CHAPTER 1: GENERAL INTRODUCTION
1.1 Diversity: context and rational
1.1.2 Richness and diversity
The species richness is simply defined by the number of different species and can be established, for instance, inside a given area, at a certain time or within a community. The biological diversity or “biodiversity” is the "variation of life at all levels of biological organization" (Gaston K. J., 2004). It can refer to the species diversity, the genetic diversity, the ecosystem diversity, or to any other biological variety. For the moment, we will focus on the species diversity, which reflects both the species richness and the number of individuals from each species (Margurran, 1988).
Nowadays, the relevance of both richness and diversity seems obvious in any biological study linked to natural populations. However, these two concepts, as they are currently used in ecological context, are quite new. Indeed, taxonomy exists since thousands of years, whereas it is only in the second part of the 19th century that biologists headed toward ecology, probably in the background of an already declining environment. Ecology, introduced by Ernst Hackel (Haeckel, 1866) and initially developed by Eugenius Warming (Warming, 1895), examines the interactions of living organisms with their environment. The development of this new field reflected thus a slide in biologists’ concerns, from a particular to a global and contextual point of view. Actually, during this period, a real and deep upheaval was occurring, in the scientific thought as well as in the experimental methods.
Biology became less contemplative and was not restricted anymore to the description and study of natural examples. On the contrary, main issues were, from that moment, to understand the relationships between biotic units and abiotic factors with the inherent purpose of acting on the overall system and modifying it.
The first crucial step of the ecological approach, and also the one which will be mainly discussed in this thesis, consists in the assessment of the diversity. Since the work of Whittaker, tree levels are widely used to define the diversity: the Alpha, Beta and Gamma diversity. They are representing respectively the within-habitat, cross-habitat and regional diversity (Whittaker, 1972). Before assessing any richness or diversity level, an ecological purpose is required. For instance, studying the impacts of industrial activity on a natural swamp will imply investigations on alpha diversity, while comparing bacterial fauna from two different types of environment will involve the Beta diversity. There are several metric
ways to quantify the species richness and diversity of an ecosystem. The most common involve the calculation of the Simpson Index (Simpson, 1949), which represents the probability that two randomly selected individuals in the habitat belong to the same species, or that of the Shannon Index (Shannon, 1948), which accounts for both abundance and evenness of the species and which is maximum if each species represented is composed of the same number of individuals. Nevertheless, some ecologists consider that species number is a poor unit for evaluating biodiversity and highly depends on sampling. For that reason, Warwick and Clarke have introduced the taxonomic diversity index and the taxonomic distinctness, which both take into account the phylogenetic separation between individuals (Warwick and Clarke, 1995).
No matter what method is chosen for the diversity assessment, the work always includes the specimen counting and their identification. Once again, numerous different ways exist for counting and identifying organisms depending on the characteristics of the group studied, like its body size range or its occurrence. Identification criteria truly depend on taxa even if morphology remains, until today, widely used. However, morphological studies are sometimes insufficient or excessively time consuming as identification tool. Biochemical analyses, such as fatty acids composition, are often performed for the identity diagnosis of the smallest organisms (Cox et al., 2006; El Menyawi et al., 2000; Roberts et al., 2006). Quite rapidly after the rise of the molecular systematics in the late 1960s, the genetic information contained in the DNA and RNA also became a standard for the identification. The use of this powerful molecular tool is now more and more systematic in the identification process but the investigated regions differ depending on the group, the family or even the genus studied. For instance, DNA sequences of some nuclear genes enabled the distinction between the African elephant species Loxodonta africana and L. cyclotis (Roca et al., 2001); small subunit ribosomal DNA (SSU rDNA) has been used to identify apicomplexan parasites of tortoises (Traversa et al., 2008) and microbiologists refer either to SSU or to internal transcribed spacer (ITS) rDNA to dissociate strains of bacteria (Chen et al., 2001). In 2003, Paul Hebert proposed that partial sequences of the cytochrome c oxidase subunit I gene (COI) from the mitochondrial DNA (mtDNA) would be kinds of species specific barcodes and would provide
“a new master key for identifying species” (Hebert et al., 2003). Unfortunately, there are now clear evidences that the COI gene does not suit to identify species in all taxonomic groups either because it may be represented by heterogenous copies (Song et al., 2008) or because it
is not diverging rapidly enough (Elias et al., 2007; Huang et al., 2008). However, continuous efforts to find reliable short DNA barcodes are still produced for each taxonomic group separately and give sometimes positive results (Huse et al., 2008). Thus, DNA barcoding (if not only based on COI) offers a competitive solution for the diversity assessment and its management, since it potentially provides a fast and relatively cheap way to identify species (Rubinoff, 2006).
As for the species identification, the specimens count is performed based on direct or indirect evidences that the species is or was indeed present in the studied area. For instance, diversity of insects is usually established by in situ trapping and direct counting (Abdullah et al., 2008). For terrestrial mammals like coyotes, number of individuals is often estimated by collecting feces (Kays et al., 2008) and for bacteria, richness can be found using clone libraries of rRNA genes (Polymenakou et al., 2009). All the methods to assess the species richness and the diversity are not equally relevant and indirect evidences can sometimes be misleading. Remains and metabolites can be dragged out of their original place by the wind, the current or another organism. The best way to be sure that a species is indeed in a given area is by observing it alive directly in its ecosystem, which is of course impossible for many taxa. Moreover, some studies suggest the presence, in marine sediments, of extracellular DNA, which could be preserved for a long time after the death of the organism it comes from (Dell'Anno and Danovaro, 2005a). These “dead” DNA molecules could potentially be amplified and included in clone libraries, inducing wrong conclusions about the species richness. Finally, a particular attention should be paid to the “active part” of the diversity.
Since molecular tools are getting more and more efficient, they enable to reveal a great richness including numerous new taxa from the environmental samples. The ecological meaning of this diversity should be taken in account, since all the species recovered by molecular analysis may not be equally involved in metabolic processes of ecosystems.
After the assessment of the diversity for a given area, an ecological approach should lead to the factors that are associated with the species richness and the species occurrence in this area. Three kinds of events can modify the local species richness and thus, the diversity:
speciation, extinction and migration in and out of the studied area from and toward a regional gene pool (Gage, 2004). Thus, to identify the factors shaping the richness, it is first required to find what could generate these three events.
An ecosystem with a set of populations from different species can only support a finite amount of biomass regarding its physicochemical characteristics like, for instance, light exposure, resources availability or nesting sites. There are two opposite ways to consider the populations occupying the ecosystem. The first one is based on the ecological niches concept (ENC) assuming that each species possesses its own characteristics, which make it suitable to occupy a particular space, so called “niche” (Grinnell, 1917). It implies that each species has a different fitness regarding the environment. After a certain time, a niche will be occupied by only one species: the one with the greatest fitness. Grinnell presents the niche as a property of the environment. According to him, the nature will supply to each new niche a new occupant, selected by evolutionary processes. However, it remains unclear whether new species are indeed produced by niches creation or whether competing species tend to use different resources to avoid competition and so, create niches. In the latter case, ecosystems should evolve by partitioning natural niches and would continuously increase their species number.
Evidently, Grinnell’s concept could be criticized for being totally devoted of randomness, since it implies that new species could only be produced by competition.
The other way to consider populations occupying an ecosystem refers to the neutral theory of Kimura, which gives a predominant place to genetic random drifts in evolution (Kimura, 1979). This will lead Hubbell to later introduce the unified neutral theory of biodiversity (UNTB), setting that all species and individuals of the same trophic level are equivalent (Hubbell, 2001). In other words, all species have “neutral” differences and similar chance of success in a given ecosystem: they have thus similar fitness. Considering a closed ecosystem and according to the UNTB, genetic drift would induce speciation at the same global frequency for each population. At the beginning of this process, population’s size could be large and obey to the same deterministic models, for instance, prey-predator interactions. When preys population increases, predator population increases too, inducing a growing consumption of preys and so on, until an equilibrium state. Balances will be successively reached between populations of smaller and smaller size, while species are drifting and speciation is occurring. As a consequence, the number of species should continuously increase with a decreasing size of their respective populations, since those sympatric species are competing for similar resources. The UNTB predicts that this process will go on and on until the populations size becomes so small that species obey to stochastic models. Random events (like fire or disease) will eliminate species as fast as others will
appear, producing, this time, an equilibrium between species (Levinton, 1979). This vision meets somehow the theory of island biogeography, describing the colonization process of a virgin island. A steady-state of the species richness is reached when there is equilibrium between immigration and local extinction (MacArthur and Wilson, 1967). According to UNTB, any new ecosystem will evolve by continuously increasing its species richness and decreasing its species respective abundance until equilibrium, where the system is biotically saturated with individuals. Thus, at steady state and without any perturbation of the system, species richness would be predictable (maximized regarding the area size) and population densities constant. These conclusions, only valid for species competing at the same trophic level, induce that diversity per unit area would tend to be the same everywhere.
Both ENC and UNTB agree that the species richness of an undisturbed area will increase with time. Assuming that, it becomes clearer that there are no factors directly associated with the species richness and the species occurrence, but rather different evolution states from the moment when the system was disturbed. Area with low species richness would thus be young ecosystem resulting from new niches partitioning or having been recently disturbed and passed through a bottleneck. Other way round, hotspots of diversity would be old undisturbed system close to the steady state.