Heterotrophic plants provide excellent opportunities to study the effects of altered selective regimes on genome evolution. Plastid genome (plastome) studies in heterotrophic plants are often based ...on one or a few highly divergent species or sequences as representatives of an entire lineage, thus missing important evolutionary-transitory events.
Here, we present the first infraspecific analysis of plastome evolution in any heterotrophic plant. By combining genome skimming and targeted sequence capture, we address hypotheses on the degree and rate of plastome degradation in a complex of leafless orchids (Corallorhizastriata) across its geographic range.
Plastomes provide strong support for relationships and evidence of reciprocal monophyly between C. involuta and the endangered C. bentleyi. Plastome degradation is extensive, occurring rapidly over a few million years, with evidence of differing rates of genomic change among the two principal clades of the complex. Genome skimming and targeted sequence capture differ widely in coverage depth overall, with depth in targeted sequence capture datasets varying immensely across the plastome as a function of GC content.
These findings will help to fill a knowledge gap in models of heterotrophic plastid genome evolution, and have implications for future studies in heterotrophs.
Barcodes are short segments of DNA that can be used to uniquely identify an unknown specimen to species, particularly when diagnostic morphological features are absent. These sequences could offer a ...new forensic tool in plant and animal conservation-especially for endangered species such as members of the Cycadales. Ideally, barcodes could be used to positively identify illegally obtained material even in cases where diagnostic features have been purposefully removed or to release confiscated organisms into the proper breeding population. In order to be useful, a DNA barcode sequence must not only easily PCR amplify with universal or near-universal reaction conditions and primers, but also contain enough variation to generate unique identifiers at either the species or population levels. Chloroplast regions suggested by the Plant Working Group of the Consortium for the Barcode of Life (CBoL), and two alternatives, the chloroplast psbA-trnH intergenic spacer and the nuclear ribosomal internal transcribed spacer (nrITS), were tested for their utility in generating unique identifiers for members of the Cycadales. Ease of amplification and sequence generation with universal primers and reaction conditions was determined for each of the seven proposed markers. While none of the proposed markers provided unique identifiers for all species tested, nrITS showed the most promise in terms of variability, although sequencing difficulties remain a drawback. We suggest a workflow for DNA barcoding, including database generation and management, which will ultimately be necessary if we are to succeed in establishing a universal DNA barcode for plants.
Recent advances in high‐throughput sequencing library preparation and subgenomic enrichment methods have opened new avenues for population genetics and phylogenetics of nonmodel organisms. To ...multiplex large numbers of indexed samples while sequencing predominantly orthologous, targeted regions of the genome, we propose modifications to an existing, in‐solution capture that utilizes PCR products as target probes to enrich library pools for the genomic subset of interest. The sequence capture using PCR‐generated probes (SCPP) protocol requires no specialized equipment, is highly flexible and significantly reduces experimental costs for projects where a modest scale of genetic data is optimal (25–100 genomic loci). Our alterations enable application of this method across a wider phylogenetic range of taxa and result in higher capture efficiencies and coverage at each locus. Efficient and consistent capture over multiple SCPP experiments and at various phylogenetic distances is demonstrated, extending the utility of this method to both phylogeographic and phylogenomic studies.
Selection together with variation in floral traits can act to mold floral form, often driven by a plant’s predominant or most effective pollinators. To investigate the evolution of traits associated ...with pollination, we developed a phylogenetic framework for evaluating tempo and mode of pollination shifts across the genus
Costus
L., known for its evolutionary toggle between traits related to bee and bird pollination. Using a target enrichment approach, we obtained 957 loci for 171 accessions to expand the phylogenetic sampling of Neotropical
Costus
. In addition, we performed whole genome resequencing for a subset of 20 closely related species with contrasting pollination syndromes. For each of these 20 genomes, a high-quality assembled transcriptome was used as reference for consensus calling of candidate loci hypothesized to be associated with pollination-related traits of interest. To test for the role these candidate genes may play in evolutionary shifts in pollinators, signatures of selection were estimated as
dN/dS
across the identified candidate loci. We obtained a well-resolved phylogeny for Neotropical
Costus
despite conflict among gene trees that provide evidence of incomplete lineage sorting and/or reticulation. The overall topology and the network of genome-wide single nucleotide polymorphisms (SNPs) indicate that multiple shifts in pollination strategy have occurred across
Costus
, while also suggesting the presence of previously undetected signatures of hybridization between distantly related taxa. Traits related to pollination syndromes are strongly correlated and have been gained and lost in concert several times throughout the evolution of the genus. The presence of bract appendages is correlated with two traits associated with defenses against herbivory. Although labellum shape is strongly correlated with overall pollination syndrome, we found no significant impact of labellum shape on diversification rates. Evidence suggests an interplay of pollination success with other selective pressures shaping the evolution of the
Costus
inflorescence. Although most of the loci used for phylogenetic inference appear to be under purifying selection, many candidate genes associated with functional traits show evidence of being under positive selection. Together these results indicate an interplay of phylogenetic history with adaptive evolution leading to the diversification of pollination-associated traits in Neotropical
Costus
.
The family of pantropical spiral gingers (Costaceae Nakai;
c.
125 spp.) can be used as a model to enhance our understanding of the mechanisms underlying Neotropical diversity. Costaceae has higher ...taxonomic diversity in South and Central America (
c.
72 Neotropical species,
c.
30 African,
c.
23 Southeast Asian), particularly due to a radiation of Neotropical species of the genus
Costus
L. (
c.
57 spp.). However, a well-supported phylogeny of the Neotropical spiral gingers including thorough sampling of proposed species encompassing their full morphologic and geographic variation is lacking, partly due to poor resolution recovered in previous analyses using a small sampling of loci. Here we use a phylogenomic approach to estimate the phylogeny of a sample of Neotropical
Costus
species using a targeted enrichment approach. Baits were designed to capture conserved elements’ variable at the species level using available genomic sequences of
Costus
species and relatives. We obtained 832 loci (generating 791,954 aligned base pairs and 31,142 parsimony informative sites) for samples that encompassed the geographical and/or morphological diversity of some recognized species. Higher support values that improve the results of previous studies were obtained when including all the available loci, even those producing unresolved gene trees and having a low proportion of variable sites. Concatenation and coalescent-based species trees methods converge in almost the same topology suggesting a robust estimation of the relationships, even under the high levels of gene tree conflict presented here. The bait set design here presented made inferring a robust phylogeny to test taxonomic hypotheses possible and will improve our understanding of the origins of the charismatic diversity of the Neotropical spiral gingers.
ObjectivesThe enormous toll of the COVID-19 pandemic has heightened the urgency of collecting and analysing population-scale datasets in real time to monitor and better understand the evolving ...pandemic. The objectives of this study were to examine the relationship of risk factors to COVID-19 susceptibility and severity and to develop risk models to accurately predict COVID-19 outcomes using rapidly obtained self-reported data.DesignA cross-sectional study.SettingAncestryDNA customers in the USA who consented to research.ParticipantsThe AncestryDNA COVID-19 Study collected self-reported survey data on symptoms, outcomes, risk factors and exposures for over 563 000 adult individuals in the USA in just under 4 months, including over 4700 COVID-19 cases as measured by a self-reported positive test.ResultsWe replicated previously reported associations between several risk factors and COVID-19 susceptibility and severity outcomes, and additionally found that differences in known exposures accounted for many of the susceptibility associations. A notable exception was elevated susceptibility for men even after adjusting for known exposures and age (adjusted OR=1.36, 95% CI=1.19 to 1.55). We also demonstrated that self-reported data can be used to build accurate risk models to predict individualised COVID-19 susceptibility (area under the curve (AUC)=0.84) and severity outcomes including hospitalisation and critical illness (AUC=0.87 and 0.90, respectively). The risk models achieved robust discriminative performance across different age, sex and genetic ancestry groups within the study.ConclusionsThe results highlight the value of self-reported epidemiological data to rapidly provide public health insights into the evolving COVID-19 pandemic.
Premise of the study:
We developed a bioinformatic pipeline that leverages a publicly available genome and published transcriptomes to design primers in conserved coding sequences flanking targeted ...introns of single‐copy nuclear loci. Paullinieae (Sapindaceae) is used to demonstrate the pipeline.
Methods and Results:
Transcriptome reads phylogenetically closer to the lineage of interest are aligned to the closest genome. Single‐nucleotide polymorphisms are called, generating a “pseudoreference” closer to the lineage of interest. Several filters are applied to meet the criteria of single‐copy nuclear loci with introns of a desired size. Primers are designed in conserved coding sequences flanking introns. Using this pipeline, we developed nine single‐copy nuclear intron markers for Paullinieae.
Conclusions:
This pipeline is highly flexible and can be used for any group with available genomic and transcriptomic resources. This pipeline led to the development of nine variable markers for phylogenetic study without generating sequence data de novo.
We developed a phylogeny of the core Bromelioideae including
Aechmea and related genera, with the specific goals of investigating the monophyly of
Aechmea and its allied genera, redefining ...monophyletic lineages for taxonomic revision, and investigating the biogeographic history of the group. Chloroplast, nuclear ribosomal, and low copy nuclear DNA sequences from 150 species within the Bromelioideae were used to develop the phylogeny. Phylogenies constructed with the combined four gene dataset provided sufficient resolution for investigating evolutionary relationships among species. Many genera are nested within
Aechmea, or are rendered para- or polyphyletic by inclusion of
Aechmea species. Several genera and subgenera of
Aechmea with species in disjunct geographic locations are found to be polyphyletic, divided into separate clades that reflect geographic distribution rather than morphological similarity. This suggests that certain morphological characteristics thought to be indicative of common ancestry have instead evolved multiple times in parallel (i.e. ecological conservatism), possibly indicative of local adaptations to an epiphytic habit across the range of the Bromelioideae. These apparently homoplastic morphological characters used to assign species to genera or subgenera may be useful taxonomically when geography is also taken into account.
Premise of the Study
We present the first plastome phylogeny encompassing all 77 monocot families, estimate branch support, and infer monocot‐wide divergence times and rates of species ...diversification.
Methods
We conducted maximum likelihood analyses of phylogeny and BAMM studies of diversification rates based on 77 plastid genes across 545 monocots and 22 outgroups. We quantified how branch support and ascertainment vary with gene number, branch length, and branch depth.
Key Results
Phylogenomic analyses shift the placement of 16 families in relation to earlier studies based on four plastid genes, add seven families, date the divergence between monocots and eudicots+Ceratophyllum at 136 Mya, successfully place all mycoheterotrophic taxa examined, and support recognizing Taccaceae and Thismiaceae as separate families and Arecales and Dasypogonales as separate orders. Only 45% of interfamilial divergences occurred after the Cretaceous. Net species diversification underwent four large‐scale accelerations in PACMAD‐BOP Poaceae, Asparagales sister to Doryanthaceae, Orchidoideae‐Epidendroideae, and Araceae sister to Lemnoideae, each associated with specific ecological/morphological shifts. Branch ascertainment and support across monocots increase with gene number and branch length, and decrease with relative branch depth. Analysis of entire plastomes in Zingiberales quantifies the importance of non‐coding regions in identifying and supporting short, deep branches.
Conclusions
We provide the first resolved, well‐supported monocot phylogeny and timeline spanning all families, and quantify the significant contribution of plastome‐scale data to resolving short, deep branches. We outline a new functional model for the evolution of monocots and their diagnostic morphological traits from submersed aquatic ancestors, supported by convergent evolution of many of these traits in aquatic Hydatellaceae (Nymphaeales).
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