Curso “Frugivoria e dispersão de sementes”, 2016

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Frugivory and Seed Dispersal Course (Portuguese/Spanish) – 7-11 March 2016

Registrations: 4 Créditos – 01 a 12/02/2016.

@UNESP_PG_EcoBio with @mauro_galetti @pedro_jordano.

Part of the Programa de Pós-Graduação em Ecologia e Biodiversidade. UNESP, Rio Claro.

Fotos: Marina Cortes, Guto Balieiro, Lindolfo Souto, Pedro Jordano.

Our paper on defaunation effects on carbon storage in tropical forests

Plant-animal mutualisms for seed dispersal are key to preserve tropical forests and many other ecosystems (e.g., Mediterranean forests). These interactions may go extinct, and pervasively affect the forests in many aspects. One of them is a substantial loss of carbon storage capacity, simply as a result of collapsed recruitment of large-seeded trees.

Our study shows that the extinction of large animals has negative impacts on climate change.

Bello C., Galetti M., Pizo M.A., Magnago L.F.S., Ferreira Rocha M., Lima R.A.F., Peres C.A., Ovaskainen O., and Jordano P. 2015. Defaunation affects carbon storage in tropical forests. Science Advances, 1(11): e1501105. doi: 10.1126/sciadv.1501105


Defaunation, the severe decline of animal populations from natural ecosystems, is a process faced by tropical forests that can go unnoticed. Several large birds and mammals are threatened by hunting and human persecution. However, the loss of animals can bring about large unforeseen impacts. The extinction of large mammals implies the loss of functions that maintain diversity and ecosystem services on which humans depend.

Our recent study published in the journal Science Advances was conducted by Brazilian researchers from the Universidade Estadual Paulista (São Paulo State University) in Rio Claro, in collaboration with researchers from Spain, England, and Finland, and demonstrated that the loss of large frugivores negatively affects the capacity of tropical forests to stock carbon and, therefore, their potential to counter climate change.

The big frugivores, such as large primates, the tapir, the toucans, among other large animals, are the only ones able to effectively disperse plants that have large seeds. Usually, the trees that have large seeds are big trees with dense wood that store more carbon.

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Figure. Large frugivores and large-seeded trees of the Atlantic Forest. Mauro Galetti author of the photos a, d, and e. Pedro Jordano author of photos b, c, and f.

When we lose large frugivores we are losing dispersal and recruitment functions of large seeded trees and therefore, the composition of tropical forests changes. The result is a new forest dominated by smaller trees with milder woods which stock less carbon.

Our study showed that when large-seeded trees are removed from the forest and are replaced by trees with smaller seeds, the carbon stock potential of the forest decreases. This is a net result of the seed dispersal and recruitment collapse that entails the large frugivores extinction.

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Replacement process of tree species composition in tropical forests when they lose large dispersers. Forests with large trees and hardwood (initial community) are replaced by forests with smaller trees with mild wood (final community).

This is the result of the loss of crucial interactions that support the Web of Life in tropical forests. Not only we are facing the loss of charismatic animals, but we are facing the loss of interactions that maintain the proper functioning and key ecosystem services such as carbon storage. To date, tropical forest degradation has been entirely defined by REDD+ programs in terms of structural forms of human disturbance such as timber extraction and wildfires. Yet, even an apparently intact but otherwise defaunated forest should be considered as degraded because the insidious carbon erosion processes we highlight in this paper are already well underway.

Our study alerts current REDD+ programs that seek to counteract climate change by storing carbon in tropical forests, about the importance of considering the animals and their functionality as a fundamental part of the maintenance of carbon stocks. The effectiveness of these programs will be improved if the preservation of ecological processes that sustain the ecosystem service of carbon storage over time is guaranteed.

The study also included Marco A. Pizo (UNESP), Otso Ovaskainen (University of Helsinki), Renato Lima (USP), Luiz Fernando S. Magnago (Federal University of Lavras) and Mariana Rocha Ferreira (Federal University of Viçosa).

Our symposium at the BES annual meeting, 2015

A brief great summary of our talks at the British Ecological Society meeting in Edinburgh (UK) this week, by CoDisperse.
The summary of the tweet feed is here.
This was the thematic topic on Tuesday afternoon, focusing on “Dispersal Processes Driving Plant Movement: Challenges for Range Shifts in a Changing World” and organized by Cristina García, Etienne Klein and myself. Big thanks CoDisperse!

Rey Jaime I Award, Environmental Sciences


 

I’m very honored with being awarded the Rey Jaime I Award in Environmental Sciences this year. I was surprised with the decision of the jury during my stay in Brazil during this year’s Ciência Sem Fronteiras stay. It was great to have many, many messages with support and congratulations from many colleagues. My sincere thanks to all them!

I’m very happy with the award, as it aids supporting conservation efforts in the natural areas where I do my field work: Cazorla, Doñana, Alcornocales, Islas Canarias.

Just published the third edition of SEEDS

The 3rd edition of the book, originally edited by Michael Fenner, “Seeds: the ecology of regeneration in natural plant communities” is just published (ISBN 978-1-78064-183-6). It has been edited by R.S. Gallagher, and you can find in it a revised and updated version of my chapter on “Fruits and frugivory”. 

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How do furgivorous birds build-up their fruit meals?

This is the third part of a trilogy of papers dedicated to understanding the evolution of fruit colors and visual signals evolved by plants to attract animal mutualists. The paper is now available online at the Proceedings of the Royal Society, Biology website.

Theory predicts that trade among mutualists requires high reliability. Here, we show that moderate reliability already allows mutualists to optimize their rewards. The colours of Mediterranean fleshy-fruits indicate lipid rewards (but not other nutrients) to avian seed dispersers on regional and local scales. On the regional scale, fruits with high lipid content were significantly darker and less chromatic than congeners with lower lipid content.

Sylvia atricapillaSylvia borin

On the local scale, two warbler species (Sylvia atricapilla and Sylvia borin, above) selected fruit colours that were less chromatic, and thereby maximized their intake of lipids—a critical resource during migration and wintering.

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Figure. The trade of resources characterizing mutualistic interactions leads to multiple, repeated interactions among individual producers and consumers. For example, birds use visual information to decide which fruits to consume. Two individual birds combine different fruit species in their meals during a short feeding bout (t0 − t1), along their foraging sequence, in which they visited different fruiting plants. M1–M4 indicate the composition of four meals, i.e. the number of fruits consumed and their species identity, different fruits with different colours. We analyzed the combination of colors in field-sampled fruit meals in relation to the nutrient composition and food “reward” obtained by the birds. Birds used markedly non-random combinations of colors in their meals, indicating a significant choice of fruit meals maximizing energy intake.

In a passage and wintering area in SW Spain where I intensively studied these birds, the two warbler species consistently selected fruit color combinations that were significantly less chromatic, evidencing the use of color as a cue of nutrient rewards during short feeding bouts. Being extremely dependent on fleshy fruits during migration and wintering, these warblers use a very diverse set of fruit species to build-up reserves required for long-distance flights (garden warbler) or winter survival (blackcap).

It is amazing how selective were these birds in their choice of fruits. Even in a short feeding bout blackcaps can ingest up to seven different fruit species. I used analyses of fecal pellets, identifying not only seeds, but also fruit skins in the remains using a microscope, which enabled me to identify the number of different fruit species consumed during a short feeding bout. The fruit meals thus combine a varied assortment of flavors, pulp types, etc. The warblers have a very short gut passage time (16 moon on average- and up to 40 min), so that a sample of faecal material indicates the previous choices of fruits made by the bird, immediately before capture. I used mist-netted birds that were released after capture.

Warblers need to maintain a high throughput of fruits when relying on fruit food because fleshy fruits are a quite “diluted” type of food: not only they are rich in water, quite succulent, but they also have indigestible seeds that occupy very valuable space within the bird’s gut. The birds need to process all this stuff very rapidly in order to get enough “reward”. In turn this is good for the plant because the seeds are readily dispersed away from the mother plant. This is a mutualistic interaction driven by the visual cues used by the birds.

Our results indicate that mutualisms require only that any association between the quality and sensory aspects of signallers is learned through multiple, repeated interactions. Because these conditions are often fulfilled, also in social communication systems, we contend that selection on reliability is less intense than hitherto assumed. This may contribute to explaining the extraordinary diversity of signals, including that of plant reproductive displays.

Now the California gull, Larus californicus

This is the California gull, Larus californicus (Lawrence, 1854). It is subs. californicus.

California gull Larus californicus Ad 1

California gull Larus californicus 3cy 7

California gull Larus californicus 3cy 1

Here we see the white mirrors in P9 and P10, which are characteristic, and the white trailing edge to inner wing. This (both photos of same individual) is an adult (at least 4cy) with the winter plumage (hindneck has dense brown streaks). These first three photos were taken at Wilder Ranch State Park, Santa Cruz, along the coast line.

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California gull Larus californicus 3cy  California gull Larus californicus 3cy

A detail of the wonderful head of this gull (same individual in these two photos, an ad). Note the dark iris, and the color pattern in the bill ring (black with red-orange tinted patch in the lower mandible). The bill is characteristically 4-colored: yellowish at the base, black ring, red-orange dot and ivory tip- this separates it from Ring-billed and Herring. The leg color is also characteristic (green-bluish) but apparently is very variable. I saw other ad birds with very yellow legs. These two photos were taken in San Lorenzo Park, Santa Cruz, CA.

California gull Larus californicus 3cy

This is a 3cy bird, finishing molt to 3rd winter. The bill ring is wholly black; there are no white patches on P feathers, nor white mirrors. The bill is longer than in Ring-billed and the head is more massive. The photo was taken at Moss Landing, Elkhorn Slough, CA.

California gull Larus californicus 2cy 6

This is a 1cy bird (juvenile molting into 1st winter plumage), with characteristic black-tipped bill with pale pink in the base. It has not yet started te molt of the scapulars, yet some grayish ones seem to be apparent- the median coverts look worn and faded, creating pale midwing-panel; so the bird is a bit delayed in its molt.

EXIF data:

e_Model NIKON D7000
e_LensModel AF-S VR Zoom-Nikkor 70-300mm f/4.5-5.6G IF-ED
e_CameraSerialNumber 6074229
e_FlashExposureComp 0
e_ISOSpeedRating 100
e_ColorModel RGB
e_Depth 16
e_FocalLength 300
e_PixelHeight 3264
e_ApertureValue 5.6
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e_ShutterSpeed 0.002
e_Flash 16
e_CaptureDayOfMonth 13
e_CaptureMonthOfYear 10
e_CaptureYear 2013

Heermann’s gull in my recent trip to California

These are some shots of my recent trip to California, last October, where I had the opportunity to do a whale watching trip offshore Monterrey Bay, from Moss Landing. I’ll be posting more photos soon…

Heermann’s (Larus heermanni (Cassin, 1852) is one of my favorite gulls, with a beautiful plain grey plumage in the adult, contrasting with the white patches and the coral-red bill, and a smooth dark brown plumage of the immature birds.  They were common birds along the coast up to Santa Cruz, quite often in large flocks. The population size is estimated in ca. 150000 pairs.

Heermann s gull Larus heermanni1

The adult birds here seem to be starting with the winter plumage, with paler grey heads.

Heermann s gull Larus heermanni 1cy 12

This is a  typical juvenile bird facing its 1st winter. The head is very dark grey, with a creamy base of the bill.

Heermann s gull Larus heermanni Ad 2

I like the broad white trailing edge of the wing. It’s a very elegant gull in flight (well, as all the gulls). I’m getting a gull-addicted, even for the commonest species, which pose very nice identification problems when you try to get to the details of the plumage patterns and molt. Even the most common species (i.e., the yellow-legged here in S Spain) pose amazing identification challenges, especially in winter.

Heermann s gull Larus heermanni 2cyw with Humpback whale

And here, with the Humpback whale…

The photos were taken with the Nikon D7000, AF-S VR Zoom-Nikkor 70-300mm f/4.5-5.6G IF-ED, f8, 1/1000, ISO 400.

Our new book, Mutualistic networks, just published by Princeton University Press

Book cover
Book cover

We have just published our book “Mutualistic Networks“, the no. 53 issue in the series Monographs in Population Biology of Princeton University Press.

Mutualistic interactions among plants and animals have played a paramount role in shaping biodiversity. Yet the majority of studies on mutualistic interactions have involved only a few species, as opposed to broader mutual connections between communities of organisms. Our book comprehensively explores this burgeoning field. Integrating different approaches, from the statistical description of network structures to the development of new analytical frameworks, we describe the architecture of these mutualistic networks and show their importance for the robustness of biodiversity and the coevolutionary process.

Making a case for why we should care about mutualisms and their complex networks, we offer a new perspective on the study and synthesis of this growing area for ecologists and evolutionary biologists.

Collared pratincoles

These are several shots of Collared pratincoles (Glareola pratincola, Glareolidae) that I took last weekend, at Marismas de Barbate, Cádiz. It was a very nice day, cloudy, but I was lucky to get close to the birds, creeping a lot. These birds are really beautiful. The geographic distribution is very patchy in the Western Palaearctic, with few areas in the Iberian Peninsula. 

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Our study on functional extinction of frugivores, published in Science

Our new paper “Functional Extinction of Birds Drives Rapid Evolutionary Changes in Seed Size”, just published in this week issue of Science.

Mauro Galetti, Roger Guevara, Marina C. Côrtes, Rodrigo Fadini, Sandro Von Matter, Abraão B. Leite, Fábio Labecca, Thiago Ribeiro, Carolina S. Carvalho, Rosane G. Collevatti, Mathias M. Pires, Paulo R. Guimarães Jr., Pedro H. Brancalion, Milton C. Ribeiro, and Pedro Jordano. 2013. Functional Extinction of Birds Drives Rapid Evolutionary Changes in Seed Size. Science 340: 1086-1090.
DOI: 10.1126/science.1233774.

Palmito collage large

Photos, from top left, descending, to right:

1. Selenidera maculisrotris (male) handling a palmito seed.
2. Palmito fruits with beak marks, dropped beneath the palm, and regurgitated seeds.
3. Turdus flavipes trying to swallow a palmito fruit.
4. Ramphastos vitellinus (subsp. vitellinus) handling a fruit.
5. Selinedera maculirostris (male) picking a fruit.
6. Palmito seedling just after germination (note the seed still attached).
7. Palmito juçara, Euterpe edulis (Arecaceae).
8. Aburria (Pipile) jacutinga.
9. Baillonius (Pteroglossus) bailloni handling a fruit.
10. Turdus amaurochalinus (young), picking a fruit.
11. View of the ompbrphilous atlantic rainfrorest (Mata Atlántica) understory in Carlos Botelho park.
12. Penelope obscura.
13. Pyroderus scutatus, swallowing a fruit.
Photos by: Edson Endrigo, Pedro Jordano, Mauro Galetti, Marina Cortes, Guto Balieiro, and Lindolfo Souto.

The selective extinction of large frugivorous birds is associated with the rapid evolutionary reduction of seed size in a keystone palm.

Local extinctions have cascading effects on ecosystem functions, yet little is known about the potential for the rapid evolutionary change of species in human-modified scenarios. We show that the functional extinction of large-gape seed dispersers in the Brazilian Atlantic forest is associated with the consistent reduction of seed size of a keystone palm species. Among 22 palm populations, areas deprived of large avian frugivores for several decades present smaller seeds than non-defaunated forests, with negative consequences for palm regeneration. Coalescence and phenotypic selection models indicate that seed size reduction most likely occurred within the last 100 years, associated with human-driven fragmentation. The fast-paced defaunation of large vertebrates is most likely causing unprecedented changes in the evolutionary trajectories and community composition of tropical forests.

When we talk about biodiversity we normally refer to the number of species found in a given area. But these species have ecological functions that are essential to the functioning of ecosystems. The loss of a species also entails the loss of the ecological role it plays in the ecosystem, and this kind of extinction happens much unnoticed. We have documented the effect of functional extinction of large fruit-eating birds on an important plant trait – seed size – of a key plant species of the Atlantic Rainforest in Brazil, one of the biodiversity “hot-spots” on the planet. Our study is a natural experiment that takes advantage of the presence of fragmented areas of forest that have remained so since the early 1800s, when the development of crops such as coffee and sugar cane triggered the extensive deforestation of the Atlantic rainforest. Only 12% of the original forest persists, and over 80% of what remains are fragments are too small to maintain large animals. Our results show that the loss of large fruit-eating birds such as toucans leads to the size reduction of the seeds of a palm tree, which is a key species in these Atlantic forests. These evolutionary changes in fruit and seed size have occurred only in defaunated forests, where only small frugivorous birds persist. These small birds only successfully disperse smaller seeds.

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We studied 22 populations of this palm tree along the SE coast of Brazil. In the defaunated areas, which persist as fragments from several decades ago, the seed sizes are consistently smaller than in well-preserved forests, and this has negative consequences for regeneration. The smaller seed size in defaunated areas is not explained by other environmental or geographic variables. Fast natural selection: Small birds such as thrushes cannot swallow and disperse large seeds. Large birds, such as aracaris and toucans, play an important role in dispersing seeds of plants, especially of large seeds. In rainforests without toucans large seeds tend to disappear over time because undispersed seeds are attacked by seed predators. Small seeds are more vulnerable to desiccation and cannot withstand projected climate change.

We have combined a number of techniques including field work, genetic analyses, evolutionary models and statistical analyses. We collected ground data on a large number of palm trees in 22 populations, by collecting fruits, observing the avian frugivore assemblage and conducting germination experiments. We have also used DNA genetic markers to employ quantitative genetic models to estimate the intensity of selection on seed traits and coalescence theoretical models to infer the time of isolation of populations. Finally, we statistically analyzed the effect of different types of data, including climatic and environmental information, on seed size variation. 

Our work provides one of the few existing evidence that evolutionary change in natural populations can happen very fast as a direct result of changes induced by human action. The extinction of large vertebrates is happening all over the world and the implication is poorly known. These large bodied species maintain mutualistic interactions with plants: while flesh-fruited plants offer fruits as food sources, frugivores disperse their seeds. Such ecological process ensures natural regeneration of the forest. Unfortunately, the effect we document in our work is probably not an isolated case. The constant extirpation of large vertebrate in natural habitats is very likely causing unprecedented changes in evolutionary trajectories of many tropical species.

Habitat loss and species extinction is causing drastic changes in the composition and structure of ecosystems. This involves the loss of key ecosystem functions that can determine evolutionary changes much faster than we anticipated. Our work highlights the importance of identifying these key functions to quickly diagnose functional collapse of ecosystems.

Components of pollination effectiveness and their consequences in insular pollinator assemblages

Our paper “Quantity and quality components of effectiveness in insular pollinator assemblages” online in Oecologia. Thanks Cande and Alfredo. This is a field study of the pollination of Isoplexis canariensis by birds and lizards in the Canary Islands, a part of Cande Rodríguez PhD project.

Ecologically isolated habitats (e.g., oceanic islands) favor the appearance of small assemblages of pollinators, generally characterized by highly contrasted life modes (e.g., birds, lizards), and opportunistic nectar-feeding behavior. Different life modes should promote a low functional equivalence among pollinators, while opportunistic nectar feeding would lead to reduced and unpredictable pollination effectiveness (PE) compared to more specialized nectarivores.

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Dissecting the quantity (QNC) and quality (QLC) components of PE, we studied the opportunistic bird–lizard pollinator assemblage of Isoplexis canariensis from the Canary Islands to experimentally evaluate these potential characteristics. Birds and lizards showed different positions in the PE landscape, highlighting their low functional equivalence. Birds were more efficient than lizards due to higher visitation frequency (QNC). Adult lizards differed from juveniles in effecting a higher production of viable seeds (QLC). The disparate life modes of birds and lizards resulted in ample intra- and inter-specific PE variance. The main sources of PE variance were visitation frequency (both lizards and birds), number of flowers probed (lizards) and proportion of viable seeds resulting from a single visit (birds).

The non-coincident locations of birds and lizards on the PE landscape indicate potential constraints for effectiveness. Variations in pollinator abundance can result in major effectiveness shifts only if QLC is relatively high, while changes in QLC would increase PE substantially only at high QNC. The low functional equivalence of impoverished, highly contrasted pollinator assemblages may be an early diagnostic signal for pollinator extinction potentially driving the collapse of mutualistic services.

Plotting effectiveness landscapes, a companion to our paper in New Phytologist

Code for plotting the effectiveness landscape of mutualisms adding isolines of equal effectiveness values.

Effectiveness landscapes are the two-dimensional representation of the possible combinations of the quantity and the quality of mutualistic services (seed dispersal, pollination) and with elevational contours representing isoclines of effectiveness. These representations can be 2D bivariate plots of multiplicative effects of any of the seed dispersal (SDE) or pollination (PE) effectiveness components.

We have addressed these components of mutualism effectiveness for the specific case of seed dispersal mutualisms in:
Schupp, E.W., Jordano, P. & Gomez, J.M. (2010). Seed dispersal effectiveness revisited: a conceptual review. New Phytol, 188, 333–353.

A number of people have asked me about the R code we used, and it is uploaded to my github repository. The page with additional explanation is here. Enjoy!

Muriquis

Muriquis (Brachyteles arachnoides) are the largest neotropical primates and the largest mammal endemic to Brazil, reaching more than 12 kg (Reis et al., 2006). They are endemic to the SE Brazil.

Previously recorded as different subspecies, muriquis are currently recognized as two distinct species, the northern muriqui B. hypoxanthus and southern muriqui B. arachnoides (Rylands et al., 1997). Aguirre (1971) estimated that before the arrival of Europeans there were about 400,000 muriquis in the Atlantic rainforest, distributed from southern Bahia to northern Paraná, and in 1971 there were no more than 3,000 individuals. Currently the northern muriqui occurs in southern Bahia, Espirito Santo and Minas Gerais and the southern muriqui occurs in southern Rio de Janeiro, São Paulo and northern Paraná (Melo and Dias 2005, Hirsch et al., 2006).

The muriquis live in groups of more than 30 individuals present social fission-fusion system where the group is divided into independent sub-groups of variable size. When in pristine areas they have a higher home ranges, ca. 1000ha, within daily displacements more than 5 km. I was fortunate enough to watch a group of 10-11 muriquis in Intervales, relatively close to the Carmo base. They were 3 males, 2-3 juveniles and 3 females, two of them carrying babies. Some of the individuals were feeding on the catkins of Cecropia glazeouvi. I approached them on a very steep slope and observed them for ca. 30 min. They were moving slowly among the canopies of the trees but with an extraordinary agility, always helping themselves with the tail. After a period close to me they moved quickly uphill.

Muriquis are herbivores, adapted to the handling, chewing and digestion of leaves or fleshy fruits, and they also consume flowers, seeds and bamboo (Strier 1991; Talebi et al., 2005). In relation to frugivory, muriquis have lower consumption of fruits (21% to 33%) in semi-deciduous Atalantic forest (Strier 1991, Martins 2006, 2008), but more intense consumption (35% to 71%) in ombrophilous Atlantic rain forests (Petroni 1993, 2000, Carvalho et al ., 2004; Talebi et al., 2005).

My friend Rafael Bueno did his master project (finished in 2010) on this species and tapirs [Frugivoria e efetividade de dispersão de sementes dos últimos grandes frugívoros da Mata Atlântica: a anta (Tapirus terrestris) e o muriqui (Brachyteles arachnoides)]. He did a great job showing the relevance of these frugivores for the dynamics of the Atlantic forest. Many tree species (at least 28 species) critically depend on their service for seed dispersal. Rafael recorded daily movements of muriqui groups ranging between 0.5 and 5.4 km. He estimated that on average, individual muriquis may disperse ca. 11,000 seeds/year. These amazing data show how relevant plant-animal mutualistic interactions are for the maintenance of tropical forests.

R libraries in ecology

We all use the general libraries for data analysis and model fitting, but a nice thing with R is that you can interface any function with others. And a bunch of packages have been developed with ecological research in mind. Recently, Scott Chamberlain posted a good  summary of new R libraries specifically useful for ecologists.

Dolph Schluter‘s page and Rodney Dyer‘s page have interesting tips for using R in evolutionary ecology and population genetics, respectively. An additional R resource for ecologists is the R programming resource center at NCEAS and the CRAN Task View for Analysis of Ecological and Environmental Data. Finally, ecological analysis with R was the core subject of a special issue of the Journal of Statistical Software in 2007.

Here is my summary of useful R packages for ecologists. I’m including here those packages that I consider more directly related to ecology and that I’ve used most. Obviously we all use many R packages for ecological research, but the idea here is to summarize those that specifically address ecological research. Some of those libraries might remain “hidden” amidst the zillions of libraries available in R. useRs interested in ecological research should consult additional R Task Views, such as the Spatial view. Additional interesting stuff for ecologists is also available in the GeneticsMultivariate, Phylogenetics and Cluster task views, among others.

General libraries for ecological research, with multiple functions

ade4. Analysis of ecological data with exploratory and euclidean methods in environmental sciences. Basically a series of functions for multivariate data analysis and graphics. true web page is here. It also has a GUI (graphic user interface), ade4TkGUI.

adehabitatHR. A collection of tools for the estimation of home range in animals.

adehabitatHS. A collection of tools for the analysis of habitat selection by animals.

adehabitatLT. A collection of tools for the analysis of animal movement patterns.

BiodiversityR. Statistical analysis of biodiversity patterns. This is a GUI (Graphical User Interface, via the R-Commander) and some utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website.

vegan. Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

ecodist. Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community data.

bio.infer. Predict environmental conditions from biological observations.

meta. Functions for meta.analysis. Fixed and random effects meta-analysis. Functions for tests of bias, forest and funnel plot.

mra. Analysis of mark-recapture data using covariates. Models: CJS open population; Huggin’s closed population. Link functions: logit, sine, hazard. Model selection and model averaging routines. Plot methods. Simulation routine. CJS methods produce estimates of population size using the Horvitz-Thompson estimator.

popbio. Analysis of matrix population models. Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).

Hmisc. Functions useful for ecological data analysis, high-level graphics, utility operations, computing sample size and power, imputing missing values, advanced table making, etc.

vegclust. Fuzzy clustering of vegetation data. This package contains functions used to perform fuzzy clustering of vegetation data under different models.

demoniche. An R-package for simulating spatially-explicit population dynamics. Nenzén et al. 2012. Ecography, 35: 577–580. doi: 10.1111/j.1600-0587.2012.07378.x.

BioMod. Functions for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships. Thuillier et al. 2009. Ecography 32, 369–373. doi: 10.1111/j.1600-0587.2008.05742.x.

simecol. Simulation of ecological (and other) dynamic systems. Object oriented framework to simulate ecological (and other) dynamic systems. It can be used for differential equations, individual-based (or agent-based) and other models as well. The package helps to organize scenarios (avoids copy and paste) and improves readability and usability of code.

fossil. Palaeoecological and palaeogeographical analysis tools. A set of analytical tools useful in analysing ecological and geographical data sets, both ancient and modern. The package includes functions for estimating species richness (Chao 1 and 2, ACE, ICE, Jacknife), shared species/beta diversity, species area curves and geographic distances and areas.

Spatial ecology. Also see the Spatial R Task View.

spatstat. A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, and space-time point patterns in any number of dimensions.

spdep. Spatial dependence: weighting schemes, statistics and models. A collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tesselations, for summarising these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial autocorrelation, including global Moran’s I, APLE, Geary’s C, Hubert/Mantel general cross product statistic, etc.

ecespa. Functions for spatial point pattern analysis. Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on spatstat), used in the book “Introducción al Análisis Espacial de Datos en Ecología y Ciencias Ambientales: Métodos y Aplicaciones”, by Marcelino de la Cruz.

spatial. Functions for kriging and point pattern analysis.

SpatialEpi. Various spatial epidemiological analyses. Cluster detection, disease mapping.

geoR. Analysis of geostatistical data. Geostatistical analysis including traditional, likelihood-based and Bayesian methods.

Molecular ecology. Also see the Genetics R Task View. useRs interested in ecological genomics should have a look to Bioconductor and the RGenetics Project.

Geneland. Functions for detecting spatial structures from genetic data within a Bayesian framework via MCMC estimation.

adegenet. Implements a number of different methods for analysing population structure using multivariate statistics, graphics and spatial statistics.

genetics. Implements classes and methods for representing genotype and haplotype data, and has several functions for population genetic analysis (e.g. functions for estimation and testing of Hardy-Weinberg and linkage disequilibria, etc.).

HardyWeinberg. Graphical representation of HW disequilibria via ternary plots.

qtl. QTL analysis and genome-wide scans.

Network ecology 

I don’t like the name ‘network ecology’, but you probably know what I mean. R libraries developed by social scientists (e.g., sna) provide many useful functions for ecological research.

bipartite. Visualising bipartite networks and calculating some (ecological) indices. Bipartite provides functions to visualise webs and calculate a series of indices commonly used to describe pattern in ecological webs. It focusses on webs consisting of only two trophic levels, e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the webs topology.

sna. Tools for Social Network Analysis. A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, p* modeling, random graph generation, and 2D/3D network visualization.

igraph. Network analysis and visualization. Routines for simple graphs and network analysis. igraph can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality indices, etc.

tnet. Analysis of Weighted, Two-mode, and Longitudinal networks.

Evolutionary ecology

Please see Scott Chamberlain‘s blog and the Phylogenetics view task. A most useful resource is the Phylogenetic comparative methods page at NEScent. In addition:

ape. Analyses of phylogenetics and evolution.

picante. Phylocom integration, community analyses, null-models, traits and evolution.

geiger. Analysis of evolutionary diversification. Running macroevolutionary simulation, and estimating parameters related to diversification from comparative phylogenetic data.

adephylo. Exploratory analyses for the phylogenetic comparative method. Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa., community analyses, null-models, traits and evolution in R.

spacodiR. Spatial and phylogenetic analysis of community diversity. SPACoDi is primarily designed to characterise the structure and phylogenetic diversity of communities using abundance or presence-absence data of species among community plots.

phylobase. Base package for phylogenetic structures and comparative data.

ouch. Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.

phangorn. Phylogenetic analysis in R: estimation of phylogenetic trees and networks using maximum likelihood, maximum parsimony, distance methods & Hadamard conjugation.

paleotree. Paleontological and phylogenetic analyses of evolution. Analyzes, time-scales and simulates phylogenies of extinct/fossil lineages, along with calculation of diversity curves. Also fits likelihood models to estimate sampling rates from stratigraphic ranges.

phylotools. Phylogenetic tools for eco-phylogenetics. Building supermatrix for DNA barcodes using different genes, calculating the inequality among lineages and phylogenetic similarity for very large dataset using slicing methods by invoking Phylocom.


Note: To automatically install the R Task Views (i.e., groups of packages useful for some specific analysis and pre-bundled in CRAN), the ctv package needs to be installed, e.g.:

install.packages("ctv")

library("ctv")

the views can then be installed via install.views or update.views (which first assesses which of the packages are already installed and up-to-date), e.g.,
install.views("Spatial")
or  update.views("Spatial").