Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...) of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

The objective of this paper is twofold. First, I present a framework called historical coherentism (Chang, 2004; Tal, 2016; Van fraassen 2008) and argue that it is the best epistemological framework available to tackle the problem of coordination, an epistemic conundrum that arises with every attempt to provide empirical content to scientific theories, models or statements. Second, I argue that the problem of coordination, which has so far been theorized only in the context of measurement practices (Reichenbach, 1927; Chang, 2001; (...) Tal, 2012; Van fraassen 2008), can be generalized beyond the philosophy of measurement. Specifically, it will be shown that the problem is embodied in classificatory practices and that, consequently, historical coherentism is well suited to analyze these practices as well as metrological ones. As a case study, I look at a contemporary debate in phylogenetics, regarding the evolutionary origin of a newly identified archaeal phylum called Methanonatronarchaeia. Exploring this debate through the lens of historical coherentism provides a detailed understanding of the dynamics of the field and a foothold for critical analyses of the standard rationale used by practitioners. (shrink)

I spell out and update the individuality thesis, that species are individuals, and not classes, sets, or kinds. I offer three complementary presentations of this thesis. First, as a way of resolving an inconsistent triad about natural kinds; second, as a phylogenetic systematics theoretical perspective; and, finally, as a novel recursive account of an evolved character. These approaches do different sorts of work, serving different interests. Presenting them together produces a taxonomy of the debates over the thesis, and isolates ways (...) it has been productive. This goes to the larger point of this paper: a defense of the individuality thesis in terms of its utility, and an update of it in light of recent theoretical developments and empirical work in biology. (shrink)

Both written and graphic accounts of history can be biased by the perspective of the historian. O’Hara (Biol Philos 7:135–160, 1992) has demonstrated that this also applies to evolutionary history and its historians, and identified four narrative devices that introduce anthropocentricisms into accounts of phylogeny. In the current paper, I identify a fifth such narrative device, viz. the left–right ordering of the taxa at the tips of cladograms. I define two measures that make it possible to quantify the degree of (...) anthropocentricism of cladograms, the human attention score and human rightness score. I then carry out an analysis of the presence of the different distorting mechanisms in phylogenetic textbooks. I deliberately chose two textbooks that adopted a cladistic perspective, since their authors can be assumed to be more conscious about the aim of avoiding anthropocentricisms. Three of the narrative devices are thus absent from cladistic works. However, there is a weak tendency that the resolution of cladogram branches is biased in favour of Homo sapiens. Furthermore, the human perspective is clear and highly significant in the positioning of taxa along the left–right axis of cladograms. I discuss the reasons for and implications of these biased presentations. (shrink)

This paper attempts to reconcile the conceptual conflict between typological and population thinking to provide a philosophical foundation for extended evolutionary synthesis. Typological thinking has been considered a pre-Darwinian, essentialist dogma incompatible with population thinking, which is the core notion of Darwinism. More recent philosophical and historical studies suggest that a non-essentialist form of typology has some advantages in the study of evolutionary biology. However, even if we adopt such an epistemological interpretation of typological thinking, there still remains an epistemological (...) and methodological conflict between these two styles of thinking. How can we relate typological thinking with population thinking in pursuit of more integrated or interconnected research into evolutionary biology? I propose that homology thinking, which is another style of thinking that recognizes homologous characters, provides a common basis for typological representations of character states and for character dynamics in an evolving population. Good examples of this bridging role are found in teratology and breeding, where variation and novelty are recognized in developmental and morphological traits, gene expression patterns, and so on. Essentialism-free, dynamic views of homology have great potential to reconcile typological and population thinking and to set the stage for the EES. (shrink)

After clarifying how Darwin understood natural selection and common ancestry, I consider how the two concepts are related in his theory. I argue that common ancestry has an evidential priority. For Darwin, arguments about natural selection often make use of the assumption of common ancestry, whereas defending common ancestry does not require the assumption that natural selection has been at work. In fact, Darwin held that the key evidence for common ancestry comes from characters whose evolution is not caused by (...) natural selection. This raises the question of why Darwin puts natural selection first and foremost in the Origin. (shrink)

Mutation and lateral transfer are two categories of processes generating genetic diversity in prokaryotic genomes. Their relative importance varies between lineages, yet both are complementary rather than independent, separable evolutionary forces. The replication process inevitably merges together their effects on the genome. We develop the concept of “open lineages” to characterize evolutionary lineages that over time accumulate more changes in their genomes by lateral transfer than by mutation. They contrast with “closed lineages,” in which most of the changes are caused (...) by mutation. Open and closed lineages are interspersed along the branches of any tree of prokaryotes. This patchy distribution conflicts with the basic assumptions of traditional phylogenetic approaches. As a result, a tree representation including both open and closed lineages is a misrepresentation. The evolution of all prokaryotic lineages cannot be studied under a single model unless new phylogenetic approaches that are more pluralistic about lineage evolution are designed. (shrink)

A series of recent studies on extant coelacanths has emphasised the slow rate of molecular and morphological evolution in these species. These studies were based on the assumption that a coelacanth is a ‘living fossil’ that has shown little morphological change since the Devonian, and they proposed a causal link between low molecular evolutionary rate and morphological stasis. Here, we have examined the available molecular and morphological data and show that: (i) low intra-specific molecular diversity does not imply low mutation (...) rate, (ii) studies not showing low substitution rates in coelacanth are often neglected, (iii) the morphological stability of coelacanths is not supported by paleontological evidence. We recall that intra-species levels of molecular diversity, inter-species genome divergence rates and morphological divergence rates are under different constraints and they are not necessarily correlated. Finally, we emphasise that concepts such as ‘living fossil’, ‘basal lineage’, or ‘primitive extant species’ do not make sense from a tree-thinking perspective.Editor's suggested further reading in BioEssays Tree thinking for all biology: the problem with reading phylogenies as ladders of progress Abstract. (shrink)

The project of this paper is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial—or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in a trivial way, their interpretation (...) is tied to foundational conceptual questions at the heart of systematics—questions whose answers are hotly disputed. I have previously argued that widely shared ideas about the meaning and interpretation of phylogenetic trees are inconsistent with species concepts other than some genealogical version of a phylogenetic species concept (Velasco 2008). Here I rely on a similar approach and concentrate on the implications of the necessary conditions underlying the inferences that we make using phylogenetic trees. I argue that common practices for the interpretation and use of trees are in conflict and that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. This is true regardless of whether the tips of the trees are themselves populations, or are species or higher taxa. Although this conclusion might be paired naturally with a view that species must be monophyletic groups, this population-centric view of trees is independent of that view of species. If we still want to have species that are paraphyletic groups of populations, this is permissible as long as we also do not treat species as the units of phylogeny. This population-centric view opposes a species-centric view of phylogeny and might be called a “rank-free” approach since it entails that we do not need to determine which groups are species (which is partly a ranking question) in order to build a tree. This conclusion and the argument for it are meant to be consistent with, but not require, acceptance of the conclusions of Velasco (2008) regarding species. (shrink)

Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing makes more and more trees available. However, their utility is compromised by widespread misconceptions about what phylogenies can tell us, and improved tree thinking is crucial. The most-serious problem comes from reading trees as ladders from left to right - many biologists assume that species-poor lineages that appear early branching or basal are ancestral - we call this the primitive lineage fallacy. This mistake causes misleading inferences about changes (...) in individual characteristics and leads to misrepresentation of the evolutionary process. The problem can be rectified by considering that modern phylogenies of present-day species and genes show relationships among evolutionary cousins. Emphasizing that these are extant entities in the 21st century will help correct inferences about ancestral characteristics, and will enable us to leave behind 19th century notions about the ladder of progress driving evolution. (shrink)

Phylogenetic trees are meant to represent the genealogical history of life and apparently derive their justification from the existence of the tree of life and the fact that evolutionary processes are treelike. However, there are a number of problems for these assumptions. Here it is argued that once we understand the important role that phylogenetic trees play as models that contain idealizations, we can accept these criticisms and deny the reality of the tree while justifying the continued use of trees (...) in phylogenetic theory and preserving nearly all of what defenders of trees have called the “importance of tree thinking.”. (shrink)

James Valentine's "On the Origin of Phyla" is divided into three main sections: "Evidence of the Origins of Metazoan Phyla," "The Metazoan Phyla," and "The Evolution of the Phyla." The second section is the zoological core of the book, a more or less conventional treatment of major animal taxa, arranged in chain-of-being fashion from sponges to cnidarians to "worms" of many kinds, and so onward to arthropods, echinoderms, chordates, and all others in between. Philosophically inclined readers will be most interested (...) in the first and third sections of the volume, which treat phylogenetic principles and macroevolution respectively. These sections are rich in detail, but Valentine adopts something of a rear-guard position on many issues, arguing in favor of a number of concepts that most systematists have now abandoned. The publisher's advertisement describes "On the Origin of Phyla" as "one of the classic scientific texts of the twentieth century," and for us in the 21st century, that may be the best way to regard it. It will be of greatest value to zoologists who want a good compendium of current comparative data, and to historians and philosophers of science who have an interest in the complex development of phylogenetic "tree-thinking" in systematic biology. (shrink)