10th Anniversary Volume 3: paleotree: A Retrospective

Post provided by David bapst

To celebrate the 10th Anniversary of the launch of Methods in Ecology and Evolution, we are highlighting an article from each volume to feature on the Methods.blog. For Volume 3, we have selected ‘paleotree: an R package for paleontological and phylogenetic analyses of evolution‘ by David W. Bapst (2012). In this post, David discusses the background to the Application he wrote as a graduate student, and how the field has changed since.

I was a fourth year graduate student when I first had the idea to make an R package. Quite a few people thought it was a bit silly, or a bit of a time-waste, but I thought it was the right thing to do at the time, and I think it has proven to be the right decision in hindsight.

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Stop, think, and beware of default options

Post provided by Paula Pappalardo (with contributions from Elizabeth Hamman, Jim Bence, Bruce Hungate & Craig Osenberg)

Esta publicación también está disponible en español.

You spent months carefully collecting data from articles addressing your favorite scientific question, you have dozens of articles neatly arranged on a spreadsheet, you found software or code to analyze the data, and then daydream about how your publication will be the most cited in your field while making cool plots. If that sounds familiar, you have probably done a meta-analysis. Meta-analysis uses statistical models to combine data from different publications to answer a specific question.

What you may not have realized when going down the meta-analysis rabbit hole, is that small, seemingly inconsequential, choices can greatly affect your results. If you want to know about one of them lurking behind the scenes… read on!

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Para, piensa, y ten cuidado con las configuraciones por defecto

Post escrito por Paula Pappalardo (con aportes de Elizabeth Hamman, Jim Bence, Bruce Hungate & Craig Osenberg)

This post is also available in English.

Pasaste meses laboriosamente colectando datos de artículos científicos acerca de tu pregunta favorita, tienes decenas de artículos perfectamente organizados en una base de datos, ya encontraste el programa o código para analizar los datos, y entonces imaginas como tu publicación va a ser la más citada en tu campo de investigación mientras haces unos gráficos lindísimos. Si esto te suena familiar, seguramente has hecho un meta-análisis. Un meta-análisis usa modelos estadísticos para combinar datos de distintas publicaciones para responder a una pregunta específica.

Lo que quizás no te diste cuenta mientras navegabas los pasos del meta-análisis, es que pequeñas decisiones (a veces pareciendo de muy poca importancia) pueden tener grandes efectos en los resultados. Si quieres saber más acerca de una de estas decisiones en particular… ¡sigue leyendo!

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MInOSSE: all you need to reconstruct past species geographic range is in the fossil record!

Post provided by Francesco Carotenuto

A very important ecological feature of a species is its geographic range, which can be described by its size, position and shape. Studying the geographic range can be useful to understand the ecological needs of a species and, thereby, to plan conservation strategies. In ecological studies, mathematical models are the new standard to reconstruct the distribution of living species on Earth because of their accuracy in predicting a species presence or absence at unsampled locations. These methods are able to reconstruct the climatic niche of a species and to project it onto a geographic domain in order to predict the species’ spatial distribution. To do this, besides the occurrences of a species, the models necessarily require the spatial maps of environmental variables, like temperature and precipitation, for all the study area.

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Gaining Genetic and Epigenetic Data from a Single Established Next-Generation Sequencing Approach

Post provided by Marco Crotti

How organisms adapt to the environment they live in is a key question in evolutionary biology. Genetic variation, i.e. how individuals within populations differ from each other in terms of their DNA, is an essential element in the process of adaptation. It can arise through different mechanisms, including DNA mutations, genetic drift, and recombination.

Example of how genetic drift can occur over generations via random sampling (i.e. random mating) in a population. (Picture credit: Gringer).

Differences in DNA sequences between individuals can results in differences in the expression of genes. This can therefore determine the organism’s capacity to grow, develop, and react to environmental stimuli. However, a growing body of literature reveals that there are other ways organisms can change the way they interact with the world without mutations in the DNA sequence.

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The Ecology of Dance

Post provided by Chloe Robinson

Dance has been part of human culture for millennia. Some scholars refer to dance as a specific language, dependent on the space and time in which it exists and dependent on the power structures that rule in that time. April 29th marks International Dance Day; a day initiated in 1982 by the International Dance Committee of the UNESCO International Theatre Institute to commemorate the birthday of Jean-Georges Noverre, a distinguished French choreographer.

Male Maratus volans peacock spider. Picture credit: Jürgen Otto.

For humans, dance is considered a sacred ritual, sometimes a form of communication and sometimes an important social and courtship activity. A recent study has even linked the innate ability to dance with greater survival rates in prehistoric times. However, for certain species of wild animal, dance-like behaviours are crucial for communication and mating. In this blog, I am going to highlight the evolutionary foundations of dance in wild animals and explore some of the ways that dance is used in ecology.

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2019 Robert May Prize Winner: Corneile Minnaar

The Robert May Prize is awarded annually for the best paper published in Methods in Ecology and Evolution by an Early Career Researcher. We’re delighted to announce that the 2019 winner is Corneile Minnaar, for his article ‘Using quantum dots as pollen labels to track the fates of individual pollen grains‘.

A central component of an organism’s fitness is its ability to successfully reproduce. This includes finding a potential mate and successful mating. For plants, movement of pollen from an anther to a conspecific stigma is essential for successful reproduction, but directly tracking movement of individual pollen grains heretofore has been impossible (with the exception of those species of orchids and milkweeds whose pollen comes in large packages (pollinia)). Knowing how pollen move around, whether or not they successfully fertilize ovules, is also central to understanding the evolution and ecology of flowering plants (angiosperms) and floral traits.

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O Problema com os ‘Fósseis Vivos’: Uma Perspectiva Filogenética Molecular

Blog escrito por: gustavo burin

This post is also available in English

Fóssil de caranguejo-ferradura (Museu de História Natural de Berlin)

Há alguns dias, me deparei com um interessante vídeo sobre os chamados “fósseis vivos”. O vídeo focou mais nos problemas de usá-los como argumentos contra a teoria da evolução, e aproveitei a oportunidade para falar mais sobre essas linhagens longevas.

Fóssil vivo‘ é um termo usado para descrever linhagens que acredita-se terem se originado há muito tempo e que mantêm características que se assemelham a seus parentes fósseis. Alguns exemplos bem conhecidos dessas linhagens são os Tuatara da Nova Zelândia (Sphenodon punctatus) e as árvores Gingkos (Gingko biloba).

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The Problem with ‘Living Fossils’: A Molecular Phylogenetic Perspective

post provided by: gustavo burin

Este post também pode ser lido em Português

Fossil of a Horseshoe crab (Museum of Natural History Berlin)

A couple of days ago I came across a nice video (in Portuguese only, sorry) about so-called “living fossils”. The video focused on the problems of using them as arguments against evolution. But I’d like to take the opportunity to talk more about these long-lived lineages.

Living fossil’ is a term used to describe lineages that are thought to have been around for a very long time and retain characteristics that resemble of their fossil relatives. A couple of well-known examples of these lineages are the Tuatara of New Zealand (Sphenodon punctatus) and the Gingko tree (Gingko biloba).

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The Evolution of Love

Post provided by Chloe Robinson

The sending of letters under the pen name ‘St. Valentine’ began back in the middle ages as a way of communicating affection during the practice of courting. Fast forward to 2020 and Valentine’s Day is a day for celebrating romance, but now it typically features the exchange of gifts and cards between lovers.

Credit: Pixabay

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