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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Reconnecting the Web of Life: Rewiring and Network Robustness

Post provided by VINICIUS A. G. BASTAZINI, JEF VIZENTIN-BUGONI and JINELLE H. SPERRY

Esta publicação no blogue também está disponível em português

Species Loss and Cascading Effects

Scale-throated Hermit (Phaethornis eurynome). ©Pedro Lorenzo.

Scale-throated Hermit (Phaethornis eurynome). ©Pedro Lorenzo.

Minimising the effects the ongoing Anthropocene mass extinction has become one of the main challenges of our era. The data suggest that the current rate of species loss is 100–1,000 greater than the background rates seen in the geological record. “But does it really matter if species are lost?” This question has permeated social and political debates. It’s usually used to demean conservation efforts. But it has also intrigued conservation scientists.

We know that species don’t occur alone in their environment. They’re entangled by their interactions, forming complex networks. In these networks the loss of one species may result in the loss of other species that depend on it. This process is known as co-extinction. Estimates of the magnitude of past and future extinction rates have often failed to account for the interdependence among species and the consequences of primary species loss on other species though. Continue reading

Religando a rede da vida: Reconexões de interações e a robustez de redes ecológicas

Postagem fornecida por VINICIUS A. G. BASTAZINI, JEF VIZENTIN-BUGONI and JINELLE H. SPERRY

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Perda de espécies e efeitos em cascata

Scale-throated Hermit (Phaethornis eurynome). ©Pedro Lorenzo.

Rabo-branco-de-garganta-rajada (Phaethornis eurynome). ©Pedro Lorenzo.

Minimizar os efeitos do atual processo de extinção em massa do Antropoceno se tornou um dos principais desafios da nossa era. Os dados sugerem que a taxa atual de perda de espécies é 100-1.000 vezes maior do que as taxas de fundo observadas no registro geológico. “Mas realmente importa se uma espécie é perdida?” Essa questão que permeia os debates sociais e políticos, geralmente para desqualificar os esforços de conservação, também tem intrigado os cientistas da conservação.

Sabemos que as espécies não ocorrem sozinhas em seu ambiente. Elas estão  interligadas por suas interações ecológicas, formando redes complexas. Nessas redes, a perda de uma espécie pode resultar em um efeito dominó, culminando na perda secundária de outras espécies. Esse processo é conhecido como co-extinção. As estimativas da magnitude das taxas de extinção passadas e futuras muitas vezes falharam em explicar a interdependência entre as espécies e as conseqüências da perda primaria de espécies. Continue reading

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