Christine N. Meynard

Spatial mismatch and congruence between taxonomic, phylogenetic and functional diversity: the need for integrative conservation strategies in a changing world

Functional and phylogenetic diversity are increasingly quantified in various fields of ecology and conservation biology. The need to maintain diversity turnover among sites, so-called beta-diversity, has also been raised in theoretical and applied ecology. In this study, we propose the first comprehensive framework for the large-scale mapping of taxonomic, phylogenetic and functional diversity and of their respective turnover. Using high-resolution data on the spatial distribution and abundance of birds at a country scale, we disentangled areas of mismatches and congruencies between biodiversity components. We further revealed unequal representation of each component in protected areas: functional diversity was significantly under-represented whereas taxonomic diversity was significantly over-represented in protected areas. Our results challenge the use of any one diversity component as a surrogate for other components and stress the need to adopt an integrative approach to biodiversity conservation.

Ecophylogenetics: advances and perspectives

Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast‐growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science.

Protected and Threatened Components of Fish Biodiversity in the Mediterranean Sea

The Mediterranean Sea (0.82% of the global oceanic surface) holds 4%-18% of all known marine species (~17,000), with a high proportion of endemism [1, 2]. This exceptional biodiversity is under severe threats [1] but benefits from a system of 100 marine protected areas (MPAs). Surprisingly, the spatial congruence of fish biodiversity hot spots with this MPA system and the areas of high fishing pressure has not been assessed. Moreover, evolutionary and functional breadth of species assemblages [3] has been largely overlooked in marine systems. Here we adopted a multifaceted approach to biodiversity by considering the species richness of total, endemic, and threatened coastal fish assemblages as well as their functional and phylogenetic diversity. We show that these fish biodiversity components are spatially mismatched. The MPA system covers a small surface of the Mediterranean (0.4%) and is spatially congruent with the hot spots of all taxonomic components of fish diversity. However, it misses hot spots of functional and phylogenetic diversity. In addition, hot spots of endemic species richness and phylogenetic diversity are spatially congruent with hot spots of fishery impact. Our results highlight that future conservation strategies and assessment efficiency of current reserve systems will need to be revisited after deconstructing the different components of biodiversity.

A phylogenetic perspective on the evolution of Mediterranean teleost fishes.

The Mediterranean Sea is a highly diverse, highly studied, and highly impacted biogeographic region, yet no phylogenetic reconstruction of fish diversity in this area has been published to date. Here, we infer the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank. We assembled a DNA supermatrix composed of four mitochondrial genes (12S ribosomal DNA, 16S ribosomal DNA, cytochrome c oxidase subunit I and cytochrome b) and two nuclear genes (rhodopsin and recombination activating gene I), including 62% of Mediterranean teleost species plus 9 outgroups. Maximum likelihood and Bayesian phylogenetic and dating analyses were calibrated using 20 fossil constraints. An additional 124 species were grafted onto the chronogram according to their taxonomic affinity, checking for the effects of taxonomic coverage in subsequent diversification analyses. We then interpreted the time-line of teleost diversification in light of Mediterranean historical biogeography, distinguishing non-endemic natives, endemics and exotic species. Results show that the major Mediterranean orders are of Cretaceous origin, specifically ∼100–80 Mya, and most Perciformes families originated 80–50 Mya. Two important clade origin events were detected. The first at 100–80 Mya, affected native and exotic species, and reflects a global diversification period at a time when the Mediterranean Sea did not yet exist. The second occurred during the last 50 Mya, and is noticeable among endemic and native species, but not among exotic species. This period corresponds to isolation of the Mediterranean from Indo-Pacific waters before the Messinian salinity crisis. The Mediterranean fish fauna illustrates well the assembly of regional faunas through origination and immigration, where dispersal and isolation have shaped the emergence of a biodiversity hotspot.

Uncertainties in predicting species distributions under climate change: a case study using Tetranychus evansi (Acari: Tetranychidae), a widespread agricultural pest.

Many species are shifting their distributions due to climate change and to increasing international trade that allows dispersal of individuals across the globe. In the case of agricultural pests, such range shifts may heavily impact agriculture. Species distribution modelling may help to predict potential changes in pest distributions. However, these modelling strategies are subject to large uncertainties coming from different sources. Here we used the case of the tomato red spider mite (Tetranychus evansi), an invasive pest that affects some of the most important agricultural crops worldwide, to show how uncertainty may affect forecasts of the potential range of the species. We explored three aspects of uncertainty: (1) species prevalence; (2) modelling method; and (3) variability in environmental responses between mites belonging to two invasive clades of T. evansi. Consensus techniques were used to forecast the potential range of the species under current and two different climate change scenarios for 2080, and variance between model projections were mapped to identify regions of high uncertainty. We revealed large predictive variations linked to all factors, although prevalence had a greater influence than the statistical model once the best modelling strategies were selected. The major areas threatened under current conditions include tropical countries in South America and Africa, and temperate regions in North America, the Mediterranean basin and Australia. Under future scenarios, the threat shifts towards northern Europe and some other temperate regions in the Americas, whereas tropical regions in Africa present a reduced risk. Analysis of niche overlap suggests that the current differential distribution of mites of the two clades of T. evansi can be partially attributed to environmental niche differentiation. Overall this study shows how consensus strategies and analysis of niche overlap can be used jointly to draw conclusions on invasive threat considering different sources of uncertainty in species distribution modelling.

Evidence of environmental niche differentiation in the striped mouse (Rhabdomys sp.): inference from its current distribution in southern Africa

The aim of this study was to characterize environmental differentiation of lineages within Rhabdomys and provide hypotheses regarding potential areas of contact between them in the Southern African subregion, including the Republic of South Africa, Lesotho, and Namibia. Records of Rhabdomys taxa across the study region were compiled and georeferenced from the literature, museum records, and field expeditions. Presence records were summarized within a 10 × 10 km grid covering the study area. Environmental information regarding climate, topography, land use, and vegetation productivity was gathered at the same resolution. Multivariate statistics were used to characterize the current environmental niche and distribution of the whole genus as well as of three mitochondrial lineages known to occur in southern Africa. Distribution modeling was carried out using MAXENT in order to generate hypotheses regarding current distribution of each taxa and their potential contact zones. Results indicate that the two species within Rhabdomys appear to have differentiated across the precipitation/temperature gradient present in the region from east to west. R. dilectus occupies the wettest areas in eastern southern Africa, while R. pumilio occupies the warmer and drier regions in the west, but also penetrates in the more mesic central part of the region. We provide further evidence of environmental differentiation within two lineages of R. dilectus. Contact zones between lineages appear to occur in areas of strong environmental gradients and topographic complexity, such as the transition zones between major biomes and the escarpment area where a sharp altitudinal gradient separates coastal and plateau areas, but also within more homogeneous areas such as within grassland and savannah biomes. Our results indicate that Rhabdomys may be more specialized than previously thought when considering current knowledge regarding mitochondrial lineages. The genus appears to have differentiated along two major environmental axes in the study region, but results also suggest dispersal limitations and biological interactions having a role in limiting current distribution boundaries. Furthermore, the projection of the potential geographic distribution of the different lineages suggests several contact zones that may be interesting study fields for understanding the interplay between ecological and evolutionary processes during speciation.

FishMed: traits, phylogeny, current and projected species distribution of Mediterranean fishes, and environmental data

The FishMed database provides traits, phylogeny, current and projected species distribution of Mediterranean fishes, and associated sea surface temperature (SST) from the regional oceanic model NEMOMED8. Data for the current geographical distributions of 635 Mediterranean fish species were compiled from a published expert knowledge atlas of fishes of the northern Atlantic and the Mediterranean (FNAM) edited between 1984 and 1986 and from an updated exotic fish species list. Two future sets of projected species distributions were obtained for the middle and end of the 21st century by using an ensemble forecasting approach for 288 coastal Mediterranean fish species based on SST according to the IPPC/SRES A2 scenario implemented with the Mediterranean climatic model NEMOMED8. The functional part of the database encompasses 12 biological and ecological traits (maximal and common lengths, vertical distribution, habitat, migration type, mode of reproduction, sex shift, semelparity, diet type (larvae and adults), social behavior, species origin, and depth) for the 635 fish species. To build the phylogeny we inferred the timing and geographic origins of Mediterranean teleost species diversity using nucleotide sequences collected from GenBank including 62% of Mediterranean teleost species plus nine outgroups. Maximum likelihood Bayesian phylogenetic and dating analyses were calibrated using 20 fossil species. An additional 124 fish species were grafted onto the chronogram according to their taxonomic affinity to obtain a phylogenetic tree including 498 species. Finally we also present the associated SST data for the observed period (1961–1980) and for the middle (2040–2059) and the end of the 21st century (2080–2099) obtained from NEMOMED8 according to the IPCC A2 scenario. The FishMed database might be of interest in the context of global anthropogenic changes as coastal Mediterranean ecosystems are currently recognized as one of the most impacted ecosystems on earth.

Comparing alternative systematic conservation planning strategies against a politically driven conservation plan

Decisions regarding the level of detail included in conservation planning and the importance given to feasibility considerations can greatly influence management in terms of total area required, achievement of conservation targets and costs. This work had two main objectives: (1) to compare priority sites proposed by the Chilean commission for the environment in a politically driven process to the results of alternative systematic conservation planning scenarios; and (2) to compare the efficacy of systematic conservation planning based on different types of conservation targets (forest types and bird species) and minimum area thresholds. To address these issues, we used vegetation cover as well as field data on forest birds in central Chile. Bird species distributions were modeled using a variety of climatic and environmental layers, allowing for the integration of environmental heterogeneity into the planning process. We then ran several conservation planning scenarios considering conservation targets based on vegetation types alone, birds alone, or a combination of vegetation and birds. Collectively these results show that conservation planning results differ significantly when considering birds or vegetation types, and that minimum area requirements for each conservation feature has a great influence on the final results. Moreover, important conservation sites are not represented in the current government plan, and these sites are related to the small representation of rare vegetation types. This study suggests that using appropriate minimum area requirements can greatly affect the results of a conservation planning exercise and therefore represents a key knowledge gap in the region.

Space use variation in co-occurring sister species: response to environmental variation or competition?

Coexistence often involves niche differentiation either as the result of environmental divergence, or in response to competition. Disentangling the causes of such divergence requires that environmental variation across space is taken into account, which is rarely done in empirical studies. We address the role of environmental variation versus competition in coexistence between two rodent species: Rhabdomys bechuanae (bechuanae) and Rhabdomys dilectus dilectus (dilectus) comparing their habitat preference and home range (HR) size in areas with similar climates, where their distributions abut (allopatry) or overlap (sympatry). Using Outlying Mean Index analyses, we test whether habitat characteristics of the species deviate significantly from a random sample of available habitats. In allopatry, results suggest habitat selection: dilectus preferring grasslands with little bare soil while bechuanae occurring in open shrublands. In sympatry, shrubland type habitats dominate and differences are less marked, yet dilectus selects habitats with more cover than bechuanae. Interestingly, bechuanae shows larger HRs than dilectus, and both species display larger HRs in sympatry. Further, HR overlaps between species are lower than expected. We discuss our results in light of data on the phylogeography of the genus and propose that evolution in allopatry resulted in adaptation leading to different habitat preferences, even at their distribution margins, a divergence expected to facilitate coexistence. However, since sympatry occurs in sites where environmental characteristics do not allow complete species separation, competition may explain reduced inter-species overlap and character displacement in HR size. This study reveals that both environmental variation and competition may shape species coexistence.

Mapping diversity indices: not a trivial issue

Mapping diversity indices, that is estimating values in all locations of a given area from some sampled locations, is central to numerous research and applied fields in ecology. Two approaches are used to map diversity indices without including abiotic or biotic variables: (i) the indirect approach, which consists in estimating each individual species distribution over the area, then stacking the distributions of all species to estimate and map a posteriori the diversity index, (ii) the direct approach, which relies on computing a diversity index in each sampled locations and then to interpolate these values to all locations of the studied area for mapping. For both approaches, we document drawbacks from theoretical and practical viewpoints and argue about the need for adequate interpolation methods. First, we point out that the indirect approach is problematic because of the high proportion of rare species in natural communities. This leads to zero-inflated distributions, which cannot be interpolated using standard statistical approaches. Secondly, the direct approach is inaccurate because diversity indices are not spatially additive, that is the diversity of a studied area (e.g. region) is not the sum of the local diversities. Therefore, the arithmetic variance and some of its derivatives, such as the variogram, are not appropriate to ecologically measure variation in diversity indices. For the direct approach, we propose to consider the β-diversity, which quantifies diversity variations between locations, by the mean of a β-gram within the interpolation procedure. We applied this method, as well as the traditional interpolation methods for comparison purposes on different faunistic and floristic data sets collected from scientific surveys...