Abstract:Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Currently, most phylogenies of extant taxa are inferred from molecules and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has rarely been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographic distributions and fossil first occurrences. For 48 pairs of … Show more
“…Poor molecular sampling usually produces non-monophyletic trees, or discordance with phylogenies based on morphology [ 10 ]. In addition, the biogeographical data may support the establishment of taxonomic limits between species [ 10 ], and actually they have been identified as providing better auxiliary information than morphology to elucidate phylogenetic relationships [ 11 ].…”
Mexico harbors ~45% of world’s cacti species richness. Their biogeography and phylogenomics were integrated to elucidate the evolutionary history of the genera Coryphantha, Escobaria, Mammillaria, Mammilloydia, Neolloydia, Ortegocactus, and Pelecyphora (Mammilloid Clade). We analyzed 52 orthologous loci from 142 complete genomes of chloroplast (103 taxa) to generate a cladogram and a chronogram; in the latter, the ancestral distribution was reconstructed with the Dispersal-Extinction-Cladogenesis model. The ancestor of these genera arose ~7 Mya on the Mexican Plateau, from which nine evolutionary lineages evolved. This region was the site of 52% of all the biogeographical processes. The lineages 2, 3 and 6 were responsible for the colonization of the arid southern territories. In the last 4 Mya, the Baja California Peninsula has been a region of prolific evolution, particularly for lineages 8 and 9. Dispersal was the most frequent process and vicariance had relevance in the isolation of cacti distributed in the south of Mexico. The 70 taxa sampled as Mammillaria were distributed in six distinct lineages; one of these presumably corresponded to this genus, which likely had its center of origin in the southern part of the Mexican Plateau. We recommend detailed studies to further determine the taxonomic circumscription of the seven genera.
“…Poor molecular sampling usually produces non-monophyletic trees, or discordance with phylogenies based on morphology [ 10 ]. In addition, the biogeographical data may support the establishment of taxonomic limits between species [ 10 ], and actually they have been identified as providing better auxiliary information than morphology to elucidate phylogenetic relationships [ 11 ].…”
Mexico harbors ~45% of world’s cacti species richness. Their biogeography and phylogenomics were integrated to elucidate the evolutionary history of the genera Coryphantha, Escobaria, Mammillaria, Mammilloydia, Neolloydia, Ortegocactus, and Pelecyphora (Mammilloid Clade). We analyzed 52 orthologous loci from 142 complete genomes of chloroplast (103 taxa) to generate a cladogram and a chronogram; in the latter, the ancestral distribution was reconstructed with the Dispersal-Extinction-Cladogenesis model. The ancestor of these genera arose ~7 Mya on the Mexican Plateau, from which nine evolutionary lineages evolved. This region was the site of 52% of all the biogeographical processes. The lineages 2, 3 and 6 were responsible for the colonization of the arid southern territories. In the last 4 Mya, the Baja California Peninsula has been a region of prolific evolution, particularly for lineages 8 and 9. Dispersal was the most frequent process and vicariance had relevance in the isolation of cacti distributed in the south of Mexico. The 70 taxa sampled as Mammillaria were distributed in six distinct lineages; one of these presumably corresponded to this genus, which likely had its center of origin in the southern part of the Mexican Plateau. We recommend detailed studies to further determine the taxonomic circumscription of the seven genera.
“…This implies significant character sampling artefacts for morphology that are less marked for molecules. Morphological characters are necessarily subjective (Neumann et al, 2021; Oyston et al, 2022), since as taxonomic level decreases, more characters tend to be included in order to distinguish between closely related species.…”
Indices of morphological disparity seek to summarise the highly multivariate morphological variation across groups of species within clades, time bins or other groups. Morphological variation can be quantified using geometric morphometric, outline or surface‐based methods. These are most effective when morphological differences are relatively modest and there are numerous ubiquitous landmarks and phase aligned features of shape variation. The most disparate samples, such as those across classes and phyla, typically necessitate the use of discrete characters. Unfortunately, such characters are often compiled subjectively in a manner reflecting the level of morphological and taxonomic focus and the intensity of taxon sampling.
Sampling intensity is often highly variable within a single data set, especially in repurposed and amalgamated cladistic matrices. Here, we propose indices of molecular disparity analogous to those of morphological disparity. Despite numerous shortcomings discussed here, molecular sequence data can be obtained in a more objective, automated and scalable manner than morphological data.
Comparisons of the morphological and molecular disparity of subclades in 16 large data sets suggest that molecular disparity is less susceptible to sampling biases than morphological disparity. Moreover, distance matrices inferred from individual genes tend to correlate strongly with each other and with distances from all concatenated genes. By contrast, morphological and molecular disparity are typically not significantly correlated across subclades, such that comparisons for groups can help to give a fuller picture of their evolution. For example, within mammals, Afrotheria have conspicuously high morphological disparity but modest molecular disparity, suggesting unusually high morphological plasticity. Even more strikingly, the molecular disparity of rodents is over five times that for Artiodactyla, despite having only half of their morphological disparity. These contrasts suggest the differential operation of geometric, biomechanical, ontogenetic and environmental constraints on form.
Given the increasing abundance of total evidence datasets in the literature and the widespread and sometimes uncritical repurposing of discrete morphological matrices, we propose the comparison of morphological and molecular disparity as a useful tool to understand subclade evolution more fully.
“…From a temporal point of view, we would give special attention for detected convergence and their historical scenarios: these species would represent proper new models for adaptative conditions on Scyphozoa (i.e. to be combined with developmental biology, ecology and genomics) 48 , 49 . Figure 5 Examples of velocities profiles used in the description of swimming kinematic analysis.…”
Ephyrae, the early stages of scyphozoan jellyfish, possess a conserved morphology among species. However, ontogenetic transitions lead to morphologically different shapes among scyphozoan lineages, with important consequences for swimming biomechanics, bioenergetics and ecology. We used high-speed imaging to analyse biomechanical and kinematic variables of swimming in 17 species of Scyphozoa (1 Coronatae, 8 “Semaeostomeae” and 8 Rhizostomeae) at different developmental stages. Swimming kinematics of early ephyrae were similar, in general, but differences related to major lineages emerged through development. Rhizostomeae medusae have more prolate bells, shorter pulse cycles and higher swimming performances. Medusae of “Semaeostomeae”, in turn, have more variable bell shapes and most species had lower swimming performances. Despite these differences, both groups travelled the same distance per pulse suggesting that each pulse is hydrodynamically similar. Therefore, higher swimming velocities are achieved in species with higher pulsation frequencies. Our results suggest that medusae of Rhizostomeae and “Semaeostomeae” have evolved bell kinematics with different optimized traits, rhizostomes optimize rapid fluid processing, through faster pulsations, while “semaeostomes” optimize swimming efficiency, through longer interpulse intervals that enhance mechanisms of passive energy recapture.
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