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Abstract Phylogenetic trees establish a historical context for the study of organismal form and function. Most phylogenetic trees are estimated using a model of evolution. For molecular data, modeling evolution is often based on biochemical observations about changes between character states. For example, there are four nucleotides, and we can make assumptions about the probability of transitions between them. By contrast, for morphological characters, we may not know a priori how many characters states there are per character, as both extant sampling and the fossil record may be highly incomplete, which leads to an observer bias. For a given character, the state space may be larger than what has been observed in the sample of taxa collected by the researcher. In this case, how many evolutionary rates are needed to even describe transitions between morphological character states may not be clear, potentially leading to model misspecification. To explore the impact of this model misspecification, we simulated character data with varying numbers of character states per character. We then used the data to estimate phylogenetic trees using models of evolution with the correct number of character states and an incorrect number of character states. The results of this study indicate that this observer bias may lead to phylogenetic error, particularly in the branch lengths of trees. If the state space is wrongly assumed to be too large, then we underestimate the branch lengths, and the opposite occurs when the state space is wrongly assumed to be too small. 

The eastern Pinesnake (Pituophis melanoleucus) is found throughout eastern United States. Taxonomy in this group has been controversial with several conflicting species designations. Three subspecies of the eastern Pinesnake have prevailed in the literature to their geographic locations and scale coloration: the northern Pinesnake (P. m. melanoleucus), the Florida Pinesnake (P. m. mugitus), and the Black Pinesnake (P. m. lodingi). Within the region, there are several major barriers to dispersal, particularly major river drainage systems and human modification of the longleaf pine habitat. Consistently, a lack of phylogenetic resolution has plagued these taxa in prior studies. The goal of this study was to examine the taxonomic validity of the eastern Pinesnake complex using single nucleotide polymorphisms (SNPs) isolated from ultra-conserved elements (UCEs) in phylogenetic and population genetic approaches. Molecular species delimitation approaches indicated that the population of eastern Pinesnake exhibits population structure across its range that may rise to the level of being new species. 

Poeciliopsis (Cyprinodontiformes: Poeciliidae) is a genus comprised of 25 species of freshwater fishes. Several well-known taxonomic uncertainties exist within the genus, especially in relation to the taxonomic status of Poeciliopsis pleurospilus and P . gracilis . However, to date, no studies have been conducted to specifically address the taxonomic status of these two species. The goal of this study was to examine the taxonomic validity of P . pleurospilus and P . gracilis using genomic data (ddRADseq) in phylogenetic, population genetic, and species delimitation frameworks. Multiple analyses support the recognition of both taxa as distinct species and also permits us to revise their respective distributions. A species delimitation analysis indicates that P . pleurospilus and P . gracilis are distinct species, each of which consists of two distinct lineages that are geographically structured. Phylogenetic and population genetic analyses provide clear evidence that individuals of P . gracilis are distributed north and west of the Isthmus of Tehuantepec in both Pacific and Atlantic river systems in Mexico, whereas individuals of P . pleurospilus are distributed in both Atlantic and Pacific river systems south and east of the Isthmus of Tehuantepec, from southern Mexico to Honduras.