2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
March 7th, 2025
Version: 1
Southeastern Louisiana University
evolutionary biology
biorxiv

Incorporating continuous characters in joint estimation of dicynodont phylogeny

Wynd, B. M.Open in Google Scholar•Khakurel, B.Open in Google Scholar•Kammerer, C. F.Open in Google Scholar•Wagner, P. J.Open in Google Scholar•Wright, A.Open in Google Scholar

Continuous characters have received comparatively little attention in Bayesian phylogenetic estima- tion. This is predominantly because they cannot be modeled by a standard phylogenetic Q-matrix approach due to their non-discrete nature. In this manuscript, we explore the use of continuous traits under two Brownian Motion models to estimate a phylogenetic tree for Dicynodontia, a well-studied group of early synapsids (stem mammals) in which continuous characters have been extensively used in parsimony-based tree reconstruction. We examine the differences in phylogenetic signal between a continuous trait partition, a discrete trait partition, and a joint analysis with both types of characters. We find that continuous and discrete traits contribute substantially different signal to the analysis, even when other parts of the model (clock and tree) are held constant. Tree topologies resulting from the new analyses differ strongly from the established phylogeny for dicynodonts, highlighting continued difficulty in incorporating truly continuous data in a Bayesian phylogenetic framework.

Similar Papers

biorxiv
Sat Jul 05 2025
Spread of a single superclone drives insecticide resistance in Acyrthosiphon kondoi across an invasive range
Populations under similar selection pressures may adapt via parallel evolution or dispersal of advantageous alleles. Here, we investigated insecticide resistance in the invasive blue-green aphid, Acyrthosiphon kondoi, which reproduces clonally in Australia and has rapidly developed resistance across geographic locations. Using genomic, transcriptomic, and experimental approaches, we explored the e...
Thia, J. A.
•
Hunt, B. J.
•
Wang, S.
•
Troczka, B. J.
...•
Hoffmann, A. A.
biorxiv
Fri Jul 04 2025
Pervasive and dynamic release of Cryptic Genetic Variation in Chironomus riparius: Rethinking adaptation in fluctuating environments
The interplay between phenotypic plasticity and cryptic genetic variation (CGV) is crucial for understanding adaptation, yet the prevailing paradigm suggests CGV is primarily exposed under novel or extreme conditions. By examining gene expression responses along a natural temperature gradient in Chironomus riparius, we challenged this view. We found that the vast majority of expressed genes (63%) ...
Pfenninger, M.
•
Nieto-Blazquez, M.-E.
•
Schell, T.
•
Geiss, M.
...•
Feldmeyer, B.
biorxiv
Fri Jul 04 2025
Pollution-Driven Selection in Riparian Ecosystems: Genome-Wide Responses to Bacillus thuringiensis israelensis and Copper in a Non-biting Midge
Riparian ecosystems are vital interfaces between aquatic and terrestrial environments but are increasingly impacted by anthropogenic pollution. In these systems, merolimnic insects serve as crucial ecological links, occupying aquatic habitats as larvae and terrestrial environments as adults, thus being an essential food source in both. Consequently, pollutant exposure during the aquatic larval sta...
Roeder, N.
•
Kolbenschlag, S.
•
Pietz, S.
•
Brennan, R. S.
...•
Schwenk, K.
biorxiv
Fri Jul 04 2025
Gamete release in Ciona robusta: roles of gonadotropin-releasing hormone and the photoreception system
Gamete release, an essential event for animals, is regulated by various factors including environmental stimuli, neural circuit, and endocrine molecules. In this study, we investigated the mechanisms regulating gamete release in the ascidian Ciona robusta, part of the sister group of vertebrates. Ciona is a hermaphrodite, releasing sperm first from orange-pigmented organ (OPO) at the end of the sp...
Osugi, T.
•
Matsubara, S.
•
Shiraishi, A.
•
Wada, A.
...•
Satake, H.
biorxiv
Fri Jul 04 2025
Songs distinguish the cryptic giant hummingbird species and clarify range limits
Vocal traits are often essential for distinguishing phenotypically cryptic taxa. The hummingbird genus Patagona comprises two species, near identical in plumage and morphology, that differ in almost every aspect of their ecology and evolution: The Northern Giant Hummingbird (Patagona peruviana) and Southern Giant Hummingbird (Patagona gigas). Here, we characterized the songs of both giant hummingb...
Robinson, B. W.
•
Zucker, R. J.
•
Witt, C. C.
•
Valqui, T.
•
Williamson, J. L.
biorxiv
Fri Jul 04 2025
Investigating the effects of chimerism on the inference of selection: quantifying genomic targets of purifying, positive, and balancing selection in common marmosets (Callithrix jacchus)
The common marmoset (Callithrix jacchus) is of considerable biomedical importance, yet there remains a need to characterize the evolutionary forces shaping empirically observed patterns of genomic variation in the species. However, two uncommon biological traits potentially prevent the use of standard population genetic approaches in this primate: a high frequency of twin-births and the prevalence...
Soni, V.
•
Versoza, C. J.
•
Pfeifer, S. P.
•
Jensen, J. D.
biorxiv
Fri Jul 04 2025
Cities as evolutionary incubators for the global spread of the Spotted Lanternfly
Habitat destruction and invasive species pose two of the greatest global threats to biodiversity. These factors do not operate in isolation, and nowhere is their interaction more apparent than in urban environments. Urban organisms rapidly evolve under novel ecological circumstances where they also encounter anthropogenic opportunities for range expansion. Here, we examine the role of urbanization...
Meng, F.
•
Snead, A. A.
•
Zhang, A. Y.
•
Munshi-South, J.
•
Winchell, K. M.
biorxiv
Fri Jul 04 2025
Functional characterization of specialized immune cells in a cnidarian reveals an ancestral antiviral program
Examining early-branching animal phyla can help reconstructing the evolutionary origins of immune cells. Here, we characterized immune-related cell programs in embryos of the sea anemone Nematostella vectensis, a model of Cnidaria, which diverged ~600 million years ago from other animals. Using a transgenic Nematostella reporter line expressing mCherry under the RLRb antiviral promoter, we identif...
Kozlovski, I.
•
Sharoni, T.
•
Levy, S.
•
Jaimes-Becerra, A.
...•
Moran, Y.
biorxiv
Fri Jul 04 2025
Rapid spread of knockdown resistance allele frequencies in a suburban population of Aedes albopictus
Aedes albopictus is a major vector of arboviral diseases and is often targeted by pyrethroid-based mosquito control in residential areas. While knockdown resistance (kdr) mutations are well documented in Ae. aegypti, their emergence in Ae. albopictus has been less studied, particularly in suburban environments where insecticide application is often uncoordinated. Understanding the temporal and spa...
Baltzegar, J. F.
•
Butler, C.
•
Beeson, C.
•
Reed, E. M.
...•
Reiskind, M. O. B.
biorxiv
Fri Jul 04 2025
Estimating the reduction in genetic diversity from background selection under non-equilibrium demography and partial selfing
The effect of natural selection on linked sites has been suggested to be a major determinant of genetic diversity. While it is in principle possible to estimate this effect from genome sequence data, interactions between selection, demography and inbreeding are expected to make inference less reliable. Here we investigate whether the genome-wide reduction in diversity due to background selection (...
Mackintosh, A.
•
Brault, M.
•
Roze, D.
•
Lascoux, M.
•
Glemin, S.