The SITE-100 Project: Site-Based Biodiversity Genomics for Species Discovery, Community Ecology, and a Global Tree-of-Life

Most insect communities are composed of evolutionarily diverse lineages, but detailed phylogenetic analyses of whole communities are lacking, in particular in species-rich tropical faunas. Likewise, our knowledge of the Tree-of-Life to document evolutionary diversity of organisms remains highly incomplete and especially requires the inclusion of unstudied lineages from species-rich ecosystems. Here we present the SITE-100 program, which is an attempt at building the Tree-of-Life from whole-community sampling of high-biodiversity sites around the globe. Combining the local site-based sets into a global tree produces an increasingly comprehensive estimate of organismal phylogeny, while also re-tracing evolutionary history of lineages constituting the local community. Local sets are collected in bulk in standardized passive traps and imaged with large-scale high-resolution cameras, which is followed by a parataxonomy step for the preliminary separation of morphospecies and selection of specimens for phylogenetic analysis. Selected specimens are used for individual DNA extraction and sequencing, usually to sequence mitochondrial genomes. All remaining specimens are bulk extracted and subjected to metabarcoding. Phylogenetic analysis on the mitogenomes produces a reference tree to which short barcode sequences are added in a secondary analysis using phylogenetic placement methods or backbone constrained tree searches. However, the approach may be hampered because (1) mitogenomes are limited in phylogenetic informativeness, and (2) site-based sampling may produce poor taxon coverage which causes challenges for phylogenetic inference. To mitigate these problems, we first assemble nuclear shotgun data from taxonomically chosen lineages to resolve the base of the tree, and add site-based mitogenome and DNA barcode data in three hierarchical steps. We posit that site-based sampling, though not meeting the criterion of “taxon-completeness,” has great merits given preliminary studies showing representativeness and evenness of taxa sampled. We therefore argue in favor of site-based sampling as an unorthodox but logistically efficient way to construct large phylogenetic trees.Copyright © 2022 Bian, Garner, Liu and Vogler. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. The attached file is the published version of the article

Effective COVID-19 prevention and control in areas of ultra-dense population: Lessons from Macau SAR

In this paper we summarise, in chronological order, all COVID-19 preventive measures undertaken by the Macau Special Administrative Region (SAR) government during the first quarter of 2020. The information and narrative contained herein may be of useful to other parts of the world in COVID-19 control and prevention, especially cities with ultra-high population densities. The four main lessons from Macau SAR are: (1) Proactive leadership and early prevention. (2) Strict adherence to community endemic control. (3) Clear prioritising of public health. (4) Planed relief for financial hardships amidst the post-pandemic recession

Independent effects on cellular and humoral immune responses underlie genotype-by- genotype interactions between Drosophila and parasitoids

It is common to find abundant genetic variation in host resistance and parasite infectivity within populations, with the outcome of infection frequently depending on genotype-specific interactions. Underlying these effects are complex immune defenses that are under the control of both host and parasite genes. We have found extensive variation in Drosophila melanogaster’s immune response against the parasitoid wasp Leptopilina boulardi. Some aspects of the immune response, such as phenoloxidase activity, are predominantly affected by the host genotype. Some, such as upregulation of the complement-like protein Tep1, are controlled by the parasite genotype. Others, like the differentiation of immune cells called lamellocytes, depend on the specific combination of host and parasite genotypes. These observations illustrate how the outcome of infection depends on independent genetic effects on different aspects of host immunity. As parasite-killing results from the concerted action of different components of the immune response, these observations provide a physiological mechanism to generate phenomena like epistasis and genotype-interactions that underlie models of coevolution.This work was funded by a Natural Environment Research Council grant NE/P00184X/ 1 to FMJ and ABL. ABL was supported by an EMBO Fellowship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscrip

Research data supporting "Independent effects on cellular and humoral immune responses underlie genotype-by-genotype interactions between Drosophila and parasitoids"

Datasets and scripts to generate each figure panel are divided in separate folders. Scripts generate and save each figure as a PDF file. Statistics are generated at the end of each script. Folders: Fig1A – The encapsulation phenotype is recorded for individual larva per treatment and genotype. Fig1B – The melanization phenotype is recorded for individual larva per treatment and genotype. Fig2 – The number of plasmatocytes and lamellocytes is recorded from pool of 6 larvae per treatment and genotype. Fig3A – Gene expression is recorded as raw Ct values from qPCR for housekeeping gene and test gene per treatment and genotype. Fig3B – Phenoloxidase activity is recorded as raw absorbance value per time point, treatment and genotype. FigS1 – The encapsulation phenotype is recorded per vial with 40 transferred larvae before infection