages of C. atrox, and provide evidence for nuclear admixture of eastern and western alleles across a broad geographic region. We identified contrasting patterns of mitochondrial and nuclear genetic variation across this genetic fusion zone that indicate partially restricted patterns of gene flow, which may be due to either pre-or post-zygotic isolating mechanisms. The failure of these two lineages to maintain complete genetic isolation, and evidence for partially-restricted gene flow, imply that these lineages were in the early stages of speciation prior to secondary contact.
Amphibians are a clade of over 8,400 species that provide unique research opportunities and chall... more Amphibians are a clade of over 8,400 species that provide unique research opportunities and challenges. With amphibians undergoing severe global declines, we posit that assessing our current understanding of amphibians is imperative. Focusing on the past five years (2016–2020), we examine trends in amphibian research, data, and systematics. New species of amphibians continue to be described at a pace of ~150 per year. Phylogenomic studies are increasing, fueling a growing consensus in the amphibian tree of life. Over 3,000 species of amphibians are now represented by expert-curated accounts or data in AmphibiaWeb, AmphibiaChina, BioWeb, or the Amphibian Disease Portal. Nevertheless, many species lack basic natural history data (e.g., diet records, morphological measurements, call recordings) and major gaps exist for entire amphibian clades. Genomic resources appear on the cusp of a rapid expansion, but large, repetitive amphibian genomes still pose significant challenges. Conservati...
AmphibiaWeb tracks the paradox: New species discovery in an era of declines • Write species accou... more AmphibiaWeb tracks the paradox: New species discovery in an era of declines • Write species accounts, or have your herpetology students contribute • Share amphibian photos, sound recordings, and videos, which are linked to species accounts • Contact AmphibiaWeb with your ideas Record and share your observations with science and fellow citizen scientists on the Global Amphibian Bioblitz. Log onto iNaturalist.org to start contributing. How to Contribute: Where else can you find AmphibiaWeb accounts? Via webservice, original and dynamically updated AmphibiaWeb species accounts appear on both EOL and iNaturalist species pages. Content is shared with partners with full credits to the original author and AmphibiaWeb. Help Record Species! Become an AmphibiaWeb contributor! Got AWeb? We have an app for that! We used the latest published phylogeny based on DNA sequence data of nearly a third of amphibian species (Pyron & Wiens 2011) to illustrate the way in which taxonomy over the past three decades has contributed to our knowledge of relationships and phylogenetic diversity. In the tree above, we highlighted in green all species that do not appear in the summary provided by Frost in 1985. More than 900 of the nearly 2,900 species included in this phylogeny (approximately one-third of the tips) represent contributions from post-1985 taxonomy to understanding the Amphibian Tree of Life. Taxonomic effort appears distributed across amphibian diversity, including new discoveries from diverse lineages representing more than 250 million years of evolution. At right, we illustrate the family tree available on AmphibiaWeb.
AmphibiaWeb Team Kellie Whittaker AmphibiaWeb Coordinator University of California at Berkeley Da... more AmphibiaWeb Team Kellie Whittaker AmphibiaWeb Coordinator University of California at Berkeley David B. Wake Director and Founder University of California at Berkeley Vance Vredenburg Associate Director, and Founder San Francisco State University Joyce Gross Database Programmer, and Founder University of California at Berkeley David C. Blackburn Senior Associate California Academy of Sciences (as of September 2011) David C. Cannatella Senior Associate University of Texas, Austin Michelle S. Koo Senior Associate University of California at Berkeley Carol L. Spencer Senior Associate University of California at Berkeley Arie van der Meijden Senior Associate CIBIO Institute, Portugal
The Mohave Rattlesnake (Crotalus scutulatus) is a highly venomous pitviper inhabiting the arid in... more The Mohave Rattlesnake (Crotalus scutulatus) is a highly venomous pitviper inhabiting the arid interior deserts, grasslands, and savannas of western North America. Currently two subspecies are recognized: the Northern Mohave Rattlesnake (C. s. scutulatus) ranging from southern California to the southern Central Mexican Plateau, and the Huamantla Rattlesnake (C. s. salvini) from the region of Tlaxcala, Veracruz, and Puebla in south-central Mexico. Although recent studies have demonstrated extensive geographic variation in venom composition and cryptic genetic diversity in this species, no modern studies have focused on geographic variation in morphology. Here we analyzed a series of qualitative, meristic, and morphometric traits from 347 specimens of C. scutulatus and show that this species is phenotypically cohesive without discrete subgroups, and that morphology follows a continuous cline in primarily color pattern and meristic traits across the major axis of its expansive distribu...
Snake venoms represent an enriched system for investigating the evolutionary processes that lead ... more Snake venoms represent an enriched system for investigating the evolutionary processes that lead to complex and dynamic trophic adaptations. It has long been hypothesized that natural selection may drive geographic variation in venom composition, yet previous studies have lacked the population genetic context to examine these patterns. We leverage range-wide sampling of Mojave Rattlesnakes (Crotalus scutulatus) and use a combination of venom, morphological, phylogenetic, population genetic, and environmental data to characterize the striking dichotomy of neurotoxic (Type A) and hemorrhagic (Type B) venoms throughout the range of this species. We find that three of the four previously identified major lineages within C. scutulatus possess a combination of Type A, Type B, and a 'mixed' Type A + B venom phenotypes, and that fixation of the two main venom phenotypes occurs on a more fine geographic scale than previously appreciated. We also find that Type A + B individuals occur in regions of inferred introgression, and that this mixed phenotype is comparatively rare. Our results support strong directional local selection leading to fixation of alternative venom phenotypes on a fine geographic scale, and are inconsistent with balancing selection to maintain both phenotypes within a single population. Our comparisons to biotic and abiotic factors further indicate that venom phenotype correlates with fang morphology and climatic variables. We hypothesize that links to fang morphology may be indicative of co-evolution of venom and other trophic adaptations, and that climatic variables may be linked to prey distributions and/or physiology, which in turn impose selection pressures on snake venoms.
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Papers by Carol Spencer