The NHM Collections Study Awards provide funding for undergraduate and graduate students to visit and study the collections of the Natural History Museum of Los Angeles County, the La Brea Tar Pits & ...

Abstract. The fossil record is incomplete, as evidenced by the pervasive presence of ghost lineages throughout the Tree of Life. For example, across placen

Macroevolutionary adaptation of a continuous trait to different discrete states across species can be modelled using a phylogenetic state-dependent Ornstein–Uhlenbeck (OU) process. Existing infere...

Abstract. One of the most transformative advances in molecular systematics over the past several decades has been our understanding of how population proce

Phylogenetic conflict—particularly hidden gene-tree discordance generated by incomplete lineage sorting (ILS)—is pervasive in multilocus and phylogenomic datasets, yet its consequences for nucleotide substitution model selection remain poorly understood. Modern molecular studies increasingly collect and concatenate large sets of independent loci sampled across distant and often poorly characterized regions of the genome, creating significant potential for heterogeneity when analyzed in combination. Here, we examine whether intra-alignment genealogical conflict can influence standard model selection procedures to favor parameter-rich substitution models even when sequences evolve under a simple substitution process. Through a series of in silico case studies, we simulated sequence evolution under the simplest rate-homogeneous Jukes–Cantor (JC69) model and generated concatenated alignments as mosaics of multiple loci, each evolving on its own gene tree drawn under the multispecies coalescent. Conflict was increased by manipulating conditions expected to elevate ILS and gene-tree heterogeneity and embedding progressively more hidden genealogies within alignments while holding total alignment length constant. Despite all data being generated under JC69, model selection frequently favored more complex models, with varying sensitivity depending on the number of taxa, the expected amount of conflict, and the specific selection criterion applied. A dominant pattern was frequent inclusion of among-site rate variation parameters (+ G4 and/or + I), and under extreme conflict, model selection increasingly favored richer substitution models (e.g., SYM, GTR). Broadly, our results showed that hidden conflict can manifest as substitutional and rate heterogeneity, driving selection procedures to compensate with additional parameters in concatenated analyses under high conflict. Broadly, our study contributes to a greater understanding and appreciation of the challenges in modeling molecular evolution in the era of multilocus phylogenetics.

Many species are characterized by trait differences between each other. For example, the brain size of different primate and human lineages varies. The que

Almost all invasive ant species studied so far form supercolonies, a dense network of interconnected nests comprising numerous queens, without aggression toward non-nestmates. Here, we show that most...

Accurate estimation of speciation ( $$\lambda $$ λ ) and extinction ( $$\mu $$ μ ) rates from phylogenetic trees is central to studies of diversification, yet it remains unclear whether commonly used ...