Phylogenetic Signal Research Articles

Uropygial gland size increases isometrically with body size in 35 North American bird species

Abstract The uropygial gland and the oils it produces have been shown to serve important functions in many bird species including plumage maintenance and chemical communication. Previous species comparisons of uropygial gland size have only been conducted in South American and European birds and have found little to no phylogenetic signal. Here, we document uropygial gland measurements of 34 different passerines, 1 hybrid chickadee population, and 1 Piciformes in eastern Pennsylvania, most of which are reported for the first time. Uropygial gland size is positively related to overall body size, controlling for phylogenetic relatedness. We show a significant phylogenetic signal of relative uropygial gland size and many of the species with the largest gland sizes belong to the Paridae. Overall, females show a nonsignificant but slight trend of larger relative uropygial gland sizes than males. This effect is stronger in some species than others and can also be seasonally dependent. We found no effect of relative total eggshell surface area or nest location on relative uropygial gland size. Together our results provide the first documentation of uropygial gland sizes in many of these North American species and provide interesting insight into factors influencing relative gland size including sex, season, and species.

Cranial variation in species and subspecies of kangaroo rats (Dipodomys, Dipodomyinae, Rodentia) according to geometric morphometrics.

Traditional Dipodomys (sub)species identification uses geography, phenotype, and external/skull measurements. Such measurements are correlated with size and thus redundant. I assessed the value of scaled cranial shape, based on two-dimensional landmarks (analyzed using geometric morphometric methods) in distinguishing Dipodomys taxa, and in summarizing their variation. My dataset includes 601 adult specimens from 20 species (49 operational taxonomic units - OTUs) across 190 localities. Cranial shape was highly useful in classifying Dipodomys taxa without considering geography. The auditory bulla was the most variable region-taxa differed in its hypertrophy, accompanied by different degrees of nearby structure crowding. Cranial shape was weakly allometric, with no significant sexual dimorphism. Weak size dimorphism was detected. (Sub)specific taxonomy is not reflective of shape variation, as the number of subspecies per species is not associated with disparity. Shape had significant phylogenetic signal, but subspecies did not always cluster with conspecifics and species did not always cluster according to phylogenetic relationship/taxonomy. Shape variation was correlated with climate, and species differed in morphological disparity and degree of specialization, which may contribute to divergence in shape variation patterns from phylogeny. D. deserti was the most specialized species, diverging greatly from the genus mean; D. heermanni was the least specialized. This study provides new insights into morphological variation of North American keystone species, several of conservation interest, for example, D. heermanni berkeleyensis, D. h. dixoni, D. nitratoides brevinasus, and D. n. nitratoides.

Evolutionary history shapes variation of wood density of tree species across the world

The effect of evolutionary history on wood density variation may play an important role in shaping variation in wood density, but this has largely not been tested. Using a comprehensive global dataset including 27,297 measurements of wood density from 2621 tree species worldwide, we test the hypothesis that the legacy of evolutionary history plays an important role in driving the variation of wood density among tree species. We assessed phylogenetic signal in different taxonomic (e.g., angiosperms and gymnosperms) and ecological (e.g., tropical, temperate, and boreal) groups of tree species, explored the biogeographical and phylogenetic patterns of wood density, and quantified the relative importance of current environmental factors (e.g., climatic and soil variables) and evolutionary history (i.e., phylogenetic relatedness among species and lineages) in driving global wood density variation. We found that wood density displayed a significant phylogenetic signal. Wood density differed among different biomes and climatic zones, with higher mean values of wood density in relatively drier regions (highest in subtropical desert). Our study revealed that at a global scale, for angiosperms and gymnosperms combined, phylogeny and species (representing the variance explained by taxonomy and not direct explained by long-term evolution process) explained 84.3% and 7.7% of total wood density variation, respectively, whereas current environment explained 2.7% of total wood density variation when phylogeny and species were taken into account. When angiosperms and gymnosperms were considered separately, the three proportions of explained variation are, respectively, 84.2%, 7.5% and 6.7% for angiosperms, and 45.7%, 21.3% and 18.6% for gymnosperms. Our study shows that evolutionary history outpaced current environmental factors in shaping global variation in wood density.

Geometric morphometrics casts light on phylogenetic relevance of cephalopod beak morphological.

The feeding organ of cephalopod species, the beak, can be used to reveal important ecological information. In this study, geometric morphometric approaches were employed to investigate the phylogenetic relevance and classification effect of beak lateral profile shape. The two-dimensional beak morphologies of 1164 pairs of 24 species from 13 genera and five families were constructed, and their evolutionary relationships and taxonomic status were confirmed using geometric morphometrics and molecular biology approaches. We also assessed the phylogenetic signals of beak shape. The analysis results show shape variation in the beak mainly in the rostrum, hood, and lateral wall. The overall shape parameters (all PCs) of the upper and lower beak are more useful for species identification. The shapes of the upper and lower beak show a strong phylogenetic signal, and the phenogram based on the beak shape basically reflected the families' taxonomic positions. We also hypothesized that the shape variation in the beaks of cephalopods may be ascribed to genetic and environmental differences. In summary, beaks are a reliable material for the classification of cephalopod species. Geometric morphometric approaches are a powerful tool to reveal the identification, phylogenetic relevance and phenotypic diversity of beak shape in cephalopods.

Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists.

Habitat type is a strong determinant of microbial composition. Habitat interfaces, such as the boundary between aquatic and terrestrial systems, present unique combinations of abiotic factors for microorganisms to contend with. Aside from the spillover of certain harmful microorganisms from agricultural soils into water (e.g. fecal coliform bacteria), we know little about the extent of soil-water habitat switching across microbial taxa. In this study, we developed a proof-of-concept system to facilitate the capture of putatively generalist microorganisms that can colonize and persist in both soil and river water. We aimed to examine the phylogenetic breadth of putative habitat switchers and how this varies across different source environments. Microbial composition was primarily driven by recipient environment type, with the strongest phylogenetic signal seen at the order level for river water colonizers. We also identified more microorganisms colonizing river water when soil was collected from a habitat interface (i.e. soil at the side of an intermittently flooded river, compared to soil collected further from water sources), suggesting that environmental interfaces could be important reservoirs of microbial habitat generalists. Continued development of experimental systems that actively capture microorganisms that thrive in divergent habitats could serve as a powerful tool for identifying and assessing the ecological distribution of microbial generalists.

Phylogenomics of the geometrid tribe Palyadini (Lepidoptera: Geometridae) reveals contrasting patterns of phylogenetic signal in wing colour characters.

Next generation sequencing techniques currently represent a practical and efficient way to infer robust evolutionary hypotheses. Palyadini is a small Neotropical tribe of geometrid moths composed of six genera that feature strikingly colourful wings. Here, we investigated patterns of evolution and amount of phylogenetic signal contained in various colour characters featured in the wings of members of this tribe by (i) inferring a robust phylogenetic hypothesis using ultraconserved elements (UCEs), and afterwards, (ii) mapping the morphological characters onto the molecular topology under a parsimonious ancestral character optimization. Our matrix, obtained with 60% completeness, includes 754 UCE loci and 73 taxa (64 ingroup, nine outgroup). Maximum likelihood and parsimony generated largely identical topologies with strongly supported nodes, except for one node inside the genus Opisthoxia. According to our topology, most wing colour characters are reconstructed as homoplastic, particularly at the tribe level, but five of the seven provide evidence supporting common ancestry at the genus level. Our results emphasize, once again, that no character system is infallible, and that more research is necessary to take our understanding of the evolution of wing colour in moths to a level comparable with the knowledge we have for butterflies.

Plant functional traits couple with range size and shape in European trees

AbstractAimPlant functional traits are frequently proposed as influential factors in species distribution. However, there is a gap in assessing how plant resource‐economic traits relate to the size and shape of a species' geographical range, and to what extent these relationships are conserved over evolutionary history. Specifically, an acquisitive strategy (characterized by heightened metabolism, shorter lifespan and quicker generation turnover) may promote isotropic range formations, resulting in less elongated and larger ranges. Here, I tested this link using data from 98 native European tree species.LocationPalaearctic.Time periodPresent.Major taxa studiedTrees.MethodsI used chorological maps to quantify two independent range attributes: species' range area and elongation. I considered 28 functional traits linked to resource‐use strategy measured in above‐ and below‐ground organs. I used multi‐response phylogenetic mixed models to calculate the conservative trait correlation (CTC) and the phylogenetically independent correlation (IND) component of each functional trait with range area and elongation.ResultsRange area positively correlated with resource acquisitive strategies, while range elongation correlated with resource conservative strategies. This pattern was consistent across the examined traits but statistically significant in seven out of the 28 traits, including specific leaf area, specific root area and root mycorrhizal colonization. Traits related to leaf and root nutritional status exhibited the weakest relationships with range attributes. Significant correlations were more frequent in the IND component and often showed contrasting trends compared to CTC.Main conclusionsPlant resource‐use strategy emerges as a relevant factor to gain insights on what shapes species' geographical distribution, alongside more established drivers such as dispersal limitation and climatic tolerance. Trait‐range relationships are driven by processes leaving a weak phylogenetic signature. These processes may result from direct selection, where functional traits impact range attributes, or indirect effects, such as the co‐variation of ranges and traits with environmental niche optima.

Morphological and molecular data combined reveal inter- and intraspecific cranial shape variations in bats of Artibeus Leach, 1821 (Chiroptera: Phyllostomidae)

Abstract Since morphological traits may overlap among species within a complex, the integration of morphological and mitochondrial data could provide crucial insights for distinguishing species, as observed in fruit-eating bats of the genus Artibeus. Therefore, the application of geometric morphometric (GM) techniques could yield more refined and robust analyses of inter- and intraspecific variations. In this study, we generated two datasets: one with molecular delimitation data based on the barcode region (COI) and the other with cranial size and shape data using GM methods. Our aims were to investigate variations between large and small species within the genus Artibeus, as well as to explore potential factors influencing such variations. The results from species delimitation revealed molecular operational taxonomic units (MOTUs) supporting the morphological identification. Analyses using GM techniques demonstrated significant inter- and intraspecific variations in cranial size and shape among Artibeus species. The combined outcomes suggest the absence of a significant phylogenetic signal influencing skull variation. This scenario indicates that potential historical ecological factors may have directly influenced the cranial morphology of these species, acting as significant selection forces in geographical space and generating intraspecific variations in Artibeus planirostris.

Evolutionary history and environmental variability structure contemporary tropical vertebrate communities

AbstractAimTropical regions harbour over half of the world's mammals and birds, but how their communities have assembled over evolutionary timescales remains unclear. To compare eco‐evolutionary assembly processes between tropical mammals and birds, we tested how hypotheses concerning niche conservatism, environmental stability, environmental heterogeneity and time‐for‐speciation relate to tropical vertebrate community phylogenetic and functional structure.LocationTropical rainforests worldwide.Time periodPresent.Major taxa studiedGround‐dwelling and ground‐visiting mammals and birds.MethodsWe used in situ observations of species identified from systematic camera trap sampling as realized communities from 15 protected tropical rainforests in four tropical regions worldwide. We quantified standardized phylogenetic and functional structure for each community and estimated the multi‐trait phylogenetic signal (PS) in ecological strategies for the four regional species pools of mammals and birds. Using linear regression models, we test three non‐mutually exclusive hypotheses by comparing the relative importance of colonization time, palaeo‐environmental changes in temperature and land cover since 3.3 Mya, contemporary seasonality in temperature and productivity and environmental heterogeneity for predicting community phylogenetic and functional structure.ResultsPhylogenetic and functional structure showed non‐significant yet varying tendencies towards clustering or dispersion in all communities. Mammals had stronger multi‐trait PS in ecological strategies than birds (mean PS: mammal = 0.62, bird = 0.43). Distinct dominant processes were identified for mammal and bird communities. For mammals, colonization time and elevation range significantly predicted phylogenetic clustering and functional dispersion tendencies respectively. For birds, elevation range and contemporary temperature seasonality significantly predicted phylogenetic and functional clustering tendencies, respectively, while habitat diversity significantly predicted functional dispersion tendencies.Main conclusionsOur results reveal different eco‐evolutionary assembly processes structuring contemporary tropical mammal and bird communities over evolutionary timescales that have shaped tropical diversity. Our study identified marked differences among taxonomic groups in the relative importance of historical colonization and sensitivity to environmental change.

Abstract 6928: Expressed mitochondrial variants capture patterns of tumor evolution at single-cell level

Abstract Single-cell lineage tracing (scLT) has recently emerged as a promising tool to investigate cancer evolution. Among other scLT markers, mitochondrial variants (MT-SNVs) have been successfully used to track clones in a variety of experimental and clinical settings. However, in spite of the dynamic accrual of such genetic mutations, analysis of MT-SNVs variation has often been limited to standard clustering procedures, not exploiting the information associated with these markers at full potential. Here, we benchmarked expressed MT-SNVs-based single-cell phylogenies. To this end, we generate two single-cell multi-omics datasets: i) a benchmarking dataset, with joint profiling of MT-SNVs, gene expression and ground truth (GT) clonal identity (from lentiviral barcodes cells), and ii) a clinical cohort of wild type and mutated SRFS2 Acute Myeloid Leukemia patients, at diagnosis, with joint profiling of MT-SNVs, gene expression and targeted nuclear SNVs. We first leveraged our benchmarking dataset for validation purposes, taking advantage of its different levels of clonal complexities (in vitro clonal mixtures vs in vivo xenografts) and its longitudinal nature (i.e., matched primary tumor-lung metastasis couples). Supervised analysis detected (GT) clonal-specific mutations rarer than previously shown, but significantly associated with GT clonal labels. The performance of tested feature selection methods varied wildly in terms of GT MT-SNVs recover, with higher False Positive than False Negative Rates. Accurate detection of GT-clones from MT-SNVs correlated with samples clonal complexity, with a substantial number of GT-clones sub-optimally detected in the highest complexity sample generated. Longitudinal analysis of matched primary tumor-metastasis couples revealed remarkable stability of MT-SNVs, corroborating evidence from other studies without longitudinal GT lentiviral clones. We then asked whether expressed MT-SNVs hold enough signal to reconstruct reliable single-cell phylogenies. Transfer Bootstrap (TS) supports of reconstructed trees correlated with clades size, with a significant number of deep clades showing high (>.70) TS values across samples and bootstrapping procedures. Moreover, GT clonal labels significantly clustered across phylogenies, suggesting high phylogenetic signal. Finally, we investigated evolutionary patterns in our clinical cohort. Here, we found independent acquisition of both nuclear- and MT-SNVs by distinct normal and malignant lineages, and characterized patterns of gene expression inheritance along recovered phylogenies. All in all, our data support the emerging role of MT-variants based lineage tracing approaches in cancer evolution studies, highlighting intrinsic limitations and potential of these endogenous markers for retrospective, phylo-phenotypic analysis. Citation Format: Andrea Cossa, Alberto Dalmasso, Andrea Tirelli, Zhan Yinxiu, Chiara Caprioli, Giulia Perticari, Pier Giuseppe Pelicci. Expressed mitochondrial variants capture patterns of tumor evolution at single-cell level [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6928.

Floral traits and their connection with Pollinators and Climate.

Floral characteristics vary significantly among plant species, and multiple underlying factors govern this diversity. Although it is widely known that spatial variation in pollinator groups can exert selection on floral traits, the relative contribution of pollinators and climate to the variation of floral traits across large geographic areas remains a little-studied area. Besides furthering our conceptual understanding of these processes, gaining insight into the topic is also of conservation relevance: understanding how climate may drive floral traits variation can serve to protect plant-pollinator interactions under global change conditions. We used Rhododendron as a model system and collected floral traits (corolla length, nectar volume and concentrations), floral visitors, and climatic data on 21 Rhododendron species across two continents (North America-Appalachians and Asia-Himalaya). Based on this we quantified the influence of climate and pollinators to floral traits using phylogeny-informed analyses. Our results indicate that there is substantial variation in pollinators and morphological traits across Rhododendron species and continents. We came across four pollinator groups: birds, bees, butterflies, and flies. Asian species were commonly visited by birds, bees, and flies, while bees and butterflies were the most common visitors of North American species. The visitor identity explained nectar trait variation, with flowers visited by birds presenting higher volumes of dilute nectar and those visited by insects producing concentrated nectar. Nectar concentration and corolla length exhibited a strong phylogenetic signal across the analysed set of species. We also found that nectar trait variation in the Himalaya could also be explained by climate, which presented significant interactions with pollinator identity. Our results indicate that both pollinators and climate contribute and interact to drive nectar trait variation, suggesting that both can affect pollination interactions and floral (and plant) evolution individually and interacting with each other.

Evolution of wing shape in geometrid moths: phylogenetic effects dominate over ecology.

Locomotory performance is an important determinant of fitness in most animals, including flying insects. Strong selective pressures on wing morphology are therefore expected. Previous studies on wing shape in Lepidoptera have found some support for hypotheses relating wing shape to environment-specific selective pressures on aerodynamic performance. Here, we present a phylogenetic comparative study on wing shape in the lepidopteran family Geometridae, covering 374 species of the northern European fauna. We focused on eleven wing traits including aspect ratio, wing roundness, and the pointedness of the apex, as well as the ratio of forewing and hindwing areas. All measures were taken from images available on the internet, using a combination of tools available in Fiji software and in R. We found that wing shape demonstrates a phylogenetically conservative pattern of evolution in Geometridae, showing similar or stronger phylogenetic signal than many of its potential predictors. Several wing traits showed statistically significant associations with predictors such as body size, phenology, and preference for forest habitats. Overall, however, all of these associations remained notably weak, with no wing shape being excluded for any value of the predictors, including body size. We conclude that, in geometrids, wing traits do not readily respond to selective pressures optimising aerodynamic performance of the moths in different environments. Selection on wing shape may nevertheless operate through other functions of the wings, with the effectiveness of crypsis at rest being a promising candidate for further studies.

Phylogenetic Economics: Animal Models and the Study of Choice

Abstract While the investigation of non-human economic decision-making is increasingly popular, it is not clear exactly what role it can play in settling debates in economics. This paper argues that—contrary to recent claims otherwise—data on animal decision-making do not help in (dis–)confirming economic theories of choice. Rather, such data help in spelling out the representationally proper domains of models of choice. To play this role, though, these data must be placed into phylogenetic comparative analyses: correlations with specific environmental features need to be assessed, and these correlations need to be corrected for the presence of phylogenetic signals.

Weak phylogenetic effect on specialist plant assemblages and their persistence on habitat islands

AbstractAimThe influence of species phylogenetic relatedness on the formation of insular assemblages remains understudied in functional island biogeography, especially for terrestrial habitat islands (i.e. distinct habitat patches embedded in a matrix that differ in the prevailing environmental conditions). Here, we tested three eco‐evolutionary hypotheses: (1) functional specialization of species (i.e. specialism) is associated with phylogenetic clustering at the habitat archipelago scale, (2) such clustering increases with insularity at the habitat island scale and (3) traits indicative of effective local persistence strategies shape island specialism.LocationTerrestrial habitat islands, Europe (Fens in the Western Carpathians, Outcrops in Moravia and Mountaintops in the Cantabrian Range).TaxonAngiosperms.MethodsWe assessed the phylogenetic relatedness of habitat specialists in three different archipelagos composed of terrestrial habitat islands based on phylogenetic signals and phylogenetic diversity (PD) measures. We estimated the effect of insularity on PD using linear models and the effect of persistence traits on specialism using phylogenetic logistic regressions.ResultsOur hypotheses were largely not supported. Outcrop and mountaintop specialist assemblages did not exhibit any phylogenetic structuring, whereas fen specialists were clustered at the archipelago scale. Therefore, insularity seems not to act as a selective force for phylogenetic structure, and ecologically important persistence traits do not operate as precursors of specialism.Main ConclusionsOur results show that species phylogenetic relatedness plays a minor role in shaping habitat island specialist assemblages. Furthermore, the effects of phylogenetic relatedness on assemblages of island specialists are system and scale dependent. Finally, accounting for species' phylogenetic relatedness on persistence traits yielded results similar to previous studies, which corroborates the positive relationship between insularity and functional traits (indicative of enhanced plant persistence abilities with increasing within‐archipelago insularity).

Qineryangia, a new genus from the Hengduan Mountains and new insights into the phylogeny of the subtribe Crepidinae (Cichorieae, Asteraceae)

AbstractThe Crepidinae are the largest subtribe of the Cichorieae (Asteraceae). Debate remains over the circumscription and phylogeny of this subtribe, mainly due to its complex morphology and the poor phylogenetic signal provided by traditional Sanger sequencing markers. In this study, a well‐resolved phylogeny of the subtribe Crepidinae, consisting of seven highly supported clades, was obtained for the first time using nuclear data with a phylogenomics approach (Hyb‐Seq). Using this phylogeny along with other evidence, we propose a new taxonomic framework for the Crepidinae with seven lines and 29 genera, which merges subtribe Chondrillinae with the Crepidinae. We also describe a new monotypic genus, Qineryangia, that is characterized by broad involucres, loose imbricate phyllaries with wavy margins, and thick pappus bristles.

Incomplete lineage sorting and gene flow within Allium (Amayllidaceae)

The phylogeny and systematics of the genus Allium have been studied with a variety of diverse data types, including an increasing amount of molecular data. However, strong phylogenetic discordance and high levels of uncertainty have prevented the identification of a consistent phylogeny. The difficulty in establishing phylogenetic consensus and evidence for genealogical discordance make Allium a compelling test case to assess the relative contribution of incomplete lineage sorting (ILS), gene flow and gene tree estimation error on phylogenetic reconstruction. In this study, we obtained 75 transcriptomes of 38 Allium species across 10 subgenera. Whole plastid genome, single copy genes and consensus CDS were generated to estimate phylogenetic trees both using coalescence and concatenation methods. Multiple approaches including coalescence simulation, quartet sampling, reticulate network inference, sequence simulation, theta of ILS and reticulation index were carried out across the CDS gene trees to investigate the degrees of ILS, gene flow and gene tree estimation error. Afterward, a regression analysis was used to test the relative contributions of each of these forms of uncertainty to the final phylogeny. Despite extensive topological discordance among gene trees, we found a fully supported species tree that agrees with the most of well-accepted relationships and establishes monophyly of the genus Allium. We presented clear evidence for substantial ILS across the phylogeny of Allium. Further, we identified two ancient hybridization events for the formation of the second evolutionary line and subg. Butomissa as well as several introgression events between recently diverged species. Our regression analysis revealed that gene tree inference error and gene flow were the two most dominant factors explaining for the overall gene tree variation, with the difficulty in disentangling the effects of ILS and gene tree estimation error due to a positive correlation between them. Based on our efforts to mitigate the methodological errors in reconstructing trees, we believed ILS and gene flow are two principal reasons for the oft-reported phylogenetic heterogeneity of Allium. This study presents a strongly-supported and well-resolved phylogenetic backbone for the sampled Allium species, and exemplifies how to untangle heterogeneity in phylogenetic signal and reconstruct the true evolutionary history of the target taxa.

The strength of the phylogenetic signal in syntactic data

While phonological change has played a central role in assessing linguistic relatedness since the nineteenth century, the usefulness of syntactic change for this purpose has remained debated – despite recent work on the question with a variety of results. In our study, we analyze the phylogenetic signal of syntactic data using state-of-the-art Bayesian algorithms and the SSWL database (Koopman 2012–). With the phylogenetic model, we infer a minimally biased family tree. We find that, generally, the phylogenetic signal in the syntactic dataset is low. The model fails to infer larger-order subgroupings that would be found further back in time. This is in contrast to the clear-cut groupings we can obtain from running this type of model on phonological databases. This raises the question how well these syntactic properties encode phylogenetic information. As it stands, the model fails to provide evidence for strong phylogenetic signal despite the rich dataset and methods.

Phylogenomics of Neogastropoda: the backbone hidden in the bush.

The molluscan order Neogastropoda encompasses over 15,000 almost exclusively marine species playing important roles in benthic communities and in the economies of coastal countries. Neogastropoda underwent intensive cladogenesis in early stages of diversification, generating a 'bush' at the base of their evolutionary tree, that has been hard to resolve even with high throughput molecular data. In the present study to resolve the bush, we use a variety of phylogenetic inference methods and a comprehensive exon capture dataset of 1,817 loci (79.6% data occupancy) comprising 112 taxa of 48 out of 60 Neogastropoda families. Our results show consistent topologies and high support in all analyses at (super)family level, supporting monophyly of Muricoidea, Mitroidea, Conoidea, and, with some reservations, Olivoidea and Buccinoidea. Volutoidea and Turbinelloidea as currently circumscribed are clearly paraphyletic. Despite our analyses consistently resolving most backbone nodes, three prove problematic: First, uncertain placement of Cancellariidae, as the sister group to either a Ficoidea-Tonnoidea clade, or to the rest of Neogastropoda, leaves monophyly of Neogastropoda unresolved. Second, relationships are contradictory at the base of the major 'core Neogastropoda' grouping. Third, coalescence-based analyses reject monophyly of the Buccinoidea in relation to Vasidae. We analysed phylogenetic signal of targeted loci in relation to potential biases, and we propose most probable resolutions in the latter two recalcitrant nodes. The uncertain placement of Cancellariidae may be explained by orthology violations due to differential paralog loss shortly after the whole genome duplication, which should be resolved with a curated set of longer loci.

Unpredictable Chemical Diversity of Essential Oils in Cinnamomum burmanni (Lauraceae) Living Collections: Beyond Maternally Inherited Phylogenetic Relationships.

The genus Cinnamomum encompasses diverse species with various applications, particularly in traditional medicine and spice production. This study focuses on Cinnamomum burmanni, specifically on a high-D-borneol-content chemotype, known as the Meipian Tree, in Guangdong Province, South China. This research explores essential oil diversity, chemotypes, and chloroplast genomic diversity among 28 C. burmanni samples collected from botanical gardens. Essential oils were analyzed, and chemotypes classified using GC-MS and statistical methods. Plastome assembly and phylogenetic analysis were conducted to reveal genetic relationships. Results showed distinct chemotypes, including eucalyptol and borneol types, with notable variations in essential oil composition. The chloroplast genome exhibited conserved features, with phylogenetic analysis revealing three major clades. Borneol-rich individuals in clade II suggested a potential maternal inheritance pattern. However, phylogenetic signals revealed that the composition of essential oils is weakly correlated with plastome phylogeny. The study underscores the importance of botanical gardens in preserving genetic and chemical diversity, offering insights for sustainable resource utilization and selective breeding of high-yield mother plants of C. burmanni.

Phylogenomics of Afrotherian mammals and improved resolution of extant Paenungulata

Molecular investigations have gathered a diverse set of mammals—predominantly African natives like elephants, hyraxes, and aardvarks—into a clade known as Afrotheria. Nevertheless, the precise phylogenetic relationships among these species remain contentious. Here, we sourced orthologous markers and ultraconserved elements to discern the interordinal connections among Afrotherian mammals. Our phylogenetic analyses bolster the common origin of Afroinsectiphilia and Paenungulata, and propose Afrosoricida as the closer relative to Macroscelidea rather than Tubulidentata, while also challenging the notion of Sirenia and Hyracoidea as sister taxa. The approximately unbiased test and the gene concordance factor uniformly recognized the alliance of Proboscidea with Hyracoidea as the dominant topology within Paenungulata. Investigation into sites with extremly high phylogenetic signal unveiled their potential to intensify conflicts in the Paenungulata topology. Subsequent exploration suggested that incomplete lineage sorting was predominantly responsible for the observed contentious relationships, whereas introgression exerted a subsidiary influence. The divergence times estimated in our study hint at the Cretaceous-Paleogene (K-Pg) extinction event as a catalyst for Afrotherian diversification. Overall, our findings deliver a tentative but insightful overview of Afrotheria phylogeny and divergence, elucidating these relationships through the lens of phylogenomics.