Diversity, Volume 12, Issue 8 (August 2020) – 30 articles

Biodiversity is vital for the stability of the planet; its ecosystem services provide essential elements for our survival and well-being. This review analyzes the national biodiversity policies and describes the main strategies for biodiversity conservation in Ecuador, one of the “mega-diverse” countries in the world with the highest species density. It deepens an analysis of in-situ and ex-situ conservation processes. Ecuador has six clear policies for biodiversity conservation. These policies strengthen biodiversity conservation through mechanisms that improve the well-being of wildlife by ensuring human, wildlife and ecosystem health. It promotes actions for the welfare of wildlife, through technical, administrative and legal tools. The National System of Protected Areas, with 60 protected areas, is the most effective in-situ conservation instrument at the country level. Several ex-situ conservation and management means for the conservation of wild species are being utilized, including nurseries, botanical gardens, zoos, germplasm banks, aquariums, species reproduction and rehabilitation centers. Ecuador is making slow progress on ex-situ conservation despite the availability of a sound policy framework, possibly due to financial, infrastructural, and/or technological challenges, and knowledge gaps. We propose fostering international research collaborations and establishing fully funded small-scale captive breeding programs at zoos, aquariums and university research facilities to help recovery of at-risk species of reptiles, amphibians, fish and species beyond Galapagos region. We recommend utilizing citizen science programs to fill the gaps of biodiversity information and increasing efforts to revive the ex-situ conservation strategies in protecting the unique biodiversity of Ecuador. Full article

Illegal wildlife trade, which mostly focuses on high-demand species, constitutes a major threat to biodiversity. However, whether poaching is an opportunistic crime within high-demand taxa such as parrots (i.e., harvesting proportional to species availability in the wild), or is selectively focused on particular, more desirable species, is still under debate. Answering this question has important conservation implications because selective poaching can lead to the extinction of some species through overharvesting. However, the challenges of estimating species abundances in the wild have hampered studies on this subject. We conducted a large-scale survey in Colombia to simultaneously estimate the relative abundance of wild parrots through roadside surveys (recording 10,811 individuals from 25 species across 2221 km surveyed) and as household, illegally trapped pets in 282 sampled villages (1179 individuals from 21 species). We used for the first time a selectivity index to test selection on poaching. Results demonstrated that poaching is not opportunistic, but positively selects species based on their attractiveness, defined as a function of species size, coloration, and ability to talk, which is also reflected in their local prices. Our methodological approach, which shows how selection increases the conservation impacts of poaching for parrots, can be applied to other taxa also impacted by harvesting for trade or other purposes. Full article

Phytosociology is a reference method to classify vegetation that relies on field data. Its classification in hierarchical vegetation units, from plant associations to class level, hierarchically reflects the floristic similarity between different sites on different spatial scales. The development of remotely sensed multispectral platforms as satellites enormously contributes to the detection and mapping of vegetation on all scales. However, the integration between phytosociology and remotely sensed data is rather difficult and little practiced despite being a goal for the modern science of vegetation. In this study, we demonstrate how normalized difference vegetation index (NDVI) time series with functional principal component analysis (FPCA) could support the analyses of phytosociologists. The approach supports the recognition and characterization of forest plant communities identified on the ground by the phytosociological approach by using NDVI time series that encode phenological behaviors. The methodology was evaluated in two study areas of central Italy, and it could characterize and discriminate six different forest plant associations that have similar dominant tree species but distinct specific composition: three dominated by black hornbeam (Ostrya carpinifolia) and three dominated by holm oak (Quercus ilex). The methodology was also able to optimize the ground data collection of unexplored areas (from a phytosociological point of view) by using a phenoclustering approach. The obtained results confirmed that by using remote sensing, it is possible to separate and distinguish plant communities in an objective/instrumental way, thus overcoming the subjectivity intrinsic to the phytosociological method. In particular, FPCA functional components (NDVI seasonalities) were significantly correlated with vegetation abundance data variation (Mantel r = 0.76, p < 0.001). Full article

Long-term monitoring programs and population demographic models have shown that the population dynamics of orchids are to a large extent dependent on prevailing weather conditions, suggesting that the changes in climatic conditions can have far reaching effects on the population dynamics and hence the distribution of orchids. Although a better understanding of the effects of climate change on the distribution of plants has become increasingly important during the final years, only a few studies have investigated the effects of changing temperature and precipitation on the distribution of orchids. In this study, we investigated the impact of climate change on the distribution of four terrestrial orchid species (Orchis anthropophora, Orchis militaris, Orchis purpurea and Orchis simia). Using bioclimatic data for current and future climate scenarios, habitat suitability, range shifts and the impact of different abiotic factors on the range of each species were modelled using Maxent. The results revealed an increase in suitable habitat area for O. anthropophora, O. purpurea and O. simia under each RCP (Representative Concentration Pathway) scenario, while a decrease was observed for O. militaris. Furthermore, all four of the orchids showed a shift to higher latitudes under the three RCPs leading to a significant range extension under mild climate change. Under severe climate change, a significant decline in the distribution area at the warm edge of their distributions was observed. Overall, these results show that mild climate change may be beneficial for the studied orchid species and lead to range expansion. However, continued warming may yet prove detrimental, as all species also showed pronounced declines at lower latitudes when temperature increases were larger than 4 °C. Full article

The aim of this research is to set a successful strategy for engaging citizen marine scientists and to obtain reliable data on marine species. The case study of this work is the bearded fireworm Hermodice carunculata, a charismatic species spreading from the southern Mediterranean probably in relation to global warming. To achieve research objectives, some emerging technologies (mainly social platforms) were combined with web ecological knowledge (i.e., data, pictures and videos about the target species published on the WWW for non-scientific purposes) and questionnaires, in order to invite people to collect ecological data on the amphinomid worm from the Adriatic Sea and to interact with involved people. In order to address future fruitful citizen science campaigns, strengths and weakness of each used method were illustrated; for example, the importance of informing and thanking involved people by customizing interactions with citizens was highlighted. Moreover, a decisive boost in people engagement may be obtained through sharing the information about citizen science project in online newspapers. Finally, the work provides novel scientific information on the polychete’s distribution, the northernmost occurrence record of H. carunculata in the Mediterranean Sea and new insights on predatory behavior on other living benthic species. Full article

We used integrative taxonomy to describe a new species of Atelopus from the lowlands of Central Amazonia in the region of Manaus, Amazonas, Brazil. The new species is geographically isolated from the southernmost species of Atelopus of the Guiana Shield. Atelopus manauensis species nova (sp. nov.) is characterized by the combination of the following characteristics: male snout-vent length range (SVL = 19.1–26.4 mm; n = 11); dorsal and lateral skin smooth; ventral surface entirely white or white with cream-colored gular region; fingers and toes lacking subarticular tubercles and fringes. The advertisement call of the new species has a call duration of 689–840 ms, contains 15–26 pulses, is emitted at an average pulse rate of 25.5 pulses per second, and has a dominant frequency ranging 3088–3610 Hz. The genetic divergence between the new species and its morphologically most similar congeners (A. spumarius and A. pulcher) is greater than 4%. Atelopus manauensis sp. nov. is closely related to species of the A. hoogmoedi complex inhabiting the Guiana Shield. The new species has a small geographic distribution (approximately 4500 km²) in a landscape that is strongly threatened by the growth of Manaus, the largest city in Brazilian Amazonia. The new species is considered critically endangered and in need of urgent conservation measures. Full article

The Mediterranean Sea is currently experiencing a decline in the abundance of several key species, as a consequence of anthropogenic pressures (e.g., increase in human population, habitat modification and loss, pollution, coastal urbanization, overexploitation, introduction of non-indigenous species and climate change). Herbaria and natural history collections are certainly fundamental for taxonomic studies, but they are also an invaluable, if currently underestimated, resource for understanding ecological and evolutionary responses of species to environmental changes. Macroalgae herbarium collections, which are really consistent (ranging from 200,000 to approximately 500,000 specimens) in some European herbaria (e.g., Muséum National d’Histoire Naturelle in Paris, University of Copenhagen, Natural History Museum in Kensington), can be successfully used as real “witnesses” to biodiversity changes. In this respect, we report some case studies from the Mediterranean Sea which summarize well the potential of macroalgae herbarium specimens to provide useful data on biodiversity changes. Indeed, these data enable the evaluation of the responses of biota, including shifts in species ranges, the detection of the presence of introduced species, and the prediction of changes in species distributions and patterns under future climate scenarios. To increase the use of this invaluable tool of research, their curation, the digitization of collections, and specimen genomics should be even more addressed. Full article

The present study aimed to investigate the structure, composition and diversity of the over-wintering aquatic bird community of Poyang Lake, including Poyang Lake National Nature Reserve (PNNR), Nanji National Nature Reserve (NNNR) and Duchang Provincial Nature Reserve (DPNR), China. After the preliminary survey, birds surveyed from vantage points at each study site between the years 2016 and 2020 in the winter season. A total of 58 bird species belonging to nine orders and 13 families were observed. The study showed variation in effective species numbers (Species richness, Shannon’s diversity and Simpson’s diversity) among the three study sites and the survey years. Nanji National Nature Reserve had the highest avian diversity, whereas Duchang Provincial Nature Reserve had the lowest. Globally threatened bird species, Siberian Crane (critically endangered), Oriental Stork (endangered), found in our study sites. However, the current management practices of the nature reserve and conservation of this globally threatened bird species are inadequate, especially of Duchang Provincial Nature Reserve. Therefore, for long term conservation of birds in these areas, it needs continuing intentional improvement of the sites and awareness creation to the local community. Full article

Fire is a key driver of natural ecosystems in Africa. However, human activity and climate change have altered fire frequency and severity, with negative consequences for biodiversity conservation. Angola ranks among the countries with the highest fire activity in sub-Saharan Africa. In this study, we investigated the spatial and temporal trends of the annual burnt area in Angola, from 2001 to 2019, and their association with terrestrial ecoregions, land cover, and protected areas. Based on satellite imagery, we analyzed the presence of significant trends in burnt area, applying the contextual Mann–Kendall test and the Theil–Sen slope estimator. Data on burnt areas were obtained from the moderate-resolution imaging spectroradiometer (MODIS) burnt area product and the analyses were processed in TerrSet. Our results showed that ca. 30% of the country’s area burned every year. The highest percentage of annual burnt area was found in northeast and southeast Angola, which showed large clusters of decreasing trends of burnt area. The clusters of increasing trends were found mainly in central Angola, associated with savannas and grasslands of Angolan Miombo woodlands. The protected areas of Cameia, Luengue-Luiana, and Mavinga exhibited large areas of decreasing trends of burnt area. Conversely, 23% of the Bicuar National Park was included in clusters of increasing trends. Distinct patterns of land cover were found in areas of significant trends, where the clusters of increasing trends showed a higher fraction of forest cover (80%) than the clusters of decreasing trends (55%). The documentation of burnt area trends was very important in tropical regions, since it helped define conservation priorities and management strategies, allowing more effective management of forests and fires in countries with few human and financial resources. Full article

Forest and land degradation is a serious problem worldwide and the Peruvian National Map of Degraded Areas indicates that 13.78% (177,592.82 km²) of the country’s territory is degraded. Forest plantations can be a restoration strategy, while conserving economically important species affected by climate change and providing forestry material for markets. This study modelled the species distribution under current conditions and climate change scenarios of five Timber Forest Species (TFS) in the Amazonas Department, northeastern Peru. Modelling was conducted with Maximum Entropy (MaxEnt) using 26 environmental variables. Of the total distribution under current conditions of Cedrelinga cateniformis, Ceiba pentandra, Apuleia leiocarpa, Cariniana decandra and Cedrela montana, 34.64% (2985.51 km²), 37.96% (2155.86 km²), 35.34% (2132.57 km²), 33.30% (1848.51 km²), and 35.81% (6125.44 km²), respectively, correspond to degraded areas and, therefore, there is restoration potential with these species. By 2050 and 2070, all TFS are projected to change their distribution compared to their current ranges, regardless of whether it will be an expansion and/or a contraction. Consequently, this methodology is intended to guide the economic and ecological success of forest plantations in reducing areas degraded by deforestation or similar activities. Full article

Ecological restoration requires balancing levels of genetic diversity to achieve present-day establishment as well as long-term sustainability. Assumptions based on distributional, taxonomic or functional generalizations are often made when deciding how to source plant material for restoration. We investigate this assumption and ask whether species-specific data is required to optimize provenancing strategies. We use population genetic and environmental data from five congeneric and largely co-distributed species of Acacia to specifically ask how different species-specific genetic provenancing strategies are based on empirical data and how well a simple, standardized collection strategy would work when applied to the same species. We find substantial variability in terms of patterns of genetic diversity and differentiation across the landscape among these five co-distributed Acacia species. This variation translates into substantial differences in genetic provenancing recommendations among species (ranging from 100% to less than 1% of observed genetic variation across species) that could not have been accurately predicted a priori based on simple observation or overall distributional patterns. Furthermore, when a common provenancing strategy was applied to each species, the recommended collection areas and the evolutionary representativeness of such artificially standardized areas were substantially different (smaller) from those identified based on environmental and genetic data. We recommend the implementation of the increasingly accessible array of evolutionary-based methodologies and information to optimize restoration efforts. Full article

Galaxiid fishes from South America are represented by three genera (Aplochiton, Brachygalaxias and Galaxias) and eight species. Their genetic patterns have been studied over the last two decades to disentangle how historical and contemporary processes influenced their biogeographic distribution and phylogeographic patterns. Here we review and synthesize this body of work. Phylogeographic approaches reveal the important role played by orogeny and the expansion/melting of glacial ice during the Quaternary. Populations retreated to glacial refugia during glacial times and some systems experienced drainage reversals from the Atlantic to the Pacific following deglaciation. Although most species expanded their populations and increased their genetic diversity during the Holocene, the introduction of salmonids and the construction of dams are likely to lead to a decline in genetic diversity for at least some species. An improvement in our understanding of the processes that influenced historical and contemporary diversity patterns among galaxiid and other native fishes in South America is necessary for addressing the cumulative and synergistic impacts of human activity on this unique freshwater fauna. Full article

Genetic diversity enrichment is urgently necessary to develop climate-resilient faba bean cultivars. The present study aimed to measure the enrichment of genetic diversity and changes in the population structure of faba bean, following induced mutagenesis. 120 samples, including 116 M₂ mutant plants, generated by exposing the ILB4347 accession to four mutagen treatments (25 and 50 Gray gamma radiation and 0.01%, and 0.05% diethyl sulfate) and four reference genotypes were characterized using 11 amplified fragment length polymorphism (AFLP) primer combinations. The AFLP markers generated 1687 polymorphic alleles, including 756 alleles (45%) that were detected infrequently (f ≤ 0.1). The total allele count of the mutant plants ranged from 117 to 545. We observed a wide range of banding patterns and counts among the mutant plants, showing the high genetic diversity induced by mutation. Mutations also changed the population structure, by altering 31.78% of the total membership coefficient (Q). Although mutations changed the population structure, Nei’s genetic distance showed that the mutant population remained closely related to its control parent. This is the first report examining genetic diversity and population changes in faba bean mutant populations and, thus, could facilitate the application of induced mutagenesis during faba bean breeding. Full article

Human activity is the major factor driving the wetland degradation in shallow lakes. Human exploitation of lake wetlands alters the habitats of wintering waterbirds, and, in turn, waterbird diversity in the shallow lakes. In the present study, we surveyed species composition, abundance, and habitat characteristics of waterbirds in three types of wetland habitats (natural lakeside wetlands, paddy fields, and aquaculture ponds) at Caizi Lake, a shallow lake in the middle and lower Yangtze River during the wintering period, and investigated the effects of habitat change driven by human activity on the diversity of wintering waterbirds. There were significant differences in species composition and abundance among the three wetland habitats (natural lakeside wetlands, aquaculture ponds, and artificial paddy fields); however, there were no significant differences among the habitats with respect to the number of waterbirds. The numbers of overwintering waterbird species and waterbird individuals in aquaculture ponds and lakeside wetlands were significantly higher than the numbers in the paddy fields, indicating that wintering waterbirds prefer natural lake wetlands and aquaculture ponds. Principal component analysis of the three wetland habitat types revealed that factors influencing waterbird diversity include wetland area, vegetation cover, water level, and degree of human interference. Therefore, minimizing human interference and ensuring suitable habitats at specific periods could facilitate the maintenance of waterbird diversity. Full article

In a quest to improve the diversity and conservation of native tree species in tropical African forests, gap regeneration remains all-important nature-promoting silviculture practice and ecosystem-based strategy for attaining these ecological goals. Nine gaps of varying sizes (286–2005 m²) were randomly selected: three each from undisturbed, slightly disturbed and disturbed areas within Bia Tano Forest Reserve of Ghana. Within individual gaps, four transects (North–South–East–West directions) followed by 10 subsampling regions of 1 m² at 2 m apart were established along each transect. Data showed 63 tree species from 21 families in the study. Although, all estimated diversity indices showed significant biodiversity improvements in all gaps at p < 0.05 level. Yet, there were no significant variations amongst gaps. Additionally, tree species differed between gaps at the undisturbed and the two disturbance-graded areas while no differences were presented between disturbance-graded areas. Balanced conservation between Green Star and Reddish Star species and imbalanced conservation between Least Concern, Near Threatened and Vulnerable species in the International Union for Conservation of Nature (IUCN) Red List were found, showing the reserve’s long-term prospects for economic and ecological benefits of forest management. Thus, there is a need for higher priority for intensive management to regulate various anthropogenic disturbances so as to protect the biological legacies of the reserve. Full article

Rhodolith seabeds function as ‘ecosystems engineers’, which globally provide a range of ‘ecosystem services’. However, knowledge on the structure, composition and distribution of rhodolith seabeds is still lacking. This Special Issue comprises six articles, addressing specific questions of rhodolith seabeds, and covering a wide range of topics. Two papers provide new large-scale information on the presence, structure and distribution of rhodolith beds at two southern hemisphere areas, in particular continental shelfs off South Africa and Brazil. Another two studies contributed to the discovery on new algal species from rhodolith beds, including Sporolithon franciscanum, a new rhodolith-forming species from Brazil, and the small benthic alga Schizocladia ischiensis. In terms of associated fauna, the taxonomic composition and patterns of abundance of decapod crustaceans are described in another article, including the description of a depth-partitioning in the abundance of juveniles and adults of the crab Nanocassiope melanodactylus. Rhodoliths are often present in fossilized deposits, so we can track changes in their presence with climate fluctuations. High temperatures during the Eocene and widespread oligotrophic conditions are finally connected with low abundances of rhodolith beds at mid and high latitudes, despite a larger presence at equatorial regions. Full article

In this paper we apply a conservation genomics approach to make evidence-based management recommendations for Acacia whibleyana, an endangered shrub endemic to Eyre Peninsula, South Australia. We used population genomic analysis to assess genetic connectivity, diversity, and historical inbreeding across all known stands of the species sampling remnant stands, revegetated stands of unknown origin, and a post-fire seedling cohort. Our results indicate a degree of historical connectivity across the landscape, but habitat loss and/or pollinator community disruption are potential causes of strong genetic structure across the remnant stands. Remnant stands had low genetic diversity and showed evidence of historical inbreeding, but only low levels of intra-stand relatedness indicating that risks of contemporary inbreeding are low. Analysis of a post-fire first generation cohort of seedlings showed they likely resulted from intra-stand matings, resulting in reduced genetic diversity compared to the parents. However, admixed seedlings in this cohort showed an increase in heterozygosity relative to likely sources and the non-admixed seedlings of the same stand. Assisted inter-stand gene flow may prove an effective management strategy to boost heterozygosity and corresponding increases in adapting capacity in this endangered species. Full article

Cyanobacteria are among the most diverse morphological microorganisms that inhabit a great variety of habitats. Their presence in the Azores, a volcanic archipelago of nine islands in the middle of the North Atlantic Ocean, has already been reported. However, due to the high diversity of cyanobacteria habitats, their biodiversity is still understudied, mainly in extreme environments. To address this, a total of 156 cyanobacteria strains from Azores lakes, streams, thermal and terrestrial habitats were isolated. Identification was made based on a polyphasic approach using classical taxonomy (morphological characteristics and environmental data) and phylogeny among 81 strains assessed by maximum likelihood and Bayesian analysis of 16S rDNA partial sequences. The 156 isolates showed a high genera diversity (38) belonging to the orders Chroococcales, Nostocales, Oscillatoriales, and Synechococcales. Eleven new genera for the Azores habitats are here reported, reinforcing that cyanobacteria biodiversity in these islands is still much understudied. Phylogenetic analysis showed 14 clusters associated with these cyanobacteria orders, with evidence for six new genera and valuable information towards Microchaete/Coleospermum taxonomic revision that better reflects species environmental distribution. These results emphasize the need for cyanobacteria taxonomy revisions, through polyphasic studies, mainly in Synechococcales order and in the Microchaete/Coleospermum, Nostoc, and Anabaena genera. Full article

The endangered Barton Springs and Austin blind salamanders (Eurycea sosorum and E. waterlooensis, respectively) are micro-endemics to the Barton Springs segment of the Edwards Aquifer and its contributing zone in Central Texas. Although vertically segregated within the aquifer system, both species are known from the same spring outflows and occasionally hybridize. We used geometric morphometrics and model-based clustering applied to a large sample of standardized salamander photographs to evaluate the potential for objective phenotypic assignment to either species, as well as putative hybrids. In addition to characterizing variation in head shape, our analyses inferred sets of clusters corresponding to ontogenetic series in both species but did not infer any distinct hybrid clusters. Eurycea sosorum and E. waterlooensis have distinctive head size to trunk length allometries, which contributed to the effective clustering of species, even at small body sizes. We also observed subtle, but significant, microgeographic variation in E. sosorum, suggesting the possibility of population substructuring, phenotypic plasticity, or undetected hybridization. Full article

The Poyang water system in Jiangxi Province, China, is important for floodwater storage, diversity maintenance, and the economy of the Poyang Lake watershed. In recent years, pollution has destroyed the ecosystem and impacted human health and the related economy. The water quality of the Poyang Lake watershed and the impact of human interference must be assessed. Conventional analysis and high-throughput sequencing were used to evaluate the structure of both zooplankton and fungi in six sub-lakes of the Poyang Lake watershed under different anthropogenic influences. The sub-lakes included were Dahuchi Lake (in natural preserve, DHC), Shahu Lake (in natural reserve, SH), Nanhu Lake (out of natural preserve, NH), Zhelinhu Lake (artificial reservoir, ZLH), Sixiahu Lake (agricultural lake artificially isolated from Poyang Lake, SXH), and Qianhu Lake (urban lake, QH). The densities and biomass of the zooplankton in DHC, SH, NH were higher compared with those in SXH, ZLH and QH (p < 0.05). Zooplankton distribution of SXH was the most strongly associated with total nitrogen (TN), total phosphorus (TP) and chlorophyll a (Chl a), while QH was highly associated with pH, conductivity (Cond), and water temperature (WT). For fungal diversity, a large number of beneficial fungi, Basidiomycota (phylum level) and Massarina (genus level) were obtained from DHC (55.3% and 27.5%, respectively), SH (54.4% and 28.9%, respectively), and NH (48.6% and 1.4%, respectively), while a large number of pathogenic Chytridiomycota (at phylum level) were identified from SXH (21.0%), ZLH (5.5%), and QH (7.5%). Manmade pollutants have impacted the natural hydrology and water quality and promoted variation between the zooplankton and fungi in the six sub-lakes, reducing the relative abundance of beneficial fungi and increasing the number of pathogens in the environment, which threatens human health and economic production. Understanding the diversity among the zooplankton and fungi in the six sub-lakes of the Poyang Lake watershed may help guide future water management practices. Full article

When designing models for predicting phytoplankton biomass or characterizing traits, it is useful to aggregate the myriad of species into a few biologically meaningful groups and focus on group-level attributes, the common practice being to combine phytoplankton species by functional types. However, biogeochemists and plankton ecologists debate the most applicable grouping for describing phytoplankton biomass patterns and predicting future community structure. Although trait-based approaches are increasingly being advocated, methods are missing for the generation of trait-based taxa as alternatives to functional types. Here we introduce such a method and demonstrate the usefulness of the resulting clustering with field data. We parameterize a Bayesian model of biomass dynamics and analyze long-term phytoplankton data collected at Station L4 in the Western English Channel between April 2003 and December 2009. We examine the tradeoffs encountered regarding trait characterization and biomass prediction when aggregating biomass by (1) functional types, (2) the trait-based clusters generated by our method, and (3) total biomass. The model conveniently extracted trait values under the trait-based clustering, but required well-constrained priors under the functional type categorization. It also more accurately predicted total biomass under the trait-based clustering and the total biomass aggregation with comparable root mean squared prediction errors, which were roughly five-fold lower than under the functional type grouping. Although the total biomass grouping ignores taxonomic differences in phytoplankton traits, it predicts total biomass change as well as the trait-based clustering. Our results corroborate the value of trait-based approaches in investigating the mechanisms underlying phytoplankton biomass dynamics and predicting the community response to environmental changes. Full article

An outline of the main distribution patterns of lichens in the ecoregions of Italy, accounting for their climatic, geographic, and environmental features, is still missing. On the basis of a GIS-based analysis, we summarized: (1) the main features (e.g., surface, climate, landscape, topographic heterogeneity, bedrock, eutrophication) of the 9 ecoregions adopted in ITALIC, the information system on Italian lichens, and (2) the patterns of richness, functional traits, and ecological requirements of lichens in the ecoregions. Our GIS-based analysis describes for the first time the main features of the 9 ecoregions adopted in ITALIC, highlighting differences which could explain the main lichen patterns. Overall, the exploration of the Italian lichen biota is still a work in progress, some regions being still underexplored, especially in the South, with new taxa being reported every year. Our research could provide a baseline for further advancements in the understanding of species richness and community composition of Italian lichens, at a regional scale. Full article

Land salinization is a major constraint for the practice of agriculture in the world. Considering the extent of this phenomenon, the rehabilitation of ecosystems degraded by salinization has become a priority to guarantee food security in semi-arid environments. The mechanical and chemical approaches for rehabilitating salt-affected soils being expensive, an alternative approach is to develop and utilize biological systems utilizing salt-tolerant plant species. Casuarina species are naturally halotolerant, but this tolerance has been shown to be improved when they are inoculated with arbuscular mycorrhizal fungi (AMF) and/or nitrogen-fixing bacteria (Frankia). Furthermore, Casuarina plantations have been proposed to promote the development of plant diversity. Thus, the aim of the current study was to evaluate the impact of a plantation comprising the species Casuarina inoculated with AMF and Frankia on the diversity of the sub-canopy and adjacent vegetation. Work was conducted on a plantation comprising Casurina equisetifolia and C. glauca variously inoculated with Frankia and Rhizophagus fasciculatus prior to field planting. The experimental area of 2500 m² was divided into randomized blocks and vegetation sampling was conducted below and outside of the Casuarina canopy in 32 m² plots. A total of 48 samples were taken annually over 3 years, with 24 taken from below the Casuarina canopy and 24 from outside the canopy. The results obtained show that co-inoculation with Frankia and Rhizophagus fasciculatus improves the height and survival rate of both species. After 4–5 years, there was greater species diversity and plant biomass in the sub-canopy environment compared with that of the adjacent environments. Our results suggest that inoculation of beneficial microbes can improve growth of Casuarina species and that planting of such species can improve the diversity of herbaceous vegetation in saline environments. Full article

Seagrass meadows are an important habitat for a variety of animals, including ecologically and socioeconomically important species. Seagrass meadows are recognised as providing species with nursery grounds, and as a migratory pathway to adjacent habitats. Despite their recognised importance, little is known about the species assemblages that occupy seagrass meadows of different depths in the coastal zone. Understanding differences in the distribution of species in seagrass at different depths, and differences in species diversity, abundance, biomass, and size spectra, is important to fully appreciate both the ecological significance and economic importance of these seagrass meadows. Here, we assess differences in the assemblage characteristics of fish, crustacea, and cephalopods (collectively, nekton) between deep (>9 m; Halophila spinulosa dominant) and shallow water (<2 m; Halodule uninervis and/or Zostera muelleri dominant) seagrass meadows of the central Great Barrier Reef coast of Queensland, Australia. Nekton assemblage structure differed between deep and shallow seagrass. Deeper meadows were typified by juvenile emperors (e.g., Lethrinus genivittatus), hairfinned leatherjacket (Paramonacanthus japonicus) and rabbitfish (e.g., Siganus fuscescens) in both biomass per unit effort (BPUE) and catch per unit effort (CPUE), whereas shallow meadows were typified by the green tiger prawn (Penaeus semisulcatus) and pugnose ponyfish (Secutor insidiator) in both BPUE and CPUE. Both meadow depths were distinct in their nekton assemblage, particularly for socioeconomically important species, with 11 species unique to both shallow and deep meadows. However, both meadow depths also included juveniles of socioeconomically important species found in adjacent habitats as adults. The total nekton CPUE was not different between deep and shallow seagrass, but the BPUE and body mass of individual animals were greater in deep than shallow seagrass. Size spectra analysis indicated that in both deep and shallow meadows, smaller animals predominated, even more so than theoretically expected for size spectra. Our findings highlight the unique attributes of both shallow and deeper water seagrass meadows, and identify the distinct and critically important role of deep seagrass meadows within the Great Barrier Reef World Heritage Area (GBRWHA) as a habitat for small and juvenile species, including those of local fisheries value. Full article

Primula palinuri Petagna is the only Mediterranean and maritime species in the genus Primula, is endemic to coastal cliffs of southern Italy, and is classified as endangered with a decreasing population trend in the IUCN Red List. For this species, the major bottleneck for long-term survival has been recognized to be recruitment failure. In this study, we investigated the seed release strategy of P. palinuri, by using field observations and laboratory experiments. We hypothesized that repetitive cycles of wet/dry conditions and external wax removal could be the environmental triggers of capsule dehiscence. Data showed that capsules treated with wet/dry cycles dehisced within 75 days, while none subjected to constant dry conditions dehisced. Once dehisced, capsules repetitively closed when made wet, and opened again upon drying. Seeds of P. palinuri can remain on plant up to 2 years, over which time capsules reclose when rained upon and reopen upon drying, highlighting the first reported occurrence of serotiny in a Primula species. Serotiny allows P. palinuri to face the dry season, by avoiding capsule dehiscence during the summer dry period and delaying seed release until the beginning of fall, when water availability in the soil is generally no longer a limiting factor. Full article

Dasybranchusgeojedoensis sp. nov., obtained from the soft sublittoral bottom in southern Korea, is described as a new species. This new species of Dasybranchus is easily distinguishable from its congeners by the protruded parapodial lobes in the final few thoracic chaetigers. Dasybranchus geojedoensis sp. nov. closely resembles D. bipartitus (Schmarda, 1861) in number and position of abdominal branchiae but differs in position of genital pores and lateral organs, range of thoracic tessellated chaetigers, and denticulation of the abdominal hooks. The partial mtCOI gene sequences of the new Korean species were significantly distinct from those of undescribed species of Dasybranchus from Australia. In this study, a key for known species of Dasybranchus is also provided. Full article

The Pseudomonas genus includes many species living in diverse environments and hosts. It is important to understand which are the major evolutionary groups and what are the genomic/proteomic components they have in common or are unique. Towards this goal, we analyzed 494 complete Pseudomonas proteomes and identified 297 core-orthologues. The subsequent phylogenomic analysis revealed two well-defined species (Pseudomonas aeruginosa and Pseudomonas chlororaphis) and four wider phylogenetic groups (Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas syringae, Pseudomonas putida) with a sufficient number of proteomes. As expected, the genus-level core proteome was highly enriched for proteins involved in metabolism, translation, and transcription. In addition, between 39–70% of the core proteins in each group had a significant presence in each of all the other groups. Group-specific core proteins were also identified, with P. aeruginosa having the highest number of these and P. fluorescens having none. We identified several P. aeruginosa-specific core proteins (such as CntL, CntM, PlcB, Acp1, MucE, SrfA, Tse1, Tsi2, Tse3, and EsrC) that are known to play an important role in its pathogenicity. Finally, a holin family bacteriocin and a mitomycin-like biosynthetic protein were found to be core-specific for P. cholororaphis and we hypothesize that these proteins may confer a competitive advantage against other root-colonizers. Full article

Phylogenetic relatedness is a key diversity measure for the analysis and understanding of how species and communities evolve across time and space. Understanding the nonrandom loss of species with respect to phylogeny is also essential for better-informed conservation decisions. However, several factors are known to influence phylogenetic reconstruction and, ultimately, phylogenetic diversity metrics. In this study, we empirically tested how some of these factors (topological constraint, taxon sampling, genetic markers and calibration) affect phylogenetic resolution and uncertainty. We built a densely sampled, species-level phylogenetic tree for spiders, combining Sanger sequencing of species from local communities of two biogeographical regions (Iberian Peninsula and Macaronesia) with a taxon-rich backbone matrix of Genbank sequences and a topological constraint derived from recent phylogenomic studies. The resulting tree constitutes the most complete spider phylogeny to date, both in terms of terminals and background information, and may serve as a standard reference for the analysis of phylogenetic diversity patterns at the community level. We then used this tree to investigate how partial data affect phylogenetic reconstruction, phylogenetic diversity estimates and their rankings, and, ultimately, the ecological processes inferred for each community. We found that the incorporation of a single slowly evolving marker (28S) to the DNA barcode sequences from local communities, had the highest impact on tree topology, closely followed by the use of a backbone matrix. The increase in missing data resulting from combining partial sequences from local communities only had a moderate impact on the resulting trees, similar to the difference observed when using topological constraints. Our study further revealed substantial differences in both the phylogenetic structure and diversity rankings of the analyzed communities estimated from the different phylogenetic treatments, especially when using non-ultrametric trees (phylograms) instead of time-stamped trees (chronograms). Finally, we provide some recommendations on reconstructing phylogenetic trees to infer phylogenetic diversity within ecological studies. Full article

The ‘green’ ciliate Paramecium bursaria lives in mutualistic symbiosis with green algae belonging to the species Chlorella variabilis or Micractinium conductrix. We analysed the diversity of algal endosymbionts and their P. bursaria hosts in nine strains from geographically diverse origins. Therefore, their phylogenies using different molecular markers were inferred. The green paramecia belong to different syngens of P. bursaria. The intracellular algae were assigned to Chl. variabilis, M. conductrix or, surprisingly, Choricystis parasitica. This usually free-living alga co-occurs with M. conductrix in the host’s cytoplasm. Addressing the potential status of Chor. parasitica as second additional endosymbiont, we determined if it is capable of symbiosis establishment and replication within a host cell. Symbiont-free P. bursaria were generated by cycloheximid treatment. Those aposymbiotic P. bursaria were used for experimental infections to investigate the symbiosis specificity not only between P. bursaria and Chor. parasitica but including also Chl. variabilis and M. conductrix. For each algae we observed the uptake and incorporation in individual perialgal vacuoles. These host-symbiont associations are stable since more than five months. Thus, Chor. parasitica and P. bursaria can form an intimate and long-term interaction. This study provides new insights into the diversity of P. bursaria algal symbionts. Full article

Floral deception has been observed in several genera in angiosperms, but is most common in the Orchidaceae. Pollination mechanisms in food deceptive plants are often difficult to assess, as visitation frequency by insects requires numerous hours of field observations to ascertain. Here, for the first time, we describe in detail and validate a simple and effective method that extends previous approaches to increase the effectiveness of pollination studies of food deceptive orchids. We used an orchid of southwest Australia, Diuris brumalis (Orchidaceae), that visually mimics model plants belonging to the genus Daviesia (Faboideae). Arrays of orchid flowers were placed and moved systematically in proximity to model plants, resulting in rapid attraction of the pollinators of D. brumalis. We compared pollinaria removal (as an indicator of pollination success) in naturally growing orchids with pollinaria removal in arrays of orchid flowers in the same sites. We showed that the proposed method greatly enhances pollinator attractiveness in food deceptive systems with very low pollination rates, and we compared its efficiency with other similar methods. The approach can be used for observing pollinator behavioural patterns and confirming effective pollinators for food deceptive species with low insect visitation rates. Full article