UPrimer: A Clade-Specific Primer Design Program Based on Nested-PCR Strategy and Its Applications in Amplicon Capture Phylogenomics

Amplicon capture is a promising target sequence capture approach for phylogenomic analyses, and the design of clade-specific nuclear protein-coding locus (NPCL) amplification primers is crucial for its successful application. In this study, we developed a primer design program called UPrimer that can quickly design clade-specific NPCL amplification primers based on genome data, without requiring manual intervention. Unlike other available primer design programs, UPrimer uses a nested-PCR strategy that greatly improves the amplification success rate of the designed primers. We examined all available metazoan genome data deposited in NCBI and developed NPCL primer sets for 21 metazoan groups with UPrimer, covering a wide range of taxa, including arthropods, mollusks, cnidarians, echinoderms, and vertebrates. On average, each clade-specific NPCL primer set comprises ∼1,000 NPCLs. PCR amplification tests were performed in 6 metazoan groups, and the developed primers showed a PCR success rate exceeding 95%. Furthermore, we demonstrated a phylogenetic case study in Lepidoptera, showing how NPCL primers can be used for phylogenomic analyses with amplicon capture. Our results indicated that using 100 NPCL probes recovered robust high-level phylogenetic relationships among butterflies, highlighting the utility of the newly designed NPCL primer sets for phylogenetic studies. We anticipate that the automated tool UPrimer and the developed NPCL primer sets for 21 metazoan groups will enable researchers to obtain phylogenomic data more efficiently and cost-effectively and accelerate the resolution of various parts of the Tree of Life.

Developing the Protocol Infrastructure for DNA Sequencing Natural History Collections

Intentionally preserved biological material in natural history collections represents a vast repository of biodiversity. Advances in laboratory and sequencing technologies have made these specimens increasingly accessible for genomic analyses, offering a window into the genetic past of species and often permitting access to information that can no longer be sampled in the wild. Due to their age, preparation and storage conditions, DNA retrieved from museum and herbarium specimens is often poor in yield, heavily fragmented and biochemically modified. This not only poses methodological challenges in recovering nucleotide sequences, but also makes such investigations susceptible to environmental and laboratory contamination. In this paper, we review the practical challenges associated with making the recovery of DNA sequence data from museum collections more routine. We first review key operational principles and issues to address, to guide the decision-making process and dialogue between researchers and curators about when and how to sample museum specimens for genomic analyses. We then outline the range of steps that can be taken to reduce the likelihood of contamination including laboratory set-ups, workflows and working practices. We finish by presenting a series of case studies, each focusing on protocol practicalities for the application of different mainstream methodologies to museum specimens including: (i) shotgun sequencing of insect mitogenomes, (ii) whole genome sequencing of insects, (iii) genome skimming to recover plant plastid genomes from herbarium specimens, (iv) target capture of multi-locus nuclear sequences from herbarium specimens, (v) RAD-sequencing of bird specimens and (vi) shotgun sequencing of ancient bovid bone samples.

Chromosome-Aware Phylogenomics of Assassin Bugs (Hemiptera: Reduvioidea) Elucidates Ancient Gene Conflict

Though the phylogenetic signal of loci on sex chromosomes can differ from those on autosomes, chromosomal-level genome assemblies for nonvertebrates are still relatively scarce and conservation of chromosomal gene content across deep phylogenetic scales has therefore remained largely unexplored. We here assemble a uniquely large and diverse set of samples (17 anchored hybrid enrichment, 24 RNA-seq, and 70 whole-genome sequencing samples of variable depth) for the medically important assassin bugs (Reduvioidea). We assess the performance of genes based on multiple features (e.g., nucleotide vs. amino acid, nuclear vs. mitochondrial, and autosomal vs. X chromosomal) and employ different methods (concatenation and coalescence analyses) to reconstruct the unresolved phylogeny of this diverse (∼7,000 spp.) and old (>180 Ma) group. Our results show that genes on the X chromosome are more likely to have discordant phylogenies than those on autosomes. We find that the X chromosome conflict is driven by high gene substitution rates that impact the accuracy of phylogenetic inference. However, gene tree clustering showed strong conflict even after discounting variable third codon positions. Alternative topologies were not particularly enriched for sex chromosome loci, but spread across the genome. We conclude that binning genes to autosomal or sex chromosomes may result in a more accurate picture of the complex evolutionary history of a clade.

Evolution of stridulatory mechanisms: vibroacoustic communication may be common in leaf-footed bugs and allies (Heteroptera: Coreoidea)

Intra- and interspecific communication is crucial to fitness via its role in facilitating mating, territoriality and defence. Yet, the evolution of animal communication systems is puzzling-how do they originate and change over time? Studying stridulatory morphology provides a tractable opportunity to deduce the origin and diversification of a communication mechanism. Stridulation occurs when two sclerotized structures rub together to produce vibratory and acoustic (vibroacoustic) signals, such as a cricket 'chirp'. We investigated the evolution of stridulatory mechanisms in the superfamily Coreoidea (Hemiptera: Heteroptera), a group of insects known for elaborate male fighting behaviours and enlarged hindlegs. We surveyed a large sampling of taxa and used a phylogenomic dataset to investigate the evolution of stridulatory mechanisms. We identified four mechanisms, with at least five evolutionary gains. One mechanism, occurring only in male Harmostini (Rhopalidae), is described for the first time. Some stridulatory mechanisms appear to be non-homoplastic apomorphies within Rhopalidae, while others are homoplastic or potentially homoplastic within Coreidae and Alydidae, respectively. We detected no losses of these mechanisms once evolved, suggesting they are adaptive. Our work sets the stage for further behavioural, evolutionary and ecological studies to better understand the context in which these traits evolve and change.

Predictors of sequence capture in a large-scale anchored phylogenomics project

Next-generation sequencing (NGS) technologies have revolutionized phylogenomics by decreasing the cost and time required to generate sequence data from multiple markers or whole genomes. Further, the fragmented DNA of biological specimens collected decades ago can be sequenced with NGS, reducing the need for collecting fresh specimens. Sequence capture, also known as anchored hybrid enrichment, is a method to produce reduced representation libraries for NGS sequencing. The technique uses single-stranded oligonucleotide probes that hybridize with pre-selected regions of the genome that are sequenced via NGS, culminating in a dataset of numerous orthologous loci from multiple taxa. Phylogenetic analyses using these sequences have the potential to resolve deep and shallow phylogenetic relationships. Identifying the factors that affect sequence capture success could save time, money, and valuable specimens that might be destructively sampled despite low likelihood of sequencing success. We investigated the impacts of specimen age, preservation method, and DNA concentration on sequence capture (number of captured sequences and sequence quality) while accounting for taxonomy and extracted tissue type in a large-scale butterfly phylogenomics project. This project used two probe sets to extract 391 loci or a subset of 13 loci from over 6,000 butterfly specimens. We found that sequence capture is a resilient method capable of amplifying loci in samples of varying age (0–111 years), preservation method (alcohol, papered, pinned), and DNA concentration (0.020 ng/μl - 316 ng/ul). Regression analyses demonstrate that sequence capture is positively correlated with DNA concentration. However, sequence capture and DNA concentration are negatively correlated with sample age and preservation method. Our findings suggest that sequence capture projects should prioritize the use of alcohol-preserved samples younger than 20 years old when available. In the absence of such specimens, dried samples of any age can yield sequence data, albeit with returns that diminish with increasing age.

Phylogenetic relationships and revised classification of the true bug infraorder Dipsocoromorpha (Insecta: Hemiptera: Heteroptera)

Currently comprising only about 430 species, Dipsocoromorpha or minute litter bugs are one of the small infraorders of Heteroptera. They are classified into five morphologically distinct families--Ceratocombidae, Dipsocoridae, Hypsipterygidae, Schizopteridae and Stemmocryptidae--but relationships among and within these families are poorly understood owing to the lack of phylogenetic studies. A phylogenetic hypothesis based on combined molecular and morphological data is important to both evaluate and revise the higher-level classification and to explore the evolutionary history of morphological features including elytriform (or beetle-like) forewings, that seem to have evolved multiple times in this group, jumping devices, and the highly modified and diverse male genitalia. We here use a dataset combining Sanger-derived (~4500 bp; 108 taxa) and Illumina-generated (~7500 bp; 24 taxa) sequence data with a morphological matrix (159 characters) and taxon sampling that comprises all currently recognized family-, subfamily- and tribal-level taxa and comprehensive genus-level sampling to investigate phylogenetic relationships within litter bugs. Our results support the monophyly of Dipsocoromorpha, Schizopteridae and Dipsocoridae, whereas Ceratocombidae and the schizopterine subfamily "Ogeriinae" are polyphyletic and paraphyletic, respectively. A new classification is proposed that recognizes six families, including Trichotonannidae, stat.n., and two subfamilies each within the two larger families Ceratocombidae and Schizopteridae. Ancestral state reconstructions outline the complex evolutionary history of many morphological characters, including 15 independent origins of elytriform forewings, and at least five shifts in the degree of genitalic asymmetry.

HyRAD-X Exome Capture Museomics Unravels Giant Ground Beetle Evolution

Advances in phylogenomics contribute toward resolving long-standing evolutionary questions. Notwithstanding, genetic diversity contained within more than a billion biological specimens deposited in natural history museums remains recalcitrant to analysis owing to challenges posed by its intrinsically degraded nature. Yet that tantalizing resource could be critical in overcoming taxon sampling constraints hindering our ability to address major evolutionary questions. We addressed this impediment by developing phyloHyRAD, a new bioinformatic pipeline enabling locus recovery at a broad evolutionary scale from HyRAD-X exome capture of museum specimens of low DNA integrity using a benchtop RAD-derived exome-complexity-reduction probe set developed from high DNA integrity specimens. Our new pipeline can also successfully align raw RNAseq transcriptomic and ultraconserved element reads with the RAD-derived probe catalog. Using this method, we generated a robust timetree for Carabinae beetles, the lack of which had precluded study of macroevolutionary trends pertaining to their biogeography and wing-morphology evolution. We successfully recovered up to 2,945 loci with a mean of 1,788 loci across the exome of specimens of varying age. Coverage was not significantly linked to specimen age, demonstrating the wide exploitability of museum specimens. We also recovered fragmentary mitogenomes compatible with Sanger-sequenced mtDNA. Our phylogenomic timetree revealed a Lower Cretaceous origin for crown group Carabinae, with the extinct Aplothorax Waterhouse, 1841 nested within the genus Calosoma Weber, 1801 demonstrating the junior synonymy of Aplothorax syn. nov., resulting in the new combination Calosoma  burchellii (Waterhouse, 1841) comb. nov. This study compellingly illustrates that HyRAD-X and phyloHyRAD efficiently provide genomic-level data sets informative at deep evolutionary scales.

New alignment-based sequence extraction software (ALiBaSeq) and its utility for deep level phylogenetics

Despite many bioinformatic solutions for analyzing sequencing data, few options exist for targeted sequence retrieval from whole genomic sequencing (WGS) data with the ultimate goal of generating a phylogeny. Available tools especially struggle at deep phylogenetic levels and necessitate amino-acid space searches, which may increase rates of false positive results. Many tools are also difficult to install and may lack adequate user resources. Here, we describe a program that uses freely available similarity search tools to find homologs in assembled WGS data with unparalleled freedom to modify parameters. We evaluate its performance compared to other commonly used bioinformatics tools on two divergent insect species (>200 My) for which annotated genomes exist, and on one large set each of highly conserved and more variable loci. Our software is capable of retrieving orthologs from well-curated or unannotated, low or high depth shotgun, and target capture assemblies as well or better than other software as assessed by recovering the most genes with maximal coverage and with a low rate of false positives throughout all datasets. When assessing this combination of criteria, ALiBaSeq is frequently the best evaluated tool for gathering the most comprehensive and accurate phylogenetic alignments on all types of data tested. The software (implemented in Python), tutorials, and manual are freely available at https://github.com/AlexKnyshov/alibaseq.

Optimized and affordable high-throughput sequencing workflow for preserved and nonpreserved small zooplankton specimens

Genomic analysis of hundreds of individuals is increasingly becoming standard in evolutionary and ecological research. Individual-based sequencing generates large amounts of valuable data from experimental and field studies, while using preserved samples is an invaluable resource for studying biodiversity in remote areas or across time. Yet, small-bodied individuals or specimens from collections are often of limited use for genomic analyses due to a lack of suitable extraction and library preparation protocols for preserved or small amounts of tissues. Currently, high-throughput sequencing in zooplankton is mostly restricted to clonal species, that can be maintained in live cultures to obtain sufficient amounts of tissue, or relies on a whole-genome amplification step that comes with several biases and high costs. Here, we present a workflow for high-throughput sequencing of single small individuals omitting the need for prior whole-genome amplification or live cultures. We establish and demonstrate this method using 27 species of the genus Daphnia, aquatic keystone organisms, and validate it with small-bodied ostracods. Our workflow is applicable to both live and preserved samples at low costs per sample. We first show that a silica-column based DNA extraction method resulted in the highest DNA yields for nonpreserved samples while a precipitation-based technique gave the highest yield for ethanol-preserved samples and provided the longest DNA fragments. We then successfully performed short-read whole genome sequencing from single Daphnia specimens and ostracods. Moreover, we assembled a draft reference genome from a single Daphnia individual (>50× coverage) highlighting the value of the workflow for non-model organisms.

Effects of sample age on data quality from targeted sequencing of museum specimens: what are we capturing in time?

Background

Next generation sequencing (NGS) can recover DNA data from valuable extant and extinct museum specimens. However, archived or preserved DNA is difficult to sequence because of its fragmented, damaged nature, such that the most successful NGS methods for preserved specimens remain sub-optimal. Improving wet-lab protocols and comprehensively determining the effects of sample age on NGS library quality are therefore of vital importance. Here, I examine the relationship between sample age and several indicators of library quality following targeted NGS sequencing of ~ 1300 loci using 271 samples of pinned moth specimens (Helicoverpa armigera) ranging in age from 5 to 117 years.

Results

I find that older samples have lower DNA concentrations following extraction and thus require a higher number of indexing PCR cycles during library preparation. When sequenced reads are aligned to a reference genome or to only the targeted region, older samples have a lower number of sequenced and mapped reads, lower mean coverage, and lower estimated library sizes, while the percentage of adapters in sequenced reads increases significantly as samples become older. Older samples also show the poorest capture success, with lower enrichment and a higher improved coverage anticipated from further sequencing.

Conclusions

Sample age has significant, measurable impacts on the quality of NGS data following targeted enrichment. However, incorporating a uracil-removing enzyme into the blunt end-repair step during library preparation could help to repair DNA damage, and using a method that prevents adapter-dimer formation may result in improved data yields.

European minnows through time: museum collections aid genetic assessment of species introductions in freshwater fishes (Cyprinidae: Phoxinus species complex)

Massive fish introductions have taken place throughout much of the world, mostly over the last 70 years, and present a major threat to the genetic diversity of native fishes. Introductions have been reported for European Phoxinus, a ubiquitous small cyprinid that populates a wide variety of habitats. Species delineation in European Phoxinus has proven difficult with one reason being ranges of distribution that often traverse drainage boundaries. The present study combines recent samples with museum samples to better understand the current distribution of Phoxinus species and their distributions prior to the massive introductions of fishes in Europe, and to evaluate the use of museum specimens for species distribution studies. For these purposes, genetic lineages from sites collected prior to 1900 (n = 14), and between 1900 and 1950 (n = 8), were analysed using two mitochondrial and nuclear markers. Although possible fish introductions were detected, our results show that the distribution of genetic lineages of museum samples is comparable to that of the extant lineages of European Phoxinus present in those areas. These observations suggest that in the studied ranges the distribution of Phoxinus lineages has been driven by natural processes.

Off-target capture data, endosymbiont genes and morphology reveal a relict lineage that is sister to all other singing cicadas

Phylogenetic asymmetry is common throughout the tree of life and results from contrasting patterns of speciation and extinction in the paired descendant lineages of ancestral nodes. On the depauperate side of a node, we find extant ‘relict’ taxa that sit atop long, unbranched lineages. Here, we show that a tiny, pale green, inconspicuous and poorly known cicada in the genus Derotettix, endemic to degraded salt-plain habitats in arid regions of central Argentina, is a relict lineage that is sister to all other modern cicadas. Nuclear and mitochondrial phylogenies of cicadas inferred from probe-based genomic hybrid capture data of both target and non-target loci and a morphological cladogram support this hypothesis. We strengthen this conclusion with genomic data from one of the cicada nutritional bacterial endosymbionts, Sulcia, an ancient and obligate endosymbiont of the larger plant-sucking bugs (Auchenorrhyncha) and an important source of maternally inherited phylogenetic data. We establish Derotettiginae subfam. nov. as a new, monogeneric, fifth cicada subfamily, and compile existing and new data on the distribution, ecology and diet of Derotettix. Our consideration of the palaeoenvironmental literature and host-plant phylogenetics allows us to predict what might have led to the relict status of Derotettix over 100 Myr of habitat change in South America.