“Species are composed of genetic material with a common historical ancestry,” said Bengt Oxelman of the Department of Biological and Environmental Sciences at the University of Gothenburg. “For phylogenetics to contribute to evolutionary theory it should focus on the genes.”
Oxelman is looking at a somewhat controversial topic which he described as having interested him since he started studying biology. “My friend who was then completing his Masters project told me that species are what a competent taxonomist says they are. I thought this was horrendous at the time, but he was right.”
“All biology is in some way related to the concept of biological taxa, which are hierarchically structured categories such as species, genus, family, or order. Biological taxonomy has during the past 50 to 60 years experienced conceptual and methodological developments, paralleled with an enormous increase in information availability,” he explained. “The concept of monophyly has provided taxonomists with a rigorous model framework where taxon hypotheses can be tested. However, while this phylogenetic tree model is widely applied to the higher categorical ranks, its application to the species rank is sometimes considered controversial.”
So controversial, that Oxelman described the topic as causing big tensions at conferences without, thus far, reaching consensus. “They will probably do sociological studies on the arguments,” he laughed.
“Our own species, Homo sapiens, is paradigmatic, but the exact spatiotemporal origin of it is hypothetical, and will remain so because of the gradual and historical nature of evolution. Most of the other 1 827 304 species listed in the 2023 version of the Catalogue of Life are also hypothetical and as there is no universal definition of what the species category represents, the nature of the specific hypotheses varies widely.”
Oxelman described how species are still described – “a taxonomist goes into the field, finds an organism that doesn’t fit any descriptions and describes it as a new species. But what does it mean that species share the same fundamentals or share category specialisation properties? Does it just make it possible to recognise them?”
Taxonomy – the practice and science of categorisation – is derived from the Greek taxis meaning arrangement and nomos, meaning law. However, the Latin word nomen means name, and therefore better conforms to the usage in biology. “Biological taxonomy is essentially about identifying, describing, ordering and naming,” said Oxelman.
Aristotle arranged species along a ladder of life with humans and ultimately Gods at the highest end. “To Aristotle, species were not confined to the living only but to anything that through development realises its essence.”
It was the Swedish biologist and physician Carl Linnaeus who formalised binomial nomenclature and is regarded as the father of modern taxonomy – “God created, Linnaeus ordered,” said Oxelman. “But he didn’t view the species as fixed but as something that could evolve and change.”
Darwin had a pragmatic and liberal view of species as groups of organisms with close resemblance. “But, after Darwin, “evolutionary theory met genetics and species became central,” said Oxelman. He noted that despite massive advances since then, Darwin’s ideas on the mechanisms of evolution remain important. “It’s amazing to read On the Origin of Species today and see how much is still valid,” he said. “I still recommend it to my students to read as a general introduction to natural selection.”
Notable work in the twentieth century highlighted by Oxelman, included that of German American evolutionary biologist and renowned taxonomist Ernst Mayr who described species as sets of interbreeding, reproductively isolated organisms and Willi Hennig, a German biologist and zoologist who is considered the founder of phylogenetic systematics (or cladistics) and developed sophisticated methods to identify monophyletic groups.
But despite these contributions, Oxelman noted that the species category definition remains controversial despite its importance in biology and its vital role in understanding biodiversity. “Species numbers are used to quantify biodiversity,” he said. “For example it’s estimated that 99.5% of viruses remain unknown. However, if there is no way to unequivocally define the species category, figures like this will, at best, be considered as very crude estimates of diversity.” He also pointed out that quantitative methods to test species status are in their infancy with the main issue being the difference between assigning individual organisms into species, versus assigning alleles (sequences of nucleotides on DNA molecules that determine individual characteristics or phenotypes).
The tree of life
Oxelman’s STIAS project therefore focuses on a recently developed multi-species coalescent model that defines species as the branches of the phylogenetic tree. In this model species have a unique ontological status different from clades (groups of species with a common ancestry). “The model makes several important assumptions including random reproduction, instantaneous split events and no generation overlaps” he explained.
The aim is to delimitate species from genetic data and Oxelman hopes to develop an approach that accounts for hybridisation and spatial scales.
“Evolution occurs in genes,” he said. “Phylogenetics is about the history of genes and gene assemblies. A fundamental property of phylogenetic taxonomy is to discover things that exist. And we have the most information from genes.”
“By viewing the genotypes (replicators) as sets of genes connected by (often sexual) reproduction, a tree model where the species constitute the branches of the phylogenetic tree, and thus being ontologically different from higher taxa, is possible. In currently available probabilistic implementations of this model, empirically recognised species are usually very different from the species that are labelled by Linnean binomials, and more in line with what biologists call local populations.”
“Therefore,” he added, “species are best viewed as a category among others in the taxonomic hierarchy, where the grouping criterion is monophyly and ranking is based on convenient criteria such as, for example, sexual compatibility. This means that in a global context, species numbers have little meaning as measures of biodiversity, but at a local, spatiotemporally restricted scale, they can have.”
“There is nothing wrong in classifying things,” he added. “But different criteria are being used in different cases. To be useful in scientific/evolutionary theories you need something that conforms to the reality, as we model it. The concept should be applied to sets of genes, not sets of organisms. Taxonomy should reflect the tree of life where shared development and characteristics reflect common ancestry.”
Michelle Galloway: Part-time media officer at STIAS
Photograph: Ignus Dreyer