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Madagascar does not have native wild felid species; however, distinct populations of free-ranging “forest cats” of unknown species are known throughout the island, including at Ankarafantsika National Park, Bezà Mahafaly Special Reserve, Makira Natural Park and the Masoala peninsula. Malagasy “forest cats” are commonly considered invasive lemur predators and competitors with endemic carnivores as well as a nuisance exotic species that kill poultry. These cats may be descendants of African wildcats, European wildcats and/or domestic cats; however, no research on their genetic origin has been published. To determine their taxonomic status, genetic data from short tandem repeat markers was assessed for three wild-caught “forest cats” from the Bezà Mahafaly Special Reserve (BMSR) and 27 “forest cats” from Ankarafantsika National Park. Bayesian analyses comparing the Malagasy “forest cats” to approximately 1900 domestic and wildcat sub-species suggest the Malagasy cats are descendents of domestic cats from the Arabian Sea region, including the islands of Lamu and Pate, Dubai, Kuwait and Oman. Additional genetic influences may descend from India and Pakistan. Combined with cultural and historical information, these data suggest that these felid populations are likely descendents from cats that immigrated to the island on trade ships, particularly along early Arab trade routes.

The hirola antelope (Beatragus hunteri) is considered to be the most endangered antelope in the world. In the ex situ translocated population at Tsavo East National Park, calf mortality and the critically low population numbers might suggest low genetic diversity and inbreeding depression. Consequently, a genetic study of the wild population is pivotal to gain an understanding of diversity and differentiation within its range before designing future translocation plans to increase the genetic diversity of the ex situ population. For that purpose, we assessed 55 individuals collected across five localities in eastern Kenya, covering its entire natural range. We used the complete mitochondrial DNA control region and microsatellite genotyping to estimate genetic diversity and differentiation across its range. Nuclear genetic diversity was moderate in comparison to other endangered African antelopes, with no signals of inbreeding. However, the mitochondrial data showed low nucleotide diversity, few haplotypes and low haplotypic differentiation. Overall, the inferred low degree of genetic differentiation and population structure suggests a single population of hirola across the natural range. An overall stable population size was inferred over the recent history of the species, although signals of a recent genetic bottleneck were found. Our results show hope for ongoing conservation management programmes and that there is a future for the hirola in Kenya.

Coastal sand dunes are dynamic ecosystems, with vegetation and biota responding to continuous changes in its typical environmental severity. Understanding vegetation patterns is relevant to early detect shifts in prevailing coastal dynamics and to refine monitoring strategies, especially in secondary sand dunes, which are under legal protection in Europe. We assessed the diversity patterns and cross-taxa congruence among lichens, bryophytes and vascular plants in secondary sand dunes under contrasting coastal dynamics (i.e. stable versus erosion sites), along a major biogeographic transition (i.e. Eurosiberian versus Mediterranean regions) in Western Europe. Our results show that the diversity patterns of bryophytes, lichens and vascular plants differ between contrasting coastal dynamics, regardless of the biogeographic context. Also, we found the absence of an explicit cross-taxa congruence among the diversity patterns of the three taxonomic groups. These results highlight the importance of taking into account the diversity of vascular plants, lichens and bryophytes, and the inclusion of other factors besides coastal dynamics, such as anthropogenic pressures. By doing so, a complementary view on the diversity patterns in secondary sand dunes can be provided to better guide conservation actions and monitoring strategies.

To protect native biodiversity and habitats from the negative impacts of biological invasions, comprehensive studies and measures to anticipate invasions are required, especially across countries in a transfrontier context. Species distribution models (SDMs) can be particularly useful to integrate different types of data and predict the distribution of invasive species across borders, both for current conditions and under scenarios of future environmental changes. We used SDMs to test whether predicting invasions and potential spatial conflicts with protected areas in a transfrontier context, under current and future climatic conditions, would provide additional insights on the patterns and drivers of invasion when compared to models obtained from predictions for individual regions/countries (different modelling strategies). The framework was tested with the invasive alien plant Acacia dealbata in North of Portugal/NW Spain Euro-region, where the species is predicted to increase its distribution under future climatic conditions. While SDMs fitted in a transfrontier context and using “the national strategy (with Portugal calibration data) presented similar patterns, the distribution of the invasive species was higher in the former. The transfrontier strategy expectedly allowed to capture a more complete and accurate representation of the species’ niche. Predictions obtained in a transfrontier context are therefore more suitable to support resource prioritisation for anticipation and monitoring impacts of biological invasions, while also providing additional support for international cooperation when tackling issues of global change. Our proposed framework provided useful information on the potential patterns of invasion by A. dealbata in a transfrontier context, with an emphasis on protected areas. This information is crucial for decision-makers focusing on the prevention of invasions by alien species inside protected areas in a transfrontier context, opening a new way for collaborative management of invasions.

Despite growing efforts to halt biodiversity loss, knowledge of species diversity and distribution is highly geographically biased, leaving some areas unexplored. Taxa distributed in remote, desert areas, such as hedgehogs (Mammalia; Eulipotyphla) in North Africa, are good examples of current knowledge gaps in systematics and biogeography. Here we studied the geographical distribution and intraspecific genetic diversity of hedgehogs in North Africa. Specimens belonging to North African and Eurasian species were analysed with mitochondrial (control region, CR) and nuclear (recombination activating gene 1, RAG1) gene fragments. This revealed a broader geographical distribution of Atelerix algirus in south-western Libya and of Paraechinus aethiopicus along the Atlantic Sahara. High intraspecific genetic differentiation was found in A. algirus and A. albiventris at the mitochondrial level, with nuclear haplotype sharing across their ranges. These findings suggest that biogeographical patterns of hedgehogs in North Africa are more complex than previously suggested, highlighting a need for further investigation in this remote and poorly known area.

Diet is important for understanding the ecology and evolution of populations. When examining animals’ diets, the lowest taxonomic rank (i.e., species level) is generally used. However, it is questionable whether dietary description varies with respect to the plant taxonomy or with the extent of plant species diversity in landscapes. We studied the diet of the Alpine mountain hare (Lepus timidus varronis) by analyzing the botanical composition of fecal pellets and comparing the results with the availability of food plants. Overall, Alpine mountain hares selected ligneous plants, whereas grasses were neutrally consumed or avoided. Plant identification at the genus and family level revealed the most information, whereas little additional information was gleaned by identifying food plants at the species level. In low-diversity spruce forests and at higher elevations, hares exhibited greater diet breadth compared to high-diversity vegetative mosaics or at lower elevations, even if they had access to the same types of plants. This is likely due to the hares’ need to diversify their diet when plant quantity is low. Greater diet breadth and selection of a larger number of different plant types at the beginning of the plant vegetation growth period suggested that more food plants suitable for Alpine mountain hares were available during this time compared to the end of the vegetation period.

Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification ofLepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1- 4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along theLepusradiation, including recent gene flow between extant species since the last glacial maximum, but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation within and among species.

Anthropogenic hybridization is one of the greatest threats to global biodiversity. It incites human-mediated gene flow between non-native/exotic and native taxa, which can have irreversible effects on native species or locally adapted populations, eventually leading to extinction. The red deer, Cervus elaphus, is a game species that, due to its extraordinary economic value, has been introduced in several regions throughout Europe. However, the consequences of those introductions on native populations, namely on their genetic background, have been poorly addressed. This study is focused on the Iberian Peninsula and aims to: (i) assess the extent of anthropogenic hybridization/introgression of introduced red deer into the native Iberian populations; (ii) evaluate the impact of red deer management regimes on the observed hybridization/introgression patterns; and (iii) assess how hybridization/introgression influence the current genetic diversity of native Iberian populations. A set of 11 microsatellites and a 329 bases pair fragment of the mitochondrial D-loop gene were used to estimate nuclear admixture and mitochondrial introgression in 1,132 individuals sampled across 46 red deer populations throughout Iberia. A Bayesian approach implemented in the STRUCTURE program was employed to investigate the proportion of admixture between native populations and non-native red deer. Results showed that 17% of individuals presented signs of non-native recent ancestors and 10.1% had non-native mitochondrial haplotypes, reaching an overall hybridization/introgression rate of 23%. Non-native or hybrid individuals were found throughout 40 Iberian red deer populations, and the percentages per population varied between 3.3 and 75.0%, independently of the management regime. Mitochondrial introgression was observed across 15 Iberian red deer populations, being more frequent in free-ranging individuals (16.2%) than in fenced populations (9.2%) but was completely absent from public-owned populations. Nuclear genetic diversity correlated positively with the proportion of hybrid individuals in public-owned populations. The genetic footprint of historical and current human-mediated translocations of non-native red deer into the Iberian Peninsula is evidenced in this study, highlighting the need to implement effective measures to avoid such practices both in Portugal and Spain, in order to preserve the endogenous genetic patrimony of the Iberian red deer populations., This work was supported by AGRIGEN – NORTE-01-0145-FEDER-000007, supported by Norte Portugal Regional Operational Programme (NORTE2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF).

The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of non-invasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.

The importance of environmental heterogeneity for biodiversity across scales is widely recognized in ecological theory and profusely supported by evidence. However, our understanding of the effects of spatiotemporal patterns of landscape functional properties on biodiversity is still rather limited. We examined the relationship between common passerine species richness and ecosystem functioning dynamics, namely seasonality, measured by satellite remote sensing. We focused on rural landscapes of a mountain National Park in Portugal undergoing rapid reshaping from agro-pastoral mosaics to early successional landscapes. We applied multi-model inference to compare the hypothesis of landscape seasonality as a driver of species richness with three competing hypotheses representing structural habitat heterogeneity, disturbance, and availability of food resources. We found support for landscape seasonality and its spatial heterogeneity in explaining passerine richness in mountain rural landscapes. Conversely, no significant support of the remaining hypotheses was found. These results highlight the role of ecosystem functioning variability in space and time. They also stress the importance of considering species-energy relationships for conservation at the landscape level. Specifically, they provide support and guidance to the identification of meaningful functional attributes of the landscape that shape its biodiversity. Our results further demonstrate the utility of remote sensing approaches and products to measure those attributes and follow their trends through time. Spatially-explicit measures of energy variability, such as the functional amplitude between winter and summer retrieved from earth observations, can link global socio-environmental change to species’ responses and support the inclusion of landscape seasonality on conservation and monitoring frameworks.

Roads represent barriers to animal movement due to physical obstruction, mortality, or behavioural avoidance. The population-level consequences of such constraints remain poorly understood, because successful crossings may be sufficient to counteract negative effects of fragmentation and isolation. Here we examine the individual- and population-level barrier effects of a motorway on the common genet Genetta genetta, by combining long-term road mortality, radio tracking and population genetics data. We found 84 genets killed at roads, of which 68% were subadults, with a peak mortality during the dispersal period. The home ranges of resident adults often bordered the motorway, and their sizes were similar close to (314 ha, n = 9) and far from (258 ha, n = 10) the motorway. The crossing rate was much higher for dispersing subadults (4.1 crossings/100 nights, n = 3) than for resident adults living near the motorway (0.2 crossings/100 nights, n = 9), though the number of tracked subadults crossing the motorway was low. Genetic kinship analysis revealed seven crossings based on father-offspring and half-sibling relationships. There was no significant genetic differentiation related to the motorway. The movement of residents were strongly constrained by the motorway, though gene flow mediated by successful crossings, particularly by subadults, likely prevented genetic differentiation. Genet movements across the motorway were probably facilitated by low traffic flow and the presence of crossing structures. Our study implies that evaluating mitigation strategies to reduce the barrier effects of roads would benefit from the integration of mortality, animal behaviour, and population genetics data, to increase effectiveness and avoid wasting scarce conservation resources.

Climate change and increasing habitat loss greatly impact species survival, requiring range shifts, phenotypic plasticity and/or evolutionary change for long-term persistence, which may not readily occur unaided in threatened species. Therefore, defining conservation actions requires a detailed assessment of evolutionary factors. Existing genetic diversity needs to be thoroughly evaluated and spatially mapped to define conservation units (CUs) in an evolutionary context, and we address that here. We also propose a multidisciplinary approach to determine corridors and functional connectivity between CUs by including genetic diversity in the modelling while controlling for isolation by distance and phylogeographic history. We evaluate our approach on a Near Threatened Iberian endemic rodent by analysing genotyping-by-sequencing (GBS) genomic data from 107 Cabrera voles (Microtus cabrerae), screening the entire species distribution to define categories of CUs and their connectivity: We defined six management units (MUs) which can be grouped into four evolutionarily significant units (ESUs) and three (putatively) adaptive units (AUs). We demonstrate that the three different categories of CU can be objectively defined using genomic data, and their characteristics and connectivity can inform conservation decision-making. In particular, we show that connectivity of the Cabrera vole is very limited in eastern Iberia and that the pre-Pyrenean and part of the Betic geographic nuclei contribute the most to the species genetic diversity. We argue that a multidisciplinary framework for CU definition is essential and that this framework needs a strong evolutionary basis. © 2018 John Wiley & Sons Ltd

Freshwater ecosystems are among the most threatened in the world, and downstream reaches of stream networks are often the most affected by multiple anthropogenic stressors. In these circumstances, many species currently restricted to stream headwaters may represent remnants of once larger populations, though this is generally difficult to ascertain due to limited historical data. Here, we document a case of range contraction into headwaters of the globally threatened Pyrenean desman Galemys pyrenaicus, a species endemic to South‐western Europe, from surveys carried out in 1993–96 and 2014–15. Geostatistical logistic mixed models were used to relate the probabilities of desman occurrence and extinction to environmental variables in 74 sites within two watersheds in NE Portugal, while controlling for linear (Euclidean) and hydrologic spatial dependencies. In 1993–96, desmans were recorded at 85.1% of sites, and their presence was positively related to stream order and slope. In 2014–15, desmans were only found at 31.1% of sites, and their presence was positively related to slope steepness and negatively to stream order and maximum temperature of the warmest month. The extinction rate across periods was 63.5%, and the probability of extinction increased with stream order and declined with slope steepness. Maps of predicted distribution and extinction indicated that while the species was widely distributed in the first period, it largely disappeared thereafter from the main rivers and the largest tributaries, persisting mostly in stream headwaters in more mountainous areas. The severe decline found in ours and other studies suggests that the conservation status of the Pyrenean desman may need to be upgraded, and highlights the importance of headwater streams for its conservation. Furthermore, this study supports the view that headwater streams may be increasingly important for biodiversity conservation in modified river systems, favouring the permanence of remnant, albeit fragmented populations.

Significant advances have been made in identifying, quantifying and valuing multiple urban ecosystem services (UES), yet this knowledge remains poorly implemented in urban planning and management. One of the reasons for this low implementation is the insufficient thematic and spatial detail in UES research to provide guidance for urban planners and managers. Acknowledging how patterns of UES delivery are related with vegetation structure and composition in urban green areas could help these stakeholders to target structural variables that increase UES provision. This investigation explored how different types of urban green spaces influence UES delivery in Porto, a Portuguese city, and how this variation is affected by a socioeconomic gradient. A stepwise approach was developed using two stratification schemes and a modelling tool to estimate urban forest structure and UES provision. This approach mapped explicit cold and hotspots of UES provision and discriminated the urban forest structural variables that influence UES at the local scale. Results revealed that different types of green spaces affect UES delivery as a direct result of the influence of structural variables of the urban forest. Furthermore, the uneven distribution of green spaces types across socioeconomic strata alters UES delivery across the city. This case study illustrates how a methodology adaptable to other geographic contexts can be used to map and analyze coupled social and ecological patterns, offering novel insights that are simple to understand and apply by urban planners and managers.

Urban areas are traditionally overlooked by ecologists, but contain a wide range of biodiversity. The existing procedures for consistent recording of habitats and biodiversity are not sufficient to adequately describe urban environments in a fine scale. A method is required to provide information on biodiversity and its spatial distribution in urban areas, for scientific objectives and urban planning. A standardized procedure is presented for the classification and mapping of urban habitats, termed Urban Habitats Biodiversity Assessment (UrHBA), designed to capture the fine detail of urban ecosystems and provide spatial data suitable for analysis and communication. Urban Habitat Categories (UHCs) have been developed based on plant life forms, and adapted to the requirements of urban areas; new Non-Life Form categories are used to define Artificial Built Elements. Site Descriptors, Vegetation Layers and species are used to add further detail. Guidelines are provided for the mapping process, with site visits being used to elaborate the initial interpretation of remote sensed images. Data are recorded on standard forms which are linked to the mapped units. Examples of the procedure are included for a park in Porto, Portugal. Because the units are defined according to consistent rules, sites can be repeatedly surveyed to monitor change. The proposed methodology can be expressed in spatial formats and designed to inform urban planning processes and decisions regarding the conservation of green spaces and biodiversity. As the categories transcend species, the method is applicable in a wide range of urban areas.

In a world facing rapid environmental changes, anticipating their impacts on biodiversity is of utmost relevance. Remotely-sensed Ecosystem Functional Attributes (EFAs) are promising predictors for Species Distribution Models (SDMs) by offering an early and integrative response of vegetation performance to environmental drivers. Species of high conservation concern would benefit the most from a better ability to anticipate changes in habitat suitability. Here we illustrate how yearly projections from SDMs based on EFAs could reveal short-term changes in potential habitat suitability, anticipating mid-term shifts predicted by climate-change-scenario models. We fitted two sets of SDMs for 41 plant species of conservation concern in the Iberian Peninsula: one calibrated with climate variables for baseline conditions and projected under two climate-change-scenarios (future conditions); and the other calibrated with EFAs for 2001 and projected annually from 2001 to 2013. Range shifts predicted by climate-based models for future conditions were compared to the 2001–2013 trends from EFAs-based models. Projections of EFAs-based models estimated changes (mostly contractions) in habitat suitability that anticipated, for the majority (up to 64%) of species, the mid-term shifts projected by traditional climate-change-scenario forecasting, and showed greater agreement with the business-as-usual scenario than with the sustainable-development one. This study shows how satellite-derived EFAs can be used as meaningful essential biodiversity variables in SDMs to provide early-warnings of range shifts and predictions of short-term fluctuations in suitable conditions for multiple species.

Knowledge regarding Ecosystem Services (ES) delivery and the socio-ecological factors that influence their proficiency is essential to allow cities to adopt policies that lead to resource-efficient planning and greater resilience. As one of the matrix elements of urban ecological structure, vegetation may play a major role in promoting ES proficiency through planting design. This research addresses the heterogeneity of ES delivered by the urban vegetation of Porto, a Portuguese city. A methodology is proposed to investigate associations between socioeconomic indicators and structural variables of the urban forest, and also which structural variables of the urban forest, if any, differ along a socioeconomic gradient. Our results reveal that before setting planning and management goals, it is crucial to understand local patterns of ES and their relationships with socioeconomic patterns, which can be affected by variables such as building age. This should be followed by the identification of structural variables of the urban forest that better explain the differences, in order to target these through planning and management goals. The conceptual framework adopted in this research can guide adaptation of our methodology to other cities, providing insights for planning and management suitable to site-specific conditions and directly usable by stakeholders.

Color molts from summer brown to winter white coats have evolved in several species to maintain camouflage year‐round in environments with seasonal snow. Despite the eco‐evolutionary relevance of this key phenological adaptation, its molecular regulation has only recently begun to be addressed. Here, we analyze skin transcription changes during the autumn molt of the mountain hare (Lepus timidus) and integrate the results with an established model of gene regulation across the spring molt of the closely related snowshoe hare (L. americanus). We quantified differences in gene expression among three stages of molt progression—“brown” (early molt), “intermediate,” and “white” (late molt). We found 632 differentially expressed genes, with a major pulse of expression early in the molt, followed by a milder one in late molt. The functional makeup of differentially expressed genes anchored the sampled molt stages to the developmental timeline of the hair growth cycle, associating anagen to early molt and the transition to catagen to late molt. The progression of color change was characterized by differential expression of genes involved in pigmentation, circadian, and behavioral regulation. We found significant overlap between differentially expressed genes across the seasonal molts of mountain and snowshoe hares, particularly at molt onset, suggesting conservatism of gene regulation across species and seasons. However, some discrepancies suggest seasonal differences in melanocyte differentiation and the integration of nutritional cues. Our established regulatory model of seasonal coat color molt provides an important mechanistic context to study the functional architecture and evolution of this crucial seasonal adaptation., We analyze skin transcription changes during the autumn color molt of the mountain hare and integrate the results with an established model of gene regulation across the spring molt of the closely related snowshoe hare. Our work provides an important mechanistic context to study the functional architecture and evolution of this crucial seasonal adaptation.

Competition is a widespread interaction among carnivores, ultimately manifested through one or more dimensions of the species' ecological niche. One of the most explicit manifestations of competitive interactions regards spatial displacement. Its interpretation under a theoretical context provides an important tool to deepen our understanding of biological systems and communities, but also for wildlife management and conservation. We used Bayesian multispecies occupancy models on camera‐trapping data from multiple sites in Southwestern Europe (SWE) to investigate competitive interactions within a carnivore guild, and to evaluate how species' ecological traits are shaping coexistence patterns. Seventeen out of 26 pairwise interactions departed from a hypothesis of independent occurrence, with spatial association being twice as frequent as avoidance. Association behaviors were only detected among mesocarnivores, while avoidance mainly involved mesocarnivores avoiding the apex predator (n = 4) and mesocarnivore‐only interactions (n = 2). Body mass ratios, defined as the dominant over the subordinate species body mass, revealed an important negative effect ( βˆ=−0.38;CI95=−0.81𝑡𝑜−0.06 ) on co‐occurrence probability, and support that spatially explicit competitive interactions are mostly expressed by larger species able to dominate over smaller ones, with a threshold in body mass ratios of ~4, above which local‐scale intraguild coexistence is unlikely. We found a weak relationship between pairwise trophic niche overlap and the probability of coexistence ( βˆ=−0.19;CI95=−0.58𝑡𝑜0.21 ), suggesting that competition for feeding resources may not be a key driver of competition, at least at the scale of our analysis. Despite local‐scale avoidance, regional‐scale coexistence appears to be maintained by the spatial structuring of the competitive environment. We provide evidence that SWE ecosystems consist of spatially structured competitive environments, and propose that coexistence among near‐sized species is likely achieved through the interplay of “facultative” and “behavioral” character displacements. Factors influencing carnivore coexistence likely include context‐dependent density and trait‐mediated effects, which should be carefully considered for a sound understanding of the mechanisms regulating these communities., This study was funded by research projects CGL2009‐10741, funded by the Spanish Ministry of Science and Innovation and EU‐FEDER, and OAPN 352/2011, funded by the Spanish Organismo Autónomo Parques Nacionales. P. Monterroso enjoyed a Ph.D. grant from the Fundação para a Ciência e a Tecnologia (FCT) (ref: SFRH/BD/37795/2007) and a postdoctoral fellowship by EU‐FEDER funds through the Operational Programme for Competitiveness Factors—COMPETE and by National Funds through FCT—Foundation for Science and Technology (ref: UID/BIA/50027/2013, POCI‐01‐0145‐FEDER‐006821). F. Díaz‐Ruiz enjoyed a research contract “Juan de la Cierva” (ref: FJCI‐2015‐24949) from the Spanish Ministry of Economy, Industry, and Competitiveness.

Background: Climatic variation and geologic change both play significant roles in shaping species distributions, thus affecting their evolutionary history. In Sahara-Sahel, climatic oscillations shifted the desert extent during the Pliocene-Pleistocene interval, triggering the diversification of several species. Here, we investigated how these biogeographical and ecological events have shaped patterns of genetic diversity and divergence in African Jerboas, desert specialist rodents. We focused on two sister and cryptic species, Jaculus jaculus and J. hirtipes, where we (1) evaluated their genetic differentiation, (2) reconstructed their evolutionary and demographic history; (3) tested the level of gene flow between them, and (4) assessed their ecological niche divergence.Results: The analyses based on 231 individuals sampled throughout North Africa, 8 sequence fragments (one mitochondrial and seven single copy nuclear DNA, including two candidate genes for fur coloration: MC1R and Agouti), 6 microsatellite markers and ecological modelling revealed: (1) two distinct genetic lineages with overlapping distributions, in agreement with their classification as different species, J. jaculus and J. hirtipes, with (2) low levels of gene flow and strong species divergence, (3) high haplotypic diversity without evident geographic structure within species, and (4) a low level of large-scale ecological divergence between the two taxa, suggesting species micro-habitat specialization. Conclusions: Overall, our results suggest a speciation event that occurred during the Pliocene-Pleistocene transition. The contemporary distribution of genetic variation suggests ongoing population expansions. Despite the largely overlapping distributions at a macrogeographic scale, our genetic results suggest that the two species remain reproductively isolated, as only negligible levels of gene flow were observed. The overlapping ecological preferences at a macro-geographic scale and the ecological divergence at the micro-habitat scale suggest that local adaptation may have played a crucial role in the speciation process of these species.

Inferring the phylogeography of species with large distributions helps deciphering major diversification patterns that may occur in parallel across taxa. Here, we infer the evolutionary history of the Cape hare, Lepus capensis sensu lato, a species distributed from southern Africa to Asia, by analyzing variation at 18 microsatellites and 9 DNA (1 mitochondrial and 8 nuclear) sequenced loci, from field and museum-collected samples. Using a combination of assignment and coalescent-based methods, we show that the Cape hare is composed of five evolutionary lineages, distributed in distinct biogeographic regions -north-western Africa, eastern Africa, southern Africa, the Near East and the Arabian Peninsula. A deep phylogenetic break possibly dating to the Early Pleistocene was inferred between the African and Asian L. capensis groups, and the latter appear more closely related to other Eurasian hare species than to African Cape hares. The inferred phylogeographic structure is shared by numerous taxa distributed across the studied range, suggesting that environmental changes, such as the progressive aridification of the Saharo-Arabian desert and the fluctuations of savannah habitats in Sub-Saharan Africa, had comparable impacts across species. Fine-scale analyses of the western Sahara-Sahel populations showed rich fragmentation patterns for mitochondrial DNA but not for microsatellites, compatible with the environmental heterogeneity of the region and female philopatry. The complex evolutionary history of L. capensis sensu lato, which possibly includes interspecific gene flow, is not reflected by taxonomy. Integrating evolutionary inference contributes to an improved characterization of biodiversity, which is fundamental to foster the conservation of relevant evolutionary units.

Local ecosystem resilience to fire disturbance can be influenced by multiple factors, from topography and climate, to fire history and pre-fire structure of biotic communities. Here we investigated the factors affecting post-fire recovery of scrub vegetation in areas under Mediterranean climate affected by frequent fires. We hypothesized that, under comparable climatic and topographic conditions, geological factors (with bedrock type as a proxy) would be at least as important as fire history in explaining patterns of post-fire recovery. We surveyed scrub vegetation in a mountain study area in Portugal, using a stratified random sampling scheme, with fire frequency, time since last fire, and bedrock type (granite vs. schist) as stratifying layers. Based on vegetation and plant community data from 40 plots, we analyzed total species richness and composition, and the relative abundance of functional groups defined on the basis of general (non fire-specific) life-history traits. We found that, at a local scale, lithology can override fire history in determining post-fire recovery. Vegetation plots on granite exhibited a considerable development of tall scrubs and higher values of total species richness. They also hosted higher numbers of animal-dispersed woody species, of trees and tall scrubs, of woody deciduous species, and of forest, edge and tall scrub species. Differences in the post-fire development of scrub vegetation and in the functional profile of plant communities highlight the need to consider local geological diversity when establishing priorities for post-fire active restoration under scenarios of limited resources.

Carnivores are elusive, nocturnal and scarce, hence, their detection is difficult. Camera trapping has become a powerful non-invasive technique for collecting information on such elusive species. Some of its major applications are species inventories and community monitoring. Some efforts have been recently devoted to standardize protocols for monitoring mammal communities in tropical areas. Nevertheless, there is a lack of standardization across studies for monitoring carnivore communities in temperate areas. We aimed to optimize camera-trapping protocols for monitoring mesocarnivore communities in Mediterranean areas, minimizing sampling effort to accurately estimate species richness. For this purpose, we assessed the effect of number of cameras, time they remain active, area covered and spatial arrangement on species richness estimates. We used between 50 and 60 camera-traps combined with generalist scent attractants in two national parks located in central Spain. We generated random sets of 5–40 cameras and evaluated the accumulated richness between 1 and 30 days since deployment. Generalized linear model analysis indicates that active days, number of cameras, covered area and study area best explained species richness. A minimum of 30 active cameras during 20 days were required for attaining the asymptotical species richness. A larger effort was required to detect all species in the study area with higher species richness (six vs. five species). These results agree with the effort required for obtaining at least one camera image of those species with the lowest detection rates. Scattered deployments required less effort (number of cameras) to reach an asymptote of species richness than clumped layouts, although differences were not significant. These findings can be used as guidelines for monitoring mesocarnivore communities with camera-traps in temperate areas, although particular monitoring requirements will depend on the community composition and density of mesocarnivore species present in a given study area., This study was funded by Organismo Autónomo Parques Nacionales, project OAPN 352/2011. F. Díaz‐Ruiz enjoyed a postdoctoral contract funded by the European Social Fund (ESF) and Junta de Comunidades de Castilla‐La Mancha (Operational Programme FSE 2007/2013). P. Monterroso was granted a postdoctoral fellowship by the project ‘Genomics Applied to Genetic Resources’ cofinanced by North Portugal Regional Operational Programme 2007/2013 (ON.2 – O Novo Norte), under the National Strategic Reference Framework (NSRF), through the European Regional Development Fund (ERDF).

Ongoing declines in biodiversity caused by global environmental changes call for adaptive conservation management, including the assessment of habitat suitability spatiotemporal dynamics potentially affecting species persistence. Remote sensing (RS) provides a wide-range of satellite-based environmental variables that can be fed into species distribution models (SDMs) to investigate species-environment relations and forecast responses to change. We address the spatiotemporal dynamics of species’ habitat suitability at the landscape level by combining multi-temporal RS data with SDMs for analysing inter-annual habitat suitability dynamics. We implemented this framework with a vulnerable plant species (Veronica micrantha), by combining SDMs with a time-series of RS-based metrics of vegetation functioning related to primary productivity, seasonality, phenology and actual evapotranspiration. Besides RS variables, predictors related to landscape structure, soils and wildfires were ranked and combined through multi-model inference (MMI). To assess recent dynamics, a habitat suitability time-series was generated through model hindcasting. MMI highlighted the strong predictive ability of RS variables related to primary productivity and water availability for explaining the test-species distribution, along with soil, wildfire regime and landscape composition. The habitat suitability time-series revealed the effects of short-term land cover changes and inter-annual variability in climatic conditions. Multi-temporal SDMs further improved predictions, benefiting from RS time-series. Overall, results emphasize the integration of landscape attributes related to function, composition and spatial configuration for improving the explanation of ecological patterns. Moreover, coupling SDMs with RS functional metrics may provide early-warnings of future environmental changes potentially impacting habitat suitability. Applications discussed include the improvement of biodiversity monitoring and conservation strategies.

Agricultural abandonment is a major driver of change in rural landscapes. Assumed to provide beneficial results to the environment and the conservation of biota, rural abandonment triggers landscape and biotic homogenization and loss of valuable species and habitats. This article focuses on the ecological effects and conservation challenges of shifts in extensive grazing regimes on marginal pastureland of Mediterranean mountains. We conceptualize a navigated socioecological transition toward conservation-oriented management after the collapse of historical land systems. The article provides examples from the LIFE+ project “Higro,” developed in mountainous protected areas in Portugal, of how management for conservation could sustain disturbance-dependent habitats. We argue that actively and regularly managing large habitat areas should be envisaged as a short-term approach to limit the immediate effects of rural abandonment. A gradual integration of conservation targets with other activities in changing rural economies is necessary to foster long-term conservation of species and habitats, building on the link between conservation-oriented habitat management and ecosystem services in rural landscapes. Conservation goals should run alongside recovery of social systems and innovation applied to traditional sources of income. This parallel development would contribute to building up social-ecological resilience by maintaining a diversity of social and ecological capital in rural areas.

The structure of mesopredators' communities is complex and results from a multidimensional web of interactions such as top-down and bottom-up regulation or intraguild interactions. However, these interactions may change geographically along species' distribution ranges. The pine marten (Martes martes) and stone marten (Martes foina) are 2 similar-sized mustelids with overlapping ecological traits and a wide distribution overlap. The absence of stone martens from potentially adequate areas has been advocated as resulting from competitive exclusion by pine martens. Particularly, the preference of both species for mammalian rodents could be the main driver of such competitive stress. However, their elusive behavior and morphological similarity of their scats often precluded the evaluation of their ecological traits in areas of co-occurrence. Using camera trapping and diet analysis on genetically identified scats, we evaluated the interactions between pine and stone martens in the southwestern limit of their range along 3 ecological niche dimensions: spatial, trophic, and temporal, under a hypothesis of competitive dominance of pine martens. We found no spatial segregation, and that coexistence was facilitated by seasonally adjusted shifts along the trophic and temporal axes. While both species often co-occurred, during the season of low food resources, pine martens exploited the less profitable feeding resource. Moreover, they not only displayed an activity pattern that limited their access to rodents, but also reduced the probabilities of direct encounters with stone martens. We suggest that the dominance position has changed in favor of the stone marten in our study area, probably as a result of habitat quality and range edge effects. These findings support the relative instability of interspecific interactions among similar-sized species, which should be evaluated using multidimensional and site-specific approaches.

After domestication, wild progenitors, such as the aurochs and the wild horse, became extinct. For the European rabbit, however, ancestral, domestic, and feral populations exist. During domestication of the rabbit, very few alleles have been fixed for selective traits, and thus, the ancestral genotypes have been preserved in lowered frequencies. This facilitates investigations on genetic processes involved in domestication as well as dedomestication, that is, where domestic strains are “rewilded.” The acquired knowledge may be useful in the search for genotypic, phenotypic, and, perhaps most importantly, ecotypic equivalents that could assist in the restoration of extinct fauna and its ecosystem functions. Such efforts could provide novel evolutionary trajectories useful in nature restoration, management, and conservation.

Although important to guide conservation management, detailed demographic studies on rare or elusive species inhabiting fragmented, human-dominated landscapes are often hampered by the species' low densities, and the logistic and ethical constraints in obtaining reliable information covering large areas. Genetic non-invasive sampling (gNIS) provides cost-effective access to demographic information, though its application to small mammals is still scarce. We used gNIS to infer on the demography of an endemic small mammal, the Cabrera vole (Microtus cabrerae), occurring as a spatially-structured population in a 462-ha Mediterranean farmland landscape. We intensively sampled fresh vole feces in four seasons, extracted the DNA, and performed individual identification based on genotypes built using nine microsatellites. We then estimated population size and individual survival relative to environmental variables, controlling for heterogeneity in capture probabilities using capture-mark-recapture modelling. Population size increased during the wet season and decreased during the dry season, while survival remained constant across the study period. Individuals captured along road-verges and around water-bodies survived longer than those captured near agricultural fields. The use of gNIS on a heterogeneous landscape such as our study area allowed us to demonstrate that human land-use activities affect Cabrera vole demographic parameters in Mediterranean farmland, with implications for conservation planning towards its long-term persistence. Our approach can be widely applied to other elusive small mammals of conservation concern, but for which informative demographic data are still scarce.

Understanding the factors that contribute to the generation of reproductively isolated forms is a fundamental goal of evolutionary biology. Cryptic species are an especially interesting challenge to study in this context since they lack obvious morphological differentiation that provides clues to adaptive divergence that may drive reproductive isolation. Geographical isolation in refugial areas during glacial cycling is known to be important for generating genetically divergent populations, but its role in the origination of new species is still not fully understood and likely to be situation dependent. We combine analysis of 35,434 single‐nucleotide polymorphisms (SNPs) with environmental niche modeling (ENM) to investigate genomic and ecological divergence in three cryptic species formerly classified as the field vole (Microtus agrestis ). The SNPs demonstrate high genomic divergence (pairwise F ST values of 0.45–0.72) and little evidence of gene flow among the three field vole cryptic species, and we argue that genetic drift may have been a particularly important mechanism for divergence in the group. The ENM reveals three areas as potential glacial refugia for the cryptic species and differing climatic niches, although with spatial overlap between species pairs. This evidence underscores the role that glacial cycling has in promoting genetic differentiation and reproductive isolation by subdivision into disjunct distributions at glacial maxima in areas relatively close to ice sheets. Future investigation of the intrinsic barriers to gene flow between the field vole cryptic species is required to fully assess the mechanisms that contribute to reproductive isolation. In addition, the Portuguese field vole (M. rozianus ) shows a high inbreeding coefficient and a restricted climatic niche, and warrants investigation into its conservation status., N.K.F was supported by an American Society of Mammalogists' Grants-in-Aid and Society for the Study of Evolution Rosemary Grant Award. P.A. is supported by the Spanish Ministerio de Economía y Competitividad (MINECO) and Universidad de Castilla-La Mancha (UCLM) through a “Ramón y Cajal” contract (RYC-2012-11970). J.P. is supported by the European Union's Horizon 2020 Research and Innovation Program under project EnvMetaGen (grant agreement no 668981).

Accurate analyses of the diets of predators are key to understand trophic interactions and defining conservation strategies. Diets are commonly assessed through analysis of non‐invasively collected scats, and the use of faecal DNA (fDNA ) analysis can reduce the species misidentifications that could lead to biased ecological inference. We review the scientific literature since publication of the first paper on amplifying fDNA , in order to assess trends in the use of genetic non‐invasive sampling (gNIS ) for predator species identification in scat‐based diet studies of North American and European terrestrial mammalian carnivores (Carnivora). We quantify error rates in morphology‐based predator species identification. We then provide an overview of how applying gNIS would improve research on trophic interactions and other areas of carnivore ecology. We found that carnivore species identity was verified by using gNIS in only 8% of 400 studies of carnivore diets based on scats. The median percentage of false positives (i.e. samples wrongly identified as belonging to the target species) in morphology‐based studies was 18%, and was consistent regardless of species’ body size. We did not find an increasing trend in the use of gNIS over time, despite the existing technical capability to identify almost all carnivore species. New directions for fDNA studies include employing high‐throughput sequencing (HTS ) and DNA metabarcoding to identify the predator species, the individual predator, the entire assemblage of consumed items, and the microbiome of the predator and pathogens. We conclude that HTS protocols and metagenomic approaches hold great promise for elevating gNIS as a fundamental cornerstone for future research in ecology and conservation biology of mammals., PM enjoyed a postdoctoral fellowship funded by FEDER funds through the Operational Programme for Competitiveness Factors - COMPETE and by National Funds through FCT - Foundation for Science and Technology (UID/BIA/50027/2013 and POCI-01-0145-FEDER-006821). RG was supported by a research contract from the Portuguese Foundation for Science and Technology (IF/564/2012). The University of Idaho, USA, provided salary support for LW. The Luso-American Development Foundation (FLAD) provided travel funding between the University of Porto, Portugal, and the University of Montana, USA.

20 páginas.- 1 figura.- 105 referencias, Alien plant species have been essential for farming and agro-forestry systems and for their supply of food, fiber, tannins, resins or wood from antiquity to the present. They also contributed to supporting functions and regulating services (water, soil, biodiversity) and to the design of landscapes with high cultural and scenic value. Some of those species were intentionally introduced, others arrived accidentally, and a small proportion escaped, naturalized and became invasive in natural ecosystems—these are known as invasive alien species (IAS). Here, invasive means that these species have some significant negative impact, either by spreading from human-controlled environments (e.g. fields, gardens) to natural ecosystems, where they can cause problems to native species, or to other production systems or urban areas, impacting on agricultural, forestry activities or human health. Socio-environmental impacts associated with plant invasions have been increasingly recognized worldwide and are expected to increase considerably under changing climate or land use. Early detection tools are key to anticipate IAS and to prevent and control their impacts. In this chapter, we focus on crop and non-crop alien plant species for which there is evidence or prediction of invasive behaviour and impacts. We provide insights on their history, patterns, risks, early detection, forecasting and management under climate change. Specifically, we start by providing a general overview on the history of alien plant species in agricultural and agroforestry systems worldwide (Sect. 1). Then, we assess patterns, risks and impacts resulting from alien plants originally cultivated and that became invasive outside cultivation areas (Sect. 2). Afterwards, we provide several considerations for managing the spread of invasive plant species in the landscape (Sect. 3). Finally, we discuss challenges of alien plant invasions for agricultural and agroforest systems, in the light of climate change (Sect. 4). © 2019, Springer Nature Switzerland AG., Joana R. Vicente was supported by POPH/FSE and FCT (Post-Doc grant SFRH/BPD/84044/2012). Ana Sofia Vaz was supported by FSE/MEC and FCT (Ph.D. grant PD/BD/52600/2014). Ana Isabel Queiroz supported by FCT—the Portuguese Foundation for Science and Technology [UID/HIS/04209/2013 and IF/00222/2013/CP1166/CT0001]. This work received financial support from the European Union (FEDER funds POCI-01-0145-FEDER-006821) and National Funds (FCT/MEC, Fundação para a Ciência e Tecnologia and Ministério da Educação e Ciência) under the Partnership Agreement PT2020 UID/BIA/50027/2013.

Rivers are amongst the most threatened ecosystems in Europe. To prevent further degradation and to improve their ecological status, effective mitigation and restoration actions are needed. Those actions are primarily based on the precision of the ecological assessment results. This study aims to assess the ecological status of two small Mediterranean rivers-the Âncora (AR) and the Ferreira (FR) rivers-through the analysis of biological (benthic macroinvertebrates and macrophytes), physico-chemical and hydromorphological quality elements. Specific objectives were to analyse variations of biotic and abiotic parameters amongst rivers, and amongst seasons and sites within each river, to confirm adequate temporal windows to develop the monitoring surveys. Results showed that only one AR site achieved a good ecological status in spring and summer, while the other sites presented a moderate ecological status in all seasons. FR sites had a moderate to bad ecological status in all seasons. Both rivers showed high levels of nutrients, particularly during spring and summer, and were found quite altered in terms of floristic composition of the riparian communities. The riparian forest and the forbs fringe were dominated by several alien woody species and nitrophilous communities, respectively. Based on a multidisciplinary approach, this study provides an in-depth description of the ecological status of two small Mediterranean rivers located in sites of European interest, as well as a sound basis for the management of the aquatic environments. Mitigation of diffuse pollution and restoration of the riparian zones are a priority to improve their ecological status.

The importance of targeting ecological and evolutionary processes in reserve design has been widely acknowledged in the literature but rarely implemented on islands. Using Socotran reptiles as models, we aim to relate richness of widespread and restricted-range species directly with landscape variables and to compare the impact of setting conservation targets for lineages versus species. Socotra Island is a UNESCO Natural World Heritage Site, containing high levels of endemism in relation to its area, especially of reptiles, the vertebrates with the most comprehensive available genetic data. We predicted the occurrences of reptile species using distribution models and used a novel approach to interpolate maps of spatial phylogenetic patterns. Patterns of intra and interspecifc diversity and differences between spatial outputs of lineage and species richeness were related to eco-geographic variables. We evaluated differences in target achievement for each conservation unit within protected areas (PAs) under the current Zoning Plan (ZP) using gap and reserve design analyses. Although intraspecific richness was strongly correlated with interspecific richness, differences in their spatial distribution reached ~30% in some areas. Differences were more pronounced for wide-ranging than restricted-range taxa. Gap analysis indicates that most conservation units are under-represented in sanctuaries and that intra and interspecific richness were significantly higher outside PAs. This work will guide local-scale conservation planning as the ZP is due to be re-evaluated. This is one of the few studies on islands using genetic data from an entire class of vertebrates to incorporate lineage diversity in reserve design. This study provides an alternative methodological framework for supporting the use of landscape and genetic tools in reserve design, circumventing the use of phylogenetic distances and deterministic spatial interpolation of lineage diversity that can be widely applied to other systems.

Genetic non-invasive sampling (gNIS) may provide valuable information for population monitoring, as it allows inferences of population density and key behavioural traits such as dispersal, kinship and reproduction. Despite its enormous potential, gNIS has rarely been applied to small mammals, for which live-trapping is still the most commonly used sampling method. Here we evaluated the applicability and cost-effectiveness of gNIS compared with live-trapping, to monitor a metapopulation of an Iberian endemic and elusive rodent: the Cabrera vole (Microtus cabrerae). We compared the genetic diversity, kinship and dispersal movements inferred using both methods. For that, we optimised microsatellite markers for individual identification of M. cabrerae, using both tissue (n = 31) and faecal samples (n = 323) collected from a metapopulation in south-western Iberia. An initial set of 20 loci was optimised for tissue samples, from which 11 were selected to amplify in faecal samples. Overall, gNIS revealed a higher number of identified individuals (65) than live-trapping (31), and the estimated genetic diversity was similar using data from tissues and gNIS. Kinship analysis showed a higher number of inferred relationships and dispersal events when including gNIS, and indicated absence of sex-biased dispersal. The total cost (fieldwork and genetic analysis) of each genotype obtained through live-trapping was three times greater than for gNIS. Our data strongly supports the high potential and cost-effectiveness of gNIS for monitoring populations of elusive and/or threatened small mammals. We also illustrate how this genetic tool can be logistically feasible in conservation.

Estimating the size of animal populations is essential for understanding the demography and conservation status of species. Genetic Non-Invasive Sampling (gNIS) combined with Spatially Explicit Capture-Recapture (SECR) modelling may provide a practical tool to obtain such estimates. Here, we evaluate for the first time the potential and limitations of this approach to estimate population densities for small mammals inhabiting patchily distributed habitats, focusing on the endemic Iberian Cabrera vole (Microtus cabrerae). Using 11 highly polymorphic microsatellites and two sex-linked introns, we compared population estimates in November/December 2011 based on live-trapping and gNIS and assessed the impact of distinct consensus criteria to differentiate unique genotypes. Live-trapping over 21 days captured 31 individuals, while gNIS over 5 days recorded 65–69 individuals. SECR models indicated that individual detectability was positively affected by live-trapping capture success on the previous occasion, while for gNIS, it was mainly affected by genotyping success rates and patch size. Live-trapping produced the lowest density estimates (mean ± SE) of 16.6 ± 3.2 individuals per hectare of suitable habitat (ind/ha). Estimates based on gNIS were higher and varied slightly between 25.2 ± 4.0 and 28.8 ± 4.5 ind/ha depending on assuming one or two genotyping errors, respectively, when differentiating individual genetic profiles. Results suggest that live-trapping underestimated the vole population, while the larger number of individuals detected through gNIS allowed better estimates with lower field effort. Overall, we suggest that gNIS combined with SECR models provides an effective tool to estimate small mammal population densities in fragmented habitats.

Global environmental changes are rapidly affecting species' distributions and habitat suitability worldwide, requiring a continuous update of biodiversity status to support effective decisions on conservation policy and management. In this regard, satellite-derived Ecosystem Functional Attributes (EFAs) offer a more integrative and quicker evaluation of ecosystem responses to environmental drivers and changes than climate and structural or compositional landscape attributes. Thus, EFAs may hold advantages as predictors in Species Distribution Models (SDMs) and for implementing multi-scale species monitoring programs. Here we describe a modelling framework to assess the predictive ability of EFAs as Essential Biodiversity Variables (EBVs) against traditional datasets (climate, land-cover) at several scales. We test the framework with a multi-scale assessment of habitat suitability for two plant species of conservation concern, both protected under the EU Habitats Directive, differing in terms of life history, range and distribution pattern (Iris boissieri and Taxus baccata). We fitted four sets of SDMs for the two test species, calibrated with: interpolated climate variables; landscape variables; EFAs; and a combination of climate and landscape variables. EFAbased models performed very well at the several scales (AUCmedian from 0.881±0.072 to 0.983±0.125), and similarly to traditional climate-based models, individually or in combination with land-cover predictors (AUCmedian from 0.882±0.059 to 0.995±0.083). Moreover, EFAbased models identified additional suitable areas and provided valuable information on functional features of habitat suitability for both test species (narrowly vs. widely distributed), for both coarse and fine scales. Our results suggest a relatively small scale-dependence of the predictive ability of satellite-derived EFAs, supporting their use as meaningful EBVs in SDMs from regional and broader scales to more local and finer scales. Since the evaluation of species' conservation status and habitat quality should as far as possible be performed based on scalable indicators linking to meaningful processes, our framework may guide conservation managers in decision-making related to biodiversity monitoring and reporting schemes., This research was developed as part of the ECOPOTENTIAL project financed by European Union's Horizon 2020 research and innovation program under grant agreement No. 641762. SAC, DAS and JPH received funding from the ECOPOTENTIAL project. JG was supported by FCT (Portuguese Science Foundation) through PhD grant SFRH/BD/90112/2012. DAS received funding from Ministerio de Educación, Cultura y Deporte, JC2015-00316 grant, and Ministerio de Ciencia e Innovación, CGL2014-61610-EXP project.

Animals that occupy temperate and polar regions have specialized traits that help them survive in harsh, highly seasonal environments. One particularly important adaptation is seasonal coat colour (SCC) moulting. Over 20 species of birds and mammals distributed across the northern hemisphere undergo complete, biannual colour change from brown in the summer to completely white in the winter. But as climate change decreases duration of snow cover, seasonally winter white species (including the snowshoe hare Lepus americanus, Arctic fox Vulpes lagopus and willow ptarmigan Lagopus lagopus) become highly contrasted against dark snowless backgrounds. The negative consequences of camouflage mismatch and adaptive potential is of high interest for conservation. Here we provide the first comprehensive review across birds and mammals of the adaptive value and mechanisms underpinning SCC moulting. We found that across species, the main function of SCC moults is seasonal camouflage against snow, and photoperiod is the main driver of the moult phenology. Next, although many underlying mechanisms remain unclear, mammalian species share similarities in some aspects of hair growth, neuroendocrine control, and the effects of intrinsic and extrinsic factors on moult phenology. The underlying basis of SCC moults in birds is less understood and differs from mammals in several aspects. Lastly, our synthesis suggests that due to limited plasticity in SCC moulting, evolutionary adaptation will be necessary to mediate future camouflage mismatch and a detailed understanding of the SCC moulting will be needed to manage populations effectively under climate change.

Freshwater biodiversity is currently threatened worldwide. In North Africa, 24.4% of Odonata are regionally threatened with extinction. In this region, freshwater resources are particularly scarce and an increasing shortage of water is expected. To better understand the current threats to the endangered North African damselfly Coenagrion mercuriale we updated information on extinct and extant populations in North Africa and characterized these localities with regard to their topography, climate and anthropogenic use (anthrome). The C. mercuriale populations are being lost and this damselfly is experiencing range contraction. In Morocco nearly 45% of the populations have become extinct in recent decades and in Tunisia a single extant population remains. This species, which occupied predominantly areas of high value for human settlement, is now mainly restricted to high altitude areas. Nevertheless, the extant populations remain under threat of extinction due to increasing demand for water, changes in agric...

DNA metabarcoding can contribute to improving cost‐effectiveness and accuracy of biological assessments of aquatic ecosystems, but significant optimization and standardization efforts are still required to mainstream its application into biomonitoring programmes. In assessments based on freshwater macroinvertebrates, a key challenge is that DNA is often extracted from cleaned, sorted and homogenized bulk samples, which is time‐consuming and may be incompatible with sample preservation requirements of regulatory agencies. Here, we optimize and evaluate metabarcoding procedures based on DNA recovered from 96% ethanol used to preserve field samples and thus including potential PCR inhibitors and nontarget organisms. We sampled macroinvertebrates at five sites and subsampled the preservative ethanol at 1 to 14 days thereafter. DNA was extracted using column‐based enzymatic (TISSUE) or mechanic (SOIL) protocols, or with a new magnetic‐based enzymatic protocol (BEAD), and a 313‐bp COI fragment was amplified. Metabarcoding detected at least 200 macroinvertebrate taxa, including most taxa detected through morphology and for which there was a reference barcode. Better results were obtained with BEAD than SOIL or TISSUE, and with subsamples taken 7–14 than 1–7 days after sampling, in terms of DNA concentration and integrity, taxa diversity and matching between metabarcoding and morphology. Most variation in community composition was explained by differences among sites, with small but significant contributions of subsampling day and extraction method, and negligible contributions of extraction and PCR replication. Our methods enhance reliability of preservative ethanol as a potential source of DNA for macroinvertebrate metabarcoding, with a strong potential application in freshwater biomonitoring. This article has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 668981 (ERA Chair in Environmental metagenomics, EnvMetaGen) and was supported by EDP‐Biodiversity Chair (EDP/FCT) and the project FRESHING funded by the Portuguese Foundation for Science and Technology (FCT) and COMPETE (PTDC/ AAGMAA/2261/2014—POCI‐01‐0145‐FEDER‐356 016824). FMSM was supported by FCT PhD grant SFRH/BD/104703/2014. PB was supported by EDP‐Biodiversity Chair, MG and JP by the EnvMetaGen, and AFF by FRESHING/FCT. We thank B. Maia‐ Carvalho for his invaluable support on the development of the BEAD protocol, and M. Monaghan for suggestions on DNA quality assessment. info:eu-repo/semantics/publishedVersion

The interactions between animals and their environment vary across species, regions, but also with gender. Sex-specific relations between individuals and the ecosystem may entail different behavioral choices and be expressed through different patterns of habitat use. Regardless, only rarely sex-specific traits are addressed in ecological modeling approaches. The European wildcat (Felis silvestris silvestris) is a species of conservation concern in Europe, with a highly fragmented and declining distribution across most of its range. We assessed sex-specific habitat selection patterns for the European wildcat, at the landscape and home range levels, across its Iberian biogeographic distribution using a multipopulation approach. We developed resource selection functions in a use-availability framework using radio-telemetry data from five wildcat populations. At the landscape level, we observed that, while both genders preferentially established home ranges in areas close to broadleaf forests and far from humanized areas, females selected mid-range elevation areas with some topographic complexity, whereas males used lowland areas. At the home range level, both females and males selected areas dominated by scrublands or broadleaf forests, but habitat features were less important at this level. The strength of association to habitat features was higher for females at both spatial levels, suggesting a tendency to select habitats with higher quality that can grant them enhanced access to shelter and feeding resources. Based on our results, we hypothesize that sex-biased behavioral patterns may contribute to the resilience of wildcats' genetic integrity through influencing the directionality of hybridization with domestic cats. Our study provides information about European wildcats' habitat use in an Iberian context, relevant for the implementation of conservation plans, and highlights the ecological relevance of considering sex-related differences in environmental preferences., This work was supported by a postdoctoral fellowship to PM by FEDER funds through the Operational Programme for Competitiveness Factors—COMPETE and by National Funds through FCT—Foundation for Science and Technology (grant numbers UID/BIA/50027/2013, POCI-01-0145-FEDER-006821); and by a research contract “Juan de la Cierva” to FD-R (grant number FJCI-2015-24949) from the Spanish Ministry of Economy, Industry, and Competitiveness.

Agriculture constitutes a dominant land cover worldwide, and rural landscapesunder extensive farming practices acknowledged due to high biodiversitylevels. The High Nature Value farmland (HNVf) concept has beenhighlighted in the EU environmental and rural policies due to their inherentpotential to help characterize and direct financial support to European landscapeswhere high nature and/or conservation value is dependent on thecontinuation of specific low-intensity farming systems. 2 Assessing the extent of HNV farmland by necessity relies on the availability of both ecological and farming systems’ data, and difficulties associated with making such assessments have been widely described across Europe. A spatially explicit framework of data collection, building out from local administrative units, has recently been suggested as a means of addressing such difficulties. 3 This manuscript tests the relevance of the proposed approach, describes the spatially explicit framework in a case study area in northern Portugal, and discusses the potential of the approach to help better inform the implementation of conservation and rural development policies. 4 Synthesis and applications: The potential of a novel approach (combining land use/cover, farming and environmental data) to provide more accurate and efficient mapping and monitoring of HNV farmlands is tested at the local level in northern Portugal. The approach is considered to constitute a step forward toward a more precise targeting of landscapes for agri-environment schemes, as it allowed a more accurate discrimination of areas within the case study landscape that have a higher value for nature conservation.

Sequential rapid radiations pose some of the greatest difficulties in phylogenetics, especially when analysing only a small number of genetic markers. Given that most of the speciation events occur in quick succession at various points in time, this creates particular challenges in determining phylogenetic relationships, i.e. branching order and divergence times. With the development of high throughput sequencing, thousands of markers can now readily be used to tackle these issues. Microtus is a speciose genus currently composed of 65 species that evolved over the last 2 million years. Although it is a well-studied group, there is still phylogenetic uncertainty at various divergence levels. Building upon previous studies that generally used small numbers of mitochondrial and/or nuclear loci, in this genomic-scale study we used both mitochondrial and nuclear data to study the rapid radiation within Microtus, using partial mitogenomes and genotyping-by-sequencing (GBS) on seven species representing five Microtus subgenera and the main biogeographic ranges where this group occurs. Both types of genome (mitochondrial and nuclear) generated similar tree topologies, with a basal split of the Nearctic (M. ochrogaster) and Holarctic (M. oeconomus) species, and then a subdivision of the five Palearctic species into two subgroups. These data support the occurrence of two European radiations, one North American radiation, and a later expansion of M. oeconomus from Asia to both Europe and North America. We further resolved the positioning of M. cabrerae as sister group of M. agrestis and refute the claim that M. cabrerae should be elevated to its own genus (Iberomys). Finally, the data support ongoing speciation events, especially within M. agrestis, with high levels of genetic divergence between the three Evolutionarily Significant Units (ESUs) previously identified. Similar high levels of divergence were also found among ESUs within M. oeconomus and M. arvalis.

Maintenance of biodiversity in a rapidly changing climate will depend on the efficacy of evolutionary rescue, whereby population declines due to abrupt environmental change are reversed by shifts in genetically driven adaptive traits. However, a lack of traits known to be under direct selection by anthropogenic climate change has limited the incorporation of evolutionary processes into global conservation efforts. In 21 vertebrate species, some individuals undergo a seasonal color molt from summer brown to winter white as camouflage against snow, whereas other individuals remain brown. Seasonal snow duration is decreasing globally, and fitness is lower for winter white animals on snowless backgrounds. Based on 2713 georeferenced samples of known winter coat color-from eight species across trophic levels-we identify environmentally driven clinal gradients in winter coat color, including polymorphic zones where winter brown and white morphs co-occur. These polymorphic zones, underrepresented by existing global protected area networks, indicate hot spots for evolutionary rescue in a changing climate.

Although whole-genome sequencing is becoming more accessible and feasible for nonmodel organisms, microsatellites have remained the markers of choice for various population and conservation genetic studies. However, the criteria for choosing microsatellites are still controversial due to ascertainment bias that may be introduced into the genetic inference. An empirical study of red deer (Cervus elaphus) populations, in which cross-specific and species-specific microsatellites developed through pyrosequencing of enriched libraries, was performed for this study. Two different strategies were used to select the species-specific panels: randomly vs. highly polymorphic markers. The results suggest that reliable and accurate estimations of genetic diversity can be obtained using random microsatellites distributed throughout the genome. In addition, the results reinforce previous evidence that selecting the most polymorphic markers leads to an ascertainment bias in estimates of genetic diversity, when compared with randomly selected microsatellites. Analyses of population differentiation and clustering seem less influenced by the approach of microsatellite selection, whereas assigning individuals to populations might be affected by a random selection of a small number of microsatellites. Individual multilocus heterozygosity measures produced various discordant results, which in turn had impacts on the heterozygosity-fitness correlation test. Finally, we argue that picking the appropriate microsatellite set should primarily take into account the ecological and evolutionary questions studied. Selecting the most polymorphic markers will generally overestimate genetic diversity parameters, leading to misinterpretations of the real genetic diversity, which is particularly important in managed and threatened populations., This work was supported by: Portuguese national funds through the FCT (Fundaçao para a Ciência e a Tecnologia) and FEDER funds (Fundo Europeu de Desenvolvimento Regional) through Programa Operacional Potencial Humano-Quadro de Referencia Estrategico Nacional (POPH-QREN) from the European Social Fund and Portuguese Ministerio da Educaçao e Ciência (SFRH/BD/73732/2010 PhD grant to JQ, Research contract IF/564/2012 to RG and SFRH/BSAB/1278/2012 sabbatical grant to PCA); FLAD (Luso-American Foundation); project ‘Genomicsand Evolutionary Biology’ cofinanced by North Portugal Regional Operational Programme 2007/2013 (ON.2 – O Novo Norte), under the National Strategic Reference Framework (NSRF),through the European Regional Development Fund (ERDF); and the Harmonized Approaches in monitoring wildlife Population Health, And Ecology and Abundance (APHAEA,219235_FP7_ERA-NET_EMIDA).

[Aim]: Climate changes in the past had a deep impact on the evolutionary history of many species and left genetic signatures that are often still detectable today. We investigated the geographical pattern of mitochondrial DNA diversity in the European wild boar (Sus scrofa). Our final aims were to clarify the influence of present and past climatic conditions, infer the geographical position of glacial refugia, and suggest post-glacial spatial dynamics. [Location]: Europe. [Methods]: D-loop sequences were obtained for 763 individuals from Portugal to western Russia. Phylogenetic, multivariate and interpolation methods were used to describe the genetic and geographical patterns. Climatic suitability during the Last Glacial Maximum (LGM) was predicted using MaxEnt. The effect of present and past suitability on the observed patterns of diversity was evaluated by multiple linear regression. [Results]: We confirmed the existence of a ubiquitous mitochondrial clade in Europe (E1), an endemic clade in Italy (E2) and a few East Asian haplotypes (A), presumably introgressed from domestic pigs. No Near Eastern haplotypes were detected. Genetic divergence was not simply related to geographical distance. A clear south-north decreasing gradient of diversity was observed, with maximum levels in putative glacial refugia. Latitudinal variation in climatic conditions during the LGM was shown to be a good predictor of current genetic diversity. Moreover, an unexpected similarity between Iberia and eastern Europe was observed, while central European populations showed a higher affinity to the Italian gene pool. [Main conclusions]: The current distribution of mitochondrial genetic diversity was highly influenced by past climatic events, especially those related to the LGM, and is consistent with a major contribution of the Italian peninsula and the Balkans to the post-glacial recolonization of northern areas. More recent processes, such as restocking and extensive hunting, probably acted at rather local scales, without great impact on the global pattern of mitochondrial diversity., Sequencing activities were funded by the Sardinian Regional Government (L.R. 7/2007 Promozione della Ricerca Scientifica e dell’Innovazione Tecnologica in Sardegna). D.B. had a PhD grant financed by the European Social Fund, Operational Programme 2007/2013 – Axis IV – Human Capital Investment. S.T.V. was supported by a PhD Fellowship for International students of the University of Ferrara. B.J. andT.B. were supported by grants N N304 253935 from the Polish Ministry of Science and Higher Education and Research Potential in Conservation and Sustainable Management of Biodiversity – BIOCONSUS from the EC’s 7th Framework Programme (contract no. 245737). Mobility between labs in Sassari and Kiel was financed by the Italy–Germany Vigoni cooperation program 2010–2011.

International audience; Genetic introgression from a resident species into an invading close relative can result from repeated hybridisation along the invasion front and/or allele surfing on the expansion wave. Cases where the phenomenon is massive and systematic, such as for hares (genus Lepus) in Iberia, would be best explained by recurrent hybridisation but this is difficult to prove because the donor populations are generally extinct. In the Pyrenean foothills, Lepus europaeus presumably replaced Lepus granatensis recently and the present species border is parallel to the direction of invasion, so that populations of L. granatensis in the contact zone represent proxies of existing variation before the invasion. Among three pairs of populations sampled across this border, we find less differentiation of mitochondrial DNA (mtDNA) across than along it, as predicted under recurrent hybridisation at the invasion front. Using autosomal microsatellite loci and X-and Y-linked diagnostic loci, we show that admixture across the border is quasi-absent, making it unlikely that lack of interspecific mtDNA differentiation results from ongoing gene flow. Furthermore, we find that the local species ranges are climatically contrasted, making it also unlikely that ongoing ecologydriven movement of the contact account for mtDNA introgression. The lack of mtDNA differentiation across the boundary is mostly due to sharing of mtDNA from a boreal species currently extinct in Iberia (Lepus timidus) whose mitochondria have thus remained in place since the last deglaciation despite successive invasions by two other species. Home-loving mitochondria thus witness past species distribution rather than ongoing exchanges across stabilised contact zones.

Introgressive hybridization is an important and widespread evolutionary process, but the relative roles of neutral demography and natural selection in promoting massive introgression are difficult to assess and an important matter of debate. Hares from the Iberian Peninsula provide an appropriate system to study this question. In its northern range, the Iberian hare, Lepus granatensis, shows a northwards gradient of increasing mitochondrial DNA (mtDNA) introgression from the arctic/boreal L. timidus, which it presumably replaced after the last glacial maximum. Here, we asked whether a south-north expansion wave of L. granatensis into L. timidus territory could underlie mtDNA introgression, and whether nuclear genes interacting with mitochondria (“mitonuc” genes) were affected. We extended previous RNA-sequencing and produced a comprehensive annotated transcriptome assembly for L. granatensis. We then genotyped 100 discovered nuclear SNPs in 317 specimens spanning the species range. The distribution of allele frequencies across populations suggests a northwards range expansion, particularly in the region of mtDNA introgression. We found no correlation between variants at 39 mitonuc genes and mtDNA introgression frequency. Whether the nuclear and mitochondrial genomes coevolved will need a thorough investigation of the hundreds of mitonuc genes, but range expansion and species replacement likely promoted massive mtDNA introgression.

Glacial refugia protected and promoted biodiversity during the Pleistocene, not only at a broader scale, but also for many endemics that contracted and expanded their ranges within refugial areas. Understanding the evolutionary history of refugial endemics is especially important in the case of endangered species to recognize the origins of their genetic structure and thus produce better informed conservation practices. The Iberian Peninsula is an important European glacial refugium, rich in endemics of conservation concern, including small mammals, such as the Cabrera vole (Microtus cabrerae). This near-threatened rodent is characterized by an unusual suite of genetic, life history and ecological traits, being restricted to isolated geographic nuclei in fast-disappearing Mediterranean subhumid herbaceous habitats. To reconstruct the evolutionary history of the Cabrera vole, we studied sequence variation at mitochondrial, autosomal and sex-linked loci, using invasive and noninvasive samples. Despite low overall mitochondrial and nuclear nucleotide diversities, we observed two main well-supported mitochondrial lineages, west and east. Phylogeographic modelling in the context of the Cabrera vole's detailed fossil record supports a demographic scenario of isolation of two populations during the Last Glacial Maximum from a single focus in the southern part of the Iberian Peninsula. In addition, our data suggest subsequent divergence within the east, and secondary contact and introgression of the expanding western population, during the late Holocene. This work emphasizes that refugial endemics may have a phylogeographic history as rich as that of more widespread species, and conservation of such endemics includes the preservation of that genetic legacy., The necessary trapping permits for this work were provided by the Portuguese Instituto da Conservação da Natureza e das Florestas (319/2012/CAPT), Comunidad de Madrid (10/076408), Generalitat Valenciana (60/2014‐VS‐FAU14‐011), Gobierno de Aragon (550201.24.2013.1031; INAGA/500201/24/2014/337), Gobierno de Castilla‐la‐Mancha (DGMEN/SEN/avp_13_013_aut; DGMEN/SEN/avp_14_022_aut), Junta de Castilla y León (EP/AV/407/2012; EP/SA/71/2014) and Región de Murcia (AUF/2013/0038; AUF/2014/0010). This work was partially supported by Programa Operacional Potencial Humano—Quadro de Referência Estratégico Nacional funds from the European Social Funds and Portuguese Ministério da Educação e Ciência through Fundação para a Ciência e Tecnologia (FCT SFRH/BD/77726/2011 PhD grant to S. Barbosa), by the European Regional Development Fund (ERDF) through COMPETE programme and Portuguese national funds through FCT (PTDC/BIA‐BEC/105110/2008, PTDC/AAG‐MAA/3227/2012 and PTDC/BIA‐BIC/6582/2014 research projects). J. Paupério had a postdoctoral grant funded by the project ‘Genomics and Evolutionary Biology’ co‐financed by North Portugal Regional Operational Programme 2007/2013 (ON.2—O Novo Norte), under the National Strategic Reference Framework, through the ERDF.

Baccharis spicata, a species native to South America (southern Brazil, Paraguay, Uruguay, and northeastern and central Argentina) is reported for the first time from Europe. In September 2015, two naturalized populations were detected in the surroundings of Porto (Matosinhos and Vila do Conde) in Portugal. Based on literature data, the species’ taxonomy and nomenclature are analyzed and it is described and illustrated. Furthermore, its ecology, habitat, biology, and possible vector of introduction are discussed. Finally, its invasive potential for the European Union is assessed, based on climatic variables and two different risk assessment methods.