Biology subjects

Benito, J.

Publications and source records attributed to Benito, J..

9 recordsLinked to original sources

bioRxiv2026

Developmental variation in pterygoid segmentation clarifies patterns of avian bony palate evolution

The morphology of the palate has long constituted the primary basis for differentiating between the two deepest clades of crown group birds, Neognathae and Palaeognathae. However, published literature on the bird palate is dominated by classical anatomical descriptions pre-dating the advent of contemporary three-dimensional imaging techniques, hindering our understanding of bird palate disparity and development. Pterygoid segmentation, the process by which the rostral portion of the pterygoid separates and fuses with the palatine during ontogeny in neognathous birds, remains a poorly understood aspect of avian cranial development despite giving rise to an important component of the cranial kinetic system. Here, we use micro-computed tomography to explore ontogenetic change of the palate during the process of pterygoid segmentation across an unprecedentedly broad taxonomic sample of immature and mature birds. With this large dataset, we present direct evidence for the full process of post-hatching pterygoid segmentation being exclusively restricted to the major avian subclade Neoaves. Further, our investigation helps refine several hypotheses of homology related to the pterygoid-palatine contact in crown birds and their close stem-group relatives: we hypothesise that the rostral projection of the pterygoid observed in Anseres (and potentially Anhimidae and Megapodiidae) is homologous with the hemipterygoid of neoavians, and that the discrete and unfused hemipterygoids of some crownward stem-birds suggest that a discrete hemipterygoid originated prior to the origin of the process of pterygoid segmentation. However, whether pterygoid segmentation represents a synapomorphy of Neornithes, Neognathae, or Neoaves remains ambiguous in light of elusive data from the fossil record and early stages of cranial development. Overall, our study clarifies the process of pterygoid segmentation in crown birds and raises new questions regarding the major morphological modifications that have characterized the evolutionary history of the avian bony palate.

paleontology↗

bioRxiv2025

Mandibular morphology clarifies phylogenetic relationships near the origin of crown birds

BackgroundThe phylogenetic relationships of fossil birds near the origin of the avian crown group remain debated, in part due to a limited amount of character evidence from incomplete fossils. The avian lower jaw provides a potentially rich source of additional character data, yet fusion of the individual bony elements composing the avian post-dentary complex has impeded efforts to explore its phylogenetic signal. Here, we use high-resolution {micro}CT-scanning to separate the individual bony elements of the mandibles of several immature crown birds and key fossil taxa, and use those data to assess support for alternative phylogenetic hypotheses for fossils near the origin of crown birds. ResultsWe find that evidence from Asteriornis fails to support interpretations of derived mandibular similarities with palaeognaths, and instead strongly favours galloanseran, and specifically galliform, affinities. Our results also illustrate striking similarities in the architecture of the lower jaws between the toothed ornithurine Ichthyornis, Pelagornithidae and Vegavis, which, in addition to the absence of derived features linking them to Galloanserae, highlights questions regarding the phylogenetic position of these perennially controversial taxa. ConclusionsOur data reveal new insight into patterns of morphological evolution near the origin of the avian crown group while raising new phylogenetic questions, emphasising the potential untapped value of detailed comparative investigations of morphological complexes such as the post-dentary complex of the mandible for informing the early evolutionary history of crown birds.

paleontology↗

bioRxiv2025

Developmental underpinnings of morphological disparity in the avian bony palate

The deepest phylogenetic divergence in crown birds gave rise to Palaeognathae and Neognathae, clades exhibiting divergent bony palate morphologies. This observation led to the longstanding hypothesis that the distinctive palate arrangement of palaeognaths retains the ancestral crown bird condition, but recent fossil evidence instead suggests that aspects of palaeognath palate morphology are derived from a neognath-like ancestral condition. While neoteny has been hypothesised as a mechanism underpinning the distinctive palatal morphologies of palaeognaths, this hypothesis has never been tested with a broad phylogenetic assessment of morphological variation through avian palate ontogeny. Here, we quantitatively assess morphological variation of the palate through the post-hatching ontogenies of 70 bird species representing all major extant phylogenetic subclades, clarifying the ontogenetic mechanisms giving rise to avian palate disparity. Though palaeognaths exhibit distinct ontogenetic changes in the PPC relative to neognaths, we find no signatures of heterochrony--including neoteny--underlying these developmental differences. However, important patterns of morphological change in the avian palate appear to be dictated by variation in developmental mode. Our results document the effects of post-hatching development on a key morphofunctional system in the avian skull, and, more broadly, highlight the influence of developmental mode on morphological evolvability across crown group birds.

evolutionary biology↗

bioRxiv2025

Shouldering the challenge of deciphering avian palate evolution

Wilken et al. (1) investigate the evolution of avian palatal kinesis using comparative morphology and biomechanical modelling. While the studys topic and approach are timely, its conclusions are marred by inadequate taxon sampling and morphological misinterpretations.

evolutionary biology↗

bioRxiv2024

The influence of soft tissue volume on estimates of skeletal pneumaticity: implications for fossil archosaurs

Air space proportion (ASP), the volume fraction in bone occupied by air, is frequently applied as a measure for quantifying the extent of skeletal pneumaticity in extant and fossil archosaurs. Nonetheless, ASP estimates rely on a key assumption: that the soft tissue mass within pneumatic bones is negligible, an assumption that has rarely been explicitly acknowledged or tested. Here, we provide the first comparisons between estimated air space proportion (where the internal cavity of a pneumatic bone is assumed to be completely air-filled) and true air space proportion (ASPt, where soft tissues present within the internal cavities of fresh specimens are considered). Using birds as model archosaurs exhibiting postcranial skeletal pneumaticity, we find that estimates of ASPt are significantly lower than estimates of ASP, raising an important consideration that should be acknowledged in investigations of the evolution of skeletal pneumaticity and bulk skeletal density in extinct archosaurs, as well as in volume-based estimates of archosaur body mass. We advocate for the difference between ASP and ASPt to be explicitly acknowledged in studies seeking to quantify the extent of skeletal pneumaticity in extinct archosaurs, to avoid the risk of systematically overestimating the volume fraction of pneumatic bones composed of air.

evolutionary biology↗

bioRxiv2023

Taphonomic damage obfuscates interpretation of the retroarticular region of the Asteriornis mandible

Asteriornis maastrichtensis, from the latest Cretaceous of Belgium, is among the oldest known crown bird fossils, and its three-dimensionally preserved skull provides the most substantial insights into the cranial morphology of early crown birds to date. Phylogenetic analyses recovered Asteriornis as a total-group member of Galloanserae (the clade uniting Galliformes and Anseriformes. One important feature supporting this placement was enlargement of the retroarticular processes, which form elongate caudal extensions of the mandible in extant Galloanserae. Here, we reinterpret the jaw of Asteriornis and illustrate that the caudalmost portion of the mandibles are in fact not preserved. Instead, the caudal extremities of both the left and right mandibular rami extend to the surface of the fossil block containing the holotype skull, where they have eroded away. The originally identified retroarticular process of the right mandible--which exhibits a morphology and orientation strikingly similar to the retroarticular processes of certain extant and fossil galloanserans, including the early Palaeogene total-clade anseriforms Conflicto and Nettapterornis--instead represents a twisted and caudally displaced medial process. Nonetheless, anatomical comparisons with extant taxa reveal that we are unable to exclude the possibility that Asteriornis exhibited robust retroarticular processes comparable to those of extant Galloanserae. In light of the reinterpreted morphology of the Asteriornis mandible, we update the original anatomical character matrix used to investigate its phylogenetic relationships, and our revised phylogenetic analyses continue to support its position as a total-group galloanseran, as initially interpreted. We demonstrate additional morphological traits of the mandible supporting this phylogenetic position and provide new data on the nature and distribution of retroarticular processes among early crown birds.

paleontology↗

bioRxiv2023

Phylogenomics and Biogeography of North American Trechine Cave Beetles (Coleoptera: Carabidae)

Cave trechines beetles (Coleoptera: Carabidae: Trechini) are members of cave communities globally and important models for understanding the colonization of caves, adaptation to cave life, and the diversification of cave-adapted lineages. In eastern North America, cave trechines are the most species-rich group of terrestrial troglobionts, comprised of over 150 taxa in six genera with no extant surface members. Previous studies have hypothesized the climate change during the Pleistocene was a major driver of cave colonization and diversification in this and other temperate terrestrial cave fauna. However, our time-calibrated molecular phylogeny resulting from the analysis of 16,794 base pairs (bp) from 68 UCE loci for 45 species of the clade supports an alternative hypothesis whereby cave colonization of the surface ancestor of eastern North American cave trechines likely began in the middle Miocene in the Appalachians Ridge and Valley (APP) and dispersed into the Interior Low Plateau (ILP) in an east to west manner around 11.5 Mya. The APP served as a cradle for diversification and also as a bridge linking the southern Appalachians and Interior Low Plateau enabling the dispersal and subsequent diversification of these cave beetles. Major clades in our time-calibrated phylogeny attained their present-day geographic distributions by the early Miocene followed by multiple additional episodes of cave colonization and diversification occurring throughout the Pliocene and Pleistocene. The genera Neaphanops, Darlingtonea, Nelsonites, and Ameroduvalius were nested within specious genus Pseudanopthalmus supporting the hypothesis that these genera are derived Pseudanophtlamus. Moreover, while several morphologically-derived species groups of Pseudanopthalmus were recovered as monophyletic, others were not warranting future taxonomic and systematic research. The molecular systematics and biogeography of these unique cave beetles offer a model for other comparative evolutionary and ecological studies of troglobionts to further our understanding of factors driving speciation and biogeographic patterns.

ecology↗

bioRxiv2022

40 new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds.

Ichthyornis has long been recognized as a pivotally important fossil taxon for understanding the latest stages of the dinosaur-bird transition, but little significant new postcranial material has been brought to light since initial descriptions of partial skeletons in the 19th Century. Here, we present new information on the postcranial morphology of Ichthyornis from 40 previously undescribed specimens, providing the most detailed morphological assessment of Ichthyornis to date. The new material includes four partially complete skeletons and numerous well-preserved isolated elements, enabling new anatomical observations such as muscle attachments previously undescribed for Mesozoic euornitheans. Among the elements that were previously unknown or poorly represented for Ichthyornis, the new specimens include an almost-complete axial series, a hypocleideum-bearing furcula, radial carpal bones, fibulae, a complete tarsometatarsus bearing a rudimentary hypotarsus, and one of the first-known nearly complete three-dimensional sterna from a Mesozoic avialan. Several pedal phalanges are preserved, revealing a remarkably enlarged pes presumably related to foot-propelled swimming. Although diagnosable as Ichthyornis, the new specimens exhibit a substantial degree of morphological variation, some of which may relate to ontogenetic changes. Phylogenetic analyses incorporating our new data and employing alternative morphological datasets recover Ichthyornis stemward of Hesperornithes and Iaceornis, in line with some recent hypotheses regarding the topology of the crownward-most portion of the avian stem group, and we establish phylogenetically-defined clade names for relevant avialan subclades to help facilitate consistent discourse in future work. The new information provided by these specimens improves our understanding of morphological evolution among the crownward-most non-neornithine avialans immediately preceding the origin of crown group birds.

paleontology↗

bioRxiv2021

BeeDNA: microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities

Pollinators are imperiled by global declines that can reduce plant reproduction, erode essential ecosystem services and resilience, and drive economic losses. Monitoring pollinator biodiversity trends is key for adaptive conservation and management, but conventional surveys are often costly, time consuming, and require taxonomic expertise. Environmental DNA (eDNA) metabarcoding surveys are booming due to their rapidity, non-invasiveness, and cost efficiency. Microfluidic technology allows multiple primer sets from different markers to be used in eDNA metabarcoding for more comprehensive species inventories whilst minimizing biases associated with individual primer sets. We evaluated microfluidic eDNA metabarcoding for pollinator community monitoring by introducing a bumblebee colony to a greenhouse flower assemblage and sampling natural flower plots. We collected nectar draws, flower swabs, or whole flower heads from four flowering species, including two occurring in both the greenhouse and field. Samples were processed using two eDNA isolation protocols before amplification with 15 primer sets for two markers (COI and 16S). Microfluidic eDNA metabarcoding detected the target bumblebee and greenhouse insects as well as common regional arthropods. Pollinator detection was maximized using whole flower heads preserved in ATL buffer and extracted with a modified Qiagen(R) DNeasy protocol for amplification with COI primers. eDNA surveillance could enhance pollinator assessment by detecting protected and endangered species and being more applicable to remote, inaccessible locations, whilst reducing survey time, effort, and expense. Microfluidic eDNA metabarcoding requires optimization to address remaining efficacy concerns but this approach shows potential in revealing complex networks underpinning critical ecosystem functions and services, enabling more accurate assessments of ecosystem resilience.

ecology↗