摘要

明确的系统发育关系 (phylogeny) 是分类学、进化事件的推断及时间校正、相关性状的祖先状态构建等的重要基础和前提。在明确了不同支系的系统发育关系的前提下，通过分析比较性状在不同类群中的演化历史，可以了解物种经受了哪些选择压力，不同性状是否倾向于共同演化或只是对相同选择压力的适应。自高通量短序列测序技术出现以后，通过广泛采样及使用大规模数据集来研究不同类群的系统发育关系的方法已经成为共识。但由于大规模全基因组测序成本高、分析难度大，简化基因组测序仍具有广泛应用前景。其中，利用转录组测序方法来获得大量适用于系统发育分析的直系同源基因具有可观的成本优势和较高的可行性。本文简要概括了基于转录组方法进行系统发育研究的主要步骤，包括样本制备、转录组测序与组装、直系同源基因筛选与评估和系统发育分析等，希望能为相关学者提供一定的参考。

Highlights

• Pollen diversity helps to trace the geographic origin of honey products.

• Metagenomic sequences are used directly as references for local honey.

• Plant identification or floral survey are no longer needed.

• Machine learning can accurately trace geographic origin at high resolution.

• Method is useful where biodiversity is used as matrix for similarity evaluation.

Abstract

The adulteration of honey is common. Recently, High Throughput Sequencing (HTS)-based metabarcoding method has been applied successfully to pollen/honey identification to determine floral composition that, in turn, can be used to identify the geographical origins of honeys. However, the lack of local references materials posed a serious challenge for HTS-based pollen identification methods. Here, we sampled 28 honey samples from various geographic origins without prior knowledge of local floral information and applied a machine learning method to determine geographical origins. The machine learning method uses a resilient backpropagation algorithm to train a neural network. The results showed that biological components in honey provided characteristic traits that enabled accurate geographic tracing for nearly all honey samples, confidently discriminating honeys to their geographic origin with > 99% success rates, including those separated by as little as 39 kilometers.

Highlights

• Analysis of genomes from all five extant and three extinct rhinoceros species

• Strong phylogenomic support for the geographical hypothesis of rhinoceros evolution

• Basal split between African and Eurasian lineages in the early Miocene (∼16 mya)

• While all rhinoceroses have low genome diversity, it is lowest in modern-day ones

Summary

Only five species of the once-diverse Rhinocerotidae remain, making the reconstruction of their evolutionary history a challenge to biologists since Darwin. We sequenced genomes from five rhinoceros species (three extinct and two living), which we compared to existing data from the remaining three living species and a range of outgroups. We identify an early divergence between extant African and Eurasian lineages, resolving a key debate regarding the phylogeny of extant rhinoceroses. This early Miocene (∼16 million years ago [mya]) split post-dates the land bridge formation between the Afro-Arabian and Eurasian landmasses. Our analyses also show that while rhinoceros genomes in general exhibit low levels of genome-wide diversity, heterozygosity is lowest and inbreeding is highest in the modern species. These results suggest that while low genetic diversity is a long-term feature of the family, it has been particularly exacerbated recently, likely reflecting recent anthropogenic-driven population declines.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Acoustic communication is enabled by the evolution of specialised hearing and sound producing organs. In this study, we performed a large-scale macroevolutionary study to understand how both hearing and sound production evolved and affected diversification in the insect order Orthoptera, which includes many familiar singing insects, such as crickets, katydids, and grasshoppers. Using phylogenomic data, we firmly establish phylogenetic relationships among the major lineages and divergence time estimates within Orthoptera, as well as the lineage-specific and dynamic patterns of evolution for hearing and sound producing organs. In the suborder Ensifera, we infer that forewing-based stridulation and tibial tympanal ears co-evolved, but in the suborder Caelifera, abdominal tympanal ears first evolved in a non-sexual context, and later co-opted for sexual signalling when sound producing organs evolved. However, we find little evidence that the evolution of hearing and sound producing organs increased diversification rates in those lineages with known acoustic communication.

A widely accepted model for the evolution of cave animals posits colonization by surface ancestors followed by the acquisition of adaptations over many generations. However, the speed of cave adaptation in some species suggests mechanisms operating over shorter timescales. To address these mechanisms, we used Astyanax mexicanus, a teleost with ancestral surface morphs (surface fish, SF) and derived cave morphs (cavefish, CF). We exposed SF to completely dark conditions and identified numerous altered traits at both the gene expression and phenotypic levels. Remarkably, most of these alterations mimicked CF phenotypes. Our results indicate that many cave-related traits can appear within a single generation by phenotypic plasticity. In the next generation, plasticity can be further refined. The initial plastic responses are random in adaptive outcome but may determine the subsequent course of evolution. Our study suggests that phenotypic plasticity contributes to the rapid evolution of cave-related traits in A. mexicanus.

Book name: Transcriptomics in entomological research

While “genomics” is becoming a household term, knowing the genome of an organism alone provides relatively little information. Between the genome and the final organism is the “transcriptome” that tells us which genes are expressed and translated into proteins in a certain cell or tissue of an organism at a given time and specific situation. The transcriptome tells you what genes are being “transcribed” at any given moment, providing the wealth of data and specificity of proteomics with the relative ease of study of genetics. Transcriptomics technology thus has myriad uses, and the goal of this book is to showcase the extraordinary diversity of ways transcriptomics can be utilised in entomological research, from basic to applied, from ecology to physiology to agricultural

Understanding diversity patterns requires accounting for the roles of both historical and contemporary factors in the assembly of communities. Here, we compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi‐State Speciation and Extinction model, to track the origins of these patterns. Further, we estimated diversification rates of the two moth assemblages and explored the effects of contemporary ecological factors. From 7,788 specimens we identified 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Moths in Yanshan mountains showed higher species diversity than in Taihang mountains. Ancestral range analysis indicated Yanshan as the origin, with significant historical dispersals from Yanshan to Taihang. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we demonstrate that a multiscale (community, population and species level) analysis incorporating both historical and contemporary factors can be useful in delineating factors contributing to community assembly and patterning in diversity.

Summary

1. Bee populations and other pollinators face multiple, synergistically acting threats, which have led to population declines, loss of local species richness and pollination services, and extinctions. However, our understanding of the degree, distribution and causes of declines is patchy, in part due to inadequate monitoring systems, with the challenge of taxonomic identification posing a major logistical barrier. Pollinator conservation would benefit from a high‐throughput identification pipeline.

2. We show that the metagenomic mining and resequencing of mitochondrial genomes (mitogenomics) can be applied successfully to bulk samples of wild bees. We assembled the mitogenomes of 48 UK bee species and then shotgun‐sequenced total DNA extracted from 204 whole bees that had been collected in 10 pan‐trap samples from farms in England and been identified morphologically to 33 species. Each sample data set was mapped against the 48 reference mitogenomes.

3. The morphological and mitogenomic data sets were highly congruent. Out of 63 total species detections in the morphological data set, the mitogenomic data set made 59 correct detections (93·7% detection rate) and detected six more species (putative false positives). Direct inspection and an analysis with species‐specific primers suggested that these putative false positives were most likely due to incorrect morphological ID s. Read frequency significantly predicted species biomass frequency (R 2 = 24·9%). Species lists, biomass frequencies, extrapolated species richness and community structure were recovered with less error than in a metabarcoding pipeline.

4. Mitogenomics automates the onerous task of taxonomic identification, even for cryptic species, allowing the tracking of changes in species richness and distributions. A mitogenomic pipeline should thus be able to contain costs, maintain consistently high‐quality data over long time series, incorporate retrospective taxonomic revisions and provide an auditable evidence trail. Mitogenomic data sets also provide estimates of species counts within samples and thus have potential for tracking population trajectories.

The advent in high-throughput-sequencing (HTS) technologies has revolutionized conventional biodiversity research by enabling parallel capture of DNA sequences possessing species-level diagnosis. However, polymerase chain reaction (PCR)-based implementation is biased by the efficiency of primer binding across lineages of organisms. A PCR-free HTS approach will alleviate this artefact and significantly improve upon the multi-locus method utilizing full mitogenomes. Here we developed a novel multiplex sequencing and assembly pipeline allowing for simultaneous acquisition of full mitogenomes from pooled animals without DNA enrichment or amplification. By concatenating assemblies from three de novo assemblers, we obtained high-quality mitogenomes for all 49 pooled taxa, with 36 species >15 kb and the remaining >10 kb, including 20 complete mitogenomes and nearly all protein coding genes (99.6%). The assembly quality was carefully validated with Sanger sequences, reference genomes and conservativeness of protein coding genes across taxa. The new method was effective even for closely related taxa, e.g. three Drosophila spp., demonstrating its broad utility for biodiversity research and mito-phylogenomics. Finally, the in silico simulation showed that by recruiting multiple mito-loci, taxon detection was improved at a fixed sequencing depth. Combined, these results demonstrate the plausibility of a multi-locus mito-metagenomics approach as the next phase of the current single-locus metabarcoding method.

Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.