Amoebozoan testate amoebae illuminate the diversity of heterotrophs and the complexity of ecosystems throughout geological time.

Heterotrophic protists are vital in Earth's ecosystems, influencing carbon and nutrient cycles and occupying key positions in food webs as microbial predators. Fossils and molecular data suggest the emergence of predatory microeukaryotes and the transition to a eukaryote-rich marine environment by 800 million years ago (Ma). Neoproterozoic vase-shaped microfossils (VSMs) linked to Arcellinida testate amoebae represent the oldest evidence of heterotrophic microeukaryotes. This study explores the phylogenetic relationship and divergence times of modern Arcellinida and related taxa using a relaxed molecular clock approach. We estimate the origin of nodes leading to extant members of the Arcellinida Order to have happened during the latest Mesoproterozoic and Neoproterozoic (1054 to 661 Ma), while the divergence of extant infraorders postdates the Silurian. Our results demonstrate that at least one major heterotrophic eukaryote lineage originated during the Neoproterozoic. A putative radiation of eukaryotic groups (e.g., Arcellinida) during the early-Neoproterozoic sustained by favorable ecological and environmental conditions may have contributed to eukaryotic life endurance during the Cryogenian severe ice ages. Moreover, we infer that Arcellinida most likely already inhabited terrestrial habitats during the Neoproterozoic, coexisting with terrestrial Fungi and green algae, before land plant radiation. The most recent extant Arcellinida groups diverged during the Silurian Period, alongside other taxa within Fungi and flowering plants. These findings shed light on heterotrophic microeukaryotes' evolutionary history and ecological significance in Earth's ecosystems, using testate amoebae as a proxy.

Using phylogenetics to infer HIV-1 transmission direction between known transmission pairs.

Inferring the transmission direction between linked individuals living with HIV provides unparalleled power to understand the epidemiology that determines transmission. Phylogenetic ancestral-state reconstruction approaches infer the transmission direction by identifying the individual in whom the most recent common ancestor of the virus populations originated. While these methods vary in accuracy, it is unclear why. To evaluate the performance of phylogenetic ancestral-state reconstruction to determine the transmission direction of HIV-1 infection, we inferred the transmission direction for 112 transmission pairs where transmission direction and detailed additional information were available. We then fit a statistical model to evaluate the extent to which epidemiological, sampling, genetic, and phylogenetic factors influenced the outcome of the inference. Finally, we repeated the analysis under real-life conditions with only routinely available data. We found that whether ancestral-state reconstruction correctly infers the transmission direction depends principally on the phylogeny's topology. For example, under real-life conditions, the probability of identifying the correct transmission direction increases from 32%-when a monophyletic-monophyletic or paraphyletic-polyphyletic tree topology is observed and when the tip closest to the root does not agree with the state at the root-to 93% when a paraphyletic-monophyletic topology is observed and when the tip closest to the root agrees with the root state. Our results suggest that documenting larger differences in relative intrahost diversity increases our confidence in the transmission direction inference of linked pairs for population-level studies of HIV. These findings provide a practical starting point to determine our confidence in transmission direction inference from ancestral-state reconstruction.

Fossil-calibrated molecular clock data enable reconstruction of steps leading to differentiated multicellularity and anisogamy in the Volvocine algae.

BACKGROUND: Throughout its nearly four-billion-year history, life has undergone evolutionary transitions in which simpler subunits have become integrated to form a more complex whole. Many of these transitions opened the door to innovations that resulted in increased biodiversity and/or organismal efficiency. The evolution of multicellularity from unicellular forms represents one such transition, one that paved the way for cellular differentiation, including differentiation of male and female gametes. A useful model for studying the evolution of multicellularity and cellular differentiation is the volvocine algae, a clade of freshwater green algae whose members range from unicellular to colonial, from undifferentiated to completely differentiated, and whose gamete types can be isogamous, anisogamous, or oogamous. To better understand how multicellularity, differentiation, and gametes evolved in this group, we used comparative genomics and fossil data to establish a geologically calibrated roadmap of when these innovations occurred. RESULTS: Our ancestral-state reconstructions, show that multicellularity arose independently twice in the volvocine algae. Our chronograms indicate multicellularity evolved during the Carboniferous-Triassic periods in Goniaceae + Volvocaceae, and possibly as early as the Cretaceous in Tetrabaenaceae. Using divergence time estimates we inferred when, and in what order, specific developmental changes occurred that led to differentiated multicellularity and oogamy. We find that in the volvocine algae the temporal sequence of developmental changes leading to differentiated multicellularity is much as proposed by David Kirk, and that multicellularity is correlated with the acquisition of anisogamy and oogamy. Lastly, morphological, molecular, and divergence time data suggest the possibility of cryptic species in Tetrabaenaceae. CONCLUSIONS: Large molecular datasets and robust phylogenetic methods are bringing the evolutionary history of the volvocine algae more sharply into focus. Mounting evidence suggests that extant species in this group are the result of two independent origins of multicellularity and multiple independent origins of cell differentiation. Also, the origin of the Tetrabaenaceae-Goniaceae-Volvocaceae clade may be much older than previously thought. Finally, the possibility of cryptic species in the Tetrabaenaceae provides an exciting opportunity to study the recent divergence of lineages adapted to live in very different thermal environments.

The rise of dietary diversity in coral reef fishes.

Diet has been identified as a major driver of reef fish lineage diversification, producing one of the most speciose vertebrate assemblages today. Yet, there is minimal understanding of how, when and why diet itself has evolved. To address this, we used a comprehensive gut content dataset, alongside a recently developed phylogenetic comparative method to assess multivariate prey use across a diverse animal assemblage, coral reef fishes. Specifically, we investigated the diversification, transitions and phylogenetic conservatism of fish diets through evolutionary time. We found two major pulses of diet diversification: one at the end-Cretaceous and one during the Eocene, suggesting that the Cretaceous-Palaeogene mass extinction probably provided the initial ecological landscape for fish diets to diversify. The birth of modern families during the Eocene then provided the foundation for a second wave of dietary expansion. Together, our findings showcase the role of extinction rebound events in shaping the dietary diversity of fishes on present-day coral reefs.

Angiosperm flowers reached their highest morphological diversity early in their evolutionary history.

Flowers are the complex and highly diverse reproductive structures of angiosperms. Because of their role in sexual reproduction, the evolution of flowers is tightly linked to angiosperm speciation and diversification. Accordingly, the quantification of floral morphological diversity (disparity) among angiosperm subgroups and through time may give important insights into the evolutionary history of angiosperms as a whole. Based on a comprehensive dataset focusing on 30 characters describing floral structure across angiosperms, we used 1201 extant and 121 fossil flowers to measure floral disparity and explore patterns of floral evolution through time and across lineages. We found that angiosperms reached their highest floral disparity in the Early Cretaceous. However, decreasing disparity toward the present likely has not precluded the innovation of other complex traits at other morphological levels, which likely played a key role in the outstanding angiosperm species richness. Angiosperms occupy specific regions of the theoretical morphospace, indicating that only a portion of the possible floral trait combinations is observed in nature. The ANA grade, the magnoliids, and the early-eudicot grade occupy large areas of the morphospace (higher disparity), whereas nested groups occupy narrower regions (lower disparity).

On the origin of bird's nest fungi: Phylogenomic analyses of fungi in the Nidulariaceae (Agaricales, Basidiomycota).

Nidulariaceae, also known as bird's nest fungi, is an understudied group of mushroom-forming fungi. The common name is derived from their nest-like morphology. Bird's nest fungi are ubiquitous wood decomposers or saprobes on dung. Recent studies showed that species in the Nidulariaceae form a monophyletic group with five sub-clades. However, phylogenetic relationships among genera and placement of Nidulariaceae are still unclear. We present phylogenomic analyses of bird's nest fungi and related Agaricales fungi to gain insight into the evolution of Nidulariaceae. A species tree with 17 newly generated genomes of bird's nest fungi and representatives from all major clades of Agaricales was constructed using 1044 single-copy genes to explore the intergeneric relationships and pinpoint the placement of Nidulariaceae within Agaricales. We corroborated the hypothesis that bird's nest fungi are sister to Squamanitaceae, which includes mushroom-shaped fungi with a stipe and pileus that are saprobes and mycoparasites. Lastly, stochastic character mapping of discrete traits on phylogenies (SIMMAP) suggests that the ancestor of bird's nest fungi likely possessed an evanescent, globose peridium without strings attaching to the spore packets (funiculi). This analysis suggests that the funiculus was gained twice and that the persistent, cupulate peridium form was gained at least four times and lost once. However, alternative coding schemes and datasets with a wider array of Agaricales produced conflicting results during ancestral state reconstruction, indicating that there is some uncertainty in the number of peridium transitions and that taxon sampling may significantly alter ancestral state reconstructions. Overall, our results suggest that several key morphological characters of Nidulariaceae have been subject to homoplasy.

Molecular phylogenetic and estimation of evolutionary divergence and biogeography of the family Schizoparmaceae and allied families (Diaporthales, Ascomycota).

The Diaporthales includes 32 families, many of which are important plant pathogens, endophytes and saprobes, e.g., members of the families Pseudoplagiostomataceae, Pyrisporaceae and Schizoparmaceae. Nucleotide sequences derived from five genetic loci including: ITS, LSU, TEF1-α, TUB2 and RPB2 were used for Bayesian evolutionary analysis to determine divergence times and evolutionary relationships within the Schizoparmaceae. Molecular clock analyses revealed that the ancestor of Schizoparmaceae split during the Upper Cretaceous period approximately 75.7 Mya (95 % highest posterior density of 60.3-91.3 Mya). Reconstructing ancestral state in phylogenies (RASP) with using the Bayesian Binary Markov chain Monte Carlo (BBM) Method to reconstruct the historical biogeography for the family Schizoparmaceae indicated its most likely origin in Africa. Based on taxonomic and phylogenetic analyses, the Pseudoplagiostomataceae and Pyrisporaceae relationships were clarified and a total of four species described herein. For Pseudoplagiostomataceae, three new species and one known species that include, Pseudoplagiostoma fafuense sp. nov., Ps. ilicis sp. nov., Ps. sanmingense sp. nov. and Ps. bambusae are described and a key of Pseudoplagiostomataceae is provided. With respect to Pyrisporaceae, we considered Pseudoplagiostoma castaneae to be a synonym of Pyrispora castaneae. In addition, a new species of Schizoparmaceae, Coniella fujianensis sp. nov. is described and illustrated.

Systematics and evolutionary dynamics of insect-fern interactions in the specialized fern-spore feeding Cuprininae (Lepidoptera, Stathmopodidae).

Fern-spore-feeding (FSF) is rare and found in only four families of Lepidoptera. Stathmopodidae is the most speciose family that contains FSF species, and its subfamily Cuprininae exclusively specializes on FSF. However, three species of Stathmopodinae also specialize on FSF. To better understand the evolutionary history of FSF and, more generally, the significance of specialization on a peculiar host, a phylogenetic and taxonomic revision for this group is necessary. We reconstructed the most comprehensive molecular phylogeny, including one mitochondrial and four nuclear genes, of Stathmopodidae to date, including 137 samples representing 62 species, with a particular focus on the FSF subfamily, Cuprininae, including 33 species (41% of named species) from 6 of the 7 Cuprininae genera. Species from two other subfamilies, Stathmopodinae and Atkinsoniinae, were also included. We found that FSF evolved only once in Stathmopodidae and that the previous hypothesis of multiple origins of FSF was misled by inadequate taxonomy. Moreover, we showed that (1) speciation/extinction rates do not differ significantly between FSF and non-FSF groups and that (2) oligophage is the ancestral character state in Cuprininae. We further revealed that a faster rate of accumulating specialists over time, and thus a higher number of specialists, was achieved by a higher transition rate from oligophagages to specialists compared to the transition rate in the opposite direction. We finish by describing three new genera, Trigonodagen. nov., Petalagen. nov., and Pediformisgen. nov., and revalidating five genera: Cuprina, Calicotis, Thylacosceles, Actinoscelis, Thylacosceloides in Cuprininae, and we provide an updated taxonomic key to genera and a revised global checklist of Cuprininae.

Plastome phylogenomics and new fossil evidence from Dominican amber shed light on the evolutionary history of the Neotropical fern genus Pecluma.

PREMISE: Molecular studies based on chloroplast markers have questioned the monophyly of the fern genus Pecluma (Polypodioideae, Polypodiaceae), which has several species of Polypodium nested within it. We explored the delimitation of Pecluma and its biogeographic pattern by evaluating the phylogenetic position of four Polypodium species not sequenced thus far and integrating the first fossil evidence of Pecluma. METHODS: Using herbarium material, we applied a genome-skimming approach to obtain a phylogenetic hypothesis of Polypodioideae; assessed the combination of character states observed in the fossil from Miocene Dominican amber using a previously published phylogeny of Polypodioideae based on four plastid markers as framework; calculated divergence times; and conducted an ancestral area estimation. RESULTS: Within Polypodioideae, Pecluma was recovered as sister to Phlebodium. Three of the newly sequenced species-Polypodium otites, P. pinnatissimum, and P. ursipes-were recovered with maximum support within the Pecluma clade, whereas P. christensenii remained within Polypodium. The closest combination of character states of the fossil was found within Pecluma. Our biogeographic analyses suggest an Eocene origin of the genus in South America, with several subsequent Oligocene and Miocene colonization events to Mexico-Central America and to the West Indies. CONCLUSIONS: Although the circumscription of Pecluma is still challenging, our results elucidate the origin and age of the genus. The newly described fossil, Pecluma hispaniolae sp. nov., supports the hypothesis that the epiphytic communities of the Greater Antilles exhibit a constant generic composition since the Miocene. We propose new combinations (Pecluma otites, Pecluma pinnatissima, and Pecluma ursipes) to accommodate three species previously classified in Polypodium.

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.

Chromosomal analysis of two Acanthodoras species (Doradidae, Siluriformes): Insights into the oldest thorny catfish clade and its karyotype evolution.

The Doradidae fishes constitute one of the most diverse groups of Neotropical freshwater environments. Acanthodoradinae is the oldest lineage and the sister group to all other thorny catfishes, and it includes only the genus Acanthodoras. The diversity of Acanthodoras remains underestimated, and the use of complementary approaches, including genetic studies, is an important step to better characterize this diversity and the relationships among the species within the genus. Therefore, we conducted a comprehensive analysis using conventional cytogenetic techniques and physical mapping of three multigene families (18S and 5S ribosomal DNA [rDNA], U2 small nuclear DNA [snDNA]) and four microsatellite motifs, namely (AC)n, (AT)n, (GA)n, and (GATA)n, in two sympatric species from the Negro River: Acanthodoras cataphractus and Acanthodoras cf. polygrammus. We found significant differences in constitutive heterochromatin (CH) content, distribution of the microsatellite (AT)n, and the number of 5S rDNA and U2 snDNA sites. These differences may result from chromosome rearrangements and repetitive DNA dispersal mechanisms. Furthermore, the characterization of the diploid number (2n) of these Acanthodoras species enables us to propose 2n = 58 chromosomes as the plesiomorphic 2n state in Doradidae based on ancestral state reconstruction. Acanthodoradinae is the oldest lineage of the thorny catfishes, and knowledge about its cytogenetic patterns is crucial for disentangling the karyotype evolution of the whole group. Thus, this study contributes to the understanding of the mechanisms behind chromosome diversification of Doradidae and highlights the importance of Acanthodoradinae in the evolutionary history of thorny catfishes.

Origination of LTR Retroelement-Derived NYNRIN Coincides with Therian Placental Emergence.

The emergence of the placenta is a revolutionary event in the evolution of therian mammals, to which some LTR retroelement-derived genes, such as PEG10, RTL1, and syncytin, are known to contribute. However, therian genomes contain many more LTR retroelement-derived genes that may also have contributed to placental evolution. We conducted large-scale evolutionary genomic and transcriptomic analyses to comprehensively search for LTR retroelement-derived genes whose origination coincided with therian placental emergence and that became consistently expressed in therian placentae. We identified NYNRIN as another Ty3/Gypsy LTR retroelement-derived gene likely to contribute to placental emergence in the therian stem lineage. NYNRIN knockdown inhibited the invasion of HTR8/SVneo invasive-type trophoblasts, whereas the knockdown of its nonretroelement-derived homolog KHNYN did not. Functional enrichment analyses suggested that NYNRIN modulates trophoblast invasion by regulating epithelial-mesenchymal transition and extracellular matrix remodeling and that the ubiquitin-proteasome system is responsible for the functional differences between NYNRIN and KHNYN. These findings extend our knowledge of the roles of LTR retroelement-derived genes in the evolution of therian mammals.

Challenging the Importance of Plastid Genome Structure Conservation: New Insights From Euglenophytes.

Plastids, similar to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations comes from studies of the primary plastids of green algae and land plants. To broaden our perspective, we obtained seven new ptDNA sequences from freshwater species of photosynthetic euglenids-a group that obtained secondary plastids, known to have dynamically evolving genome structure, via endosymbiosis with a green alga. Our analyses have demonstrated that the evolutionary history of euglenid plastid genome structure is exceptionally convoluted, with a patchy distribution of inverted ribosomal operon (rDNA) repeats, as well as several independent acquisitions of tandemly repeated rDNA copies. Moreover, we have shown that inverted repeats in euglenid ptDNA do not share their genome-stabilizing property documented in chlorophytes. We hypothesize that the degeneration of the quadripartite structure of euglenid plastid genomes is connected to the group II intron expansion. These findings challenge the current global paradigms of plastid genome architecture evolution and underscore the often-underestimated divergence between the functionality of shared traits in primary and complex plastid organelles.

Ancestrally Reconstructed von Willebrand Factor Reveals Evidence for Trench Warfare Coevolution between Opossums and Pit Vipers.

Opossums in the tribe Didelphini are resistant to pit viper venoms and are hypothesized to be coevolving with venomous snakes. Specifically, a protein involved in blood clotting (von Willebrand factor [vWF] which is targeted by snake venom C-type lectins [CTLs]) has been found to undergo rapid adaptive evolution in Didelphini. Several unique amino acid changes in vWF could explain their resistance; however, experimental evidence that these changes disrupt binding to venom CTLs was lacking. Furthermore, without explicit testing of ancestral phenotypes to reveal the mode of evolution, the assertion that this system represents an example of coevolution rather than noncoevolutionary adaptation remains unsupported. Using expressed vWF proteins and purified venom CTLs, we quantified binding affinity for vWF proteins from all resistant taxa, their venom-sensitive relatives, and their ancestors. We show that CTL-resistant vWF is present in opossums outside clade Didelphini and likely across a wider swath of opossums (family Didelphidae) than previously thought. Ancestral reconstruction and in vitro testing of vWF phenotypes in a clade of rapidly evolving opossums reveal a pattern consistent with trench warfare coevolution between opossums and their venomous snake prey.

Evolutionary patterns of host switching, lifestyle mode, and the diversification history in symbiotic zoantharians.

Symbioses play important roles in forming the structural and distributional patterns of marine diversity. Understanding how interspecies interactions through symbioses contribute to biodiversity is an essential topic. Host switching has been considered as one of the main drivers of diversification in symbiotic systems. However, its process and patterns remain poorly investigated in the marine realm. Hexacoral species of the order Zoantharia (=zoantharians) are often epizoic on other marine invertebrates and generally use specific taxa as hosts. The present study investigates the patterns of host switching and the diversification history of zoantharians based on the most comprehensive molecular phylogenetic analyses to date, using sequences from three mitochondrial and three nuclear markers from representatives of 27 of 29 genera. Our results indicate that symbiotic zoantharians, in particular those within suborder Macrocnemina, diversified through repeated host switching. In addition, colonization of new host taxa appears to have driven morphological and ecological specialization in zoantharians. These findings have important implications for understanding the role of symbioses in the morphological and ecological evolution of marine invertebrates.

The phylogeny and global biogeography of Primulaceae based on high-throughput DNA sequence data.

The angiosperm family Primulaceae is morphologically diverse and distributed nearly worldwide. However, phylogenetic uncertainty has obstructed the identification of major morphological and biogeographic transitions within the clade. We used target capture sequencing with the Angiosperms353 probes, taxon-sampling encompassing nearly all genera of the family, tree-based sequence curation, and multiple phylogenetic approaches to investigate the major clades of Primulaceae and their relationship to other Ericales. We generated dated phylogenetic trees and conducted broad-scale biogeographic analyses as well as stochastic character mapping of growth habit. We show that Ardisia, a pantropical genus and the largest in the family, is not monophyletic, with at least 19 smaller genera nested within it. Neotropical members of Ardisia and several smaller genera form a clade, an ancestor of which arrived in the Neotropics and began diversifying about 20 Ma. This Neotropical clade is most closely related to Elingamita and Tapeinosperma, which are most diverse on islands of the Pacific. Both Androsace and Primula are non-monophyletic by the inclusion of smaller genera. Ancestral state reconstructions revealed that there have either been parallel transitions to an herbaceous habit in Primuloideae, Samolus, and at least three lineages of Myrsinoideae, or a common ancestor of nearly all Primulaceae was herbaceous. Our results provide a robust estimate of phylogenetic relationships across Primulaceae and show that a revised classification of Myrsinoideae and several other clades within the family is necessary to render all genera monophyletic.

Evolution of posture in amniotes-Diving into the trabecular architecture of the femoral head.

Extant amniotes show remarkable postural diversity. Broadly speaking, limbs with erect (strongly adducted, more vertically oriented) posture are found in mammals that are particularly heavy (graviportal) or show good running skills (cursorial), while crouched (highly flexed) limbs are found in taxa with more generalized locomotion. In Reptilia, crocodylians have a "semi-erect" (somewhat adducted) posture, birds have more crouched limbs and lepidosaurs have sprawling (well-abducted) limbs. Both synapsids and reptiles underwent a postural transition from sprawling to more erect limbs during the Mesozoic Era. In Reptilia, this postural change is prominent among archosauriforms in the Triassic Period. However, limb posture in many key Triassic taxa remains poorly known. In Synapsida, the chronology of this transition is less clear, and competing hypotheses exist. On land, the limb bones are subject to various stresses related to body support that partly shape their external and internal morphology. Indeed, bone trabeculae (lattice-like bony struts that form the spongy bone tissue) tend to orient themselves along lines of force. Here, we study the link between femoral posture and the femoral trabecular architecture using phylogenetic generalized least squares. We show that microanatomical parameters measured on bone cubes extracted from the femoral head of a sample of amniote femora depend strongly on body mass, but not on femoral posture or lifestyle. We reconstruct ancestral states of femoral posture and various microanatomical parameters to study the "sprawling-to-erect" transition in reptiles and synapsids, and obtain conflicting results. We tentatively infer femoral posture in several hypothetical ancestors using phylogenetic flexible discriminant analysis from maximum likelihood estimates of the microanatomical parameters. In general, the trabecular network of the femoral head is not a good indicator of femoral posture. However, ancestral state reconstruction methods hold great promise for advancing our understanding of the evolution of posture in amniotes.

Evolution of vertebral numbers in primates, with a focus on hominoids and the last common ancestor of hominins and panins.

The primate vertebral column has been extensively studied, with a particular focus on hominoid primates and the last common ancestor of humans and chimpanzees. The number of vertebrae in hominoids-up to and including the last common ancestor of humans and chimpanzees-is subject to considerable debate. However, few formal ancestral state reconstructions exist, and none include a broad sample of primates or account for the correlated evolution of the vertebral column. Here, we conduct an ancestral state reconstruction using a model of evolution that accounts for both homeotic (changes of one type of vertebra to another) and meristic (addition or loss of a vertebra) changes. Our results suggest that ancestral primates were characterized by 29 precaudal vertebrae, with the most common formula being seven cervical, 13 thoracic, six lumbar, and three sacral vertebrae. Extant hominoids evolved tail loss and a reduced lumbar column via sacralization (homeotic transition at the last lumbar vertebra). Our results also indicate that the ancestral hylobatid had seven cervical, 13 thoracic, five lumbar, and four sacral vertebrae, and the ancestral hominid had seven cervical, 13 thoracic, four lumbar, and five sacral vertebrae. The last common ancestor of humans and chimpanzees likely either retained this ancestral hominid formula or was characterized by an additional sacral vertebra, possibly acquired through a homeotic shift at the sacrococcygeal border. Our results support the 'short-back' model of hominin vertebral evolution, which postulates that hominins evolved from an ancestor with an African ape-like numerical composition of the vertebral column.

Phylogeny of the carpenter bees (Apidae: Xylocopinae) highlights repeated evolution of sociality.

Many groups of animals have evolved social behaviours in different forms, from intimate familial associations to the complex eusocial colonies of some insects. The subfamily Xylocopinae, including carpenter bees and their relatives, is a diverse clade exhibiting a wide range of social behaviours, from solitary to obligate eusociality with distinct morphological castes, making them ideal focal taxa in studying the evolution of sociality. We used ultraconserved element data to generate a broadly sampled phylogeny of the Xylocopinae, including several newly sequenced species. We then conducted ancestral state reconstructions on the evolutionary history of sociality in this group under multiple coding models. Our results indicate solitary origins for the Xylocopinae with multiple transitions to sociality across the tree and subsequent reversals to solitary life, demonstrating the lability and dynamic nature of social evolution in carpenter bees. Ultimately, this work clarifies the evolutionary history of the Xylocopinae, and expands our understanding of independent origins and gains and losses of social complexity.

When can we reconstruct the ancestral state? Beyond Brownian motion.

Reconstructing the ancestral state of a group of species helps answer many important questions in evolutionary biology. Therefore, it is crucial to understand when we can estimate the ancestral state accurately. Previous works provide a necessary and sufficient condition, called the big bang condition, for the existence of an accurate reconstruction method under discrete trait evolution models and the Brownian motion model. In this paper, we extend this result to a wide range of continuous trait evolution models. In particular, we consider a general setting where continuous traits evolve along the tree according to stochastic processes that satisfy some regularity conditions. We verify these conditions for popular continuous trait evolution models including Ornstein-Uhlenbeck, reflected Brownian Motion, bounded Brownian Motion, and Cox-Ingersoll-Ross.