We are living in a time of rapid biodiversity loss. Numerous studies have shown that modern extinction rates are higher than pre-human background rates. However, these biodiversity studies almost exclusively focus on large vertebrates: mammals, birds, fish and reptiles. We lack sufficient long-term records for many invertebrate taxa to track biodiversity loss. Aquatic, benthic, calcareous invertebrates, however, have the advantage of leaving a long-term record that can readily be sampled along with living communities. They leave easily-fossilized remains in the form of mineralized skeletons that accumulate in the very same sediments in which they live. These so called “death assemblages” contain an underutilized record for long-term monitoring. Here, we leverage calcareous micro- and macro- faunal remains from three aquatic environments spanning a two-dimensional gradient from freshwater to fully marine and polluted to remediated. We find death assemblages of lacustrine, calcareous microcrustaceans (Ostracoda) faithfully record human impacts, both pollution and remediation, across a fresh to hypersaline environmental gradient today. Death assemblages from calcareous marine, macrofauna (Bivalvia) also faithfully reconstruct temporal variation in human impact encompassing pristine, polluted, and successful remediation. We thus establish that death assemblages can act as useful gauges of changes in community assembly and population structures at local and regional scales which would be impossible with only contemporaneous monitoring of the living communities. These examples demonstrate that death assemblages from easily-fossilized taxa represent an effective tool for environmental managers to establish baselines for conservation targets and identify when community assembly approaches natural conditions in remediated ecosystems, rendering previously unrecognized biodiversity loss visible.

Genetic mutation occurs within genes and is responsible for the observed phenotypic variation between breeds within a species. It is known that indigenous sheep breeds are more robust and able to reproduce in adverse conditions in comparison to exotic sheep breeds. Therefore, the aim of this study was to determine whether there are any genetic mutations between indigenous breeds in known fecundity genes, growth differentiation factor 9 (GDF9) and bone morphogenetic protein receptor type 1B (BMPR1B/FecB), in four South African indigenous sheep breeds. A total of 52 blood samples were collected from four sheep breeds (Karakul = 8; Damara = 8; Zulu = 18; Pedi = 18). Unlabeled forward and reverse primers were used to amplify the GDF9 and BMPR1B genes. The PCR products were sequenced by a standard capillary sequencer. Sequencing results were analyzed using BioEdit, thereafter the detection of single nucleotide polymorphisms (SNPs), and phylogenetic analysis with the MEGA-X software. The results indicated that there are point mutations between sheep breeds in the GDF9 and BMPR1B gene compared to that of the Ovis aries complete coding sequence found in GenBank. Mutations of GDF9 gene (c.142C>T) and (c.151G>C) were detected in individuals of the Karakul, Damara, and Zulu sheep. The results also show that BMPR1B gene has mutation (c.80G>C) between individuals of the Zulu and Pedi sheep. Molecular phylogenetic analysis for both genes using the Neighbor-Joining method indicates relatedness between the Zulu and Pedi sheep. Damara breeds are more distantly related to Zulu and Pedi but show more relatedness with Karakul sheep. Polymorphism between and within the sheep breeds could be an indication of genetic variation that is potentially associated with higher prolificacy in indigenous sheep breeds.

Sampling of environmental DNA (eDNA), coupled with state-of-the-art molecular detection approaches, can potentially overcome many limitations of traditional biodiversity monitoring. The concept of eDNA utilizes nucleic acids of organisms directly from the environment. Recent studies have detected a wide spectrum of prokaryotic and eukaryotic eDNA from a variety of environments, which are ancient or modern, terrestrial or aquatic. The numerous sources of eDNA promise to establish this approach as a tool for diverse scientific settings. Here, we propose and establish spider webs as a source of eDNA with far reaching implications. First, in a field study, we tracked specific arthropod targets from different type of spider webs. Second, we used high-throughput amplicon sequencing of taxonomic barcodes to investigate the utility of eDNA from spider webs for biodiversity monitoring of animals, fungi and bacteria. We show that even the smallest target organisms can be detected by their genetic remains on spider webs. We also demonstrate that eDNA from spider webs is useful in community compositions research in different domains of life, and argue that spider webs potentially offer highly detailed temporal and spatial information.

We describe the application of the computerized deep learning methodology to the recognition of corals in a shallow reef in the Gulf of Eilat, Red Sea. This project is aimed at applying deep neural network analysis, based on thousands of underwater images, to the automatic recognition of some common species among the 100 species reported to be found in the Eilat coral reefs.
This is a challenging task, since even in the same colony, corals exhibit significant within-species
morphological variability, in terms of age, depth, current, light, geographic location, and interspecific competition. Since deep learning procedures are based on photographic images, the task is further challenged by image quality, distance from the object, angle of view, and light conditions. We
produced a large dataset of over 5,000 coral images that were classified into 11 species in the present automated deep learning classification scheme. We demonstrate the efficiency and reliability of the method, as compared to painstaking manual classification. Specifically, we demonstrated that this
method is readily adaptable to include additional species, thereby providing an excellent tool for future studies in the region, that would allow for real time monitoring the detrimental effects of global climate change and anthropogenic impacts on the coral reefs of the Gulf of Eilat and elsewhere, and
that would help assess the success of various bioremediation efforts.

Soil is one of the most important, non-renewable natural resources of human beings. Soils are needed to produce food and thus it is crucial to maintain soil health. Earthworms are one of the best indicators of soil health. Farming systems have a tremendous impact on soil biota. This effect can be both negative and positive. Less intensive farming systems, such as organic and permaculture farming are known to be more favorable for soil life while intensive farms are widely known for their negative effects. Our aim was to compare different farming systems based on the density of earthworms. Fifteen small-scale (0.3–2 hectares) farms in North-Central Hungary with similar agroecological features were selected for comparison. All of them are horticultural farms with diverse crops in the crop rotation, the only difference is the farming systems, i.e. one intensive (conventional), and two extensive types (organic and permaculture). Earthworms were sampled in May and September 2020, six replicates on each site, by hand sorting of 25x25x25 cm soil blocks. In May, abundance of juvenile and adult earthworms were significantly higher in case of permaculture farms compared to organic and also conventional farms. However, we did not find significant differences in earthworm abundance in September. There was no significant difference in the abundance of earthworm species neither in May, nor in September. Based on our soil-wise experiences it is of great importance to know as much soil information as possible (i.e. soil thickness, soil organic matter content, texture, soil management, fertilizers used, soil moisture content at the time of the counting, soil cover etc.) for considering earthworms data as a good indicator for soil quality assessment.

Transhumance is an extensive livestock technique that consist on the seasonal movement of herds to take advantage of natural high-quality pastures. Extensive pastoralism modulates the landscape, provide ecosystem services as well as feeding opportunities for scavengers. However, transhumance is in decline mainly due to socio-economic changes, so the availability of food for scavengers may be changing. With the aim to evaluate the remaining effect of transhumance, we explored the changes that occur in a summer pasture ecosystem according to the presence or absence of livestock. The study was located in a high plateau of pastures in the south of the Iberian Peninsula, located in the Natural Park of Sierra de Cazorla, Segura y las Villas where about 35,000 units of livestock, mainly sheep, move there to graze in summer. We evaluated the changes in the abundance of obligate and facultative scavengers by field surveys, as well as the response of local wild ungulates in presence and absence of livestock. We also evaluated the individual foraging behavior of the main scavengers by GPS monitoring of 30 adult griffon vultures (Gyps fulvus) for four years. Surveys shown a positive populational response of griffon vultures in presence of livestock and an increase of GPS locations, especially noteworthy in non-breeding individuals. However, facultative scavengers and wild ungulates abundances remain unaltered throughout the year. The combination of census sampling and GPS monitoring allowed us to better understand the ecosystem dynamics. Traditional extensive livestock farming has a functional ecological response in scavengers, so current changes in this practice may affect them in future scenarios.

Bark and ambrosia beetles are considered the main forest pest groups and also biological indicators in natural areas, due to their especial participation in wood rot process. However, there are few investigations exploring the aspects related to the temperature influence, as well as the host plant availability along the geographical distribution, abundance and diversity of these beetles in anthropized areas. Thus, we aimed to access such parameters to Scolytinae in three different anthropized environments in the south of Brazil and verify their possible correlation with temperature and distinct host plants. It was installed flight interception alcohol traps to monitor the beetles. The experimental areas were divided in uncovered soil area with grass fragments; reforestation area composed exclusively to Mimosa scabrella, a native plant from south of Brazil; agroforestry system with native and exotic plant species. It was collected 357 Scolytinae individuals, distributed in 6 tribes, 15 genus and 42 species. Individuals from the Corthylini tribe dominated in abundance (~78%) and diversity (24 spp.). From this group, ~58% from all species belong to Corthylus. We also observed a correlation between the temperature and Scolytinae abundance, since the higher number of species were collected during the lowest temperatures. The abundance and diversity similarity between M. scabrella and the agroforestry areas demonstrated that a higher diversity of plants does not indicate a higher diversity of ambrosia beetles. Therefore, in anthropized areas, the Corthylini beetles do not seem to be potential bioindicators, which can be related to their polyphagous ability.

Invasive alien species pose a significant threat to biodiversity in the area where they have been introduced. In South Africa, most of ornamental fishes sold are imported from other countries. The parasites of alien species can be transported along with their hosts and become co-invasive. An invasive parasite from Asia, Camallanus cotti was reported in Africa for the first time in the year 2017 from the guppy, an ornamental fish which established a feral population. This is proof that ornamental fish may introduce alien parasites. Three ornamental fish species were imported (Red rainbowfish, pearl gourami and clown loach) from Indonesia. Standard methods were used for the dissection of fish, examination, fixation and preservation of parasites. The prevalence and mean intensity of different parasites of each fish species were determined and they were identified to genus and species level where possible. Nematodes (Camallanus cotti and Procamallanus sp), cestodes (Neogryporhynchus cheilancristrotus and Dendrouterina herodiae), a copepod (Lernaea cyprinacea) and monogeneans were found from the imported fishes. Two new species of monogeneans (here named Ancyrocephalidae sp. 1 and Ancyrocephalidae sp. 2) not belonging to any established genus were discovered. Cestodes were only found from pearl gourami and the copepod from red rainbowfish. The clown loach had no parasites. Red rainbowfish had the highest prevalence and mean intensity for mongeneans and nematodes.

Heterogeneity in species diversity is driven by the dynamics of speciation and extinction, potentially influenced by organismal and environmental factors. Here, we explore macroevolutionary trends on a phylogeny of golden orbweavers (spider family Nephilidae). Our initial inference detects heterogeneity in speciation and extinction, with accelerated extinction rates in the extremely sexually size dimorphic Nephila and accelerated speciation in Herennia, a lineage defined by highly derived, arboricolous webs, and pronounced island endemism. We evaluate potential drivers of this heterogeneity that relate to organisms and their environment. Primarily, we test two continuous organismal factors for correlation with diversification in nephilids: phenotypic extremeness (female and male body length, and sexual size dimorphism as their ratio) and dispersal propensity (through range sizes as a proxy). We predict a bell-shaped relationship between factor values and speciation, with intermediate phenotypes exhibiting highest diversification rates. Analyses using SSE-class models fail to support our two predictions, suggesting that phenotypic extremeness and dispersal propensity cannot explain patterns of nephilid diversification. Furthermore, two environmental factors (tropical versus subtropical and island versus continental species distribution) indicate only marginal support for higher speciation in the tropics. Although our results may be affected by methodological limitations imposed by a relatively small phylogeny, it seems that the tested organismal and environmental factors play little to no role in nephilid diversification. In the phylogeny of golden orbweavers, the recent hypothesis of universal diversification dynamics may be the simplest explanation of macroevolutionary patterns.

Cyphalonotus is a poorly studied araneid spider genus with species from Africa and Asia whose phylogenetic proximity remains unknown due to the paucity of morphological and molecular data. We here report on a taxonomic and evolutionary research on these spiders with three main objectives: i) to test the taxonomic composition of Cyphalonotus; ii) to test its phylogenetic placement; and iii) to place the male and female size variation of Cyphalonotus and related genera in an evolutionary context. Our original collection and field observations from Taiwan and China facilitated description of a new and a known species, and newly provided sequence data enable species delimitation, and phylogenetic analyses. The phylogenetic results reject all four classification hypotheses from the literature, and instead recover a well-supported clade Cyphalonotus + Poltys. We review the male and female size variation in Cyphalonotus, Poltys, and related genera. These data reveal that all known species of Poltys are extremely sexually size dimorphic (eSSD = females over twice the male size) reaching values exceeding 10-fold differences, while Cyphalonotus and other genera in their phylogenetic proximity are relatively sexually monomorphic (SSD < 2.0). This confirms an independent origin of eSSD in Poltys, one of multiple convergent evolutionary outcomes in orbweb spiders.