Refined DNA Tool Tracks Native and Invasive Fish

Below is a press release about the Methods paper ‘Long-range PCR allows sequencing of mitochondrial genomes from environmental DNA‘ taken from the Cornell University.

©Nick Hobgood

Rather than conduct an aquatic roll call with nets to know which fish reside in a particular body of water, scientists can now use DNA fragments suspended in water to catalog invasive or native species.

The research from Cornell University, the University of Notre Dame and Hawaii Pacific University was published July 14 in Methods in Ecology and Evolution.

“We’ve sharpened the environmental DNA (eDNA) tool, so that if a river or a lake has threatened, endangered or invasive species, we can ascertain genetic detail of the species there,” said senior author David Lodge, the Francis J. DiSalvo Director of the Atkinson Center for a Sustainable Future at Cornell, and professor of ecology and evolutionary biology. “Using eDNA, scientists can better design management options for eradicating invasive species, or saving and restoring endangered species.” Continue reading

Issue 7.6: Methods in Ecology and Evolution 5th Anniversary Special Feature

Issue 7.6 is now online!

The June issue of Methods, which includes our latest Special Feature – “5th Anniversary of Methods in Ecology and Evolution” – is now online!

Our 5th Anniversary Special Feature is a collection of six articles (plus an Editorial from Executive Editor Rob Freckleton) that highlights the breadth and depth of topics covered by the journal so far. It grew out of our 5th Anniversary Symposium – a joint event held in London, UK and Calgary, Canada and live-streamed around the world in April 2015 – and contains papers by Associate Editors, a former Robert May prize winner and regular contributors to the journal.

The six articles are based on talks given at last May’s Symposium. They focus on:

In his Editorial for the Special Feature, Rob Freckleton looks to the future. In his words: “we hope to continue to publish a wide range of papers on as diverse a range of topics as possible, exemplified by the diversity of the papers in this feature”.

All of the articles in the Special Feature will be freely available for a limited time. In addition to this, two of the articles (Shedding light on the ‘dark side’ of phylogenetic comparative methods and Perturbation analysis of transient population dynamics using matrix projection models) are Open Access.
Continue reading

A New Modelling Strategy for Conservation Practice? Ensembles of Small Models (ESMS) for Modelling Rare Species

Post provided by FRANK BREINER, ARIEL BERGAMINI, MICHAEL NOBIS and ANTOINE GUISAN

Rare Species and their Protection

Erythronium dens-canis L. – a rare and threatened species used for modelling in Switzerland. ©Michael Nobis

Erythronium dens-canis L. – a rare and threatened species used for modelling in Switzerland. ©Michael Nobis

Rare species can be important for ecosystem functioning and there is also a high intrinsic interest to protect them as they are often the most original and unique components of local biodiversity. However, rare species are usually those most threatened with extinction.

In order to help prioritizing conservation efforts, the International Union for Conservation of Nature (IUCN) has published criteria to categorize the status of threatened species, which are then published in Red Lists. Changes in a species’ geographical distribution is one of the several criteria used to assign a threat status. For rare species, however, the exact distribution is often inadequately known. In conservation science, Species Distribution Models (SDMs) have recurrently been used to estimate the potential distribution of rare or insufficiently sampled species. Continue reading

Ecological Transcriptomics for Endangered Species: Avoiding the “Successful Operation, but the Patient Died” Problem

Post provided by TILL CZYPIONKA, DANIEL GOEDBLOED, ARNE NOLTE and LEON BLAUSTEIN

Ecological Transcriptomics and Endangered Species

 The small size of the rockpool and the salamander population makes non-invasive sampling a necessity (from left: Tamar Krugman, Alan Templeton, Leon Blaustein). © Arne Nolte

The small size of the rockpool and the salamander population makes non-invasive sampling a necessity (from left: Tamar Krugman, Alan Templeton, Leon Blaustein). © Arne Nolte

Friday was Endangered Species Day – so this is a good time to reflect on what science and scientists can do to support conservation efforts and to reduce the rate of species extinctions. One obvious answer is that we need to study endangered species to understand their habitat requirements as well as their potential for acclimatization and adaptation to changing environmental conditions. This information is crucial to for the design of informed conservation planning. However, for most endangered species the relevant phenotypes are not known a priori, which leaves the well-intentioned scientist asking “which traits should I measure?”. Transcriptome analysis is often a good way to answer to this question.

Transcriptome analysis measures the expression levels of thousands of genes in parallel. This amount of data circumvents the need to decide on a reduced number of traits of unknown relevance and allows for a relatively unbiased phenotypic screen of many traits. In particular, physiological changes, which often influence a species’ distributional range, can be studied using transcriptome analysis. Also, transcriptomics provide a direct connection to the genetic level. This is essential for in-depth analyses of aspects of evolution and might even be helpful for a new kind of conservation planning, which aims to foster endangered species by promoting (supposedly) beneficial hybridization. The integration of transcriptomic analysis with ecological studies is known as ‘Ecological transcriptomics’. Continue reading

Bringing Ecologists and Statisticians Together for the Conservation of Endangered Species

Post provided by Cecilia Pinto and Luigi Spezia

The Benefits of High Frequency Data

One of the tagged flapper skates showing the three different kinds of tags. ©Cecilia Pinto

One of the tagged flapper skates showing the three different kinds of tags. ©Cecilia Pinto

High frequency data, like those obtained from individual electronic tags, carries the potential of giving us detailed information on the behaviour of species at the individual level. Such data are particularly useful for marine species, as we can’t observe them directly for long periods of time.

Understanding how individuals use water columns – both at daily and seasonal scales – can help define conservation measures such as restricting fishing activity to reduce by-catch or defining protected areas to help recovering populations or protect spawning and nursery areas. High frequency data have become popular as they give insight to detailed individual foraging behaviour and therefore the specific energetic needs that are linked to reproduction and fitness. Continue reading

Demography and Big Data

Post provided by BRITTANY TELLER, KRISTIN HULVEY and ELISE GORNISH

Follow Brittany (@BRITTZINATOR) and Elise (@RESTORECAL) on Twitter

To understand how species survive in nature, demographers pair field-collected life history data on survival, growth and reproduction with statistical inference. Demographic approaches have significantly contributed to our understanding of population biology, invasive species dynamics, community ecology, evolutionary biology and much more.

As ecologists begin to ask questions about demography at broader spatial and temporal scales and collect data at higher resolutions, demographic analyses and new statistical methods are likely to shed even more light on important ecological mechanisms.

Population Processes

Midsummer Opuntia cactus in eastern Idaho, USA. © B. Teller.

Midsummer Opuntia cactus in eastern Idaho, USA. © B. Teller.

Traditionally, demographers collect life history data on species in the field under one or more environmental conditions. This approach has significantly improved our understanding of basic biological processes. For example, rosette size is a significant predictor of survival for plants like wild teasel (Werner 1975 – links to all articles are at the end of the post), and desert annual plants hedge their bets against poor years by optimizing germination strategies (Gremer & Venable 2014).

Demographers also include temporal and spatial variability in their models to help make realistic predictions of population dynamics. We now know that temporal variability in carrying capacity dramatically improves population growth rates for perennial grasses and provides a better fit to data than models with varying growth rates because of this (Fowler & Pease 2010). Moreover, spatial heterogeneity and environmental stochasticity have similar consequences for plant populations (Crone 2016). Continue reading

On the Tail of Reintroduced Canada Lynx: Leveraging Archival Telemetry Data to Model Animal Movement

Post provided by FRANCES E. BUDERMAN

Animal Movement

218 Canada lynx were reintroduced to the San Juan Mountains between 1999 and 2006 with VHF/Argos collars. © Colorado Parks and Wildlife

218 Canada lynx were reintroduced to the San Juan Mountains between 1999 and 2006 with VHF/Argos collars. © Colorado Parks and Wildlife

Animal movement is a driving factor underlying many ecological processes including disease transmission, extinction risk and range shifts. Understanding why, when and how animals traverse a landscape can provide much needed information for landscape-level conservation and management practices.

The theoretical underpinnings for modelling animal movement were developed about seventy years ago. Technological developments followed, with radio-collars initially deployed on large mammals such as grizzly bears and elk. We can now monitor animal movement of a wide variety of species, including those as small as a honeybee, at an unprecedented temporal and spatial scale.

However, location-based data sets are often time consuming and costly to collect. For many species, especially those that are rare and elusive, pre-existing data sets may be the only viable data source to inform management decisions. Continue reading

Safeguarding Sturgeon: Satellite measurements of ocean color and temperature help researchers predict sturgeon locations

Below is a press release about the Methods paper ‘Dynamic seascapes predict the marine occurrence of an endangered species: Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus‘ taken from the University of Delaware.

New clues are helping University of Delaware researchers develop an online map to help Mid-Atlantic fishermen avoid catching Atlantic sturgeon.

Researchers at the University of Delaware are one step closer to developing an online map that would help Mid-Atlantic fishermen avoid catching Atlantic sturgeon.

The research team, led by Matthew J. Oliver, Patricia and Charles Robertson Professor of Marine Science and Policy, found they could make useful predictions about sturgeon locations using satellite measurements of ocean color and temperature. They reported their findings Feb. 3 in the journal Methods in Ecology and Evolution.

The researchers believe this to be an important step toward helping both fishermen and the vulnerable fish. If they can reliably predict where sturgeon or other “species of concern” are congregating or migrating, they can relay this information to fishermen through a daily fishing forecast, similar to a weather forecast. Continue reading

Progress and Future Directions for Passive Acoustic Monitoring: Listening Out for New Conservation Opportunities

Post provided by Ammie Kalan (Post-doctoral researcher at the Max Planck Institute for Evolutionary Anthropology, Department of Primatology)

A Primate Call in a Forest is like a ‘Needle in a Haystack’

An ARU powered by solar energy recording in the Taï national park, Côte d’Ivoire. ©Ammie Kalan

A solar-powered ARU recording in the Taï national park, Côte d’Ivoire.
©Ammie Kalan

Finding a call of a particular primate species within hours and hours of audio recordings of a forest is no easy task; like finding a ‘needle in a haystack’ so to speak. Automated acoustic monitoring relies on the ability of researchers to easily locate and isolate acoustic signals produced by species of interest from all other sources of noise in the forest, i.e. the background noise. This can be much harder than it sounds. Think about whenever you have to use any kind of voice recognition system: seeking out a quiet room will greatly improve the chances you are understood by the robot-like voice on the other end of the phone. If you ever set foot in a rainforest the first thing you’ll notice is that it is anything but quiet. In fact characterizing and quantifying soundscapes has become a marker for the complexity of the biodiversity present in a given environment.

Primate monitoring programmes can learn a great deal from cetacean research where Passive Acoustic Monitoring (PAM) is the norm (since individuals are rarely observable visually). Research on bats and birds can provide excellent examples to follow as well. Automated algorithm approaches including machine learning techniques, spectral cross-correlation, Gaussian mixture models, and random forests have been used in these fields to be able to detect and classify audio recordings using a trained automated system. Such automated approaches are often investigated for a single species but impressive across-taxa efforts have also been initiated within a framework of real-time acoustic monitoring. Implementing these in other research fields could lead to significant advances. Continue reading