Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets that are independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. The inclusion or exclusion of mitochondrial data had a limited impact upon analyses upon analyses using either concatenated data or multispecies coalescent methods. Some of the key phylogenetic findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order

A Macroevolutionary Perspective on Multiple Sexual Traits in the Phasianidae (Galliformes)

Traits involved in sexual signaling are ubiquitous among animals. Although a single trait appears sufficient to convey information, many sexually dimorphic species exhibit multiple sexual signals, which may be costly to signalers and receivers. Given that one signal may be enough, there are many microevolutionary hypotheses to explain the evolution of multiple signals. Here we extend these hypotheses to a macroevolutionary scale and compare those predictions to the patterns of gains and losses of sexual dimorphism in pheasants and partridges. Among nine dimorphic characters, including six intersexual signals and three indicators of competitive ability, all exhibited both gains and losses of dimorphism within the group. Although theories of intersexual selection emphasize gain and elaboration, those six characters exhibited greater rates of loss than gain; in contrast, the competitive traits showed a slight bias towards gains. The available models, when examined in a macroevolutionary framework, did not yield unique predictions, making it difficult to distinguish among them. Even with this limitation, when the predictions of these alternative models were compared with the heterogeneous patterns of evolution of dimorphism in phasianids, it is clear that many different selective processes have been involved in the evolution of sexual signals in this group

Speciation in Duckweeds (Lemnaceae): Phylogenetic and Ecological Inferences

Species of duckweeds (Letnnaceae) that were resolved as sister taxa in a phylogeny based on combined molecular and non-molecular data were compared for morphological, physiological, and ecological attributes to infer factors important in the initial divergence leading to speciation. The ability to survive extreme conditions such as desiccation and cold temperatures is the most common difference identified between species. Two morphological characters facilitating survival in extreme environments are production of special resting buds called turions and increased seed production. The prevalent geographic pattern for species pairs consists of one restricted species occurring on the periphery of a more widespread taxon; this pattern indicates that divergence of peripheral isolates is a common geographical mode of speciation in duckweeds. Other species differ in optimal environmental conditions for growth, and these species are largely sympatric. In only one instance does it appear that divergence and speciation occurred following long-distance dispersal. Sympatric species pairs have the lowest molecular divergence; widespread primarily allopatric, and distantly allopatric species have the highest molecular divergence. Despite infrequent sexual reproduction, some degree of detectable variation (molecular, physiological, etc.) occurs within populations and among populations of the same species. Molecular evidence indicates that variation within duckweeds extends from the population and intraspecific levels to very different levels of divergence among recognized species. Contrary to the appearance of morphological and ecological uniformity implied by their reduced morphology and restricted occurrence in fresh water habitats, duckweeds are not a group in evolutionary stasis. Rather, these smallest of all flowering plants are dynamic evolutionarily, and comprise a model system for studying plant evolution and speciation

Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions

Homoplastic Microinversions and the Avian Tree of Life

Background Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasy-free evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. Results We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. Conclusions Microinversions can provide valuable phylogenetic information, although power analysis indicates that large amounts of sequence data will be necessary to identify enough inversions (and similar RGCs) to resolve short branches in the tree of life. Moreover, microinversions are not perfect characters and should be interpreted with caution, just as with any other character type. Independent of their use for phylogenetic analyses, microinversions are important because they have the potential to complicate alignment of non-coding sequences. Despite their low rate of accumulation, they have clearly contributed to genome evolution, suggesting that active identification of microinversions will prove useful in future phylogenomic studies

Phylogenetic definitions for 25 higher-level clade names of birds

Knowledge of the higher-level phylogenetic relationships of birds has grown substantially during the past two decades due to the application of genomic data. However, the nomenclature of higher-level taxa has not become more stable, due to the lack of regulation of taxon names above the level of superfamily by the ICZN, and the usage of rank-based nomenclature, which is not tied to clades in a phylogeny. Lack of regulation and the instability of rank-based nomenclature impede effective communication among systematists. Here we review support for higher-level avian clades using a set of 10 phylogenomic data sets, and identify clades that are supported by congruency of at least four of these. We provide formal definitions of the names of these clades based on the rules of the recently published PhyloCode. The names of 25 clades are here defined using minimum-crown-clade (n = 23), minimum-clade (n = 1) and maximum-crown-clade (n = 1) definitions. Four new names are introduced here: Dinocrypturi, Pteroclimesites, Musophagotides and Pelecanes. We also review diagnostic apomorphies of the relevant clades, and identify known synonyms and homonyms. By establishing a formal link between higher-level taxon names and well-supported phylogenetic hypotheses, our phylogenetic definitions will provide a solid basis for the stabilization of avian higher-level nomenclature

Phylogenomics of manakins (Aves: Pipridae) using alternative locus filtering strategies based on informativeness

Target capture sequencing effectively generates molecular marker arrays useful for molecular systematics. These extensive data sets are advantageous where previous studies using a few loci have failed to resolve relationships confidently. Moreover, target capture is well-suited to fragmented source DNA, allowing data collection from species that lack fresh tissues. Herein we use target capture to generate data for a phylogeny of the avian family Pipridae (manakins), a group that has been the subject of many behavioral and ecological studies. Most manakin species feature lek mating systems, where males exhibit complex behavioral displays including mechanical and vocal sounds, coordinated movements of multiple males, and high speed movements. We analyzed thousands of ultraconserved element (UCE) loci along with a smaller number of coding exons and their flanking regions from all but one species of Pipridae. We examined three different methods of phylogenetic estimation (concatenation and two multispecies coalescent methods). Phylogenetic inferences using UCE data yielded strongly supported estimates of phylogeny regardless of analytical method. Exon probes had limited capability to capture sequence data and resulted in phylogeny estimates with reduced support and modest topological differences relative to the UCE trees, although these conflicts had limited support. Two genera were paraphyletic among all analyses and data sets, with Antilophia nested within Chiroxiphia and Tyranneutes nested within Neopelma. The Chiroxiphia-Antilophia Glade was an exception to the generally high support we observed; the topology of this Glade differed among analyses, even those based on UCE data. To further explore relationships within this group, we employed two filtering strategies to remove low-information loci. Those analyses resulted in distinct topologies, suggesting that the relationships we identified within Chiroxiphia-Antilophia should be interpreted with caution. Despite the existence of a few continuing uncertainties, our analyses resulted in a robust phylogenetic hypothesis of the family Pipridae that provides a comparative framework for future ecomorphological and behavioral studies.Peer reviewe

Foreyt

This study evaluated the effectiveness of nondieting versus dieting treatments for overweight, bingeeating women. Participants (N = 219) were randomly assigned to 1 of 3 groups: diet treatment (DT), nondiet treatment (NDT), or wait-list control (WLC). DT received a balanced-deficit diet reinforced with behavioral strategies. NDT received therapy designed to help participants break out of their dieting cycles. Treatment in both conditions was administered in weekly groups for 6 months, followed by 26 biweekly maintenance meetings, for a total of 18 months of contact. At 6 months posttreatment, DT lost 0.6 kg while NDT gained 1.3 kg. Both treatment groups reduced their Binge Eating Scale scores significantly more than WLC. At 18-month follow-up, both treatment groups experienced weight gain but maintained similar reductions in binge eating. Results indicate that neither intervention was successful in producing short-or long-term weight loss. Therapist biases, which may have affected treatment integrity, and other methodological issues are discussed in relation to the small weight losses achieved. Estimates of binge eating among obese patients range from 20% to 50%, depending on the criteria used and the study population (Bruce & Wilfiey, 1996; It is unclear whether or not binge-eating obese patients experience greater difficulty in treatment programs as a result of these liabilities. Obese binge eaters have been found to respond to weight loss programs similarly to nonbingers, and experience similar or lower attrition rates This research was supported by National Institute of Diabetes and Digestive and Kidney Diseases Grant DK43109 and by a Minority Scientist Development Award from the American Heart Association and its Puerto Rican Affiliate. Correspondence concerning this article should be addressed to G. Ken Goodrick, Behavioral Medicine Research Center, Baylor College of Medicine, 6535 Fannin, Mailstop F-700, Houston, Texas 77030. outcomes Several nondieting therapeutic approaches have been developed for the treatment of obesity The purpose of this prospective, randomized, controlled study was to evaluate the effectiveness of this nondieting approach in the treatment of obese, binge-eating women, compared with a standardized, behavioral dieting treatment and a control group. Method Participants The mean age of participants was 40 years (SD = 6.3, range = 25 to 50 years). Participants' mean pretreatment weight was 88 kg (SD = 9.6, range = 66 to 110 kg). The mean body mass index (BMI) was 33 kg/m 2 (SD = 3.4), with a range of 26 to 43 kg/m 2. The ethnic-racial composition of the sample was 85% White, 8% Black, and 7% Hispanic. Of the total participants, 62% were married, 21% were single or divorced, and 17% were never married. Twenty-four percent of the participants had a college degree, 65% had some college, and 11% had a high school diploma or less. Sixty-nine percent were employed full time, and 9% part time. Procedure Female participants were recruited from Houston and the surrounding area using print and electronic media to publicize the study. Those 36

A Phylogenomic Supertree of Birds

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well

Homoplastic microinversions and the avian tree of life

Background: Microinversions are cytologically undetectable inversions of DNA sequences that accumulate slowly in genomes. Like many other rare genomic changes (RGCs), microinversions are thought to be virtually homoplasyfree evolutionary characters, suggesting that they may be very useful for difficult phylogenetic problems such as the avian tree of life. However, few detailed surveys of these genomic rearrangements have been conducted, making it difficult to assess this hypothesis or understand the impact of microinversions upon genome evolution. Results: We surveyed non-coding sequence data from a recent avian phylogenetic study and found substantially more microinversions than expected based upon prior information about vertebrate inversion rates, although this is likely due to underestimation of these rates in previous studies. Most microinversions were lineage-specific or united well-accepted groups. However, some homoplastic microinversions were evident among the informative characters. Hemiplasy, which reflects differences between gene trees and the species tree, did not explain the observed homoplasy. Two specific loci were microinversion hotspots, with high numbers of inversions that included both the homoplastic as well as some overlapping microinversions. Neither stem-loop structures nor detectable sequence motifs were associated with microinversions in the hotspots. Conclusions: Microinversions can provide valuable phylogenetic information, although power analysis indicate