A paradigm shift in our view of species drives current trends in biological classification

Abstract

Discontent about changes in species classifications has grown in recent years. Many of these changes are seen as arbitrary, stemming from unjustified conceptual and methodological grounds, or leading to species that are less distinct than those recognised in the past. We argue that current trends in species classification are the result of a paradigm shift toward which systematics and population genetics have converged and that regards species as the phylogenetic lineages that form the branches of the Tree of Life. Species delimitation now consists of determining which populations belong to which individual phylogenetic lineage. This requires inferences on the process of lineage splitting and divergence, a process to which we have only partial access through incidental evidence and assumptions that are themselves subject to refutation. This approach is not free of problems, as horizontal gene transfer, introgression, hybridisation, incorrect assumptions, sampling and methodological biases can mislead inferences of phylogenetic lineages. Increasing precision is demanded through the identification of both sister relationships and processes blurring or mimicking phylogeny, which has triggered, on the one hand, the development of methods that explicitly address such processes and, on the other hand, an increase in geographical and character data sampling necessary to infer/test such processes. Although our resolving power has increased, our knowledge of sister relationships – what we designate as species resolution – remains poor for many taxa and areas, which biases species limits and perceptions about how divergent species are or ought to be. We attribute to this conceptual shift the demise of trinominal nomenclature we are witnessing with the rise of subspecies to species or their rejection altogether; subspecies are raised to species if they are found to correspond to phylogenetic lineages, while they are rejected as fabricated taxa if they reflect arbitrary partitions of continuous or non‐hereditary variation. Conservation strategies, if based on taxa, should emphasise species and reduce the use of subspecies to avoid preserving arbitrary partitions of continuous variation; local variation is best preserved by focusing on biological processes generating ecosystem resilience and diversity rather than by formally naming diagnosable units of any kind. Since many binomials still designate complexes of species rather than individual species, many species have been discovered but not named, geographical sampling is sparse, gene lineages have been mistaken for species, plenty of species limits remain untested, and many groups and areas lack adequate species resolution, we cannot avoid frequent changes to classifications as we address these problems. Changes will not only affect neglected taxa or areas, but also popular ones and regions where taxonomic research remained dormant for decades and old classifications were taken for granted.

Misinterpretation of Genomic Data Matters for Endangered Species Listing: The Sub-specific Status of the Peñasco Least Chipmunk (Neotamias minimus atristriatus)

“…Given the lack of phylogenetic resolution recovered from exon capture data, Puckett et al (2021) may have benefited by reporting additional analyses with their data, or minimally by discussing shortcomings, leaving the door open for further future analyses that might more accurately test hypotheses of uniqueness for N. m. atristriatus (Padial and De la Riva, 2021). For instance, exon data are known to evolve more slowly than intron data and other genomic elements including microsatellites, and may not be most suitable for resolving the tips of the tree of life (Bi et al, 2012).…”

Conceptual issues in hominin taxonomy: Homo heidelbergensis and an ethnobiological reframing of species

“…Whether or not Hennig intended for these cladograms to be seen as phylogenetic trees, inevitably they were. The depiction of species as end points on branches has had a powerful impact on how we perceive them (Padial & De la Riva, 2021; Tassy, 2011). Other illustrated classification schemes throughout the history of taxonomy such as ladders, nested tables, networks, and trellises that do not center species as unique end‐products have been relatively uncommon in the past 50 years.…”

Revision and annotation of DNA barcode records for marine invertebrates: report of the 8thiBOL conference hackathon

“…First, there are discordances that are due to real biological complexities. Some of these are merely a reflection of the inherent uncertainties and dynamics of alpha taxonomy (e.g., De La Riva 2006, Padial andDe la Riva 2020). Others originate from a mismatch between morphological and molecular diagnosis of species boundaries, that is, species that, for intrinsic reasons, can be diagnosed morphologically but not through short DNA sequences, or reciprocally.…”

“…The experience level of the identifier may play a role in such errors, but often taxonomic keys, drawings and descriptions are incomplete or have poor quality, contributing to misidentifications. This may happen for some species that are frequently, but wrongly, recorded across the globe as cosmopolitan species for the simple reason that the original description is vague enough to accommodate various other species that remain undetected (Gómez et al 2007, Padial andDe la Riva 2020). Taxonomic variants such as synonyms and alternate representation designating the same taxon, are an additional source of mismatches (e.g., Magallana gigas and its alternate representation, but widely used name, Crassostrea gigas, Salvi et al 2014, Bayne et al 2017, Backeljau 2018.…”