BOLD v4: A Centralized Bioinformatics Platform for DNA-Based Biodiversity Data.

BOLD, the Barcode of Life Data System, supports the acquisition, storage, validation, analysis, and publication of DNA barcodes, activities requiring the integration of molecular, morphological, and distributional data. Its pivotal role in curating the reference library of DNA barcodes, coupled with its data management and analysis capabilities, makes it a central resource for biodiversity science. It enables rapid, accurate identification of specimens and also reveals patterns of genetic diversity and evolutionary relationships among taxa.Launched in 2005, BOLD has become an increasingly powerful tool for advancing the understanding of planetary biodiversity. It currently hosts 17 million specimen records and 14 million barcodes that provide coverage for more than a million species from every continent and ocean. The platform has the long-term goal of providing a consistent, accurate system for identifying all species of eukaryotes.BOLD's integrated analytical tools, full data lifecycle support, and secure collaboration framework distinguish it from other biodiversity platforms. BOLD v4 brought enhanced data management and analysis capabilities as well as novel functionality for data dissemination and publication. Its next version will include features to strengthen its utility to the research community, governments, industry, and society-at-large.

Taming the terminological tempest in invasion science.

Standardised terminology in science is important for clarity of interpretation and communication. In invasion science - a dynamic and rapidly evolving discipline - the proliferation of technical terminology has lacked a standardised framework for its development. The result is a convoluted and inconsistent usage of terminology, with various discrepancies in descriptions of damage and interventions. A standardised framework is therefore needed for a clear, universally applicable, and consistent terminology to promote more effective communication across researchers, stakeholders, and policymakers. Inconsistencies in terminology stem from the exponential increase in scientific publications on the patterns and processes of biological invasions authored by experts from various disciplines and countries since the 1990s, as well as publications by legislators and policymakers focusing on practical applications, regulations, and management of resources. Aligning and standardising terminology across stakeholders remains a challenge in invasion science. Here, we review and evaluate the multiple terms used in invasion science (e.g. 'non-native', 'alien', 'invasive' or 'invader', 'exotic', 'non-indigenous', 'naturalised', 'pest') to propose a more simplified and standardised terminology. The streamlined framework we propose and translate into 28 other languages is based on the terms (i) 'non-native', denoting species transported beyond their natural biogeographic range, (ii) 'established non-native', i.e. those non-native species that have established self-sustaining populations in their new location(s) in the wild, and (iii) 'invasive non-native' - populations of established non-native species that have recently spread or are spreading rapidly in their invaded range actively or passively with or without human mediation. We also highlight the importance of conceptualising 'spread' for classifying invasiveness and 'impact' for management. Finally, we propose a protocol for classifying populations based on (i) dispersal mechanism, (ii) species origin, (iii) population status, and (iv) impact. Collectively and without introducing new terminology, the framework that we present aims to facilitate effective communication and collaboration in invasion science and management of non-native species.

Economic costs of invasive rodents worldwide: the tip of the iceberg.

Background: Rodents are among the most notorious invasive alien species worldwide. These invaders have substantially impacted native ecosystems, food production and storage, local infrastructures, human health and well-being. However, the lack of standardized and understandable estimation of their impacts is a serious barrier to raising societal awareness, and hampers effective management interventions at relevant scales. Methods: Here, we assessed the economic costs of invasive alien rodents globally in order to help overcome these obstacles. For this purpose, we combined and analysed economic cost data from the InvaCost database-the most up-to-date and comprehensive synthesis of reported invasion costs-and specific complementary searches within and beyond the published literature. Results: Our conservative analysis showed that reported costs of rodent invasions reached a conservative total of US$ 3.6 billion between 1930 and 2022 (annually US$ 87.5 million between 1980 and 2022), and were significantly increasing through time. The highest cost reported was for muskrat Ondatra zibethicus (US$ 377.5 million), then unspecified Rattus spp. (US$ 327.8 million), followed by Rattus norvegicus specifically (US$ 156.6 million) and Castor canadensis (US$ 150.4 million). Of the total costs, 87% were damage-related, principally impacting agriculture and predominantly reported in Asia (60%), Europe (19%) and North America (9%). Our study evidenced obvious cost underreporting with only 99 documents gathered globally, clear taxonomic gaps, reliability issues for cost assessment, and skewed breakdowns of costs among regions, sectors and contexts. As a consequence, these reported costs represent only a very small fraction of the expected true cost of rodent invasions (e.g., using a less conservative analytic approach would have led to a global amount more than 80-times higher than estimated here). Conclusions: These findings strongly suggest that available information represents a substantial underestimation of the global costs incurred. We offer recommendations for improving estimates of costs to fill these knowledge gaps including: systematic distinction between native and invasive rodents' impacts; monetizing indirect impacts on human health; and greater integrative and concerted research effort between scientists and stakeholders. Finally, we discuss why and how this approach will stimulate and provide support for proactive and sustainable management strategies in the context of alien rodent invasions, for which biosecurity measures should be amplified globally.

Deadly and venomous Lonomia caterpillars are more than the two usual suspects.

Caterpillars of the Neotropical genus Lonomia (Lepidoptera: Saturniidae) are responsible for some fatal envenomation of humans in South America inducing hemostatic disturbances in patients upon skin contact with the caterpillars' spines. Currently, only two species have been reported to cause hemorrhagic syndromes in humans: Lonomia achelous and Lonomia obliqua. However, species identifications have remained largely unchallenged despite improved knowledge of venom diversity and growing evidence that the taxonomy used over past decades misrepresents and underestimates species diversity. Here, we revisit the taxonomic diversity and distribution of Lonomia species using the most extensive dataset assembled to date, combining DNA barcodes, morphological comparisons, and geographical information. Considering new evidence for seven undescribed species as well as three newly proposed nomenclatural changes, our integrative approach leads to the recognition of 60 species, of which seven are known or strongly suspected to cause severe envenomation in humans. From a newly compiled synthesis of epidemiological data, we also examine the consequences of our results for understanding Lonomia envenomation risks and call for further investigations of other species' venom activities. This is required and necessary to improve alertness in areas at risk, and to define adequate treatment strategies for envenomed patients, including performing species identification and assessing the efficacy of anti-Lonomia serums against a broader diversity of species.

Deadly and venomous Lonomia caterpillars are more than the two usual suspects

Caterpillars of the Neotropical genus Lonomia (Lepidoptera: Saturniidae) are responsible for some fatal envenomation of humans in South America inducing hemostatic disturbances in patients upon skin contact with the caterpillars’ spines. Currently, only two species have been reported to cause hemorrhagic syndromes in humans: Lonomia achelous and Lonomia obliqua. However, species identifications have remained largely unchallenged despite improved knowledge of venom diversity and growing evidence that the taxonomy used over past decades misrepresents and underestimates species diversity. Here, we revisit the taxonomic diversity and distribution of Lonomia species using the most extensive dataset assembled to date, combining DNA barcodes, morphological comparisons, and geographical information. Considering new evidence for seven undescribed species as well as three newly proposed nomenclatural changes, our integrative approach leads to the recognition of 60 species, of which seven are known or strongly suspected to cause severe envenomation in humans. From a newly compiled synthesis of epidemiological data, we also examine the consequences of our results for understanding Lonomia envenomation risks and call for further investigations of other species’ venom activities. This is required and necessary to improve alertness in areas at risk, and to define adequate treatment strategies for envenomed patients, including performing species identification and assessing the efficacy of anti-Lonomia serums against a broader diversity of species.

A diversification relay race from Caribbean-Mesoamerica to the Andes: historical biogeography of Xylophanes hawkmoths.

The regions of the Andes and Caribbean-Mesoamerica are both hypothesized to be the cradle for many Neotropical lineages, but few studies have fully investigated the dynamics and interactions between Neotropical bioregions. The New World hawkmoth genus Xylophanes is the most taxonomically diverse genus in the Sphingidae, with the highest endemism and richness in the Andes and Caribbean-Mesoamerica. We integrated phylogenomic and DNA barcode data and generated the first time-calibrated tree for this genus, covering 93.8% of the species diversity. We used event-based likelihood ancestral area estimation and biogeographic stochastic mapping to examine the speciation and dispersal dynamics of Xylophanes across bioregions. We also used trait-dependent diversification models to compare speciation and extinction rates of lineages associated with different bioregions. Our results indicate that Xylophanes originated in Caribbean-Mesoamerica in the Late Miocene, and immediately diverged into five major clades. The current species diversity and distribution of Xylophanes can be explained by two consecutive phases. In the first phase, the highest Xylophanes speciation and emigration rates occurred in the Caribbean-Mesoamerica, and the highest immigration rates occurred in the Andes, whereas in the second phase the highest immigration rates were found in Amazonia, and the Andes had the highest speciation and emigration rates.

Description of three new species of Automeris Hübner, 1819 from Colombia and Brazil (Lepidoptera, Saturniidae, Hemileucinae).

The Saturniidae is one of the most emblematic families of moths, comprising nearly 3000 species distributed globally. In this study, DNA barcode analysis and comparative morphology were combined to describe three new species within the genus Automeris, which is the most diverse genus in the family. Automeris llaneros Decaëns, Rougerie & Bonilla, sp. nov., Automeris mineros Decaëns, Rougerie & Bonilla, sp. nov., and Automeris belemensis Decaëns, Rougerie & Bénéluz, sp. nov. are described from the Colombian Orinoco watershed, the Colombian Eastern Cordillera, and the area of endemism of Belém in the Brazilian Amazonia, respectively. They all belong to the Automeris bilinea (Walker, 1855) species subgroup, which comprises a number of species that are sometimes difficult to distinguish from each other using morphology alone. Here, the description of these three new species is based on significant differences from their closest relatives, either in terms of wing patterns, genitalia, DNA barcodes or a combination of these features.

Non-English languages enrich scientific knowledge: The example of economic costs of biological invasions.

We contend that the exclusive focus on the English language in scientific research might hinder effective communication between scientists and practitioners or policy makers whose mother tongue is non-English. This barrier in scientific knowledge and data transfer likely leads to significant knowledge gaps and may create biases when providing global patterns in many fields of science. To demonstrate this, we compiled data on the global economic costs of invasive alien species reported in 15 non-English languages. We compared it with equivalent data from English documents (i.e., the InvaCost database, the most up-to-date repository of invasion costs globally). The comparison of both databases (~7500 entries in total) revealed that non-English sources: (i) capture a greater amount of data than English sources alone (2500 vs. 2396 cost entries respectively); (ii) add 249 invasive species and 15 countries to those reported by English literature, and (iii) increase the global cost estimate of invasions by 16.6% (i.e., US$ 214 billion added to 1.288 trillion estimated from the English database). Additionally, 2712 cost entries - not directly comparable to the English database - were directly obtained from practitioners, revealing the value of communication between scientists and practitioners. Moreover, we demonstrated how gaps caused by overlooking non-English data resulted in significant biases in the distribution of costs across space, taxonomic groups, types of cost, and impacted sectors. Specifically, costs from Europe, at the local scale, and particularly pertaining to management, were largely under-represented in the English database. Thus, combining scientific data from English and non-English sources proves fundamental and enhances data completeness. Considering non-English sources helps alleviate biases in understanding invasion costs at a global scale. Finally, it also holds strong potential for improving management performance, coordination among experts (scientists and practitioners), and collaborative actions across countries. Note: non-English versions of the abstract and figures are provided in Appendix S5 in 12 languages.

A global food plant dataset for wild silkmoths and hawkmoths and its use in documenting polyphagy of their caterpillars (Lepidoptera: Bombycoidea: Saturniidae, Sphingidae).

BACKGROUND: Herbivorous insects represent a major fraction of global biodiversity and the relationships they have established with their food plants range from strict specialists to broad generalists. Our knowledge of these relationships is of primary importance to basic (e.g. the study of insect ecology and evolution) and applied biology (e.g. monitoring of pest or invasive species) and yet remains very fragmentary and understudied. In Lepidoptera, caterpillars of families Saturniidae and Sphingidae are rather well known and considered to have adopted contrasting preferences in their use of food plants. The former are regarded as being rather generalist feeders, whereas the latter are more specialist. NEW INFORMATION: To assemble and synthesise the vast amount of existing data on food plants of Lepidoptera families Saturniidae and Sphingidae, we combined three major existing databases to produce a dataset collating more than 26,000 records for 1256 species (25% of all species) in 121 (67%) and 167 (81%) genera of Saturniidae and Sphingidae, respectively. This dataset is used here to document the level of polyphagy of each of these genera using summary statistics, as well as the calculation of a polyphagy score derived from the analysis of Phylogenetic Diversity of the food plants used by the species in each genus.

Megafauna Seed Dispersal in the Neotropics: A Meta-Analysis Shows No Genetic Signal of Loss of Long-Distance Seed Dispersal.

Restricted gene flow may lead to the loss of genetic diversity and higher genetic differentiation among populations, but the genetic consequences of megafauna extinction for plant populations still remain to be assessed. We performed a phylogenetic-independent meta-analysis across 102 Neotropical plants to test the hypothesis that plant species with megafaunal seed dispersal syndrome have a lower genetic diversity and a higher genetic differentiation than those without it. We classified as megafauna-dependent plant species those that potentially relied only on megafauna to seed dispersal, and as megafauna-independent those that relied on megafauna and other seed dispersers. Our data comprised 98 studies using microsatellite markers. We found no statistical difference in genetic diversity and differentiation between plants with megafauna and non-megafauna seed dispersal syndrome, although the statistical power to detect differences in genetic differentiation was low. Moreover, we found no statistical difference between megafauna-dependent and megafauna-independent plant species. We then used generalized linear mixed models and phylogenetic generalized least square models to investigate the effects of megafaunal seed dispersal syndromes and reproductive traits on variation in genetic diversity and genetic differentiation. We found no effect of megafaunal syndrome, rather, reproductive traits, such as pollination mode, mating, and breeding systems, showed significant effects. Our findings show that the genetic studies of Neotropical plants performed so far show no difference in genetic diversity and differentiation in plants with megafaunal compared to those with non-megafaunal seed dispersal syndromes. Our results also provide evidence pointing out that plant species with megafaunal seed dispersal syndromes may have used different strategies to counterbalance the extinction of their mutualistic megafauna dispersers, such as the dispersal by extant mammals that may promote long-distance seed dispersal. Our results also reinforce the importance of pollination to long-distance gene flow in Neotropical plants.

A global checklist of the Bombycoidea (Insecta: Lepidoptera).

BACKGROUND: Bombycoidea is an ecologically diverse and speciose superfamily of Lepidoptera. The superfamily includes many model organisms, but the taxonomy and classification of the superfamily has remained largely in disarray. Here we present a global checklist of Bombycoidea. Following Zwick (2008) and Zwick et al. (2011), ten families are recognized: Anthelidae, Apatelodidae, Bombycidae, Brahmaeidae, Carthaeidae, Endromidae, Eupterotidae, Phiditiidae, Saturniidae and Sphingidae. The former families Lemoniidae and Mirinidae are included within Brahmaeidae and Endromidae respectively. The former bombycid subfamilies Oberthueriinae and Prismostictinae are also treated as synonyms of Endromidae, and the former bombycine subfamilies Apatelodinae and Phitditiinae are treated as families. NEW INFORMATION: This checklist represents the first effort to synthesize the current taxonomic treatment of the entire superfamily. It includes 12,159 names and references to their authors, and it accounts for the recent burst in species and subspecies descriptions within family Saturniidae (ca. 1,500 within the past 10 years) and to a lesser extent in Sphingidae (ca. 250 species over the same period). The changes to the higher classification of Saturniidae proposed by Nässig et al. (2015) are rejected as premature and unnecessary. The new tribes, subtribes and genera described by Cooper (2002) are here treated as junior synonyms. We also present a new higher classification of Sphingidae, based on Kawahara et al. (2009), Barber and Kawahara (2013) and a more recent phylogenomic study by Breinholt et al. (2017), as well as a reviewed genus and species level classification, as documented by Kitching (2018).

Correction: Pollination Mode and Mating System Explain Patterns in Genetic Differentiation in Neotropical Plants.

[This corrects the article DOI: 10.1371/journal.pone.0158660.].

Climatic changes can drive the loss of genetic diversity in a Neotropical savanna tree species.

The high rates of future climatic changes, compared with the rates reported for past changes, may hamper species adaptation to new climates or the tracking of suitable conditions, resulting in significant loss of genetic diversity. Trees are dominant species in many biomes and because they are long-lived, they may not be able to cope with ongoing climatic changes. Here, we coupled ecological niche modelling (ENM) and genetic simulations to forecast the effects of climatic changes on the genetic diversity and the structure of genetic clusters. Genetic simulations were conditioned to climatic variables and restricted to plant dispersal and establishment. We used a Neotropical savanna tree as species model that shows a preference for hot and drier climates, but with low temperature seasonality. The ENM predicts a decreasing range size along the more severe future climatic scenario. Additionally, genetic diversity and allelic richness also decrease with range retraction and climatic genetic clusters are lost for both future scenarios, which will lead genetic variability to homogenize throughout the landscape. Besides, climatic genetic clusters will spatially reconfigure on the landscape following displacements of climatic conditions. Our findings indicate that climate change effects will challenge population adaptation to new environmental conditions because of the displacement of genetic ancestry clusters from their optimal conditions.

Pollination Mode and Mating System Explain Patterns in Genetic Differentiation in Neotropical Plants.

We studied genetic diversity and differentiation patterns in Neotropical plants to address effects of life history traits (LHT) and ecological attributes based on an exhaustive literature survey. We used generalized linear mixed models (GLMMs) to test the effects as fixed and random factors of growth form, pollination and dispersal modes, mating and breeding systems, geographical range and habitat on patterns of genetic diversity (HS, HeS, π and h), inbreeding coefficient (FIS), allelic richness (AR) and differentiation among populations (FST) for both nuclear and chloroplast genomes. In addition, we used phylogenetic generalized least squares (pGLS) to account for phylogenetic independence on predictor variables and verify the robustness of the results from significant GLMMs. In general, GLMM revealed more significant relationships among LHTs and genetic patterns than pGLS. After accounting for phylogenetic independence (i.e., using pGLS), FST for nuclear microsatellites was significantly related to pollination mode, mating system and habitat. Plants specifically with outcrossing mating system had lower FST. Moreover, AR was significantly related to pollination mode and geographical range and HeS for nuclear dominant markers was significantly related to habitat. Our findings showed that different results might be retrieved when phylogenetic non-independence is taken into account and that LHTs and ecological attributes affect substantially the genetic pattern in Neotropical plants, hence may drive key evolutionary processes in plants.

Indirect interactions among tropical tree species through shared rodent seed predators: a novel mechanism of tree species coexistence.

The coexistence of numerous tree species in tropical forests is commonly explained by negative dependence of recruitment on the conspecific seed and tree density due to specialist natural enemies that attack seeds and seedlings ('Janzen-Connell' effects). Less known is whether guilds of shared seed predators can induce a negative dependence of recruitment on the density of different species of the same plant functional group. We studied 54 plots in tropical forest on Barro Colorado Island, Panama, with contrasting mature tree densities of three coexisting large seeded tree species with shared seed predators. Levels of seed predation were far better explained by incorporating seed densities of all three focal species than by conspecific seed density alone. Both positive and negative density dependencies were observed for different species combinations. Thus, indirect interactions via shared seed predators can either promote or reduce the coexistence of different plant functional groups in tropical forest.

Forests as promoters of terrestrial life-history strategies in East African amphibians.

Many amphibian lineages show terrestrialization of their reproductive strategy and breeding is partially or completely independent of water. A number of causal factors have been proposed for the evolution of terrestrialized breeding. While predation has received repeated attention as a potential factor, the influence of other factors such as habitat has never been tested using appropriate data or methods. Using a dataset that comprises 180 amphibian species from various East African habitats, we tested whether species occurring in different habitats show different patterns of terrestrialization in their breeding strategy. We recovered a significant association between terrestrialized breeding strategies and forest habitats. In general, forest seems to act as a facilitator, providing a permissive environment for the evolution of terrestrialized breeding strategies. However, while terrestrial oviposition is strongly correlated with lowland and montane forest habitat, complete terrestrial development is significantly correlated with montane forest only, indicating different selective pressures acting at different steps towards complete terrestrial development.