Phylogenetic Methods Research Articles

A new dentition-based phylogeny of Litopterna (Mammalia: Placentalia) and ‘archaic’ South American ungulates

Abstract Ever since the discovery of Macrauchenia patachonica by Charles Darwin in 1834, the affinities of litopterns—a group of extinct South American Native Ungulates (SANUs)—have been elusive. In particular, the interfamilial relationships and timing of the familial diversification within the order Litopterna have not been addressed with adequate taxon and character sampling, and modern phylogenetic methods. We address these issues using a new morphological matrix of 703 dental and mandibular characters, scored for the earliest litopterns alongside early SANUs of other orders (Astrapotheria, Notoungulata, Pyrotheria, and Xenungulata). We also included members of families that have been often included within Litopterna, such as Didolodontidae, Protolipternidae, Indaleciidae, and Notonychopidae, the last two sometimes grouped in the order Notopterna. We conducted maximum parsimony and undated and tip-dated Bayesian phylogenetic analyses. Our results indicate that (1) didolodontids, protolipternids, and kollpaniines should be considered early SANUs, but not particularly closely related to any order, (2) Indaleciidae and Notonychopidae usually form a monophyletic group (Notopterna), and (3) Litopterna is a monophyletic unit composed of four families [Adianthidae, Anisolambdidae (subfamilies Anisolambdinae and Sparnotheriodontinae), Macraucheniidae, Proterotheriidae], and tentatively the notoptern families Indaleciidae and Notonychopidae with a probable origin ~64.0 Mya in the Early Palaeocene.

The resurgence of influenza A/H3N2 virus in Australia after the relaxation of COVID-19 restrictions during the 2022 season.

This study retrospectively analyzed the genetic characteristics of influenza A H3N2 (A/H3N2) viruses circulating in New South Wales (NSW), the Australian state with the highest number of influenza cases in 2022, and explored the phylodynamics of A/H3N2 transmission within Australia during this period. Sequencing was performed on 217 archived specimens, and A/H3N2 evolution and spread within Australia were analyzed using phylogenetic and phylodynamic methods. Hemagglutinin genes of all analyzed NSW viruses belonged to subclade 3C.2a1b.2a.2 and clustered together with the 2022 vaccine strain. Complete genome analysis of NSW viruses revealed highly frequent interclade reassortments between subclades 3C.2a1b.2a.2 and 3C.2a1b.1a. The estimated earliest introduction time of the dominant subgroup 3C.2a1b.2a.2a.1 in Australia was February 22, 2022 (95% highest posterior density: December 19, 2021-March 13, 2022), following the easing of Australian travel restrictions, suggesting a possible international source. Phylogeographic analysis revealed that Victoria drove the transmission of A/H3N2 viruses across the country during this season, while NSW did not have a dominant role in viral dissemination to other regions. This study highlights the importance of continuous surveillance and genomic characterization of influenza viruses in the postpandemic era, which can inform public health decision-making and enable early detection of novel strains with pandemic potential.

First Molecular Diagnosis of Oestrus ovis (Linnaeus, 1758) Larvae Causing Conjunctival Ophthalmomyiasis in Mexico City, Mexico.

Human ophthalmomyiasis is a rare ocular parasitosis that results from the accidental infestation of dipteran larvae of several species, including Oestrus ovis (Linnaeus, 1758). This study aims to present the fourth documented human case of ophthalmomyiasis in Mexico, identifying the etiological agent through morphological and molecular analyses. Additionally, we investigated the phylogenetic position and genetic distances among different specimens globally characterized based on mitochondrial Cox1 sequences. A total of five larval specimens were extracted from the patient's eye, with two specimens allocated for identification based on morphological features using a stereomicroscope, and the remaining three preserved in absolute ethanol, one of them used for subsequent analysis using molecular methods. The mitochondrial Cox1 region was amplified and sequenced using automated Sanger sequencing. The resulting sequence was deposited in GenBank under accession number OR440699 and subjected to BlastN analysis against 35 other Cox1 sequences of O. ovis from GenBank. The identity and phylogenetic position of the strains were further explored using parsimony and maximum likelihood phylogenetic methods. Morphological examination of the larval specimens extracted from the patient's eye unequivocally identified them as O. ovis species. BlastN analysis and comprehensive phylogenetic investigations involving a total of 36 Cox1 sequences confirmed the taxonomic identity of the larvae. Notably, our sequence was positioned within the cluster formed by the Brazilian and two Iranian samples. This finding underscores a shared genetic ancestry among these distinct geographical isolates and provides valuable insights into the evolutionary relationships within O. ovis populations. The presence of O. ovis infestation in Mexico City suggests potential shifts in environmental conditions favoring fly proliferation, highlighting the need for vigilance in urban healthcare settings.

Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2.

Public health researchers and practitioners commonly infer phylogenies from viral genome sequences to understand transmission dynamics and identify clusters of genetically-related samples. However, viruses that reassort or recombine violate phylogenetic assumptions and require more sophisticated methods. Even when phylogenies are appropriate, they can be unnecessary or difficult to interpret without specialty knowledge. For example, pairwise distances between sequences can be enough to identify clusters of related samples or assign new samples to existing phylogenetic clusters. In this work, we tested whether dimensionality reduction methods could capture known genetic groups within two human pathogenic viruses that cause substantial human morbidity and mortality and frequently reassort or recombine, respectively: seasonal influenza A/H3N2 and SARS-CoV-2. We applied principal component analysis (PCA), multidimensional scaling (MDS), t-distributed stochastic neighbor embedding (t-SNE), and uniform manifold approximation and projection (UMAP) to sequences with well-defined phylogenetic clades and either reassortment (H3N2) or recombination (SARS-CoV-2). For each low-dimensional embedding of sequences, we calculated the correlation between pairwise genetic and Euclidean distances in the embedding and applied a hierarchical clustering method to identify clusters in the embedding. We measured the accuracy of clusters compared to previously defined phylogenetic clades, reassortment clusters, or recombinant lineages. We found that MDS embeddings accurately represented pairwise genetic distances including the intermediate placement of recombinant SARS-CoV-2 lineages between parental lineages. Clusters from t-SNE embeddings accurately recapitulated known phylogenetic clades, H3N2 reassortment groups, and SARS-CoV-2 recombinant lineages. We show that simple statistical methods without a biological model can accurately represent known genetic relationships for relevant human pathogenic viruses. Our open source implementation of these methods for analysis of viral genome sequences can be easily applied when phylogenetic methods are either unnecessary or inappropriate.

Influence of life-history traits on mitochondrial DNA substitution rates exceeds that of metabolic rates in teleost fishes

Abstract Understanding the molecular relevance of metabolic rate (MR) is crucial for unveiling the mechanisms driving the evolution of animals. In this study, we investigated the association between mitochondrial DNA characteristics and both resting and maximal MRs in conjunction with life-history traits among 139 species of teleost fish. We gathered fish MR data from various sources and procured sequences of 13 mitochondrial protein-encoding genes. We calculated the absolute substitution rate for entire nucleotide sequences and 4-fold degenerate sites of each gene, along with encoding amino acid sequences. Using the phylogenetic comparative method, we then explored the associations between MR and mitochondrial DNA absolute substitution rate. Additionally, we screened MR-associated single nucleotide variants in mitochondrial DNA. The findings indicate no positive correlation between MRs and any substitution rate values of both combined sequences and individual mitochondrial protein-coding genes, refuting the MR hypothesis. Instead, both maximum body size and longevity correlated negatively with molecular substitution rates, suggesting their influences on both mutation and fixation within mitochondrial genes in fish. Results also revealed significant correlations between base variation at ATP6_169 and both resting MR and maximum MR, identifying the unique ATP6_169G in Scombridae fish, which results in an extremely low isoelectric point (pI) value of the ATP6 protein. Considering its functional significance, the ATP6_169G in Scombridae fish might link to their lifestyle characterized by fast locomotion and high metabolic demands alongside a slower molecular evolutionary rate.

Functional redundancy in carrion decomposition by temperate forest ant communities

Abstract Scavenging of small avian corpses may provide ants with a valuable source of nutrients, a possibility poorly studied. Here, we assessed whether ants are efficient carrion‐decomposers of avian corpses in Mediterranean dehesas through an exclusion experiment comparing decomposition rates among three treatments: vertebrate exclusion, vertebrate + invertebrate exclusion and control. Treatments were applied in a paired design in bird cavities and on the ground in two zones to assess functional redundancy. Ant community was characterized by pitfall traps, and key functional traits influencing ants' presence on carrion were identified by using phylogenetic comparative methods. Carrion decomposition was influenced by the exclusion treatment, being significantly faster when ants and other invertebrates were not excluded, but not by location (cavity/ground). Vertebrates were less likely to detect baits in cavities and removed more bait mass in the most transformed zone. Twelve of 25 ant species in the community were found foraging on baits. Ant communities differed between carrion location and localities. Phylogenetic analyses revealed that the proneness of ant species to forage on carrion was unrelated to morphological or social traits, but behavioural, being higher among species foraging collectively. Our results show that ants play a functionally unique role in the decomposition of small corpses in dehesas, and particularly so in trees and less transformed pastureland. Decomposition involves different species in different microhabitats, suggesting high functional redundancy across ants. Our findings provide new insights into the role of ants as scavengers and expand our understanding of the functioning of Mediterranean communities.

Deciphering the Plastome and Molecular Identities of Six Medicinal "Doukou" Species.

The genus Amomum includes over 111 species, 6 of which are widely utilized as medicinal plants and have already undergone taxonomic revision. Due to their morphological similarities, the presence of counterfeit and substandard products remains a challenge. Accurate plant identification is, therefore, essential to address these issues. This study utilized 11 newly sequenced samples and extensive NCBI data to perform molecular identification of the six medicinal "Doukou" species. The plastomes of these species exhibited a typical quadripartite structure with a conserved gene content. However, independent variation shifts of the SC/IR boundaries existed between and within species. The comprehensive set of genetic sequences, including ITS, ITS1, ITS2, complete plastomes, matK, rbcL, psbA-trnH, and ycf1, showed varying discrimination of the six "Doukou" species based on both distance and phylogenetic tree methods. Among these, the ITS, ITS1, and complete plastome sequences demonstrated the highest identification success rate (3/6), followed by ycf1 (2/6), and then ITS2, matK, and psbA-trnH (1/6). In contrast, rbcL failed to identify any species. This research established a basis for a reliable molecular identification method for medicinal "Doukou" plants to protect wild plant resources, promote the sustainable use of medicinal plants, and restrict the exploitation of these resources.

RRmorph—a new R package to map phenotypic evolutionary rates and patterns on 3D meshes

The study of evolutionary rates and patterns is the key to understand how natural selection shaped the current and past diversity of phenotypes. Phylogenetic comparative methods offer an array of solutions to undertake this challenging task, and help understanding phenotypic variation in full in most circumstances. However, complex, three-dimensional structures such as the skull and the brain serve disparate goals, and different portions of these phenotypes often fulfil different functions, making it hard to understand which parts truly were recruited by natural selection. In the recent past, we developed tools apt to chart evolutionary rate and patterns directly on three-dimensional shapes, according to their magnitude and direction. Here, we present further developments of these tools, which now allow to restitute the mapping of rates and patterns with full biological realism. The tools are condensed in a new R software package.

Early detection of highly transmissible viral variants using phylogenomics.

As demonstrated by the SARS-CoV-2 pandemic, the emergence of novel viral strains with increased transmission rates poses a serious threat to global health. Statistical models of genome sequence evolution may provide a critical tool for early detection of these strains. Using a novel stochastic model that links transmission rates to the entire viral genome sequence, we study the utility of phylogenetic methods that use a phylogenetic tree relating viral samples versus count-based methods that use case counts of variants over time exclusively to detect increased transmission rates and identify candidate causative mutations. We find that phylogenies in particular can detect novel transmission-enhancing variants very soon after their origin and may facilitate the development of early detection systems for outbreak surveillance.

Phylogenetic relationships and lineage-specific mitochondrial gene rearrangement in Ophiuroidea: insights from mitochondrial genomes

Ophiuroids, the most diverse group of echinoderms, inhabit a vast array of ecological niches and play vital roles in benthic ecosystems as suspension feeders, scavengers and opportunists. Despite the important ecological roles played by Ophiuroidea, their evolutionary history and phylogenetic relationship is not yet fully understood. In this study, 47 mitochondrial genomes of ophiuroids, including 21 newly sequenced ones, were analyzed. tRNA duplication was firstly discovered in four species and a new start codon was identified for Ophiuroidea. Eighteen phylogenetic trees based on mitochondrial genomes consistently supported two major lineages, Ophintegrida and Euryophiurida. It further confirmed the monophyly of Euryalida and Ophiurida, respectively, as well as families represented by multiple species. Among 18 trees, only the two ML trees based on amino acid sequences using IQtree method supported monophyly of Amphilepidida and Ophiacanthida, consistent with current phylogenetic system of Ophiuroidea. This result highlighted the effect of phylogenetic analysis methods and datasets on tree topology, indicating that amino acid sequence data maybe more suitable for higher taxonomic level phylogenetic analysis of ophiuroids than nucleotide sequences. Four new gene orders of 13 protein-coding genes + two rRNAs and 12 new gene orders of all 37 genes were identified. Mitochondrial gene orders were highly variable in Ophiacanthida, but were extremely conserved in Eurylida. Additionally, both branch lengths and estimated positive selection varied among the four orders, and a positive relationship between branch lengths and mitochondrial gene rearrangement rates was revealed, suggesting distinctly different evolutionary history among the four major clades of Ophiuroidea. Overall, we (1) reconstructed the phylogenetic relationship based on mitochondrial genome, supporting the current phylogenetic system in Ophiuroidea, (2) revealed a high variability in mitochondrial gene rearrangement among the four orders, (3) provided the first evidence to link gene rearrangement and nucleotide substitution in Echinodermata.

Comparative muscle anatomy of the anuran pelvis and hindlimb in relation to locomotor mode.

Frogs have a highly conserved body plan, yet they employ a diverse array of locomotor modes, making them ideal organisms for investigating the relationships between morphology and locomotor function, in particular whether anatomical complexity is a prerequisite for functional complexity. We use diffusible iodine contrast-enhanced microCT (diceCT) imaging to digitally dissect the gross muscle anatomy of the pelvis and hindlimbs for 30 species of frogs representing five primary locomotor modes, including the first known detailed dissection for some of the world's smallest frogs, forming the largest digital comparative analysis of musculoskeletal structure in any vertebrate clade to date. By linking musculoskeletal dissections and phylogenetic comparative methods, we then quantify and compare relationships between anatomy and function across over 160 million years of anuran evolution. In summary, we have found that bone lengths and pelvic crest sizes are generally not reliable predictors of muscle sizes, which highlights important implications for future palaeontological studies. Our investigation also presents previously unreported differences in muscle anatomy between frogs specialising in different locomotor modes, including several of the smallest frog hindlimb muscles, which are extremely difficult to extract and measure using traditional approaches. Furthermore, we find evidence of many-to-one and one-to-many mapping of form to function across the phylogeny. Additionally, we perform the first quantitative analysis of how the degree of muscle separation can differ between frogs. We find evidence that phylogenetic history is the key contributing factor to muscle separation in the pelvis and thigh, while the separation of shank muscles is influenced more strongly by locomotor mode. Finally, our anatomical 3D reconstructions are published alongside this manuscript to contribute towards future research and serve as educational materials.

Genomic data provide insights into the classification of extant termites

The higher classification of termites requires substantial revision as the Neoisoptera, the most diverse termite lineage, comprise many paraphyletic and polyphyletic higher taxa. Here, we produce an updated termite classification using genomic-scale analyses. We reconstruct phylogenies under diverse substitution models with ultraconserved elements analyzed as concatenated matrices or within the multi-species coalescence framework. Our classification is further supported by analyses controlling for rogue loci and taxa, and topological tests. We show that the Neoisoptera are composed of seven family-level monophyletic lineages, including the Heterotermitidae Froggatt, Psammotermitidae Holmgren, and Termitogetonidae Holmgren, raised from subfamilial rank. The species-rich Termitidae are composed of 18 subfamily-level monophyletic lineages, including the new subfamilies Crepititermitinae, Cylindrotermitinae, Forficulitermitinae, Neocapritermitinae, Protohamitermitinae, and Promirotermitinae; and the revived Amitermitinae Kemner, Microcerotermitinae Holmgren, and Mirocapritermitinae Kemner. Building an updated taxonomic classification on the foundation of unambiguously supported monophyletic lineages makes it highly resilient to potential destabilization caused by the future availability of novel phylogenetic markers and methods. The taxonomic stability is further guaranteed by the modularity of the new termite classification, designed to accommodate as-yet undescribed species with uncertain affinities to the herein delimited monophyletic lineages in the form of new families or subfamilies.

A Guided Tour of Phylogenetic Comparative Methods for Studying Trait Evolution

Phylogenetic comparative methods are important tools in biology, providing insights into the way traits evolve. There are many technical resources describing how these methods work. Our aim here is to complement these with an overview of the types of biological questions that can be addressed by different methods and to outline potential pitfalls and considerations when embarking on comparative studies. First, we introduce what comparative methods are and why they are important. Second, we outline how they can be used to understand when, where, and how frequently traits evolve. Third, we examine how the coevolution of traits within and between species can be studied, along with patterns of causality. Finally, we discuss how to approach comparative analyses and the ways in which different types of data, such as published relationships, omic, and remote sensing data, can be integrated.

Detecting branching rate heterogeneity in multifurcating trees with applications in lineage tracing data.

Understanding cellular birth rate differences is crucial for predicting cancer progression and interpreting tumor-derived genetic data. Lineage tracing experiments enable detailed reconstruction of cellular genealogies, offering new opportunities to measure branching rate heterogeneity. However, the lineage tracing process can introduce complex tree features that complicate this effort. Here, we examine tree characteristics in lineage tracing-derived genealogies and find that editing window placement leads to multifurcations at a tree's root or tips. We propose several ways in which existing tree topology-based metrics can be extended to test for rate heterogeneity on trees even in the presence of lineage-tracing associated distortions. Although these methods vary in power and robustness, a test based on the statistic effectively detects branching rate heterogeneity in simulated lineage tracing data. Tests based on other common statistics ( and the Sackin index) show interior performance to . We apply our validated methods to xenograft experimental data and find widespread rate heterogeneity across multiple study systems. Our results demonstrate the potential of tree topology statistics in analyzing lineage tracing data, and highlight the challenges associated with adapting phylogenetic methods to these systems.

Non‐linear phylogenetic regression using regularised kernels

Abstract Phylogenetic regression is a type of generalised least squares (GLS) method that incorporates a modelled covariance matrix based on the evolutionary relationships between species (i.e. phylogenetic relationships). While this method has found widespread use in hypothesis testing via phylogenetic comparative methods, such as phylogenetic ANOVA, its ability to account for non‐linear relationships has received little attention. To address this, here we implement a phylogenetic Kernel Ridge Regression (phyloKRR) method that utilises GLS in a high‐dimensional feature space, employing linear combinations of phylogenetically weighted data to account for non‐linearity. We analysed two biological datasets using the Radial Basis Function and linear kernel function. The first dataset contained morphometric data, while the second dataset comprised discrete trait data and diversification rates as response variable. Hyperparameter tuning of the model was achieved through cross‐validation rounds in the training set. In the tested biological datasets, phyloKRR reduced the error rate (as measured by RMSE) by around 20% compared to linear‐based regression when data did not exhibit linear relationships. In simulated datasets, the error rate decreased almost exponentially with the level of non‐linearity. These results show that introducing kernels into phylogenetic regression analysis presents a novel and promising tool for complementing phylogenetic comparative methods. We have integrated this method into Python package named phyloKRR, which is freely available at: https://github.com/ulises‐rosas/phylokrr.

Functional trait mismatch between native and introduced bee pollinators servicing a global fruit crop

BackgroundUnderstanding connections between biodiversity and ecosystem services can be enhanced by shifting focus from species richness to functional trait-based approaches, that when paired with comparative phylogenetic methods can provide even deeper insights. We investigated the functional ecology and phylogenetic diversity of pollination services provided by hymenopteran insects visiting apple flowers in orchards surrounded by either ‘natural’ or ‘disturbed’ landscapes in New South Wales, Australia. We assessed whether morphological and behavioural traits (hairiness, body size, glossa length, pollen load purity, and probability of loose pollen) exhibited non-random phylogenetic patterns. Then, explored whether bees, the primary pollinators in this system, filled unique or overlapping functional entities (FEs). For each landscape, we calculated phylogenetic diversity and used FEs to assess functional richness, evenness, and diversion.ResultsA phylogenomic matrix based on ultraconserved elements (UCEs; 1,382,620 bp from 1,969 loci) was used to infer a fully-resolved and well-supported maximum likelihood phylogeny for 48 hymenopteran morphospecies. There was no significant difference in species richness between landscape categories. Pollinator communities at natural sites had higher phylogenetic complexity (X = 2.37) and functional divergence (x̄ = 0.74 ± 0.02 s.e.) than disturbed sites (X = 1.65 and x̄ = 0.6 ± 0.01 s.e.). Hairiness showed significant phylogenetic clustering (K = 0.94), whereas body size, glossa length, and loose pollen showed weaker non-random phylogenetic patterns (K between 0.3–0.5). Pollen load purity showed no association with phylogeny. The assemblage of 17 bee morphospecies comprised nine FEs: eight FEs consisted of native bees with three containing 65% of all native bee taxa. The introduced honey bee (Apis mellifera) occupied a unique FE, likely due to its different evolutionary history. Both landscape types supported six FEs each with three overlapping: two native bee FEs and the honey bee FE.ConclusionsBee hairiness was the only functional trait to exhibit demonstrable phylogenetic signal. Despite differences in species richness, and functional and phylogenetic diversity between orchard landscape types, both maintained equal bee FE numbers. While no native bee taxon was analogous to the honey bee FE, four native bee FEs shared the same hairiness level as honey bees. Health threats to honey bee populations in Australia will likely disrupt pollination services to apple, and other pollination-dependent food crops, given the low level of functional redundancy within the investigated pollinator assemblages.

A macroevolutionary analysis of European Late Upper Palaeolithic stone tool shape using a Bayesian phylodynamic framework.

Phylogenetic models are commonly used in palaeobiology to study the patterns and processes of organismal evolution. In the human sciences, phylogenetic methods have been deployed for reconstructing ancestor-descendant relationships using linguistic and material culture data. Within evolutionary archaeology specifically, phylogenetic analyses based on maximum parsimony and discrete traits dominate, which sets limitations for the downstream role cultural phylogenies, once derived, can play in more elaborate analytical pipelines. Recent methodological advances in Bayesian phylogenetics, however, now allow us to infer evolutionary dynamics using continuous characters. Capitalizing on these developments, we here present an exploratory analysis of cultural macroevolution of projectile point shape evolution in the European Final Palaeolithic and earliest Mesolithic (approx. 15 000-11 000 BP) using a Bayesian phylodynamic approach and the fossilized birth-death process model. This model-based approach leaps far beyond the application of parsimony, in that it not only produces a tree, but also divergence times, and diversification rates while incorporating uncertainties. This allows us to compare rates to the pronounced climatic changes that occurred during our time frame. While common in cultural evolutionary analyses of language, the extension of Bayesian phylodynamic models to archaeology arguably represents a major methodological breakthrough.

Multivariate analysis of phenotypic diversity elite bread wheat (Triticum aestivum L.) genotypes from ICARDA in Ethiopia

Wheat is an important crop for food security, providing a source of protein and energy for the growing population in Ethiopia. However, both biotic and abiotic factors limit national wheat productivity. The availability of genetically diverse wheat genotypes is crucial for developing new wheat varieties that are both high-yielding and resilient to stress. Therefore, this field trial aimed to assess phenotypic variation and relationship among ICARDA-derived bread wheat genotypes using multivariate analysis techniques. The trial was conducted at three locations: Enewari, Wogere, and Kulumsa using an alpha lattice design with two replications during the main cropping seasons of 2022 and 2023. Phenotypic data on eight agronomic traits and the severity of yellow rust were collected and R programming was used for data analysis. Individual and combined location data analysis of variance showed significant differences (p ≤ 0.05) among genotypes for most of the studied traits. The highest heritability and genetic advance as a percentage of the mean were observed in days to heading (90.8, 21.29), plant height (72.4, 28.6), seeds per spike (61.7, 28), thousand kernel weight (61.9, 12), and area under the disease progress curve (67, 39.8), suggesting a predominance of additive gene action. Grain yield showed a strong positive correlation with days to maturity, plant height, spike length, spikelet per spike, and thousand kernel weight for each location. Dendrogram and phylogenetic tree methods were used to group genotypes into four genetically distinct clusters. Cluster II and III had the greatest inter-cluster distance, indicating higher diversity among their genotypes. This study identified new candidate genotypes with superior agronomic performance, high grain yield traits, and robust resistance to yellow rust, making them valuable for both current and future wheat breeding programs. Additionally, the comprehensive dataset produced in this study could facilitate the identification of genetic variations influencing desirable traits through genome-wide association analysis.

Nest site correlates with nest type and body size in Troglodytidae passerines.

Nest characteristics are highly variable in the Passeriformes, but the macroevolutionary patterns observable for birds in general are not necessarily valid for specific families, suggesting that both global and within-family studies are needed. Here, we used phylogenetic comparative methods to address the evolutionary patterns of nest type, nest site and habitat in the Troglodytidae, a passerine group with diversified nest and habitat characteristics. The common ancestor of the Troglodytidae likely constructed enclosed nests within sheltered sites (cavity or crevice), but the radiation of the group was characterized by (i) shifts to exposed nest sites (vegetation) with retention of enclosed nests or (ii) retention of sheltered sites with nest simplification (cup nests). Nest site and nest type presented strong phylogenetic conservatism and evolved interdependently, while habitat was poorly correlated with nest evolution. A phylogenetic mixed modelling approach showed that sheltered nest sites were associated with small body size, likely to avoid competition with other animals for these places. With these results, we improve the understanding of nest character evolution in the Troglodytidae and reveal evolutionary aspects not observed so far for passerine birds.

The meaning of mass extinctions and what the fossil record tells us about angiosperm survival at K-Pg: a reply to Hagen (2024).

Last year, we published research using phylogenetic comparative methods (PCMs) to reveal no phylogenetic evidence for elevated lineage-level extinction rates in angiosperms across K-Pg (Thompson JB, Ramírez-Barahona S. 2023 No phylogenetic evidence for angiosperm mass extinction at the Cretaceous-Palaeogene (K-Pg) boundary. Biol. Lett. 19, 20230314. (doi:10.1098/rsbl.2023.0314)), results that are in step with the global angiosperm fossil record. In a critique of our paper (Hagen ER. 2024 A critique of Thompson and Ramírez-Barahona (2023) or: how I learned to stop worrying and love the fossil record. EcoEvoRxiv. (doi:10.32942/X2631W)), simulation work is presented to argue we erred in our methodological choices and interpretations, and that we should have deferred to fossil evidence. In our opinion, underlying this critique are poor methodological choices on simulations and philosophical problems surrounding the definition of a mass extinction event, which leads to incorrect interpretations of both the fossil record and PCMs. We further argue that deferring to one source of evidence in favour of the other shuts the door to important evolutionary and philosophical questions.