Diversity

Ojo Guareña Natural Monument in Burgos (Spain) is an important and large karstic system. It consists of more than 110 kilometers of surveyed galleries, and it has rich sources of organic material from the surface and permanent water circulation. It is the fourth largest cave system in the Iberian Peninsula, and one of the 10 largest in Europe. Ojo Guareña also ranks 23rd among the world's largest caves. To date, only volcanic caves in the Canary Islands, in which between 28 and 38 subterranean species occur, are considered subterranean diversity hotspots in Spain. Here, we provide the first list of subterranean taxa present in Ojo Guareñ, which is comprised of 54 taxa that includes 46 stygobiotic and eight troglobiotic species (some still unidentified at the species level), revealing Ojo Guareña as the largest known subterranean biodiversity hotspot in Spain and Portugal. In addition, we provide a list of an additional 48 taxa, 34 stygophiles and 14 troglophiles, found in the system, whose ecological status could change with detailed biological studies, which may change the number of strictly subterranean species present in the system. Indeed, at present, these numbers are provisional as they correspond to a small part of this sizeable cave system. The biodiversity of large areas of the system remains unknown as these areas have yet to be explored from the biological point of view. In addition, a large number of samples of both terrestrial and aquatic fauna are still under study by specialists. Furthermore, evidence of cryptic species within Bathynellacea (Crustacea) indicates an underestimation of biodiversity in the karstic system. Despite these limitations, the data available reveal the typical uneven distribution of subterranean aquatic fauna, and suggest that the great heterogeneity of the microhabitats in this wide and highly connected karstic extension led to the great richness of aquatic subterranean species. Full article

Brazil has the highest number of parrots in the world and the greatest number of threatened species. The Golden Conure is endemic to the Brazilian Amazon forest and it is currently considered as threatened by extinction, although it is fairly common in captivity. Here we report the first reintroduction of this species. The birds were released in an urban park in Belem, capital of Para State, where the species was extinct more than a century ago. Birds were trained to recognize and consume local food and to avoid predators. After the soft-release, with food supplementation and using nest boxes, we recorded breeding activity in the wild. The main challenges before the release were the territorial disputes within the aviary and the predation by boa snakes. During the post-release monitoring the difficulties were the fast dispersion of some individuals and the dangers posed by anthropic elements such as power lines that caused some fatalities. Released birds were very successful at finding and consuming native foods, evading predators, and one pair reproduced successfully. Monitoring continues and further releases are programmed to establish an ecologically viable population. Full article

Root-associated endophytic fungi (RAF) are found asymptomatically in almost all plant groups. However, little is known about the compositions and potential functions of RAF communities associated with most Orchidaceae species. In this study, the diversity of RAF was examined in four wild epiphytic orchids, Acampe rigida, Doritis pulcherrima, Renanthera coccinea, and Robiquetia succisa, that occur in southern China. A culture-independent method involving Illumina amplicon sequencing, and an in vitro culture method, were used to identify culturable fungi. The RAF community diversity differed among the orchid roots, and some fungal taxa were clearly concentrated in a certain orchid species, with more OTUs being detected. By investigating mycorrhizal associations, the results showed that 28 (about 0.8%) of the 3527 operational taxonomic units (OTUs) could be assigned as OMF, while the OTUs of non-mycorrhizal fungal were about 99.2%. Among the OMFs, Ceratobasidiaceae OTUs were the most abundant with different richness, followed by Thelephoraceae. In addition, five Ceratobasidium sp. strains were isolated from D. pulcherrima, R. succisa, and R. coccinea roots with high separation rates. These culturable Ceratobasidium strains will provide materials for host orchid conservation and for studying the mechanisms underlying mycorrhizal symbiosis. Full article

Presence of mollusk assemblages was studied within red coralligenous algae Corallina officinalis L. along the southern Istrian coast. C. officinalis turfs can be considered a biodiversity reservoir, as they shelter numerous invertebrate species. The aim of this study was to identify mollusk species within these settlements using DNA barcoding as a method for detailed identification of mollusks. Nine locations and 18 localities with algal coverage range above 90% were chosen at four research areas. From 54 collected samples of C. officinalis turfs, a total of 46 mollusk species were identified. Molecular methods helped identify 16 gastropod, 14 bivalve and one polyplacophoran species. COI sequences for two bivalve species (Musculus cf. costulatus (Risso, 1826) and Gregariella semigranata (Reeve, 1858)) and seven gastropod species (Megastomia winfriedi Peñas & Rolán, 1999, Eatonina sp. Thiele, 1912, Eatonina cossurae (Calcara, 1841), Crisilla cf. maculata (Monterosato, 1869), Alvania cf. carinata (da Costa, 1778), Vitreolina antiflexa (Monterosato, 1884) and Odostomia plicata (Montagu, 1803)) represent new BINs in BOLD database. This study contributes to new findings related to the high biodiversity of mollusks associated with widespread C. officinalis settlements along the southern coastal area of Istria. Full article

Landraces are generally neglected by industrialized agriculture, regardless of their potential to provide valuable genetic material for breeding and to diversifying the available assortment for producers and markets. They may also excel in certain plant protection issues with possible resistance or tolerance to plant pathogens. This is the first report on the disease susceptibility traits of Hungarian on certain indeterminate and determinate tomato gene bank accessions under on-farm organic conditions. For this, a three-year on-farm experiment was conducted in two management systems, open-field and protected. Yield and disease symptoms data obtained from ten tomato landraces were compared to commercial varieties. The incidence and severity of three important diseases (caused by late blight ‘Phytophthora infestans’, early blight ‘Alternaria solani’ and Septoria leafspot ‘Septoria lycopersici’), as well as yield, were recorded and assessed. According to these results, there were no significant difference between landraces and control varieties (San Marzano, Kecskeméti 549) regarding the studied parameters, and year was a determinant factor in the occurrence and severity of the infection of the studied diseases. In 2016, rainy, humid weather induced a severe late blight infection, causing serious damage to the open field, while the weather in 2015 and 2017 was favorable for tomato production and our measurements. There were some differences within and between landraces in terms of susceptibility. The investigation revealed that certain accessions can be highly recommended, e.g., the indeterminate ‘Fadd’ (RCAT030275) and ‘Mátrafüred’ (RCAT057656) had suitably high yields with significantly lower susceptibility to late blight, and the determinate ‘Szentlőrinckáta’ (RCAT078726) with high yield as well as tolerance to early blight is also recommendable, but it is sensitive to late blight under an adverse environment. This study suggests that landraces are competitive with the studied commercial varieties under organic production systems. Considering yield and the prevention of the major diseases of tomato, the studied tomato gene bank accessions are recommended for organic field and protected management systems. Full article

Two sibling bare-backed bat species (Pteronotus fulvus and P. gymnonotus) have been traditionally differentiated by their size. However, intermediate specimens between the two species have been found in sympatric populations along southern Mexico and it has been suggested that they may be the outcome of a hybridization process between the two species. We used one mitochondrial (COI), three nuclear markers (PRKCL, STAT5A and RAG2) and 13 microsatellites to explore the evolutionary relationships between these two species and elucidate whether the intermediate morphotypes correspond to hybrid individuals. These markers have been analyzed in sympatric and allopatric populations of the two species plus the closely related species Pteronotus davyi. We confirmed the species-level differentiation of the three lineages (P. fulvus, P. davyi and P. gymnonotus), but the phylogenetic hypotheses suggested by the nuclear and mitochondrial markers were discordant. We confirm that the discordance between markers is due to genetic introgression through the mitochondrial capture of P. fulvus in P. gymnonotus populations. Such introgression was found in all P. gymnonotus specimens across its sympatric distribution range (Mexico to Costa Rica) and is related to expansion/retraction species distribution pulses associated with changes in forest distribution during the Quaternary climate cycles. Microsatellite analyses showed contemporary genetic contact between the two sympatric species and 3.0% of the samples studied were identified as hybrids. In conclusion, we found a historical and asymmetric genetic introgression (through mitochondrial capture) of P. fulvus into P. gymnonotus in Mexico and Central America and a limited contemporary gene exchange between the two species. However, no relationship was found between hybridization and the intermediate-sized specimens from southern Mexico, which might likely result from a clinal variation with latitude. These results confirm the need for caution when using forearm size to identify these species in the field and when differentiating them in the laboratory based on mitochondrial DNA alone. Full article

Anguillid eels are widely acknowledged for their ecological and socio-economic value in many countries. Yet, knowledge regarding their biodiversity, distribution and abundance remains superficial—particularly in tropical countries such as Indonesia, where demand for anguillid eels is steadily increasing along with the threat imposed by river infrastructure developments. We investigated the diversity of anguillid eels on the western Indonesian islands of Sumatra and Java using automated molecular classification and genetic species delimitation methods to explore temporal patterns of glass eel cohorts entering inland waters. A total of 278 glass eels were collected from monthly samplings along the west coast of Sumatra and the south coast of Java between March 2017 and February 2018. An automated, DNA-based glass eel identification was performed using a DNA barcode reference library consisting of 64 newly generated DNA barcodes and 117 DNA barcodes retrieved from BOLD for all nine Anguilla species known to occur in Indonesia. Species delimitation methods converged in delineating eight Molecular Operational Taxonomic Units (MOTUs), with A. nebolusa and A. bengalensis being undistinguishable by DNA barcodes. A total of four MOTUs were detected within the glass eel samples, corresponding to Anguilla bicolor, A. interioris, A. marmorata, and A. nebulosa/A. bengalensis. Monthly captures indicated that glass eel recruitment peaks in June, during the onset of the dry season, and that A. bicolor is the most prevalent species. Comparing indices of mitochondrial genetic diversity between yellow/silver eels, originating from several sites across the species range distribution, and glass eels, collected in West Sumatra and Java, indicated a marked difference. Glass eels displayed a much lower diversity than yellow/silver eels. Implications for the management of glass eel fisheries and species conservation are discussed. Full article

Sweet, grain, and dual-purpose sorghums differ in a number of important traits, including biomass production, total solutes in the stem juice, and sugar accumulation across the stem. Ten dual-purpose hybrids, two sweet genotypes, and two grain landraces of sorghums were characterized under temperate environmental conditions to determine their potential for bioethanol production. Five sorghum hybrids (Ganymed, Hannibal, Tarzan, Merlin, and Zerberus) performed better with respect to cane yield, juice yield, potential sugar, and ethanol yields compared to sweet and grain genotypes. While the sweet genotype KIT1 produced the highest sugar concentration in the stem, the lowest concentration was produced by the grain landrace Razinieh. The study showed that plant height, leaf number, leaf weight, cane yield, and juice yield were positively correlated with the sugar yield in fresh stalk. Sugar accumulation was higher in the central internodes of all genotypes. Clustering analysis showed that sweet genotypes are located more closely to dual-purpose hybrids than grain landraces. We discuss the results with respect to the potential of dual-purpose sorghum hybrids for bio-economy in Germany. Full article

The order Psittaciformes is one of the most prevalent groups in the illegal wildlife trade. Efforts to understand this threat have focused on describing the elements of the trade itself: actors, extraction rates, and routes. However, the development of policy-oriented interventions also requires an understanding of how research aims and actions are distributed across the trade chain, regions, and species. We used an action-based approach to review documents published on illegal Psittaciformes trade at a global scale to analyze patterns in research aims and actions. Research increased exponentially in recent decades, recording 165 species from 46 genera, with an over representation of American and Australasian genera. Most of the research provided basic knowledge for the intermediary side of the trade chain. Aims such as the identification of network actors, zoonosis control, and aiding physical detection had numerous but scarcely cited documents (low growth rate), while behavior change had the highest growth rate. The Americas had the highest diversity of research aims, contributing with basic knowledge, implementation, and monitoring across the whole trade chain. Better understanding of the supply side dynamics in local markets, actor typology, and actor interactions are needed. Protecting areas, livelihood incentives, and legal substitutes are actions under-explored in parrots, while behavior change is emerging. Full article

Copepods are one of the most abundant and diverse live food sources for mesopelagic and bathypelagic fishes and crustaceans. They could contribute to the overlap of the transition period from live feed to an artificial weaning diet in marine larvae production. However, the culture conditions still need optimization to provide sufficient production to cover the increasing demand for marine hatcheries. Therefore, the present study investigated the effects of different salinity levels (5, 10, 15, 20, 25, and 30 ppt) on the population growth, growth rate, and population composition (males, females, copepodite, and nauplii ratio) of the marine copepod, Oithona nana. The experiment continued for 15 days, under laboratory-controlled conditions of temperature (27 ± 1 °C), pH (7.7 ± 0.15), and continuous gentle aeration in 30 L glass aquaria. The copepod culture aquaria were supplemented with a mixture of soybean and yeast (0.5 g 10⁻⁶ individual⁻¹ 24-h⁻¹) as a feed source. The highest significant population growth and population growth rate of O. nana were achieved with a salinity level of 20 ppt. Regarding population composition, O. nana cultured at the salinity level of 20 ppt recorded the highest significant percentages of copepodite and nauplii. The results concluded that copepod, O. nana, is capable of withstanding abrupt changes in the salinity, but there are limits to their tolerance, with an optimal salinity level of 20 ppt. This salinity level achieved the highest population growth and the highest percentages of copepodite and nauplii of marine Copepoda, O. nana. Full article

Urban gardens are important for human well-being, biodiversity and other ecosystem functions. Biodiversity-promoting initiatives would benefit from their owners being aware of the state of biodiversity in their gardens. We examined whether garden owners’ perceptions match actual biodiversity in their gardens and whether perceptions are influenced by the owners’ ecological knowledge. We used a structured interview to assess the motivations and biodiversity knowledge of owners of 33 domestic gardens in the city of Basel (Switzerland) and related them to a survey of native plants and several groups of ground-dwelling invertebrates in their gardens. Owners showed different priorities, with promotion of habitat for biodiversity, receiving, on average, higher scores than cultivation, recreation and garden designing. Owners prioritizing biodiversity promotion had gardens with high habitat richness. The garden owners’ perceptions of both native plant and overall invertebrate diversity were not correlated with actual diversity data for native plants and ground-dwelling invertebrates. The perceptions of the abundance of invertebrate groups by garden owners with good biodiversity knowledge were not more accurate than those from owners with less knowledge. Despite their willingness, many owners do not know all the opportunities to promote biodiversity. Initiatives to further biodiversity-friendly gardening should thus transfer knowledge. Full article

We investigated the effect of varying storage time and storage temperature on fungal species’ isolation as part of a case study of Illinois cave sediment samples. A deeper understanding of cave fungal communities may influence eco-epidemiology studies of emerging or re-emerging cave fungal pathogens. Using culture-dependent techniques, we isolated geophilic fungi from homogeneous cave sediment samples from three Illinois caves. Each sample was stored under five different temperatures ranging from −80 °C to 22 °C. Cave sediment was periodically removed at five different time periods from 48 h to 1 year, serially diluted with distilled water, lawn plated onto two different media, and monitored for fungal colonies. We isolated colonies and confirmed identity through nrDNA sequence similarity. Our results suggest that storage time was more important than storage temperature for the isolation of a wide diversity of geophilic fungal taxa. Importantly, our results show that varying storage conditions will alter both the kind of taxa and abundance of those taxa, suggesting that comparative studies of fungal diversity across studies should employ similar storage conditions. Lastly, future investigations should utilize multiple genetic markers because the fungal barcode region lacked species-level resolution for many isolates within common Illinois geophilic fungal genera. Full article

Seahorses (Hippocampus spp.) are threatened as a result of habitat degradation and overfishing. They have commercial value as traditional medicine, curio objects, and pets in the aquarium industry. There are 48 valid species, 27 of which are represented in the international aquarium trade. Most species in the aquarium industry are relatively large and were described early in the history of seahorse taxonomy. In 2002, seahorses became the first marine fishes for which the international trade became regulated by CITES (Convention for the International Trade in Endangered Species of Wild Fauna and Flora), with implementation in 2004. Since then, aquaculture has been developed to improve the sustainability of the seahorse trade. This review provides analyses of the roles of wild-caught and cultured individuals in the international aquarium trade of various Hippocampus species for the period 1997–2018. For all species, trade numbers declined after 2011. The proportion of cultured seahorses in the aquarium trade increased rapidly after their listing in CITES, although the industry is still struggling to produce large numbers of young in a cost-effective way, and its economic viability is technically challenging in terms of diet and disease. Whether seahorse aquaculture can benefit wild populations will largely depend on its capacity to provide an alternative livelihood for subsistence fishers in the source countries. For most species, CITES trade records of live animals in the aquarium industry started a few years earlier than those of dead bodies in the traditional medicine trade, despite the latter being 15 times higher in number. The use of DNA analysis in the species identification of seahorses has predominantly been applied to animals in the traditional medicine market, but not to the aquarium trade. Genetic tools have already been used in the description of new species and will also help to discover new species and in various other kinds of applications. Full article

One of the obstacles to detecting regional trends in jellyfish populations is the lack of a defined baseline. In the Adriatic Sea, the jellyfish fauna (Scyphozoa and Ctenophora) is poorly studied compared to other taxa. Therefore, our goal was to collect and systematize all available data and provide a baseline for future studies. Here we present phenological data and relative abundances of jellyfish based on 2010–2019 scientific surveys and a “citizen science” sighting program along the eastern Adriatic. Inter-annual variability, seasonality and spatial distribution patterns of Scyphomedusae and Ctenophore species were described and compared with existing historical literature. Mass occurrences with a clear seasonal pattern and related to the geographical location were observed for meroplanktonic Scyphomedusae Aurelia solida, Rhizostoma pulmo, and to a lesser extent Chrysaora hysoscella, Cotylorhiza tuberculata and Discomedusa lobata. Holoplanktonic Pelagia noctiluca also formed large aggregations, which were seasonally less predictable and restricted to the central and southern Adriatic. Four species of Ctenophora produced blooms limited to a few areas: Bolinopsis vitrea, Leucothea multicornis, Cestum veneris and the non-native Mnemiopsis leidyi. However, differences between Adriatic subregions have become less pronounced since 2014. Our results suggest that gelatinous organisms are assuming an increasingly important role in the Adriatic ecosystem, which may alter the balance of the food web and lead to harmful and undesirable effects. Full article

Rear-edge populations are of significant scientific interest because they can contain allelic variation not found in core-range populations. However, such populations can differ in their level of genetic diversity and divergence reflecting variation in life-history traits, demographic histories and human impacts. Using 13 EST-microsatellites, we investigated the genetic diversity and differentiation of rear-edge populations of the Japanese endemic conifer Thuja standishii (Gordon) Carr. in southwest Japan from the core-range in northeast Japan. Range-wide genetic differentiation was moderate (Fst = 0.087), with northeast populations weakly differentiated (Fst = 0.047), but harboring high genetic diversity (average population-level Ar = 4.76 and Ho = 0.59). In contrast, rear-edge populations were genetically diverged (Fst = 0.168), but contained few unique alleles with lower genetic diversity (Ar = 3.73, Ho = 0.49). The divergence between rear-edge populations exceeding levels observed in the core-range and results from ABC analysis and species distribution modelling suggest that these populations are most likely relicts of the Last Glacial Maximum. However, despite long term persistence, low effective population size, low migration between populations and genetic drift have worked to promote the genetic differentiation of southwest Japan populations of T. standishii without the accumulation of unique alleles. Full article

As the extent of hypoxia in coastal waters increases, the survivorship of jellyfish polyps relative to that of competing sessile organisms often increases, enabling them to reproduce more prolifically, leading to a medusa bloom in the following year. Quantifying the population of polyps can be used to predict when these blooms will occur. We used a time-delayed logistic equation to quantify the response to variable dissolved oxygen (DO) concentrations and temperatures in a population of moon jellyfish (Aurelia coerulea) polyps on substrates that carried competing sessile organisms. The availability of substrate depends on the DO threshold for each competitor, and substrates only become available to the polyps during hypoxic periods. We used the median sublethal concentration (SLC₅₀) thresholds of hypoxia for different groups of benthic organisms to calculate the DO-dependent survivorship of A. coerulea polyps competing on the substrate. Since the median lethal time (LT₅₀) for cnidarians is close to 240 h, we chose a 10-day delay in the time-delayed logistic equation. The carrying capacity is determined every 10 days depending on DO concentrations and temperature. The polyps reproduce by budding at a temperature-dependent rate after settling on the substrate during the hypoxic period, and thus, the annual polyp reproduction rate is determined by multiplying the temperature-dependent budding rate by the DO-dependent survivorship. The duration of hypoxia is a key factor determining the polyp population, which can increase more as the duration of hypoxia increases. Modeling simulations were compared to observed data. In this model, the DO and temperature distribution data make it possible to quantify variations in the population of the A. coerulea polyps, which can be used to predict the abundance and appearance of medusa the following year. Full article

Karstic landscapes are immense reservoirs of biodiversity and range-restricted endemism. Nowhere is this more evident than in the world’s third-largest vertebrate genus Cyrtodactylus (Gekkonidae) which contains well over 300 species. A stochastic character mapping analysis of 10 different habitat preferences across a phylogeny containing 344 described and undescribed species recovered a karst habitat preference occurring in 25.0% of the species, whereas that of the other eight specific habitat preferences occurred in only 0.2–11.0% of the species. The tenth category—general habitat preference—occurred in 38.7% of the species and was the ancestral habitat preference for Cyrtodactylus and the ultimate origin of all other habitat preferences. This study echoes the results of a previous study illustrating that karstic landscapes are generators of species diversity within Cyrtodactylus and not simply “imperiled arks of biodiversity” serving as refugia for relics. Unfortunately, the immense financial returns of mineral extraction to developing nations largely outweighs concerns for biodiversity conservation, leaving approximately 99% of karstic landscapes with no legal protection. This study continues to underscore the urgent need for their appropriate management and conservation. Additionally, this analysis supports the monophyly of the recently proposed 31 species groups and adds one additional species group. Full article

Ilex guayusa Loes. is a shrub native to the Neotropics, traditionally consumed as an infusion. Despite its cultural value and extensive use, genetic research remains scarce. This study examined the genetic and clonal diversity of guayusa in three different Ecuadorian Amazon regions using 17 species-specific SSR markers. The results obtained suggest a moderately low degree of genetic diversity (He = 0.396). Among the 88 samples studied, 71 unique multilocus genotypes (MLGs) were identified, demonstrating a high genotypic diversity. A Discriminant Analysis of Principal Components (DAPC) revealed the existence of two genetic clusters. We propose that a model of isolation-by-environment (IBE) could explain the genetic differentiation between these clusters, with the main variables shaping the population’s genetic structure being temperature seasonality (SD × 100) (Bio 4) and isothermality ×100 (Bio 3). Nonetheless, we cannot dismiss the possibility that human activities could also impact the genetic diversity and distribution of this species. This study gives a first glance at the genetic diversity of I. guayusa in the Ecuadorian Amazon. It could assist in developing successful conservation and breeding programs, which could promote the economic growth of local communities and reinforce the value of ancestral knowledge. Full article