Significance: Traditional interpretation of animal phylogeny suggests traits, such as mesoderm, muscles, and neurons, evolved only once given the assumed placement of sponges as sister to all other animals. In contrast, placement of ctenophores as the first branching animal lineage raises the possibility of multiple origins of many complex traits considered important for animal diversification and success. We consider sources of potential error and increase taxon sampling to find a single, statistically robust placement of ctenophores as our most distant animal relatives, contrary to the traditional understanding of animal phylogeny. Furthermore, ribosomal protein genes are identified as creating conflict in signal that caused some past studies to recover a sister relationship between ctenophores and cnidarians.

Ctenophora, comprising approximately 200 described species, is an important lineage for understanding metazoan evolution and is of great ecological and economic importance. Ctenophore diversity includes species with unique colloblasts used for prey capture, smooth and striated muscles, benthic and pelagic lifestyles, and locomotion with ciliated paddles or muscular propulsion. However, the ancestral states of traits are debated and relationships among many lineages are unresolved. Here, using 27 newly sequenced ctenophore transcriptomes, publicly available data and methods to control systematic error, we establish the placement of Ctenophora as the sister group to all other animals and refine the phylogenetic relationships within ctenophores. Molecular clock analyses suggest modern ctenophore diversity originated approximately 350 million years ago ± 88 million years, conflicting with previous hypotheses, which suggest it originated approximately 65 million years ago. We recover Euplokamis dunlapae—a species with striated muscles—as the sister lineage to other sampled ctenophores. Ancestral state reconstruction shows that the most recent common ancestor of extant ctenophores was pelagic, possessed tentacles, was bioluminescent and did not have separate sexes. Our results imply at least two transitions from a pelagic to benthic lifestyle within Ctenophora, suggesting that such transitions were more common in animal diversification than previously thought.

This is the first American Fisheries Society conservation assessment of freshwater gastropods (snails) from Canada and the United States by the Gastropod Subcommittee (Endangered Species Committee). This review covers 703 species representing 16 families and 93 genera, of which 67 species are considered extinct, or possibly extinct, 278 are endangered, 102 are threatened, 73 are vulnerable, 157 are currently stable, and 26 species have uncertain taxonomic status. Of the entire fauna, 74% of gastropods are imperiled (vulnerable, threatened, endangered) or extinct, which exceeds imperilment levels in fishes (39%) and crayfishes (48%) but is similar to that of mussels (72%). Comparison of modern to background extinction rates reveals that gastropods have the highest modern extinction rate yet observed, 9,539 times greater than background rates. Gastropods are highly susceptible to habitat loss and degradation, particularly narrow endemics restricted to a single spring or short stream reaches. Compilation of this review was hampered by a paucity of current distributional information and taxonomic uncertainties. Although research on several fronts including basic biology, physiology, conservation strategies, life history, and ecology are needed, systematics and curation of museum collections and databases coupled with comprehensive status surveys (geographic limits, threat identification) are priorities. RESUMEN esta es la primera evaluación sobre el estado que guarda la conservación de los gasterópodos (caracoles) de Canadá y los EE.UU., realizada por el Subcomité para los Gasterópodos (Comité de Especies Amenazadas) de la Sociedad Americana de Pesquerías. Esta revisión comprende 703 especies, pertenecientes a 16 familias y 93 géneros, de las cuales 67 se consideran extintas o probablemente extintas; 278 están en peligro, 102 amenazadas, 73 vulnerables, 157 cuentan con poblaciones estables y 26 especies presentan un estado taxonómico incierto. De la totalidad de la fauna, 74% de los gasterópodos se encuentran en alguna categoría de vulnerabilidad (amenazados, en peligro o vulnerables) o extintos, lo cual excede al nivel de amenaza al que está sujeto el grupo de los peces (39%) y los langostinos (48%), pero es similar al de los mejillones (72%). Comparando las tasas de extinción actuales contra las tasas de extinción de fondo en el grupo de los gasterópodos, se tiene que en la actualidad son las más altas registradas: 9,539 veces la tasa de extinción de fondo. Los gasterópodos son altamente susceptibles a la degradación y pérdida de hábitat, en particular aquellas especies endémicas cuya distribución está restringida a un solo manantial o a arroyos pequeños. La compilación realizada para esta revisión se dificultó por la falta de información sobre la incertidumbre en la distribución y taxonomía del grupo. Si bien se necesita desarrollar investigación en distintos frentes como biología básica, fisiología, estrategias de conservación, historias de vida y ecología, se consideran como prioridades la sistemática, curación de colecciones museográficas y bases de datos acopladas con muestreos sistemáticos integrales (para establecer límites geográficos, identificación de amenazas).

As phylogenetic datasets have increased in size, site-heterogeneous substitution models such as CAT-F81 and CAT-GTR have been advocated in favor of other models because they purportedly suppress long-branch attraction (LBA). These models are two of the most commonly used models in phylogenomics, and they have been applied to a variety of taxa, ranging from Drosophila to land plants. However, many arguments in favor of CAT models have been based on tenuous assumptions about the true phylogeny, rather than rigorous testing with known trees via simulation. Moreover, CAT models have not been compared to other approaches for handling substitutional heterogeneity such as data partitioning with site-homogeneous substitution models. We simulated amino acid sequence datasets with substitutional heterogeneity on a variety of tree shapes including those susceptible to LBA. Data were analyzed with both CAT models and partitioning to explore model performance; in total over 670,000 CPU hours were used, of which over 97% was spent running analyses with CAT models. In many cases, all models recovered branching patterns that were identical to the known tree. However, CAT-F81 consistently performed worse than other models in inferring the correct branching patterns, and both CAT models often overestimated substitutional heterogeneity. Additionally, reanalysis of two empirical metazoan datasets supports the notion that CAT-F81 tends to recover less accurate trees than data partitioning and CAT-GTR. Given these results, we conclude that partitioning and CAT-GTR perform similarly in recovering accurate branching patterns. However, computation time can be orders of magnitude less for data partitioning, with commonly used implementations of CAT-GTR often failing to reach completion in a reasonable time frame (i.e., for Bayesian analyses to converge). Practices such as removing constant sites and parsimony uninformative characters, or using CAT-F81 when CAT-GTR is deemed too computationally expensive, cannot be logically justified. Given clear problems with CAT-F81, phylogenies previously inferred with this model should be reassessed.