Estimating alpha, beta, and gamma diversity through deep learning

The reliable mapping of species richness is a crucial step for the identification of areas of high conservation priority, alongside other value considerations. This is commonly done by overlapping range maps of individual species, which requires dense availability of occurrence data or relies on assumptions about the presence of species in unsampled areas deemed suitable by environmental niche models. Here we present a deep learning approach that directly estimates species richness, skipping the step of estimating individual species ranges. We train a neural network model based on species lists from inventory plots, which provide ground truthing for supervised machine learning. The model learns to predict species richness based on spatially associated variables, including climatic and geographic predictors, as well as counts of available species records from online databases. We assess the empirical utility of our approach by producing independently verifiable maps of alpha, beta, and gamma plant diversity at high spatial resolutions for Australia, a continent with highly contrasting diversity patterns. Our deep learning framework provides a powerful and flexible new approach for estimating biodiversity patterns.

Vertebrate Subfossil Localities in Taylorsville MetroPark, Montgomery County, Ohio, USA

Karst features in the Silurian dolomites of Taylorsville MetroPark (Dayton Metropolitan Area, Ohio, United States) were explored from 2017 to 2018 to identify sites of paleontological interest. Initial landscape surveys recovered 124 skeletal elements (from 12 sites) that were attributed to 17 vertebrate species—including evidence of such extirpated animals as bobcats (Lynx rufus) and rattlesnakes (Crotalus sp.). Of the 12 sites, 9 sites contained remains from the historical era and 3 sites contained much older remains (n = 17) that were radiocarbon dated to approximately 1,400 years before present (YBP). Human remains at one site, butchered bones at another, and artifacts from a third suggest a long period of pre-colonial human use of the area. The presence of rare taxa expands pre-historical species lists and confirms the coexistence of many previously undocumented taxa from the area during the late, pre-colonial, Holocene Epoch.

Legislative Approach in Managing Environment Pollution by Alien Fish Species in Malaysia

River pollution has been a major problem in Malaysia and significantly affects the environment. One of the contributing issues would be the spread of invasive alien fish species that has given negative impacts on the environment and ecological disaster, the human health, harming the native animals and plants, as well the economy. Based on the National Committee on Invasive Alien Species Report in 2018, that 46 invasive alien species from a total of 130 species in the established main invasive alien species lists in Malaysia. The alien fishes have been known to make their presence in our dams, lakes and rivers but not much attention has been paid to their existence. Based on these facts, it is proven that the issue poses a significant risk hence an urgent attention is required in managing this pollution through proactive legal measures to enforce strictly the existing law so as to prevent the halt of the spread of invasive species. A legal doctrinal and non-doctrinal modes of research are used to examine and review on the existing laws and/or policy governing this issue. This research will help to provide reference and strategic planning via legal approach for better controlling the invasion in our Malaysian waters.

A review of tangle-veined flies (Nemestrinidae, Diptera) in Egypt

The Egyptian fauna of the genus Nemestrinus Latreille, 1802 is revised. In 1967, Steyskal and El-Bialy listed 12 species from the region, but only six species are now recognized. The primary type specimens of the species N. aegyptiacus (Wiedemann, 1828), N. rufipes (Olivier, 1810), and N. lateralis Wiedemann, 1828 (N. lateralis being a synonym of N. rufipes) deposited in the Museum für Naturkunde, Berlin, Germany were examined. Two species (N. abdominalis Olivier, 1811 and N. fascifrons (Bigot, 1888) are placed as new synonyms of N. ater (Olivier, 1811), and N. ruficornis Macquart, 1840 is synonymized with N. rufipes (Olivier, 1811). Nemestrinus jullieni (Efflatoun, 1925) is confirmed as a synonym of N. aegyptiacus. Furthermore, three species (N. caucasicus Fischer, 1806, N. pallipes (Olivier, 1811), and N. persicus Lichtwardt, 1909) have been removed and are doubtful records from Egypt. A key to the species, lists of specimens examined, and Illustrations and distributions for each species are provided. The status of species of doubtful occurrence in Egypt is discussed.

Environmental DNA analysis needs local reference data to inform taxonomy-based conservation policy:A case study from Aotearoa / New Zealand

Effective management of biodiversity requires regular surveillance of multiple species. Analysis of environmental DNA by metabarcoding (eDNA) holds promise to achieve this relatively easily. However, taxonomic inquiries into eDNA data need suitable molecular reference data, which are often lacking. We evaluate the impact of this reference data void in a case study of fish diversity in the remote fiords of New Zealand. We compared eDNA-derived species identifications against Baited Remote Underwater Video (BRUV) data collected at the same time and locations as the eDNA data. Furthermore, we cross referenced both eDNA and BRUV data against species lists for the same region obtained from literature surveys and the Ocean Biodiversity Information System (OBIS). From all four data sources, we obtained a total of 116 species records (106 ray-finned fishes, 10 cartilaginous fishes; 59 from literature, 44 from eDNA, 25 from BRUV, 25 from OBIS). Concordance of taxonomies between the data sources dissolved with lowering taxonomic levels, most decisively so for eDNA data. BRUV agreed with local biodiversity information much better and fared better in detecting regional biodiversity dissimilarities. We provide evidence that eDNA metabarcoding will remain a powerful but impaired tool for species-level biodiversity management without locally generated reference data.

A Hotspot of Arid Zone Subterranean Biodiversity: The Robe Valley in Western Australia

Knowledge of subterranean fauna has mostly been derived from caves and streambeds, which are relatively easily accessed. In contrast, subterranean fauna inhabiting regional groundwater aquifers or the vadose zone (between surface soil layers and the watertable) is difficult to sample. Here we provide species lists for a globally significant subterranean fauna hotspot in the Robe Valley of the Pilbara region, Western Australia. This fauna was collected from up to 50 m below ground level using mining exploration drill holes and monitoring wells. Altogether, 123 subterranean species were collected over a distance of 17 km, comprising 65 troglofauna and 58 stygofauna species. Of these, 61 species were troglobionts and 48 stygobionts. The troglofauna occurs in small voids and fissures in mesas comprised mostly of an iron ore formation, while the stygofauna occurs in the alluvium of a river floodplain. The richness of the Robe Valley is not a localized aberration, but rather reflects the richness of the arid Pilbara region. While legislation in Western Australia has recognized the importance of subterranean fauna, mining is occurring in the Robe Valley hotspot with conditions of environmental approval that are designed to ensure species persistence.

The Louisiana Amphibian Monitoring Program from 1997 to 2017: Results, analyses, and lessons learned

To determine trends in either frog distribution or abundance in the State of Louisiana, we reviewed and analyzed frog call data from the Louisiana Amphibian Monitoring Program (LAMP). The data were collected between 1997 and 2017 using North American Amphibian Monitoring Program protocols. Louisiana was divided into three survey regions for administration and analysis: the Florida Parishes, and 2 areas west of the Florida parishes called North and South. Fifty-four routes were surveyed with over 12,792 stops and 1,066 hours of observation. Observers heard 26 species of the 31 species reported to be in Louisiana. Three of the species not heard were natives with ranges that did not overlap with survey routes. The other two species were introduced species, the Rio Grande Chirping Frog (Eleutherodactylus cystignathoides) and the Cuban Treefrog (Osteopilus septentrionalis). Both seem to be limited to urban areas with little to no route coverage. The 15 most commonly occurring species were examined in detail using the percentage of stops at which they observed along a given survey and their call indices. Most species exhibited a multimodal, concave, or convex pattern of abundance over a 15-year period. Among LAMP survey regions, none of the species had synchronous population trends. Only one group of species, winter callers, regularly co-occur. Based on the species lists, the North region could be seen as a subset of the South. However, based on relative abundance, the North was more similar to Florida parishes for both the winter and summer survey runs. Our analyses demonstrate that long-term monitoring (10 years or more) may be necessary to determine population and occupancy trends, and that frog species may have different local demographic patterns across large geographic areas.

Calliphoridae (Diptera) on Decomposing Pig Carcasses and Human Cadavers in the Upper Midwest of North America

The geographic ranges of forensically informative taxa on decomposing remains vary across regions. To determine which calliphorid flies would be expected to occur in Minnesota and the upper Midwest, individual freshly killed pig carcasses (Sus scrofa L.) were placed in the field in St. Paul, MN, at monthly intervals from May to October 2017 and May to September 2018. Aerial nets, forceps, and pitfall traps were used to collect and preserve associated adult and immature insects. Sixty-four forensically informative insect taxa were recorded, representing three insect orders and 14 families. Ten informative calliphorid species were recorded on carcasses, adding four new Minnesota records. Comparison of species lists from 26 human forensic cases indicated agreement between the two lists, except for Lucilia coeruleiviridis Macquart, Calliphora vomitoria (L.), and Cynomya cadaverina Robineau-Desvoidy, which occurred on pig carcasses but not human remains, and Calliphora livida Hall, which occurred on human remains, but not carcasses. The composite fauna list from cadavers agreed largely with the 2-yr list from pig carcasses.

IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics

The advent and continual improvement of high-throughput sequencing technologies has made immunoglobulin repertoire sequencing accessible and informative regardless of study species. However, to fully map changes in polyclonal dynamics, precise annotation of these constantly rearranging genes is pivotal. For this reason, data agnostic tools able to learn from presented data are required. Most sequence annotation tools are designed primarily for use with human and mouse antibody sequences which use databases with fixed species lists, applying very specific assumptions which select against unique structural characteristics. We present IgMAT, which utilises a reduced amino acid alphabet, incorporates multiple HMM alignments into a single consensus and enables the incorporation of user defined databases to better represent their species of interest.Availability and implementationIgMAT has been developed as a python module, and is available on GitHub (https://github.com/TPI-Immunogenetics/igmat) for download under GPLv3 license.Supplementary informationModel Breakdowns

NEW RECORD OF THE SPIDER CRAB Mithrax tortugae RATHBUN, 1920 IN THE NORTHEAST OF BRAZIL, FIRST RECORD ON THE COAST OF RIO GRANDE DO NORTE

The Northeast region of Brazil has gaps in the distribution of several species of crustaceans. In the last decade, the increase in the sampling effort and the elaboration of species lists have minimized this problem. In some cases, studies suggest that these “gaps” in the distribution of some organisms may be a natural part of a discontinuity in their geographical limits. During the lobster fishing expeditions on coral reefs in the north coast of Rio Grande do Norte (RN), for the first time, the spider crab Mithrax tortugae was captured in RN. After capture, some specimens were sent to the UFRN aquatic fauna laboratory for identification and biometrics. After confirmation of identification, they were deposited in the UFRN invertebrate collection. Thus, the present work aims to update the distribution area of the species, and to fill an existing gap for the Northeast region, bringing the first record of Mithrax tortugae on the coast of Rio Grande do Norte.