David Wake

David Wake
University of California, Berkeley | UCB · Department of Integrative Biology

Ph. D.

About

370
Publications
109,026
Reads
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23,140
Citations
Introduction
Evolutionary Biology, biogeography, comparative morphology, focus on amphibians, especially salamanders.
Additional affiliations
July 1969 - present
University of California, Berkeley
Position
  • Director (1971-1998), Curator of Herpetology
July 1969 - present
University of California, Berkeley
Position
  • Professor (Associate); Professor; Professor of the Graduate School
October 1964 - September 1969
University of Chicago
Position
  • Instructor; Assistant Professor
Education
September 1958 - August 1964
University of Southern California
Field of study
  • Biological Sciences
September 1954 - June 1958
Pacific Lutheran College
Field of study
  • Biology

Publications

Publications (370)
Article
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Human activities are increasingly responsible for moving organisms far beyond natural dispersal distances and range boundaries. Here we describe the 1st documented instance of a slender salamander (genus Batrachoseps; B. attenuatus specifically) in Washington State, in the Seattle suburb of Kirkland. We molecularly identified this individual as bel...
Article
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Evolutionary biologists are always interested in deciphering the geographic context of diversification, therefore they introduced the concept of comparative phylogeography, which helps to identify common mechanisms that contribute to shared genetic structures among organisms from the same region. Here, we used multi-locus genetic data along with en...
Article
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Emerging infectious diseases have been especially devastating to amphibians, the most endangered class of vertebrates. For amphibians, the greatest disease threat is chytridiomycosis, caused by one of two chytridiomycete fungal pathogens Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans ( Bsal ). Research over the last two d...
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In 2020, the Reptile Database (RDB) and AmphibiaWeb (AW) celebrated their 25th and 20th anniversaries, respectively. Here, we briefly review their history and highlight the biodiversity informatics context in which AmphibiaWeb and the Reptile Database have grown for a quarter century. More specifically, we outline the similarities and differences o...
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Background The southern California biodiversity hotspot has had a complex geological history, with both plate tectonic forces and sea level changes repeatedly reconfiguring the region, and likely driving both lineage splittings and extinctions. Here we investigate patterns of genetic divergence in two species of slender salamanders (Plethodontidae:...
Article
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The genus Chiropterotriton is endemic to Mexico with a geographical distribution along the Sierra Madre Oriental, the Trans Mexican Volcanic Belt and the Sierra de Juárez. The recent use of molecular tools has shown that Mexico’s amphibian diversity is highly underestimated, including a large number of cryptic, unnamed species. Chiropterotriton has...
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We present a taxonomic revision of the black salamander (Aneides flavipunctatus) complex of northwestern California and extreme southeastern Oregon. The revision is based on a number of published works as well as new molecular and morphological data presented herein. The subspecies Aneides flavipunctatus niger Myers & Maslin 1948 is raised in rank...
Article
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Tibetan frogs, Nanorana parkeri, are differentiated genetically but not morphologically along geographical and elevational gradients in a challenging environment, presenting a unique opportunity to investigate processes leading to speciation. Analyses of whole genomes of 63 frogs reveal population structuring and historical demography, characterize...
Article
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The Shasta salamander, Hydromantes shastae, is a geographically restricted lungless salamander (Plethodontidae) exhibiting remarkable evolutionary diversification at small spatial scales. Tissue samples were sequenced for the mitochondrial cytochrome b and 16S genes. Bayesian phylogenetic analyses revealed five statistically supported clades with l...
Article
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Chiropterotriton is a relatively small genus that comprises 15 species with great morphological and ecological diversity. In previous studies, molecular data provided evidence for a considerable number of species that remain undescribed. In this study, we describe one new species, Chiropterotriton chico sp. nov. based on molecular and morphological...
Article
From the time of Cope's first analysis of plethodontid systematics through Dunn's era of consolidation and integration to the present time, there have been persistent themes. Criteria for recognition of species continue to evolve as methods of data acquisition have progressed and new methods of analysis of data have been developed. Species descript...
Article
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Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of f...
Article
A ring species is a ring of populations in which there is only a single species boundary. Two contacting forms behave as distinct species yet are connected by a long chain of populations through which there is gradual or stepwise change. Such situations provide an illustration of how the process of speciation, by which one species splits into two,...
Article
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We describe three new species of minute salamanders, genus Thorius, from the Sierra Madre del Sur of Oaxaca, Mexico. Until now only a single species, T. minutissimus, has been reported from this region, although molecular data have long shown extensive genetic differentiation among geographically disjunct populations. Adult Thorius pinicola sp. nov...
Article
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Ring species are widely recognized as one of the best natural illustrations of species formation. A ring species is a circular arrangement of populations with one boundary characterized by reproductive isolation, but intergradation among populations elsewhere. They form when populations disperse around a central barrier and form a secondary contact...
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Deep phylogenetic relationships of the largest salamander family Plethodontidae have been difficult to resolve, probably reflecting a rapid diversification early in their evolutionary history. Here, data from 50 independent nuclear markers (total 48,582 bp) are used to reconstruct the phylogeny and divergence times for plethodontid salamanders, usi...
Chapter
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Background Phylogeography is an important tool that can be used to reveal cryptic biodiversity and to better understand the processes that promote lineage diversification. We studied the phylogeographic history of the Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to the California floristic province. We used multi-locus dat...
Article
In the mid-20th century, Ernst Mayr (1942) and Theodosius Dobzhansky (1958) championed the significance of ‘circular overlaps’ or ‘ring species’ as the perfect demonstration of the gradual nature of species formation. As an ancestral species expands its range, wrapping around a geographic barrier, derived taxa within the ring display interactions t...
Article
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The Neotropical bolitoglossine salamanders represent an impressive adaptive radiation, comprising roughly 40% of global salamander species diversity. Despite decades of morphological studies and molecular work, a robust multilocus phylogenetic hypothesis based on DNA sequence data is lacking for the group. We estimated species trees based on multil...
Article
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The cloud forests of Mesoamerica are notable for their high endemism, and plethodontid salamanders provide a striking example of divergence and microendemism across cloud forest blocks at a regional level. Salamanders that make use of arboreal bromeliad microhabitats in the cloud forest appear to be especially prone to divergence driven by natural...
Article
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In the midst of an ongoing sixth mass extinction ( 1 ), more than 40% of all amphibians are threatened ( 2 ). Chytridiomycosis, an emerging infectious disease (EID) caused by the fungal pathogen Batrachochytrium dendrobatidis ( Bd ), has been more devastating than any infectious wildlife disease recorded, with >200 amphibian species collapsing to o...
Article
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Although we are used to the idea that many organisms stop growing when they reach a predictable size, in many taxa, growth occurs throughout the life of an organism, a phenomenon referred to as indeterminate growth. Our comparative analysis suggests that indeterminate growth may indeed represent the ancestral condition, whereas the permanent arrest...
Article
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Osteological variation is recorded among and within four of the most distinctive species of the Mexican salamander genus Chiropterotriton. Analysis of the data is consistent with the monophyletic status of the genus and documents previously unrecorded intraspecific and interspecific variation. Most of the recorded variation involves qualitative and...
Article
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Aim: Phylogeographical structure in the black salamander (Aneides flavipunctatus) was inferred using two independent genetic datasets. Concordance between the datasets was sought in order to evaluate earlier suggestions of species-level breaks and evidence of vicariance and long-term isolation within the complex. We hypothesized that major phylogeo...
Chapter
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My goal is to present my perspectives on a 50-year exploration of homoplasy in salamanders, using the 1981 Dahlem conference on Evolution and Development (Bonner 1982) as a centerpiece. I summarize my early work on homoplasy and show how it was relevant to the planning of the original conference. I then examine how the conference influenced my late...
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A newly discovered population of Red-bellied Newts (Taricha rivularis) in the Stevens Creek watershed in Santa Clara County, California, represents a significant southerly range extension of this species, by approximately 130 km from the nearest records in Sonoma County, California. To investigate the origin of this population we sequenced two mito...
Data
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45 At a time when amphibian populations globally are in decline, the recent discoveries of large numbers of new frog species on Sri Lanka, an island from which the pathogenic chytrid fungus has not yet been reported, may seem heartening (Meegaskumbura et al. 2002). A total of 42 new species of anurans have been described since 1993, and many more s...
Article
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Global declines of amphibians refer to the phenomenon of the population declines and even extinctions of amphibian species around the world. Assessments of the world's amphibians found that nearly a third of the known species of amphibians are globally threatened with extinction and that at least 42% of known amphibian species are experiencing popu...
Article
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Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent distinct genetic populations based on prio...
Data
The small size and apparent external morphological similarity of the minute salamanders of the genus Thorius have long hindered evolutionary studies of the group. We estimate gene and species trees within the genus using mitochondrial and nuclear DNA from nearly all named and many candidate species and find three main clades. We use this phylogenet...
Article
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Anura (frogs and toads) constitute over 88% of living amphibian diversity but many important questions about their phylogeny and evolution remain unresolved. For this study, we developed an efficient method for sequencing anuran mtDNAs by amplifying the mitochondrial genome in 12 overlapping fragments using frog-specific universal primer sets. Base...
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Background The currently recognized species richness of South American salamanders is surprisingly low compared to North and Central America. In part, this low richness may be due to the salamanders being a recent arrival to South America. Additionally, the number of South American salamander species may be underestimated because of cryptic diversi...
Data
Bayesian chronogram with 95% highest posterior density for Central and South American Bolitoglossa based on Rag1 and Cytb.
Data
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Divergence time estimates based on alternative calibrations.
Data
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List of specimens (species, GenBank accession, continent) included in the divergence time analysis.
Data
Best likelihood models of sequence evolution for each codon position and combined positions.
Data
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Multilocus combined phylogeny.
Data
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Inter-individual K2P corrected sequence divergence at cytochrome b. Sensu lato interspecific comparisons are shaded grey.
Data
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Inter-individual uncorrected sequence divergence at Rag1.Sensu lato interspecific comparisons are shaded grey.
Article
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The salamander fauna of Colombia is very poorly known, probably because most research efforts have been devoted to anurans during the last two decades. Here, we describe two new species of the genus Bolitoglossa (Eladinea) from the eastern flank of the Eastern Colombian Andes (Cordillera Oriental), near the border with Venezuela. Bolitoglossa tamae...
Data
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Recently published research addressing the question of relationships and biogeography of European plethodontid salamanders has refined time estimates for divergence from American relatives. The recently discovered Korean plethodontid Karsenia is either the sister-taxon of Hydromantes (which has members in Europe and California), or a close relative...
Data
Full-text available
Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent distinct genetic populations based on prio...
Article
Full-text available
Here we characterize the genetic structure of Black Salamanders (Aneides flavipunctatus) in the Klamath Mountains of northwestern California and southwestern Oregon using mitochondrial and nuclear DNA sequences. We hypothesized that the Sacramento, Smith, Klamath, and Rogue River watersheds would represent distinct genetic populations based on prio...
Article
Full-text available
Background The complex geological history of Mesoamerica provides the opportunity to study the impact of multiple biogeographic barriers on population differentiation. We examine phylogeographic patterns in a clade of lowland salamanders (Bolitoglossa subgenus Nanotriton) using two mitochondrial genes and one nuclear gene. We use several phylogeogr...
Data
Table S1. Museum catalog numbers, locality information, geographic coordinates, and GenBank accession numbers for all tissues used in phylogenetic analyses.
Data
Table S4. General time reversible (GTR) distances between POMC haplotypes used in phylogenetic analyses.
Data
Table S2. General time reversible (GTR) distances between 16S haplotypes used in phylogenetic analyses.
Data
Table S3. General time reversible (GTR) distances between cytb haplotypes used in phylogenetic analyses.
Article
Full-text available
Papenfuss and Wake (1987) described a new species of plethodontid salamander from northern Oaxaca, Mexico, which they named Nototriton adelos. The species was assigned to Nototriton primarily on the basis of its similarity to members of that widespread genus, which as then constituted ranged from Oaxaca, Mexico, to east-central Costa Rica. At that...
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Several recent publications have made recommendations for changes in the taxonomy of plethodontid salamanders. Here formal taxonomic proposals are made, in accordance with the Code, regarding family-group taxa. Subfamilies Hemidactyliinae and Plethodontinae are recognized, the former with four tribes and the latter with five tribes. Genera are assi...
Article
Aim Montane Central America offers an ideal system for testing geographical hypotheses of species diversification. We examined how the complex geological history of Nuclear Central America has shaped the diversification of a genus of cloud-forest-inhabiting salamanders (Dendrotriton). We applied parametric models of geographical range evolution to...
Article
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We describe five new species of lungless salamanders (Plethodontidae) from high mountain habitats along the border between Costa Rica and Panama: Bolitoglossa splendida, Bolitoglossa aureogularis, Bolitoglossa kamuk, Nototriton matama, and Oedipina nimaso. We also present phylogenetic hypotheses for the new taxa (with the exception of the Oedipina)...