Diversity, Volume 11, Issue 10 (October 2019) – 29 articles

Spiders are a diverse group with a high eco-morphological diversity, which complicates anatomical descriptions especially with regard to its terminology. New terms are constantly proposed, and definitions and limits of anatomical concepts are regularly updated. Therefore, it is often challenging to find the correct terms, even for trained scientists, especially when the terminology has obstacles such as synonyms, disputed definitions, ambiguities, or homonyms. Here, we present the Spider Anatomy Ontology (SPD), which we developed combining the functionality of a glossary (a controlled defined vocabulary) with a network of formalized relations between terms that can be used to compute inferences. The SPD follows the guidelines of the Open Biomedical Ontologies and is available through the NCBO BioPortal (ver. 1.1). It constitutes of 757 valid terms and definitions, is rooted with the Common Anatomy Reference Ontology (CARO), and has cross references to other ontologies, especially of arthropods. The SPD offers a wealth of anatomical knowledge that can be used as a resource for any scientific study as, for example, to link images to phylogenetic datasets, compute structural complexity over phylogenies, and produce ancestral ontologies. By using a common reference in a standardized way, the SPD will help bridge diverse disciplines, such as genomics, taxonomy, systematics, evolution, ecology, and behavior. Full article

Here we present a comprehensive review of the diversity revealed by research in limnology and microbial ecology conducted in Byers Peninsula (Livingston Island, South Shetland Islands, Antarctica) during the last two decades. The site constitutes one of the largest ice-free areas within the Antarctic Peninsula region. Since it has a high level of environmental protection, it is less human-impacted compared to other sites within the South Shetland archipelago. The main investigations in Byers Peninsula focused on the physical and chemical limnology of the lakes, ponds, rivers, and wetlands, as well as on the structure of their planktonic and benthic microbial communities, and on the functional ecology of the microbial food webs. Lakes and ponds in Byers range along a productivity gradient that extends from the less productive lakes located upland to the eutrophic coastal lakes. Their planktonic assemblages include viruses, bacteria, a metabolically diverse community of protists (i.e., autotrophs, heterotrophs, and mixotrophs), and a few metazooplankton species. Most of the studies conducted in the site demonstrate the strong influence of the physical environment (i.e., temperature, availability of light, and water) and nutrient availability in structuring these microbial communities. However, top-down biotic processes may occur in summer, when predation by zooplankton can exert a strong influence on the abundance of protists, including flagellates and ciliated protozoa. As a consequence, bacterioplankton could be partly released from the grazing pressure exerted by these protists, and proliferates fueled by external nutrient subsidies from the lake’s catchment. As summer temperatures in this region are slightly above the melting point of water, biotic processes, such as those related to the productivity of lakes during ice-free periods, could become even more relevant as warming induced by climate change progresses. The limnological research carried out at the site proves that Byers Peninsula deserves special attention in the framework of the research in extreme environments. Together with nearby sites, such as Signy Island, Byers Peninsula comprises a featuring element of the Maritime Antarctic region that represents a benchmark area relative to the global distribution and diversity of aquatic microorganisms. Full article

Elevational gradients provide a unique opportunity to explore species responses to changing environmental conditions. Here, we focus on an elevational gradient in Crete, a climate-vulnerable Mediterranean plant biodiversity hotspot and explore the diversity patterns and underlying mechanisms of different plant life forms. We found that the significant differences in life forms’ elevational and environmental ranges are reflected in α- diversity (species richness at local scale), γ-diversity (species richness at regional scale) and β-diversity (variation in species composition). The α- and γ-diversity decreased with elevation, while β-diversity followed a hump-shaped relationship, with the peak varying between life forms. However, β-deviation (deviation from null expectations) varied significantly with elevation but was life formindependent. This suggests that species composition is shaped by the size of the available species pool which depends on life form, but also by other deterministic or stochastic processes that act in a similar way for different life forms. The strength of these processes varies with elevation, with hotter–drier conditions and increased human activities filtering species composition at lowlands and large-scale processes determining the species pool size overriding local ecological processes at higher elevations. Full article

The lowland rainforests of the Amazon basin harbor some of the most species-rich reptile communities on Earth. However, there is considerable heterogeneity among climatically-similar sites across the Amazon basin, and faunal surveys for southwestern Amazonia in particular have revealed lower species diversity relative to sites in the northwestern and central Amazon. Here, we report a herpetofaunal inventory for Los Amigos Biological Station (LABS), a lowland site located in the Madre de Dios watershed of southern Peru. By combining active search and passive trapping methods with prior records for the site, we provide a comprehensive species list for squamate reptiles from LABS. We also estimate an “expected” list for LABS by tabulating additional taxa known from the regional species pool that we consider to have a high probability of detection with further sampling. The LABS total of 60 snake and 26 lizard taxa is perhaps the highest for any single site in the southern Amazon. Our estimate of the regional species pool for LABS suggests that the southwestern Amazonian lowlands harbor at least 25% fewer species of snakes relative to the western equatorial Amazon, a diversity reduction that is consistent with patterns observed in several other taxonomic groups. We discuss potential causes of this western Amazonian richness gradient and comment on the relationship between spatial diversity patterns in squamates and other taxa in the Amazon basin. Full article

Modern agriculture has responded to the growing pressure for animal-protein consumption in the global human population by selecting for specific production traits, which, over the last fifty years, has resulted in a loss of genetic diversity. Most rare and endangered breeds of livestock have not experienced the same selection pressures for production and therefore may contain useful genetic traits not found within modern breeds. In an effort to maintain biodiversity of livestock breeds, the SVF Foundation, a non-profit organization founded to preserve the genetic diversity of food and fiber livestock, has established an ex situ repository of genetic material from endangered North American cattle, sheep, and goats. This genetic material includes in vivo and in vitro produced embryos, semen, fibroblasts, serum, and whole blood DNA cards. The majority of samples in the SVF repository are cryopreserved, creating a genome resource bank for future use. Through the Smithsonian and SVF Biodiversity Preservation Project, this repository will be maintained at the Smithsonian’s Front Royal, VA, facility. This effort represents an excellent model for understanding and sustaining the genetic diversity of rare breeds in the US and in other countries. Full article

Anti-seasonal drying-wetting cycles since 2010 have substantially altered its soil and vegetation status in the drawdown zone of China’s Three Gorges Reservoir (TGR). Such alternations may thus affect the composition and functioning of soil microbial communities, including the beneficial arbuscular mycorrhizal fungi (AMF), which enhance plant performance. Moreover, limited information is available if AMF communities are different in soils and roots, particularly under contrasting land-use changes. By combining the Illumina Miseq sequencing with bioinformatics analyses, AMF communities in both rhizosphere soils and roots of a stoloniferous and rhizomatous C₄ perennial of Cynodon dactylon were characterized under three land-use types: (1) crop cultivated, (2) non-cultivated non-disturbed, and (3) disturbed non-cultivated land. A total of 35 and 26 AMF taxa were respectively detected from C. dactylon rhizosphere soils and roots from these three land-use types, which had endured four anti-seasonal drying/summer-wetting/winter cycles. Contrasting differentiations in the AMF community composition and structure were displayed in the C. dactylon rhizosphere soils and roots, and between land-use types. Nonmetric multidimensional scaling analyses revealed that AMF communities significantly correlated to soil organic carbon in the rhizosphere soils and roots of C. dactylon, to land-use types only in rhizosphere soils, whereas to soil moisture only in roots. Our results highlight the effects of soil nutrients and land-use changes on AMF community composition and diversity under the canopy of C. dactylon in TGR. The identified dominant AMF taxa can be employed to vegetation restoration in such degraded habitats globally. Full article

We analyze the structure of diameter, richness, and diversity of the forests in the upper limit of the great Amazon basin located in the Ecuadorian territory of the Cordilleras del Cóndor and Cutucú. Our hypothesis was that the forests of the eastern mountain ranges are not homogeneous, but rather present differences in their structure, richness, and floristic diversity. Our main objective was to classify the types of forests based on the characteristics of the diameter structure and the species composition of the Amazonian forests of the eastern mountain ranges in southern Ecuador, and we determined the influence of critical edaphic, environmental, and geomorphological factors, For this we installed eight permanent plots of one hectare in homogeneous and well preserved forest stands, four plots in the province of Zamora Chinchipe and four in the province of Morona Santiago. We identified and measured all trees >10 cm at chest height and for each plot, soil samples, as well as environmental and slope data were taken. We performed an non-metric multidimensional scaling analysis (NMDS) analysis to evaluate changes in climatic and geomorphological gradients, and used the CCA analysis to assess the relationship between the composition of the species at the plot level and the edapho-climatic variables. Finally, we modeled the change in diversity ad species (Fisher’s alpha) in relation to climatic, altitudinal, and geomorphological gradients using a GLM. We determined the existence of two different types of forest, the first called Terra Firme, characterized by the presence of a greater number of species and individuals per plot as compared to the second type of forest called Tepuy or Sandstone forest. Species richness was negatively correlated with the phosphorus content of the soil and the pH, annual average temperature, annual rainfall, and altitude. Terra Firme forests, settled in more stable and nutrient-rich climatic areas, were more diverse and Sandstone forests are poor in nutrients and develop in areas with greater seasonality. Full article

Bacterial and archaeal diversity and succession were studied during a mesocosm experiment that investigated whether changing light regimes could affect the onset of phytoplankton blooms. For this, 454-pyrosequencing of the bacterial V1-V3 and archaeal V3-V9 16S rRNA regions was performed in samples collected from four mesocosms receiving different light irradiances at the beginning and the end of the experiment and during phytoplankton growth. In total, 46 bacterial operational taxonomic units (OTUs) with ≥1% relative abundance occurred (22–34 OTUs per mesocosm). OTUs were affiliated mainly with Rhodobacteraceae, Flavobacteriaceae and Alteromonadaceae. The four mesocosms shared 11 abundant OTUs. Dominance increased at the beginning of phytoplankton growth in all treatments and decreased thereafter. Maximum dominance was found in the mesocosms with high irradiances. Overall, specific bacterial OTUs had different responses in terms of relative abundance under in situ and high light intensities, and an early phytoplankton bloom resulted in different bacterial community structures both at high (family) and low (OTU) taxonomic levels. Thus, bacterial community structure and succession are affected by light regime, both directly and indirectly, which may have implications for an ecosystem’s response to environmental changes. Full article

Straw retention, an alternative to artificial fertilization, commonly mitigates soil degradation and positively affects soil fertility. In this study, we investigated the succession of soil bacteria during two sugarcane straw retention treatments (control (CK) and sugarcane straw retention (SR)) and at four depths (0–10, 10–20, 20–30, and 30–40 cm) in fallow soil in a sugarcane cropping system. Using an Illumina MiSeq (16S rRNA) and soil enzyme activity, we explored the SR influence on soil bacterial communities and enzyme activities and its inclusive impact on soil fertility, with an emphasis on topsoil (0–10 cm) and subsoil (10–40 cm). Our results show that SR effectively improved soil fertility indicators (C, N, and P), including enzyme activities (C and N cycling), throughout the soil profile: these soil parameters greatly improved in the topsoil compared to the control. Sugarcane straw retention and soil depth (0–10 cm vs. 10–40 cm) were associated with little variation in bacterial species richness and alpha diversity throughout the soil profile. Subsoil and topsoil bacterial communities differed in composition. Compared to the CK treatment, SR enriched the topsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, and Nitrospirae, while the subsoil was depleted in Nitrospirae and Acidobacteria. Similarly, SR enriched the subsoil with Proteobacteria, Verrucomicrobia, Actinobacteria, Chloroflexi, Gemmatimonadetes, and Bacteroidetes, while the topsoil was depleted in Acidobacteria, Gemmatimonadetes, and Planctomycetes compared to the CK. At the genus level, SR enriched the topsoil with Gp1, Gp2, Gp5, Gp7, Gemmatimonas, Kofleria, Sphingomonas, and Gaiella, which decompose lignocellulose and contribute to nutrient cycling. In summary, SR not only improved soil physicochemical properties and enzyme activities but also enriched bacterial taxa involved in lignocellulosic decomposition and nutrient cycling (C and N) throughout the soil profile. However, these effects were stronger in topsoil than in subsoil, suggesting that SR enhanced fertility more in topsoil than in subsoil in fallow land. Full article

This study investigated the spatial variation in the components of a microbial food web (viruses, picoplankton, nanoflagellates, and ciliates) in different hydrographic environments in the Taiwan Strait during winter. Water temperature and salinity varied spatially, with lower temperatures (15.3–22.8 °C) and salinities (32.2–33.4 psu) in the northern part of the Taiwan Strait, largely affected by runoff from the coast of China. Concentrations of nutrients and Chl a were significantly higher in the northern part than that in the southern part of the study area. Synechococcus spp., nanoflagellate, and ciliate abundance also varied significantly, with the northern strait having higher abundances of these communities. In contrast, a higher abundance of bacteria was found in the southern part of the Taiwan Strait. The results of this study, which describes two different ecosystems in the Taiwan Strait, suggest that during winter, a “viral loop” might play an important role in controlling bacterial production in the southern part of the Taiwan Strait, while nanofalgellate grazing of picophytoplankton may contribute mainly to the flux of energy in the northern part. Full article

Invasive plant species are increasingly altering species composition and the functioning of ecosystems from a local to a global scale. The grass species Pennisetum setaceum has recently raised concerns as an invader on different archipelagos worldwide. Among these affected archipelagos are the Canary Islands, which are a hotspot of endemism. Consequently, conservation managers and stakeholders are interested in the potential spreading of this species in the archipelago. We identify the current extent of the suitable habitat for P. setaceum on the island of La Palma to assess how it affects island ecosystems, protected areas (PAs), and endemic plant species richness. We recorded in situ occurrences of P. setaceum from 2010 to 2018 and compiled additional ones from databases at a 500 m × 500 m resolution. To assess the current suitable habitat and possible distribution patterns of P. setaceum on the island, we built an ensemble model. We projected habitat suitability for island ecosystems and PAs and identified risks for total as well as endemic plant species richness. The suitable habitat for P. setaceum is calculated to cover 34.7% of the surface of La Palma. In open ecosystems at low to mid elevations, where native ecosystems are already under pressure by land use and human activities, the spread of the invader will likely lead to additional threats to endemic plant species. Forest ecosystems (e.g., broadleaved evergreen and coniferous forests) are not likely to be affected by the spread of P. setaceum because of its heliophilous nature. Our projection of suitable habitat of P. setaceum within ecosystems and PAs on La Palma supports conservationists and policymakers in prioritizing management and control measures and acts as an example for the potential threat of this graminoid invader on other islands. Full article

Keratinolytic and keratinophilic fungi, such as dermatophytes, are frequently a cause of infections in humans and animals. Underground ecosystems are inhabited by various animals and are of interest for tourists. Therefore, the main goal of our research was the first evaluation of sediment and soil samples taken inside and outside the Harmanecká Cave in Slovakia for the occurrence of keratinolytic and keratinophilic fungi. Tests with Vanbreuseghema bait, as well as phenotyping and molecular methods, showed that all of the sampling sites contained ten isolates, all of the same species of keratinophilic fungi, belonging to the Microsporum cookei clade and with close affinities to Paraphyton cookei (Ajello) Y. Gräser, Dukik & de Hoog. Our research showed that, dependent on the medium, its mycelium varied in color and showed different growth rates. It also produced metabolites alkalizing DTM (dermatophyte test medium) medium. It dissolved keratin in in vitro hair perforation tests and was able to utilize most substrates in the API® 20C AUX, except for MDG (α-methyl-D-glucoside). In addition, the vegetative structures of mycelium were viable after storage at temperatures from −72 to −5 °C for 56 days, and actively grew after 28 days at a temperature range from 15 to 37 °C, with 25 °C being optimal. It showed weak, but active, growth at 5 and 10 °C after 56 days. We can assume that due to the low temperature in the caves, this fungus will not be able to actively grow rapidly on keratin substrates, but the contact with mammals, along with other favorable factors, might lead to an infection. Full article

Two main aspects of the study of diversity can be distinguished: the first is related to the inventory of living organisms, the second is related to the organization of life at the level of biotic communities. Quantitative assessment of diversity is two-components as the richness of elements and their evenness. A model of the ecosystem continuum is proposed. The greatest indicators of diversity should be expected in the middle part of the environmental gradients with temporal stability. Study of producers and consumers in water bodies of Ukraine showed a regular change in their community structure in the gradient of saprobity indices. The decreasing of community diversity estimated by the Shannon index and by species richness was found at both high and low values of the saprobity indices. The fundamental coincidence of the empirical point fields of the Shannon index for the communities of invertebrates and phytoplankton with the field points of the empirical model indicates the universality of the bimodal distribution of diversity indicators in the trophic gradient. It is shown that the estimates by zoobenthos overestimate organic pollution compared with the calculations of the same indicators by phytoplankton. Full article

In aquatic settings, animals directly affect ecosystem functions through excretion of dissolved nutrients. However, the comparative role of egestion as an animal-mediated nutrient flux remains understudied. We conducted a literature survey and meta-analysis to directly compare nitrogen (N), phosphorus (P), and N:P of egestion compared to excretion rates and ratios across freshwater animals. Synthesizing 215 datasets across 47 animal species (all primary consumers or omnivores), we show that the total N and P egestion rates exceed inorganic N and P excretion rates but not total N and P excretion rates, and that proportions of P egested compared to excreted depend on body size and animal phylum. We further show that variance of egestion rates is often greater than excretion rates, reflecting greater inter-individual and temporal variation of egestion as a nutrient flux in comparison to excretion. At phylogenetic levels, our analysis suggests that Mollusca exhibit the greatest rates and variance of P egestion relative to excretion, especially compared to Arthropoda. Given quantitative evidence of egestion as a dominant and dynamic animal-mediated nutrient flux, our synthesis demonstrates the need for additional studies of rates, stoichiometry, and roles of animal egestion in aquatic settings. Full article

The need for improved aquaculture productivity has led to widespread pressure to introduce the Genetically Improved Farmed Tilapia (GIFT) strains of Nile tilapia (Oreochromis niloticus) into Africa. However, the physical and regulatory infrastructures for preventing the escape of farmed stocks into wild populations and ecosystems are generally lacking. This study characterized the genetic background of O. niloticus being farmed in Ghana and assessed the genetic effects of aquaculture on wild populations. We characterized O. niloticus collected in 2017 using mitochondrial and microsatellite DNA markers from 140 farmed individuals sampled from five major aquaculture facilities on the Volta Lake, and from 72 individuals sampled from the wild in the Lower Volta River downstream of the lake and the Black Volta tributary upstream of the lake. Our results revealed that two farms were culturing non-native O. niloticus stocks, which were distinct from the native Akosombo strain. The non-native tilapia stocks were identical to several GIFT strains, some of which showed introgression of mitochondrial DNA from non-native Oreochromis mossambicus. We also found that the non-native cultured tilapias have escaped into the wild and interbred with local populations, and also observed potentially admixed individuals on some farms. Our results highlight aquaculture as a vector in the spread of invasive non-native species and strains, and underscore the importance of genetic baseline studies to guide conservation planning for wild populations. Full article

Relative to mammals and birds, little is known about the mortality trajectories of perennial plants, as there are few long-term demographic studies following multiple yearly cohorts from birth to death. This is particularly important because if reproductively mature individuals show actuarial senescence, current estimations of life spans assuming constant survival would be incorrect. There is also a lack of studies documenting how life history trade-offs and disturbance influence the mortality trajectories of plants. We conducted Bayesian survival trajectory analyses (BaSTA) of a 33-year individual-based dataset of Pulsatilla vulgaris ssp. gotlandica. Mortality trajectories corresponded to “Type III” survivorship patterns, with rapidly decreasing annual mortality rates for young plants, but with constant mortality for reproductively mature individuals. We found trade-off effects resulting in a cost of growth for non-reproductive plants but no apparent cost of reproduction. Contrarily to our expectation, young plants that had previously shrunk in size had a lower mortality. However, accounting for trade-offs and disturbance only had minor effects on the mortality trajectories. We conclude that BaSTA is a useful tool for assessing mortality patterns in plants if only partial age information is available. Furthermore, if constant mortality is a general pattern in polycarpic plants, long-term studies may not be necessary to assess their age-dependent demography. Full article

Soil nitrogen abundance, as well as nitrogen use efficiency (NUE), significantly affect the crop yield and grain protein content (GPC). Depending on the genotype, a negative correlation between the yield and GPC can occur. The aim of the study was to assess the agronomic performance, and to explore physiological pathways for the efficient use of N fertilizer for two durum wheat cultivars, “Aureo” and “Vespucci”. After fertilization, the nitrogen content and values of some of the agronomic parameters and yield-related traits increased in both cultivars; nevertheless, a simultaneous rise in both the yield and GPC occurred only in Aureo. The biochemical parameters, analyzed at tillering, confirm the genotypic specificity of nitrogen use. In Vespucci’s roots, the nitrogen supply did not affect the nitrate reductase (NR), but greatly increased the amino acids and proteins, suggesting that ammonium is preferentially assimilated. In Aureo, nitrate is in part assimilated by the roots, as suggested by the ammonium increase and NR enhancement. In the leaves of both cultivars, organic nitrogen significantly increased after fertilization; however, the rise in amino acids, as well as in NR activity, was higher in Aureo than in Vespucci. These results indicate that the different nitrogen use, and in particular the diverse NR behavior, at tillering, are in part responsible of the cultivar differences in grain yield and GPC. Full article

The Sense Acuity and Behavioral (SAAB) Hypothesis proposes that the swimming capabilities and sensorial acuity of temperate fish larvae allows them to find and swim towards coastal nursery areas, which are crucial for their recruitment. To gather further evidence to support this theory, it is necessary to understand how horizontal swimming capability varies along fish larvae ontogeny. Therefore, we studied the swimming capability of white seabream Diplodus sargus (Linnaeus, 1758) larvae along ontogeny, and their relationship with physiological condition. Thus, critical swimming speed (U_crit) and the distance swam (km) during endurance tests were determined for fish larvae from 15 to 55 days post-hatching (DPH), and their physiological condition (RNA, DNA and protein contents) was assessed. The critical swimming speed of white seabream larvae increased along ontogeny from 1.1 cm s⁻¹ (15 DPH) to 23 cm s⁻¹ (50 and 55 DPH), and the distance swam by larvae in the endurance experiments increased from 0.01 km (15 DPH) to 86.5 km (45 DPH). This finding supports one of the premises of the SAAB hypothesis, which proposes that fish larvae can influence their transport and distribution in coastal areas due to their swimming capabilities. The relationship between larvae’s physiological condition and swimming capabilities were not evident in this study. Overall, this study provides critical information for understanding the link between population dynamics and connectivity with the management and conservation of fish stocks. Full article

The cyanobacteriosponge Terpios hoshinota has been reported throughout the Indo-Pacific including the Great Barrier Reef, Australia. The species encrusts live coral, giant clams, and other benthos and can be a threat to benthic communities on coral reefs. The Kimberley region of Western Australia has some of the least impacted reefs globally. We report for the first time the presence of T. hoshinota in the eastern Indian Ocean on Kimberley inshore coral reefs. Given its invasive potential, reef health surveys should include this species, and monitoring approaches developed to audit the remote Kimberley for this and other invasive species. Full article

The spread of non-native species raises concerns about native species displacement, while other negative effects on native species (e.g., habitat degradation) should also be considered. The highly invasive non-native apple snail Pomacea maculata has raised such concerns as it has become established in a wide range of aquatic systems worldwide. While monitoring native Florida P. paludosa populations in Lake Tohopekaliga (LTOHO) from 2001 to 2009 and in Water Conservation Area 3A (WCA3A, Everglades) from 2006 to 2015, we opportunistically documented the establishment and distribution of P. maculata. We estimated snail densities and recorded egg cluster presence in three study sites (12 total plots, LTOHO) and 137 sites (WCA3). On LTOHO, native snails were absent or at very low densities prior to finding P. maculata. Few snails of either species were found in high-stem-density vegetation of the littoral zone. Pomacea maculata immigration into the littoral zone occurred following managed vegetation removal, and Hydrilla verticillata proliferation in LTOHO likely contributed to the spread of P. maculata. We found both native and non-native apple snail species in many WCA3A sites following P. maculata invasion. We initially found the non-native snail in two sites in southern WCA3A; they were mostly restricted to within three kilometers of initial sites over the next four years. Overall plant community compositions in LTOHO and WCA3A appeared less impacted than expected based on previous reports of P. maculata invasions. Full article

Wildlife hosts are important reservoirs of a wide range of human and livestock infections worldwide, and in some instances, wildlife populations are threatened by disease. Yet wildlife diseases are difficult to monitor, and we often lack an understanding of basic epidemiological parameters that might inform disease management and the design of targeted interventions. The impacts of disease on host survival are generally associated with age, yet traditional epidemiological models tend to use simplistic categories of host age. Mortality trajectory analysis provides the opportunity to understand age-specific impacts of disease and uncover epidemiological patterns across complete life histories. Here, we use Bayesian survival trajectory analysis (BaSTA) software to analyse capture-mark-recapture data from a population of wild badgers Meles meles naturally infected with Mycobacterium bovis, the causative agent of tuberculosis in badgers and cattle. We reveal non-constant mortality trajectories, and show that infection exaggerates an age-dependent increase in late-life mortality. This study provides evidence for actuarial senescence in badgers, a species previously believed to display constant mortality throughout life. Our case study demonstrates the application of mortality trajectory analysis in wildlife disease research, but also highlights important limitations. We recommend BaSTA for mortality trajectory analysis in epidemiological research, but also suggest combining approaches that can include diagnostic uncertainty and the movement of hosts between disease states as they age. We recommend future combinations of multi-state and multi-event modelling frameworks for complex systems incorporating age-varying disease states. Full article

Mycorrhizas play a vital role in ecosystem function, diversity and productivity. However, mycorrhizas in tropical forests are considered to be a neglected area of research in contrast to the well-studied diversity patterns of macro organisms. To this end, soil samples from 0 to 30 cm in depth were collected from six or four elevations in a typical tropical forest of Mt. Jianfeng and Mt. Diaoluo in China. The arbuscular mycorrhizal fungal (AMF) diversity and community composition were explored among different elevations based on high-throughput barcoded sequencing on the Illumina MiSeq platform. Environmental variables of soil characteristics, and elevation on AMF community assembly were analyzed using canonical correspondence analysis. In total, 316 AMF operational taxonomic units (OTUs) were found to belong to four identified and one unclassified order, and Glomus was the most dominant genus in tropical forest. AMF communities or diversity did not clearly reflect local environmental conditions, the spatial distance between mountains and elevation. In total, 68% and 56% of taxa of AMF were observed on multiple elevations in Mt. Jianfeng and Mt. Diaoluo, respectively. Furthermore, 8.9% and 19% of OTUs were exhibited on all elevations in Mt. Jianfeng and Mt. Diaoluo, respectively. The AMF alpha diversity, richness and evenness were similar across the two surveyed tropical mountains. The influence of elevation showed no distinct role on the diversity of AMF taxa. Overall, AMF communities and diversity are abundant in tropical forests and with little influence of elevation in tropical forests of China. Full article

Galling arthropods represent one of the most specialized herbivore groups. On an evolutionary scale, different taxa of insects and mites have convergently adapted to a galling lifestyle. In this study, we have used a multi-taxonomic approach to analyze the interaction specialization between gall-inducing mites and insects and their host plants in the Nitra City Park (Nitra, Slovakia). We used four ecological descriptors for describe plant-galling interactions: number of host plant species used by each arthropod species, galling specificity on host plant species (specificity), exclusivity of interactions between galling and plant species (specialization) and overlap of the interactions between arthropod species (similarity). We have found 121 species of gall-inducing arthropods, totaling 90 insects and 31 mites occurring on 65 host plant species. Our results reveal that mites have high specialization and low similarity of interactions in comparison to insects. A multiple-taxonomic comparison showed that these differences are triggered by gall-wasps (Hymenoptera: Cynipidae), the taxon with the lowest levels of specificity of plant-galling interactions (i.e., occurring on different host plant species). Our findings are indicative of different patterns of interaction between distinct gall-inducing arthropods taxa and their host plants, despite the ecological convergence of different taxa to a highly specialized herbivorous habitat. Full article

Bacteria play a vital role in the quality of soil, health, and the production of plants. This has led to several studies in understanding the diversity and structure in the plant rhizosphere. Over the years, there have been overwhelming advances in molecular biology which have led to the development of omics techniques which utilize RNA, DNA, or proteins as biomolecules; these have been gainfully used in plant–microbe interactions. The bacterial community found in the rhizosphere is known for its colonization around the roots due to availability of nutrients, and composition, and it affects the plant growth directly or indirectly. Metabolic fingerprinting enables a snapshot of the metabolic composition at a given time. We review metabolites with ample information on their benefit to plants and which are found in rhizobacteria such as Pseudomonas spp. and Bacillus spp. Exploring plant-growth-promoting rhizobacteria using omics techniques can be a true success story for agricultural sustainability. Full article

“Genomic Analyses of Avian Evolution” is a “state of the art” showcase of the varied and rapidly evolving fields of inquiry enabled and driven by powerful new methods of genome sequencing and assembly as they are applied to some of the world’s most familiar and charismatic organisms—birds. The contributions to this Special Issue are as eclectic as avian genomics itself, but loosely interrelated by common underpinnings of phylogenetic inference, de novo genome assembly of non-model species, and genome organization and content. Full article

Breeds of domesticated animals are often overlooked as contributing to biodiversity. Their unique role at the junction of natural and human-influenced environments makes them important potential contributors to biodiversity and ecosystem function. Effective conservation of livestock breeds rests upon valid recognition of breeds as repeatable genomic packages with a reasonably high level of predictability for performance. Local or landrace breeds that lack breeder organization are especially difficult to conserve due to lack of formal recognition as breeds. Achieving success with them involves three major steps: Discover, Secure, and Sustain. Early in the process an evaluation of candidate populations for status as genetic resources is essential. This process is aided by a phenotypic matrix which can be used alongside historical investigations and genetic (DNA) studies. The goal is to include all qualifying animals and to exclude all those that do not qualify. Securing some populations depends on careful rescue protocols for maximizing the recovery of genetic variation, and this can then be followed by breeding protocols that provide for maintaining the population’s production potential along with a healthy and viable genetic structure for long-term survival and use. Sustaining breeds for the long term is also enabled by assuring market demand for the breed and its products. Full article

Shallow water coral reefs are the most diverse marine ecosystems, but there is an immense gap in knowledge when it comes to understanding the diversity of the vast majority of marine biota in these ecosystems. This is especially true when it comes to understudied small and cryptic coral reef taxa in understudied ecosystems, such as mesophotic coral reef ecosystems (MCEs). MCEs were reported in Japan almost fifty years ago, although only in recent years has there been an increase in research concerning the diversity of these reefs. In this study we describe the first stoloniferous octocoral from MCEs, Hadaka nudidomus gen. nov. et sp. nov., from Iriomote and Okinawa Islands in the southern Ryukyus Islands. The species is zooxanthellate; both specimens host Cladocopium LaJeunesse & H.J.Jeong, 2018 (formerly Symbiodinium ‘Clade C’) and were collected from depths of ~33 to 40 m. Additionally, H. nudidomus gen. nov. et sp. nov. is both sclerite-free and lacks free pinnules, and both of these characteristics are typically diagnostic for octocorals. The discovery and morphology of H. nudidomus gen. nov. et sp. nov. indicate that we still know very little about stoloniferous octocoral diversity in MCEs, their genetic relationships with shallower reef species, and octocoral–symbiont associations. Continued research on these subjects will improve our understanding of octocoral diversity in both shallow and deeper reefs. Full article

Acquarossa river (Viterbo, Italy) was the site of a prospering Etruscan civilization thanks to metallurgical activity around 625–550 B.C. This caused the spread of heavy metals throughout the area. Rocks along the river probably act as a filter for these elements and they are covered by two different biofilms (epilithons). They differ for both color and bacterial composition. One is red and is enriched with Pseudomonas strains, while the other one is black and Acinetobacter is the most represented genus. Along the river lay the Infernaccio waterfalls, whose surrounding rocks are covered only by the red epilithon. The bacterial composition of this biofilm was analyzed through high throughput sequencing and compared to those ones of red and black epilithons of Acquarossa river. Moreover, cultivable bacteria were isolated and their phenotype (i.e., resistance against antibiotics and heavy metals) was studied. As previously observed in the case of Acquarossa river, characterization of bacterial composition of the Infernaccio red epilithon revealed that the two most represented genera were Acinetobacter and Pseudomonas. Nonetheless, these strains differed from those isolated from Acquarossa, as revealed by RAPD analysis. This work, besides increasing knowledge about the ecological properties of this site, allowed to isolate new bacterial strains, which could potentially be exploited for biotechnological applications, because of their resistance against environmental pollutants. Full article

The Cleveland Bay (CB) is the United Kingdom’s oldest established horse breed. In this study we analyzed the genetic variability in CB horses and investigated its genetic relationships with other horse breeds. We examined the genetic variability among 90 CB horses sampled in the USA compared to a total of 3447 horses from 59 other breeds. Analysis of the genetic diversity and population structure was carried out using 15 microsatellite loci. We found that genetic diversity in CB horses was less than that for the majority of other tested breeds. The genetic similarity measures showed no direct relationship between the CB and Thoroughbred but suggested the Turkman horses (likely in the lineage of ancestors of the Thoroughbred) as a possible ancestor. Our findings reveal the genetic uniqueness of the CB breed and indicate its need to be preserved as a genetic resource. Full article