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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 partitioning of global biodiversity into biogeographic regions is critical for understanding the impacts of global-scale ecological and evolutionary processes on species assemblages as well as prioritizing areas for conservation. However, the lack of globally comprehensive data on species distributions precludes fine-scale estimation of biogeographical regionalization for numerous taxa of ecological, economic and conservation interest. Using a recently published phylogeny and novel curated native range maps for over 10 000 species of butterflies around the world, we delineated biogeographic regions for the world’s butterflies using phylogenetic dissimilarity. We uncovered 19 distinct phylogenetically delimited regions (phyloregions) nested within 6 realms. Regional boundaries were predicted by spatial turnover in modern-day temperature and precipitation seasonality, but historical climate change also left a pronounced fingerprint on deeper- (realm-) level boundaries. We use a culturally and ecologically important group of insects to expand our understanding of how historical and contemporary factors drive the distribution of organismal lineages on the Earth. As insects and global biodiversity more generally face unprecedented challenges from anthropogenic factors, our research provides the groundwork for prioritizing regions and taxa for conservation, especially with the goal of preserving the legacies of our biosphere’s evolutionary history. This article is part of the discussion meeting issue ‘Bending the curve towards nature recovery: building on Georgina Mace's legacy for a biodiverse future’. 

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. 

Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in data sets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become “inapplicable” across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological data sets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded data set on palaeognathid birds. We find that in small, simulated data sets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger data sets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures—a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a data set, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space. 

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.