Plant DNA barcodes and assessment of phylogenetic community structure of a tropical mixed dipterocarp forest in Brunei Darussalam (Borneo)

DNA barcoding is a fast and reliable tool to assess and monitor biodiversity and, via community phylogenetics, to investigate ecological and evolutionary processes that may be responsible for the community structure of forests. In this study, DNA barcodes for the two widely used plastid coding regions rbcL and matK are used to contribute to identification of morphologically undetermined individuals, as well as to investigate phylogenetic structure of tree communities in 70 subplots (10 × 10m) of a 25-ha forest-dynamics plot in Brunei (Borneo, Southeast Asia). The combined matrix (rbcL + matK) comprised 555 haplotypes (from ≥154 genera, 68 families and 25 orders sensu APG, Angiosperm Phylogeny Group, 2016), making a substantial contribution to tree barcode sequences from Southeast Asia. Barcode sequences were used to reconstruct phylogenetic relationships using maximum likelihood, both with and without constraining the topology of taxonomic orders to match that proposed by the Angiosperm Phylogeny Group. A third phylogenetic tree was reconstructed using the program Phylomatic to investigate the influence of phylogenetic resolution on results. Detection of non-random patterns of community assembly was determined by net relatedness index (NRI) and nearest taxon index (NTI). In most cases, community assembly was either random or phylogenetically clustered, which likely indicates the importance to community structure of habitat filtering based on phylogenetically correlated traits in determining community structure. Different phylogenetic trees gave similar overall results, but the Phylomatic tree produced greater variation across plots for NRI and NTI values, presumably due to noise introduced by using an unresolved phylogenetic tree. Our results suggest that using a DNA barcode tree has benefits over the traditionally used Phylomatic approach by increasing precision and accuracy and allowing the incorporation of taxonomically unidentified individuals into analyses

Tribe Shoreae (Dipterocarpaceae subfamily Dipterocarpoideae) Finally Dissected.

The dipterocarp tribe Shoreae, perhaps more than any other members of this elegant family of often giant emergent trees, is familiar to all who visit the once ubiquitous lowland forests of tropical Asia. Timbers of the genus comprised the bulk of hardwood traded on international markets for thirty years, since the nineteen seventies. Distinct species groups came to be recognised by taxonomists: for their characteristic androecia, and sometimes differences in bark and wood anatomy, while generic status for some was then proposed on embryological evidence. A new molecular phylogeny of the family, and this tribe, substantially confirms the embryological case. This paper formalises resultant nomenclatural changes. Those of us who recall the majestic forested former landscapes of the Sunda lands may regret this decision. But now, with landscapes irretrievably changed by serried ranks of oil palm and forest degradation, the case for recognition of the proposed new entities can guide conservation planners in recognising and making the case for permanently conserving surviving undisturbed stands of exceptional composition or diversity

Molecular phylogeny helps to delimit <i>Plectranthus</i> <i>hadiensis</i> from its related morph occurring in Sri Lanka

Plectranthus hadiensis is an important medicinal plant in Sri Lanka. It was considered a separate species, P. zeylanicus, endemic to the island until its inclusion, as P. hadiensis var. tomentosus, together with morphs from southern Africa in the revised species concept of P. hadiensis. However, there are morphological, chemical, and therapeutic differences between the African and Sri Lankan morphs. We used eight molecular markers in a phylogenetic study to clarify the species concept of P. hadiensis and to investigate whether it should include the Sri Lankan morph. We examined the position of the two P. hadiensis morphs in relation to eight other Plectranthus species. The maximum likelihood tree revealed three clades: a weakly supported clade including P. calycinus, P. glabratus, P. fruticosus, and P. malabaricus; a highly supported clade including P. amboinicus and African and Sri Lankan specimens of P. hadiensis; and a highly supported clade formed by P. barbatus, P. caninus, and P. hadiensis var. tomentosus. The African P. hadiensis specimens form a highly supported subclade sister to a subclade containing the Sri Lankan P. hadiensis, suggesting that the subclades correspond to either two sister species or two subspecies. We propose that they are more likely to be sister species given the differences in morphology, chemistry, and chromosome number

Conservation of Three-Dimensional Structure of Lepidoptera and Trichoptera L-Fibroins for 290 Million Years

The divergence of sister orders Trichoptera (caddisflies) and Lepidoptera (moths and butterflies) from a silk-spinning ancestor occurred around 290 million years ago. Trichoptera larvae are mainly aquatic, and Lepidoptera larvae are almost entirely terrestrial&mdash;distinct habitats that required molecular adaptation of their silk for deployment in water and air, respectively. The major protein components of their silks are heavy chain and light chain fibroins. In an effort to identify molecular changes in L-fibroins that may have contributed to the divergent use of silk in water and air, we used the ColabFold implementation of AlphaFold2 to predict three-dimensional structures of L-fibroins from both orders. A comparison of the structures revealed that despite the ancient divergence, profoundly different habitats, and low sequence conservation, a novel 10-helix core structure was strongly conserved in L-fibroins from both orders. Previously known intra- and intermolecular disulfide linkages were accurately predicted. Structural variations outside of the core may represent molecular changes that contributed to the evolution of insect silks adapted to water or air. The distributions of electrostatic potential, for example, were not conserved and present distinct order-specific surfaces for potential interactions with or modulation by external factors. Additionally, the interactions of L-fibroins with the H-fibroin C-termini are different for these orders; lepidopteran L-fibroins have N-terminal insertions that are not present in trichopteran L-fibroins, which form an unstructured ribbon in isolation but become part of an intermolecular &beta;-sheet when folded with their corresponding H-fibroin C-termini. The results are an example of protein structure prediction from deep sequence data of understudied proteins made possible by AlphaFold2

Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium

The accurate analyses of massive amounts of data obtained through next¿generation sequencing depend on the selection of appropriate evolutionary models. Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region, using a concatenate ¿supergene¿ approach. The effects of molecular evolutionary models and character partition strategies on plastome¿based phylogenies have generally been evaluated at higher taxonomic levels in green plants. Using plastome data from 32 species of Amphilophium, a genus of Neotropical lianas, we explored potential sources of topological incongruence with different plastid genome datasets and approaches. Specifically, we evaluated the effects of compositional heterogeneity, codon usage bias, positive selection, and incomplete lineage sorting as sources of systematic error (i.e., the recovery of well¿supported conflicting topologies). We compared different datasets (e.g., non¿coding regions, exons, and codon¿aligned and translated amino acids) using concatenated approaches under site¿heterogeneous and site¿homogeneous models, as well as multispecies coalescent (MSC) methods. We found incongruences in recovered phylogenetic relationships, which were mainly located in short internodes. The MSC and concatenated approaches recovered similar topologies. The analysis of GC content and codon usage bias indicated higher substitution rates and AT excess at the third codon positions, and we found evidence of positive selection in 3% of amino acid sites. There were no significant differences among species in site biochemical profiles. We argue that the selection of appropriate partition strategies and evolutionary models is important to increase accuracy in phylogenetic relationships, even when using plastome datasets, which is still the primarily used genome in plant phylogenetics

Genome size evolution in the diverse insect order Trichoptera

Background: Genome size is implicated in the form, function, and ecological success of a species. Two principally different mechanisms are proposed as major drivers of eukaryotic genome evolution and diversity: polyploidy (i.e., whole-genome duplication) or smaller duplication events and bursts in the activity of repetitive elements. Here, we generated de novo genome assemblies of 17 caddisflies covering all major lineages of Trichoptera. Using these and previously sequenced genomes, we use caddisflies as a model for understanding genome size evolution in diverse insect lineages. Results: We detect a ∼14-fold variation in genome size across the order Trichoptera. We find strong evidence that repetitive element expansions, particularly those of transposable elements (TEs), are important drivers of large caddisfly genome sizes. Using an innovative method to examine TEs associated with universal single-copy orthologs (i.e., BUSCO genes), we find that TE expansions have a major impact on protein-coding gene regions, with TE-gene associations showing a linear relationship with increasing genome size. Intriguingly, we find that expanded genomes preferentially evolved in caddisfly clades with a higher ecological diversity (i.e., various feeding modes, diversification in variable, less stable environments). Conclusion: Our findings provide a platform to test hypotheses about the potential evolutionary roles of TE activity and TE-gene associations, particularly in groups with high species, ecological, and functional diversities. © 2022 The Author(s) 2022. Published by Oxford University Press GigaScience.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]