The emergence of SARS-CoV-2 variants of concern is driven by acceleration of the evolutionary rate

The ongoing SARS-CoV-2 pandemic has seen an unprecedented amount of rapidly generated genome data. These data have revealed the emergence of lineages with mutations associated to transmissibility and antigenicity, known as variants of concern (VOCs). A striking aspect of VOCs is that many of them involve an unusually large number of defining mutations. Current phylogenetic estimates of the evolutionary rate of SARS-CoV-2 suggest that its genome accrues around 2 mutations per month. However, VOCs can have around 15 defining mutations and it is hypothesised that they emerged over the course of a few months, implying that they must have evolved faster for a period of time. We analysed genome sequence data from the GISAID database to assess whether the emergence of VOCs can be attributed to changes in the evolutionary rate of the virus and whether this pattern can be detected at a phylogenetic level using genome data. We fit a range of molecular clock models and assessed their statistical fit. Our analyses indicate that the emergence of VOCs is driven by an episodic increase in the evolutionary rate of around 4-fold the background phylogenetic rate estimate that may have lasted several weeks or months. These results underscore the importance of monitoring the molecular evolution of the virus as a means of understanding the circumstances under which VOCs may emerge.

Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia

Bacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere). Interactions between eukaryotes and bacteria range from cooperative to competitive, with the associated microorganisms affecting their host`s development, growth and health. Since the advent of non-culture dependent analytical techniques such as metagenome sequencing, consortia have been described at the phylogenetic level but rarely functionally. Multifaceted analysis of the microbial consortium of the ancient phytoplankton Botryococcus as an attractive model food web revealed that its all abundant bacterial members belong to a niche of biotin auxotrophs, essentially depending on the microalga. In addition, hydrocarbonoclastic bacteria without vitamin auxotrophies seem adversely to affect the algal cell morphology. Synthetic rearrangement of a minimal community consisting of an alga, a mutualistic and a parasitic bacteria underpins the model of a eukaryote that maintains its own mutualistic microbial community to control its surrounding biosphere. This model of coexistence, potentially useful for defense against invaders by a eukaryotic host could represent ecologically relevant interactions that cross species boundaries. Metabolic and system reconstruction is an opportunity to unravel the relationships within the consortia and provide a blueprint for the construction of mutually beneficial synthetic ecosystems.

The Role of Botanical Families in Medicinal Ethnobotany: A Phylogenetic Perspective

Studies suggesting that medicinal plants are not chosen at random are becoming more common. The goal of this work is to shed light on the role of botanical families in ethnobotany, depicting in a molecular phylogenetic frame the relationships between families and medicinal uses of vascular plants in several Catalan-speaking territories. The simple quantitative analyses for ailments categories and the construction of families and disorders matrix were carried out in this study. A Bayesian approach was used to estimate the over- and underused families in the medicinal flora. Phylogenetically informed analyses were carried out to identify lineages in which there is an overrepresentation of families in a given category of use, i.e., hot nodes. The ethnobotanicity index, at a specific level, was calculated and also adapted to the family level. Two diversity indices to measure the richness of reported taxa within each family were calculated. A total of 47,630 use reports were analysed. These uses are grouped in 120 botanical families. The ethnobotanicity index for this area is 14.44% and the ethnobotanicity index at the family level is 68.21%. The most-reported families are Lamiaceae and Asteraceae and the most reported troubles are disorders of the digestive and nutritional system. Based on the meta-analytic results, indicating hot nodes of useful plants at the phylogenetic level, specific ethnopharmacological research may be suggested, including a phytochemical approach of particularly interesting taxa.

Avian phenotypic convergence is subject to low genetic constraints based on genomic evidence

Background Phenotypic convergence between distinct species provides an opportunity to examine the predictability of genetic evolution. Unrelated species sharing genetic underpinnings for phenotypic convergence suggests strong genetic constraints, and thus high predictability of evolution. However, there is no clear big picture of the genomic constraints on convergent evolution. Genome-based phylogenies have confirmed many cases of phenotypic convergence in birds, making them a good system for examining genetic constraints in phenotypic convergence. In this study, we used hierarchical genomic approaches to estimate genetic constraints in three convergent avian traits: nocturnality, raptorial behavior and foot-propelled diving. Results Phylogeny-based hypothesis tests and positive selection tests were applied to compare 16 avian genomes, representing 14 orders, and identify genes with strong convergence signals. We found 43 adaptively convergent genes (ACGs) associated with the three phenotypic convergence cases and assessed genetic constraints in all three cases, from (amino acid) site mutations to genetic pathways. We found that the avian orders shared few site mutations in the ACGs that contributed to the convergent phenotypes, and that these ACGs were not enriched in any genetic pathways. In addition, different pairs of orders with convergent foot-propelled diving or raptorial behaviors shared few ACGs. We also found that closely related orders that shared foot-propelled diving behavior did not share more ACGs than did distinct orders, suggesting that convergence among these orders could not be explained by their initial genomic backgrounds. Conclusions Our analyses of three avian convergence events suggest low constraints for phenotypic convergence across multiple genetic levels, implying that genetic evolution is unpredictable at the phylogenetic level of avian order. Ours is one of first studies to apply hierarchical genomic examination to multiple avian convergent cases to assess the genetic constraints in life history trait evolution.

A cautionary note on the use of genotype callers in Phylogenomics

Next-generation-sequencing genotype callers are commonly used in studies to call variants from newly-sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However, when these callers are used at the phylogenetic level, the consequences for downstream analyses can be substantial. Here, we performed simulations to compare the performance between the genotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show that the genotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also found that the accuracy of heterozygote calls declines with increasing distance to the reference genome. We quantified this decline, and found that it is very sharp in GATK, while ATLAS maintains a high accuracy even at moderately-divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies.

Morphological variability and taxonomic concepts of Broad-leaved Helleborine ingroup Epipactis helleborine (L.) Crantz / Raznolikost morfoloških lastnosti in taksonomski koncepti oblikovnega kroga širokolistne močvirnice Epipactis helleborine (L.) Crantz

The Broad-leaved Helleborine (Epipactis helleborine s.l.) represents a taxonomically complex group with wide morphological diversity and close genetic relationships among the Epipactis taxa. The transition of some taxa to self-pollination leads to initial speciation from the paraphyletic background of the Broad-leaved Helleborine. In the last twenty years, several new taxa have been awarded species status. However, these taxa are morphologically poorly defined, the descriptions are often contradictory and they actually merit the rank of a subspecies, variety or a form. The taxonomic issue is being explored by several research groups at molecular phylogenetic level. Their results are difficult to integrate into a precise phylogenetic tree, as researchers most often address few local taxa using a variety of more or less supportive molecular markers. In the present review article, the use of an appropriate combination of morphological and molecular markers has been emphasized as being crucial in resolving taxonomic relationships within the Broad-leaved Helleborine. Key words: Epipactis helleborine s.l., Broad-leaved Helleborine, taxonomic problems, speciation Izvleček Oblikovni krog širokolistne močvirnice (Epipactis helleborine s.l.) predstavlja taksonomsko zapleteno skupino s široko morfološko raznolikostjo in ožjo genetsko sorodnostjo taksonov. Na težavnost določanja nekaterih taksonov vpliva prehod k samoopraševanju, ki vodi k začetni speciaciji iz parafiletskega ozadja širokolistne močvirnice. V zadnjih dvajsetih letih je bilo opisanih več novih taksonov, vendar so ti morfološko slabo opredeljeni, opisi so pogosto nasprotujoči. Taksonomski nivo vrste je večinoma neupravičen in bi jih morali umestiti na nivo podvrste ali različice. Filogenetsko problematiko znotraj oblikovnega kroga širokolistne močvirnice proučuje nekaj raziskovalnih skupin. Njihove rezultate je težko povezati v jasno filogenetsko drevo, saj raziskovalci največkrat obravnavajo nekaj lokalnih taksonov, pri čemer uporabljajo različne, bolj ali manj podporne molekulske metode. V preglednem članku izpostavljamo, da je pri reševanju taksonomskih odnosov ključna uporaba ustrezne kombinacije tako morfoloških kot tudi molekulskih markerjev. Ključne besede: Epipactis helleborine s.l., širokolistna močvirnica, taksonomska problematika, speciacija

A cautionary note on the use of haplotype callers in Phylogenomics

Next-generation-sequencing haplotype callers are commonly used in studies to call variants from newly-sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional haplotype callers such as the one from GATK, is that they are optimized for variant calling at the population level, but not at the phylogenetic level. Thus, the consequences for downstream analyses can be substantial. Here, through simulations, we compare the performance between the haplotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show how the haplotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also quantified the level at which the accuracy of heterozygote calls declines with increasing distance to the reference genome. Such decrease is very sharp in GATK, while ATLAS maintains a high accuracy in variant calling, even at moderately-divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies.

TINGKAT FILOGENETIK RHOPALOCERA DI TAMAN WISATA ALAM KERANDANGAN KABUPATEN LOMBOK BARAT

This study aimed to determine the existence of the sub-order species Rhopalocera in Kerandangan Nature Tourism Park (NTP) area and the extent of its phylogenetic level between species found. This type of research was quantitative descriptive research. The sampling location consists of two location points namely the location of the park (the front part of NTP) as station I and the waterfall area of the cave wallet used as station II. Sampling was carried out by estimating the distribution of time ie morning and afternoon with observations for 2 (two) weeks. Sample footage used exploratory survey (roaming) with entrapping method. Data were analyzed descriptively to show a description of the morphology of the species found. Then the similarity level index of soransen was calculated with a limit of 9 species based on the number of species found. The results showed that the types of sub-order Rhopalocera found were Troides helena, Papilio memnom, Graphium sarpedon, Papilio peranthus, Doleschallia bisaltide, Cupha erymanthis, Mycalesis sp., and Jamides alecto. While the closest phylogenetic level falls on Papilio polytes and Papilio peranthus is 100% and species with the farthest kinship level are between species of Papilio polytes and Doleschallia bisaltide with a percentage of phylogenetic is 57,9%.

A new species of the genus Hilethera Uvarov, 1923 (Orthoptera: Acrididae: Oedipodinae) from China and its complete mitochondrial genome

The new species, Hilethera xinjiangensis sp. nov. (Orthoptera: Acrididae: Oedipodinae) is described based on specimens collected from Xinjiang, northern China. The new species is similar to H. brevipennis Zheng & Lu, 2002 and H. turanica Uvarov, 1925, but differs from: (1) dark brown in general coloration, (2) darker coloration in forewings, (3) forewings longer than H. brevipennis but shorter than H. turanica, (4) cubital area of forewings boarder than H. brevipennis and H. turanica, (5) hind tibiae dark brown with two light yellow pre-basal rings, while dark with one fade pre-basal ring in H. brevipennis and light yellow with three dark rings in H. turanica.In addition, the complete mitogenome of holotype was sequenced using next-generation sequencing technology. The total length of the assembled mitogenome is 16,145 bp, representing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one noncoding region (D-loop region). The new mitogenome sequence is compared with published Oedipodinae mitogenomes and the phylogenetic relationships within the subfamily are reconstructed. The results infer that the gene cox1 could be a useful marker for higher phylogenetic level, while the genes nd5 and rrnL could be potentially useful markers between closely related species.

Larval nutritional mode and swimming behaviour in ciliated marine larvae

Swimming propagules (embryos and larvae) are a critical component of the life histories of benthic marine animals. Larvae that feed (planktotrophic) have been assumed to swim faster, disperse farther and have more complex behavioural patterns than non-feeding (lecithotrophic) larvae. However, a number of recent studies challenge these early assumptions, suggesting a need to revisit them more formally. The current review presents a quantitative analysis of swimming speed and body size in planktotrophic and lecithotrophic propagules across five major marine phyla (Porifera, Cnidaria, Annelida, Mollusca and Echinodermata). Results of the comparative study showed that swimming speed differences among ciliated propagules can be driven by taxonomy, adult mobility (motile vs sessile) and/or larval nutritional mode. On a phylogenetic level, distinct patterns emerge across phyla and life stages, whereby planktotrophic propagules swim faster in some of them, and lecithotrophic propagules swim faster in others. Interestingly, adults with sessile and sedentary lifestyles produce propagules that swam faster than the propagules produced by motile adults. Understanding similarities and differences among marine propagules associated with different reproductive strategies and adult lifestyles are significant from ecological, evolutionary and applied perspectives. Patterns of swimming can directly impact the dispersal/recruitment potential with incidence on the design of larval rearing methods and marine protected areas.