The world’s biodiversity is in crisis. Species are declining at an alarming rate. And this is happening at just the time we are really beginning to understand this diversity through an unprecedented cataloging and compiling of information. Data repositories are filled with hundreds of thousands of entries about species, where they live, how they live, and who they are related to. And this is only the beginning. New DNA-based surveys are exploding onto the scene and our ideas and understanding of biodiversity are improving everyday.
So when and how do we use this burgeoning knowledge of biodiversity in biodiversity conservation?
We take a stab at this question in our recent paper out in Nature by analysing the world’s bird and mammal diversity from a conservation perspective. We ask how much of the world’s bird and mammal diversity is currently protected and how much better we could do if protected areas were to be expanded. We consider diversity to be not only species, but also phylogenetic and functional diversity. The use of these types of diversity means we have a better chance of meeting big policy goals of preserving biodiversity that benefits humans and ecosystems than with a sole focus on species. Continue reading Where in the world is the unprotected diversity? New paper out in Nature→
We have a new paper out in Nature Climate Change that combines Species Distribution Models (SDMs), climate change and phylogenetic diversity metrics. This is very exciting as it is the first paper from our PD working group.
-We explore the effect of climate change on various PD metrics (including endemism-based metrics) for all eucalypts across Australia. Eucalypts are stand dominants in many forests across the continent and are also of course inherently awesome.
-We present the first complete phylogenetic tree for eucalypts (657 species)
-We include SDMs for dispersal and no-dispersal scenarios for all species for the present and future projections (more on the models soon..)
-The results? Overall, there is a loss of PD within cells as well as between cells- so an increasingly homogenous PD landscape. Rare, ancient lineages are the most impacted, and some areas, such as the Kimberley Region will likely be increasingly important refugia for PD. The southern coastline is an important reservoir of both ‘old’ and ‘young’ lineages. This distinction is important as we might value old and young lineages for different reasons from a conservation perspective.
After a long road, that began with a comment, ‘Of course related eucalypts don’t coexist, most of them are distributed allopatrically, and if they do re-mix, they will hybridise anyway’.. followed by many years of field-work, lab work, running models, revisions, more revisions, even more revisions.. we came to the conclusion, that indeed, evolutionary history probably explains why closely related species don’t co-occur.
Ecology is also important. Species in plots tend to have similar trait values (especially specific leaf area). One cool thing about a model-based approach is that we can estimate how much different factors influence co-occurrence and we can detect interactions- e.g. similar species co-occur unless they hybridise. The negative effect of reproductive compatibility was nearly as strong as the positive effect of having similar traits.
An SDM models the response of a species to a set of predictor variables (usually environmental variables). The model can be extended across a landscape with a probability of occurrence of species in grid cells**. The external branches (tips) of the phylogeny correspond to a particular taxon (let’s assume we have a species-level tree). Therefore, each external branch can simply be the probability of that species occurring in each cell (a,b,c,e,f in figure above). Now, for the internal branches. Continue reading Linking species distribution models (SDM) and phylogenies→
Why is evolutionary history rarely considered in actual conservation planning? Well, there are many reasons. Conservation practitioners might not be aware that evolutionary diversity can be used in conservation. If they are aware, maybe it doesn’t compete with the vast number of other conservation concerns. Or maybe they do value it, and would like to use it, but are not sure how.
We have a new paper out in PhilTransRocSocB that addresses this last problem. We show how to use phylogenetic diversity in spatial prioritisation software. The advantage of using this software is that diversity can be considered alongside other concerns–extinction risk, connectivity, cost etc.
What do you need to do this?
1-distribution data (occurrence in grids or a species distribution model-SDM)
How do we best preserve the world’s remaining biodiversity? That was the topic of a conference I attended last week at the Royal Society in London on ‘Phylogeny, extinction risk and conservation’. The two-day conference included a range of interesting presentations on global to regional conservation efforts.
Obviously the extinction story can be a depressing one—the Yangtze River Dolphin is most likely extinct and one in five plant species are threatened with extinction. However, even given the looming threats to biodiversity, there is a huge effort underway to make informed decisions about how to prevent further losses. Continue reading Keeping the tree of life intact→
We have a new paper out at MEE. It is a guide on how to use Joint Species Distribution Models (JSDMs) originally known (to us) as Multivariate Probit models (MVP), a name which thankfully didn’t stick.
Locating areas where species will likely persist in future climate changes has recently become a conservation priority. How do we find these areas? A good first step is to look for places that species persisted through past climate changes (often termed ‘refugia’). We think we may have identified mini or micro-refugia for trees on deep, protected soils in the Grampians ranges, Victoria. Continue reading Where in the landscape are the refugia?→
We have a new paper out in Ecography. The aim was to link functional traits to environmental gradients. There are existing methods that do this, but they generally involve multiple steps. We created a hierarchical model that effectively joins a species distribution model with species trait values in one step. We were quite happy with the model because it worked well-better than we anticipated for rare species-and, importantly, produced sensible and interpretable results. Here is one example.
Specific leaf area (SLA) represents a tissue allocation strategy of either growing quickly or growing slowly with more tissue devoted to protection or conserving resources. SLA modifies species responses to rock cover. So, species with low SLA (thick, tough leaves) tend to increase in occurrence on increasingly rocky areas. Species with higher SLA (flimsy leaves) tend to be found on deeper, less rocky soil (see Figure).
The y-axis label looks complicated, but it’s simply the expected change in probability of species occurrence for a given change in surface rock cover. (technically, this is a partial response)..
Some key aspects of the model are:
1- species trait values actually modify species responses to environmental gradients. This may be useful for improving species distribution models when trait values are known.
2- rare species borrowed strength from common species. Species that are uncommon or have restricted distributions are usually quite difficult or impossible to model. I think this type of multi-species modelling shows real promise in this area.