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 translocations2-5. 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 area3,6.

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 »





Successful movers responding to climate change

16 06 2020

tropical fishes range shiftsEcologists often rely on measuring certain elements of a species’ characteristics, behaviour, or morphology to determine if these — what we call ‘traits’ — give them certain capacities to exploit their natural environments. While sometimes a bit arbitrarily defined, the traits that can be measured are many indeed, and sometimes they reveal rather interesting elements of a species’ resilience in the face of environmental change.

As we know, climate change is changing the way species are distributed around the planet, for the main (and highly simplified) reason that the environments in which they’ve evolved and to which they have adapted are changing.

In the simplest case, a warming climate means that there is a higher and higher chance you’ll experience temperatures that really don’t suit you that well (think of a koala or a flying fox baking in a tree when the thermometer reads +45° in the shade). Just like you seeking those nice, air-conditioned spaces on a scorcher of a day, species like to move to where conditions are more acceptable to their particular physiologies and behaviours.

When they can’t change fast enough, they go extinct.

Ecologists use life-history traits to predict which species have the highest probability of moving to new areas in response to climate change. Most studies into this phenomenon have largely ignored that range shifts in fact occur in sequential stages: (1) the species arrives in a new place for the first time, (2) its population increases in size (and extent), and (3) it can continue to persist in the new spot. Read the rest of this entry »





A plant’s adaptive traits don’t follow climate conditions as you might expect

27 03 2020

mountain

Just a quick post today, my last one for March. Like probably most of you, I’ve been trying to pretend to be as normal as possible despite the COVID-19 surrealism all around me. But even COVID-19 has shifted my research to a small degree.

But I’m not going to talk about the global pandemic right now (I can almost hear the collective sigh of relief). Instead, I’m going to go back to topic and discuss a paper that I’ve just co-authored.

Last year I went to China’s Yunnan Province where I met some fantastic colleagues at the Xishuangbanna Tropical Botanical Garden who were doing some very cool stuff with the variation in plant functional traits across environmental gradients.

Well, those colleagues invited me to participate in one those research projects, and I’m happy to say that the result has just been published in Forests.

Measuring the functional traits of different alpine trees species in the Changbai Mountains of far north-eastern China (no, I didn’t get to go there), the research set out to test how these varied among species and elevation.

Of course, one expects that different trees use different combinations of traits to survive the rigours of mountain life (high variation in temperature, freezing, wind, etc.), but generally speaking, you might expect things like xylem vessel diameter and density to change more or less monotonically (i.e., changing in a consistent manner as elevation rises or falls). This is because trees should adapt their traits to the local conditions as best they can. Read the rest of this entry »





Heat tolerance highly variable among populations and species

14 01 2020

Many ecological studies have examined the tolerance of terrestrial wildlife to high and low air temperatures over global scales (e.g., 1, 2, 3). This topic has been boosted in the last two decades by ongoing and predicted impacts of climate change on biodiversity (see summary of 2019 United Nation’s report here and here).

However, it is unfortunate that for most species, studies have measured thermal tolerance from a single location or population. Researchers interested in global patterns of thermal stress collect those measurements from the literature for hundreds to thousands of species [recently compiled in the GlobTherm database] (4), and are therefore often restricted to analysing one value of thermal tolerance per species.

CB_FunctionalEcology_jan2020_Photo

Three of the 15 species of Iberian lacertids sampled in our study of thermal tolerance (9), including the populations of Algerian psammodromus (Psammodromus algirus), Geniez’s wall lizard (Podarcis virescens) and Western green lizard (Lacerta bilineata) sampled in Navacerrada (Madrid), Fuertescusa (Cuenca) and Moncayo (Soria), respectively. Photos by S. Herrando-Pérez

Using this approach, ecologists have concluded that cold tolerance is far more variable than heat tolerance across species from the tropics to the boreal zone (5-8). Consequently, tolerance to heat stress might be a species trait with limited potential to change in response to global warming compared to cold tolerance (5). Read the rest of this entry »





Less snow from climate change pushes evolution of browner birds

7 09 2017
© Bill Doherty

© Bill Doherty

Climate changes exert selective pressures on the reproduction and survival of species. A study of tawny owls from Finland finds that the proportion of two colour morphs varies in response to the gradual decline of snowfall occurring in the boreal region.

Someone born in the tropics who travels to the Antarctic or the Himalaya can, of course, stand the cold (with a little engineering help from clothing, however). The physiology of our body is flexible enough to tolerate temperatures alien to those of our home. We can acclimate and, if we are healthy, we can virtually reside anywhere in the world.

However, modern climate change is steadily altering the thermal conditions of the native habitats of many species. Like us, some can live up to as much heat or cold as their genetic heritage permits, because each species can express a range of morphological, physiological, and behavioural variation (plasticity). Others can modify their genetic make-up, giving way to novel species-specific features or genotypes (evolution).

When genetic changes are speedy, that is, within a few generations, we are witnessing ‘microevolution’ — in contrast to ‘macroevolution’ across geological time scales as originally reported by Darwin and Wallace (1). To date, the detection of microevolution in response to modern climate change remains elusive, and many studies claiming so seem to lack the appropriate data to differentiate microevolution from phenotypic plasticity (i.e., the capacity of a single genotype to exhibit variable phenotypes in different environments) (2, 3). Read the rest of this entry »





It’s not all about temperature for corals

31 05 2017

CB_ClimateChange6_Photo

Three of the coral species studied by Muir (2): (a) Acropora pichoni: Pohnpei Island, Pacific Ocean — deep-water species/IUCN ‘Near threatened’; (b) Acropora divaricate: Maldives, Indian ocean — mid-water species/IUCN ‘Near threatened’; and (c) Acropora gemmifera: Orpheus Island, Australia — shallow-water species/IUCN ‘Least Concern’. The IUCN states that the 3 species are vulnerable to climate change (acidification, temperature extremes) and demographic booms of the invading predator, the crown-of-thorns starfish Acanthaster planci. Photos courtesy of Paul Muir.

Global warming of the atmosphere and the oceans is modifying the distribution of many plants and animals. However, marine species are bound to face non-thermal barriers that might preclude their dispersal over wide stretches of the sea. Sunlight is one of those invisible obstacles for corals from the Indian and Pacific Oceans.

If we were offered a sumptuous job overseas, our professional success in an unknown place could be limited by factors like cultural or linguistic differences that have nothing to do with our work experience or expertise. If we translate this situation into biodiversity terms, one of the best-documented effects of global warming is the gradual dispersal of species tracking their native temperatures from the tropics to the poles (1). However, as dispersal progresses, many species encounter environmental barriers that are not physical (e.g., a high mountain or a wide river), and whose magnitude could be unrelated to ambient temperatures. Such invisible obstacles can prevent the establishment of pioneer populations away from the source.

Corals are ideal organisms to study this phenomenon because their life cycle is tightly geared to multiple environmental drivers (see ReefBase: Global Information System for Coral Reefs). Indeed, the growth of a coral’s exoskeleton relies on symbiotic zooxanthellae (see video and presentation), a kind of microscopic algae (Dinoflagellata) whose photosynthetic activity is regulated by sea temperature, photoperiod and dissolved calcium in the form of aragonite, among other factors.

Read the rest of this entry »





Spring asynchrony in migratory birds

15 05 2017
CB_ClimateChange5_BirdLateMigratoryArrival_Photo

Brent geese flock in the Limfjorden (Denmark)courtesy of Kevin Clausen. The Brent goose (Branta bernicla) is a migratory goose that breeds in Arctic coasts, as well as in northern Eurasia and the Americas, starting from late May to early June. Adults are about 0.5 m long, weigh some 2 kg and live up to 30 years. Their nests are placed in the ground, where reproductive pairs incubate a single clutch (≤ 5 eggs) for a couple of months. They are herbivores, feeding on algae (mainly Zostera marina in Limfjord) and seagrass in estuaries, fjords, intertidal areas and rocky beaches during fall and winter. During summer they feed on tundra herbs, moss, lichens, as well as aquatic plants in rivers and lakes. The species is ‘Least Concern’ for the IUCN, with a global population at some 600,000 individuals.

Migratory birds synchronise their travel from non-breeding to breeding quarters with the seasonal conditions optimal for reproduction. Above all, they decide when to migrate on the basis of the climate of their wintering areas while they are there. As climate change involves earlier springs in the Arctic but not in the wintering areas, there is a lack of synchronisation that leads to a demographic decline of these birds in the polar regions where they breed.

When I think about how species respond to climate change, the song from the ClashShould I stay or should I go” comes to mind. As climate changes, species eventually have to face an ultimate choice: (i) stay and adapt to novel conditions or become locally extinct if adaptation fails, (ii) or move to other regions where climatic conditions should be more suitable. Migratory species have to face this decision every time they have to move back and forth from non-breeding to breeding grounds.

Migration is a behavioural strategy shared by different animal groups like sea turtles, mammals, amphibians, insects or birds. Species move from one area to another usually to feed and reproduce in the best climatic conditions possible. For birds, migration is a common phenomenon that typically entails large movements between breeding and wintering grounds. These vertebrates boast some of the longest migratory distances known in the animal kingdom, particularly seabirds like Artic terns, which can complete up to a round-world trip in a single migratory event between the UK and the Antarctic (1). There are several theories about the mechanisms triggering bird migration, including improving body condition and fitness through unexploited resources (2), reducing parasite load (3), minimizing predation risk (4), maximizing day-light (5), or reducing competition (6, 7). Whatever the cause, birds have to decide when the best moment to migrate is, counting only with the (usually climatic) clues they have at the departure site. Read the rest of this entry »





Singin’ in the heat

9 03 2017
coqui & forest

Common coqui frog male (Eleutherodactylus coqui, snout-to vent length average ~ 3 cm) camouflaged in the fronds of an epiphyte in the El Yunque National Forest (Puerto Rico), along with an image of the enchanted forest of the Sierra de Luquillo where Narins & Meenderink did their study (4) – photos courtesy of Thomas Fletcher. This species can be found from sea level to the top of the highest peak in Puerto Rico (Cerro Punta = 1338 m). Native to mesic ecosystems, common coquis are well adapted to a terrestrial life, e.g., they lack interdigital webbing that support swimming propulsion in many amphibians, and youngsters hatch directly from the egg without transiting a tadpole stage. The IUCN catalogues the species as ‘Least Concern’ though alerts recent declines in high-altitude populations caused by chytrid fungus – lethal to amphibians at a planetary scale (9). Remarkably, the species has been introduced to Florida, Hawaii, the Dominican Republic and the Virgin Islands where it can become a pest due to high fertility rates (several >20 egg clutches/female/year).

Frog songs are species-specific and highly useful for the study of tropical communities, which host the highest amphibian diversities globally. The auditory system of females and the vocal system of males have co-evolved to facilitate reproductive encounters, but global warming might be disrupting the frequency of sound-based encounters in some species..

It is a rainy night, and Don (Gene Kelly) has just left his love, Kathy (Debbie Reynolds), at home, starting one of the most famous musical movie scenes ever: Singin’ in the rain 

Amphibians (see Amphibians for kids by National Geographic) also love to sing in rainy nights when males call for a partner, but now they have to do it in hotter conditions as local climates become warmer. Vocal behaviour is a critical trait in the life history of many frog species because it mediates recognition between individuals, including sexual selection by females (1).

With few exceptions, every species has a different and unique call, so scientists can use call features to identify species, and this trait is particularly useful in the inventory of diverse tropical communities (2). Differences in call frequency, duration and pitch, and in note, number, and repetition pattern, occur from one species to another. And even within species, songs can vary from individual to individual (as much as there are not two people with the same voice), and be tuned according to body size and environmental temperature (3). Read the rest of this entry »





Where do citizens stand on climate change?

2 01 2017
Talk to the hand

Talk to the hand

Climate change caused by industrialisation is modifying the structure and function of the Biosphere. As we uncork 2017, our team launches a monthly section on plant and animal responses to modern climate change in the Spanish magazine Quercus – with an English version in Conservation Bytes. The initiative is the outreach component of a research project on the expression and evolution of heat-shock proteins at the thermal limits of Iberian lizards (papers in progress), supported by the British Ecological Society and the Spanish Ministry of Economy, Industry and Competitiveness. The series will feature key papers (linking climate change and biodiversity) that have been published in the primary literature throughout the last decade. To set the scene, we start off putting the emphasis on how people perceive climate change.

Salvador Herrando-Pérez, David R. Vieites & Miguel B. Araújo

“I would like to mention a cousin of mine, who is a Professor in Physics at the University of Seville – and asked about this matter [climate change], he stated: listen, I have gathered ten of the top scientists worldwide, and none has guaranteed what the weather will be like tomorrow in Seville, so how could anyone predict what is going to occur in the world 300 years ahead?”

Mariano Rajoy (Spanish President from 2011 to date) in a public speech on 22 October 2007

Weather (studied by meteorology) behaves like a chaotic system, so a little variation in the atmosphere can trigger large meteorological changes in the short term that are hard to predict. On the contrary, climate (studied by climatology) is a measure of average conditions in the long term and thus far more predictable than weather. There is less uncertainty in a climate prediction for the next century than in a weather prediction for the next month. The incorrect statement made by the Spanish President reflects harsh misinformation and/or lack of environment-related knowledge among our politicians.

Climate has changed consistently from the onset of the Industrial Revolution. The IPCC’s latest report stablishes with 95 to 100% certainty (solid evidence and high consensus given published research) that greenhouse gases from human activities are the main drivers of global warming since the second half of the 20th Century (1,2). The IPCC also flags that current concentrations of those gases have no parallel in the last 800,000 years, and that climate predictions for the 21st Century vary mostly according to how we manage our greenhouse emissions (1,3). Read the rest of this entry »





How to find fossils

30 03 2016

Many palaeontologists and archaeologists might be a little put out by the mere suggestion that they can be told by ecologists how to do their job better. That is certainly not our intention.

Like fossil-hunting scientists, ecologists regularly search for things (individuals of species) that are rare and difficult to find, because surveying the big wide world for biodiversity is a challenge that we have faced since the dawn of our discipline. In fact, much of the mathematical development of ecology stems from this probabilistic challenge — for example, species distribution models are an increasingly important component of both observational and predictive ecology.

IMG_1277But the palaeo types generally don’t rely on mathematical models to ‘predict’ where fossils might be hiding just under the surface. Even I’ve done what most do when trying to find a fossil — go to a place where fossils have already been found and start fossicking. I’ve done this now with very experienced sedimentary geologists in the Flinders Rangers looking for 550 million year-old Ediacaran fossils, and most recently searching for Jurassic fossils (mainly ammonites) on the southern coast of England (Devon’s Jurassic Coast). My prized ammonite find is shown in the photo to the left.

If you’ve read anything on this blog before, you’ll probably know that I’m getting increasingly excited about palaeo-ecology, with particular emphasis on Australia’s late-Pleistocene and early Holocene mass-extinction of megafauna. So with a beautiful, brand-new, shiny, and quality-rated megafauna dataset1, we cheekily decided to take fossil hunting to the next level by throwing mathematics at the problem.

Just published2 in PloS One, I’m happy to announce our newest paper entitled Where to dig for fossils: combining climate-envelope, taphonomy and discovery models.

Of course, we couldn’t just treat fossil predictions like ecological ones — there are a few more steps involved because we are dealing with long-dead specimens. Our approach therefore involved three steps: Read the rest of this entry »





InvaCost – estimating the economic damage of invasive insects

7 11 2014

insectinvasionThis is a blosh (rehash of someone else’s blog post) of Franck Courchamp‘s posts on an exciting new initiative of which I am excited to be a part. Incidentally, Franck’s spending the week here in Adelaide.

Don’t forgot to vote for the project to receive 50 000 € public-communication grant!

Climate change will make winters milder and habitats climatically more suitable year-round for cold-blooded animals like insects, but there are many questions remaining regarding whether such insects will be able to invade other regions as the climate shifts. There are many nasty bugs out there.

For example, the Asian predatory wasp is an invasive hornet in Europe that butchers pollinating insects, especially bees, thereby affecting the production of many wild and cultivated plants. I hope that we all remember what Einstein said about pollinators:

If bees were to disappear, humans will disappear within a few years.

(we all should remember that because it’s one of the few things he said that most of us understood). The highly invasive red fire ant is feared for its impacts on biodiversity, agriculture and cattle breeding, and the thousands of anaphylactic shocks inflicted to people by painful stings every year (with hundreds of deaths). Between the USA and Australia, over US$10 billion is spent yearly on the control of this insect alone. Tiger mosquitoes are vectors of pathogens that cause dengue fever, chikungunya virus and of about 30 other viruses. We could go on.

Most of these nasty creatures are now unable to colonise northern regions of Europe or America, or southern regions of Australia, for example, because they cannot survive cold temperatures. But how will this change? Where, when and which species will invade with rising temperatures? What will be the costs in terms of species loss? In terms of agricultural or forestry loss? In terms of diseases to cattle, domestic animals and humans? What will be the death toll if insects that are vectors of malaria can establish in new, highly populated areas?

We’ve proposed to study these and others from a list of 20 of the worst invasive insect species worldwide, and we got selected (i.e., financed!) by the Fondation BNP Paribas. In addition, the Fondation BNP Paribas has selected five scientific programmes on climate change and will give 50,000 € (that’s US$62,000) to the one selected by the public, for a communication project on their scientific programme. This is why we need you to vote for our project: InvaCost. Read the rest of this entry »





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

16 01 2014
© T. Brandon

© T. Brandon

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 »





Shrinking global range projected for the world’s largest fish

7 08 2013
© W. Osborn (AIMS)

© W. Osborn (AIMS)

My recently finished PhD student, Ana Sequeira, has not only just had a superb paper just accepted in Global Change Biology, she’s recently been offered (and accepted) a postdoctoral position based at the University of Western Australia‘s Oceans Institute (in partnership with AIMS and CSIRO). As any supervisor, I’m certainly pleased when a student completes her PhD, but my pride as an academic papa truly soars when she gets her first job. Well done, Ana. This post by Ana is about her latest paper.

Following our previous whale shark work (see herehereherehere, here, here and here), especially the recent review where we inferred global connectivity and suggest possible pathways for their migration, we have now gone a step further and modelled the habitat suitability for the species at at global scale. This paper sets a nice scene regarding current habitat suitability, which also demonstrates the potential connectivity pathways we hypothesised previously. But the paper goes much further; we extend our predictions to a future scenario for 2070 when water temperatures are expected to increase on average by 2 °C.

Sequeira et al_GCB_Figure 3

Global predictions of current seasonal habitat suitability for whale sharks. Black triangles indicate known aggregation locations. Solid line delineates areas where habitat suitability > 0.1 was predicted.

Regarding the current range of whale sharks (i.e., its currently suitable habitat), we already know that whale sharks span latitudes between about 35 º North to South. We also know that this geographical range has been exceeded on several occasions. What we did not know was whether conditions were suitable enough for whale sharks to cross from the Indian Ocean to the Atlantic Ocean – in other words, whether they could travel between ocean basins south of South Africa. Our global model results demonstrate that suitable habitat in this region does exist at least during the summer, thus supporting our hypotheses regarding global connectivity!

It’s true that the extensive dataset we used (30 years’ worth of whale shark sightings collected by tuna purse seiners in the three major oceans – data provided by the IRD, IOTC and SPC) has many caveats (as do all opportunistically collected data), but we went to great trouble to deal with them in this paper (you can request a copy here or access it directly here). And the overall result: the current global habitat suitability for whale sharks does agree well with current locations of whale shark occurrence, with the exception of the Eastern Pacific for where we did not have enough data to validate. Read the rest of this entry »





Ecosystem functions breaking down from climate change

17 05 2010

I’m particularly proud to present to ConservationBytes.com readers a new paper we’ve just had published online in Journal of Animal Ecology: Mechanisms driving change: altered species interactions and ecosystem function through global warming (Lochran Traill, Matt Lim, Navjot Sodhi and me).

It wasn’t easy to write a review discussing climate change effects on biodiversity, mainly because so many have been written already and we needed to examine the issue from a fresh perspective. The evidence for single species’ responses to rapidly shifting climates around the world is overwhelming (see for a few thousand examples, see the following: Stenseth et al. 2002; Parmesan et al. 2003, 2006; Roessig et al. 2004; Thomas et al. 2004; Poloczanska et al. 2007; Skelly et al. 2004; Dunn et al. 2009). It’s rather remarkable how many things are moving in response, with reduction in range size being more common than expansion.

However, predicting extinction risk from climate change is far more problematic because traditionally there have been too few data on species interactions to make heads or tails of a particular species’ eventual response (e.g., see comment on Chris Thomas’ famous paper regarding this matter). As systems heat up, some species will change in abundance, thereby affecting the abundance of others (think predators and prey, pollinators and their host plants, etc.) – this whole complicated process combined with single-species’ responses makes predicting what a future ecosystem might look like nearly impossible. Add in all the other ecosystem damage we’ve done from forest clearance, invasive species and over-harvesting, it’s a right mess.

It is for this reason we focussed on reviewing the links between species rather than on the species’ responses per se. We looked specifically at ecosystem function, that is, “the processes that facilitate energy transfer along food webs, and the major processes that allow the cycling of carbon, oxygen and nitrogen. ‘Function’ also includes ecosystem services.” Read the rest of this entry »





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…

182kydeee9pyxjpgOne 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

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