Phylogenetic signal in characters from Aristotle’s History of Animals

The influential Greek philosopher Aristotle (384-322 BCE) is almost unanimously acclaimed as the founder of zoology. There is a consensus that he was interested in attributes of animals, but whether or not he tried to develop a zoological taxonomy remains controversial. Fürst von Lieven and Humar compiled a data matrix from Aristotle’s Historia animalium and showed, through a parsimony analysis published in 2008, that these data produced a hierarchy that matched several taxa recognized by Aristotle. However, their analysis leaves some questions unanswered because random data can sometimes yield fairly resolved trees. In this study, we update the scores of many cells and add four new characters to the data matrix (147 taxa scored for 161 characters) and quote passages from Aristotle’s Historia animalium to justify these changes. We confirm the presence of a phylogenetic signal in these data through a test using skewness in length distribution of a million random trees, which shows that many of the characters discussed by Aristotle were systematically relevant. Our parsimony analyses on the updated matrix recover far more trees than reported by Fürst von Lieven and Humar, but their consensus includes many taxa that Aristotle recognized and apparently named for the first time, such as selachē (selachians) and dithyra (Bivalvia Linnaeus, 1758). This study suggests that even though taxonomy was obviously not Aristotle’s chief interest in Historia animalium, it was probably among his secondary interests. These results may pave the way for further taxonomic studies in Aristotle’s zoological writings in general. Despite being almost peripheral to Aristotle’s writings, his taxonomic contributions are clearly major achievements.

Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumanniicomplex

Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes isolated from their functional contexts. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and micro-synteny conservation analyses. This allowed to delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with, or are found preferentially in, the pathogenic ACB clade. They unveil, at an unprecedented resolution, the genetic makeup that coincides with the manifestation of the pathogenic phenotype in the last common ancestor of the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. Specifically, we could show that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. They disclose promising routes for future therapeutic strategies.

Diversity of cave Phlebotomines (Diptera: Psychodidae) from a Colombian cave

Sandflies are vector species of Leishmania, among many other pathogens, with a global distribution and a variety of ecological niches. Previous samplings have found that karstic formations (i.e., caves and folds formed by the erosion of limestone) serve as a natural habitat to sandfly species. The majority of samplings of cave sandfly diversity have occurred in Brazil and to date none have studied the species composition in a cave in the Northern Andes. We collected sandflies in the Cave-Los Guacharos-, in the state of Antioquia, Colombia. The sampling was carried out during two consecutive nights in September 2019. CDC-type light traps were installed inside the cavern and in other surrounding karst systems (caves and folds). In total, we identified 18 species of sandfly from the cave and surrounding karst systems, including three new records for Colombia (Bichromomyia olmeca nociva, Brumptomyia brumpti, and Warileya leponti), and provide the first karstic reports for four other species (Lutzomyia gomezi, Lutzomyia hartmanni, Pintomyia ovallesi, and Psychodopygus panamensis). We then used the results of our survey and published literature to test two hypotheses. First, that sandfly diversity in Neotropical caves is richest nearer to the equator and second that there is a phylogenetic signal of karstic habitat use in sandflies. Counter to our predictions, we found no evidence that diversity follows a latitudinal gradient. Further, we find no evidence of a phylogenetic signal of karstic habitat use, instead finding that the use of caves likely evolved multiple times across several genera. Our results highlight the importance of a wide sampling to understand the natural habitat of sandflies and other disease vectors.

Mitogenomes of Nine Asian Skipper Genera and Their Phylogenetic Position (Lepidoptera: Hesperiidae: Pyrginae)

In this study, complete mitochondrial genomes of nine species representing three tribes in the subfamily Pyrginae sensu lato were newly sequenced. The mitogenomes are closed double-stranded circular molecules, with the length ranging from 15,232 bp to 15,559 bp, which all encode 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region. The orientation and gene order of these nine mitogenomes are identical to the inferred ancestral arrangement of insects. All PCGs exhibit the typical start codon ATN except for cox1 (using CGA) and cox2 (using TTG) in Mooreana trichoneura. Most of the PCGs terminate with a TAA stop codon, while cox1, cox2, nad4, and nad5 end with the incomplete codon single T. For the different datasets, we found that the one comprising all 37 genes of the mitogenome produced the highest nodal support, indicating that the inclusion of RNAs improves the phylogenetic signal. This study re-confirmed the status of Capila, Pseudocoladenia, and Sarangesa; namely, Capila belongs to the tribe Tagiadini, and Pseudocoladenia and Sarangesa to the tribe Celaenorrhini. Diagnostic characters distinguishing the two tribes, the length of the forewing cell and labial palpi, are no longer significant. Two populations of Pseudocoladenia dan fabia from China and Myanmar and P. dan dhyana from Thailand are confirmed as conspecific.

A divide-and-conquer phylogenomic approach based on character supermatrices resolves early steps in the evolution of the Archaea

Background The recent rise in cultivation-independent genome sequencing has provided key material to explore uncharted branches of the Tree of Life. This has been particularly spectacular concerning the Archaea, projecting them at the center stage as prominently relevant to understand early stages in evolution and the emergence of fundamental metabolisms as well as the origin of eukaryotes. Yet, resolving deep divergences remains a challenging task due to well-known tree-reconstruction artefacts and biases in extracting robust ancient phylogenetic signal, notably when analyzing data sets including the three Domains of Life. Among the various strategies aimed at mitigating these problems, divide-and-conquer approaches remain poorly explored, and have been primarily based on reconciliation among single gene trees which however notoriously lack ancient phylogenetic signal. Results We analyzed sub-sets of full supermatrices covering the whole Tree of Life with specific taxonomic sampling to robustly resolve different parts of the archaeal phylogeny in light of their current diversity. Our results strongly support the existence and early emergence of two main clades, Cluster I and Cluster II, which we name Ouranosarchaea and Gaiarchaea, and we clarify the placement of important novel archaeal lineages within these two clades. However, the monophyly and branching of the fast evolving nanosized DPANN members remains unclear and worth of further study. Conclusions We inferred a well resolved rooted phylogeny of the Archaea that includes all recently described phyla of high taxonomic rank. This phylogeny represents a valuable reference to study the evolutionary events associated to the early steps of the diversification of the archaeal domain. Beyond the specifics of archaeal phylogeny, our results demonstrate the power of divide-and-conquer approaches to resolve deep phylogenetic relationships, which should be applied to progressively resolve the entire Tree of Life.

The Male Hindwing Costal Roll in Cochylina (Lepidoptera: Tortricidae): Morphological Variation, Phylogenetic Distribution, and Relationship to Host Utilization

This is the first morphological study of the male hindwing costal roll (CR), a scent organ of tortricid moths of the subtribe Cochylina (Lepidoptera, Tortricidae). This composite organ varies from a simple membranous roll of the hindwing costa to a complex roll that incorporates a hairpencil and two types of microscales. All the components show taxon-dependent traits. Both optical and electron microscopy are used to elucidate the structure. The costal roll is associated primarily with the Aethes Billberg, Saphenista Walsingham, Phalonidia Le Marchand, and Cochylis Treitschke groups of genera. The general notions that wing male scent organs are phylogenetically labile and that they may have arisen among closely related species as a consequence of habitat sharing are explored using network analysis and phylogenetic signal. Taxa with a costal roll certainly support a more complex area of the food web, however, the character shows a strong phylogenetic signal and is not the result of a sporadic evolution.

Review of the current objectives and modern approaches to studying extant and extinct shrews (Soricomorpha: Soricidae) investigation: the origin of the modern subfamilies and diversity of Crocidosoricinae

The current review is devoted to topical issues of the origin of modern shrew’ subfamilies Soricinae Fischer, 1817 and Crocidurinae Milne-Edwards, 1868 (Soricomorpha: Soricidae), as well as to the consideration of the possibility of using morphological analysis to search for ancestral groups of modern soricine and crocidurine shrews within the extinct subfamily Crocidosoricinae Reumer, 1987. The data on the taxonomic composition of the Crocidosoricinae subfamily and the preliminary results of a comparative analysis of the Neogene shrews Miosorex Kretzoi, 1959 and Shargainosorex Zazhigin et Voyta, 2018 (Crocidosoricinae) shrews with the representatives of Soricinae and Crocidurinae according to the shape of the first upper molar M1 are presented as an example to substantiate urgent problems in this area. The problem of relations of molecular and morphological data are discussed using individual groups as examples. Modern approaches of geometric morphometry are described, which together with phylogenetic data allow assessing the expression of the phylogenetic signal when analysing the shape of morphological structures. Possible prospects for the practical application of these approaches for the study of fossil material and the search for ancestral lineages of modern shrews among Crocidosoricinae are described.

Morphometric variation of Middle-American cichlids: Theraps– Paraneetroplus clade (Actinopterygii: Cichliformes: Cichlidae)

This study assesses the patterns of variation in body shape, and relations of morphological similarity among species of the Theraps–Paraneetroplus clade in order to determine whether body shape may be a trait in phylogenetic relations. A total of 208 specimens belonging to 10 species of the Theraps–Paraneetroplus clade were examined. The left side of each specimen was photographed; in each photograph, 27 fixed landmarks were placed to identify patterns in body shape variation. Images were processed by using geometric morphometrics, followed by a phylogenetic principal component analysis. The phylogenetic signal for body shape was then calculated. To determine the relations in morphological similarity, a dendrogram was created using the unweighted pair group method and arithmetic mean values, while a Procrustes ANOVA and post-hoc test were used to evaluate significant differences between species and habitats. We found three morphological groups that differed in body length and depth, head size, and the position of the mouth and eyes. The body shape analysis recovered the morphotypes of seven species, and statistical differences were demonstrated in eight species. Based on traits associated with cranial morphology, Wajpamheros nourissati (Allgayer, 1989) differed the most among the species examined. No phylogenetic signal was found for body shape; this trait shows independence from ancestral relatedness, indicating that there is little congruence between morphological and genetic interspecific patterns. As evidenced by the consistently convergent morphology of the species in the Theraps–Paraneetroplus clade, the diversification of the group is related to an ecological opportunity for habitat use and the exploitation of food resources. Although no phylogenetic signal was detected for body shape, there appears to be an order associated with cranial morphology-based phylogeny. However, it is important to evaluate the intraspecific morphologic plasticity produced by ecological segregation or partitioning of resources. Therefore, future morphological evolutionary studies should consider cranial structures related to the capture and processing of food.