First Report and Molecular Variability of Belonolaimus longicaudatus Associated with Turfgrass in Maryland.

Turfgrass is a crop used extensively in athletic fields and golf courses in Maryland. A soil sample collected in July 2023 from an athletic field in Baltimore County, Maryland, part of a turfgrass nematode survey, contained Belonolaimus longicaudatus. In the southeastern United States, B. longicaudatus is an economically important pathogen of warm season turfgrass. The density was four individuals/100 cm3 of soil, and no visual symptoms were observed in the bermudagrass field. Morphological features and morphometrics of males and females were consistent with B. longicaudatus and placed the Maryland population in a subclade that was geographically represented by populations from north and west Florida, Texas, and South Carolina. Sequencing of the internal transcribed spacer region ITS1 and ITS2 and 28S large ribosomal subunit D2-23 expansion region confirmed the species' identity. Phylogenetic trees and parsimony network analysis placed the Maryland isolate in a large grouping of B. longicaudatus populations including those from Alabama, Delaware, Florida, Indiana, Mississippi, South Carolina, and Texas. To our knowledge, this is the first report of B. longicaudatus in Maryland.

Bounding the Softwired Parsimony Score of a Phylogenetic Network.

In comparison to phylogenetic trees, phylogenetic networks are more suitable to represent complex evolutionary histories of species whose past includes reticulation such as hybridisation or lateral gene transfer. However, the reconstruction of phylogenetic networks remains challenging and computationally expensive due to their intricate structural properties. For example, the small parsimony problem that is solvable in polynomial time for phylogenetic trees, becomes NP-hard on phylogenetic networks under softwired and parental parsimony, even for a single binary character and structurally constrained networks. To calculate the parsimony score of a phylogenetic network N, these two parsimony notions consider different exponential-size sets of phylogenetic trees that can be extracted from N and infer the minimum parsimony score over all trees in the set. In this paper, we ask: What is the maximum difference between the parsimony score of any phylogenetic tree that is contained in the set of considered trees and a phylogenetic tree whose parsimony score equates to the parsimony score of N? Given a gap-free sequence alignment of multi-state characters and a rooted binary level-k phylogenetic network, we use the novel concept of an informative blob to show that this difference is bounded by k + 1 times the softwired parsimony score of N. In particular, the difference is independent of the alignment length and the number of character states. We show that an analogous bound can be obtained for the softwired parsimony score of semi-directed networks, while under parental parsimony on the other hand, such a bound does not hold.

Exploring geography and evolutionary history as drivers of variation in floral scent chemistry in western sessile-flowered Trillium using parsimony-constrained phylogenetics.

BACKGROUND AND AIMS: The sessile-flowered Trillium species from western North America have been challenging to distinguish morphologically due to overlapping characters and intraspecific variation. Molecular phylogenetic analyses, currently inconclusive for this group, have not sampled multiple populations of the different species to account for this. Here, we query the diversity of floral volatile composition to understand its bearings on the taxonomy, distribution and evolution of this group. METHODS: We explored taxonomic and geographic patterns in average floral volatile composition (105 different compounds) among 42 wild populations of four sessile-flowered Trillium species and the outgroup, Pseudotrillium, in California, Oregon and Washington by means of parsimony-constrained phylogenetic analyses. To assess the influence of character construction, we coded compound abundance in three different ways for the phylogenetic analyses and compared the results with those of statistical analyses using the same dataset and previously published statistical analyses. KEY RESULTS: Different codings of floral volatile composition generated different phylogenetic topologies with different levels of resolution. The different phylogenies provide similar answers to taxonomic questions but support different evolutionary histories. Monophyly of most populations of each taxon suggests that floral scent composition bears phylogenetic signal in the western sessile-flowered Trillium. Lack of correlation between the distribution of populations and their position in scent-based phylogenies does not support a geographic signal in floral scent composition. CONCLUSIONS: Floral scent composition is a valuable data source for generating phylogenetic hypotheses. The way scent composition is coded into characters is important. The phylogenetic patterns supported by floral volatile compounds are incongruent with previously reported phylogenies of the western sessile-flowered Trillium obtained using molecular or morphological data. Combining floral scent data with gene sequence data and detailed morphological data from multiple populations of each species in future studies is needed for understanding the evolutionary history of western sessile-flowered Trillium.

Foveapeltis gen. nov., an unusual cleroid genus with large hypomeral cavities from mid-Cretaceous amber (Coleoptera: Cleroidea).

Beetles have a remote evolutionary history dating back to the Carboniferous, with Mesozoic fossils playing a pivotal role in elucidating the early evolution of extant families. Despite their exceptional preservation in amber, deciphering the systematic positions of Mesozoic trogossitid-like beetles remains challenging. Here, we describe and illustrate a new trogossitid-like lineage from mid-Cretaceous Kachin amber, Foveapeltis rutai Li, Kolibác, Liu & Cai, gen. et sp. nov. Foveapeltis stands out within the Cleroidea due to the presence of a significant large cavity on each hypomeron. While the exact phylogenetic placement of Foveapeltis remains uncertain, we offer a discussion on its potential affinity based on our constrained phylogenetic analyses.

Measuring complexity for hierarchical models using effective degrees of freedom.

Hierarchical models can express ecological dynamics using a combination of fixed and random effects, and measurement of their complexity (effective degrees of freedom, EDF) requires estimating how much random effects are shrunk toward a shared mean. Estimating EDF is helpful to (1) penalize complexity during model selection and (2) to improve understanding of model behavior. I applied the conditional Akaike Information Criterion (cAIC) to estimate EDF from the finite-difference approximation to the gradient of model predictions with respect to each datum. I confirmed that this has similar behavior to widely used Bayesian criteria, and I illustrated ecological applications using three case studies. The first compared model parsimony with or without time-varying parameters when predicting density-dependent survival, where cAIC favors time-varying demographic parameters more than conventional Akaike Information Criterion. The second estimates EDF in a phylogenetic structural equation model, and identifies a larger EDF when predicting longevity than mortality rates in fishes. The third compares EDF for a species distribution model fitted for 20 bird species and identifies those species requiring more model complexity. These highlight the ecological and statistical insight from comparing EDF among experimental units, models, and data partitions, using an approach that can be broadly adopted for nonlinear ecological models.

Please Mind the Gap: Indel-Aware Parsimony for Fast and Accurate Ancestral Sequence Reconstruction and Multiple Sequence Alignment Including Long Indels.

Despite having important biological implications, insertion, and deletion (indel) events are often disregarded or mishandled during phylogenetic inference. In multiple sequence alignment, indels are represented as gaps and are estimated without considering the distinct evolutionary history of insertions and deletions. Consequently, indels are usually excluded from subsequent inference steps, such as ancestral sequence reconstruction and phylogenetic tree search. Here, we introduce indel-aware parsimony (indelMaP), a novel way to treat gaps under the parsimony criterion by considering insertions and deletions as separate evolutionary events and accounting for long indels. By identifying the precise location of an evolutionary event on the tree, we can separate overlapping indel events and use affine gap penalties for long indel modeling. Our indel-aware approach harnesses the phylogenetic signal from indels, including them into all inference stages. Validation and comparison to state-of-the-art inference tools on simulated data show that indelMaP is most suitable for densely sampled datasets with closely to moderately related sequences, where it can reach alignment quality comparable to probabilistic methods and accurately infer ancestral sequences, including indel patterns. Due to its remarkable speed, our method is well suited for epidemiological datasets, eliminating the need for downsampling and enabling the exploitation of the additional information provided by dense taxonomic sampling. Moreover, indelMaP offers new insights into the indel patterns of biologically significant sequences and advances our understanding of genetic variability by considering gaps as crucial evolutionary signals rather than mere artefacts.

Neither Ethical nor Prudent: Why Not to Choose Normothermic Regional Perfusion.

In transplant medicine, the use of normothermic regional perfusion (NRP) in donation after circulatory determination of death raises ethical difficulties. NRP is objectionable because it restores the donor's circulation, thus invalidating a death declaration based on the permanent cessation of circulation. NRP's defenders respond with arguments that are tortuous and factually inaccurate and depend on introducing extraneous concepts into the law. However, results comparable to NRP's-more and higher-quality organs and more efficient allocation-can be achieved by removing organs from deceased donors and using normothermic machine perfusion (NMP) to support the organs outside the body, without jeopardizing confidence in transplantation's legal and ethical foundations. Given the controversy that NRP generates and the convoluted justifications made for it, we recommend a prudential approach we call "ethical parsimony," which holds that, in the choice between competing means of achieving a result, the ethically simpler one is to be preferred. This approach makes clear that policy-makers should favor NMP over NRP.

Common Methods for Phylogenetic Tree Construction and Their Implementation in R.

A phylogenetic tree can reflect the evolutionary relationships between species or gene families, and they play a critical role in modern biological research. In this review, we summarize common methods for constructing phylogenetic trees, including distance methods, maximum parsimony, maximum likelihood, Bayesian inference, and tree-integration methods (supermatrix and supertree). Here we discuss the advantages, shortcomings, and applications of each method and offer relevant codes to construct phylogenetic trees from molecular data using packages and algorithms in R. This review aims to provide comprehensive guidance and reference for researchers seeking to construct phylogenetic trees while also promoting further development and innovation in this field. By offering a clear and concise overview of the different methods available, we hope to enable researchers to select the most appropriate approach for their specific research questions and datasets.

Dollo Parsimony Overestimates Ancestral Gene Content Reconstructions.

Ancestral reconstruction is a widely used technique that has been applied to understand the evolutionary history of gain and loss of gene families. Ancestral gene content can be reconstructed via different phylogenetic methods, but many current and previous studies employ Dollo parsimony. We hypothesize that Dollo parsimony is not appropriate for ancestral gene content reconstruction inferences based on sequence homology, as Dollo parsimony is derived from the assumption that a complex character cannot be regained. This premise does not accurately model molecular sequence evolution, in which false orthology can result from sequence convergence or lateral gene transfer. The aim of this study is to test Dollo parsimony's suitability for ancestral gene content reconstruction and to compare its inferences with a maximum likelihood-based approach that allows a gene family to be gained more than once within a tree. We first compared the performance of the two approaches on a series of artificial data sets each of 5,000 genes that were simulated according to a spectrum of evolutionary rates without gene gain or loss, so that inferred deviations from the true gene count would arise only from errors in orthology inference and ancestral reconstruction. Next, we reconstructed protein domain evolution on a phylogeny representing known eukaryotic diversity. We observed that Dollo parsimony produced numerous ancestral gene content overestimations, especially at nodes closer to the root of the tree. These observations led us to the conclusion that, confirming our hypothesis, Dollo parsimony is not an appropriate method for ancestral reconstruction studies based on sequence homology.

When better is the enemy of good: two cautionary tales of conceptual validity versus parsimony in clinical psychometric research.

This paper presents an empirical challenge to the assumption that an item-response theory analysis always yields a better measure of a clinical construct. We summarize results from two measurement development studies that showed that such an analysis lost important content reflecting the conceptual model ("conceptual validity"). The cost of parsimony may thus be too high. Conceptual models that form the foundation of QOL measurement reflect the patient's experience. This experience may include concepts and items that are psychometrically "redundant" but capture distinct features of the concept. Good measurement is likely a balance between relying on IRT's quantitative metrics and recognizing the importance of conceptual validity and clinical utility.

DNA Barcoding of Invasive Terrestrial Plant Species in India.

Invasive plants are known to cause biodiversity loss and pose a major risk to human health and environment. Identification of invasive plants and distinguishing them from native species has been relied on morphological examination. Stringent requirement of floral characters and decreasing number of expert taxonomists are making conventional morphology-based identification system tedious and resource-intensive. DNA barcoding may help in quick identification of invasive species if distinct sequence divergence pattern at various taxonomic levels is observed. The present work evaluates the utility of four molecular markers; rbcL, matK, their combination (rbcL + matK), and psbA-trnH for identification of 37 invasive plant species from India and also in distinguishing them from 97 native species. A psbA-trnH locus was found to be of restricted utility in this work as it was represented by the members of a single family. A hierarchical increase in K2P mean divergence across different taxonomic levels was found to be the maximum for matK alone followed by rbcL + matK and rbcL alone, respectively. NJ clustering analysis, however, confirmed the suitability of combined locus (rbcL + matK) over individual rbcL and matK as the DNA barcode. RbcL showed the lowest resolution power among the three markers studied. MatK exhibited much better performance compared to rbcL alone in identifying most of the species accurately although it failed to show monophyly of genus Dinebra. Two families; Asteraceae and Poaceae, remained polyphyletic in the trees constructed by all three markers. Combined locus (rbcL + matK) was found to be the most suitable marker as it raised the resolution power of both the markers and could identify more than 90% of genera correctly. Phylogenetic tree constructed by Maximum-Parsimony method using combined locus as a molecular marker exhibited the best resolution, thus, supporting the significance of two-locus combination of rbcL + matK for barcoding invasive plant species from India. Present study contributes to the global barcode data of invasive plant species by adding fifty-one new sequences to it. Effective barcoding of additional number of native as well as invasive plant species from India is possible using this dual locus if it is combined with one or more new molecular plastid markers. Expansion of barcode database with a focus on barcode performance optimisation to improve discrimination ability at species level can be undertaken in future.

Elucidating the evolution of monkeypox virus genomes through phylo-geo-network and haplogroup analysis.

BACKGROUND: As the world settles down from the COVID-19 pandemic, many countries are faced with an unexpected outbreak of monkeypox infection. Monkeypox is a zoonotic disease caused by monkeypox virus (MPXV), which is an enveloped, double stranded DNA virus belonging to the Poxviridae family. Presently, we construct and analyze the phylo-geo-network and the corresponding haplogroups. Presently, we performed the haplogroup analysis with their defining mutations and phylogenetic lineage study along with geographical distributions with the aim to understand the evolutionary path of the MPXV across the world. RESULTS: Information about 719 full length genomes of MPXV were collected from GISAID repository and the sequences extracted from NCBI. The alignment of 719 MPXV genomes and their subsequent analysis revealed a total of 1530 segregating sites of which 330 were parsimony informative (PI) sites. The variations had a positive value of Tajima's D statistic indicating some mutations being prevalent and hence balancing selection. A total of 39 haplogroups were observed in the phylo-geo-network and their defining mutations along with the evolutionary path has been discussed. The phylo-geo-network revealed the nodal haplogroup is represented by GISAID ID 13889450, haplogroup A1, an isolate from Germany, having a total of 296 identical sequences in the study incident across 22 countries. The localized evolution is highlighted by country specific sequences and haplogroups. USA had a total of 58 genomes and 13 haplogroups as compared to Peru (89 genomes, 7 haplogroups) and Germany (26 genomes, 6 haplogroups). CONCLUSIONS: The evolution of MPXV can be happening in a localized manner and hence accumulation of variations in the MPXV genomes needs to be monitored in order to be prepared for any possible threats.

Nothing to it: a reply to Wheeler's "much ado about nothing".

Wheeler (Cladistics 2023, 39, 475) recently suggested that the issues with inapplicable characters in phylogenetic analysis can be dealt with directly by treating observed absences of a feature not in a separate absence/presence character but as insertion/deletion events in a complex character that describes the feature in all its variation; and that this dynamic homology view can be achieved by imposing a sequence or linear order on a set of characters and by analysing the resulting sequence character using custom alphabet tree alignment algorithms. As Wheeler observed, this approach can lead to considering inappropriate character states (such as a head state and a foot state) homologous. We show that it is also sensitive to the specific ordering assumption used and that such different character orders can lead to a preference for different trees. We present a simple four-taxon dataset with observations of absence, but no inapplicable characters or other kinds of character dependence, for which the dynamic homology framework gives different results to classic algorithms for independent characters, including an optimal tree with biologically impossible reconstructions at inner nodes (every terminal has a head but the inner nodes are headless). We show how these issues can be solved by removing the character ordering assumption that the approach requires. Doing so, the dynamic homology framework reduces in general to Maddison's (Syst. Biol. 1993, 42, 576) well-known proposal to deal with inapplicability using step matrix analysis of complex characters. If in addition costs are interpreted in terms of homology, it reduces to Goloboff et al.'s (Cladistics 2021, 37, 596) step matrix implementation for maximization of homology as applied to inapplicable characters. However, if used with homogeneous costs, as Wheeler suggested, it reduces to unordered analysis of such complex characters, which is known to treat tails that may share many observed features as irrelevant for establishing kinship when they differ in just one feature, e.g. colour.

An enigmatic Cretaceous beetle with possible affinity to Erotylidae (Coleoptera: Cucujiformia).

The morphology of beetles of the recently defined superfamilies Erotyloidea, Nitiduloidea and Cucujoidea is varied. Determining the systematic positions of Mesozoic fossils within these groups can often be challenging. Here we describe and illustrate a puzzling cucujiform beetle, Isocryptophilus exilipunctus Li & Cai gen. & sp. nov., based on an individual from mid-Cretaceous Burmese amber. While we cannot definitively pinpoint the exact phylogenetic position of Isocryptophilus, its possible affinity to Erotylidae is discussed in light of our phylogenetic analyses. A broader-sampled morphological matrix, coupled with a robust molecular phylogeny of these groups, will be promising for clarifying the systematic placement of the fossil.

Dollo-CDP: a polynomial-time algorithm for the clade-constrained large Dollo parsimony problem.

The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem for the Dollo criterion score in [Formula: see text] time, where n is the number of leaves, k is the number of characters, and [Formula: see text] is the set of clades used as constraints. Dollo parsimony, which requires traits/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. This motivated us to implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility for analyzing retroelement insertion presence / absence patterns for bats, birds, toothed whales as well as simulated data. Our results show that Dollo-CDP can improve upon heuristic search from a single starting tree, often recovering a better scoring tree. Moreover, Dollo-CDP scales to data sets with much larger numbers of taxa than branch-and-bound while still having an optimality guarantee, albeit a more restricted one. Lastly, we show that our algorithm for Dollo parsimony can easily be adapted to Camin-Sokal parsimony but not Fitch parsimony.

Female semiochemicals stimulate male courtship but dampen female sexual receptivity.

Chemical communication plays a vital role in mate attraction and discrimination among many insect species. Here, we document a unique example of semiochemical parsimony, where four chemicals act as both aphrodisiacs and anti-aphrodisiacs in different contexts in Bactrocera dorsalis. Specifically, we identified four female-specific semiochemicals, ethyl laurate, ethyl myristate, ethyl cis-9-hexadecenoate, and ethyl palmitate, which serve as aphrodisiacs to attract male flies and arouse male courtship. Interestingly, these semiochemicals, when sexually transferred to males during mating, can function as anti-aphrodisiacs, inhibiting the receptivity of subsequent female mates. We further showed that the expression of elongase11, a key enzyme involved in the biosynthesis of these semiochemicals, is under the control of doublesex, facilitating the exclusive biosynthesis of these four semiochemicals in females and guaranteeing effective chemical communication. The dual roles of these semiochemicals not only ensure the attractiveness of mature females but also provide a simple yet reliable mechanism for female mate discrimination. These findings provide insights into chemical communication in B. dorsalis and add elements for the design of pest control programs.

Representing and extending ensembles of parsimonious evolutionary histories with a directed acyclic graph.

In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but the collection of high-quality trees. This goal is typically addressed using Bayesian techniques, however, current Bayesian methods do not scale to large data sets. Furthermore, for large data sets with relatively low signal one cannot even store every good tree individually, especially when the trees are required to be bifurcating. In this paper, we develop a novel object called the "history subpartition directed acyclic graph" (or "history sDAG" for short) that compactly represents an ensemble of trees with labels (e.g. ancestral sequences) mapped onto the internal nodes. The history sDAG can be built efficiently and can also be efficiently trimmed to only represent maximally parsimonious trees. We show that the history sDAG allows us to find many additional equally parsimonious trees, extending combinatorially beyond the ensemble used to construct it. We argue that this object could be useful as the "skeleton" of a more complete uncertainty quantification.

Implications of outgroup selection in the phylogenetic inference of hominoids and fossil hominins.

Understanding the phylogenetic relationships among hominins and other hominoid species is critical to the study of human origins. However, phylogenetic inferences are dependent on both the character data and taxon sampling used. Previous studies of hominin phylogenetics have used Papio and Colobus as outgroups in their analyses; however, these extant monkeys possess many derived traits that may confound the polarities of morphological changes among living apes and hominins. Here, we consider Victoriapithecus and Ekembo as more suitable outgroups. Both Victoriapithecus and Ekembo are anatomically well known and are widely accepted as morphologically primitive stem cercopithecoid and hominoid taxa, respectively, making them more appropriate for inferring polarity for later-occurring hominoid- and hominin-focused analyses. Craniodental characters for both taxa were scored and then added to a previously published matrix of fossil hominin and extant hominoid taxa, replacing outgroups Papio and Colobus over a series of iterative analyses using both parsimony and Bayesian inference methods. Neither the addition nor replacement of outgroup taxa changed tree topology in any analysis. Importantly, however, bootstrap support values and posterior probabilities for nodes supporting their relationships generally increased compared to previous analyses. These increases were the highest at extant hominoid and basal hominin nodes, recovering the molecular ape phylogeny with considerably higher support and strengthening the inferred relationships among basal hominins. Interestingly, however, the inclusion of both extant and fossil outgroups reduced support for the crown hominid node. Our findings suggest that, in addition to improving character polarity estimation, including fossil outgroups generally strengthens confidence in relationships among extant hominoid and basal hominins.

All quiet on the western front? The evolutionary history of monogeneans (Dactylogyridae: Cichlidogyrus, Onchobdella) infecting a West and Central African tribe of cichlid fishes (Chromidotilapiini).

Owing to the largely unexplored diversity of metazoan parasites, their speciation mechanisms and the circumstances under which such speciation occurs - in allopatry or sympatry - remain vastly understudied. Cichlids and their monogenean flatworm parasites have previously served as a study system for macroevolutionary processes, e.g., for the role of East African host radiations on parasite communities. Here, we investigate the diversity and evolution of the poorly explored monogeneans infecting a West and Central African lineage of cichlid fishes: Chromidotilapiini, which is the most species-rich tribe of cichlids in this region. We screened gills of 149 host specimens (27 species) from natural history collections and measured systematically informative characters of the sclerotised attachment and reproductive organs of the parasites. Ten monogenean species (Dactylogyridae: Cichlidogyrus and Onchobdella) were found, eight of which are newly described and one redescribed herein. The phylogenetic positions of chromidotilapiines-infecting species of Cichlidogyrus were inferred through a parsimony analysis of the morphological characters. Furthermore, we employed machine learning algorithms to detect morphological features associated with the main lineages of Cichlidogyrus. Although the results of these experimental algorithms remain inconclusive, the parsimony analysis indicates that West and Central African lineages of Cichlidogyrus and Onchobdella are monophyletic, unlike the paraphyletic host lineages. Several instances of host sharing suggest occurrences of intra-host speciation (sympatry) and host switching (allopatry). Some morphological variation was recorded that may also indicate the presence of species complexes. We conclude that collection material can provide important insights on parasite evolution despite the lack of well-preserved DNA material.

Title: À l'Ouest, rien de nouveau ? L'histoire évolutive des monogènes (Dactylogyridae : Cichlidogyrus, Onchobdella) infectant une tribu de poissons cichlidés (Chromidotilapiini) d'Afrique occidentale et centrale. Abstract: En raison de la nature largement inexplorée de la diversité des parasites métazoaires, leurs mécanismes de spéciation et les circonstances dans lesquelles cette spéciation se produit­allopatrie ou sympatrie­restent très peu étudiés. Les cichlidés et leurs parasites Plathelminthes monogènes ont déjà servi de modèle pour l'étude des processus macro-évolutifs, par exemple pour le rôle des radiations d'hôtes de l'Afrique de l'Est sur les communautés de parasites. Ici, nous étudions la diversité et l'évolution des monogènes peu étudiées qui infestent une lignée de poissons cichlidés d'Afrique occidentale et centrale : les Chromidotilapiini, qui est la tribu de cichlidés la plus riche en espèces dans cette région. Nous avons examiné les branchies de 149 spécimens hôtes (27 espèces) provenant de musées d'histoire naturelle et mesuré systématiquement les caractères informatifs des pièces sclérifiées du hapteur et des organes copulateurs des parasites. Dix espèces de monogènes (Dactylogyridae : Cichlidogyrus et Onchobdella) ont été trouvées ; huit sont nouvelles pour la science et une est redécrite. Les positions phylogénétiques des espèces de Cichlidogyrus infectant les chromidotilapiines ont été déduites par une analyse de parcimonie des caractères morphologiques. En outre, nous avons utilisé des algorithmes d'apprentissage automatique pour détecter les caractéristiques morphologiques associées aux principales lignées de Cichlidogyrus. Bien que les résultats de ces algorithmes expérimentaux restent peu concluants, l'analyse de parcimonie indique que les lignées de Cichlidogyrus et d'Onchobdella de l'Afrique de l'Ouest et Central sont monophylétiques, contrairement aux lignées d'hôtes qui sont paraphylétiques. Plusieurs cas de partage d'hôtes suggèrent des occurrences de spéciation synxénique (sympatrie) et de changement d'hôte (allopatrie). Certaines variations morphologiques ont été enregistrées et peuvent également indiquer la présence de complexes d'espèces. Nous concluons donc que le matériel de collection peut fournir des informations importantes sur l'évolution des parasites malgré le manque d'ADN exploitable.

On parsimony and clustering.

This work is motivated by applications of parsimonious cladograms for the purpose of analyzing non-biological data. Parsimonious cladograms were introduced as a means to help understanding the tree of life, and are now used in fields related to biological sciences at large, e.g., to analyze viruses or to predict the structure of proteins. We revisit parsimonious cladograms through the lens of clustering and compare cladograms optimized for parsimony with dendograms obtained from single linkage hierarchical clustering. We show that despite similarities in both approaches, there exist datasets whose clustering dendogram is incompatible with parsimony optimization. Furthermore, we provide numerical examples to compare via F-scores the clustering obtained through both parsimonious cladograms and single linkage hierarchical dendograms.