Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2025.01.17.633553

Towards a comprehensive anatomical matrix for crown birds: phylogenetic insights from the pectoral girdle and forelimb skeleton

Chen, A.·Steell, E. M.·Benson, R. B. J.·Field, D. J.
View original source ↗Export metadata ↓

Abstract

Phylogenetic analyses of phenotypic characters in crown-group birds often recover results that are strongly incongruous with the findings of recent phylogenomic analyses. Furthermore, existing morphological datasets for crown birds are frequently limited by restricted taxon or character sampling, inconsistent character construction, incorrect scoring, or a combination of several of these factors. As part of an effort to address these limitations, in this study we focus on identifying phylogenetically informative characters of the avian pectoral girdle and forelimb skeleton, elements of which are commonly preserved as avian fossils. We assembled and vetted a dataset of 204 characters, which were then scored for a phylogenetically diverse range of 75 extant avian taxa and incorporated into phylogenetic analyses. Analyses run without topological constraints exhibited notable conflicts with the results of recent phylogenomic studies, possibly due to functional convergence and rapid cladogenesis in the early evolutionary history of crown birds. Qualitative anatomical comparisons and quantitative metrics of homoplasy further highlighted the fact that similar morphologies in pectoral girdle and forelimb elements have evolved repeatedly in distantly related groups of birds, representing a major confounding factor in avian morphological phylogenetics. However, the implementation of molecular scaffolds allowed identification of diagnostic character combinations for numerous avian clades previously only recognized through molecular data, such as Phaethontimorphae, Aequornithes, and Telluraves. Although large morphological datasets may not guarantee increased congruence with molecular phylogenetic studies, they can nonetheless be valuable tools for identifying anatomical synapomorphies of key clades, placing fossils into phylogenetic context, and studying macroevolutionary patterns within major groups of organisms.

Source connections

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Chen, A., Steell, E. M., Benson, R. B. J., Field, D. J.. 2025-01-21. Towards a comprehensive anatomical matrix for crown birds: phylogenetic insights from the pectoral girdle and forelimb skeleton. https://doi.org/10.1101/2025.01.17.633553

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Denisovan introgression left differential selection regimes in Humans and Neanderthals on the SLC30A9 gene

Signals of positive selection around the SLC30A9 gene have been reported in human populations outside Africa. Selection likely acted on a highly differentiated single-nucleotide polymorphism, rs1047626, leading to a non-synonymous substitution in the encoded zinc transporter. Because of the striking similarity between the putatively selected SLC30A9 haplotype observed in several current human populations and the Denisovan individual, previous work has proposed adaptive introgression. Yet alternative explanations, including ancient human variation, and the precise archaic source -Neanderthal or Denisovan- remained unresolved. Considering the potentially complex evolution of SLC30A9, we applied Approximate Bayesian Computation (ABC) algorithms coupled to machine learning to investigate the most plausible evolutionary origin of this substitution. After modelling different evolutionary scenarios with forward-in-time simulations, our results highlight that the most probable scenario is a Denisovan origin of the rs1047626 polymorphism. However, the allele likely introgressed into Neanderthals first and was then passed into non-African modern humans. Moreover, the derived allele frequency for rs1047626 across several African populations is consistent with back-to-Africa migrations. Finally, our ABC analyses indicate strong positive selection in East Asian populations and other out-of-Africa populations, whereas in Neanderthal populations, the selection coefficient was probably neutral or slightly deleterious.

evolutionary biology↗
bioRxiv2026

RELAX does not reproduce its own estimates at default settings, and its output does not show it

Selection-intensity estimates from RELAX are reported as a point value of K with a likelihood-ratio P. We report that, at default settings and on data of ordinary size, the program does not reproduce its own fits. Of 27 enzyme entries refitted under two optimiser configurations, none reproduced its log-likelihood to within 0.01 units; the median change was 103 units, the largest over 3,400, and four verdicts reversed. Eighty null orthologues reproduced none. A byte-identical command returned a distinct likelihood on every repetition, single-threaded, across three releases, and on alignments simulated under the fitted model, where 3.3 per cent of replicates reproduced. The documented random-number seed never reaches the generator when assigned on the command line, yet reads back as the value supplied. PAML localises the cause: its two-ratio model, without site classes, reproduced its log-likelihood for all 288 genes; its site-class models agreed for 27 to 67 per cent. The instability follows the mixture over sites, not the program. The output does not show it: 46 of 410 fits ended with a negative likelihood-ratio statistic, impossible under convergence, and 123 of 410 report a K re-estimated under a domain restriction rather than the unconstrained maximum. Of 234 published studies using RELAX, none reported a seed. Seeding while holding the thread count at one reproduced sixty of sixty runs on twenty genes under two releases; the seed alone reproduced none of five, and no documentation states the second condition. We recommend that fits be repeated and their dispersion published.

evolutionary biology↗
bioRxiv2026

Sequential accumulation of adaptive alleles forms an inversion supergene in deer mice

Supergenes are clusters of co-inherited loci that affect multiple or complex phenotypes. Despite the growing number of chromosomal inversions identified as supergenes in natural populations, their molecular basis and evolutionary history often remain obscure. Here, we identified two candidate genes, Slc45a2 and Npr3, within a 41-Mb inversion supergene in the deer mouse (Peromyscus maniculatus) that respectively drive darker coats and longer tails - two traits associated with forest adaptation. Mice homozygous for the inversion (inv/inv) exhibit elevated Slc45a2 expression in melanocytes relative to the congenic standard genotype (std/std), disrupting pheomelanin production. In parallel, downregulation of Npr3 in inv/inv mouse growth plates prolongs postnatal growth of caudal vertebrae, resulting in tail elongation. Population-level analyses further implicate that this supergene arose through the subsequent accumulation of the Npr3 allele within the inversion, rather than by capturing all beneficial mutations at its origin.

evolutionary biology↗