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There are considerable phylogenetic incongruencies between morphological and phylogenomic data for the deep evolution of animals. This has contributed to a heated debate over the earliest-branching lineage of the animal kingdom: the sister to all other Metazoa (SOM). Here, we use published phylogenomic data sets (⁠|$\sim $| 45,000–400,000 characters in size with |$\sim $| 15–100 taxa) that focus on early metazoan phylogeny to evaluate the impact of incorporating morphological data sets (⁠|$\sim $| 15–275 characters). We additionally use small exemplar data sets to quantify how increased taxon sampling can help stabilize phylogenetic inferences. We apply a plethora of common methods, that is, likelihood models and their "equivalent" under parsimony: character weighting schemes. Our results are at odds with the typical view of phylogenomics, that is, that genomic-scale data sets will swamp out inferences from morphological data. Instead, weighting morphological data 2–10 |$\times $| in both likelihood and parsimony can in some cases "flip" which phylum is inferred to be the SOM. This typically results in the molecular hypothesis of Ctenophora as the SOM flipping to Porifera (or occasionally Placozoa). However, greater taxon sampling improves phylogenetic stability, with some of the larger molecular data sets (⁠|$>$| 200,000 characters and up to |$\sim $| 100 taxa) showing node stability even with |$\geqq100\times $| upweighting of morphological data. Accordingly, our analyses have three strong messages. 1) The assumption that genomic data will automatically "swamp out" morphological data is not always true for the SOM question. Morphological data have a strong influence in our analyses of combined data sets, even when outnumbered thousands of times by molecular data. Morphology therefore should not be counted out a priori. 2) We here quantify for the first time how the stability of the SOM node improves for several genomic data sets when the taxon sampling is increased. 3) The patterns of "flipping points" (i.e. the weighting of morphological data it takes to change the inferred SOM) carry information about the phylogenetic stability of matrices. The weighting space is an innovative way to assess comparability of data sets that could be developed into a new sensitivity analysis tool. [Metazoa; Morphology; Phylogenomics; Weighting.] [ABSTRACT FROM AUTHOR]

Phylogenies based on gene content rely on statements of primary homology to characterize gene presence or absence. These statements (hypotheses) are usually determined by techniques based on threshold similarity or distance measurements between genes. This fundamental but problematic step can be examined by evaluating each homology hypothesis by the extent to which it is corroborated by the rest of the data. Here we test the effects of varying the stringency for making primary homology statements using a range of similarity (e-value) cutoffs in 166 fully sequenced and annotated genomes spanning the tree of life. By evaluating each resulting data set with tree-based measurements of character consistency and information content, we find a set of homology statements that optimizes overall corroborration. The resulting data set produces well-resolved and well-supported trees of life and greatly ameliorates previously noted inconsistencies such as the misclassification of small genomes. The method presented here, which can be used to test any technique for recognizing primary homology, provides an objective framework for evaluating phylogenetic hypotheses and data sets for the tree of life. It also can serve as a technique for identifying well-corroborated sets of homologous genes for functional genomic applications. [CCM; consistency; corroboration; gene content; homology; ILD; phylogeny; presence absence; tree of life.] [ABSTRACT FROM AUTHOR]

The article discusses the preservation and long-term storage of biological specimens, derived materials and associated data, which are essential to ensure comparability and reproducibility in all areas of biological research. Natural history museums and herbaria now face the challenging task of preserving the genetic library of life for generations to come. However, the lack and/or poor condition of preservation of molecular vouchers generated from often fragile and rare specimens have been problems too often underestimated or not addressed. The article seeks to bring genetic resource collections, and the issues of preservation of genetic resources, to the awareness of the systematic biology community through the case study of the American Museum of Natural History's new cryogenic repository.

When a data set is partitioned, the resulting subsets may contain phylogenetically conflicting signals if they have different evolutionary histories. In a data set with many taxa, a single taxon that contains multiple phylogenetic histories may result in global incongruence, but no methods are available in a parsimony framework to localize incongruence to specific clades in a phylogeny or to test the significance of incongruence on a local scale. Here we present a new method to quantify the conflict between data partitions for any clade in a phylogeny and to test the statistical significance of that conflict by using a metric called the local incongruence length difference. We apply this method to the evolutionary history of the nuclear receptor superfamily, a large group of transcriptional regulators that play essential roles in metazoan development and physiology. All nuclear receptors are composed of several discrete domains, including one that binds to DNA response elements on specific target genes and another that binds to the appropriate ligand. We have performed combined and separate phylogenetic analyses of these two domains and have tested the hypothesis that nuclear receptors evolved by a simple process of lineage splitting and divergence, without domain shuffling or other forms of sequence transfer between proteins. Our analysis indicates that significant conflict exists between the partitioned domains at a few nodes on the tree, suggesting that several groups of receptors are "hybrid proteins" formed by domain shuffling or other forms of sequence transfer between more ancient nuclear receptors. [ABSTRACT FROM AUTHOR]

Discusses the resolution of a supertree and supermatrix paradox. Phylogenetic relationships of paraxonians based on explicit character data and a combined supertree analysis; Parsimony analysis of the supertree data set; Problems in the supertree data set; Supermatrix analysis of paraxonia.

A phylogenetic hypothesis of relationships among 33 species of stalk-eyed flies was generated from a molecular data set comprising three mitochondrial and three nuclear gene regions. A combined analysis of all the data equally weighted produced a single most-parsimonious cladogram with relatively strong support at the majority of nodes. The phylogenetic utility of different classes of molecular data was also examined. In particular, using a number of different measures of utility in both a combined and separate analysis framework, we focused on the distinction between mitochondrial and nuclear genes and between faster-evolving characters and slower-evolving characters. For the first comparison, by nearly any measure of utility, the nuclear genes are substantially more informative for resolving diopsid relationships than are the mitochondrial genes. The nuclear genes exhibit less homoplasy, are less incongruent with one another and with the combined data, and contribute more support to the combined analysis topology than do the mitochondrial genes. Results from the second comparison, however, provide little evidence of a clear difference in utility. Despite indications of rapid divergence and saturation, faster-evolving characters in both the nuclear and mitochondrial data sets still provide substantial phylogenetic signal. In general, inclusion of the more rapidly evolving data consistently improves the congruence among partitions. [Diopsidae; incongruence; nuclear genes; partitioned Bremer support; saturation.]. [ABSTRACT FROM AUTHOR]

Morphological and molecular data sets favor robustly supported, contradictory interpretations of crocodylian phylogeny. A longstanding perception in the field of systematics is that such significantly conflicting data sets should be analyzed separately. Here we utilize a combined approach, simultaneous analyses of all relevant character data, to summarize common support and to reconcile discrepancies among data sets. By conjoining rather than separating incongruent classes of data, secondary phylogenetic signals emerge from both molecular and morphological character sets and provide solid evidence for a unified hypothesis of crocodylian phylogeny. Simultaneous analyses of four gene sequences and paleontological data suggest that putative adaptive convergences in the jaws of gavialines (gavials) and tomistomines (false gavials) offer character support for a grouping of these taxa, making Gavialinae an atavistic taxon. Simple new methods for measuring the influence of extinct taxa on topological support indicate that in this vertebrate order fossils generally stabilize relationships and accentuate hidden phylogenetic signals. Remaining inconsistencies in minimum length trees, including concentrated hierarchical patterns of homoplasy and extensive gaps in the fossil record, indicate where future work in crocodylian systematics should be directed. [ABSTRACT FROM AUTHOR]