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In 2020, the Reptile Database (RDB) and AmphibiaWeb (AW) celebrated their 25th and 20th anniversaries, respectively. Here, we briefly review their history and highlight the biodiversity informatics context in which AmphibiaWeb and the Reptile Database have grown for a quarter century. More specifically, we outline the similarities and differences 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).
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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.
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... In Brazil, most snake species from the Elapid family are from the Micrurus genus, popularly known as coral snakes. To date, 34 Micrurus species found throughout the country in diverse biomes are described [1]. Micrurus venoms are composed mainly of two toxin families, the phospholipase A 2 (PLA 2 ) [2] and the three-finger toxin (3FTx) [3,4], conferring a phenotypic dichotomy pattern [5]. ...
Full-text available
Coral snake venoms from the Micrurus genus are a natural library of components with multiple targets, yet are poorly explored. In Brazil, 34 Micrurus species are currently described, and just a few have been investigated for their venom activities. Micrurus venoms are composed mainly of phospholipases A2 and three-finger toxins, which are responsible for neuromuscular blockade—the main envenomation outcome in humans. Beyond these two major toxin families, minor components are also important for the global venom activity, including Kunitz-peptides, serine proteases, 5′ nucleotidases, among others. In the present study, we used the two-microelectrode voltage clamp technique to explore the crude venom activities of five different Micrurus species from the south and southeast of Brazil: M. altirostris, M. corallinus, M. frontalis, M. carvalhoi and M. decoratus. All five venoms induced full inhibition of the muscle-type α1β1δε nAChR with different levels of reversibility. We found M. altirostris and M. frontalis venoms acting as partial inhibitors of the neuronal-type α7 nAChR with an interesting subsequent potentiation after one washout. We discovered that M. altirostris and M. corallinus venoms modulate the α1β2 GABAAR. Interestingly, the screening on KV1.3 showed that all five Micrurus venoms act as inhibitors, being totally reversible after the washout. Since this activity seems to be conserved among different species, we hypothesized that the Micrurus venoms may rely on potassium channel inhibitory activity as an important feature of their envenomation strategy. Finally, tests on NaV1.2 and NaV1.4 showed that these channels do not seem to be targeted by Micrurus venoms. In summary, the venoms tested are multifunctional, each of them acting on at least two different types of targets.
... Snakes compose a monophyletic group that represents one of the most successful vertebrate radiations, comprising more than 3900 species inhabiting almost all continents [1][2][3]. ...
Full-text available
Interspecific differences in snake venom compositions can result from distinct regulatory mechanisms acting in each species. However, comparative analyses focusing on identifying regulatory elements and patterns that led to distinct venom composition are still scarce. Among venomous snakes, Bothrops cotiara and Bothrops fonsecai represent ideal models to complement our understanding of the regulatory mechanisms of venom production. These recently diverged species share a similar specialized diet, habitat, and natural history, but each presents a distinct venom phenotype. Here, we integrated data from the venom gland transcriptome and miRNome and the venom proteome of B. fonsecai and B. cotiara to better understand the regulatory mechanisms that may be acting to produce differing venom compositions. We detected not only the presence of similar toxin isoforms in both species but also distinct expression profiles of phospholipases A2 (PLA2) and some snake venom metalloproteinases (SVMPs) and snake venom serine proteinases (SVSPs) isoforms. We found evidence of modular expression regulation of several toxin isoforms implicated in venom divergence and observed correlated expression of several transcription factors. We did not find strong evidence for miRNAs shaping interspecific divergence of the venom phenotypes, but we identified a subset of toxin isoforms whose final expression may be fine-tuned by specific miRNAs. Sequence analysis on orthologous toxins showed a high rate of substitutions between PLA2s, which indicates that these toxins may be under strong positive selection or represent paralogous toxins in these species. Our results support other recent studies in suggesting that gene regulation is a principal mode of venom evolution across recent timescales, especially among species with conserved ecotypes.
... Liolaemus is a Southern South America lizard genus distributed across a wide range of latitude and elevation, from Per u to the very southern end of South America and from Pacific to Atlantic coasts (Cei, 1986(Cei, , 1993. This genus is particularly rich in species (nearly 293 species; Uetz et al., 2021) and the variation in lifestyles is well known (Cei, 1993;Cruz et al., 2005;Espinoza et al., 2004;O'Grady et al., 2005;Pincheira-Donoso et al., 2013. Nearly, 50% of Liolaemus species are viviparous, most of them occurring in cold climates (Esquerr e et al., 2019). ...
Evolutionary transitions in life‐history strategies, such as the shift from egg‐laying to live birth (viviparity) are of great interest to evolutionary biologists. In squamate reptiles, several hypotheses have been proposed to explain viviparity including the cold climate hypothesis, maternal manipulation hypothesis, hypoxia hypothesis, and several others. We used two approaches: first we studied 45 species of Liolaemus, a genus where nearly 50% of species are viviparous, using a diverse ecophysiological dataset to examine the cold climate and maternal manipulation hypotheses. We collected environmental thermal data (accounting for elevational differences among species), physiological traits including preferred body temperature and its coefficient of variation as an indicator of precision in thermoregulation. Additionally, we collected standard metabolic rates for 23 of the 45 species. In one clade (the darwinii group of species) with both reproductive modes, we ran our second approach. We tested for differences in thermal physiology and metabolic rates between viviparous and oviparous species during pregnancy and non‐pregnancy periods. The cold climate hypothesis received strong support because viviparous species occur in sites with colder air temperatures (including areas at both higher elevations and latitudes) compared with oviparous species. Our detailed analysis showed that the maternal manipulation hypothesis also is supported; pregnant viviparous females show lower variation in their selected temperature. Our evidence suggests that the Andean orogeny is likely to have played a key role in the diversification of Liolaemus lizards and the evolution of viviparity in this clade may have been driven by a variety of physiological advantages accrued at different stages of embryogenesis and over evolutionary time. Thus, historical climate changes may have led to egg retention and may have been accompanied by other adaptations such as thermoregulation precision. Several hypotheses have been proposed to explain viviparity in Reptiles including the cold climate hypothesis, maternal manipulation hypothesis, hypoxia hypothesis, and several others. We collected environmental thermal data, preferred body temperature, its coefficient of variation (as an indicator of precision in thermoregulation) and standard metabolic rates for several species of Liolaemus. We tested for differences in thermal physiology and metabolic rates between viviparous and oviparous species during pregnancy and non‐pregnancy periods. Both, the cold climate and the maternal manipulation hypotheses were supported. Viviparous species occur in sites with colder air temperatures and pregnant viviparous females show lower variation in their selected temperature than oviparous gravid females. Historical climate changes may have led to egg retention and may have been accompanied by other adaptations such as thermoregulation precision.
... Many of the core activities of AmphibiaWeb have not changed in the last two decadesa web page for every amphibian species with literature-based accounts and spatial data. Much of the data we track (e.g., species accounts, type localities, range maps and traits) have been used in research studies (reviewed in (Uetz et al. 2021)), including in this article. ...
Full-text available
Amphibians are a clade of over 8,400 species that provide unique research opportunities and challenges. With amphibians undergoing severe global declines, taking stock of our current understanding of amphibians is imperative. Focusing on 2016–2020, we assessed trends in amphibian publishing, conservation research, systematics, and community resources. We show that while research and data availability are increasing rapidly, information is not evenly distributed across research fields, clades, or geographic regions, leading to substantial knowledge gaps. A complete review of amphibian NCBI resources indicates that genomic data are poised for rapid expansion, but amphibian genomes pose significant challenges. A review of recent conservation literature and cataloged threats on 1,261 species highlight the need to address land use change and disease using adaptive management strategies. We underscore the importance of database integration for advancing amphibian research and conservation and suggest other understudied or imperiled clades would benefit from similar assessments.
... The Reptile Database (RDB) curates the literature and taxonomy for about 14,000 species and subspecies of reptiles (Uetz et al. 2021). Together with a few other databases, the RDB curates the literature for about 70,000 species of fish, amphibians, reptiles, birds and mammals. ...
Full-text available
The Reptile Database (RDB) curates the literature and taxonomy for about 14,000 species and subspecies of reptiles (Uetz et al. 2021). Together with a few other databases, the RDB curates the literature for about 70,000 species of fish, amphibians, reptiles, birds and mammals. While it acts as a current name list for extant reptile taxa, including synonymies, it also collects images (currently ~18,000, representing half of all species), type information, diagnoses and descriptions, and a bibliography of 62,000 references, most of which are linked to online sources. The database is also extensively cross-referenced to citizen science projects (iNaturalist), the NCBI taxonomy, the IUCN Red List, and several others, and serves as data provider (for reptiles) for the Catalogue of Life. A major challenge for the Reptile database is the consistent curation of the literature, which requires the addition of about 2000 papers a year, including about 200 new species descriptions and numerous taxonomic changes. For instance, during the past five years, almost 1000 species changed their names, in addition to the ~900 species that were newly described, i.e., almost 20% of all reptile species were described or changed their name within just a half decade! While the database can keep track of name changes, it remains a largely unsolved problem of how these name changes can or should be translated into related databases such as the National Center for Biotechnology Information (NCBI), which keeps track of the literature independently (but exchanges data with the RDB). Some sites use the web services of the RDB to update their taxonomy, such as Calphotos or iNaturalist, but many do not or have not been able to implement automated name tracking. The RDB also works with the Global Assessment of Reptile Distributions (GARD Initiative) to keep track of range changes. After GARD published a collection of ~10,000 range maps for reptiles in 2017, more than half of these maps have changed in area size by more than 5% since the initial release. The database has developed several avenues for streamlining and optimizing curation of the literature, e.g., (semi-) automated requests for publications, species descriptions, and photos from authors, but the process is far from fully automated. Questions remain: how can taxonomic databases develop, share, and exchange better tools for curation? Can we standardize data collection and processing? How can we automatically exchange data with other data sources? How can we optimize the process of scientific publication to streamline databasing and automated information extraction?
... Such analysis risks providing a false sense of assurance that we understand the dimensions of trade, while in reality the trade may be spanning far more species than those actively monitored (Marshall et al., 2020). Marshall et al., 2020, highlighted the discrepancy in protection within the reptile trade, with only 8.3% under CITES regulations yet over 36% in trade and over 70% of individuals from some taxa (e. g., lizards) harvested from the wild (Marshall et al., 2020;Uetz et al., 2021). Whilst trade of wildcollected individuals is not necessarily unsustainable, such a judgement should rely on data, as unregulated harvest from the wild, especially for rare or small-ranged species could potentially pose a significant risk to the continued survival of such populations (Auliya et al., 2016). ...
Full-text available
As the biodiversity crisis continues, we must redouble efforts to understand and curb pressures pushing species closer to extinction. One major driver is the unsustainable trade of wildlife. Trade in internationally regulated species gains the most research attention, but this only accounts for a minority of traded species and we risk failing to appreciate the scale and impacts of unregulated legal trade. Despite being legal, trade puts pressure on wild species via: direct collection, introduced pathogens, and invasive species. Smaller species-rich vertebrates, such reptiles, fish, and amphibians, may be particularly vulnerable to trading because of gaps in regulations, small distributions, and demand of novel species. Here we combine data from five sources: online web searches in six languages, CITES trade database, LEMIS trade inventory, IUCN assessments, and a recent literature review, to characterise the global trade in amphibians, and also map use by purpose including meat, pets, medicinal and for research. We show that 1,215 species are being traded (17% of amphibian species), almost three times previous recorded numbers, 345 are threatened, and 100 data deficient or unassessed. Traded species origin hotspots include South American, China, and Central Africa; sources indicate 42% of amphibians are taken from the wild. Newly described species can be rapidly traded (mean time lag of 6.5 years), including threatened and unassessed species. The scale and limited regulation of the amphibian trade, paired with the triptych of connected pressures (collection, pathogens, invasive species), warrants a re-examination of the wildlife trade status-quo, application of the precautionary principle in regards to wildlife trade, and a renewed push to achieve global biodiversity goals.
... Such analysis risks providing a false sense of assurance that we understand the dimensions of trade, while in reality the trade may be spanning far more species than those actively monitored (Marshall et al., 2020). Marshall et al., 2020, highlighted the discrepancy in protection within the reptile trade, with only 8.3% under CITES regulations yet over 36% in trade and over 70% of individuals from some taxa (e. g., lizards) harvested from the wild (Marshall et al., 2020;Uetz et al., 2021). Whilst trade of wildcollected individuals is not necessarily unsustainable, such a judgement should rely on data, as unregulated harvest from the wild, especially for rare or small-ranged species could potentially pose a significant risk to the continued survival of such populations (Auliya et al., 2016). ...
In order to adapt to diverse habitats, organisms often evolve corresponding adaptive mechanisms to cope with their survival needs. The species-rich family of Scincidae contains both limbed and limbless species, which differ fundamentally in their locomotor demands, such as relying on the movement of limbs or only body swing to move. Locomotion requires energy, and different types of locomotion have their own energy requirements. Mitochondria are the energy factories of living things, which provide a lot of energy for various physiological activities of organisms. Therefore, mitochondrial genomes could be tools to explore whether the limb loss of skinks are selected by adaptive evolution. Isopachys gyldenstolpei is a typical limbless skink. Here, we report the complete mitochondrial genomes of I. gyldenstolpei, Sphenomorphus indicus, and Tropidophorus hainanus. The latter two species were included as limbed comparator species to the limbless I. gyldenstolpei. The results showed that the full lengths of the mitochondrial genomes of I. gyldenstolpei, S. indicus, and T. hainanus were 17,210, 16,944, and 17,001 bp, respectively. Three mitochondrial genomes have typical circular double-stranded structures similar to other reptiles, including 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and the control region. Three mitochondrial genomes obtained in this study were combined with fifteen mitochondrially complete genomes of Scincidae in the NCBI database; the phylogenetic relationship between limbless I. gyldenstolpei and limbed skinks (S. indicus and T. hainanus) is discussed. Through BI and ML trees, Sphenomorphinae and Mabuyinae were monophyletic, while the paraphyly of Scincinae was also recovered. The limbless skink I. gyldenstolpei is closer to the species of Tropidophorus, which has formed a sister group with (T. hainanus + T. hangman). In the mitochondrial genome adaptations between limbless I. gyldenstolpei and limbed skinks, one positively selected site was found in the branch-site model analysis, which was located in ND2 (at position 28, BEB value = 0.907). Through analyzing the protein structure and function of the selected site, we found it was distributed in mitochondrial protein complex I. Positive selection of some mitochondrial genes in limbless skinks may be related to the requirement of energy to fit in their locomotion. Further research is still needed to confirm this conclusion though.
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Beyond providing critical information to biologists, species distributions are useful for naturalists, curious citizens, and applied disciplines including conservation planning and medical intervention. Venomous snakes are one group that highlight the importance of having accurate information given their cosmopolitan distribution and medical significance. Envenomation by snakebite is considered a neglected tropical disease by the World Health Organization and venomous snake distributions are used to assess vulnerability to snakebite based on species occurrence and antivenom/healthcare accessibility. However, recent studies highlighted the need for updated fine-scale distributions of venomous snakes. Pitvipers (Viperidae: Crotalinae) are responsible for >98% of snakebites in the New World. Therefore, to begin to address the need for updated fine-scale distributions, we created VenomMaps, a database and web application containing updated distribution maps and species distribution models for all species of New World pitvipers. With these distributions, biologists can better understand the biogeography and conservation status of this group, researchers can better assess vulnerability to snakebite, and medical professionals can easily discern species found in their area.
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.