Lineages, splits and divergence challenge whether the terms anagenesis and cladogenesis are necessary

Rapid clade divergence and phyletic gradualism in an interacting particle model of sympatric speciation

The coexistence of cladogenesis, i.e., the branching of lineages along an evolutionary tree as observed in the fossil record, and anagenesis, which is the progressive evolution within populations, lacks a clear explanation. In this study, we examine a simple model that simulates the evolutionary changes occurring within populations inhabiting the same environment in sympatry, and driven by ecological competition. Our model characterizes populations through a set of evolving morphological traits represented by mathematical points within a two-dimensional morphospace. Such points may reproduce or die due to overcrowding, implying competition in morphospace as suggested by the ecological phenomenon of character displacement. By focusing on the morphospace rather than physical space, the model effectively captures the simultaneous evolution of coexisting populations. Central to the model is the delicate balance between the range of competition and the range of reproduction within the morphospace. Interesting patterns emerge when the ratio between the competition to reproducetion ranges, referred to as CR ratio, changes from values slightly smaller to significantly larger than unity. When competition acts over short distances relative to the reproduction range (low CR), the phylogenetic tree takes on a nearly uniform appearance, gradually transforming into a more bush-like structure for slightly higher CR values. With further increases in CR, evolutionary lineages become more discernible, and the morphogenetic pattern shifts from a bush-like shape to a more tree-like arrangement and few branches for very large CRs. At specific time sections, the synthetic phylogenetic tree appears as an assembly of clusters of individuals within the morphospace. These clusters, interpretable as simulated models of species, exhibit distinct separation within the morphospace and are subject to dynamic inter-cluster repulsion. Notably, clusters tend to be resistant to change. They maintain relatively constant abundances while gradually shifting their positions within the morphospace-a phase that aligns with the concept of phyletic gradualism. However, this predictable pattern is occasionally upset by the abrupt divisions into multiple groups, interpreted as cladogenesis events. The intricacies of the splitting process are explored, revealing that in scenarios with large CR values, the splitting can emerge much more rapidly than phyletic changes. This accelerated process of splitting is initiated by one or few individuals at the fringes of a cluster, where competition is minimal. The newly generated cluster then undergoes deformation, swiftly followed by divergence and splitting (seen as branching in the synthetic phylogenetic tree), as if an inherent "repulsion" triggered the division between species. The simple rules implied in the interacting-particle model may provide insight into the coexistence of gradualism and cladogenesis along lineages, illustrating the capacity for rapid shifts during cladogenesis and the more gradual process of anagenesis.

Cell types as species: Exploring a metaphor

The concept of "cell type," though fundamental to cell biology, is controversial. Cells have historically been classified into types based on morphology, physiology, or location. More recently, single cell transcriptomic studies have revealed fine-scale differences among cells with similar gross phenotypes. Transcriptomic snapshots of cells at various stages of differentiation, and of cells under different physiological conditions, have shown that in many cases variation is more continuous than discrete, raising questions about the relationship between cell type and cell state. Some researchers have rejected the notion of fixed types altogether. Throughout the history of discussions on cell type, cell biologists have compared the problem of defining cell type with the interminable and often contentious debate over the definition of arguably the most important concept in systematics and evolutionary biology, "species." In the last decades, systematics, like cell biology, has been transformed by the increasing availability of molecular data, and the fine-grained resolution of genetic relationships have generated new ideas about how that variation should be classified. There are numerous parallels between the two fields that make exploration of the "cell types as species" metaphor timely. These parallels begin with philosophy, with discussion of both cell types and species as being either individuals, groups, or something in between (e.g., homeostatic property clusters). In each field there are various different types of lineages that form trees or networks that can (and in some cases do) provide criteria for grouping. Developing and refining models for evolutionary divergence of species and for cell type differentiation are parallel goals of the two fields. The goal of this essay is to highlight such parallels with the hope of inspiring biologists in both fields to look for new solutions to similar problems outside of their own field.

Lineage Identification Affects Estimates of Evolutionary Mode in Marine Snails

In order to study evolutionary pattern and process, we need to be able to accurately identify species and the evolutionary lineages from which they are derived. Determining the concordance between genetic and morphological variation of living populations, and then directly comparing extant and fossil morphological data, provides a robust approach for improving our identification of lineages through time. We investigate genetic and shell morphological variation in extant species of Penion marine snails from New Zealand, and extend this analysis into deep time using fossils. We find that genetic and morphological variation identify similar patterns and support most currently recognized extant species. However, some taxonomic over-splitting is detected due to shell size being a poor trait for species delimitation, and we identify incorrect assignment of some fossil specimens. We infer that a single evolutionary lineage (Penion sulcatus) has existed for 22 myr, with most aspects of shell shape and shell size evolving under a random walk. However, by removing samples previously classified as the extinct species P. marwicki, we instead detect morphological stasis for one axis of shell shape variation. This result demonstrates how lineage identification can change our perception of evolutionary pattern and process. [Genotyping by sequencing; geometric morphometrics; morphological evolution; Neogastropoda; phenotype; speciation; stasis.].

A molecular assessment of species diversity in Tympanopleura and Ageneiosus catfishes (Auchenipteridae: Siluriformes)

In order to test the congruence of genetic data to the morphologically defined Neotropical catfish genera Tympanopleura and Ageneiosus and explore species diversity, we generated 17 DNA barcodes from five of six species of Tympanopleura and 12 of 13 species of Ageneiosus. To discriminate limits between species, an automatic barcode gap discovery (ABGD), a generalised mixed yule-coalescent model (GYMC) and fixed distance thresholds Kimura two-parameter (K2P; 3%) were used to discriminate putative species limits from the DNA barcodes. The ABGD, GMYC and K2P methods agreed by each generating 13 clusters: six in Tympanopleura (five nominal plus one undescribed species) and seven in Ageneiosus. These clusters corresponded broadly to the described species, except in the case of the Ageneiosus ucayalensis group (A. akamai, A. dentatus, A. intrusus, A. ucayalensis, A. uranophthalmus and A. vittatus). Haplotype sharing and low divergences may have prevented molecular methods from distinguishing these species. We hypothesise that this is the result of a recent radiation of a sympatric species group distributed throughout the Amazon Basin. One putative new species of Tympanopleura was also supported by the molecular data. These results taken together highlight the utility of molecular methods such as DNA barcoding in understanding patterns of diversification across large geographic areas and in recognising overlooked diversity.

Off-target capture data, endosymbiont genes and morphology reveal a relict lineage that is sister to all other singing cicadas

Phylogenetic asymmetry is common throughout the tree of life and results from contrasting patterns of speciation and extinction in the paired descendant lineages of ancestral nodes. On the depauperate side of a node, we find extant ‘relict’ taxa that sit atop long, unbranched lineages. Here, we show that a tiny, pale green, inconspicuous and poorly known cicada in the genus Derotettix, endemic to degraded salt-plain habitats in arid regions of central Argentina, is a relict lineage that is sister to all other modern cicadas. Nuclear and mitochondrial phylogenies of cicadas inferred from probe-based genomic hybrid capture data of both target and non-target loci and a morphological cladogram support this hypothesis. We strengthen this conclusion with genomic data from one of the cicada nutritional bacterial endosymbionts, Sulcia, an ancient and obligate endosymbiont of the larger plant-sucking bugs (Auchenorrhyncha) and an important source of maternally inherited phylogenetic data. We establish Derotettiginae subfam. nov. as a new, monogeneric, fifth cicada subfamily, and compile existing and new data on the distribution, ecology and diet of Derotettix. Our consideration of the palaeoenvironmental literature and host-plant phylogenetics allows us to predict what might have led to the relict status of Derotettix over 100 Myr of habitat change in South America.

Evolutionary lineages of marine snails identified using molecular phylogenetics and geometric morphometric analysis of shells

The relationship between morphology and inheritance is of perennial interest in evolutionary biology and palaeontology. Using three marine snail genera Penion, Antarctoneptunea and Kelletia, we investigate whether systematics based on shell morphology accurately reflect evolutionary lineages indicated by molecular phylogenetics. Members of these gastropod genera have been a taxonomic challenge due to substantial variation in shell morphology, conservative radular and soft tissue morphology, few known ecological differences, and geographical overlap between numerous species. Sampling all sixteen putative taxa identified across the three genera, we infer mitochondrial and nuclear ribosomal DNA phylogenetic relationships within the group, and compare this to variation in adult shell shape and size. Results of phylogenetic analysis indicate that each genus is monophyletic, although the status of some phylogenetically derived and likely more recently evolved taxa within Penion is uncertain. The recently described species P. lineatus is supported by genetic evidence. Morphology, captured using geometric morphometric analysis, distinguishes the genera and matches the molecular phylogeny, although using the same dataset, species and phylogenetic subclades are not identified with high accuracy. Overall, despite abundant variation, we find that shell morphology accurately reflects genus-level classification and the corresponding deep phylogenetic splits identified in this group of marine snails.

Anagenesis, Cladogenesis, and Speciation on Islands

Anagenesis and cladogenesis are fundamental evolutionary concepts, but are increasingly being adopted as speciation models in the field of island biogeography. Here, we review the origin of the terms 'anagenetic' and 'cladogenetic' speciation, critique their utility, and finally suggest alternative terminology that better describes the geographical relationships of insular sister species.

Peripatric speciation in an endemic Macaronesian plant after recent divergence from a widespread relative

The Macaronesian Scrophularia lowei is hypothesized to have arisen from the widespread S. arguta on the basis of several phylogenetic studies of the genus, but sampling has been limited. Although these two annual species are morphologically distinct, the origin of S. lowei is unclear because genetic studies focused on this Macaronesian species are lacking. We studied 5 S. lowei and 25 S. arguta populations to determine the relationship of both species and to infer the geographical origin of S. lowei. The timing of S. lowei divergence and differentiation was inferred by dating analysis of the ITS region. A phylogenetic analysis of two nuclear (ITS and ETS) and two chloroplast (psbJ–petA and psbA–trnH) DNA regions was performed to study the relationship between the two species, and genetic differentiation was analysed by AMOVA. Haplotype network construction and Bayesian phylogeographic analysis were conducted using chloroplast DNA regions and a spatial clustering analysis was carried out on a combined dataset of all studied regions. Our results indicate that both species constitute a well-supported clade that diverged in the Miocene and differentiated in the Late Miocene-Pleistocene. Although S. lowei constitutes a well-supported clade according to nDNA, cpDNA revealed a close relationship between S. lowei and western Canarian S. arguta, a finding supported by the spatial clustering analysis. Both species have strong population structure, with most genetic variability explained by inter-population differences. Our study therefore supports a recent peripatric speciation of S. lowei—a taxon that differs morphologically and genetically at the nDNA level from its closest relative, S. arguta, but not according to cpDNA, from the closest Macaronesian populations of that species. In addition, a recent dispersal of S. arguta to Madeira from Canary Islands or Selvagens Islands and a rapid morphological differentiation after the colonization to generate S. lowei is the most likely hypothesis to explain the origin of the last taxon.

A new tyrannosaur with evidence for anagenesis and crocodile-like facial sensory system

A new species of tyrannosaurid from the upper Two Medicine Formation of Montana supports the presence of a Laramidian anagenetic (ancestor-descendant) lineage of Late Cretaceous tyrannosaurids. In concert with other anagenetic lineages of dinosaurs from the same time and place, this suggests that anagenesis could have been a widespread mechanism generating species diversity amongst dinosaurs, and perhaps beyond. We studied the excellent fossil record of the tyrannosaurid to test that hypothesis. Phylogenetic analysis places this new taxon as the sister species to Daspletosaurus torosus. However, given their close phylogenetic relationship, geographic proximity, and temporal succession, where D. torosus (~76.7-75.2 Ma) precedes the younger new species (~75.1-74.4 Ma), we argue that the two forms most likely represent a single anagenetic lineage. Daspletosaurus was an important apex predator in the late Campanian dinosaur faunas of Laramidia; its absence from later units indicates it was extinct before Tyrannosaurus rex dispersed into Laramidia from Asia. In addition to its evolutionary implications, the texture of the facial bones of the new taxon, and other derived tyrannosauroids, indicates a scaly integument with high tactile sensitivity. Most significantly, the lower jaw shows evidence for neurovasculature that is also seen in birds.