Error-free genetic repositories: case of amphibians

18 08 2020

In our new study, we curated > 39,000 amphibian mitochondrial DNA (mtDNA) sequences from GenBank, identified > 2,000 sequencing and taxonomic errors, and published the quality-checked records as a curated dataset with an automated workflow in R. High-quality genetic data should help quantify and protect the diversity of the most threatened vertebrate group on Earth.

frogs

Upper left: species of Boophis from Andasibe, Madagascar. Upper right: Dendropsophus anceps from State of Rio de Janeiro, Brazil. Lower left; Dendropsophus bipunctatus from State of Rio de Janeiro, Brazil. Lower right: Bufo bufo from Gelderland, The Netherlands. All images from the author.

Scientists from a broad range of biological disciplines use genetic information like DNA sequences to test ecological and evolutionary hypotheses. Critically, genetics are today essential for naming species and therefore quantifying biodiversity, as well as determining where species live and how many individuals of a species occur in the wild.

Researchers are routinely asked, and more recently frequently required, by scientific journals to submit their DNA sequences to GenBank (among other public repositories of genetic data) as a requirement for publishing a paper. Although GenBank provides some quality controls (e.g., to filter sequences with bacterial contaminants and those from other kingdoms), authors are responsible for the quality of their genetic data and have full freedom to assign these to species in the taxonomy database of GenBank. Notably, once sequences have been deposited in GenBank, records are rarely updated in light of identified errors often resulting from taxonomic progress.

Two important notions emerge from the former status quo: Read the rest of this entry »





Heat tolerance highly variable among populations and species

14 01 2020

Many ecological studies have examined the tolerance of terrestrial wildlife to high and low air temperatures over global scales (e.g., 1, 2, 3). This topic has been boosted in the last two decades by ongoing and predicted impacts of climate change on biodiversity (see summary of 2019 United Nation’s report here and here).

However, it is unfortunate that for most species, studies have measured thermal tolerance from a single location or population. Researchers interested in global patterns of thermal stress collect those measurements from the literature for hundreds to thousands of species [recently compiled in the GlobTherm database] (4), and are therefore often restricted to analysing one value of thermal tolerance per species.

CB_FunctionalEcology_jan2020_Photo

Three of the 15 species of Iberian lacertids sampled in our study of thermal tolerance (9), including the populations of Algerian psammodromus (Psammodromus algirus), Geniez’s wall lizard (Podarcis virescens) and Western green lizard (Lacerta bilineata) sampled in Navacerrada (Madrid), Fuertescusa (Cuenca) and Moncayo (Soria), respectively. Photos by S. Herrando-Pérez

Using this approach, ecologists have concluded that cold tolerance is far more variable than heat tolerance across species from the tropics to the boreal zone (5-8). Consequently, tolerance to heat stress might be a species trait with limited potential to change in response to global warming compared to cold tolerance (5). Read the rest of this entry »





Microclimates: thermal shields against global warming for small herps

22 11 2017

Thermal microhabitats are often uncoupled from above-ground air temperatures. A study focused on small frogs and lizards from the Philippines demonstrates that the structural complexity of tropical forests hosts a diversity of microhabitats that can reduce the exposure of many cold-blooded animals to anthropogenic climate warming.

Luzon forest frogs

Reproductive pair of the Luzon forest frogs Platymantis luzonensis (upper left), a IUCN near-threatened species restricted to < 5000 km2 of habitat. Lower left: the yellow-stripped slender tree lizard Lipinia pulchella, a IUCN least-concerned species. Both species have body lengths < 6 cm, and are native to the tropical forests of the Philippines. Right panels, top to bottom: four microhabitats monitored by Scheffers et al. (2), namely ground vegetation, bird’s nest ferns, phytotelmata, and fallen leaves above ground level. Photos courtesy of Becca Brunner (Platymantis), Gernot Kunz (Lipinia), Stephen Zozaya (ground vegetation) and Brett Scheffers (remaining habitats).

If you have ever entered a cave or an old church, you will be familiar with its coolness even in the dog days of summer. At much finer scales, from centimetres to millimetres, this ‘cooling effect’ occurs in complex ecosystems such as those embodied by tropical forests. The fact is that the life cycle of many plant and animal species depends on the network of microhabitats (e.g., small crevices, burrows, holes) interwoven by vegetation structures, such as the leaves and roots of an orchid epiphyte hanging from a tree branch or the umbrella of leaves and branches of a thick bush.

Much modern biogeographical research addressing the effects of climate change on biodiversity is based on macroclimatic data of temperature and precipitation. Such approaches mostly ignore that microhabitats can warm up or cool down in a fashion different from that of local or regional climates, and so determine how species, particularly ectotherms, thermoregulate (1). To illustrate this phenomenon, Brett Scheffers et al. (2) measured the upper thermal limits (typically known as ‘critical thermal maxima’ or CTmax) of 15 species of frogs and lizards native to the tropical forest of Mount Banahaw, an active volcano on Luzon (The Philippines). The > 7000 islands of this archipelago harbour > 300 species of amphibians and reptiles (see video here), with > 100 occurring in Luzon (3).

Read the rest of this entry »