Bats. They’re amazing creatures. Long-lived (with relevance to their body size), echolocating (for microbats and some megabats), metabolically-resilient (apparently resilient to most virus infections) flying mammals (with heart beats up to 1200 bpm for hours during flight). There are 1,411 species of this incredible creature. But very little is known about their physiology and unique biological traits. And detailed evolutionary analysis has only just begun.
The problem is, they’re an ‘exotic’ animal (wildlife that most people do not come into contact with). Being a long-lived animal producing minimal offspring (most only have one baby per year), they’re not suited to the kind of experimental studies we do with other animals like mice. Unavoidably, some aspects of biology require the use of tissues and cells. These samples can be used for sequencing, genomics, molecular evolution studies, detailed transcriptomic analysis, functional experiments with specific cell types and much more. Some methodology is beginning to be published – such as capture techniques and wing punch/genomic isolation – but there’s been an absence of protocols for the processing of bats. This is essential for the field to maximise the potential application of each individual and for minimising non-essential specimen collection.
Knowing how many individuals there are in a population is a fundamental objective in ecology and conservation biology. But estimating abundance is often extremely difficult. It’s particularly difficult in the management of exploited marine, anadromous and freshwater populations. In marine fisheries, abundance estimation traditionally relies on demographic models, costly and time consuming mark recapture (MR) approaches if they are feasible at all, and the relationship between fishery catches and effort (catch per unit effort or CPUE). CPUEs can be subject to bias and uncertainty. This is why they tend to be considered relatively unreliable and contentious.
Close-Kin Mark-Recapture: Reducing Bias and Uncertainty
There is an alternative method though. It’s known as “Close-Kin Mark-Recapture” (CKMR), and is grounded in genomics and was first proposed by Skaug in 2001. The method is based on the principle that an individual’s genotype can be considered a “recapture” of the genotypes of each of its parents. Assuming the sampling of offspring and parents is independent of each other, the number of Parent-Offspring pairs (POP) genetically identified in a large collection of both groups can be used to estimate abundance. Continue reading →
We’ve got six papers that are freely available to absolutely everyone this month too. You can find out about two of the Open Access papers in the Applications and Practical Tools section below. In the third, Chen et al. show that tree assemblages in tropical forest ecosystems can present a strong signal of extensive distributional interspersion.
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?
Pathogens and the infectious diseases that they cause can have devastating impacts on host individuals and populations. To better understand how pathogens are able to cause disease, we can investigate the genetic mechanisms underlying the infection process. Hosts may respond to infection by upregulating defence pathways. Pathogens, in turn, evade these host immune responses as they infect and cause disease. As this process unfolds and each organism responds to the other, gene expression changes in both the host and the pathogen. These gene expression changes can be captured by dual RNA‐seq, which simultaneously captures the gene expression profiles of a host and of a pathogen during infection. Continue reading →
A fossilized species of the diatom Thalassiosira. B. A species of the dinoflagellate Prorocentrum. (Image provided by A. Ndhlovu).
As any reader of Methods in Ecology and Evolution will know, advances in technologies and methodologies used by ecologists and evolutionary biologists are never-ending. Coupled with the tendency for researchers to become ever more specialised, this means that keeping up to date with all the advances is challenging at best. Occasionally, new advances revolutionise the kinds of questions we ask and encourage us to develop new approaches to answer them. One of these huge advances emerged from the ‘-omics’ revolution.
The application of -omics methodologies to evolution and ecology has been particularly rapid. These technologies usually aren’t part of the basic science education in these fields – it’s more usual for computational biologists to cross over to ecology and evolution than the other way around. The review by Simon Creer and colleagues ’The ecologist’s field guide to sequence-based identification of biodiversity’ helps bridge this gap. It’s not too technical, but sufficiently detailed, and it provides a very handy overview of how genomics, transcriptomics and their meta-analyses can be applied to evolutionary ecology. The paper is filled with enormously helpful workflows, pointers, examples and, as the title suggests, is a guide for those who are not experts in sequence based technologies. Continue reading →
This double-size issue contains six Applications articles (one of which is Open Access) and two Open Access research articles. These eight papers are freely available to everyone, no subscription required.
–Temperature Manipulation: Welshofer et al. present a modified International Tundra Experiment (ITEX) chamber design for year-round outdoor use in warming taller-stature plant communities up to 1.5 m tall.This design is a valuable tool for examining the effects of in situ warming on understudied taller-stature plant communities
–Zoon: The disjointed nature of the current species distribution modelling (SDM) research environment hinders evaluation of new methods, synthesis of current knowledge and the dissemination of new methods to SDM users. The zoon R package aims to overcome these problems by providing a modular framework for constructing reproducible SDM workflows.
–BEIN R Package: The Botanical Information and Ecology Network (BIEN) database comprises an unprecedented wealth of cleaned and standardised botanical data. The bien r package allows users to access the multiple types of data in the BIEN database. This represents a significant achievement in biological data integration, cleaning and standardisation.
The BES Microbial Ecology Special Interest Group is running a workshop today (Thursday 2 November) on Novel Tools for Microbial Ecology. To compliment this workshop, Xavier Harrison has edited a Virtual Issue of the best Methods in Ecology and Evolution articles on advances in methods of studying microbial evolution and ecology from the past few years.
Advances in Next-Generation Sequencing (NGS) technology now allow us to study associations between hosts and their microbial communities in unprecedented detail. However, studies investigating host-microbe interactions in the field of ecology and evolution are dominated by 16S and ITS amplicon sequencing. While amplicon sequencing is a useful tool for describing microbial community composition, it is limited in its ability to quantify the function(s) performed by members of those communities. Characterising function is vital to understanding how microbes and their hosts interact, and consequently whether those interactions are adaptive for, or detrimental to, the host. The articles in this Virtual Issue cover a broad suite of approaches that allow us to study host-microbe and microbe-microbe interactions in novel ways.
“My research is broadly focussed on the evolution of complexity. Many of my projects are related to the evolutionary ecology of programmed cell death (PCD) in unicellular organisms; how PCD impacts microbial communities; and how the philosophy of levels of selection informs our understanding of PCD evolution. I have also examined other aspects of complexity evolution such as the origin of life and group formation in unicellular chlorophytes in response to predation. The model organisms I typically use are phytoplankton. With specific reference to submissions to Methods in Ecology and Evolution, I have used a range of methods in my research, including general cell and molecular biology tools, biochemical assays, microscopy, flow cytometry, bioinformatics and computational algorithms.”
“I’m a molecular ecologist who uses genetic and genomic tools to ask questions ranging from surveillance and monitoring to biodiversity and phylogeography. My work includes development of novel molecular detection tools and metabarcoding applications for aquatic invasive species. I’m also interested in applying molecular tools to ask questions related to the evolution and biodiversity of benthic marine invertebrates in Antarctica.”
This month’s issue contains two Applications articles and two Open Access articles, all of which are freely available.
– MO-Phylogenetics: A software tool to infer phylogenetic trees optimising two reconstruction criteria simultaneously and integrating a framework for multi-objective optimisation with two phylogenetic software packages.
– PHYLOMETRICS: An efficient algorithm to construct the null distributions (by generating phylogenies under a trait state-dependent speciation and extinction model) and a pipeline for estimating the false-positive rate and the statistical power of tests on phylogenetic metrics..