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History of species distribution models

21 07 2020

This little historical overview by recently completed undergraduate student, Sofie Costin (soon to join our lab!), nicely summarises the history, strengths, and limitations of species distribution modelling in ecology, conservation and restoration. I thought it would be an excellent resource for those who are just entering the world of species distribution models.

SDM

Of course, there is a strong association between and given species and its environment¹. As such, climate and geographical factors have been often used to explain the distribution of plant and animal species around the world.

Predictive ecological models, otherwise known as ‘niche models’ or ‘species distribution models’ have become a widely used tool for the planning of conservation strategies such as pest management and translocations^2-5. In short, species distribution models assess the relationship between environmental conditions and species’ occurrences, and then can estimate the spatial distribution of habitats suited to the study species outside of the sampling area^3,6.

While the application of species distribution models can reduce the time and cost associated with conservation research, and conservation managers are relying increasingly on them to inform their conservation strategies⁴, species distribution models are by no means a one-stop solution to all conservation issues. Read the rest of this entry »

Koala extinctions past, present, and future

12 06 2019

Photo by John Llewelyn

Koalas are one of the most recognised symbols of Australian wildlife. But the tree-living marsupial koala is not doing well throughout much of its range in eastern Australia. Ranging as far north as Cairns in Queensland, to as far west as Kangaroo Island in South Australia, the koala’s biggest threats today are undeniably deforestation, road kill, dog attacks, disease, and climate change.

With increasing drought, heatwaves, and fire intensity and frequency arising from the climate emergency, it is likely that koala populations and habitats will continue to decline throughout most of their current range.

But what was the distribution of koalas before humans arrived in Australia? Were they always a zoological feature of only the eastern regions?

The answer is a resounding ‘no’ — the fossil record reveal a much more complicated story.

Read the rest of this entry »

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Tags: climate envelope, Eucalypt, Eucalyptus, koala, marsupial, niche, Phascolarctos, Phascolarctos cinereus, potential niche, SDM
Categories : Australia, biodiversity, biogeography, climate change, climate shift, conservation, conservation biology, conservation ecology, decline, deforestation, ecology, extinction, fragmentation, habitat loss, mammal, modelling, niche model, palaeo-ecology, research, science, southern Australia, species distribution model, threatened species, vegetation

Job: Koala Data Research Technician

6 03 2017

koala If you live in South Australia, and in Adelaide especially, you would have had to be living under a rock not to have heard of the Great Koala Counts 1 and 2. So I’m not really writing this for those sotto pietra types. If you are a regular reader of CB.com, you’ll also know that I’ve been involved in helping analyse the data from GKC1, as well as improving the design of the GKC2.

Well, the data are in for GKC2 and we need help to analyse them. Just as a little reminder, the GKCs are designed to provide better data to estimate the distribution and density of koalas in South Australia (especially in the Mount Lofty Ranges). We’ve already written one scientific article from GKC1, but we now have a more expansive and quality-controlled dataset, so it’s now time to write the second. Read the rest of this entry »

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Tags: data, employment, job, koala, marsupial, part-time, research assistant, technician
Categories : conservation, niche model, South Australia, southern Australia, species distribution model

Palaeo-ecology PhD scholarships

1 03 2017

With my new position as Matthew Flinders Fellow in Global Ecology at Flinders University, I am in the agreeable position to be able to offer two PhD scholarships to the best candidates from around the world. If you feel that you’re up to the challenge, I look forward to hearing from you.

These projects will be in the following palaeo-ecology topics:

PhD Project #1. Ecological networks to examine community cascades of Late Quaternary megafauna extinctions Read the rest of this entry »

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Tags: applications, PhD, PhD scholarships, scholarships, Students
Categories : bottom-up ecology, community ecology, conservation, ecology, Flinders University, metapopulation, niche model, palaeo-ecology, population dynamics, top-down ecology

You know it’s hot when it’s too hot to ….

16 01 2014

My post’s title might be a good candidate title for a punk song in the 2030s (maybe by a re-incarnation of the Dead Kennedys).

I am currently sitting under my solar-powered ceiling fan as Adelaide is declared the world’s hottest city (and not in the funky, cultural, fun way), and I can’t help but contemplate climate change models predicting the fate of biodiversity over the coming decades. Because it’s far, far too hot to work outside, I’m perusing the latest interesting articles on the subject and I came across this recent little gem.

Also recommended on F1000Prime by Ary Hoffman, the paper, Using physiology to predict the responses of ants to climatic warming, by Sarah Diamond and colleagues touches on many aspects of climate predictions that need to be considered. I summarise these briefly here.

While no physiologist, I have dabbled in the past, although up until quite recently I didn’t see that physiology per se had much to do with conservation. It turns out that climate change has spawned an entire sub-discipline called ‘conservation physiology‘, which focuses inter alia on how species can/will/might respond and adapt to a warmer, climatically disrupted world.

What struck me about Diamond & colleagues’ paper was that yet again, it’s not as simple as heat-stressing a species experimentally and making a prediction on its future distribution (ecology is complex). No, the complexity comes in various forms that makes each species a little different from each other. Using North American ant species subjected to various warming scenarios in large (5 m) enclosures, they found the following: Read the rest of this entry »

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Tags: ants, climate change, climate disruption, fitness, foraging, Global warming, niche models, physiology, species distribution models, survival, thermal niche
Categories : bioclimatic envelope, climate change, conservation, decline, ecology, extinction, niche model, species distribution model

Global Ecology postgraduate opportunities

12 08 2012

I should have published these ages ago, but like many things I have should have done earlier, I didn’t.

I also apologise for a bit of silence over the past week. After coming back from the ESP Conference in Portland, I’m now back at Stanford University working with Paul Ehrlich trying to finish our book (no sneak peaks yet, I’m afraid). I have to report that we’ve completed about about 75 % it, and I’m starting to feel like the end is in sight. We hope to have it published early in 2013.

So here they are – the latest 9 PhD offerings from us at the Global Ecology Laboratory. If you want to get more information, contact the first person listed as the first supervisor at the end of each project’s description.

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1. Optimal survey and harvest models for South Australian macropods (I’ve advertised this before, but so far, no takers):

The South Australia Department of Environment, Water and Natural Resources (DEWNR) is custodian of a long-term macropod database derived from the State’s management of the commercial kangaroo harvest industry. The dataset entails aerial survey data for most of the State from 1978 to present, annual population estimates, quotas and harvests for three species: red kangaroo (Macropus rufus), western grey kangaroo (Macropus fuliginosus), and the euro (Macropus robustus erubescens).

DEWNR wishes to improve the efficiency of surveys and increase the precision of population estimates, as well as provide a more quantitative basis for setting harvest quotas.

We envisage that the PhD candidate will design and construct population models:

to predict population size/densities with associated uncertainty, linking fluctuations to environmental variability (including future climate change projections)
to evaluate the efficiency of spatially explicit aerial surveys
to estimate demographic parameters (e.g., survival rate) from life tables and
to estimate spatially explicit sustainable harvest quotas

Supervisors: me, A/Prof. Phill Cassey, Dr Damien Fordham, Dr Brad Page (DEWNR), Professor Michelle Waycott (DEWNR).

2. Correcting for the Signor-Lipps effect

The ‘Signor-Lipps effect’ in palaeontology is the notion that the last organism of a given species will never be recorded as a fossil given the incomplete nature of the fossil record (the mirror problem is the ‘Jaanusson effect’, where the first occurrence is delayed past the true time of origination). This problem makes inference about the timing and speed of mass extinctions (and evolutionary diversification events) elusive. The problem is further complicated by the concept known as the ‘pull of the recent’, which states that the more time since an event occurred, the greater the probability that evidence of that event will have disappeared (e.g., erased by erosion, hidden by deep burial, etc.).

In a deep-time context, these problems confound the patterns of mass extinctions – i.e., the abruptness of extinction and the dynamics of recovery and speciation. This PhD project will apply a simulation approach to marine fossil time series (for genera and families, and some individual species) covering the Phanerozoic Aeon, as well as other taxa straddling the K-T boundary (Cretaceous mass extinction). The project will seek to correct for taphonomic biases and assess the degree to which extinction events for different major taxa were synchronous.

The results will also have implications for the famous Sepkoski curve, which describes the apparent logistic increase in marine species diversity over geological time with an approximate ‘carrying capacity’ reached during the Cenozoic. Despite recent demonstration that this increase is partially a taphonomic artefact, a far greater development and validation/sensitivity analysis of underlying statistical models is needed to resolve the true patterns of extinction and speciation over this period.

The approach will be to develop a series of models describing the interaction of the processes of speciation, local extinction and taphonomic ‘erasure’ (pull of the recent) to simulate how these processes interact to create the appearance of growth in numbers of taxa over time (Sepkoski curve) and the abruptness of mass extinction events. The candidate will estimate key parameters in the model to test whether the taphonomic effect is strong enough to be the sole explanation of the apparent temporal increase in species diversity, or whether true diversification accounts for this.

Supervisors: me, Prof. Barry Brook

3. Genotypic relationships of Australian rabbit populations and consequences for disease dynamics

Historical evidence suggests that there were multiple introduction events of European rabbits into Australia. In non-animal model weed systems it is clear that biocontrol efficacy is strongly influenced by the degree of genetic diversity and number of breed variants in the population.

The PhD candidate will build phylogenetic relationships for Australian rabbit populations and develop landscape genetic models for exploring the influence of myxomatosis and rabbit haemorrhagic disease virus (RHDV) on rabbit vital rates (survival, reproduction and dispersal) at regional and local scales. Multi-model synthesis will be used to quantify the relative roles of environment (including climate) and genotype on disease prevalence and virulence in rabbit populations.

Supervisors: A/Prof Phill Cassey, Dr Damien Fordham, Prof Barry Brook Read the rest of this entry »

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Tags: Adelaide, biodiversity, climate change, Doctor of Philosophy, extinction, invasion biology, invasive species, Paleontology, PhD, rabbit, scholarship, The University of Adelaide, turtle, university
Categories : alien species, Australia, conservation, conservation biology, disease, environmental science, health, invasive species, kangaroo, mathematics, niche model, population dynamics, science, South Australia, The University of Adelaide

Pickled niches

2 08 2011

Another fine contribution from Salvador Herrando-Pérez (see previous posts here, here, here and here).

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Sometimes evolution fails to shape new species that are able to expand the habitat of their ancestors. This failure does not rein in speciation, but forces it to take place in a habitat that changes little over geological time. Such evolutionary outcomes are important to predict the distribution of groups of phylogenetically related species.

Those who have ever written a novel, a biography, or even a court application, will know that a termite-eaten photo or an old hand-written letter can help rebuild moments of our lives with surgical precision. Likewise, museums of natural sciences store historical biodiversity data of great value for modern research and conservation¹.

A notable example is the study of chameleons from Madagascar by Chris Raxworthy and colleagues². By collating 621 records of 11 species of the tongue-throwing reptiles, these authors subsequently concentrated survey efforts on particular regions where they discovered the impressive figure of seven new species to science, which has continued to expand³ (see figure below). The trick was to characterise the habitat at historical and modern chameleon records on the basis of satellite data describing climate, hydrology, topography, soil and vegetation, then extrapolate over the entire island to predict what land features were most likely to harbour other populations and species. This application of species distribution models⁴ supports the idea that the phenotypic, morphological and ecological shifts brought about by speciation can take place at slower rates than changes in the habitats where species evolve – the so-called ‘niche conservatism’ (a young concept with already contrasting definitions, e.g.,^5-7).

Read the rest of this entry »

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Tags: biodiversity, climate change, environment, niche, speciation, Species distribution, species distribution model
Categories : climate change, conservation, modelling, niche model

生态学 = ‘Ecology’ in China

13 05 2011

I’m just heading home after a very inspiring workshop organised by Fangliang He at Sun Yat-sen University in Guangzhou, China (I’m writing this from the Qantas Club in the Hong Kong airport).

Before I proceed to regale you with the salient details of the ‘International Symposium for Biodiversity and Theoretical Ecology‘, I am compelled to state publicly that I offer my sincerest condolences to Fangliang and his family; unfortunately Fangliang’s brother passed away while we were at the workshop and so Fangliang wasn’t able to spend much time reaping the fruits of his organisational labour. If you know Fangliang, please send him a supporting email.

That sad note aside, I am delighted to say that the workshop was compelling, challenging and also rather fortuitous. I was one of many overseas invitees, and I must say that I was at times overwhelmed by the size of the brains they managed to pack into the auditorium. Many colleagues I didn’t know attended, and I hope that many will become collaborators. The international invitees were: Read the rest of this entry »

Comments : 3 Comments »
Tags: biodiversity, China, ecology, environment, Fangliang He, Sun Yat-sen University
Categories : alien species, biodiversity, biogeography, China, climate change, conference, demography, ecology, ecosystem function, extinction, invasive species, mathematics, modelling, neutral theory, niche model, population dynamics, speciation, tropical

Mega-meta-model manager

24 07 2010

As Barry Brook just mentioned over at BraveNewClimate.com, I’ll be travelling with him and several of our lab to Chicago tomorrow to work on some new aspects of linked climate, disease, meta-population, demographic and vegetation modelling. Barry has this to say, so I won’t bother re-inventing the wheel:

… working for a week with Dr Robert Lacy, Prof Resit Akcakaya and collaborators, on integrating spatial-demographic ecological models with climate change forecasts, and implementing multi-species projections (with the aim of improving estimates of extinction risk and provide better ranking of management and adaptation options). This work builds on a major research theme at the global ecology lab, and consequently, a whole bunch of my team are going with me — Prof Corey Bradshaw (lab co-director), my postdocs Dr Damien Fordham, Dr Mike Watts and Dr Thomas Prowse and Corey’s and my ex-postdoc, Dr Clive McMahon. This builds on earlier work that Corey and I had been pursuing, which he described on ConservationBytes last year.

The ‘mega-meta-model manager’ part is a clever piece of control-centre software that integrates these disparate ecological, climate and disease dynamic inputs. Should be some good papers coming out of the work soon.

Of course, I’ll continue to blog over the coming week. I’m not looking forward to the 30-hour travel tomorrow to Chicago, but it should be fun and productive once I get there.

CJA Bradshaw

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Tags: Barry Brook, Bob Lacy, Chicago, ecological modelling, RAMAS, Resit Akcakaya, software, travel, Vortex
Categories : climate change, connectivity, conservation biology, disease, mathematics, metapopulation, modelling, niche model, population dynamics, population viability analysis, PVA, USA

Life and death on Earth: the Cronus hypothesis

13 10 2009

Cronus

Bit of a strange one for you today, but here’s a post I hope you’ll enjoy.

My colleague, Barry Brook, and I recently published a paper in the very new and perhaps controversial online journal , the Journal of Cosmology. Cosmology? According to the journal, ‘cosmology’ is:

“the study and understanding of existence in its totality, encompassing the infinite and eternal, and the origins and evolution of the cosmos, galaxies, stars, planets, earth, life, woman and man”.

The journal publishes papers dealing with ‘cosmology’ and is a vehicle for those who wish to publish on subjects devoted to the study of existence in its totality.

Ok. Quite an aim.

Our paper is part of the November (second ever) issue of the journal entitled Asteroids, Meteors, Comets, Climate and Mass Extinctions, and because we were the first to submit, we managed to secure the first paper in the issue.

Our paper, entitled The Cronus hypothesis – extinction as a necessary and dynamic balance to evolutionary diversification, introduces a new idea in the quest to find that perfect analogy for understanding the mechanisms dictating how life on our planet has waxed and waned over the billions of years since it first appeared.

Gaia

In the 1960s, James Lovelock conceived the novel idea of Gaia – that the Earth functions like a single, self-regulating organism where life itself interacts with the physical environment to maintain conditions favourable for life (Gaia was the ancient Greeks’ Earth mother goddess). Embraced, contested, denounced and recently re-invigorated, the idea has evolved substantially since it first appeared. More recently (this year, in fact), Peter Ward countered the Gaia hypothesis with his own Greek metaphor – the Medea hypothesis. Essentially this view holds that life instead ‘seeks’ to destroy itself in an anti-Gaia manner (Medea was the siblicidal wife of Jason of the Argonauts). Ward described his Medea hypothesis as “Gaia’s evil twin”.

One can marvel at the incredible diversity of life on Earth (e.g., conservatively, > 4 million protists, 16600 protozoa, 75000-300000 helminth parasites, 1.5 million fungi, 320000 plants, 4-6 million arthropods, > 6500 amphibians, 10000 birds and > 5000 mammals) and wonder that there might be something in the ‘life makes it easier for life’ idea underlying Gaia. However, when one considers that over 99 % of all species that have ever existed are today extinct, then a Medea perspective might dominate.

Medea

Enter Cronus. Here we posit a new way of looking at the tumultuous history of life and death on Earth that effectively relegates Gaia and Medea to opposite ends of a spectrum. Cronus (patricidal son of Gaia overthrown by his own son, Zeus, and banished to Hades) treats speciation and extinction as birth and death in a ‘metapopulation’ of species assemblages split into biogeographic realms. Catastrophic extinction events can be brought about via species engineering their surroundings by passively modifying the delicate balance of oxygen, carbon dioxide and methane – indeed, humans might be the next species to fall victim to our own Medean tendencies. But extinction opens up new niches that eventually elicit speciation, and under conditions of relative environmental stability, specialists evolve because they are (at least temporarily) competitive under those conditions. When conditions change again, extinction ensues because not all can adapt quickly enough. Just as all individuals born in a population must eventually die, extinction is a necessary termination.

We think the Cronus metaphor has a lot of advantages over Gaia and Medea. The notion of a community of species as a population of selfish individuals retains the Darwinian view of contestation; self-regulation in Cronus occurs naturally as a result of extinction modifying the course of future evolution. Cronus also makes existing mathematical tools developed for metapopulation theory amenable to broader lines of inquiry.

For example, species as individuals with particular ‘mortality’ (extinction) rates, and lineages with particular ‘birth’ (speciation) rates, could interact and disperse among ‘habitats’ (biogeographical realms). ‘Density’ feedback could be represented as competitive exclusion or symbioses. As species dwindle, feedbacks such as reduced community resilience that further exacerbate extinction risk (Medea-like phase), and stochastic fluctuation around a ‘carrying capacity’ (niche saturation) arising when environmental conditions are relatively stable is the Gaia-like phase. Our Cronus framework is also scale-invariant – it could be applied to microbial diversity on another organism right up to inter-planetary exchange of life (panspermia).

What’s the relevance to conservation? We’re struggling to prevent extinction, so understanding how it works is an essential first step. Without the realisation that extinction is necessary (albeit, at rates preferably slower than they are currently), we cannot properly implement conservation triage, i.e., where do we invest in conservation and why?

We had fun with this, and I hope you enjoy it too.

CJA Bradshaw

Bradshaw, C.J.A., & Brook, B.W. (2009). The Cronus Hypothesis – extinction as a necessary and dynamic balance to evolutionary diversification Journal of Cosmology, 2, 201-209 Other: http://journalofcosmology.com/Extinction100.html

Comments : 4 Comments »
Tags: biodiversity, Cronus, evolution, extinction, Gaia, Medea, science, speciation
Categories : biodiversity, conservation, demography, extinction, habitat loss, harvest, invasive species, metapopulation, modelling, niche model, population dynamics, speciation

Moving forward with extinction risk predictions from climate change

15 10 2008

A little belated, but I thought this was worth mentioning for the Potential list…

—

One from Keith and colleagues in Biology Letters entitled Predicting extinction risks under climate change: coupling stochastic population models with dynamic bioclimatic habitat models is a nice example of a way forward to predict the extremely complex array of ecological processes and patterns that may arise from rapid climate change.

One of the major problems with predicting how biodiversity might respond to climate change is the typical simplicity of single-species ‘envelope’ models – these models basically use tolerance limits (generally, physiological) or optimum conditions to predict how a species’ distribution might change. Unfortunately, this usually negates the complex dynamics of populations, the dispersal capacity of individuals, and interactions with other species that may all dominate possible responses. In other words, climatic envelope models may be way, way off (and probably vastly optimistic).

Keith and colleagues have brought us a step closer to better predictions of (and hopefully, better responses to) climate change effects on species. They linked a time series of habitat suitability models with spatially explicit stochastic population models to explore factors that influence the viability of plant species populations in South African fynbos, a global biodiversity hotspot. They discovered that complex interactions between life history, disturbance regimes and distribution patterns mediate species extinction risks under climate change.

Well done! Our next challenge is to incorporate multiple species’ interactions into such models (just to make them as mind-bogglingly complex as possible) to give us better approaches for managing our depauperate future.

CJA Bradshaw