David Wake

• Ph. D.
• Professor at University of California, Berkeley

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...

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...

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 dec...

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...

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:...

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...

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...

Significance Central topics in evolutionary biology include uncovering the processes and genetic bases of speciation and documenting environmental adaptations and processes responsible for them. The challenging environment of the Qinghai-Tibetan Plateau (QTP) facilitates such investigations, and the Tibetan frog, Nanorana parkeri , offers a unique...

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...

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...

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...

Significance Frogs are the dominant component of semiaquatic vertebrate faunas. How frogs originated and diversified has long attracted the attention of evolutionary biologists. Here, we recover their evolutionary history by extensive sampling of genes and species and present a hypothesis for frog evolution. In contrast to prior conclusions that th...

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,...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

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...

Bayesian chronogram with 95% highest posterior density for Central and South American Bolitoglossa based on Rag1 and Cytb.

Divergence time estimates based on alternative calibrations.

List of specimens (species, GenBank accession, continent) included in the divergence time analysis.

Best likelihood models of sequence evolution for each codon position and combined positions.

Multilocus combined phylogeny.

Inter-individual K2P corrected sequence divergence at cytochrome b. Sensu lato interspecific comparisons are shaded grey.

Inter-individual uncorrected sequence divergence at Rag1.Sensu lato interspecific comparisons are shaded grey.

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...

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...

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...

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...

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...

Table S1. Museum catalog numbers, locality information, geographic coordinates, and GenBank accession numbers for all tissues used in phylogenetic analyses.

Table S4. General time reversible (GTR) distances between POMC haplotypes used in phylogenetic analyses.

Table S2. General time reversible (GTR) distances between 16S haplotypes used in phylogenetic analyses.

Table S3. General time reversible (GTR) distances between cytb haplotypes used in phylogenetic analyses.

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...

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...

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...

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)...

AbstractWe describe a new species of Bolitoglossa (Nanotriton) from the Sierra de Juárez and Sierra Mixe of Oaxaca, Mexico. Bolitoglossa chinanteca sp. n. is distinguished from the three other species in the subgenus Nanotriton by its more robust body, by having substantial numbers of maxillary teeth and differences in relative head width, foot wid...

In the mid 20th century, Ernst Mayr and Theodosius Dobzhansky championed the significance of circular overlaps or ring species as the perfect demonstration of speciation, yet in the over 50 years since, only a handful of such taxa are known. We developed a topographic model to evaluate whether the geographic barriers that favor processes leading to...

Barrier permeability as measured by fragmentation and shape. Left: barrier permeability (fragmentation) vs. size (area). Right: barrier permeability (shape as measured by the perimeter-to-area ratio) vs. size (area). Vertical lines identify barriers that are 50,000 km2. Gray points identify all barriers on the planet, as defined by the topographic...

Use of the topographic ring model to identify candidate taxa for ring diversification around a focal barrier in the Iberian Peninsula (southern Europe) that is topographically similar to the reference barrier for the Drakensberg Massif (South Africa), which has promoted ring diversification in a tree species, Acacia karroo. Extensive field-based st...

Use of the topographic ring model to identify candidate taxa for ring diversification around a focal barrier on the island of New Guinea that is topographically similar to the reference barrier for the Central Valley (California, USA), which has promoted ring diversification in a salamander, Ensatina eschscholtzii. The focal barrier (upper right pa...

Use of the topographic ring model to identify candidate taxa for ring diversification around a focal barrier near the Baja California Peninsula (USA and Mexico) that is topographically similar to the reference barrier for the Drakensberg Massif (South Africa), which has promoted ring diversification in a tree species, Acacia karroo. The focal barri...

Use of the topographic ring model to identify candidate taxa for ring diversification around a focal barrier in Costa Rica and Panama that is topographically similar to the reference barrier for the Central Valley (California, USA), which has promoted ring diversification in a salamander, Ensatina eschscholtzii. A: The focal barrier is a long-stand...

Use of the topographic ring model to identify candidate taxa for ring diversification around a focal barrier in Madagascar that is topographically "in between" (Figure 3) reference barriers for the Drakensberg Massif (South Africa), which has promoted ring diversification in a tree species, Acacia karroo, and the Tibetan Plateau (Central Asia), whi...

Amphibian populations worldwide are under threat as a result of additive effects of multiple stressors.

Slender salamanders of the genus Batrachoseps achieve relatively high diversity in the Kern Canyon region at the southern end of the Sierra Nevada of California through high turnover of species with small geographic ranges. The status of several populations of Batrachoseps in this region is enigmatic, and both morphological and molecular data have...

For the kingdom Animalia, 1,552,319 species have been described in 40 phyla in a new evolutionary classification. Among these, the phylum Arthropoda alone represents 1,242,040 species, or about 80% of the total. The most successful group, the Insecta (1,020,007 species), accounts for about 66% of all animals. The most successful insect order, Coleo...

We describe a new species of Oedipina (subgenus Oedipina) from premontane elevations of three isolated mountains in northern Nicaragua. The new cryptic species differs in molecular characters from its closest relatives: Oedipina cyclocauda (an Atlantic lowland species with a distributional range from central Panama to extreme southeastern Nicaragua...

Reproductive isolation (RI) is widely accepted as an important "check point" in the diversification process, since it defines irreversible evolutionary trajectories. Much less consensus exists about the processes that might drive RI. Here, we employ a formal quantitative analysis of genetic interactions at several stages of divergence within the ri...

Principal component analysis on 19 climatic variables for spatially unique observations of Ensatina within California. PC1 is responsible for 41.2% of the climatic variation and reflects wet and cold gradients (Mean Temperature of Coldest Quarter, Mean Temperature of Wettest Quarter, Min Temperature of Coldest Period, and Precipitation Seasonality;...

Collecting localities for mtDNA data, geographic location and GenBank Accession numbers.

Additional ring-distributed taxa surrounding reference barriers. A: The bird species complex Alauda (sp. arvensis and gulgula): Central Asia. B: The bird species Parus major: Central Asia. C: The bird species complex Charadrius (sp. hiaticula and semipalmatus): Arctic Ocean. Barriers are shown by the red polygons, species' distributions by the blac...

Amphibians highlight the global biodiversity crisis because ∼40% of all amphibian species are currently in decline. Species have disappeared even in protected habitats (e.g., the enigmatic extinction of the golden toad, Bufo periglenes, from Costa Rica). The emergence of a fungal pathogen, Batrachochytrium dendrobatidis (Bd), has been implicated in...

Understanding the diversification of phenotypes through time—“descent with modification”—has been the focus of evolutionary biology for 150 years. If, contrary to expectations, similarity evolves in unrelated taxa, researchers are guided to uncover the genetic and developmental mechanisms responsible. Similar phenotypes may be retained from common...

We describe a new species of Pseudoeurycea from the cloud forests of Huatusco in the state of Veracruz, México. This species belongs to the P. cephalica complex. Pseudoeurycea cafetalera sp. nov. is sister to the clade formed by P. cephalica and P. quetzalanensis. The new species is diagnosed by a stout body, long stout legs, short digits, somewhat...

We describe a new species of Oedipina (subgenus Oeditriton) from the highlands of north-central Nicaragua. The new species is most closely related to Oedipina kasios, a premontane species from north-central Honduras, and O. quadra, a lowland species from northern and eastern Honduras. It differs from O. kasios and O. quadra in molecular characters...

Asian frogs of the tribe Paini (Anura: Dicroglossidae) range across several first-order tectono-morphological domains of the Cenozoic Indo-Asian collision that include the Tibetan Plateau, the Himalayas, and Indochina. We show how the tectonic events induced by the Indo-Asian collision affected the regional biota and, in turn, how the geological hi...

The recent discovery of a plethodontid salamander, Karsenia koreana, in Korea challenged our understanding of the biogeographic history of the family Plethodontidae, by far the largest family of salamanders, which otherwise is distributed in the New World with a few European species. Molecular studies suggest that Karsenia forms a clade with Hydrom...

We are deeply disturbed by the recent escalation of political assaults on scientists in general and on climate scientists in particular. All citizens should understand some basic scientific facts. There is always some uncertainty associated with scientific conclusions; science never absolutely proves anything. When someone says that society should...

Ecological niches evolve through time, but at different rates and to different degrees. An integrated approach using diverse databases, methods, and analytical tools is used to estimate climate envelopes for species of salamanders (family Salamandridae). These species, which range widely across the Holarctic and have a rich and long fossil record,...

M odern concepts central to current studies of biogeog-raphy, changing climates and evolution of ecological niches were born approximately a hun-dred years ago. In 1908, the Regents of the University of California established the Museum of Vertebrate Zoology at Berkeley, in accordance with the wishes of Annie M. Alexander (1867–1950). Alexander con...

El grupo de Bolitoglossa macrinii (limitado geográficamente al sur de Oaxaca y el suroeste de Guerrero, México) es un conjunto monofilético constituido por cinco especies, B. macrinii, Bolitoglossa riletti, Bolitoglossa hermosa, Bolitoglossa oaxacensis sp. nov., and Bolitoglossa zapoteca sp. nov. Se analizaron secuencias de ADN con un total de 1164...