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.

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.

Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than de novo and Maximum-Likelihood Implementations.

Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have often relied on tools designed for de novo phylogenetic inference, in which all data are collected before any analysis is performed and the phylogeny is inferred once from scratch. SARS-CoV-2 data sets do not fit this mold. There are currently over 14 million sequenced SARS-CoV-2 genomes in online databases, with tens of thousands of new genomes added every day. Continuous data collection, combined with the public health relevance of SARS-CoV-2, invites an "online" approach to phylogenetics, in which new samples are added to existing phylogenetic trees every day. The extremely dense sampling of SARS-CoV-2 genomes also invites a comparison between likelihood and parsimony approaches to phylogenetic inference. Maximum likelihood (ML) and pseudo-ML methods may be more accurate when there are multiple changes at a single site on a single branch, but this accuracy comes at a large computational cost, and the dense sampling of SARS-CoV-2 genomes means that these instances will be extremely rare because each internal branch is expected to be extremely short. Therefore, it may be that approaches based on maximum parsimony (MP) are sufficiently accurate for reconstructing phylogenies of SARS-CoV-2, and their simplicity means that they can be applied to much larger data sets. Here, we evaluate the performance of de novo and online phylogenetic approaches, as well as ML, pseudo-ML, and MP frameworks for inferring large and dense SARS-CoV-2 phylogenies. Overall, we find that online phylogenetics produces similar phylogenetic trees to de novo analyses for SARS-CoV-2, and that MP optimization with UShER and matOptimize produces equivalent SARS-CoV-2 phylogenies to some of the most popular ML and pseudo-ML inference tools. MP optimization with UShER and matOptimize is thousands of times faster than presently available implementations of ML and online phylogenetics is faster than de novo inference. Our results therefore suggest that parsimony-based methods like UShER and matOptimize represent an accurate and more practical alternative to established ML implementations for large SARS-CoV-2 phylogenies and could be successfully applied to other similar data sets with particularly dense sampling and short branch lengths.

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.

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.

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.

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.

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.

Ongoing Recombination in SARS-CoV-2 Revealed through Genealogical Reconstruction.

The evolutionary process of genetic recombination has the potential to rapidly change the properties of a viral pathogen, and its presence is a crucial factor to consider in the development of treatments and vaccines. It can also significantly affect the results of phylogenetic analyses and the inference of evolutionary rates. The detection of recombination from samples of sequencing data is a very challenging problem and is further complicated for SARS-CoV-2 by its relatively slow accumulation of genetic diversity. The extent to which recombination is ongoing for SARS-CoV-2 is not yet resolved. To address this, we use a parsimony-based method to reconstruct possible genealogical histories for samples of SARS-CoV-2 sequences, which enables us to pinpoint specific recombination events that could have generated the data. We propose a statistical framework for disentangling the effects of recurrent mutation from recombination in the history of a sample, and hence provide a way of estimating the probability that ongoing recombination is present. We apply this to samples of sequencing data collected in England and South Africa and find evidence of ongoing recombination.

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.

An updated analysis of hominin phylogeny with an emphasis on re-evaluating the phylogenetic relationships of Australopithecus sediba.

The discovery and description of Australopithecus sediba has reignited the debate over the evolutionary history of the australopiths and the genus Homo. It has been suggested that A. sediba may be an ancestor of Homo because it possesses a mosaic of derived Homo-like and primitive australopith-like traits. However, an alternative hypothesis proposes that the majority of the purported Homo-like craniodental characters can be attributed to the juvenile status of the type specimen, MH1. We conducted an independent character assessment of the craniodental morphology of A. sediba, with particular emphasis on evaluating whether the ontogenetic status of MH1 may have affected its purported Homo-like characteristics. In doing so, we have also expanded fossil hypodigms to incorporate the new Australopithecus anamensis cranium from Woranso-Mille (MRD-VP-1/1), as well as recently described Paranthropus robustus cranial remains from Drimolen (DNH 7, DNH 155). Morphological character data were analyzed using both standard parsimony and Bayesian techniques. In addition, we conducted a series of Bayesian analyses constrained to evaluate the hypothesis that Australopithecus africanus and A. sediba are sister taxa. Based on the results of the parsimony and Bayesian analyses, we could not reject the hypothesis that A. sediba shares its closest phylogenetic affinities with the genus Homo. Therefore, based on currently available craniodental evidence, we conclude that A. sediba is plausibly the terminal end of a lineage that shared a common ancestor with the earliest representatives of Homo. We caution, however, that the discovery of new A. sediba fossils preserving adult cranial morphology or the inclusion of postcranial characters may ultimately necessitate a re-evaluation of this hypothesis.

Diddensiella parasantjacobensis f.a., sp. nov., a yeast species from forest habitats.

Six conspecific yeast strains, representing an undescribed species, were isolated from rotten wood collected in different locations in Hungary and Germany and an additional one from fungal fruiting body in Taiwan. The seven strains share identical nucleotide sequences in the D1/D2 domain of the nuclear large subunit (LSU) rRNA gene. The Hungarian and Taiwanese isolates share identical internal transcribed spacer (ITS) sequences as well, while the two German isolates differ from them merely by three substitutions and four indels in this region. The investigated strains are very closely related to Diddensiella santjacobensis. Along their LSU D1/D2 domain they differ only by one substitution from the type strain of D. santjacobensis. However, in the ITS region of Hungarian and Taiwanese strains we detected 3.5 % divergence (nine substitutions and nine indels) between the undescribed species and D. santjacobensis, while the German strains differed by 13 substitutions and nine indels from D. santjacobensis. This ITS sequence divergence has raised the possibility that the strains investigated in this study may represent a different species from D. santjacobensis. This hypothesis was supported by comparisons of partial translation elongation factor 1-α (EF-1α) and cytochrome oxidase II (COX II) gene sequences. While no difference and 1-2 substitutions among the partial EF-1α and COX II gene sequences of the strains of the undescribed species, respectively, were detected; the undescribed species differ by about 4 % (36 substitutions) and 10 % (50-51 substitutions) from D. santjacobensis in these regions. Parsimony network analysis of the partial COX II gene sequences also separated the investigated strains from the type strain of D. santjacobensis. In this paper we propose Diddensiella parasantjacobensis f.a., sp. nov. (holotype: NCAIM Y.02121; isotypes: CBS 17819, DSM 114156) to accommodate the above-noted strains.

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.

Caution is required when considering sentience in animals: a response to the commentary by Briffa (2022) on "Hermit crabs, shells, and sentience" (Elwood 2022).

My recent review examined the complex and intimate relationship between hermit crabs and the empty gastropod shells upon which they depend for survival. Because shells come with costs as well as benefits, the crabs are highly selective about which ones they prefer to occupy. Thus, a new shell is investigated and the information that is gathered appears to be compared with their existing shell before a decision is made. This is often prolonged and complex. Crabs also fight for shells and again the information that is gathered and used to inform fight decisions is complex. In my review, I consider these and other situations with reference to the possibility of sentience (including awareness). The excellent commentary from Mark Briffa expands on aspects of sentience and invokes the use of Lloyd Morgan's Canon to avoid suggesting complex abilities when simpler explanations would suffice. I agree with this approach. However, I also suggest that when simpler explanations appear not to explain the data, then it is reasonable to consider if more complex mental abilities might be used. I also like Briffa's suggestion that the use of an apparently higher mental faculty might result in a mechanism that is simpler than a large number of apparently simple decisions used to make complex decisions.

When should we ascribe sentience to animals? A commentary on "Hermit crabs, shells and sentience" (Elwood 2022).

In a new review article, experiments on hermit crab behaviour are discussed in the context of possible animal sentience. Sentience can be defined as the ability to experience feelings such as pleasure or pain but there are also broader definitions that include elements of awareness. Here I suggest that of the different levels of awareness described as components of sentience, only the higher levels (assessment and executive awareness) seem distinct from the basic non-sentient cognitive tasks of gathering, processing and storing information, which are demonstrated by most animals. Studies that attempt to differentiate between basic cognitive functions and higher levels of awareness are rare for most animal taxa, including hermit crabs. Therefore, while results such as those obtained from studies of hermit crab behaviour are compatible with sentience they cannot yet be distinguished from simpler explanations based on basic cognitive functions, which we should prefer for the time-being. Nevertheless, hermit crabs are promising model systems for investigating awareness in animals.

Patterns of endemism of the Chinese Larentiinae (Lepidoptera: Geometridae).

Chinese Larentiinae is exceptionally rich in species since it spans the Palearctic realm and the Oriental realm, comprising 715 species belonging to 130 genera. Among them, nearly half species are endemic. This taxon is considered an ideal object for the study of endemic patterns. In this study, parsimony analysis of endemicity was used to delineate areas of endemisms (AOEs), and track compatibility analysis (TCA) was used to perform the TCA. Eight AOEs were supported. Except for five AOEs around the Qinghai-Tibet plateau (QTP), two AOEs from northern China and Taiwan islands were found. Twenty-two generalized tracks were obtained from the combination of the track analysis and the AOEs. The uplift of the QTP was assumed to greatly influence these endemic patterns, presented an appearance of highly centralized endemism and diversity in the eastern and southern edges of the QTP. And the AOE of Mt. Hengduan was considered as a major center of development through recent geological history, where strong evolutionary radiation might have taken place, resulting in the migration routes described by the generalized tracks from this center to various regions in various directions.

The principle of simplicity for Qutb al-Din Shirazi.

This paper seeks to show how Qutb al-Din Shirazi, a prominent astronomer of the Islamic age of science, employed the principle of simplicity in choosing among rival planetary models. Following some previous studies, we distinguish syntactic and ontological accounts of simplicity. Shirazi explicitly refers to these methodological principles and utilizes them to reduce the number of orbs in the planetary models. We provide cases where Shirazi applies the former account of simplicity, and others where he uses the latter. In some complicated cases, however, he appeals to a third kind of simplicity in favor of conceptual consistency. We argue that retaining the uniform motion of orbs plays a critical role in his favoring a particular account of simplicity.

Maximum parsimony reconciliation in the DTLOR model.

BACKGROUND: Analyses of microbial evolution often use reconciliation methods. However, the standard duplication-transfer-loss (DTL) model does not account for the fact that species trees are often not fully sampled and thus, from the perspective of reconciliation, a gene family may enter the species tree from the outside. Moreover, within the genome, genes are often rearranged, causing them to move to new syntenic regions. RESULTS: We extend the DTL model to account for two events that commonly arise in the evolution of microbes: origin of a gene from outside the sampled species tree and rearrangement of gene syntenic regions. We describe an efficient algorithm for maximum parsimony reconciliation in this new DTLOR model and then show how it can be extended to account for non-binary gene trees to handle uncertainty in gene tree topologies. Finally, we describe preliminary experimental results from the integration of our algorithm into the existing xenoGI tool for reconstructing the histories of genomic islands in closely related bacteria. CONCLUSIONS: Reconciliation in the DTLOR model can offer new insights into the evolution of microbes that is not currently possible under the DTL model.

MAPLE: A Microbiome Analysis Pipeline Enabling Optimal Peptide Search and Comparative Taxonomic and Functional Analysis.

Metaproteomics by mass spectrometry (MS) is a powerful approach to profile a large number of proteins expressed by all organisms in a highly complex biological or ecological sample, which is able to provide a direct and quantitative assessment of the functional makeup of a microbiota. The human gastrointestinal microbiota has been found playing important roles in human physiology and health, and metaproteomics has been shown to shed light on multiple novel associations between microbiota and diseases. MS-powered proteomics generally relies on genome data to define search space. However, metaproteomics, which simultaneously analyzes all proteins from hundreds to thousands of species, faces significant challenges regarding database search and interpretation of results. To overcome these obstacles, we have developed a user-friendly microbiome analysis pipeline (MAPLE, freely downloadable at http://maple.rx.umaryland.edu/), which is able to define an optimal search space by inferring proteomes specific to samples following the principle of parsimony. MAPLE facilitates highly comparable or better peptide identification compared to a sample-specific metagenome-guided search. In addition, we implemented an automated peptide-centric enrichment analysis function in MAPLE to address issues of traditional protein-centric comparison, enabling straightforward and comprehensive comparison of taxonomic and functional makeup between microbiota.

Minimal models provide maximally parsimonious explanations.

We are delighted that Diniz-Filho et al. agree with the main premise of our paper, and we welcome their critique, as constructive debate will help foster a better understanding of size evolution on islands. Our perspective on each of their criticisms is discussed in greater detail below.