ArticlePDF Available

Abstract and Figures

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 of each project, their operation and content, and review their histories, activities, users, and shared challenges. Amphibians and reptiles represent almost one-third of all vertebrates, and may contain more species than birds and mammals combined (but see Dickinson and Christidis 2014, Dickinson and Remsen 2014, Barrowclough et al. 2016, Padial and de la Riva 2021). Conservation concerns, a growing body of literature, and the rise of the internet in the 1990s led to the creation of several major efforts to provide online biodiversity databases, including AW and the RDB (Table 1).
Content may be subject to copyright.
Herpetological Review 52(2), 2021
Herpetological Review, 2021, 52(2), 246–255.
© 2021 by Society for the Study of Amphibians and Reptiles
A Quarter Century of Reptile and Amphibian Databases
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 of each project, their
operation and content, and review their histories, activities,
users, and shared challenges.
Amphibians and reptiles represent almost one-third of
all vertebrates, and may contain more species than birds and
mammals combined (but see Dickinson and Christidis 2014,
Dickinson and Remsen 2014, Barrowclough et al. 2016, Padial
and de la Riva 2021). Conservation concerns, a growing body
of literature, and the rise of the internet in the 1990s led to the
creation of several major efforts to provide online biodiversity
databases, including AW and the RDB (Table 1).
wHy dAtAbASES?
The tenth edition of Systema Naturae, published by Linneaus
in 1758, contained data on more than 4000 animal species, which
one could view as the first taxonomic database. As research and
exploration ramped up in the 19th century, so did taxonomy,
the discipline of classifying and identifying species. Taxonomic
advances were facilitated by the founding of the Zoological
Record in 1864, which aided efforts to collect all published
zoological literature. In 1900, the Zoological Record listed about
260 papers published on reptiles and amphibians. By 1925, that
number had reached about 800 per year, with steady increases
throughout the 20th and 21st centuries to what is now thousands
of new articles per year. During the 20th century, data generation
also steadily increased with better technology for research, travel,
and publications, eventually leading to digital publications,
online journals, and databases. Prior to the 1990’s, there were few
alternatives to making daily library forays and searching through
numerous books and journals before the internet revolutionized
information retrieval in the last three decades.
By the early 2000s, numerous projects had started to collect a
diversity of biological data, ranging from taxonomic surveys (e.g.,
Constable et al. 2010, Catalog of Life) and geographic maps (e.g.,
Grenyer et al. 2006), to conservation (e.g., Hofmann et al. 2010)
and DNA sequences (e.g., Schoch et al. 2020). The information
challenge for researchers has moved beyond issues of convenience
and speed and is now a matter of handling increasingly large
data sets and analyses that are organized and easily accessible.
AmphibiaWeb and Reptile Database have been working on these
issues and here we reflect on our success and work yet to come.
But how did it all get started?
The Reptile Database started in 1995 as a side project at the
European Molecular Biology Laboratory (EMBL) in Heidelberg,
Germany, where Peter Uetz was a graduate student from 1993–
1997. EMBL had just set up its first online DNA sequence database
and had already included taxonomic data. While the precursor
of RDB was a simple species list on a static web page in 1995, a
searchable version went online in early 1996 as the EMBL Reptile
Database. While the first few versions of the database had little
more than species names, families, and basic distribution data,
it was already linked to the EMBL DNA sequence database.
Virginia Commonwealth University, Richmond, Virginia 23284, USA
Museum of Vertebrate Zoology, University of California,
Berkeley, California 94720, USA; e-mail:
Monash University, University of Melbourne, Museums Victoria,
Melbourne, Australia
Virginia Commonwealth University, Richmond, Virginia 23284, USA
Florida International University, Miami, Florida 33199, USA
Museum of Vertebrate Zoology, University of California,
Berkeley California 94720, USA
School of Zoology, Faculty of Life Sciences, Tel Aviv University 6997801,
Tel Aviv, Israel
Scotts Mills, Oregon, USA
Berkeley Natural History Museums, University of California,
Berkeley, California 94720, USA
Karlsruhe, Germany
Ostrava, Czech Republic
Department of Environmental Science, Policy, and Management,
University of California, Berkeley, California 94720, USA;
Washington Department of Fish and Wildlife
Virginia Commonwealth University, Richmond, Virginia 23284, USA
Museum of Vertebrate Zoology, University of California,
Berkeley, California 94720, USA
Department of Biology, East Carolina University,
Greenville, North Carolina 27858, USA
Museum of Vertebrate Zoology and Department of Integrative Biology,
University of California, Berkeley, California 94720, USA
San Francisco State University, California 94132, USA
Museum of Vertebrate Zoology and Department of Integrative Biology,
University of California, Berkeley, California 94720, USA
1 Reptile Database
2 AmphibiaWeb
*Except for corresponding authors, all others in alphabetical order;
rst two authors contributed equally
Herpetological Review 52(2), 2021
Unfortunately, EMBL closed the database when the last person
on the original team, Ramu Chenna, left EMBL in 2006; hence,
the RDB had to move to a different server. When Uetz worked at
The Institute of Genomic Research (TIGR), the database operated
briefly as TIGR Reptile Database until he left TIGR in 2010. The
main server moved to the Czech Republic where it has been
operated by Jiří Hošek since then (see Uetz and Etzold 1996, Uetz
2016 for more details).
AmphibiaWebs origin was motivated by a University of
California Berkeley (UCB) seminar on amphibian declines led
by David Wake in 1998, attended by Vance Vredenburg and
Joyce Gross. Vredenburg was then a graduate student studying
declines in high-elevation Sierra Nevada frog species (Rana
muscosa and R. sierrae), and Gross was a programmer for the
UCB Digital Library Project. The seminar participants saw the
need for a central resource for biological, life history, taxonomic,
and conservation status for all amphibians. Simultaneously in
the early 2000s, museum informatics were increasingly moving
information and their access online and were becoming more
robust in aggregating data (e.g., HerpNET, VertNet), allowing AW
to incorporate data-driven, species-level information including
maps as well as other web services. AmphibiaWeb thus began
producing comprehensive snapshots of species information, with
a dedicated web page for every species of amphibian.
Around the same time, Amphibian Species of the World (ASW),
another taxonomic database, came online. ASW was founded and
managed by Darrel Frost at the American Museum of Natural
History and has its 22nd anniversary this year (Frost, pers. comm).
The original Amphibian Species of the World database actually
dates to a book published in 1985 with the same title (Frost
1985). The focus of the ASW database is to comprehensively track
taxonomy and literature. Both AW and ASW reciprocally link to
each other from species pages.
oPErAtionS, FundinG, And GoVErnAnCE
Both RDB and AW continue to be administered from academic
units at the respective universities of the principals, Virginia
Commonwealth University and the Museum of Vertebrate
Zoology at the University of California Berkeley, respectively.
This serves the practical needs of hosting a website, database
maintenance, and providing updated and new content on a
spare budget. Because neither project has independent funding,
direct donations and grant support are essential. Grant support
for “maintenance” is difficult to obtain and this has been true
of the limited grants awarded to AW. With the exception of its
seed funding from the Turner Foundation in 1999, awards to
AW have been to support specific research (e.g., AmphibiaTree)
development and integration projects, mainly from the National
Science Foundation (NSF). Similarly, RDB was initially funded
by the EU through a partner program of the Catalogue of Life /
Species 2000 project (approximately 2004–2006, with follow-
up approximately 2008–2010). Both projects depend on stable
university employment for PIs, support staff, and students.
Equally important are volunteer contributions for governance
and content (e.g., content, literature curation and data collection).
From its launch in 2000, AW has been run as a collaborative
project within the Museum of Vertebrate Zoology, where three AW
principals (Director David Wake, Associate Director Michelle Koo,
Coordinator Ann Chang) have appointments. Other leads include
programmer Gross of the Berkeley Natural History Museums and
Associate Director Vredenburg, now a professor at San Francisco
State University. AW is governed by its directors, who consult with
a steering committee made of amphibian experts from several
institutions in the US and Australia. The AW members will often
break into smaller working groups, which may include students
and other volunteers to focus on specific immediate or long-term
RDB is managed by a central Editor (Uetz) who coordinates
with experts, the Scientific Advisory Board (SAB), photo editor
Paul Freed, and content contributors. The SAB advises on general
strategic decisions as well as on controversial taxonomic issues.
RDB currently has four part-time core staff who are responsible
for taxonomic content, photos, and technical infrastructure.
tAXonomy trACKinG And SHArinG
A central activity of both projects has been to properly track
taxonomy. Both databases use three main routes to track new
species and the taxonomic literature in general: 1) by following
specific journals and their content alerts (e.g., Zootaxa, etc.), 2)
by using Google Scholar alerts and sources such as Zoological
Record, and 3) by direct communication from experts.
AmphibiaWeb relies on a subcommittee of taxonomists
originally led by David Wake, which includes David Blackburn,
David Cannatella, and Jodi Rowley, to track the literature,
add new species, and make recommendations on taxonomic
updates. They function by consensus and contact experts in
difficult cases (AmphibiaWeb 2020 Taxonomy). AW has explicitly
outlined its criteria for taxonomic decisions, with these central
table 1. Major taxonomic databases for vertebrates, with approximate number of species, accessed 7 January 2021. *Ornithologists have mul-
tiple global species checklists available via Avibase. EBird ( has a searchable database but summary data and species lists
are not readily available.
Database Website Species
Fishbase 34,500
Catalog of Fishes 35,704
AmphibiaWeb 8,275
Amphibian Species of the World 8,275
Reptile Database 11,440
Avibase ~10,720*
ASM Mammal Database 6,513
All vertebrates total ~72,000
Herpetological Review 52(2), 2021
considerations: 1) monophyly; 2) stability of continuing name
associations (this is important for policy and conservation); 3)
expertise of authors; 4) usefulness or general acceptance by the
amphibian community; 5) ranked taxa; 6) degree of divergence
(whether genetic or phenotypic, with respect to time since
separation for its sister taxa), especially balancing long-term name
usage and monophyly; 7) degree of support, which includes the
quality of evidence provided as well as how well supported are any
provided phylogenetic models (AmphibiaWeb 2020 Taxonomy).
The RDB uses similar criteria, although not explicitly written
out, given the heterogeneity of the literature, with each issue
requiring individual, and often preliminary, decisions. Uetz leads
the literature curation at RDB, although he routinely contacts
experts in specific cases, or the Scientific Advisory Board (SAB),
which is made up of taxonomic experts from around the world, for
more general or more wide-ranging decisions (e.g., whether the
~400 species of Anolis should be split into 8 genera, whether lab-
created species should be recognized, how to deal with taxonomic
Literature curation and taxonomic decisions pose particular
challenges for these projects. Inevitably, taxonomic organization,
which almost always relies on incomplete data, can require
subjective decisions. A common issue faced by both projects
occurs when a new publication makes conclusions about the
taxonomic organization of a clade that overreach the quality
or quantity of available data. For instance, species are often
superficially described or documented, sometimes based on
only one or a few specimens (Meiri et al. 2017), or only on
mitochondrial data, which can create misleading phylogenetic
patterns that are later revised when more data become available
(e.g., compare trees in Poe et al. 2017 and Reynolds et al. 2018).
Nonetheless, RDB and AW have to make decisions on whether
or not to include these taxonomic changes, and if so, whether
to include decision-making notes in their comments. With
increasing splitting of species, it becomes more difficult to make
objective decisions about their validity, especially with low DNA
sequence differences or little morphological differentiation, a
problem that is exacerbated by small numbers of specimens or
large geographic variation (e.g., see the recent controversy over
kingsnake classification; Chambers and Hillis 2019).
Although RDB and AW necessarily make taxonomic decisions
as part of their database maintenance, neither project considers
itself a taxonomic authority. Nevertheless, RDB and AW taxonomy
are often adopted as reference taxonomy databases. Hence we
highlight that for controversial taxonomic decisions, users are
encouraged to refer to the primary literature to decide whether or
not they would follow our recommendation. While the RDB and
AW try to represent and reflect the scientific literature, decisions
by the projects can reverberate through other databases and
be adopted by authors themselves, thus risking an unintended
positive feedback loop.
AW and the Amphibian Species of the World (ASW) can
sometimes differ in conclusions; however, these disagreements
on taxonomy are generally few in number. Reciprocal links from
each respective website allow users the opportunity to compare
taxonomies and decisions. In contrast, the RDB often uses
authoritative checklists as preferred data sources (especially for
species names), such as the Turtle Taxonomy Working Group
(2017) or SSAR checklists (Crother 2017) for turtles and North
American reptiles, respectively.
Images, sound recordings, and videos attract users to
biodiversity databases and enhance their value. Both AW and the
RDB have substantial collections of images, either hosted by their
respective databases or by external sources (such as CalPhotos
or iNaturalist). Both projects rely on volunteer contributors who
tAblE 2. Comparing AmphibiaWeb and Reptile Database. Data accessed 20 December 2020.
AmphibiaWeb Reptile Database Notes
Species number / subspecies number 8,268* 11,440 / 2,213 Total ssp. without nominate ssp. *AW does not
track subspecies
Species descriptions 3,338 5,299 Number of species with descriptions / diagnosis
Photos available 41,510* 16,740 *includes habitat photos
Species with photos 4,674 (56%) 5,568 (48%)
Ranges available 6,650 (~80%) ~8,000 maps via IUCN
Synonyms 11,971 ~44,000 Total unique names/combinations
Life history accounts 3,000 ~9,000 *Not separated out into categories
—diet 267
—reproduction 8,819
References 7,703* ~56,000 *Stored in AW database, other references are
tracked in a public Zotero group
Etymology ~ 2,250 6,192
Web Services Taxonomy, Taxonomy,
synonymy (XML, JSON); synonymy (JSON)
species accounts (XML)
Herpetological Review 52(2), 2021
generously share their images and expertise. Both AW and RDB
use CalPhotos, an online image sharing site developed and
maintained by the Berkeley Natural History Museums. In turn,
CalPhotos uses the taxonomy of both RDB and AW, checking
any uploaded identification to ensure that the name exists in the
respective taxonomy. Identifications of any CalPhotos image can
be updated or commented publicly through its online system. As
of December 2020, RDB had photos of 49% of all reptile species, or
close to 70%, when external links are included (Marshall et al.
2020b). In addition to over 41,500 images of amphibians (close to
57% of known species, see Table 2), AW also serves over 510 videos
(on Youtube and in the database) and over 820 sound files. The
sound files are important for identification, especially in frogs,
although videos are as important for all groups to document
behaviors or other dynamic features.
Fig. 1. AmphibiaWeb and Reptile Database users in 2020. Top panel: active users in 1, 7, and 28 day moving windows during 2020. Note
seasonal (and possibly Covid-related) fluctuations, including weekly fluctuations in the 1-day series (with user numbers dropping on
weekends). Bottom panel: most active countries as measured by active users in 2020. Note overlap between databases with only a few
countries not present among the top-10 countries in the other database (shown in gray italics). All data based on Google Analytics.
Herpetological Review 52(2), 2021
From its inception, AW incorporated distribution data into
its species accounts, as either static maps from the literature or
from atlases. Later the website began to display locality data from
HerpNET (later updated to VertNet) as species range estimates in
an interactive web map using a service called BerkeleyMapper.
These range polygons are based on both the IUCN Red List
assessment maps and curated species ranges produced by
AmphibiaWeb GIS assistants or volunteers, mainly for newly
described species, North American species, and species without
Red List assessments. Additionally, AW tracks type localities for
newly described species; these are also viewable from their species
page. Currently over 80% of species have distributional data.
Given the sources of the spatial data (unvetted point data from
collections via VertNet, range maps based on expert opinion or the
literature), some errors are inevitable, but presenting the data with
links to original provenance allows users to decide how best to use
these data. Range maps are still invaluable to species accounts
and for describing family distributions, which are viewable as
cartographic products and downloadable as PDFs on AW. Both
AW and RDB maintain country checklists based on the literature.
While maps are currently not directly available on RDB, locations
are searchable by country (and often smaller subdivisions such as
states) and links to maps on the IUCN site are provided.
How tHE Community uSES tHE rEPtilE dAtAbASE And AmPHibiAwEb
We assess usage data from website statistics (Google Analytics),
direct user feedback, citation data, and focused user surveys. The
AW website currently has an average of 28,000 users per month
making 2.6 million page views in 2020 (Fig. 1). By far, most of the
visitors land on AW after using a search engine (ca. 72% of total
visitors), and then visit AW to search for information on a specific
species (through its species search page). A consistent proportion
(5%) of visitors to AW result from Google searches for ‘amphibian
declines’ or related ‘disease’ or ‘chytrid’ information. The
COVID-19 pandemic has not appreciably changed AW site traffic
except for modest increases overall in users (ca. +5%) and sessions
(+2%); however, there were large increases in page views (+33%)
and pages per session (+30%) compared to previous years. Five
regions comprised over 60% of traffic, namely the US, followed by
Brazil, Mexico, India and Europe. Many AW users were researchers
and students who requested help via emails with identification of
amphibians encountered in backyards or in the wild.
The RDB had about 60,000 active users per month in 2020,
resulting in 2000 to 3000 searches per day. Most of the users hailed
from the US, Brazil, India, and Europe. Perhaps unsurprisingly,
8 of the 10 most active countries on the two sites are the same,
with only two countries not represented among the top-10 on the
other site. It is also encouraging that some of the most biodiverse
countries (Brazil, India, Mexico, Indonesia, Australia, China) are
among the heaviest users of both databases (Fig. 1).
Every year, herpetology courses in the US rely on AW and RDB
as sources of species’ information, and AW has made concerted
effort to include and create content useful to both professors
and students. Material beyond the species accounts used in
courses include family summary pages with richness maps, a
family tree, a primer on amphibians, a primer on taxonomy and
phylogeny including lessons on how to read a phylogenetic tree,
and several articles on conservation and declines of amphibians.
Many of these are downloadable as PDFs. AmphibiaWeb also
engages directly with herpetology courses by offering professors
the option of assigning students to write species accounts. AW
Fig. 2. Number of citations (2005–2020) for AmphibiaWeb and Reptile Database from Web of Science (WoS).
Herpetological Review 52(2), 2021
provides an account template and research tips for students;
these species accounts are edited and reviewed by AW staff before
publishing online with author credit for these students. AW also
runs an undergraduate apprenticeship program through UC
Berkeley where students are trained in writing species accounts,
conducting literature researches, and using GIS to help create and
update content.
The RDB is less focused on authored content, mainly because
the database tries to produce more structured data as opposed
to free text. Hence, RDB focuses on adding data from outside
sources, such as published supplementary data files. Nevertheless,
RDB receives an average of three or four emails a day (>1000 per
year) referring to specific content, requiring frequent updates or
additions to the database.
Another metric of usage is citations of AW and RDB in
publications. Both projects have been increasingly cited since
their launch either as a website (AW) or as both a website and
publication (RDB) (Fig. 2).
wHo uSES rEPtilE dAtAbASE?
Based on a long-term user survey (2016–2020), RDB is used by
professional biologists, students and by a significant percentage
of casual visitors and hobbyists (Fig. 3). However, this survey is not
really representative, given that recipients of the RDB newsletter
(mostly professionals) were actively encouraged to participate.
Professional users are thought to be the most likely to respond to
such surveys.
The most common use cases involved searches for names (or
lists of names), synonyms, distribution data and literature (Fig. 3B).
The most wanted features were distribution maps and help with
species identification. Links to other data such as phylogenetic
trees, GBIF or VertNet were also high on the wish-lists of users.
Among the free-text responses, a variety of “wanted items” were
provided, ranging from sellers of reptile pets and care sheets to
venom information, country checklists, and quick photos guides.
GrEAtESt nEEdS And CHAllEnGES in tHE nEXt 25 yEArS
Scientific publishing.—The limiting step for any modern
scientific database is to convert relevant information from
published papers (or other sources) into a structured, machine-
readable format, so it can be further processed, ideally by both
computers and human users. Currently all data on AW and most
data on RDB are hand-curated by humans, an expensive and
inefficient process. Numerous attempts have been proposed to
automate text-mining but the available tools are not ready for
routine use. Nevertheless, standards have been proposed and will
be incrementally implemented by journals (Leaman et al. 2020).
Importantly, journals need to require authors to structure their
papers in a way that information can be more easily extracted.
Herpetological Review (HR) could become a role model for such
improvements by formatting geographic or natural history notes
by (visible or invisible) tags so that species names, geographic
locations, or certain key words may be easier to extract by either
humans or computers. An early effort to make HR content more
accessible to databases (by Paul Freed) includes a complete
indexed listing of all the scientific names of amphibians and
reptiles from the very first issue of HR to the present (pending),
which would help automated linking of relevant HR content
to AW and RDB. However, we are working with HR to automate
this further so that species names and localities can be extracted
semi-automatically from future articles. Similarly, species
descriptions, published in any journal, need to be standardized, so
that each description has the same minimal data (type specimens,
character tables, localities, etc.), formatted so that information
can be easily imported into a database and displayed spatially
and on species account pages. This is a bottleneck for AW; with
more than 150 new amphibian species described each year, it is
laborious to stay updated. Ultimately, scientific publishing needs
to adapt to modern data processing so that published data can
be more easily transferred into electronic databases (see below).
Other biological data.—A major gap in current biodiversity
databases, including AW and RDB, is the lack of structured trait
data, both morphological and otherwise, such as life history or
genome data (see also Meiri 2018, Grundler 2020). Structured trait
data would allow users to identify species, refine phylogenetic
studies, or do more biological research, e.g., into the relationship
between genotype and phenotype and thus evolutionary
adaptations. Ecomorphology of Anolis is a perfect example for the
evolutionary and biological insights to be gained by integrating
trait data (Losos 2009). Similarly, there is relatively little structured
habitat data, and distribution data is still sparse and not easily
available in machine-readable formats (despite the fact that
Roll et al. 2017 have provided a large number of range maps for
reptiles, but their polygons are still too coarse for many studies).
AmphiBIO (Oliveira et al. 2017) compiled a useful set of 17 traits
for many species of amphibians, using AW as a data source, but for
the vast majority of species, such data are still missing. We predict
that fewer natural history data will be traditionally published in
journal articles but rather directly deposited into specifically
created databases, such as NSF-funded FuTRES (https://futres.
org), which has established itself as a vertebrate morphological
trait database with strict ontology rules. Similar with publications,
we need new attribution technologies, so that small contributions
and deposited data can have authors and thus citations, features
that will remain important especially for academic careers.
Integration of databases and collections.—A critical goal of
biodiversity informatics is to connect the numerous data sets to
their original physical entities, such as the voucher specimens,
DNA samples, associated pathogen or parasite samples, or
localities, often referred to as the “extended-specimen networks
(e.g., Lendemer et al. 2020; Webster 2017). Creating and
maintaining these specimen and dataset networks is especially
challenging with respect to tracking taxonomic histories and
changing species concepts or delimitations, many of which are
not reflected in physical museum collections or their database
management systems. AW and RDB can serve as a central nexus
to support the extended specimen network specifically with an
updated taxonomy and its respective links to these biodiversity
resources (Fig. 4), including genetic and genomic repositories
at GenBank, specimen aggregators (e.g., VertNet), taxonomy
resources (e.g., Catalog of Life, NCBI, Amphibian Species of the
World), species traits (e.g., Encyclopedia of Life), conservation
(e.g., assessments at Amphibian Ark and IUCN Red List), and,
most fundamentally, to the primary scientific literature. AW and
RDB thus become an extended species network serving connected
data for biodiversity research.
Long-term funding and maintenance.—Few agencies
fund scientific databases or their maintenance. Databases
are long-term projects that require regular maintenance and
management, to which funders are reluctant to commit—a
problem that is even true for major model organism databases
(Kaiser 2016). Hence, a large number of databases cease to exist
Herpetological Review 52(2), 2021
after a few years (Wren et al. 2017). Long-term maintenance
is thus critical, especially since new data on species is steadily
Can AmphibiaWeb and Reptile Database help to solve the
biodiversity crisis?—Successful conservation actions require
up-to-date and complete information about species identities,
species ranges, taxonomic nomenclature, and conservation
status. This information is especially important when
conservation is focused on hyperdiverse biodiversity hotspots
where hundreds or thousands of species may occur (Roll et al.
2017). Both the Reptile Database and AmphibiaWeb work with
conservation organizations such as IUCN and Red List teams to
coordinate for correct taxonomies, and they link to conservation
assessment data from the respective websites. However, new
research is constantly changing the landscape of taxonomy.
For example, a new species of amphibian has been described
on average every week from 1980 to the present, and there are
increasing instances of species splitting, which can complicate
Fig. 3. Reptile Database user survey results: A) User types; B) information searched for at last visit; C) most useful features in RDB; D)
most wanted features in RDB. Survey based on ~700 responses [not all questions were always answered], 2016–2020). The survey was
launched both on the RDB website and through its newsletter, with the latter being dominated by professional herpetologists and biol-
ogy students.
Herpetological Review 52(2), 2021
conservation efforts further. Thus, updating taxonomies has
become a critical but ever-increasing challenge that we can
only solve by encouraging close cooperation between scientists
and conservationists. Further, the informatic expertise and
infrastructure our databases can provide may be extremely
valuable for conservation data. For example, emerging
infectious diseases are recognized as a growing threat to wildlife
all over the world (Daszak 2007). For amphibians, the disease
chytridiomycosis, which is caused by a fungal pathogen (Berger
et al. 1998), has decimated many species on all continents save
Antarctica (Fisher et al. 2009). AW has provided overall summaries
of our knowledge on chytridiomycosis, a bibliography on the
fungal pathogen, instructional videos on sampling live and
preserved amphibians for the pathogen, and many more actions
to address this crisis. AW has also provided summaries and links
to peer-reviewed literature and media explaining monitoring
protocols that can be used to test museum or wild specimens
for infection status (e.g., Cheng et al. 2011), and thus track
pathogen invasion over the past century (e.g., Huss et al. 2013;
Vredenburg et al. 2013; Fong et al. 2015; Sette et al. 2015; Talley et
al. 2015; Vredenburg et al. 2019). In 2013, with the discovery of a
second chytrid fungus fatal to amphibians, B. salamandrivorans
(Martel et al 2013), AW principals (Koo and Vredenburg) joined
the international North American Bsal Task Force (https:// to work with governmental agencies
and others to coordinate research, surveillance and chytrid data.
The resulting predictive models (in part using AW data) helped
convince federal authorities to limit international trade in live
amphibians as pets (Yap et al. 2015). Unfortunately, even the best
scientific information can be misused. For example, biodiversity
databases often provide type localities (and other locality
records) and have been suspected of being used by poachers to
harvest newly described species or threatened species illegally
(Marshall et al. 2020a).
Can AmphibiaWeb and Reptile Database address inequities in
science?—Like the extended-specimen network, we represent the
extended-species network (see Fig. 4). And similar to the efforts
to democratize museum collections through digitization, we,
too, see opportunities to correct imbalances of knowledge access
(Drew et al. 2017). Specifically AW and RDB aim to address issues
of equity and inclusion by making scientific species information
freely and openly available. This is especially important in
Fig. 4. Relations between AmphibiaWeb (AW) and Reptile Database (RDB) to genetic, scientific, conservation and taxonomic resources
and websites. Arrows indicate relationship type and direction. Solid Black: data flow direction for both AW and RDB; Dotted Black: web
links on both AW and RDB (e.g., links on species detail pages); Solid and Dotted Orange: Links and data only for RDB; Dotted Blue: Links
only for AW. (CalPhotos images of Hyperolius bolifambae by Brian Freiermuth; Crotaphytus bicinctores by William Flaxington)
Herpetological Review 52(2), 2021
biodiversity hotspots, which, for amphibians and reptiles, are
often in countries where academic resources may be limited,
especially access to literature and scientific references. As a
community-based resource—both projects rely on contributions
of media, content, and feedback from users—we recognize that
some of our most valuable contributions come from students
and citizen scientists from these regions.
How can you contribute?—Databases such as AW and RDB
are made for their users, yet equally depend on them, both for
feedback on utility and needs, but also for content and quality
control. Given the constant funding shortages, volunteers are
a critical part of most database efforts and users like you can
help in many ways, such as submitting data (e.g., papers or
photos) but even more importantly, by helping to curate new
or published data into machine-readable content (e.g., data
tables), and being sure to reference or cite usage of AW and RDB.
More specifically, AW and RDB are increasingly collecting trait
data (morphological and ecological), and AW always needs help
with species accounts. We welcome contributions. As we have
shown (Fig. 2), citations are critical to demonstrate use and
acknowledge the value of our efforts. Please contact the authors
of this paper if you want to get involved, provide feedback on our
sites, or sign up for our newsletters.
Acknowledgments.The RDB and AW thank our many volun-
teers and contributors over the years. The Reptile Database es-
pecially recognizes its longstanding collaborators Shai Meiri and
the GARD team and all colleagues who have submitted their data,
papers, photographs, and other feedback. Mark Herr and Amy
McLeod are acknowledged for managing the RDB Social Media
activities. AmphibiaWeb thanks Darrel Frost and Amphibian Spe-
cies of the World, its many cohorts of UC Berkeley apprentices,
herpetology class students around the USA, and to our friends and
colleagues, who have contributed their energy, expertise, and feed-
back to our efforts.
We dedicate this paper to David Wake, whose intellectual
greatness was only eclipsed by his modesty and generosity.
AmphibiaWeb would not exist without David Wake and his
dedication to amphibians, conservation, and education.
literature cited
AmPHibiAwEb. 2020. Taxonomy [web application]. https://amphibi- University of California,
Berkeley, California. Accessed 11 December 2020.
bArrowClouGH, G. F., j. CrACrAFt, j. KliCKA, r. m. zinK. 2016. How
many kinds of birds are there and why does it matter? PLoS ONE
bErGEr, l., r. SPEArE, P. dASzAK, d. E. GrEEn, A. A. CunninGHAm, , C. l.
GoGGin, r. SloCombE, m. A. rAGAn, A. d. HyAtt, K. r. mCdonAld, H.
b. HinES, K. r. liPS, G. mArAntElli, And H. PArKES. 1998. Chytridio-
mycosis causes amphibian mortality associated with population
declines in the rain forests of Australia and Central America. PNAS
CHAmbErS, E. A., And d. m. HilliS. 2019. The multispecies coalescent
over-splits species in the case of geographically widespread taxa.
Syst. Biol. 69:184–193.
CHEnG, t. l., S. m. roVito, d. b. wAKE, And V. t. VrEdEnburG. 2011. Coin-
cident mass extinction of neotropical amphibians with the emer-
gence of the fungal pathogen Batrachochytrium dendrobatidis.
PNAS 108:9502–9507
ConStAblE, H., r. GurAlniCK, j. wiECzorEK, C. SPEnCEr, A. t. PEtErSon, And
tHE VErtnEt StEErinG Commit tEE. 2010. VertNet: A new model for
biodiversity data sharing. PLoS Biol. 8:e1000309.
crother, b. i. (ed.). 2017. Scientific and Standard English Names of
Amphibians and Reptiles of North America North of Mexico, with
Comments Regarding Confidence in Our Understanding. 8th ed.
SSAR Herpetol. Circ. 43:1–104.
dicKinson, e. c., and l. christidis (eds.) 2014. The Howard and Moore
Complete Checklist of the Birds of the World. Volume 2. Passer-
ines. 4th ed. Aves Press, Eastbourne, UK. 804 pp.
———, and J. V. reMsen (eds.) 2013. The Howard and Moore Complete
Checklist of the Birds of the World. Volume 1. Non-passerines. 4th
ed. Aves Press, Eastbourne, UK. 461 pp.
drEw, j. A., C. S. morEAu, And m. l. j. StiASSny. 2017. Digitization of
museum collections holds the potential to enhance researcher di-
versity. Nature Ecol. Evol. 1:1789–1790.
FiSHEr, m. P., t. w. j. GArnEr, And S. F. wAlKEr. 2009. Global emergence
of Batrachochytrium dendrobatidis and amphibian chytridiomy-
cosis in space, time, and host. Annu. Rev. Microbiol. 63:291–310.
FonG, j. j., t. l. CHEnG, A. bAtAillE, A. P. PESSiEr, b. wAldmAn, And V. t.
VrEdEnburG. 2015. Early 1900s Detection of Batrachochytrium den-
drobatidis in Korean amphibians. PLoS ONE 10: e0115656.
FroSt, d. r. (Ed.) 1985. Amphibian Species of the World: A Taxonomic
and Geographical Reference. Allen Press and the Association of
Systematics Collections, Lawrence, Kansas. 732 pp.
FutrES. 2020. Functional Trait Resource for Environmental Studies
Project [web application]. University of Or-
egon, Eugene, Oregon. Accessed 11 December 2020.
GrEnyEr, r., C. d. l. ormE, S. F. jACKSon, G. H. tHomAS, r. G. dAViES, t.
j. dAViES, K. E. jonES, V. A. olSon, r. S. ridGEly, P. C. rASmuSSEn, t.- S.
dinG, P. m. bEnnEtt, t. m. blACKburn, K. j. GASton, j. l. GittlEmAn, And
i. P. F. owEnS. 2006. Global distribution and conservation of rare
and threatened vertebrates. Nature 444:93–96.
GrundlEr, m. C. 2020. SquamataBase: a natural history database and
R package for comparative biology of snake feeding habits. Biodi-
versity Data J. 8:e49943.
KAiSEr, j. 2016. Funding for key data resources in jeopardy. Science
lEAmAn r, C.- H. wEi, A. Allot A, A. lu. 2020. Ten tips for a text-mining-
ready article: How to improve automated discoverability and in-
terpretability. PLoS Biol. 18:e3000716.
lEndEmEr j., b. tHiErS, A. K. monFilS, j. zASPEl, E. r. Ellwood, A. bEnt-
lEy, K. lEVAn, j. bAtES, d. jEnninGS, d. ContrErAS, l. lAGomArSino, P.
mAbEE, l. S. Ford, r. GurAlniCK, r. E. GroPP, m. rEVElEz, n. Cobb, K.
SEltmAnn, And m. C. AimE. 2020. The Extended Specimen Network: A
strategy to enhance US biodiversity collections, promote research
and education. BioScience 70:23–30.
loSoS, j. b. 2009. Lizards in an Evolutionary Tree: Ecology and Adap-
tive Radiation of Anoles. University of California Press, Berkeley,
California. 528 pp.
mArSHAll, b. m., C. StrinE, C. And A. C. HuGHES. 2020a. Thousands of
reptile species threatened by under-regulated global trade. Nature
Commun. 11:4738.
———, P. FrEEd, l. Vitt, P. bErnArdo, G. VoGEl, S. lotzKAt, m. FrAnzEn, j.
hallerMann, r. d. sage, b. bush, M. ribeiro-duarte, l. J. aVila, d. Jan-
dziK, b. KluSmEyEr, And P. uEtz. 2020b. An inventory of online reptile
images. Zootaxa 4896:251–264.
mArtEl, A., A. PPitzEn-VAn dEr SluliS, m. blooi, w. bErt, r. duCAtEllE,
m. C. FiSHEr, A. woEltjES, w. boSmAn, K. CHiErS, F. boSSuyt, And F. PAS-
mAnS. 2013. Batrachochytrium salamandrivorans sp. nov. causes
chytridiomicosis in amphibians. PNAS 110:15325–15329.
mEiri, S. 2018. Traits of lizards of the world: Variation around a suc-
cessful evolutionary design. Global Ecol. Biogeogr. 27:1168–1172.
———, a. M. bauer, a. allison, F. castro-herrera, l. chirio, g. colli,
i. das, t. M. doan, F. glaW, l. l. grisMer, M. hoogMoed, F. Kraus, M.
lEbrEton, d. mEirtE, z. t. nAGy, C. dE noGuEirA, P. oliVEr, o. S. G.
PAuwElS, d. PinCHEirA-donoSo, G. SHEA, r. SindACo, o. j. S. tAllowin,
o. torrES-CArVAjAl, j. F. trAPE, P. uEtz, P. wAGnEr, y. wAnG, t. ziEGlEr,
And u. roll. 2017. Extinct, obscure or imaginary: the lizard species
with the smallest ranges. Divers. Distrib. 24:262–273.
oliVEirA, b. F., V. A. São-PEdro, G. SAntoS-bArrErA, G., C. PEnonE, And G.
Herpetological Review 52(2), 2021
C. CoStA. 2017. AmphiBIO, a global database for amphibian eco-
logical traits. Sci. Data 4:170123.
PoE, S., A. niEto-montES dE oCA, o. torrES-CArVAjAl, K. dE QuEiroz, j. A.
VElASCo, b. truEtt, l. n. GrAy, m. j. ryAn, G. KöHlEr, F. AyAlA-VArElA,
And i. lAtEllA. 2017. A phylogenetic, biogeographic, and taxonomic
study of all extant species of Anolis (Squamata; Iguanidae). Syst.
Biol. 66:663–697.
rEynoldS, r. G., A. r. PuEntE-rolón, A. l. CAStlE, m. VAn dE SCHoot,
And A. j. GEnEVA. 2018. Herpetofauna of Cay Sal Bank, Bahamas and
phylogenetic relationships of Anolis fairchildi, Anolis sagrei, and
Tropidophis curtus from the region. Breviora 560:1–19.
roll, u., a. FeldMan, M. noVosoloV, a. allison, a. M. bauer, r. ber-
nArd, m. böHm, F. CAStro-HErrErA, l. CHirio, b. CollEn, G. r. Colli,
l. dAbool, i. dAS, t. m. doAn, l. l. GriSmEr, m. HooGmoEd, y. itESCu,
F. Kraus, M. lebreton, a. leWin, M. Martins, e. Maza, d. Meirte, z. t.
nAGy, C. dE C. noGuEirA, o. S. G. PAuwElS, d. PinCHEirA-donoSo, G. d.
PownEy, r. SindACo, o. j. S. tAllowin, o. torrES-CArVAjAl, j.- F. trAPE,
E. VidAn, P. uEtz, P. wAGnEr, y. wAnG, C. d. l. ormE, r. GrEnyEr And
S. mEiri. 2017. The global distribution of tetrapods reveals a need
for targeted reptile conservation. Nature Ecol. Evol. 1:1677–1682.
SEttE, C., V. t. VrEdEnburG, And A. zinK. 2015. Reconstructing historical
and contemporary disease dynamics: A case study using the Cali-
fornia slender salamander. Biol. Conserv. 192:20–29.
schoch, c. l., s. ciuFo, M. doMracheV, c. l. hotton, s. Kannan, r.
KHoVAnSKAyA, d. lEiPE, r. mCVEiGH, K. o’nEill, b. robbErtSE, S. SHArmA,
V. SouSSoV, j. P. SulliVAn, l. Sun, S. turnEr, And i. KArSCH-mizrACHi.
2020 NCBI Taxonomy: a comprehensive update on curation, re-
sources and tools. Database 2020:baaa062.
tAllEy, b. l., C. mulEtz, r. FlEiSCHEr, V. t. VrEdEnburG, And K. r. liPS.
2015. A Century of Batrachochytrium dendrobatidis in Illinois
Amphibians (1888–1989). Biol. Conserv. 182:254–261.
turtlE tAXonomy worKinG GrouP [A. G. j. rHodin, j. b. iVErSon, r. bour,
u. Fritz, A. GEorGES, H. b. SHAFFEr, And P. P. VAn dijK]. 2017. Turtles of
the World: Annotated Checklist and Atlas of Taxonomy, Synonymy,
Distribution, and Conservation Status. 8th ed. In A. G. J. Rhodin,
J. B. Iverson, P. P. van Dijk, R. A. Saumure, K. A. Buhlmann, P. C.
H. Pritchard, and R. A. Mittermeier (eds.), Conservation Biology
of Freshwater Turtles and Tortoises: A Compilation Project of the
IUCN/SSC Tortoise and Freshwater Turtle Specialist Group. Che-
lonian Research Monographs 7:1–292.
uEtz, P. 2016. The Reptile Database turns 20. Herpetol. Rev. 47:330–
———, And t. Etzold. 1996. The EMBL/EBI Reptile Database. Herpe-
tol. Rev. 27:174–175.
VrEdEnburG, V. t., S. A. FElt, E. C. morGAn, S. V. G. mCnAlly, S. wilSon,
And S. l. GrEEn. 2013. Prevalence of Batrachochytrium dendroba-
tidis in Xenopus collected in Africa (1871–2000) and in California
(2001–2010). PLoS ONE 8:e63791.
———, S. V. G. mCnAlly, H. SulAEmAn, H. m. butlEr, t. yAP, m. S. Koo,
d. SCHmEllEr, C. dodGE, t. CHEnG, G. lAu, And C. j. briGGS. 2019.
Pathogen invasion history elucidates contemporary host patho-
gen dynamics. PLoS ONE 14:e0219981.
wEbStEr, m. S. 2017. The extended specimen. In M. S. Webster (ed.),
The Extended Specimen: Emerging Frontiers in Collections-Based
Ornithological Research, pp. 1–9. Studies in Avian Biology 50. CRC
Press, Boca Raton, Florida.
wrEn j. d., C. GEorGESCu, C. b. GilES, And j. HEnnESSEy. 2017. Use it or
lose it: Citations predict the continued online availability of pub-
lished bioinformatics resources. Nucleic Acids Res. 45:3627–3633.
yAP, t., m. S. Koo, r. F. AmbroSE, d. b. wAKE, And V. t. VrEdEnburG. 2015.
Averting a biodiversity crisis. Science 349:481–482.
... Significance statement: Chameleons are a clade of highly specialized squamate 21 reptiles widely studied for their capacity to change skin coloration and many other and high-fidelity (HiFi) Pacbio sequencing technologies on whole genome sequencing, 10 made it feasible to resolve high-quality genome assembly for non-model species ...
... Teyssier et al. 2015). Chameleons are also frequently studied for many21 specialized traits adaptive to arboreal life, including zygodactylous feet and a prehensile no reference genome is currently available for chameleons. The closet3 genomes available are from the family Agamidae (Pinto et al. 2023), which diverged 4 from Chamaeleonidae about 107 million years ago (Kumar et al. 2017). ...
... No contig assembly error20 was identified using Hi-C data (figure s2). A single round of automated scaffolding21 resulted in 11 super-scaffolds, corresponding to 11 chromosomes of F. pardalis high continuity of the genome(figure s3, table s1). Furthermore, 10 out3 of the 11 pseudo-chromosomes have telomere repeats (["TAACCC"] × n) at both ends, 4 and three chromosomes (Chr3, Chr7, Chr10) are telomere-to-telomere gapless of Illumiina short reads can be properly mapped to the assembled genome and 8 94.6% of BUSCO sequences for sauropsida were complete (table S2), showing 9 excellent completeness and accuracy of the genome. ...
Full-text available
Most amniote genomes are diploid, moderate in size (approximately 1-6 Gbp), and contain a large proportion of repetitive sequences. The development of next-generation sequencing technology, especially the emergence of high-fidelity (HiFi) long-read data, has made it feasible to resolve high-quality genome assembly for non-model species efficiently. However, reference genomes for squamate reptiles has lagged behind other amniote lineages. Here we de novo assembled the first genome from the Chameleonidae family, the panther chameleon (Furcifer pardalis). We obtained telomere-to-telomere contigs using only HiFi data, reaching a contig N50 of 158.72 Mbp. The final chromosome-level assembly is 1.61 Gbp in size and 100% of primary contigs were placed to pseudochromosomes using Hi-C interaction data. We also found that sequencing depth > 30 folds can ensure both the integrity and accuracy of the genome, while insufficient depth led to false increase in genome size and proportion of duplicated genes. We provide a high-quality reference genome valuable for evolutionary and ecological studies in chameleons as well as providing comparative genomic resources for squamate reptiles.
... Snakes represent one of the most successful vertebrates groups with a global radiation of ~4000 extant species (McDiarmid et al., 1999;Uetz et al., 2021). Recent advances in phylogenomic-scale data generation have vastly improved our understanding of the relationships within and between many groups of snakes, but one group that has received relatively little attention is the Scolecophidiacommonly known in English as 'blindsnakes'. ...
... They are mostly fossorial and prey on soft-bodied invertebrates (Kley, 2001;Mizuno and Kojima, 2015;Shine and Webb, 1990;Webb and Shine, 1993). Despite their conservative morphology (Hedges et al., 2014), blindsnakes represent ~12% of global snake diversity, with over 450 described extant species (Uetz et al., 2021). ...
... Scolecophidians are believed to have originated in Gondwana 160 -125 Ma (Vidal et al., 2010) and today comprises five extant families of superficially similar snakes including Anomalepididae (20 species in the Neotropics), Leptotyphlopidae (142 species in Africa, Arabia, and the New World), Gerrhopilidae (21 species in South Asia, the Malay Archipelago and Melanesia), Xenotyphlopidae (1 species in Madagascar) and Typhlopidae (275 species in the Neotropics, Africa, Madagascar, Southeastern Europe, Southern Asia, and Australia) (Midtgaard, 2021;Uetz et al., 2021). Despite external similarities, various molecular phylogenetic datasets suggest that the Scolecophidia are paraphyletic with respect to other extant snakes Miralles et al., 2018). ...
... [4][5][6][7] These efforts may soon cover identification of the entire 12,000 species of non-avian reptiles described so far. 8 The order Squamata is by far the largest group of non-avian reptiles, often representing a significant proportion of the terrestrial vertebrate species in arid environments, including North Africa and the Middle East. Although squamate species have been inventoried in these regions, the species in Qatar are not extensively described. ...
... 14 Species identity and updated species names were further verified using The Reptile Database. 8 About 25 mg of muscle tissues or 20 µL of whole blood were collected per sample. DNA extraction was completed using the Qiagen DNeasy Blood & Tissue Kit following the manufacturer's recommendations. ...
Full-text available
Background: DNA barcoding allows for species identification and description of genetic diversity. However, in the Middle East, information on genetic diversity is accumulating at a slower pace compared to that of other regions. Methods: The COI sequence of 24 lizard and snake species in Qatar that represent major families within the order Squamata were sampled and amplified via PCR using RepCOI primers (apart from one species). Purified amplicons were then aligned, and high-quality sequences were uploaded to BOLD. Using Sphenodon punctatus as the outgroup, the phylogenetic analysis was conducted using raxmlGUI software following the maximum likelihood method. Results: The COI sequence from each of the species was obtained and the consensus sequences were submitted to GenBank. In the phylogenetic analysis, a close relationship between members of the Agamidae and Serpentes was confirmed. While members of the same genus often showed sister-taxa relationships, and species in the same family were clustered with reasonably high bootstrap supports, the COI-based phylogeny was not able to resolve the relationships among genera within the families or identify relationships with high resolution at deeper lineages. Conclusion: Although ideal for species identification, COI gene sequencing is limited in phylogenetic inference due to high mutation rates that restrict its effectiveness for resolving relationships at deep phylogenetic levels. However, COI gene sequencing can be combined with nuclear markers for a more in-depth analysis.
... Australia abounds with a globally unique diversity of elapid snakes, many of which are amongst the most toxic serpents known to man [1]. A particularly enigmatic group of Australian elapids are the black snakes of the genus Pseudechis, a group of large snakes currently consisting of nine generally accepted species [2]. Members of Pseudechis are venomous and capable of delivering bites to cause severe envenoming leading to morbidity and death [3]. ...
... Members of Pseudechis are venomous and capable of delivering bites to cause severe envenoming leading to morbidity and death [3]. The genus further contains some of Australia's most prominent snakes, including the king brown or mulga snake (Pseudechis australis) and the Collett's snake (Pseudechis colletti) [2]. Another member of this genus that receives noteworthy recognition among the broader public is the red-bellied black snake (Pseudechis porphyriacus). ...
Full-text available
The red-bellied black snake (Pseudechis porphyriacus) is a member of the Elapidae family and is distributed on the east coast of Australia. The species is known to feed on a variety of ecto-thermic prey, including frogs and lizards. It is also known to be ophiophagous (snake-feeding), and stomach-content analyses suggest that P. porphyriacus also exhibits cannibalistic behavior, yet this extreme case of ophiophagy has rarely been documented. Here, a case of cannibalism in P. porphyri-acus, which was observed in Lamington (Queensland, Australia), has been photographically documented and is described.
... With nearly 290 described species (Abdala and Quinteros 2014; Uetz et al. 2021), the genus Liolaemus is one of the most specious in the world. This genus has broad latitudinal and elevational distributions, from central Western Perú in the North to Tierra del Fuego in the South and from the Pacific to Atlantic coasts (Cruz et al. 2022). ...
Full-text available
Environmental, morphological, and phylogenetic agents may explain the clutch size in lizards. Some lineages do not fit the established correlates, however, and the causes of the variations are poorly understood. We evaluated the fecundity (in terms of clutch size) of 20 oviparous Liolaemus lizards of the boulengeri group using environmental variables under a phylogenetic framework. We used Pagel's Phylogenetic Signal Test to determine if the patterns observed respond to phylogenetic relatedness or other factors. We also ran phylogenetic generalized least squares models to determine which variable better explains differences in clutch size in these species. We found that female body size showed a strong phylogenetic signal. The clutch size of these lizards is mainly related to the daily thermal amplitude and showed a weak phylogenetic signal. Female body size weakly explains fecundity at the lineage level. It seems that thermal amplitude and, to a lesser degree, female body size and relative humidity are the critical factors for clutch size in these lizards, probably because it provides the females the conditions to reach a better body condition for reproduction.
... Initiatives to standardize, maintain, and organize relevant communities around taxonomic backbones have made important progress towards this goal. Yet, taxonomic efforts often face regional-specific [39], taxonomic-specific [40], temporal-specific [41], or fundingspecific [42] constraints, leading to a spectrum of longevity, interoperability, and maintenance hurdles that limit effective research and conservation applications [43][44][45]. ...
Full-text available
All aspects of biodiversity research, from taxonomy to conservation, rely on data associated with species names. Effective integration of names across multiple fields is paramount and depends on the coordination and organization of taxonomic data. We assess current efforts and find that even key applications for well-studied taxa still lack commonality in taxonomic information required for integration. We identify essential taxonomic elements from our interoperability assessment to support improved access and integration of taxonomic data. A stronger focus on these elements has the potential to involve taxonomic communities in biodiversity science and overcome broken linkages currently limiting research capacity. We encourage a community effort to democratize taxonomic expertise and language in order to facilitate maximum interoperability and integration.
... Squamates (Order Squamata) are a near-globally distributed clade of reptiles including 11,000 extant species of lizards, snakes, and amphisbaenians [1]. The large number of species and extensive phenotypic variation observed across squamates make them one of the most diverse and successful of the vertebrate orders. ...
Full-text available
Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, and display a dazzling diversity of phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce and define squamates (Order Squamata) and review the history and promise of genomic investigations into the patterns and processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, and evolutionary analysis. We survey the most recently available whole genome assemblies for squamates, including the taxonomic distribution of available squamate genomes, and assess their quality metrics and usefulness for research. We then focus on disagreements in squamate phylogenetic inference, how methods of high-throughput phylogenomics affect these inferences, and demonstrate the promise of whole genomes to settle or sustain persistent phylogenetic arguments for squamates. We review the role transposable elements play in vertebrate evolution, methods of transposable element annotation and analysis, and further demonstrate that through the understanding of the diversity, abundance, and activity of transposable elements in squamate genomes, squamates can be an ideal model for the evolution of genome size and structure in vertebrates. We discuss how squamate genomes can contribute to other areas of biological research such as venom systems, studies of phenotypic evolution, and sex determination. Because they represent more than 30% of the living species of amniote, squamates deserve a genome consortium on par with recent efforts for other amniotes (i.e., mammals and birds) that aim to sequence most of the extant families in a clade.
... Limbless and gape-limited predators may feed on prey that can have dangerous antipredator defenses, and both skull morphology and behavior can be adapted to this task (Savitzky 1983;Forbes 1989;Ferry-Graham et al. 2002;Mukherjee and Heithaus 2013). Within terrestrial vertebrates, snakes are the largest group of limbless, gape-limited predators, and the ∼4000 species allow for the analysis of wide variations in morphology, behavior, and diet (Uetz et al. 2021). While some types of subduing behavior have been well studied for vertebrate prey (e.g., coiling, constriction, and envenomation), how snakes feed on other unusual or well-defended prey remains poorly known (Cundall and Greene 2000;Moon et al. 2019). ...
Full-text available
Synopsis Feeding is a complex process that involves an integrated response of multiple functional systems. Animals evolve phenotypic integration of complex morphological traits to covary and maximize performance of feeding behaviors. Specialization, such as feeding on dangerous prey, can further shape the integration of behavior and morphology as traits are expected to evolve and maintain function in parallel. Feeding on centipedes, with their powerful forcipules that pinch and inject venom, has evolved multiple times within snakes, including the genus Tantilla. However, the behavioral and morphological adaptations used to consume this dangerous prey are poorly understood. By studying snakes with varying degrees of dietary specialization, we can test the integration of diet, morphology, and behavior to better understand the evolution of consuming difficult prey. We studied the prey preference and feeding behavior of Tantilla using the flat-headed snake (T. gracilis) and the crowned snake (T. coronata), which differ in the percentage of centipedes in their diet. We then quantified cranial anatomy using geometric morphometric data from CT scans. To test prey preference, we offered multiple types of prey and recorded snake behavior. Both species of snakes showed interest in multiple prey types, but only struck or consumed centipedes. To subdue centipedes, crowned snakes used coiling and holding (envenomation) immediately after striking, while flat-headed snakes used the novel behavior of pausing and holding onto centipedes for a prolonged time prior to the completion of swallowing. Each skull element differed in shape after removing the effects of size, position, and orientation. The rear fang was larger in crowned snakes, but the mechanical advantage of the lower jaw was greater in flat-headed snakes. Our results suggest that the integration of behavioral and morphological adaptations is important for the success of subduing and consuming dangerous prey.
Aim Shifts in diversification rates of Australian flora and fauna have been associated with aridification, but the relationship between diversification rates and aridity has never been quantified. We employed multiple approaches to reconstruct paleoenvironments of Australia for the first time. We used this information, and phylogenetic‐based analyses, to explore how changes in temperature and increasing aridity during the Neogene influenced the diversification of the Australian blindsnakes. We tested whether diversification rates differ between arid‐adapted and mesic‐adapted lineages. Taxon Typhlopidae, Anilios blindsnakes. Location Australia. Materials and Methods We estimated the historical biogeography of blindsnakes using BioGeoBEARS. We synthesised multiple approaches to reconstruct paleotemperature and paleoaridity of Australia during the Neogene. We fitted several birth‐death models and estimated diversification rates under paleoenvironmental conditions using RPANDA. We further compared diversification rates between arid‐adapted lineages versus mesic‐adapted lineages using ClaDS and GeoHiSSE. Results Ancestral area estimation indicated Australian blindsnakes have tropical grassland origins. We found that Australia‐specific regional paleotemperature and paleoaridity provided a better explanation for diversification rate variation than global paleotemperature. Specifically, our best‐fitting model indicated that speciation rates of blindsnakes decreased with increasing aridity. We found no difference in diversification rates between arid‐ and mesic‐adapted lineages. Main Conclusions Soon after dispersing to Australia, the common ancestors of Australian blindsnakes diversified rapidly in mesic habitats during the early Miocene. However, as the continent became increasingly arid, diversification rates decreased. We found that shifts in the environment led to the emergence of two major clades: one remaining in primarily mesic habitats and the other adapting to the expanding arid biome. Our results emphasise the importance of both arid and tropical biomes as sources and sinks of diversification.
Full-text available
Wildlife trade is a key driver of the biodiversity crisis. Unregulated, or under-regulated wildlife trade can lead to unsustainable exploitation of wild populations. International efforts to regulate wildlife mostly miss ‘lower-value’ species, such as those imported as pets, resulting in limited knowledge of trade in groups like reptiles. Here we generate a dataset on web-based private commercial trade of reptiles to highlight the scope of the global reptile trade. We find that over 35% of reptile species are traded online. Three quarters of this trade is in species that are not covered by international trade regulation. These species include numerous endangered or range-restricted species, especially hotspots within Asia. Approximately 90% of traded reptile species and half of traded individuals are captured from the wild. Exploitation can occur immediately after scientific description, leaving new endemic species especially vulnerable. Pronounced gaps in regulation imply trade is having unknown impacts on numerous threatened species. Gaps in monitoring demand a reconsideration of international reptile trade regulations. We suggest reversing the status-quo, requiring proof of sustainability before trade is permitted.
Full-text available
Data-driven research in biomedical science requires structured, computable data. Increasingly, these data are created with support from automated text mining. Text-mining tools have rapidly matured: although not perfect, they now frequently provide outstanding results. We describe 10 straightforward writing tips—and a web tool, PubReCheck—guiding authors to help address the most common cases that remain difficult for text-mining tools. We anticipate these guides will help authors’ work be found more readily and used more widely, ultimately increasing the impact of their work and the overall benefit to both authors and readers. PubReCheck is available at
Full-text available
Public databases in taxonomy, phylogenetics and geographic and fossil occurrence records are key research tools that provide raw materials, on which broad-scale analyses and synthesis in their respective fields are based. Comparable repositories for natural history observations are rare. Publicly available natural history data on traits like diet, habitat and reproduction are scattered across an extensive primary literature and remain relatively inaccessible to researchers interested in using these data for broad-scale analyses in macroecology and macroevolution. In this paper, I introduce SquamataBase, an open-source R package and database of predator-prey records involving the world’s snakes. SquamataBase facilitates the discovery of natural history observations for use in comparative analyses and synthesis and, in its current form, contains observations of at least 18,304 predator individuals comprising 1,227 snake species and at least 58,633 prey items comprising 3,231 prey taxa. To facilitate integration with comparative analysis workflows, the data are distributed inside an R package, which also provides basic functionality for common data manipulation and filtering operations. Moving forward, the continued development of public natural history databases and their integration with existing digitisation efforts in biodiversity science should become a priority.
Full-text available
For more than two centuries, biodiversity collections have served as the foundation for scientific investigation of and education about life on Earth (Melber and Abraham 2002, Cook et al. 2014, Funk 2018). The collections that have been assembled in the past and continue to grow today are a cornerstone of our national heritage that have been treated as such since the founding of the United States (e.g., Jefferson 1799, Goode 1901a, 1901b, Meisel 1926). A diverse array of institutions throughout the United States, from museums and botanical gardens to universities and government agencies, maintain our biodiversity collections as part of their research and education missions. Collectively, these institutions and their staff are stewards for at least 1 billion biodiversity specimens that include such diverse objects as dinosaur bones, pressed plants, dried mushrooms, fish preserved in alcohol, pinned insects, articulated skeletons, eggshells, and microscopic pollen grains. In turn, these collections are a premier resource for exploring life, its forms, interactions, and functions, across evolutionary, temporal, and spatial scales (Bebber et al. 2010, Monfils et al. 2017, Schindel and Cook 2018). Biodiversity collections have historically consisted of physical objects and the infrastructure to support those objects (Bradley et al. 2014). However, the last two decades have witnessed a remarkable wave of digitization that has reshaped the collections paradigm to include digital data and infrastructure (Nelson and Ellis 2018), opening vast new areas for integrative biological research (e.g., a single plant specimen mounted on an herbarium sheet may be analyzed in multitude ways to yield data on flower morphology, DNA for applications from systematic studies to genome sequences, and isotopes for analyses of nitrogen to understand the mechanisms of phenology in relation to nitrogen uptake). In the United States, investment by the federal government through the National Science Foundation's (NSF) Advancing Digitization of Biodiversity Collections (ADBC) program has facilitated the digitization of approximately 62 million US biodiversity specimens since 2011 through 24 thematic collection networks connecting over 700 collections. These networks have helped to develop a collaborative infrastructure connecting specimen data, human resources, research, and education among institutions. The ADBC program has also provided support to iDigBio (the Integrated Digitized Biocollections), which is the central coordinating unit for the digitization effort. The final ADBC grants will be awarded in 2021. During the last several years, the Biodiversity Collections Network has led an effort to gather input from primary stakeholder communities regarding future directions for collections and their use in research and education. The effort culminated in a workshop held from 30 October through 1 November 2018 at Oak Spring Garden in Upperville, Virginia, during which a strategy was developed to maximize the value of collections for future research and education that builds on and leverages the accomplishments of the ADBC program. The strategy that was informed by stakeholders, refined by workshop participants, and vetted through public comment from scientific community is presented in the present article.
Full-text available
Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically-distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014; Syst. Biol. 63:231-250). We show that over-reliance on the program BPP, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.
Full-text available
The distributions of amphibians, birds and mammals have underpinned global and local conservation priorities, and have been fundamental to our understanding of the determinants of global biodiversity. In contrast, the global distributions of reptiles, representing a third of terrestrial vertebrate diversity, have been unavailable. This prevented the incorporation of reptiles into conservation planning and biased our understanding of the underlying processes governing global vertebrate biodiversity. Here, we present and analyse the global distribution of 10,064 reptile species (99% of extant terrestrial species). We show that richness patterns of the other three tetrapod classes are good spatial surrogates for species richness of all reptiles combined and of snakes, but characterize diversity patterns of lizards and turtles poorly. Hotspots of total and endemic lizard richness overlap very little with those of other taxa. Moreover, existing protected areas, sites of biodiversity significance and global conservation schemes represent birds and mammals better than reptiles. We show that additional conservation actions are needed to effectively protect reptiles, particularly lizards and turtles. Adding reptile knowledge to a global complementarity conservation priority scheme identifies many locations that consequently become important. Notably, investing resources in some of the world’s arid, grassland and savannah habitats might be necessary to represent all terrestrial vertebrates efficiently.
Full-text available
Current ecological and evolutionary research are increasingly moving from species- to trait-based approaches because traits provide a stronger link to organism’s function and fitness. Trait databases covering a large number of species are becoming available, but such data remains scarce for certain groups. Amphibians are among the most diverse vertebrate groups on Earth, and constitute an abundant component of major terrestrial and freshwater ecosystems. They are also facing rapid population declines worldwide, which is likely to affect trait composition in local communities, thereby impacting ecosystem processes and services. In this context, we introduce AmphiBIO, a comprehensive database of natural history traits for amphibians worldwide. The database releases information on 17 traits related to ecology, morphology and reproduction features of amphibians. We compiled data from more than 1,500 literature sources, and for more than 6,500 species of all orders (Anura, Caudata and Gymnophiona), 61 families and 531 genera. This database has the potential to allow unprecedented large-scale analyses in ecology, evolution, and conservation of amphibians.
Full-text available
Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles. Our new taxonomic treatment achieves the supposed advantages of recent subdivisions of anoles that employed ranked Linnaean–based nomenclature while avoiding the pitfalls of those approaches regarding artificial constraints imposed by ranks. Our biogeographic analyses demonstrate complexity in the dispersal history of anoles, including multiple crossings of the Isthmus of Panama, two invasions of the Caribbean, single invasions to Jamaica and Cuba, and a single evolutionary dispersal from the Caribbean to the mainland that resulted in substantial anole diversity. Our comprehensive phylogenetic estimate of anoles should prove useful for rigorous testing of many comparative evolutionary hypotheses.