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The lichen-forming genus Pertusaria under its current circumscription is polyphyletic and its phylogenetic affiliations are uncertain. Here we study the species of the genera Pertusaria and Varicellaria which containlecanoric acid as major constituent, have disciform apothecia, strongly amyloid asci, non-amyloid hymenial gel, 1-2-spored asci, and 1- or 2-celled ascospores with thick, 1-layered walls. We infer phylogenetic relationships using maximum likelihood and Bayesian analyses based on four molecular loci (mtSSU, nuLSU rDNA, and the protein-coding, nuclear RPB1 and MCM7 genes). Our results show that the lecanoric acid-containing species form a well-supported, monophyletic group, which is only distantly related to Pertusaria s.str. The phylogenetic position of this clade is unclear, but placement in Pertusaria s.str. is rejected using alternative hypothesis testing. The circumscription of the genus Varicellaria is enlarged to also include species with non-septate ascospores. Seven species are accepted in the genus: Varicellaria culbersonii (Vězda) Schmitt & Lumbsch, comb. nov., Varicellaria hemisphaerica (Flörke) Schmitt & Lumbsch, comb. nov., Varicellaria kasandjeffii (Szatala) Schmitt & Lumbsch, comb. nov., Varicellaria lactea (L.) Schmitt & Lumbsch, comb. nov., Varicellaria philippina (Vain.) Schmitt & Lumbsch, comb. nov., Varicellaria rhodocarpa (Körb.) Th. Fr., and Varicellaria velata (Turner) Schmitt & Lumbsch, comb. nov. A key to the species of Varicellaria is provided.
An updated inventory of the Bromeliaceae for Costa Rica is presented including citations of representative specimens for each species. The family comprises 18 genera and 198 species in Costa Rica, 32 species being endemic to the country. Additional 36 species are endemic to Costa Rica and Panama. Only 4 of the 8 bromeliad subfamilies occur in Costa Rica, with a strong predominance of Tillandsioideae (7 genera/150 spp.; 75.7% of all bromeliad species in Costa Rica). 124 species (62.6%) grow exclusively epiphytic, additional 59 spp. (29.8%) are facultative epiphytes. The most diverse genus is Werauhia, with 59 species (29.8% of the Costa Rican bromeliad flora), followed by Tillandsia with 40 species (20.2%) and Guzmania with 28 spp. (8.6%).
We report new localities for the lizard Anolis salvini Boulenger, 1885, along the Pacific slopes of the Cordillera Central in Chiriquí province and the Comarca Ngöbe-Buglé of western Panama. These records extend the known geographic distribution of this species about 70 km eastwards. They also extend the known vertical distribution approximately 70 m uphill. Additionally, we provide the first record for the Caribbean slopes, an updated distribution map, photos of specimens from different localities, an analysis of a distress call, and comments on the morphology of this species.
Background: The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text.
Results: We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities.
Conclusions: The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established vocabularies or ontologies, but rather serve as an overarching framework based on which different application- and domain-specific ontologies, thesauri and vocabularies of phenotypes observed in flowering plants can be integrated.
The existence of individual variation in males' motivation to mate remains a conundrum as directional selection should favour high mating frequencies. Balancing selection resulting from (context-dependent) female mate choice could contribute to the maintenance of this behavioural polymorphism. In dichotomous choice tests, mosquitofish (Gambusia holbrooki) females preferred virtual males showing intermediate mating frequencies, reflecting females' tendencies to avoid harassment by highly sexually active males. When tested in the presence of a female shoal—which protects females from male harassment—focal females showed significantly stronger preferences for high sexual activity. A trade-off between (indirect) benefits and (direct) costs of mating with sexually active males probably explains context-dependent female mate choice, as costs depend on the social environment in which females choose their mates. No preference was observed when we tested virgin females, suggesting that the behavioural pattern described here is part of the learned behavioural repertoire of G. holbrooki females.
Background: Taxonomy offers precise species identification and delimitation and thus provides basic information for biological research, e.g. through assessment of species richness. The importance of molecular taxonomy, i.e., the identification and delimitation of taxa based on molecular markers, has increased in the past decade. Recently developed exploratory tools now allow estimating species-level diversity in multi-locus molecular datasets.
Results: Here we use molecular species delimitation tools that either quantify differences in intra- and interspecific variability of loci, or divergence times within and between species, or perform coalescent species tree inference to estimate species-level entities in molecular genetic datasets. We benchmark results from these methods against 14 morphologically readily differentiable species of a well-defined subgroup of the diverse Drusinae subfamily (Trichoptera, Limnephilidae). Using a 3798 bp (6 loci) molecular data set we aim to corroborate a geographically isolated new species by integrating comparative morphological studies and molecular taxonomy.
Conclusions: Our results indicate that only multi-locus species delimitation provides taxonomically relevant information. The data further corroborate the new species Drusus zivici sp. nov. We provide differential diagnostic characters and describe the male, female and larva of this new species and discuss diversity patterns of Drusinae in the Balkans. We further discuss potential and significance of molecular species delimitation. Finally we argue that enhancing collaborative integrative taxonomy will accelerate assessment of global diversity and completion of reference libraries for applied fields, e.g., conservation and biomonitoring.
Importance of latrine communication in European rabbits shifts along a rural–to–urban gradient
(2016)
Background: Information transfer in mammalian communication networks is often based on the deposition of excreta in latrines. Depending on the intended receiver(s), latrines are either formed at territorial boundaries (between-group communication) or in core areas of home ranges (within-group communication). The relative importance of both types of marking behavior should depend, amongst other factors, on population densities and social group sizes, which tend to differ between urban and rural wildlife populations. Our study is the first to assess (direct and indirect) anthropogenic influences on mammalian latrine-based communication networks along a rural-to-urban gradient in European rabbits (Oryctolagus cuniculus) living in urban, suburban and rural areas in and around Frankfurt am Main (Germany).
Results: The proportion of latrines located in close proximity to the burrow was higher at rural study sites compared to urban and suburban ones. At rural sites, we found the largest latrines and highest latrine densities close to the burrow, suggesting that core marking prevailed. By contrast, latrine dimensions and densities increased with increasing distance from the burrow in urban and suburban populations, suggesting a higher importance of peripheral marking.
Conclusions: Increased population densities, but smaller social group sizes in urban rabbit populations may lead to an increased importance of between-group communication and thus, favor peripheral over core marking. Our study provides novel insights into the manifold ways by which man-made habitat alterations along a rural-to-urban gradient directly and indirectly affect wildlife populations, including latrine-based communication networks.
Erratum to doi:10.1186/s13071-016-1853-2
Background: Aedes albopictus and Ae. japonicus are two of the most widespread invasive mosquito species that have recently become established in western Europe. Both species are associated with the transmission of a number of serious diseases and are projected to continue their spread in Europe.
Methods: In the present study, we modelled the habitat suitability for both species under current and future climatic conditions by means of an Ensemble forecasting approach. We additionally compared the modelled MAXENT niches of Ae. albopictus and Ae. japonicus regarding temperature and precipitation requirements.
Results: Both species were modelled to find suitable habitat conditions in distinct areas within Europe: Ae. albopictus within the Mediterranean regions in southern Europe, Ae. japonicus within the more temperate regions of central Europe. Only in few regions, suitable habitat conditions were projected to overlap for both species. Whereas Ae. albopictus is projected to be generally promoted by climate change in Europe, the area modelled to be climatically suitable for Ae. japonicus is projected to decrease under climate change. This projection of range reduction under climate change relies on the assumption that Ae. japonicus is not able to adapt to warmer climatic conditions. The modelled MAXENT temperature niches of Ae. japonicus were found to be narrower with an optimum at lower temperatures compared to the niches of Ae. albopictus.
Conclusions: Species distribution models identifying areas with high habitat suitability can help improving monitoring programmes for invasive species currently in place. However, as mosquito species are known to be able to adapt to new environmental conditions within the invasion range quickly, niche evolution of invasive mosquito species should be closely followed upon in future studies.
Speolepta leptogaster (Winnertz, 1863) is frequently occurring in European subterranean environments. As for most cave animals, studies addressing non-anatomical aspects are sparse. Here we present the first molecular study on S. leptogaster. We investigated the demographic structure (i.e. COI locus) of 69 specimens from 36 underground populations in Hesse (Central German Uplands) to get first insights into the species’ dispersal ability.
In total, 14 haplotypes were revealed. Haplotype diversity was relatively high, whereas nucleotide diversity was low. Furthermore, a significant but low pattern of isolation-by-distance and (a) past population expansion event(s) were detected.
Our genetic results suggest a (good) active dispersal ability for Speolepta leptogaster. The occurrence of several surface records of adult specimens corroborates this hypothesis. We discuss the developmental stages of S. leptogaster in the context of the ecological classification system and regard the species as a eutroglophile. Evidence has been found to distinguish two larval types. A reconstructed life-cycle of the species is provided.
We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced ‘cybertype’ notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.
Reporting on the first locality in Bocas del Toro province of extreme western Panama, we extend the known geographic distribution of the lizard Leposoma rugiceps (Cope, 1869) about 275 km westwards from the nearest locality in Panamá province. We provide photos of Panamanian specimens, comment on their morphology, and map the distribution of this binational endemism.
Reporting on the southernmost locality in Costa Rica and the first two localities in Panama, we extend the known geographic distribution of the lizard Potamites apodemus (Uzzell, 1966) roughly 20 km eastwards, 40 km southwards, and 175 m in elevation. We provide photos of Panamanian specimens, comment on their morphology, and map the distribution of this unique species.
We report on new localities for Anolis gruuo Köhler, Ponce, Sunyer and Batista, 2007 along the Serranía de Tabasará in the Comarca Ngöbe-Buglé and Veraguas province of western Panama. These records extend the known geographic distribution of this lizard about 80 km eastward, and the known vertical distribution approximately 40 m lower and 630 m higher. We provide photos of specimens from different localities and comment on their morphology. Only the easternmost populations of this Panamanian endemic live inside a protected area.
The partial faunal reserve of Pama is situated in the province of Kompienga, in the South-East of Burkina Faso, with typical Sudanian savanna vegetation. Adjacent to the Arli National Park and the Pendjari National Park, it is part of the so-called WAP complex, one of the largest wildlife areas in West Africa. Up to now, only little has been known about its flora. The present study aimed at reducing this gap in knowledge, and represents an important tool for conservation and research. The list of species was compiled from the surveys carried out from 2001 to 2004, additional relevé data, and herbarium specimens. We found 450 species, which belong to 244 genera and 73 families. The most species-rich family is Poaceae (83 species), followed by Fabaceae (64), Cyperaceae (24), Rubiaceae (22), Euphor- biaceae (20), Combretaceae (15), Asteraceae (14), Caesalpiniaceae (14), Mimosaceae (12), and Convolvulaceae (11).
Gallery forests (GFs) are floristically and functionally distinct forests along rivers and watercourses. The GFs of the West African savannas form thin stripes with a particular, species-rich flora differing significantly from the surrounding vegetation. Due to their relative isolation in the savannas and their dependence on rivers, GFs are particularly endangered by the expected global climate changes in the 21st century. Despite their high diversity, little is known about the ecology and biogeography of GFs in West Africa. Especially, their response to climate changes and their vegetation dynamics remain largely unknown. This thesis combines floristic, phylo-geographic and ecological data to investigate the biodiversity, historical and recent biogeography and conservation status of GF species in Burkina Faso (BFA) as a model for West Africa.
Southern African protected areas (PAs) harbour a great diversity of animals, which represent a large potential for wildlife tourism. In this region, global change is expected to result in vegetation changes, such as bush encroachment and increases in vegetation density. However, little is known on the influence of vegetation structure on wildlife tourists’ wildlife viewing experience and satisfaction. In this study, we collected data on vegetation structure and perceived mammal densities along 196 road transects (each 5 km long) and conducted a social survey with 651 questionnaires across four PAs in three Southern African countries. Our objectives were 1) to assess visitors’ attitude towards vegetation, 2) to test the influence of perceived mammal density and vegetation structure on the easiness to spot animals, and 3) on visitors’ satisfaction during their visit to PAs. Using a Boosted Regression Tree procedure, we found mostly negative non-linear relationships between vegetation density and wildlife tourists’ experience, and positive relationships between perceived mammal densities and wildlife tourists’ experience. In particular, wildlife tourists disliked road transects with high estimates of vegetation density. Similarly, the easiness to spot animals dropped at thresholds of high vegetation density and at perceived mammal densities lower than 46 individuals per road transect. Finally, tourists’ satisfaction declined linearly with vegetation density and dropped at mammal densities smaller than 26 individuals per transect. Our results suggest that vegetation density has important impacts on tourists’ wildlife viewing experience and satisfaction. Hence, the management of PAs in savannah landscapes should consider how tourists perceive these landscapes and their mammal diversity in order to maintain and develop a sustainable wildlife tourism.
Large-scale genetic census of an elusive carnivore, the European wildcat (Felis s. silvestris)
(2016)
The European wildcat, Felis silvestris silvestris, serves as a prominent target species for the reconnection of central European forest habitats. Monitoring of this species, however, appears difficult due to its elusive behaviour and the ease of confusion with domestic cats. Recently, evidence for multiple wildcat occurrences outside its known distribution has accumulated in several areas across Central Europe, questioning the validity of available distribution data for this species. Our aim was to assess the fine-scale distribution and genetic status of the wildcat in its central European distribution range. We compiled and analysed genetic samples from roadkills and hundreds of recent hair-trapping surveys and applied phylogenetic and genetic clustering methods to discriminate wild and domestic cats and identify population subdivision. 2220 individuals were confirmed as either wildcat (n = 1792) or domestic cat (n = 342), and the remaining 86 (3.9 %) were identified as hybrids between the two. Remarkably, genetic distinction of domestic cats, wildcats and their hybrids was only possible when taking into account the presence of two highly distinct genetic lineages of wildcats, with a suture zone in central Germany. 44 % of the individual wildcats where sampled outside the previously published distribution. Our analyses confirm a relatively continuous spatial presence of wildcats across large parts of the study area in contrast to previous analyses indicating a highly fragmented distribution. Our results suggest that wildcat conservation and management should take advantage of the higher than previously assumed dispersal potential of wildcats, which may use wildlife corridors very efficiently.
Climate change indicators are tools to assess, visualize and communicate the impacts of climate change on species and communities. Indicators that can be applied to different taxa are particularly useful because they allow comparative analysis to identify which kinds of species are being more affected. A general prediction, supported by empirical data, is that the abundance of warm-adapted species should increase over time, relative to the cool-adapted ones within communities, under increasing ambient temperatures. The community temperature index (CTI) is a community weighted mean of species’ temperature preferences and has been used as an indicator to summarize this temporal shift. The CTI has the advantages of being a simple and generalizable indicator; however, a core problem is that temporal trends in the CTI may not only reflect changes in temperature. This is because species’ temperature preferences often covary with other species attributes, and these other attributes may affect species response to other environmental drivers. Here, we propose a novel model-based approach that separates the effects of temperature preference from the effects of other species attributes on species’ abundances and subsequently on the CTI. Using long-term population data of breeding birds in Denmark and demersal marine fish in the southeastern North Sea, we find differences in CTI trends with the original approach and our model-based approach, which may affect interpretation of climate change impacts. We suggest that our method can be used to test the robustness of CTI trends to the possible effects of other drivers of change, apart from climate change.
Over the last decades agroforestry parklands in Burkina Faso have come under increasing demographic as well as climatic pressures, which are threatening indigenous tree species that contribute substantially to income generation and nutrition in rural households. Analyzing the threats as well as the species vulnerability to them is fundamental for priority setting in conservation planning. Guided by literature and local experts we selected 16 important food tree species (Acacia macrostachya, Acacia senegal, Adansonia digitata, Annona senegalensis, Balanites aegyptiaca, Bombax costatum, Boscia senegalensis, Detarium microcarpum, Lannea microcarpa, Parkia biglobosa, Sclerocarya birrea, Strychnos spinosa, Tamarindus indica, Vitellaria paradoxa, Ximenia americana, Ziziphus mauritiana) and six key threats to them (overexploitation, overgrazing, fire, cotton production, mining and climate change). We developed a species-specific and spatially explicit approach combining freely accessible datasets, species distribution models (SDMs), climate models and expert survey results to predict, at fine scale, where these threats are likely to have the greatest impact. We find that all species face serious threats throughout much of their distribution in Burkina Faso and that climate change is predicted to be the most prevalent threat in the long term, whereas overexploitation and cotton production are the most important short-term threats. Tree populations growing in areas designated as ‘highly threatened’ due to climate change should be used as seed sources for ex situ conservation and planting in areas where future climate is predicting suitable habitats. Assisted regeneration is suggested for populations in areas where suitable habitat under future climate conditions coincides with high threat levels due to short-term threats. In the case of Vitellaria paradoxa, we suggest collecting seed along the northern margins of its distribution and considering assisted regeneration in the central part where the current threat level is high due to overexploitation. In the same way, population-specific recommendations can be derived from the individual and combined threat maps of the other 15 food tree species. The approach can be easily transferred to other countries and can be used to analyze general and species specific threats at finer and more local as well as at broader (continental) scales in order to plan more selective and efficient conservation actions in time. The concept can be applied anywhere as long as appropriate spatial data are available as well as knowledgeable experts.