amphibians | ConservationBytes.com

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.

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 »

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Tags: amphibians, cytochrome b, frogs, GeneBank, herpetology, mitochondrial DNA, mtDNA, sequencing
Categories : amphibian, biodiversity, conservation, conservation biology, frog, genetic diversity, genetics

Singin’ in the heat

9 03 2017

Common coqui frog male (Eleutherodactylus coqui, snout-to vent length average ~ 3 cm) camouflaged in the fronds of an epiphyte in the El Yunque National Forest (Puerto Rico), along with an image of the enchanted forest of the Sierra de Luquillo where Narins & Meenderink did their study (4) – photos courtesy of Thomas Fletcher. This species can be found from sea level to the top of the highest peak in Puerto Rico (Cerro Punta = 1338 m). Native to mesic ecosystems, common coquis are well adapted to a terrestrial life, e.g., they lack interdigital webbing that support swimming propulsion in many amphibians, and youngsters hatch directly from the egg without transiting a tadpole stage. The IUCN catalogues the species as ‘Least Concern’ though alerts recent declines in high-altitude populations caused by chytrid fungus – lethal to amphibians at a planetary scale (9). Remarkably, the species has been introduced to Florida, Hawaii, the Dominican Republic and the Virgin Islands where it can become a pest due to high fertility rates (several >20 egg clutches/female/year).

Frog songs are species-specific and highly useful for the study of tropical communities, which host the highest amphibian diversities globally. The auditory system of females and the vocal system of males have co-evolved to facilitate reproductive encounters, but global warming might be disrupting the frequency of sound-based encounters in some species..

It is a rainy night, and Don (Gene Kelly) has just left his love, Kathy (Debbie Reynolds), at home, starting one of the most famous musical movie scenes ever: Singin’ in the rain …

Amphibians (see Amphibians for kids by National Geographic) also love to sing in rainy nights when males call for a partner, but now they have to do it in hotter conditions as local climates become warmer. Vocal behaviour is a critical trait in the life history of many frog species because it mediates recognition between individuals, including sexual selection by females (1).

With few exceptions, every species has a different and unique call, so scientists can use call features to identify species, and this trait is particularly useful in the inventory of diverse tropical communities (2). Differences in call frequency, duration and pitch, and in note, number, and repetition pattern, occur from one species to another. And even within species, songs can vary from individual to individual (as much as there are not two people with the same voice), and be tuned according to body size and environmental temperature (3). Read the rest of this entry »

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Tags: amphibians, behavioural shift, calls, climate change, Global warming, vocalisation
Categories : amphibian, behaviour, bioclimatic envelope, biodiversity, climate change, climate shift, decline, extinction, function, rain forests, research, South America, tropical

The Evidence Strikes Back — What Works 2017

16 01 2017

Bat gantry on the A590, Cumbria, UK. Photo credit: Anna Berthinussen

Tired of living in a world where you’re constrained by inconvenient truths, irritating evidence and incommodious facts? 2016 must have been great for you. But in conservation, the fight against the ‘post-truth’ world is getting a little extra ammunition this year, as the Conservation Evidence project launches its updated book ‘What Works in Conservation 2017’.

Conservation Evidence, as many readers of this blog will know, is the brainchild of conservation heavyweight Professor Bill Sutherland, based at Cambridge University in the UK. Like all the best ideas, the Conservation Evidence project is at once staggeringly simple and breathtakingly ambitious — to list every conservation intervention ever cooked up around the world, and see how well, in the cold light of evidence, they actually worked. The project is ongoing, with new chapters of evidence added every year grouped by taxa, habitat or topic — all available for free on www.conservationevidence.com.

‘What Works in Conservation’ is a book that summarises the key findings from the Conservation Evidence website, and presents them in a simple, clear format, with links to where more information can be found on each topic. Experts (some of us still listen to them, Michael) review the evidence and score every intervention for its effectiveness, the certainty of the evidence and any harmful side effects, placing each intervention into a colour coded category from ‘beneficial’ to ‘likely to be ineffective or harmful.’ The last ‘What Works’ book included chapters on birds, bats, amphibians, soil fertility, natural pest control, some aspects of freshwater invasives and farmland conservation in Europe; new for 2017 is a chapter on forests and more species added to freshwater invasives. Read the rest of this entry »

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Tags: amphibians, bat bridges, bats, Bill Sutherland, biodiversity, birds, Cambridge, Claire Wordley, conservation evidence, farmland, invasive species, nest boxes, pest control, Soil
Categories : agriculture, alien species, amphibian, biodiversity, biowealth, birds, book, climate change, connectivity, conservation, conservation biology, fish, frog, management, planning, predator, recovery, restoration, roads

World’s greatest conservation tragedy you’ve probably never heard of

13 10 2016

I admit that I might be stepping out on a bit of a dodgy limb by claiming ‘greatest’ in the title. That’s a big call, and possibly a rather subjective one at that. Regardless, I think it is one of the great conservation tragedies of the Anthropocene, and few people outside of a very specific discipline of conservation ecology seem to be talking about it.

I’m referring to freshwater biodiversity.

I’m no freshwater biodiversity specialist, but I have dabbled from time to time, and my recent readings all suggest that a major crisis is unfolding just beneath our noses. Unfortunately, most people don’t seem to give a rat’s shit about it.

Sure, we can get people riled by rhino and elephant poaching, trophy hunting, coral reefs dying and tropical deforestation, but few really seem to appreciate that the stakes are arguably higher in most freshwater systems. Read the rest of this entry »

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Tags: amphibians, biodiversity, conservation, extinction, Fish, fishes, fresh water, freshwater biodiversity, frogs, invertebrates, lakes, rivers, streams, threat, threatened species, water, wetlands
Categories : agriculture, alien species, amphibian, anthropocene, biodiversity, climate change, conservation, water

Killing us slowly

6 07 2010

I’m currently attending the 2010 International Congress for Conservation Biology in Edmonton, Canada. I thought it would be good to tweet and blog my way through on topics that catch my attention. This is my second post from the conference.

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I silently scoffed inside when the plenary speaker was being introduced. It was boldly claimed that we were about to hear one of the best presentations any of us had ever seen at a scientific conference before.

I cannot say for certain whether it was indeed ‘the best’, but bloody hell, it was excellent.

Our speaker is certainly well-known in the endocrinology world (very well published), is a bane to certain chemical industries and is revered as a scientist who puts his money where is mouth is.

Professor Tyrone Hayes of the University of California Berkeley is an ‘eco-endocrinologist’ who blew the lid on the devastating health effects of the most available and ubiquitous agricultural herbicide in use today – evil atrazine. As my readers know, I am certainly pushing the empirical basis for the link between environmental degradation and deterioration of human health (my talk here at the ICCB on Wednesday will be on this very topic), so this topic interests me greatly.

It’s no secret that atrazine has devastating feminising effects on amphibians (and many other taxa), and has been linked convincingly to increasing the risk of cancer in humans. It’s banned in Europe, but still widely used pretty much everywhere else. Read the rest of this entry »