An advanced sequence clustering and designation workflow reveals the enzootic maintenance of a dominant West Nile virus subclade in Germany

West Nile virus (WNV) is the most widespread arthropod-borne (arbo) virus and the primary cause of arboviral encephalitis globally. Members of WNV species genetically diverged and are classified into different hierarchical groups below species rank. However, the demarcation criteria for allocating WNV sequences into these groups remain individual and inconsistent, and the use of names for different levels of the hierarchical levels is unstructured. In order to have an objective and comprehensible grouping of WNV sequences, we developed an advanced grouping workflow using the 'affinity propagation clustering' algorithm and newly included the 'agglomerative hierarchical clustering' algorithm for the allocation of WNV sequences into different groups below species rank. In addition, we propose to use a fixed set of terms for the hierarchical naming of WNV below species level and a clear decimal numbering system to label the determined groups. For validation, we applied the refined workflow to WNV sequences that have been previously grouped into various lineages, clades, and clusters in other studies. Although our workflow regrouped some WNV sequences, overall, it generally corresponds with previous groupings. We employed our novel approach to the sequences from the WNV circulation in Germany 2020, primarily from WNV-infected birds and horses. Besides two newly defined minor (sub)clusters comprising only three sequences each, Subcluster 2.5.3.4.3c was the predominant WNV sequence group detected in Germany from 2018 to 2020. This predominant subcluster was also associated with at least five human WNV infections in 2019-20. In summary, our analyses imply that the genetic diversity of the WNV population in Germany is shaped by enzootic maintenance of the dominant WNV subcluster accompanied by sporadic incursions of other rare clusters and subclusters. Moreover, we show that our refined approach for sequence grouping yields meaningful results. Although we primarily aimed at a more detailed WNV classification, the presented workflow can also be applied to the objective genotyping of other virus species.

A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx)

To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data records is the associated taxon concept. Unlike Linnaean taxon names, the traditional way in which taxon concepts are provided, phylogenetic definitions are native to phylogenetic trees and offer well-defined semantics that can be transformed into formal, computationally evaluable logic expressions. These attributes make them highly suitable for phylogeny-driven comparative biology by allowing computationally verifiable and reproducible integration of taxon-linked data against Tree of Life-scale phylogenies. To achieve this, the first step is transforming phylogenetic definitions from the natural language text in which they are published to a structured interoperable data format that maintains strong ties to semantics and lends itself well to sharing, reuse, and long-term archival. To this end, we developed the Phyloreference Exchange Format (Phyx), a JSON-LD-based text format encompassing rich metadata for all elements of a phylogenetic definition, and we created a supporting software library, phyx.js, to streamline computational management of such files. Together they form a foundation layer for digitizing and computing with phylogenetic definitions of clades.

Naming diversity in an evolutionary context: Phylogenetic definitions of the Roucela clade (Campanulaceae/Campanuloideae) and the cryptic taxa within

In recent times, evolution has become a central tenet of taxonomy, but nomenclature has consistently been decoupled from the tree-thinking process, often leading to significant issues in reconciling traditional (Linnaean) names with clades in the Tree of Life. Recent evolutionary studies on the Roucela clade, a group of endemic plants found in the Mediterranean Basin, motivated the establishment of phylogenetic concepts to formally anchor clade names on the Campanuloideae (Campanulaceae) tree. These concepts facilitate communication of clades that approximate traditionally defined groups, in addition to naming newly discovered cryptic diversity in a phylogenetic framework.

Population and phylogenomic decomposition via genotyping-by-sequencing in Australian Pelargonium

Species delimitation has seen a paradigm shift as increasing accessibility of genomic-scale data enables separation of lineages with convergent morphological traits and the merging of recently diverged ecotypes that have distinguishing characteristics. We inferred the process of lineage formation among Australian species in the widespread and highly variable genus Pelargonium by combining phylogenomic and population genomic analyses along with breeding system studies and character analysis. Phylogenomic analysis and population genetic clustering supported seven of the eight currently described species but provided little evidence for differences in genetic structure within the most widely distributed group that containing P. australe. In contrast, morphometric analysis detected three deep lineages within Australian Pelargonium; with P. australe consisting of five previously unrecognized entities occupying separate geographic ranges. The genomic approach enabled elucidation of parallel evolution in some traits formerly used to delineate species, as well as identification of ecotypic morphological differentiation within recognized species. Highly variable morphology and trait convergence each contribute to the discordance between phylogenomic relationships and morphological taxonomy. Data suggest that genetic divergence among species within the Australian Pelargonium may result from allopatric speciation while morphological differentiation within and among species may be more strongly driven by environmental differences.

Impacts of phylogenetic nomenclature on the efficacy of the U.S. Endangered Species Act

Cataloging biodiversity is critical to conservation efforts because accurate taxonomy is often a precondition for protection under laws designed for species conservation, such as the U.S. Endangered Species Act (ESA). Traditional nomenclatural codes governing the taxonomic process have recently come under scrutiny because taxon names are more closely linked to hierarchical ranks than to the taxa themselves. A new approach to naming biological groups, called phylogenetic nomenclature (PN), explicitly names taxa by defining their names in terms of ancestry and descent. PN has the potential to increase nomenclatural stability and decrease confusion induced by the rank-based codes. But proponents of PN have struggled with whether species and infraspecific taxa should be governed by the same rules as other taxa or should have special rules. Some proponents advocate the wholesale abandonment of rank labels (including species); this could have consequences for the implementation of taxon-based conservation legislation. I examined the principles of PN as embodied in the PhyloCode (an alternative to traditional rank-based nomenclature that names biological groups based on the results of phylogenetic analyses and does not associate taxa with ranks) and assessed how this novel approach to naming taxa might affect the implementation of species-based legislation by providing a case study of the ESA. The latest version of the PhyloCode relies on the traditional rank-based codes to name species and infraspecific taxa; thus, little will change regarding the main targets of the ESA because they will retain rank labels. For this reason, and because knowledge of evolutionary relationships is of greater importance than nomenclatural procedures for initial protection of endangered taxa under the ESA, I conclude that PN under the PhyloCode will have little impact on implementation of the ESA.