The nuclear and mitochondrial genome assemblies of Tetragonisca angustula (Apidae: Meliponini), a tiny yet remarkable pollinator in the Neotropics.

BACKGROUND: The field of bee genomics has considerably advanced in recent years, however, the most diverse group of honey producers on the planet, the stingless bees, are still largely neglected. In fact, only eleven of the ~ 600 described stingless bee species have been sequenced, and only three using a long-read (LR) sequencing technology. Here, we sequenced the nuclear and mitochondrial genomes of the most common, widespread and broadly reared stingless bee in Brazil and other neotropical countries-Tetragonisca angustula (popularly known in Brazil as jataí). RESULTS: A total of 48.01 Gb of DNA data were generated, including 2.31 Gb of Pacific Bioscience HiFi reads and 45.70 Gb of Illumina short reads (SRs). Our preferred assembly comprised 683 contigs encompassing 284.49 Mb, 62.84 Mb of which (22.09%) corresponded to 445,793 repetitive elements. N50, L50 and complete BUSCOs reached 1.02 Mb, 91 contigs and 97.1%, respectively. We predicted that the genome of T. angustula comprises 17,459 protein-coding genes and 4,108 non-coding RNAs. The mitogenome consisted of 17,410 bp, and all 37 genes were found to be on the positive strand, an unusual feature among bees. A phylogenomic analysis of 26 hymenopteran species revealed that six odorant receptor orthogroups of T. angustula were found to be experiencing rapid evolution, four of them undergoing significant contractions. CONCLUSIONS: Here, we provided the first nuclear and mitochondrial genome assemblies for the ecologically and economically important T. angustula, the fourth stingless bee species to be sequenced with LR technology thus far. We demonstrated that even relatively small amounts of LR data in combination with sufficient SR data can yield high-quality genome assemblies for bees.

Impacts of Taxon-Sampling Schemes on Bayesian Tip Dating Under the Fossilized Birth-Death Process.

Evolutionary timescales can be inferred by molecular-clock analyses of genetic data and fossil evidence. Bayesian phylogenetic methods such as tip dating provide a powerful framework for inferring evolutionary timescales, but the most widely used priors for tree topologies and node times often assume that present-day taxa have been sampled randomly or exhaustively. In practice, taxon sampling is often carried out so as to include representatives of major lineages, such as orders or families. We examined the impacts of different densities of diversified sampling on Bayesian tip dating on unresolved fossilized birth-death (FBD) trees, in which fossil taxa are topologically constrained but their exact placements are averaged out. We used synthetic data generated by simulations of nucleotide sequence evolution, fossil occurrences, and diversified taxon sampling. Our analyses under the diversified-sampling FBD process show that increasing taxon-sampling density does not necessarily improve divergence-time estimates. However, when informative priors were specified for the root age or when tree topologies were fixed to those used for simulation, the performance of tip dating on unresolved FBD trees maintains its accuracy and precision or improves with taxon-sampling density. By exploring three situations in which models are mismatched, we find that including all relevant fossils, without pruning off those that are incompatible with the diversified-sampling FBD process, can lead to underestimation of divergence times. Our reanalysis of a eutherian mammal data set confirms some of the findings from our simulation study, and reveals the complexity of diversified taxon sampling in phylogenomic data sets. In highlighting the interplay of taxon-sampling density and other factors, the results of our study have practical implications for using Bayesian tip dating to infer evolutionary timescales across the Tree of Life. [Bayesian tip dating; eutherian mammals; fossilized birth-death process; phylogenomics; taxon sampling.].

Functional and phylogenetic relationships link predators to plant diversity via trophic and non-trophic pathways.

Human-induced biodiversity loss negatively affects ecosystem function, but the interactive effects of biodiversity change across trophic levels remain insufficiently understood. We sampled arboreal spiders and lepidopteran larvae across seasons in 2 years in a subtropical tree diversity experiment, and then disentangled the links between tree diversity and arthropod predator diversity by deconstructing the pathways among multiple components of diversity (taxonomic, phylogenetic and functional) with structural equation models. We found that herbivores were major mediators of plant species richness effects on abundance, species richness, functional and phylogenetic diversity of predators, while phylogenetic, functional and structural diversity of trees were also important mediators of this process. However, the strength and direction differed between functional, structural and phylogenetic diversity effects, indicating different underlying mechanisms for predator community assembly. Abundance and multiple diversity components of predators were consistently affected by tree functional diversity, indicating that the variation in structure and environment caused by plant functional composition might play key roles in predator community assembly. Our study highlights the importance of an integrated approach based on multiple biodiversity components in understanding the consequences of biodiversity loss in multitrophic communities.

Tree dissimilarity determines multi-dimensional beta-diversity of herbivores and carnivores via bottom-up effects.

Global biodiversity decline and its cascading effects through trophic interactions pose a severe threat to human society. Establishing the impacts of biodiversity decline requires a more thorough understanding of multi-trophic interactions and, more specifically, the effects that loss of diversity in primary producers has on multi-trophic community assembly. Within a synthetic conceptual framework for multi-trophic beta-diversity, we tested a series of hypotheses on neutral and niche-based bottom-up processes in assembling herbivore and carnivore communities in a subtropical forest using linear models, hieratical variance partitioning based on linear mixed-effects models (LMMs) and simulation. We found that the observed taxonomic, phylogenetic and functional beta-diversity of both herbivorous caterpillars and carnivorous spiders were significantly and positively related to tree dissimilarity. Linear models and variance partitioning for LMMs jointly suggested that as a result of bottom-up effects, producer dissimilarities were predominant in structuring consumer dissimilarity, the strength of which highly depended on the trophic dependencies on producers, the diversity facet examined, and data quality. Importantly, linear models for standardized beta-diversities against producer dissimilarities implied a transition between niche-based processes such as environmental filtering and competitive exclusion, which supports the role of bottom-up effect in determining consumer community assembly. These findings enrich our mechanistic understanding of the 'Diversity Begets Diversity' hypothesis and the complexity of higher-trophic community assembly, which is fundamental for sustainable biodiversity conservation and ecosystem management.

Tree communities and functional traits determine herbivore compositional turnover.

There are many factors known to drive species turnover, although the mechanisms by which these operate are less clear. Based on comprehensive datasets from the largest tree diversity experiment worldwide (BEF-China), we used shared herbivore species (zeta diversity) and multi-site generalized dissimilarity modelling to investigate the patterns and determinants of species turnover of Lepidoptera herbivores among study plots across a gradient in tree species richness. We found that zeta diversity declined sharply with an increasing number of study plots, with complete changes in caterpillar species composition observed even at the fine spatial scale of our study. Plant community characteristics rather than abiotic factors were found to play key roles in driving caterpillar compositional turnover, although these effects varied with an increasing number of study plots considered, due to the varying contributions of rare and common species to compositional turnover. Our study reveals details of the impact of phylogeny- and trait-mediated processes of trees on herbivore compositional turnover, which has implications for forest management and conservation and shows potential avenues for maintenance of heterogeneity in herbivore communities.

The impact of heavy metal pollution on wild bee communities in smallholder farmlands.

Wild bees provide important pollination services, but they face numerous stressors that threaten them and their ecosystem services. Wild bees can be exposed to heavy metal pollution through the consumption of nectar, pollen, and water, which might cause bee decline. While some studies have measured heavy metal concentrations in honeybees, few studies have monitored heavy metal concentrations in wild bees or explored their potential effects on wild bee communities. To investigate the impact of heavy metal pollution on wild bee communities, heavy metal concentrations, including vanadium (V), chromium (Cr), nickel (Ni), cadmium (Cd), Zinc (Zn) and lead (Pb) in multiple wild bee species were measured. Multiple wild bee species, including: Xylocopa tranquabaroroum, Eucera floralia, Apis cerana, and small bee mixtures (representing multiple small wild bee species) were sampled from 18 sites in Quzhou, Zhejiang Province, China. The findings demonstrated that there were significant differences in heavy metal concentrations among different bee species. The concentrations of V, Zn, Cd, and Pb in X. tranquabaroroum, the largest bee species in this study, were lower than that in the other three sample groups. Furthermore, there were significant negative correlations between heavy metal pollution and wild bee diversity and species richness, but not with abundance. Particularly, there was no significant relationship between heavy metal pollution and the abundance of small bees. Given these worrying findings, monitoring multiple heavy metals in wild bees should be conducted for protecting wild bee diversity and securing their pollination services.

Patterns of endemism of the Chinese Larentiinae (Lepidoptera: Geometridae).

Chinese Larentiinae is exceptionally rich in species since it spans the Palearctic realm and the Oriental realm, comprising 715 species belonging to 130 genera. Among them, nearly half species are endemic. This taxon is considered an ideal object for the study of endemic patterns. In this study, parsimony analysis of endemicity was used to delineate areas of endemisms (AOEs), and track compatibility analysis (TCA) was used to perform the TCA. Eight AOEs were supported. Except for five AOEs around the Qinghai-Tibet plateau (QTP), two AOEs from northern China and Taiwan islands were found. Twenty-two generalized tracks were obtained from the combination of the track analysis and the AOEs. The uplift of the QTP was assumed to greatly influence these endemic patterns, presented an appearance of highly centralized endemism and diversity in the eastern and southern edges of the QTP. And the AOE of Mt. Hengduan was considered as a major center of development through recent geological history, where strong evolutionary radiation might have taken place, resulting in the migration routes described by the generalized tracks from this center to various regions in various directions.

A Simulation-Based Evaluation of Tip-Dating Under the Fossilized Birth-Death Process.

Bayesian molecular dating is widely used to study evolutionary timescales. This procedure usually involves phylogenetic analysis of nucleotide sequence data, with fossil-based calibrations applied as age constraints on internal nodes of the tree. An alternative approach is tip-dating, which explicitly includes fossil data in the analysis. This can be done, for example, through the joint analysis of molecular data from present-day taxa and morphological data from both extant and fossil taxa. In the context of tip-dating, an important development has been the fossilized birth-death process, which allows non-contemporaneous tips and sampled ancestors while providing a model of lineage diversification for the prior on the tree topology and internal node times. However, tip-dating with fossils faces a number of considerable challenges, especially, those associated with fossil sampling and evolutionary models for morphological characters. We conducted a simulation study to evaluate the performance of tip-dating using the fossilized birth-death model. We simulated fossil occurrences and the evolution of nucleotide sequences and morphological characters under a wide range of conditions. Our analyses of these data show that the number and the maximum age of fossil occurrences have a greater influence than the degree of among-lineage rate variation or the number of morphological characters on estimates of node times and the tree topology. Tip-dating with the fossilized birth-death model generally performs well in recovering the relationships among extant taxa but has difficulties in correctly placing fossil taxa in the tree and identifying the number of sampled ancestors. The method yields accurate estimates of the ages of the root and crown group, although the precision of these estimates varies with the probability of fossil occurrence. The exclusion of morphological characters results in a slight overestimation of node times, whereas the exclusion of nucleotide sequences has a negative impact on inference of the tree topology. Our results provide an overview of the performance of tip-dating using the fossilized birth-death model, which will inform further development of the method and its application to key questions in evolutionary biology.

Multi-trophic communities re-establish with canopy cover and microclimate in a subtropical forest biodiversity experiment.

Plant diversity affects multi-trophic communities, but in young regrowth forests, where forest insects are in the process of re-establishment, other biotic and also abiotic factors might be more important. We studied cavity-nesting bees, wasps and their natural enemies along an experimental tree diversity gradient in subtropical South-East China. We compared insect communities of experimental young forests with communities of established natural forests nearby the experiment and tested for direct and indirect effects of tree diversity, tree basal area (a proxy of tree biomass), canopy cover and microclimate on bee and wasp community composition, abundance and species richness. Finally, we tested if the trophic levels of bees, herbivore-hunting wasps, spider-hunting wasps and their natural enemies respond similarly. Forest bee and wasp community composition re-established towards communities of the natural forest with increasing tree biomass and canopy cover. These factors directly and indirectly, via microclimatic conditions, increased the abundance of bees, wasps and their natural enemies. While bee and wasp species richness increased with abundance and both were not related to tree diversity, abundance increased directly with canopy cover, mediated by tree biomass. Abundance of natural enemies increased with host (bee and wasp) abundance irrespective of their trophic position. In conclusion, although maximizing tree diversity is an important goal of reforestation and forest conservation, rapid closure of canopies is also important for re-establishing communities of forest bees, wasps and their natural enemies.

Comparison of two criteria on the essential number calculation of Andrena camellia.

Andrena camellia Wu is one of the primary pollinators of Camellia oleifera A. in China. In this paper, the essential number of individuals for efficient pollination by this species was calculated via two criteria, based on various indicators including counts of pollen grains in provisions, from single visits, and from single foraging trips overall; single flower visit duration; single flight period duration; number of eggs laid by a single female over their lifetime; and the average number of flowers per plant. Based on the number of pollen grains collected per flower visit, the essential number of females necessary is 2107 in a 1-ha Camellia oleifera garden with 1800 plants, while only 1998 female individuals are essentially needed when estimated based on the mean number of pollen grains collected in a single flight period. We argue that the essential number estimated by the former method is more reasonable and accurate for practical applications.