Capturing the Contribution of Rare and Common Species to Turnover: A Multi-Site Version of Generalised Dissimilarity Modelling

Post provided by Guillaume Latombe and Melodie A. McGeoch

Understanding how biodiversity is distributed and its relationship with the environment is crucial for conservation assessment. It also helps us to predict impacts of environmental changes and design appropriate management plans. Biodiversity across a network of local sites is typically described using three components:

  1. alpha (α) diversity, the average number of species in each specific site of the study area
  2. beta (β) diversity, the difference in species composition between sites
  3. gamma (γ) diversity, the total number of species in the study area.
Two tawny frogmouths, a species native to Australia. ©Marie Henriksen.

Two tawny frogmouths, a species native to Australia. ©Marie Henriksen.

Despite the many insights provided by the combination of alpha, beta and gamma diversity, the ability to describe species turnover has been limited by the fact that they do not consider more than two sites at a time. For more than two sites, the average beta diversity is typically used (multi-site measures have also been developed, but suffer shortcomings, including difficulties of interpretation). This makes it difficult for researchers to determine the likely environmental drivers of species turnover.

We have developed a new method that combines two pre-existing advances, zeta diversity and generalised dissimilarity modelling (both explained below). Our method allows the differences in the contributions of rare versus common species to be modelled to better understand what drives biodiversity responses to environmental gradients. Continue reading

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Conifers for Christmas: Evolution above the level of species

Post provided by  Aelys Humphreys

Conifers for Christmas

It’s somehow fitting that the centre piece of an ancient midwinter tradition in Europe – that of decorating and worshipping an evergreen tree – is an ancient seed plant, a conifer. In Europe, we tend to think of conifers as “Christmas trees” – evergreen trees with needles and dry cones, restricted to cold and dry environments – but conifers are much more diverse and widespread than that. There are broad-leaved, tropical conifers with fleshy cones and even a parasitic species that is thought to parasitise on members of its own family!

Conifer diversity. Classic Christmas tree style conifers in the snow; a broadleaved, tropical podocarp (© Ming-I Weng); the only parasitic gymnosperm, Parasitaxus usta (©W. Baker).

Conifer diversity. Classic Christmas tree style conifers in the snow; a broadleaved, tropical podocarp (© Ming-I Weng); the only parasitic gymnosperm, Parasitaxus usta (©W. Baker).

However, while today’s distribution of conifers is global – spanning tropical, temperate and boreal zones – it is fragmented. The conifer fossil record extends well into the Carboniferous and bears witness to a lineage that was once much more abundant, widespread and diverse. So we can tell that today’s diversity and distribution have been shaped by hundreds of millions of years of speciation, extinction and migration. Continue reading

Issue 6.11

Issue 6.11 is now online!

The November issue of Methods is now online!

This month’s issue contains two Applications articles and one Open Access article, all of which are freely available.

mvMORPH: A package of multivariate phylogenetic comparative methods for the R statistical environment which allows fitting a range of multivariate evolutionary models under a maximum-likelihood criterion. Its use can be extended to any biological data set with one or multiple covarying continuous traits.

Low-cost soil CO2 efflux and point concentration sensing systems: The authors use commercially available, low-cost and low-power non-dispersive infrared (NDIR) CO2 sensors to develop a soil CO2 efflux system and a point CO2 concentration system. Their methods enable terrestrial ecologists to substantially improve the characterization of CO2 fluxes and concentrations in heterogeneous environments.

This month’s Open Access article comes from Jolyon Troscianko and Martin Stevens. In ‘Image calibration and analysis toolbox – a free software suite for objectively measuring reflectance, colour and pattern‘ they introduce a toolbox that can convert images to correspond to the visual system (cone-catch values) of a wide range of animals, enabling human and non-human visual systems to be modelled. The toolbox is freely available as an addition to the open source ImageJ software and will considerably enhance the appropriate use of digital cameras across multiple areas of biology. In particular, researchers aiming to quantify animal and plant visual signals will find this useful. This article received some media attention upon Early View publication over the summer. You can read the Press Release about it here.

Our November issue also features articles on Population Genetics, Macroevolution, Modelling species turnover, Abundance modelling, Measuring stress and much more. Continue reading