You will find here a summary of the research I have conducted the past couple of years. My main focus is to understand the mechanisms underlying the distribution of biodiversity across different spatial and temporal scales and I am particularly interested in working at the interface between different levels of biodiversity, from variation within species (genes, traits) to variation among ecosystems. Specifically, my approach builds on the metapopulation and the metacommunity concepts to understand how local dynamics of populations and communities generate patterns at larger spatial scales. At the population level, my research has challenged the metapopulation concept using both demographic and genetic data, and has resulted in a better understanding of the interplay between ecological and evolutionary dynamics. At the community level, I have tackled the problem of how species diversity covaries with genetic diversity in complex landscapes using a synthesis of empirical and theoretical approaches. I am also focused on characterizing the spatial and temporal scales at which biodiversity varies in response to natural and anthropogenic drivers based on long-term survey data. I have so far focused on three main ecosystems: freshwater rivers and ponds from the West-Indies, coral reefs in French Polynesia and kelp forests off the California coast.
The four main axes of my research are the following:
1. challenging metapopulation theory using demographic and genetic data
2. understanding the interplay between ecological and evolutionary dynamics in a metacommunity
3. unifying genetic and species diversity theory
4. quantifying pattern of biodiversity across temporal and spatial scales
Research axe 1: challenging metapopulation theory using demographic and genetic data
The metapopulation concept is central in modern ecological and evolutionary literature as it allows the integration of local processes with landscape scale dynamics. Surprisingly, however, there are few empirical examples of metapopulation dynamics. Work on metapopulations has long been hindered by the difficulty of detecting species in field surveys, as well as by the existence of unobservable forms in many species (e.g., seed banks in plants, resting eggs in animals). Although these issues have been raised for many years, my research was one of the first to tackle them in a common framework and quantify how the presence of cryptic forms may bias the estimation of critical metapopulation parameters.
To achieve this goal, I worked on a freshwater snail metacommunity that inhabits a network of ephemeral ponds on a tropical island (Guadeloupe, Lesser Antilles). Some of these ponds are permanent, but many of them completely dry out, either yearly or more irregularly, during the dry season. Rainfall during the rainy season causes overflow of many of these freshwater environments, inducing transient aquatic connection of ponds belonging to the same catchment area. Freshwater snails are the most common species in these habitats and include twenty-nine species exhibiting short life cycles and various life-history strategies including simultaneous hermaphrodites.
The freshwater snail metacommunity from the Guadeloupe archipelago
I conducted intensive fieldwork (yearly community and environmental surveys of 240 sites for three years, designed to be compatible with a previous eight-year survey), and assessed the spatio-temporal genetic composition of 42 populations, that I genotyped at microsatellite markers, of one focal snail species, Drepanotrema depressissimum, which relies on aestivation to persist in desiccated ponds. I detected no genetic signatures of extinction events based on temporal changes in allele frequencies, even when demographic surveys suggested otherwise or when ponds were totally desiccated (Lamy et al. 2012 Mol Ecol).
Based on these striking results I developed a general multistate occupancy model that allows estimation of species persistence for both normal and resistant forms and take into account species detectability issues. This model successfully predicted the dynamics of the resistant form and removed biases inherent to more naive models (Lamy et al. 2013 Am Nat). Based on this model we made the striking discovery that the persistence of the species was much higher at unstable sites, whereas its extinction probability was much higher in more speciose and stable sites. This result suggests that this species exhibits a persistence-competition trade-off and adds to our understanding of species coexistence mechanisms.
The methodology I developed to take into account these hidden stages (Lamy et al. 2013 Am Nat) is widely applicable, and for it I received the MCED award for young modelers from the Ecological Society of Germany, Austria and Switzerland in 2013. I also extended this model to other species of the snail metacommunity and results suggest that the ability to tolerate habitat instability varies greatly among species and may be an important trait underlying species coexistence.
Research axe 2: understanding the interplay between ecological and evolutionary dynamics in a metacommunity
Metapopulation and metacommunity dynamics can have a strong influence on the evolution of species life-history traits, which in turn play a key role in affecting species persistence and coexistence. Using the Guadeloupe freshwater snail metacommunity, I tested how ecological and evolutionary dynamics could interact with each other. For instance, in simultaneous hermaphroditic species the ability to self fertilize can be a major competitive advantage as it provides reproductive assurance when mates are scarce, such as when colonizing new sites. Hence, I tested whether metapopulation dynamics could drive the evolution of self fertilization toward higher selfing rates as a response of habitat instability in the species D. depressissimum. To that aim I measured selfing rates based on molecular data and detected no sign of selfing in natural populations (Lamy et al. 2012 Evol Ecol, Lamy et al. 2012 Mol Ecol, Lamy et al. 2013 Mol Ecol). Next I sampled natural populations and conducted a quantitative genetics experiment to test how self-fertilized individuals performed in common-garden conditions and found they suffered near-total inbreeding depression. These results suggest that D. depressissimum may overcome periods of mate shortage associated with habitat instability without relying on selfing, and the metapopulation persistence of this species is probably due to its dormant form rather than through recolonization by rare immigrants.
Species interactions are also important determinants of coexistence in a metacommunity; for example, species with overlapping niches may mutually exclude each other. In the Guadeloupe freshwater snail metacommunity this issue is particularly relevant, since only half of the 29 recorded species are native as a result of repeated introductions over the last 50 years. We found that a pair of closely related species, one native and one nonnative, occupy a similar niche, yet they persist in the metacommunity. In a collaborative effort we tested whether the coexistence of these species could be explained through rapid evolution and character displacement. We compared in the lab, populations of the two related freshwater snails that have been in contact for varying time periods, as documented by long-term survey data. We found that after a few years of contact, populations of the two species diverged in life-history trait space, mostly as a consequence of fast evolution of the native species towards an ‘r-selected’ strategy (Chapuis et al. Submitted). The evolutionary response of species traits in ecological time are a poorly explored aspect of species coexistence with strong ramifications for theories of species interaction and persistence in metacommunities.
Invasions and coexistence of species occupying similar niches through adaptative character displacement. Site occupancy through time of Physa acuta (red), and Aplexa marmorata (blue) derived from Bayesian hierarchical occupancy models. P. acuta invaded freshwater habitat in less than ten years and occupies the same environmental niche as the native species A. marmorata. A study of life-history traits in both species reveals adaptative character displacement in the native species toward r-like reproductive strategy.
Research axe 3: unifying genetic and species diversity theory: toward a theoretical and methodological framework to understand the distribution of both genes and species
The similarities between neutral theories of genetic diversity and species diversity are striking. This observation led to the idea that parallel effects of different processes on both levels of diversity should promote non-random relationships between species diversity and neutral genetic diversity. Specifically, variation in size and connectivity among sites within a metacommunity should generate positive correlations between the genetic diversity within species and species diversity, so-called species-genetic diversity correlations (SGDCs). I tested this prediction using the Guadeloupe freshwater snail metacommunity by combining long-term ecological surveys with the genetic diversity of 75 populations of two focal species that I assessed at microsatellite markers. I found highly significant correlations between the genetic diversity of the two species and the species diversity of local communities (Lamy et al. 2013 Mol Ecol). Next, I tested whether parallel processes (such as migration or drift) were affecting both genes and species in the same way. To do this, I developed a framework to quantify the importance of different habitat characteristics (e.g. habitat instability, landscape connectivity, patch size) underlying these correlations. I showed that landscape connectivity was responsible for 59 to 71% of the SGDCs but that other variables could contribute negatively such as habitat instability. These results suggest that SGDCs arise due to migration, as most species display the same passive dispersal mode. This study supported the intuitive idea that positive SGDCs should be a common pattern in nature.
However, the assumptions behind this assertion rely only on neutral processes (drift, migration) and are likely overly simplistic. We developed the first neutral theory of both genes and species to study SGDCs in metacommunities and provided the theoretical evidence that positive SGDCs emerge under purely neutral assumptions (Laroche et al. 2015 Am Nat). However, we also showed that negative SGDCs can arise under certain neutral circumstances, for example when mutation rate is high.
In a synthesis paper we further showed that although a large number of published SGDCs are portrayed as positive, only 17% of them are statistically significant, a fraction that is similar to the significantly negative ones (Lamy et al. submitted). Indeed, ecological equivalence among species, which lies at the core of the neutral theory of biodiversity, does not hold in many ecological systems. We extended our neutral model of SGDCs to include both neutral and non-neutral processes into a common conceptual framework. Our aim is to outline a larger set of factors that can potentially affect SGDCs either positively or negatively. To clarify these ideas and direct future research we introduced three categories of factors affecting SGDCs and provided methods that allow decomposition of any empirical SGDC into the positive and negative contributions of a given factor (Lamy et al. submitted).
Research axe 4: quantifying pattern of biodiversity across temporal and spatial scales
Since I have started the postdoctoral adventure in 2012, I have developed my quantitative skills to gain a better understanding of the factors that can affect variation in species composition across temporal and spatial scales. To achieve this goal, I have developed and relied on diverse set of sophisticated multivariate methods to deal with long-term community surveys from two ecosystems: coral reefs from the island of Moorea in French Polynesia (Pacific Ocean) and temperate reefs from the Santa Barbara Channel in California. In Moorea, my research has helped to characterize the mechanisms shaping coral reef ecosystems in the face of severe natural disturbances. Based on three decades of data, I showed that the structure and function of fish and coral communities were consistently changing over time solely due to the impact of repeated natural disturbances. This result highlights the importance of historical contingency to understanding present day coral reef condition (Lamy et al. 2016 Coral Reefs).
At a shorter temporal scale (one decade), I further investigated the taxonomic and functional changes associated with a major disturbance – the outbreak of a coral predator, the crown of thorn starfish. Crown of thorns led to a 90% decline in coral cover (Lamy et al. 2015 Plos One), apparently degrading habitat quality for fishes. Yet I showed that fish biomass remained extremely stable through this disturbance and fish composition remained spatially heterogeneous. However, there were compensatory changes among species: in particular, herbivores were favored as predation on corals increased algal abundance. This response in the fish community maintained a high level of grazing pressure, a key mechanism of resilience and future recovery in these ecosystems (Lamy et al. 2015 Plos One).
Spatial redundancy in the temporal responses of herbivore species to natural disturbances promotes resilience of coral reefs in Moorea. These are the seven species that displayed the most important temporal changes in response to two natural disturbances (left figure). In the middle figure, polygon lengths are proportional to the species temporal response. Positive response (in blue) indicate species whose biomasses increased through time, while negative response (red) indicate species whose biomasses decreases through time. Right figure: Biomass through time for two species at two different reefs.
More recently I began working as a postdoctoral researcher on a new NASA-funded Marine Biodiversity Observation Network at UCSB, where I am collaborating with multiple faculty and researchers across departments. Using a set of temperate reef data of unprecedented spatial and temporal resolution, my aim is to characterize the scales at which major community changes are occurring and understand the corresponding drivers. This work will enable prediction and detection of change in marine communities over time as climate changes.