Contributions of paraecologists and parataxonomists to research, conservation, and social development

The importance of Indigenous and local people for cataloging biodiversity

Indigenous and local peoples' (ILPs) role in cataloging life on Earth has been significant but underappreciated. ILPs knowledge faces growing cultural and biological threats. Greater participation by ILPs in research would make science more efficient, conservation more sustainable, and traditional knowledge stronger, but formidable obstacles remain.

Diversity and conservation of terrestrial vertebrates (birds, mammals, and reptiles) of Sierra Cucapá, Mexicali, Baja California, Mexico

Knowledge about the biodiversity of Baja California has been obtained mainly from natural protected areas (NPAs), while some unprotected natural areas have been poorly studied. The Sierra Cucapá in the northeast of the peninsula is one example. The objectives of this study are 1) to integrate existing knowledge of bird, mammal, and reptile diversity in Cucapá from public databases, citizen science platforms, and information generated from fieldwork, 2) to identify the spatial distribution of records in the study area, 3) to compare the composition of vertebrate species of Cucapá with that of NPAs of northern part of the peninsula, and 4) to assess the biological conservation value of Cucapá. We obtained records of 150 species of native vertebrates (102 birds, 34 mammals, and 14 reptiles) of which 10 species of birds, four mammals, and seven reptiles are included in a risk extinction category. The different sources of information contributed in a complementary way to the species inventories. Large areas in western and northern Cucapá lack records. The total difference in species composition between Cucapá and nearby NPAs ranged between 58 and 69% for birds, 61 and 79% for mammals, and 69 and 87% for reptiles. The species richness of Cucapá, its particular species composition, the presence of species in risk extinction categories, and the number and size of unexplored areas indicate that this area represents an opportunity for biological conservation in the northern part of the Peninsula. This work provides compelling data for the protection of Cucapá.

Guidelines to Facilitate Human-Wildlife Interactions in Conservation Translocations

Species reintroductions and translocations are widely used management interventions to restore locally extinct or augment severely depleted species. In such projects, the human dimension issues that influence the success of these conservation interventions are encountered at five different stages of the project life cycle: (1) planning, (2) initiation, (3) implementation, (4) ending stage, and (5) post-exit. Overlooking or failing to consider the human dimension in any of these phases could jeopardise the conservation translocation project's success. When the human dimensions are included there is greater possibility of community involvement, peers' acceptance and support from various interest groups and avoidance of conflict situations. The Human-Wildlife Interactions Working Group (HWIWG) was formed in 2018 by members of the IUCN Conservation Translocation Specialist Group (CTSG). HWIWG has facilitated online discussions and workshops with practitioners, researchers and academics from across the globe, on a range of aspects of human-wildlife interactions in conservation translocations, as well as leading discussion sessions during international research conferences. These events have provided a rich source of material from which to draw a series of recommendations. In this paper we discuss findings from the HWIWG that illustrate how, in each of the five stages of the project life cycle, human-dimensions influenced conservation translocation projects. Our aim is to provide useful and multidimensional insights for those working in species' reintroductions and translocations.

Chile (Capsicum spp.) as Food-Medicine Continuum in Multiethnic Mexico

Mexico is the center of origin and diversification of domesticated chile (Capsicum annuum L.). Chile is conceived and employed as both food and medicine in Mexico. In this context, the objective of this paper is to describe and analyze the cultural role of chile as food and as medicine for the body and soul in different cultures of Mexico. To write it, we relied on our own fieldwork and literature review. Our findings include a) the first matrix of uses of chile across 67 indigenous and Afrodescendants cultures within Mexican territory and b) the proposal of a new model of diversified uses of chile. Traditional knowledge, uses and management of chile as food and medicine form a continuum (i.e., are not separated into distinct categories). The intermingled uses of Capsicum are diversified, deeply rooted and far-reaching into the past. Most of the knowledge, uses and practices are shared throughout Mexico. On the other hand, there is knowledge and practices that only occur in local or regional cultural contexts. In order to fulfill food, medicinal or spiritual functions, native communities use wild/cultivated chile.

Rapid coral reef assessment using 3D modelling and acoustics: acoustic indices correlate to fish abundance, diversity and environmental indicators in West Papua, Indonesia

BACKGROUND

Providing coral reef systems with the greatest chance of survival requires effective assessment and monitoring to guide management at a range of scales from community to government. The development of rapid monitoring approaches amenable to collection at community level, yet recognised by policymakers, remains a challenge. Technologies can increase the scope of data collection. Two promising visual and audio approaches are (i) 3D habitat models, generated through photogrammetry from video footage, providing assessment of coral cover structural metrics and (ii) audio, from which acoustic indices shown to correlate to vertebrate and invertebrate diversity, can be extracted.

METHODS

We collected audio and video imagery using low cost underwater cameras (GoPro Hero7™) from 34 reef samples from West Papua (Indonesia). Using photogrammetry one camera was used to generate 3D models of 4 m2 reef, the other was used to estimate fish abundance and collect audio to generate acoustic indices. We investigated relationships between acoustic metrics, fish abundance/diversity/functional groups, live coral cover and reef structural metrics.

RESULTS

Generalized linear modelling identified significant but weak correlations between live coral cover and structural metrics extracted from 3D models and stronger relationships between live coral and fish abundance. Acoustic indices correlated to fish abundance, species richness and reef functional metrics associated with overfishing and algal control. Acoustic Evenness (1,200-11,000 Hz) and Root Mean Square RMS (100-1,200 Hz) were the best individual predictors overall suggesting traditional bioacoustic indices, providing information on sound energy and the variability in sound levels in specific frequency bands, can contribute to reef assessment.

CONCLUSION

Acoustics and 3D modelling contribute to low-cost, rapid reef assessment tools, amenable to community-level data collection, and generate information for coral reef management. Future work should explore whether 3D models of standardised transects and acoustic indices generated from low cost underwater cameras can replicate or support 'gold standard' reef assessment methodologies recognised by policy makers in marine management.

Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts

MOTIVATION

Biomedical literature is growing at a rate that outpaces our ability to harness the knowledge contained therein. To mine valuable inferences from the large volume of literature, many researchers use information extraction algorithms to harvest information in biomedical texts. Information extraction is usually accomplished via a combination of manual expert curation and computational methods. Advances in computational methods usually depend on the time-consuming generation of gold standards by a limited number of expert curators. Citizen science is public participation in scientific research. We previously found that citizen scientists are willing and capable of performing named entity recognition of disease mentions in biomedical abstracts, but did not know if this was true with relationship extraction (RE).

RESULTS

In this article, we introduce the Relationship Extraction Module of the web-based application Mark2Cure (M2C) and demonstrate that citizen scientists can perform RE. We confirm the importance of accurate named entity recognition on user performance of RE and identify design issues that impacted data quality. We find that the data generated by citizen scientists can be used to identify relationship types not currently available in the M2C Relationship Extraction Module. We compare the citizen science-generated data with algorithm-mined data and identify ways in which the two approaches may complement one another. We also discuss opportunities for future improvement of this system, as well as the potential synergies between citizen science, manual biocuration and natural language processing.

AVAILABILITY AND IMPLEMENTATION

Mark2Cure platform: https://mark2cure.org; Mark2Cure source code: https://github.com/sulab/mark2cure; and data and analysis code for this article: https://github.com/gtsueng/M2C_rel_nb.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation

Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon. Because of difficulties in morphological identification and taxonomic uncertainty of amphibian species observed in the area, we integrated a DNA barcoding analysis into the project to improve the overall quality and accuracy of the species inventory. Based on morphology alone, 48 species were recognized in the field and voucher specimens of each were collected. We used tissue samples from specimens collected at our field site, material available from amphibians collected in other parts of Gabon and the Republic of Congo to initiate a DNA barcode library for west Central African amphibians. We then compared our sequences with material in GenBank for the genera recorded at the study site to assist in identifications. The resulting COI and 16S barcode library allowed us to update the number of species documented at the study site to 28, thereby providing a more accurate assessment of diversity and distributions. We caution that because sequence data maintained in GenBank are often poorly curated by the original submitters and cannot be amended by third-parties, these data have limited utility for identification purposes. Nevertheless, the use of DNA barcoding is likely to benefit biodiversity inventories and long-term monitoring, particularly for taxa that can be difficult to identify based on morphology alone; likewise, inventory and monitoring programs can contribute invaluable data to the DNA barcode library and the taxonomy of complex groups. Our methods provide an example of how non-taxonomists and parataxonomists working in understudied parts of the world with limited geographic sampling and comparative morphological material can use DNA barcoding and publicly available sequence data (GenBank) to rapidly identify the number of species and assign tentative names to aid in urgent conservation management actions and contribute to taxonomic resolution.

GuiaTreeKey, a multi-access electronic key to identify tree genera in French Guiana

The tropical rainforest of Amazonia is one of the most species-rich ecosystems on earth, with an estimated 16000 tree species. Due to this high diversity, botanical identification of trees in the Amazon is difficult, even to genus, often requiring the assistance of parataxonomists or taxonomic specialists. Advances in informatics tools offer a promising opportunity to develop user-friendly electronic keys to improve Amazonian tree identification. Here, we introduce an original multi-access electronic key for the identification of 389 tree genera occurring in French Guiana terra-firme forests, based on a set of 79 morphological characters related to vegetative, floral and fruit characters. Its purpose is to help Amazonian tree identification and to support the dissemination of botanical knowledge to non-specialists, including forest workers, students and researchers from other scientific disciplines. The electronic key is accessible with the free access software Xper², and the database is publicly available on figshare: https://figshare.com/s/75d890b7d707e0ffc9bf (doi: 10.6084/m9.figshare.2682550).