Ultraconserved Elements are Widely Shared across the Tree of Life

Post provided by SILAS BOSSERT

Large-scale phylogenies are increasingly fueled by genomic-data from Ultraconserved Elements. ©Silas Bossert

Large-scale phylogenies are increasingly fuelled by genomic-data from Ultraconserved Elements. ©Silas Bossert

Sequencing ultraconserved DNA for phylogenetic research is a hot topic in evolution right now. As the name implies, Ultraconserved Elements (UCEs) are regions of the genome that are nearly identical among distantly related organisms. They can provide useful information for difficult phylogenetic questions. The list of advantages is long – among others, UCEs are:

A key reason for the method’s success is the developers’ commitment to full transparency, active tutoring, and willingness to help next-gen sequencing newbies like me to get started. Help is just a github-issue post away.

It took little to convince me that I wanted to use UCEs to reconstruct the phylogeny of one of my favourite groups of bees. I eventually met that objective but it won’t be part of this post. This blog post is about the journey to get there—the background story to the article ‘On the universality of target‐enrichment baits for phylogenomic research’. Continue reading

The Dark and Bright Sides of Phylogenetics and Comparative Methods

Five years ago at Evolution 2014, ‘The Dark Side of Phylogenetics’ symposium (organised by Natalie Cooper) explored some of the issues with phylogenetic comparative methods (PCMs). This year at Evolution 2019, Michael Landis and Rosana Zenil-Ferguson are organising a contrasting ‘Bright Side of Phylogenetics‘ spotlight session (featuring Michael Matschiner). They aim to promote research that has overcome these pitfalls and that explores innovations in phylogenetics. Clearly they found our lack of faith disturbing.

Natalie and Michael have created a Virtual Issue to complement the spotlight session: Phylogenetics and Comparative Methods: The Bright and Dark Sides. It highlights recent Methods in Ecology and Evolution papers that feature either the ‘Bright Side’ or ‘Dark Side’ of phylogenetics and comparative methods. This Virtual Issue also highlights the diversity of researchers around the world working on these exciting questions. We hope you have a good feeling about it! Continue reading

Stereo DOV: A Non-Invasive, Non-Destructive Way to Study Fish Populations

It’s more important than ever for us to have accurate information to help marine conservation efforts. Jordan Goetze and his colleagues have provided the first comprehensive guide for researchers using diver operated stereo-video methods (or stereo-DOVs) to survey fish assemblages and their associated habitat.

But what is Stereo DOV? What makes it a better method than the traditional UVC (Underwater Visual Census) method? And when should you use it? Find out in this video:

To find out more about stereo DOVs, read the full Methods in Ecology and Evolution article ‘A field and video analysis guide for diver operated stereo‐video
(No Subscription Required).

If you’re using interesting new field techniques like this, why not submit a Practical Tools manuscript about them? You can find out more about Practical Tools manuscripts here.

Using Molecular Power to Reconstruct Hyperdiverse Food Webs

Post provided by JORDAN CASEY

Coral Reefs: The Ocean’s Most Extravagant Buffet

Coral reefs are home to an incredibly diverse array of species ©Jordan Casey

Coral reefs are home to an incredibly diverse array of species ©Jordan Casey

There are an estimated 830,000 species on coral reefs worldwide. At some stage in their lives, nearly all of these species are consumed as prey items. In this super diverse buffet of fishes, corals, crabs, worms, and other critters, the number of possible interactions between predators and prey is nearly inexhaustible.

The extreme diversity of coral reefs has fascinated naturalists for centuries. Pinpointing predator-prey dynamics is essential to fully understand coral reef ecosystem dynamics, and visual analysis of gut contents has been a staple technique of coral reef ecologists. While the joy of spending copious hours looking through a microscope at half-digested marine mush is undeniable, this type of visual inspection has limitations. Even so, visual gut content analysis (along with stable isotope analysis and behavioural observations) has showcased a highly complex dietary network.

To digest this extreme complexity and surmount the hurdle of dietary unknowns, researchers frequently lump fishes into broad trophic categories, such as ‘mobile herbivores’. Broad generalisations are pragmatic and may be help us detect broad ecological trends, but they oversimplify species’ actual dietary preferences. As coral reefs are changing due to anthropogenic disturbances, it’s critical to thoroughly examine how well trophic groupings capture dietary linkages among reef organisms. Continue reading

Analysing Big Datasets while Answering Big Ecological Questions: #BESQuantMove2019

Post provided by LAURA GRAHAM and THEONI PHOTOPOULOU

Last week we heard about the importance of small conferences from Natalie Cooper. Hopefully she inspired you to look into smaller meetings going on this summer. If so, how about joining the Quantitative and Movement Special Interest Groups in Sheffield on 9 and 10 July for our back-to-back annual meetings?

This joint meeting will take advantage of shared strengths as well as shared challenges between the two groups and foster links between them. Both days will be a mix of keynotes, short contributed talks, poster sessions and discussion. Plus lots of all-important networking.

The meeting will be along the common theme of analysing big datasets while answering big ecological questions and the challenges associated with it. We welcome submissions of talks and posters. There will also be discussions on general issues with computation; integrating different datasets; and propagating uncertainty in ecological analyses.

The registration deadline is FRIDAY 7 JUNE – just three days away at the time of posting! Attendees will have the opportunity to attend one, or both annual meetings. A quick insider tip for registration: it’s cheaper to join the BES as a member and register for a BES member ticket, than to register for the non-BES member ticket. Continue reading

In Praise of Small Conferences

Post provided by NATALIE COOPER

Conferences come in many shapes and sizes, from mega-conferences like the Ecological Society of America (ESA) or Evolution with up to 5000 attendees, to small BES Special Interest Group (SIG) meetings with fewer than 100 attendees. There are pros and cons to both kinds of conference, but I’d like to take this opportunity to focus on small meetings*. Here are five reasons why I think they’re great, and why they’re particularly good for Early Career Researchers.

1. Networking is Much Easier

At a big conference networking can be really hard. Not only do you have to find the people you want to talk to, but you also have to compete with all the other people who want to talk to them! This is even worse if you’re also nervous about approaching them.

Networking more generally (i.e. without specific targets in mind), or just finding people to hang out with, can also be harder. Large meetings tend to cause groups to close ranks**. The sheer numbers of people around can make it really intimidating (there are some tips for networking at bigger meetings here). Continue reading

Assessing Sea Turtle Populations: Can We Get a Hand From Drones and Deep Learning?

Post provided by PATRICK GRAY

An olive ridley sea turtle in Ostional, Costa Rica. ©Vanessa Bézy.

Understanding animal movement and population size is a challenge for researchers studying any megafauna species. Sea turtles though, add a whole additional level of complexity. These wide-ranging, swift, charismatic animals spend much of their time underwater and in remote places. When trying to track down and count turtles, this obstacle to understanding population size becomes a full-on barricade.

Censusing these animals doesn’t just satisfy our scientific curiosity. It’s critical for understanding the consequences of unsound fishing practices, the benefits of conservation policy, and overall trends in population health for sea turtles, of which, six out of seven species range from vulnerable to critically endangered. Continue reading

Where do Animals Spend Their Time and Energy? Theory, Simulations and GPS Trackers Can Help Us Find Out

Post provided by MATT MALISHEV (@DARWINANDDAVIS)

 An adult sleepy lizard with a GPS tracker and body temperature logger strapped to her tail. ©Mike Bull.


An adult sleepy lizard with a GPS tracker and body temperature logger strapped to her tail. ©Mike Bull.

Changes in temperature and available food determine where and when animals move, reproduce, and survive. Our understanding of how environmental change impacts biodiversity and species survival is well-established at the landscape, country and global scales. But, we know less about what could happen at finer space and time scales, such as within habitats, where behavioural responses by animals are crucial for daily survival.

Simulating Movement and Daily Survival with Individual-Based Movement Models

Key questions at these scales are how the states of individuals (things like body temperature and nutritional condition) influence movement decisions in response to habitat change, and how these decisions relate to patchiness in microclimates and food. So we need tools to make reliable forecasts of how fine-scale habitat use will change under future environments. Individual-based movement simulation models are powerful tools for these kinds of studies. They let you construct habitats that vary in temperature and food conditions in both space and time and ask ‘what if’ questions. By populating these models with activity, behaviour, and movement data of animals, we can simulate different habitat conditions and predict how animals will respond to future change. Continue reading

Early Spring: Predicting Budburst with Genetics

Below is a press release about the Methods in Ecology and Evolution article ‘On the importance of accounting for intraspecific genomic relatedness in multi‐species studies‘ taken from the Université de Montréal.

Bud of American beech (Fagus grandifolia). ©Tim Savas

Researchers from Canada and the USA found that tree and shrub genetics can be used to produce more accurate predictions of when leaves will burst bud in the spring. Their study was published in Methods in Ecology and Evolution.

Although climate sceptics might find it hard to believe with this year’s endless snow and freezing temperatures, climate change is making warm, sunny early springs increasingly common. And that affects when trees start to leaf out. But how much?

Simon Joly, biology professor at Université de Montréal and Elizabeth Wolkovich, an ecology professor at University of British Columbia, showed that a plant’s genetics can be used to produce more accurate predictions of when its leaves will burst bud in spring. Continue reading

ViXeN: View eXtract aNnotate Multimedia Data

Post provided by KadaMbari Devarajan

At a time when data is everywhere, and data science is being talked about as the future in different fields, a method that produces huge amounts of multimedia data is camera-trapping. We need ways to manage these kinds of media data efficiently. ViXeN is an attempt to do just that.

Camera traps have been a game-changer for ecological studies, especially those involving mammals in the wild. This has resulted in an increasing amount of camera trap datasets. However, the tools to manage camera trap data tend to be very specific and customised for images. They typically come with stringent data organisation requirements. There’s a growing amount of multimedia datasets and a lack of tools that can manage several types of media data.

In ‘ViXeN: An open‐source package for managing multimedia data’ we try to fix this visible gap. Camera trap management is a very specific a use-case. We thought that the field was missing general-purpose tools, capable of handling a variety of media data and formats, that were also free and open source. ViXeN was born from this idea. It stands for View eXtract aNnotate (media data). The name is also an ode to the canids I was studying at the time which included two species of foxes.


Example camera trap video Continue reading