Phylogenies, Trait Evolution and Fancy Glasses

Post provided by Daniel S. Caetano

Phylogenetic trees represent the evolutionary relationships among different lineages. These trees give us two crucial pieces of information:

  1. the relationships between lineages (which we can tell from the pattern of the branches (i.e., topology))
  2. the point when lineages separated from a common ancestor (which we can tell from the length of the branches, when estimated from genetic sequences and fossils).
Phylogeny of insects inferred from genetic sequences showing the time of divergence between ants and bees.

Phylogeny of insects inferred from genetic sequences showing the time of divergence between ants and bees.

As systematic biologists, we are interested in the evolutionary history of life. We use phylogenetic trees to uncover the past, understand the present, and predict the future of biodiversity on the planet. Among the tools for this thrilling job are the comparative methods, a broad set of statistical tools built to help us understand and interpret the tree of life.

Here’s a Tree, Now Tell Me Something

The comparative methods we use to study the evolution of traits are mainly based on the idea that since species share a common evolutionary history, the traits observed on these lineages will share this same history. In the light of phylogenetics, we can always make a good bet about how a species will look if we know how closely related it is to another species or group. Comparative models aim to quantify the likelihood of our bet being right and use the same principle to estimate how fast evolutionary changes accumulate over time. Continue reading

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Issue 8.8

Issue 8.10 is now online!

The October issue of Methods is now online!

This double-sized issue contains three Applications articles and two Open Access articles. These five papers are freely available to everyone, no subscription required.

 Phylogenetic TreesThe fields of phylogenetic tree and network inference have advanced independently, with only a few attempts to bridge them. Schliep et al. provide a framework, implemented in R, to transfer information between trees and networks.

 Emon: Studies, surveys and monitoring are often costly, so small investments in preliminary data collection and systematic planning of these activities can help to make best use of resources. To meet recognised needs for accessible tools to plan some aspects of studies, surveys and monitoring, Barry et al. developed the R package emon, which includes routines for study design through power analysis and feature detection.

 Haplostrips: A tool to visualise polymorphisms of a given region of the genome in the form of independently clustered and sorted haplotypes. Haplostrips is a command-line tool written in Python and R, that uses variant call format files as input and generates a heatmap view.

Continue reading

Imperfect Pathogen Detection: What to Do When Sampling and Diagnostic Tests Produce Inaccurate Results

Post Provided by Graziella DiRenzo

A salamander having its skin swabbed to test for Bsal infection.

A salamander having its skin swabbed to test for Bsal infection.

Imagine you’re at the doctor’s office. You’re waiting to hear back on a critical test result. With recent emerging infectious diseases in human populations, you are worried you may be infected after a sampling trip to a remote field site. The doctor walks in. You sit nervously, sensing a slight tremble in your left leg. The doctor confidently declares, “Well, your tests results came back negative.” In that moment, you let out a sigh of relief, the kind you feel throughout your body. Then, thoughts start flooding your mind. You wonder– what are the rates of false negatives associated with the test? How sensitive is the diagnostic test to low levels of infection? The doctor didn’t sample all of your blood, so how can they be sure I’m not infected? Is the doctor’s conclusion right?

 Now, let’s say I’m the doctor and my patient is an amphibian. I don’t have an office where the amphibian can come in and listen to me explain the diagnosis or the progression of disease − BUT I do regularly test amphibians in the wild for a fatal fungal pathogen, known as Batrachochytrium dendrobatidis (commonly known as Bd). Diseases like Bd are among the leading causes of the approximately one-third of amphibian species that are threatened, near threatened, or vulnerable to extinction. To test for Bd, and the recently emerged sister taxon Batrachochytrium salamandrivorans (hereafter referred to as: Bsal), disease ecologists rely on non-invasive skin swabs. Continue reading

Monitoring the Distribution and Abundance of Sea Otters

Post provided by Perry Williams

Sea otters (Enhydra lutris) are an apex predator of the nearshore marine ecosystem – the narrow band between terrestrial and oceanic habitat. During the commercial maritime fur trade in the 18th and 19th centuries, sea otters were nearly hunted to extinction across their range in the North Pacific Ocean. By 1911, only a handful of small isolated populations remained.

Sea otters resting in Glacier Bay National Park. © Jamie Womble, NPS. USFWS Permit #14762C-0, NPS Permit #GLBA-2016- SCI-0022.

Sea otters resting in Glacier Bay National Park. © Jamie Womble, NPS. USFWS Permit #14762C-0, NPS Permit #GLBA-2016- SCI-0022.

But sea otter populations have recovered in many areas due to a few changes. The International Fur Seal Treaty in 1911 and the Marine Mammal Protection Act (1972) protected sea otters from most human harvest. Wildlife agencies helped sea otter colonisation by transferring them to unoccupied areas. Eventually, sea otters began to increase in abundance and distribution, and they made their way to Glacier Bay, a tidewater glacier fjord and National Park in southeastern Alaska. Continue reading

A New Way to Study Bee Cognition in the Wild

Understanding how animals perceive, learn and remember stimuli is critical for understanding both how cognition is shaped by natural selection, and how ecological factors impact behaviour.Unfortunately, the limited number of protocols currently available for studying insect cognition has restricted research to a few commercially available bee species, in almost exclusively laboratory settings.
In a new video Felicity Muth describes a simple method she developed with Trenton Cooper, Rene Bonilla and Anne Leonard for testing both lab- and wild-caught bees for their preferences, learning and memory. They hope this method will be useful for students and researchers who have not worked on cognition in bees before. The video includes a tutorial for carrying out the method and describes the data presented in their Methods in Ecology and Evolution article, also titled ‘A novel protocol for studying bee cognition in the wild‘.

This video is based on the article ‘A novel protocol for studying bee cognition in the wild by Muth et al.

 

Tracing New and Old Resources in Estuarine Ecosystems

Post provided by Thomas Larsen, Kim Vane & Ricardo Fernandes

This week, more than 150 events along the US shores will celebrate estuaries and educate the public and policy makers of the many benefits we get from healthy and thriving ecosystems. But why do we need to pay more attention to estuaries?

A woman collecting snails in the Yellow River estuary, China. Estuaries are important habitats for marine gastropods and nurturing grounds for marine fishes. ©Thomas Larsen

Estuaries are important habitats for marine gastropods and nurturing grounds for marine fishes. ©Thomas Larsen

Estuaries are biological hotspots and by far the most productive ecosystems on our planet. The shallow waters where streams and rivers meet the sea often harbour a rich terrestrial and aquatic flora and are home to many animals. They’re important feeding and reproduction areas for a diverse array of wildlife such as birds and fish, which can include both freshwater and marine species. A large portion of the world’s marine fisheries today depend on the ecosystem services of estuaries; it has been estimated that well over half of all marine fishes develop in the protective environment of an estuary. Historically, humans have been attracted to these large expanses of shallow water that could sustain their basic needs. Nowadays, these estuaries also have economic value as recreational and touristic destinations as for example fishing, boating and swimming spots.

However, our understanding of how estuaries function and sustain this amount of biodiversity is limited. As is the case for most ecosystems on our planet, estuaries are under increasing pressure from human activities. Estuaries are subjected to intensive land reclamation and developments like harbours and aquacultural farms. They also receive excessive amounts of of nutrients, soil and organic matter from intensive farms and urban landscapes via small streams and large rivers. These stressors are accentuated by environmental changes such as sea level rise, increasing water temperatures and extreme weather conditions causing droughts and flooding. Continue reading

Learn to be a Reviewer: Peer Reviewer Mentoring Scheme

Today is the first day of peer review week. One of the issues that many people bring up about the current system of peer review is that there is very little formal training. There are guidance documents available (including the BES Guide to Peer Review), workshops on peer review can be found at some conferences and some senior academics teach their PhD students or post-docs about the process. In general though, peer review training is fairly hard to come by.

This is something that people have told us (the BES publications team) at conferences and through surveys, so we’re doing something about it. From October 2017 until April 2018 Methods in Ecology and Evolution is going to be partnering with the BES Quantitative Ecology Special Interest Group to run a trial Peer Review Mentoring Scheme.

The trial scheme is going to focus on statistical ecology (as we receive a lot of statistical papers at Methods in Ecology and Evolution), but if it goes well, we’ll be looking at other areas of expertise too.

Applications for Mentor and Mentee positions are now open. If you’re an experienced statistical ecologist or evolutionary biologist or an Early Career Researcher in those fields, we’d love to receive an application from you. Continue reading

Issue 8.9

Issue 8.9 is now online!

The September issue of Methods is now online!

This issue contains two Applications articles and three Open Access articles. These five papers are freely available to everyone, no subscription required.

 qfasar: A new R package for diet estimation using quantitative fatty acid signature analysis methods. It also provides functionality to evaluate and potentially improve the performance of a library of prey signature data, compute goodness-of-fit diagnostics, and support simulation-based research.

 biomass: An r package designed to compute both AGB/AGC estimate and its associated uncertainty from forest plot datasets, using a Bayesian inference procedure. The package builds upon previous work on pantropical and regional biomass allometric equations and published datasets by default, but it can also integrate unpublished or complementary datasets in many steps.

Continue reading

Multi-State Species Distribution Models: What to do When Species Need Multiple Habitats

Post provided by Jan Engler, Veronica Frans and Amélie Augé

The north, south, east, and west boundaries of a species’ range tell us very little about what is happening inside…

― Robert H. MacArthur (1972, p. 149)

When You Enter the Matrix, Things Become Difficult!

New Zealand sea lion mother and pup. © Amélie Augé

New Zealand sea lion mother and pup. © Amélie Augé

Protecting wildlife calls for a profound understanding of species’ habitat demands to guide concrete conservation actions. Quantifying the relationships between species and their environment using species distribution models (SDMs) has attracted tremendous attention over the past two decades. Usually these species-environment relationships are estimated on coarse spatial scales, using globally-interpolated long-term climate data sets. While they’re useful for studies on large-scale species distributions, these environmental predictors have limited applications for conservation management.

Climatic data were the first environmental information available with global coverage, but a wide range of Earth observation techniques have increased the availability of much finer environmental information. This allows us to quantify species-environment relationships in unprecedented detail. We can now shift the scale that SDMs operate at, resulting in more useful applications in conservation – SDMs now enter the matrix.

This shift in scale brings new challenges, especially for species using multiple distinct habitat types to survive. The landscape matrix, which has been negligible at the broad (global) scale, is hugely important at the fine (local) scale. It is not only that we need to quantify certain habitat types but also need to consider their arrangement in the landscape, which is basically what the landscape matrix is about. But as we enter the matrix, things become difficult. Continue reading