Accounting for uncertainty in predictions of a marine species: Integrating population genetics to verify past distributions

We develop a new perspective on the uncertainties affecting the predictions of coastal species distributions using patterns of genetic diversity to assess the congruence of hindcasted distribution models. We model the niche of the subtidal seagrass Cymodocea nodosa, for which previous phylogeographic findings are used to contrast hypotheses for the Last Glacial Maximum (LGM) in the Mediterranean and adjacent Atlantic coastal regions. We focus on amelioration of sampling bias, and explore the influence of other sources of uncertainty such as the number of variables, Ocean General Circulation Models (OGCMs), and thresholds used. To do that, we test geographical and environmental filtering of presences, and a species-specific weighted filter related to political boundaries for background data. Contrary to our initial hypothesis that reducing sampling bias by means of geographical, environmental or background filtering would enhance predictive power and reliability of the models, none of these approaches consistently improved performance. These counter-intuitive results might be explained by the higher relative occurrence area (ROA) inherent to linear coastal study areas in relation to terrestrial regions, which may cause worse predictions and, thus, higher variability among models. We found that the Ocean General Circulation Models (OGCMs), the threshold and, to a smaller extent, the number of variables used, conditioned greatly the variability of the predictions in both accuracy and geographic range. Despite these uncertainties, all models achieved the goal of identifying long-term persistence regions (glacial refugia) where the highest genetic diversity for Cymodocea nodosa is found nowadays. However, only the CCSM corroborated the hypothesis, raised in previous studies, of a vicariant process in shaping the species' genetic structure. (C) 2017 Elsevier B.V. All rights reserved.Fundacao para a Ciencia e a Tecnologia (FCT, Portugal) [SFRH/BPD/85040/2012]Pew Foundation (USA)[UID/Multi/04326/2013]info:eu-repo/semantics/publishedVersio

Abandonment of traditional saltworks facilitates degradation of halophytic plant communities and Carpobrotus edulis invasion

Aims In Mediterranean countries, traditional salt exploitation has been practiced over centuries. However, there is a progressive reduction of active saltworks, causing changes in the adjacent halophytic communities and, ultimately, the invasion by opportunistic plant species. Assessing the impact of land use change is key to understanding and protecting these fragile wetland ecosystems. Here, we explore how the abandonment of saltworks is impacting plant communities. We assess if the reduction in saltworks activity alters the composition of protected halophytic communities and favours the invasion by Carpobrotus edulis, an invasive species in many coastal regions throughout the world. Location The Natural Park of Ria Formosa (Algarve, Portugal). Methods We studied variations in the structure of halophytic communities affected to different degrees by C. edulis over three saltworks land use regimes in the Ria Formosa. Plant cover and soil salinity were estimated in a total of 60 transects pertaining to two saltworks complexes harbouring different land use and hydrologic regimes. We performed a non-metric multidimensional scaling ordination of saltworks based on plant cover and identified the indicator species of each saltworks class. Results We found that plant communities significantly varied among types of saltworks according to the pattern of soil salinity and hydrologic regime. We identified C. edulis as the main indicator species of the abandoned saltworks' communities, characterized by less saline soils and being desiccated in summer. Conclusions Land-use change caused by the abandonment of salinas facilitated the transition of halophytic into psammophytic communities and the invasiveness of C. edulis. The maintenance of traditional saltworks activities is vital for the preservation of this fragile wetland ecosystem.FCT - Foundation for Science and TechnologyPortuguese Foundation for Science and Technology [UID/Multi/04326/2019]FCT project PORBIOTA through a postdoctoral fellowshipUniversity of Algarv

Niche conservatism and spread of seaweed invasive lineages with different residence time in the Mediterranean Sea

Marine algae invasions attract a lot of interest as they are altering the structure of marine ecosystems. However, niche dynamics and risk predictions of marine invasions integrating phylogeographic structure in the analyses have not yet been investigated. In this study, we perform a comprehensive analysis of two invasive lineages of Caulerpa taxifolia with different residence time in the Mediterranean Sea for a better understanding of their invasive processes. We performed lineage-based and species-based niche models to assess the risk of invasion, the spatial overlap, and the variables delimiting the distribution of the two lineages. We also compared the effect of using different extents on niche overlap and niche shift analyses. Intraspecific models with pooled occurrences accurately found two separate regions susceptible of invasion for each invasive lineage in the Mediterranean, while species-based predictions underestimated invaded regions. The invasive lineages spread across colder coastal areas than the species. Altogether, we provide evidence that different invasive lineages of algae show dissimilar environmental responses and invasive ranges that are not detectable by species-based analyses. Moreover, niche overlap and niche shift analyses seem to depend greatly on the geographical extent used. According to the most appropriate extent (worldwide), the invaded range did not show niche shift, and thus, no evidence of a post-introduction adaptation scenario was found as both lineages invaded habitats similar to their Australian native locations. Actions to prevent further spreading of the most recent invasive lineage are needed.SFRH/BPD/109452/2015info:eu-repo/semantics/publishedVersio

Modelos predictivos aplicados a la conservación de invertebrados protegidos ibero-baleares

Tesis doctoral inédita. Universidad Autónoma de Madrid, Facultad de Ciencias, Departamento de Biología. Fecha de lectura: 05-05-201

Environmental niche divergence among three dune shrub sister species with parapatric distributions

Background and Aims The geographical distributions of species are constrained by their ecological requirements. The aim of this work was to analyse the effects of environmental conditions, historical events and biogeographical constraints on the diversification of the three species of the western Mediterranean shrub genus Stauracanthus, which have a parapatric distribution in the Iberian Peninsula. Methods Ecological niche factor analysis and generalized linear models were used to measure the response of all Stauracanthus species to the environmental gradients and map their potential distributions in the Iberian Peninsula. The bioclimatic niche overlap between the three species was determined by using Schoener's index. The genetic differentiation of the Iberian and northern African populations of Stauracanthus species was characterized with GenalEx. The effects on genetic distances of the most important environmental drivers were assessed through Mantel tests and non-metric multidimensional scaling. Key Results The three Stauracanthus species show remarkably similar responses to climatic conditions. This supports the idea that all members of this recently diversified clade retain common adaptations to climate and consequently high levels of climatic niche overlap. This contrasts with the diverse edaphic requirements of Stauracanthus species. The populations of the S. genistoides-spectabilis clade grow on Miocene and Pliocene fine-textured sedimentary soils, whereas S. boivinii, the more genetically distant species, occurs on older and more coarse-textured sedimentary substrates. These patterns of diversification are largely consistent with a stochastic process of geographical range expansion and fragmentation coupled with niche evolution in the context of spatially complex environmental fluctuations. Conclusions: The combined analysis of the distribution, realized environmental niche and phylogeographical relationships of parapatric species proposed in this work allows integration of the biogeographical, ecological and evolutionary processes driving the evolution of species adaptations and how they determine their current geographical ranges.FCT [UID/Multi/04326/2013, SFRH/BD/65659/2009, SFRH/BPD/85040/2012]; Portuguese FCT project COMDUNES [EXPL/BIA-BIC/2311/2013]; FCT BI grant by project COMDUNES; Atraccion de Talento Investigador Programme (Gobierno de Extremadura) [TA13032]info:eu-repo/semantics/publishedVersio

Landscape metrics as indicators of coastal morphology and its use in ecological niche modelling of seagrass species

Dependence of some species on landscape structure has been proved in numerous studies. So far, however, little progress has been made in the integration of landscape metrics in the prediction of species associated with coastal features. Specific landscape metrics were tested as predictors of coastal shape using three coastal features of the Iberian Peninsula (beaches, capes and gulfs) at different scales. We used the landscape metrics in combination with environmental variables to model the niche and find suitable habitats for a seagrass species (Cymodocea nodosa) throughout its entire range of distribution. Landscape metrics able to capture variation in the coastline enhanced significantly the accuracy of the models, despite the limitations caused by the scale of the study. We provided the first global model of the factors that can be shaping the environmental niche and distribution of C. nodosa throughout its range. Sea surface temperature and salinity were the most relevant variables. We identified areas that seem unsuitable for C. nodosa as well as those suitable habitats not occupied by the species. We also present some preliminary results of testing historical biogeographical hypotheses derived from distribution predictions under Last Glacial Maximum conditions and genetic diversity data

Marine forests of the Mediterranean-Atlantic Cystoseira tamariscifolia complex show a southern Iberian genetic hotspot and no reproductive isolation in parapatry

Climate-driven range-shifts create evolutionary opportunities for allopatric divergence and subsequent contact, leading to genetic structuration and hybrid zones. We investigate how these processes influenced the evolution of a complex of three closely related Cystoseira spp., which are a key component of the Mediterranean-Atlantic seaweed forests that are undergoing population declines. The C. tamariscifolia complex, composed of C. tamariscifolia s.s., C. amentacea and C. mediterranea, have indistinct boundaries and natural hybridization is suspected. Our aims are to (1) infer the genetic structure and diversity of these species throughout their distribution ranges using microsatellite markers to identify ancient versus recent geographical populations, contact zones and reproductive barriers, and (2) hindcast past distributions using niche models to investigate the influence of past range shifts on genetic divergence at multiple spatial scales. Results supported a single, morphologically plastic species the genetic structure of which was incongruent with a priori species assignments. The low diversity and low singularity in northern European populations suggest recent colonization after the LGM. The southern Iberian genetic hotspot most likely results from the role of this area as a climatic refugium or a secondary contact zone between differentiated populations or both. We hypothesize that life-history traits (selfing, low dispersal) and prior colonization effects, rather than reproductive barriers, might explain the observed genetic discontinuities.Pew Charitable Trusts (USA); MARINERA, Spain [CTM2008-04183-E/MAR]; FCT (Portugal) [FCT-BIODIVERSA/004/2015, CCMAR/Multi/04326/2013, SFRH/BPD/107878/2015, SFRH/BPD/85040/2012]; FPU fellowship of the Spanish Ministry of Education; European Community ASSEMBLE visiting grant [00399/2012]; University of Cadi

Can we use niche models of indicator species to predict the distribution of endangered communities?

European-wide conservation policies are based on the identification of priority habitats. However, research on conservation biogeography often relies on the results and projections of species distribution models to assess species' vulnerability to global change. We assess whether the distribution and structure of threatened communities can be predicted by the suitability of the environmental conditions for their indicator species. We present some preliminary results elucidating if using species distribution models of indicator species at a regional scale is a valid approach to predict these endangered communities. Dune plant assemblages, affected by severe conditions, are excellent models for studying possible interactions among their integrating species and the environment. We use data from an extensive survey of xerophytic inland sand dune scrub communities from Portugal, one of the most threatened habitat types of Europe. We identify indicator shrub species of different types of communities, model their geographical response to the environment, and evaluate whether the output of these niche models are able to predict the distribution of each type of community in a different region

Environmental drivers of distribution and reef development of the Mediterranean coral Cladocora caespitosa

Cladocora caespitosa is the only Mediterranean scleractinian similar to tropical reef-building corals. While this species is part of the recent fossil history of the Mediterranean Sea, it is currently considered endangered due to its decline during the last decades. Environmental factors affecting the distribution and persistence of extensive bank reefs of this endemic species across its whole geographic range are poorly understood. In this study, we examined the environmental response of C. caespitosa and its main types of assemblages using ecological niche modeling and ordination analysis. We also predicted other suitable areas for the occurrence of the species and assessed the conservation effectiveness of Mediterranean marine protected areas (MPAs) for this coral. We found that phosphate concentration and wave height were factors affecting both the occurrence of this versatile species and the distribution of its extensive bioconstructions in the Mediterranean Sea. A set of factors (diffuse attenuation coefficient, calcite and nitrate concentrations, mean wave height, sea surface temperature, and shape of the coast) likely act as environmental barriers preventing the species from expansion to the Atlantic Ocean and the Black Sea. Uncertainties in our large-scale statistical results and departures from previous physiological and ecological studies are also discussed under an integrative perspective. This study reveals that Mediterranean MPAs encompass eight of the ten banks and 16 of the 21 beds of C. caespitosa. Preservation of water clarity by avoiding phosphate discharges may improve the protection of this emblematic species.Spanish Ministry of Economy and Competitiveness [CTM2014-57949-R]info:eu-repo/semantics/publishedVersio

A utilização do ATLANTIS – Tierra 2.0 e de ferramentas SIG para predizer a distribuição espacial e a adequação do habitat de espécies endémicas

O conhecimento da distribuição de espécies raras requer muito esforço devido às dificuldades inerentes à detecção das suas populações. Neste capítulo, apresenta-se um exemplo de modelação da distribuição potencial de espécies endémicas de insectos, que constituem uma preocupação de conservação nos Açores. São analisados dados extraídos da base de dados ATLANTIS com o objectivo de desenvolver mapas preditivos da distribuição de quatro escaravelhos endémicos (Insecta, Coleoptera) na ilha Terceira: Cedrorum azoricus azoricus Borges & Serrano, 1993; Trechus terceiranus Machado, 1988; Trechus terrabravensis Borges, Serrano & Amorim, 2004; e Alestrus dolosus (Crotch, 1867). São usadas duas técnicas amplamente aplicadas nestas situações (BIOCLIM e BioMapper) de forma a desenvolver os mapas de distribuição, mas igualmente a obter a descrição do nicho ecológico de cada espécie. Todas as espécies, excepto T. terceiranus, apresentam grandes restrições de habitat. As outras três espécies parecem estar ambientalmente restringidas a duas áreas espaciais bem definidas, localizadas nas partes oeste (Serra de Santa Bárbara) e central (Terra Brava) da ilha Terceira. Contudo, enquanto A. dolosus estará potencialmente espalhado em ambas as áreas, de acordo com os seus requisitos de habitat, C. azoricus azoricus e T. terrabravensis parecem possuir adaptações ambientais muito mais restritivas. No entanto, como os dados sobre a distribuição conhecida destas espécies se revelaram escassos, a eficácia dos mapas de predição não é propriamente a ideal. Deste modo, é discutida de forma exaustiva a utilidade das técnicas utilizadas, num contexto de gestão da conservação. São igualmente discutidos os problemas surgidos durante o processo de modelação dos dados e como estes podem ser resolvidos. Finalmente são apresentadas sugestões para melhorar a informação a obter da base de dados ATLANTIS.ABSTRACT: Ranges of rare species require great efforts to be mapped due to the low detect ability of their populations. In this chapter, we provide an example focusing on several endemic insect species of conservation concern in the Azores. We explore the use of data extracted from ATLANTIS database to develop predictive maps of the distribution of four endemic beetle species (Insecta, Coleoptera) in Terceira Island: Cedrorum azoricus azoricus Borges & Serrano, 1993; Trechus terceiranus Machado, 1988; Trechus terrabravensis Borges, Serrano & Amorim, 2004; and Alestrus dolosus (Crotch, 1867). We use two widely used methodologies (BIOCLIM and BioMapper) to develop such maps, as well as to provide a description of the niche of these species. All species except for T. terceiranus presented highly restricted habitat requirements. The other three species seem to be environmentally restricted to two spatially well-defined areas, placed in the west (Serra de Santa Bárbara) and the centre of the island (Terra Brava). However, while A. dolosus seems to be potentially widespread in these two areas according to its habitat requirements, C. azoricus azoricus and T. terrabravensis appear to have very restricted environmental adaptations. As data (recorded presences) for these species is scarce, the performance of the predictions was not ideal. Therefore, we discuss extensively the utility of such methodologies in the context of conservation management. We also discuss how the problems arose during this work can be overcome, and how ATLANTIS information could be improved