THE IMPORTANCE OF TAXONOMY ON BASE SCIENCE

Although species identification is a central component on Biological Sciences, misidentifications are quite common generating error cascade effects on other environmental studies, resulting on erroneous population estimates, status, trends, and distribution data. One of the main causes of these errors occurs when dealing with damaged material, immature specimens, sexual dimorphism, intraspecific variation, and species with poor or outdated descriptions. Furthermore, usually there is no material retained as voucher of the specimens studied in scientific collections, hindering confirmation the identified species, in morphoanatomical and genetic scope. Even with this reliance on species identification taxonomy has been in decline for many years. In this study, we present the case study of the crustaceans identified for the Minho River estuary (NW Iberian Peninsula), using a taxonomic approach comparing these results with the biological surveys obtained through various ecology studies performed for 4 decades. A total of 64 species of crustaceans were identified within this study, in which 44 were new records for the Minho River estuary, compared to the 25 species identified on the biological surveys analyzed. Being one of the first studies of this nature in the Minho River, the main objective will be to provide taxonomic support in future projects in this area, contributing to the knowledge of the fauna of Portugal and the Iberian Peninsula.

Comparison of materials for rapid passive collection of environmental DNA

Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive, efficient, and requires minimal equipment, making it suited to high density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3 million litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibers and 1% chitosan, cotton fibres, hemp fibres and sponge with either zeolite or active carbon) for intervals between five and 1080 minutes. We show that for most materials, with as little as five minutes submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 to 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19-32). Using scanning electron microscopy, we visualised biological matter adhered to the surface of materials, rather than entrapped, with images also revealing a diversity in size and structure of putative eDNA particles. Environmental DNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost and time-sensitive biological surveys, and where access to equipment is limited.

Comparison of materials for rapid passive collection of environmental DNA

Passive collection is an emerging sampling method for environmental DNA (eDNA) in aquatic systems. Passive eDNA collection is inexpensive, efficient, and requires minimal equipment, making it suited to high density sampling and remote deployment. Here, we compare the effectiveness of nine membrane materials for passively collecting fish eDNA from a 3 million litre marine mesocosm. We submerged materials (cellulose, cellulose with 1% and 3% chitosan, cellulose overlayed with electrospun nanofibers and 1% chitosan, cotton fibres, hemp fibres and sponge with either zeolite or active carbon) for intervals between five and 1080 minutes. We show that for most materials, with as little as five minutes submersion, mitochondrial fish eDNA measured with qPCR, and fish species richness measured with metabarcoding, was comparable to that collected by conventional filtering. Furthermore, PCR template DNA concentrations and species richness were generally not improved significantly by longer submersion. Species richness detected for all materials ranged between 11 to 37 species, with a median of 27, which was comparable to the range for filtered eDNA (19-32). Using scanning electron microscopy, we visualised biological matter adhered to the surface of materials, rather than entrapped, with images also revealing a diversity in size and structure of putative eDNA particles. Environmental DNA can be collected rapidly from seawater with a passive approach and using a variety of materials. This will suit cost and time-sensitive biological surveys, and where access to equipment is limited.

Comparing the reliability of relative bird abundance indices from standardized surveys and community science data at finer resolutions

Biodiversity loss is a global ecological crisis that is both a driver of and response to environmental change. Understanding the connections between species declines and other components of human-natural systems extends across the physical, life, and social sciences. From an analysis perspective, this requires integration of data from different scientific domains, which often have heterogeneous scales and resolutions. Community science projects such as eBird may help to fill spatiotemporal gaps and enhance the resolution of standardized biological surveys. Comparisons between eBird and the more comprehensive North American Breeding Bird Survey (BBS) have found these datasets can produce consistent multi-year abundance trends for bird populations at national and regional scales. Here we investigate the reliability of these datasets for estimating patterns at finer resolutions, inter-annual changes in abundance within town boundaries. Using a case study of 14 focal species within Massachusetts, we calculated four indices of annual relative abundance using eBird and BBS datasets, including two different modeling approaches within each dataset. We compared the correspondence between these indices in terms of multi-year trends, annual estimates, and inter-annual changes in estimates at the state and town-level. We found correspondence between eBird and BBS multi-year trends, but this was not consistent across all species and diminished at finer, inter-annual temporal resolutions. We further show that standardizing modeling approaches can increase index reliability even between datasets at coarser temporal resolutions. Our results indicate that multiple datasets and modeling methods should be considered when estimating species population dynamics at finer temporal resolutions, but standardizing modeling approaches may improve estimate correspondence between abundance datasets. In addition, reliability of these indices at finer spatial scales may depend on habitat composition, which can impact survey accuracy.

Biogeographic and fragmentation-related research biases on antbirds and non-flying small mammals in Brazil

Major biogeographic and taxonomic biases are recurrent in biological surveys, including fragmentation studies. Detecting biases and subsequent gaps is crucial to steer future research and suitable conservation policies. We evaluated biogeographic and fragmentation-related biases on antbirds and non-flying small mammals in Brazil, two oversampled and vulnerable taxonomic groups, by surveying papers in the Scielo and the Web of Science. We found 566 articles published from 1945 to 2018, including 55 and 43 fragmentation studies for antbirds and small mammals, respectively. Considering the species richness for each group across the Brazilian biomes, the number of publications for small mammals tended to disproportionately increase while increasing richness. The Atlantic Forest, the most degraded and densely populated biome, contained the highest number of publications. However, the Amazon included a disproportionately high number of papers considering its low population density. Conversely, non-forest biomes such as the Caatinga, Pampa and Pantanal were mostly overlooked. Our results show that research effort for small mammals and antbirds in Brazil is biogeographically biased. We call future research to consider more studies across non-forest biomes and vast unexplored areas within forest biomes to overcome major knowledge gaps on diversity, distribution and ecology of antbirds and small mammals in Brazil.

Assessing the potential environmental factors affecting cladoceran assemblage composition in arsenic-contaminated lakes near abandoned silver mines

Silver mining has a long history in Cobalt (Ontario, Canada), and it has left a complex environmental legacy where many lakes are contaminated with arsenic-rich mine tailings. In this exploratory survey, we examined subfossil Cladocera remains in the surface sediments of 22 lakes in the abandoned mining region to assess which environmental variables may be influencing the recent assemblage structure. Further, using a “top-bottom” paleolimnological approach, we compared the recent (top) and older (bottom) assemblages from a subset of 16 lakes to determine how cladoceran composition has changed in these lakes. Our regional survey suggests that the cladoceran assemblages in the Cobalt area are primarily structured by differences in lake depth, while site-specific limnological characteristics, including those related to past mining activities, may have limited roles in shaping the recent cladoceran compositions. The top-bottom paleolimnological analysis suggests that the cladoceran assemblages have changed in most lakes around Cobalt, however the magnitude and nature of changes varied across the study sites. As with most regional biological surveys, the responses to historical mining activities were not uniform across all sites, which further emphasizes the importance of considering site-specific limnological characteristics and multiple environmental stressors when assessing the impacts of mining pollution.

The Subhabitat Dependence of Biogeographic Pattern

We introduce and test the subhabitat dependence hypothesis (SDH) in biogeography. This hypothesis posits that biogeographic pattern within a region differs when determined with species abundance data from different subhabitat types. It stems from the notion that the main abiotic factors that drive species distribution in different subhabitat types across a biogeographic region often vary differently across space. To test the SDH, we measured the abundance of algae and sessile invertebrates in two different subhabitats (high intertidal zone and mid-intertidal zone) at eight locations along the Atlantic Canadian coast. We conducted multivariate analyses of the species abundance data to compare alongshore biogeographic pattern between both zones. For both subhabitat types, location groupings based on community similarity not always responded to geographic proximity, leading to biogeographic patchiness to some extent. Nonetheless, both biogeographic patterns were statistically unrelated, thus supporting the SDH. This lack of concordance was most evident for southern locations, which clustered together based on high-intertidal data but showed considerable alongshore patchiness based on mid-intertidal data. We also found that the ordination pattern of these eight locations based on sea surface temperature data was significantly related to biogeographic pattern for the mid-intertidal zone but not for the high intertidal zone. This finding supports the rationale behind the SDH due to the longer periods of submergence experienced by the mid-intertidal zone. Overall, we conclude that biogeographic pattern within a region can depend on the surveyed subhabitat type. Thus, biological surveys restricted to specific subhabitats may not properly reveal biogeographic pattern for a biota as a whole or even just for other subhabitats. As many studies generate biogeographic information with data only for specific subhabitats, we recommend testing the SDH in other systems to determine its domain of application.

The fauna of caves and other subter-ranean habitats of North Carolina, USA

Over 1,500 caves have been documented in North Carolina, however, cave fauna in the Blue Ridge Mountains and Piedmont regions of North Carolina have been overlooked historically compared to the cave-rich karst terrains in the Appalachian Valley and Ridge and Interior Low Plateau to the west. Here, we provide the first comprehensive faunal list of caves and other subterranean habitats in the state based on over 40 years of periodic surveys and compilation of literature, biodiversity databases, and museum records. We report 475 occurrences from 127 caves, springs, and wells in 29 counties, representing 5 phyla, 17 classes, 43 orders, 90 families, 124 genera, and at least 164 species. Vertebrate fauna comprised 32 species, including 4 fishes, 9 salamanders, 1 lizard, 4 snakes, 2 birds, and 12 mammals (8 bats). Diverse invertebrate groups included spiders (11 families and 18 genera), springtails (7 families and 9 genera), segmented worms (3 families and 8 genera), and snails (6 families and 9 genera). At least 25 taxa are troglobites/stygobites (cave obligates), including 5 species of cave flatworms, 5 cave springtails, and 5 cave amphipods. Most troglobitic/stygobitic fauna documented in this study are endemic to North Carolina. Counties with the greatest cave biodiversity include Rutherford, McDowell, Swain, Henderson, Polk, and Avery counties. Over 20 species documented are of conservation concern, including 14 troglobites and 3 federally-listed bats. Although not as diverse as adjacent states, caves and other subterranean habitats in North Carolina support a diverse community of invertebrates and vertebrates. Our review serves as a base line for future cave biological surveys in the state and highlights the importance of subterranean habitats for North Carolina biodiversity.

A new velvet gecko (Oedura: Diplodactylidae) from Groote Eylandt, Northern Territory

Over the last decade, the combination of biological surveys, genetic diversity assessments and systematic research has revealed a growing number of previously unrecognised vertebrate species endemic to the Australian Monsoonal Tropics. Here we describe a new species of saxicoline velvet gecko in the Oedura marmorata complex from Groote Eylandt, a large island off the eastern edge of the Top End region of the Northern Territory. Oedura nesos sp. nov. differs from all congeners in combination of moderate size, and aspects of tail morphology and colouration. It has not been reported from the nearby mainland regions (eastern Arnhem Land) suggesting it may be an insular endemic, although further survey work is required to confirm this. While Groote Eylandt is recognised as a contemporary ecological refuge for declining mammal species of northern Australia, newly detected endemic species suggest it may also be of significance as an evolutionary refuge for many taxa, especially those associated with sandstone escarpments.

The role of microhabitats in structuring cave invertebrate communities in Guatemala

Several studies have tried to elucidate the main environmental features driving invertebrate community structure in cave environments. They found that many factors influence the community structure, but rarely focused on how substrate types and heterogeneity might shape these communities. Therefore, the objective of this study was to assess which substrate features and whether or not substrate heterogeneity determines the invertebrate community structure (species richness and composition) in a set of limestone caves in Guatemala. We hypothesized that the troglobitic fauna responds differently to habitat structure regarding species richness and composition than non-troglobitic fauna because they are more specialized to live in subterranean habitats. Using 30 m2 transects, the invertebrate fauna was collected and the substrate features were measured. The results showed that community responded to the presence of guano, cobbles, boulders, and substrate heterogeneity. The positive relationship between non-troglobitic species composition with the presence of guano reinforces the importance of food resources for structuring invertebrate cave communities in Guatemalan caves. Furthermore, the troglobitic species responded to different substrate features when compared to non-troglobitic species. For them, instead of the presence of organic matter, a higher variety of abiotic microhabitats seem to be the main driver for species diversity within a cave. The high specialization level of troglobitic organisms might be the reason why they respond differently to environmental conditions. The findings of this study highlight the importance of biological surveys for understanding cave biodiversity and give insights on how this biodiversity might be distributed within a cave. Conservation measures should keep in mind the target organisms and if such measures aim to protect a broad variety of organisms, then one should aim to preserve as many microhabitats and trophic resources as possible.