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This scientific article explores the phylogenetic relationships among different bird species, specifically focusing on the Neoaves group. The authors reanalyzed a dataset from a previous study and discovered that the new phylogeny did not support the traditional division between land birds and waterbirds. They also identified errors in the dataset that could affect the accuracy of phylogenetic analysis. The authors stress the importance of using proper procedures to ensure accurate sequence alignments and improve our understanding of bird evolution. [Extracted from the article]

Different species of toothed whales (Odontoceti) exhibit a variety of tooth forms and enamel types. Some odontocetes have highly prismatic enamel with Hunter-Schreger bands, whereas enamel is vestigial or entirely lacking in other species. Different tooth forms and enamel types are associated with alternate feeding strategies that range from biting and grasping prey with teeth in most oceanic and river dolphins to the suction feeding of softer prey items without the use of teeth in many beaked whales. At the molecular level, previous studies have documented inactivating mutations in the enamel-specific genes of some odontocete species that lack complex enamel. At a broader scale, however, it is unclear whether enamel complexity across the full diversity of extant Odontoceti correlates with the relative strength of purifying selection on enamel-specific genes. Here, we employ sequence alignments for seven enamel-specific genes (ACP4, AMBN, AMELX, AMTN, ENAM, KLK4, MMP20) in 62 odontocete species that are representative of all extant families. The sequences for 33 odontocete species were obtained from databases, and sequences for the remaining 29 species were newly generated for this study. We screened these alignments for inactivating mutations (e.g., frameshift indels) and provide a comprehensive catalog of these mutations in species with one or more inactivated enamel genes. Inactivating mutations are rare in Delphinidae (oceanic dolphins) and Platanistidae/Inioidea (river dolphins) that have higher enamel complexity scores. By contrast, mutations are much more numerous in clades such as Monodontidae (narwhal, beluga), Ziphiidae (beaked whales), Physeteroidea (sperm whales), and Phocoenidae (porpoises) that are characterized by simpler enamel or even enamelless teeth. Further, several higher-level taxa (e.g., Hyperoodon, Kogiidae, Monodontidae) possess shared inactivating mutations in one or more enamel genes, which suggests loss of function of these genes in the common ancestor of each clade. We also performed selection (dN/dS) analyses on a concatenation of these genes and used linear regression and Spearman's rank-order correlation to test for correlations between enamel complexity and two different measures of selection intensity (# of inactivating mutations per million years, dN/dS values). Selection analyses revealed that relaxed purifying selection is especially prominent in physeteroids, monodontids, and phocoenids. Linear regressions and correlation analyses revealed a strong negative correlation between selective pressure (dN/dS values) and enamel complexity. Stronger purifying selection (low dN/dS) is found on branches with more complex enamel and weaker purifying selection (higher dN/dS) occurs on branches with less complex enamel or enamelless teeth. As odontocetes diversified into a variety of feeding modes, in particular, the suction capture of prey, a reduced reliance on the dentition for prey capture resulted in the relaxed selection of genes that are critical to enamel development. [ABSTRACT FROM AUTHOR]

The transition in Mysticeti (Cetacea) from capture of individual prey using teeth to bulk filtering batches of small prey using baleen ranks among the most dramatic evolutionary transformations in mammalian history. We review phylogenetic work on the homology of mysticete feeding structures from anatomical, ontogenetic, and genomic perspectives. Six characters with key functional significance for filter-feeding behavior are mapped to cladograms based on 11 morphological datasets to reconstruct evolutionary change across the teeth-to-baleen transition. This comparative summary within a common parsimony framework reveals extensive conflicts among independent systematic efforts but also broad support for the newly named clade Kinetomenta (Aetiocetidae + Chaeomysticeti). Complementary anatomical studies using CT scans and ontogenetic series hint at commonalities between the developmental programs for teeth and baleen, lending further support for a 'transitional chimaeric feeder' scenario that best explains current evidence on the transition to filter feeding. For some extant mysticetes, the ontogenetic sequence in fetal specimens recapitulates the inferred evolutionary transformation: from teeth, to teeth and baleen, to just baleen. Phylogenetic mapping of inactivating mutations reveals mutational decay of 'dental genes' related to enamel formation before the emergence of crown Mysticeti, while 'baleen genes' that were repurposed or newly derived during the evolutionary elaboration of baleen currently are poorly characterized. Review and meta-analysis of available data suggest that the teeth-to-baleen transition in Mysticeti is one of the best characterized macroevolutionary shifts due to the diversity of data from the genome, the fossil record, comparative anatomy, and ontogeny that directly bears on this remarkable evolutionary transformation. [ABSTRACT FROM AUTHOR]

Retroelement insertions (RIs) are low-homoplasy characters that are ideal data for addressing deep evolutionary radiations, where gene tree reconstruction errors can severely hinder phylogenetic inference with DNA and protein sequence data. Phylogenomic studies of Neoaves, a large clade of birds (>9000 species) that first diversified near the Cretaceous–Paleogene boundary, have yielded an array of robustly supported, contradictory relationships among deep lineages. Here, we reanalyzed a large RI matrix for birds using recently proposed quartet-based coalescent methods that enable inference of large species trees including branch lengths in coalescent units, clade-support, statistical tests for gene flow, and combined analysis with DNA-sequence-based gene trees. Genome-scale coalescent analyses revealed extremely short branches at the base of Neoaves, meager branch support, and limited congruence with previous work at the most challenging nodes. Despite widespread topological conflicts with DNA-sequence-based trees, combined analyses of RIs with thousands of gene trees show emergent support for multiple higher-level clades (Columbea, Passerea, Columbimorphae, Otidimorphae, Phaethoquornithes). RIs express asymmetrical support for deep relationships within the subclade Afroaves that hints at ancient gene flow involving the owl lineage (Strigiformes). Because DNA-sequence data are challenged by gene tree-reconstruction error, analysis of RIs represents one approach for improving gene tree-based methods when divergences are deep, internodes are short, terminal branches are long, and introgressive hybridization further confounds species–tree inference. [ABSTRACT FROM AUTHOR]

A potential shortcoming of concatenation methods for species tree estimation is their failure to account for incomplete lineage sorting. Coalescent methods address this problem but make various assumptions that, if violated, can result in worse performance than concatenation. Given the challenges of analyzing DNA sequences with both concatenation and coalescent methods, retroelement insertions (RIs) have emerged as powerful phylogenomic markers for species tree estimation. Here, we show that two recently proposed quartet-based methods, SDPquartets and ASTRAL_BP, are statistically consistent estimators of the unrooted species tree topology under the coalescent when RIs follow a neutral infinite-sites model of mutation and the expected number of new RIs per generation is constant across the species tree. The accuracy of these (and other) methods for inferring species trees from RIs has yet to be assessed on simulated data sets, where the true species tree topology is known. Therefore, we evaluated eight methods given RIs simulated from four model species trees, all of which have short branches and at least three of which are in the anomaly zone. In our simulation study, ASTRAL_BP and SDPquartets always recovered the correct species tree topology when given a sufficiently large number of RIs, as predicted. A distance-based method (ASTRID_BP) and Dollo parsimony also performed well in recovering the species tree topology. In contrast, unordered, polymorphism, and Camin–Sokal parsimony (as well as an approach based on MDC) typically fail to recover the correct species tree topology in anomaly zone situations with more than four ingroup taxa. Of the methods studied, only ASTRAL_BP automatically estimates internal branch lengths (in coalescent units) and support values (i.e. local posterior probabilities). We examined the accuracy of branch length estimation, finding that estimated lengths were accurate for short branches but upwardly biased otherwise. This led us to derive the maximum likelihood (branch length) estimate for when RIs are given as input instead of binary gene trees; this corrected formula produced accurate estimates of branch lengths in our simulation study provided that a sufficiently large number of RIs were given as input. Lastly, we evaluated the impact of data quantity on species tree estimation by repeating the above experiments with input sizes varying from 100 to 100,000 parsimony-informative RIs. We found that, when given just 1000 parsimony-informative RIs as input, ASTRAL_BP successfully reconstructed major clades (i.e. clades separated by branches |$>0.3$| coalescent units) with high support and identified rapid radiations (i.e. shorter connected branches), although not their precise branching order. The local posterior probability was effective for controlling false positive branches in these scenarios. [Coalescence; incomplete lineage sorting; Laurasiatheria; Palaeognathae; parsimony; polymorphism parsimony; retroelement insertions; species trees; transposon.] [ABSTRACT FROM AUTHOR]

Objectives: The new data provide an important genomic resource for the Critically Endangered Cuban crocodile (Crocodylus rhombifer). Cuban crocodiles are restricted to the Zapata Swamp in southern Matanzas Province, Cuba, and readily hybridize with the widespread American crocodile (Crocodylus acutus) in areas of sympatry. The reported de novo assembly will contribute to studies of crocodylian evolutionary history and provide a resource for informing Cuban crocodile conservation. Data description: The final 2.2 Gb draft genome for C. rhombifer consists of 41,387 scaffolds (contigs: N50 = 104.67 Kb; scaffold: N50-518.55 Kb). Benchmarking Universal Single-Copy Orthologs (BUSCO) identified 92.3% of the 3,354 genes in the vertebrata_odb10 database. Approximately 42% of the genome (960Mbp) comprises repeat elements. We predicted 30,138 unique protein-coding sequences (17,737 unique genes) in the genome assembly. Functional annotation found the top Gene Ontology annotations for Biological Processes, Molecular Function, and Cellular Component were regulation, protein, and intracellular, respectively. This assembly will support future macroevolutionary, conservation, and molecular studies of the Cuban crocodile. [ABSTRACT FROM AUTHOR]

Homology is perhaps the most central concept of phylogenetic biology. At difficult to resolve polytomies that are deep in theTree of Life, a few homology errors in phylogenomic data can drive spurious phylogenetic results. Feijoo and Parada (2017) assembled three phylogenomic data sets for mammals and reported methodological discrepancies and unexpected results that contradict the monophyly of well-established clades in Pinnipedia and Yangochiroptera. Examination of Feijoo and Parada's (2017) data sets reveals extensive homology errors (paralogous sequences, alignments of different exons to each other) and cross-contamination of sequences from different species. These problems predictably result in distorted estimates of gene trees, species trees, bootstrap support, and branch lengths. Correction of these errors resulted in robust support for conventional relationships in Pinnipedia and Yangochiroptera. Phylogenomic data sets are not immune to the problems of homology errors in sequence alignments. Rather, sequence alignments underlie all inferences in molecular phylogenetics and evolution and should be spot-checked for obvious errors via manual inspection of alignments and gene trees. [ABSTRACT FROM AUTHOR]

Homology is perhaps the most central concept of phylogenetic biology. Molecular systematists have traditionally paid due attention to the homology statements that are implied by their alignments of orthologous sequences, but some authors have suggested that manual gene-by-gene curation is not sustainable in the phylogenomics era. Here, we show that there are multiple ways to efficiently screen for and detect homology errors in phylogenomic data sets. Application of these screening approaches to two phylogenomic data sets, one for birds and another for mammals, shows that these data are replete with homology errors including alignments of different exons to each other, alignments of exons to introns, and alignments of paralogues to each other. The extent of these homology errors weakens the conclusions of studies based on these data sets. Despite advances in automated phylogenomic pipelines, we contend that much of the long, difficult, and sometimes tedious work of systematics is still required to guard against pervasive homology errors. This conclusion is underscored by recent studies that show that just a few outlier genes can impact phylogenetic results at short, tightly spaced internodes that are deep in the Tree of Life. The view that widespread DNA sequence alignment errors are not a major concern for rigorous systematic research is not tenable. If a primary goal of phylogenomics is to resolve the most challenging phylogenetic problems with the abundant data that are now available, researchers must employ effective procedures to screen for and correct homology errors prior to performing downstream phylogenetic analyses. [ABSTRACT FROM AUTHOR]

MC5R is one of five melanocortin receptor genes found in placental mammals. MC5R plays an important role in energy homeostasis and is also expressed in the terminal differentiation of sebaceous glands. Among placental mammals there are multiple lineages that either lack or have degenerative sebaceous glands including Cetacea (whales, dolphins, and porpoises), Hippopotamidae (hippopotamuses), Sirenia (manatees and dugongs), Proboscidea (elephants), Rhinocerotidae (rhinos), and Heterocephalus glaber (naked mole rat). Given the loss or diminution of sebaceous glands in these taxa, we procured MC5R sequences from publicly available genomes and transcriptomes, supplemented by a newly generated sequence for Choeropsis liberiensis (pygmy hippopotamus), to determine if this gene remains intact or is inactivated in association with loss/reduction of sebaceous glands. Our data set includes complete MC5R sequences for 114 placental mammal species including two individuals of Mammuthus primigenius (woolly mammoth) from Oimyakon and Wrangel Island. Complete loss or inactivation of the MC5R gene occurs in multiple placental lineages that have lost sebaceous glands (Cetacea, West Indian manatee, African elephant, white rhinoceros) or are characterized by unusual skin (pangolins, aardvarks). Both M. primigenius individuals share inactivating mutations with the African elephant even though sebaceous glands have been reported in the former. MC5R remains intact in hippopotamuses and the naked mole rat, although slightly elevated dN/dS ratios in these lineages allow for the possibility that the accumulation of inactivating mutations in MC5R may lag behind the relaxation of purifying selection. For Cetacea and Hippopotamidae, the absence of shared inactivating mutations in two different skin genes ( MC5R, PSORS1C2 ) is consistent with the hypothesis that semi-aquatic lifestyles were acquired independently in these clades following divergence from a common ancestor. [ABSTRACT FROM AUTHOR]

Summary coalescence methods have emerged as a popular alternative for inferring species trees with large genomic datasets, because these methods explicitly account for incomplete lineage sorting. However, statistical consistency of summary coalescence methods is not guaranteed unless several model assumptions are true, including the critical assumption that recombination occurs freely among but not within coalescence genes (c-genes), which are the fundamental units of analysis for these methods. Each c-gene has a single branching history, and large sets of these independent gene histories should be the input for genome-scale coalescence estimates of phylogeny. By contrast, numerous studies have reported the results of coalescence analyses in which complete protein-coding sequences are treated as c-genes even though exons for these loci can span more than a megabase of DNA. Empirical estimates of recombination breakpoints suggest that c-genes may be much shorter, especially when large clades with many species are the focus of analysis. Although this idea has been challenged recently in the literature, the inverse relationship between c-gene size and increased taxon sampling in a dataset--the 'recombination ratchet'--is a fundamental property of c-genes. For taxonomic groups characterized by genes with long intron sequences, complete protein-coding sequences are likely not valid c-genes and are inappropriate units of analysis for summary coalescence methods unless they occur in recombination deserts that are devoid of incomplete lineage sorting (ILS). Finally, it has been argued that coalescence methods are robust when the no-recombination within loci assumption is violated, but recombination must matter at some scale because ILS, a by-product of recombination, is the raison d'etre for coalescence methods. That is, extensive recombination is required to yield the large number of independently segregating c-genes used to infer a species tree. If coalescent methods are powerful enough to infer the correct species tree for difficult phylogenetic problems in the anomaly zone, where concatenation is expected to fail because of ILS, then there should be a decreasing probability of inferring the correct species tree using longer loci with many intralocus recombination breakpoints (i.e., increased levels of concatenation). [ABSTRACT FROM AUTHOR]

Recent phylogenetic analyses of a large dataset for mammalian families (169 taxa, 26 loci) portray contrasting results. Supermatrix (concatenation) methods support a generally robust tree with only a few inconsistently resolved polytomies, whereas MP- EST coalescence analysis of the same dataset yields a weakly supported tree that conflicts with many traditionally recognized clades. Here, we evaluate this discrepancy via improved coalescence analyses with reference to the rich history of phylogenetic studies on mammals. This integration clearly demonstrates that both supermatrix and coalescence analyses of just 26 loci yield a congruent, well-supported phylogenetic hypothesis for Mammalia. Discrepancies between published studies are explained by implementation of overly simple DNA substitution models, inadequate tree-search routines and limitations of the MP- EST method. We develop a simple measure, partitioned coalescence support ( PCS), which summarizes the distribution of support and conflict among gene trees for a given clade. Extremely high PCS scores for outlier gene trees at two nodes in the mammalian tree indicate a troubling bias in the MP- EST method. We conclude that in this age of phylogenomics, a solid understanding of systematics fundamentals, choice of valid methodology and a broad knowledge of a clade's taxonomic history are still required to yield coherent phylogenetic inferences. [ABSTRACT FROM AUTHOR]

Various toothed whales (Odontoceti) are unique among mammals in lacking olfactory bulbs as adults and are thought to be anosmic (lacking the olfactory sense). At the molecular level, toothed whales have high percentages of pseudogenic olfactory receptor genes, but species that have been investigated to date retain an intact copy of the olfactory marker protein gene ( OMP ), which is highly expressed in olfactory receptor neurons and may regulate the temporal resolution of olfactory responses. One hypothesis for the retention of intact OMP in diverse odontocete lineages is that this gene is pleiotropic with additional functions that are unrelated to olfaction. Recent expression studies provide some support for this hypothesis. Here, we report OMP sequences for representatives of all extant cetacean families and provide the first molecular evidence for inactivation of this gene in vertebrates. Specifically, OMP exhibits independent inactivating mutations in six different odontocete lineages: four river dolphin genera ( Platanista, Lipotes, Pontoporia, Inia ), sperm whale ( Physeter ), and harbor porpoise ( Phocoena ). These results suggest that the only essential role of OMP that is maintained by natural selection is in olfaction, although a non-olfactory role for OMP cannot be ruled out for lineages that retain an intact copy of this gene. Available genome sequences from cetaceans and close outgroups provide evidence of inactivating mutations in two additional genes ( CNGA2, CNGA4 ), which imply further pseudogenization events in the olfactory cascade of odontocetes. Selection analyses demonstrate that evolutionary constraints on all three genes ( OMP, CNGA2, CNGA4 ) have been greatly reduced in Odontoceti, but retain a signature of purifying selection on the stem Cetacea branch and in Mysticeti (baleen whales). This pattern is compatible with the ‘echolocation-priority’ hypothesis for the evolution of OMP , which posits that negative selection was maintained in the common ancestor of Cetacea and was not relaxed significantly until the evolution of echolocation in Odontoceti. [ABSTRACT FROM AUTHOR]

Observed Variability (OV) and Tree Independent Generation of Evolutionary Rates (TIGER) are quick and easy-to-apply tree-independent methods that have been proposed to provide unbiased estimates of each character’s rate of evolution and serve as the basis for excluding rapidly evolving characters. Both methods have been applied to multiple phylogenomic datasets, and in many cases the authors considered their trees inferred from the OV- and TIGER-delimited sub-matrices to be better estimates of the phylogeny than their trees based on all characters. In this study we use four sets of simulations and an empirical phylogenomic example to demonstrate that both methods share a systematic bias against characters with more symmetric distributions of character states, against characters with greater observed character-state space, and against large clades in the context of character conflict. As a result these methods can favor convergences and reversals over synapomorphy, exacerbate long-branch attraction, and produce mutually exclusive phylogenetic inferences that are dependent upon differential taxon sampling. We assert that neither OV nor TIGER should be relied upon to increase the ratio of phylogenetic to non-phylogenetic signal in a data matrix. We also assert that skepticism is warranted for empirical phylogenetic results that are based on OV- and/or TIGER-based character deletion wherein a small clade is supported after deletion of characters, yet is contradicted by a larger clade when the entire data matrix was analyzed. [ABSTRACT FROM AUTHOR]

Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are required to unravel deep-level phylogenetic problems that have stymied concatenation. Here, we reanalyze Song et al.'s (2012) data and leverage these re-analyses to explore key issues in systematics including the recombination ratchet, gene tree stoichiometry, the proportion of gene tree incongruence that results from deep coalescence versus other factors, and simulations that compare the performance of coalescence and concatenation methods in species tree estimation. Song et al. (2012) reported an average locus length of 3.1 kb for the 447 protein-coding genes in their phylogenomic dataset, but the true mean length of these loci (start codon to stop codon) is 139.6 kb. Empirical estimates of recombination breakpoints in primates, coupled with consideration of the recombination ratchet, suggest that individual coalescence genes (c-genes) approach 12 bp or less for Song et al.'s (2012) dataset, three to four orders of magnitude shorter than the c-genes reported by these authors. This result has general implications for the application of coalescence methods in species tree estimation. We contend that it is illogical to apply coalescence methods to complete protein-coding sequences. Such analyses amalgamate c-genes with different evolutionary histories (i.e., exons separated by >100,000 bp), distort true gene tree stoichiometry that is required for accurate species tree inference, and contradict the central rationale for applying coalescence methods to difficult phylogenetic problems. In addition, Song et al.'s (2012) dataset of 447 genes includes 21 loci with switched taxonomic names, eight duplicated loci, 26 loci with non-homologous sequences that are grossly misaligned, and numerous loci with >50% missing data for taxa that are misplaced in their gene trees. These problems were compounded by inadequate tree searches with nearest neighbor interchange branch swapping and inadvertent application of substitution models that did not account for among-site rate heterogeneity. Sixty-six gene trees imply unrealistic deep coalescences that exceed 100 million years (MY). Gene trees that were obtained with better justified models and search parameters show large increases in both likelihood scores and congruence. Coalescence analyses based on a curated set of 413 improved gene trees and a superior coalescence method (ASTRAL) support a Scandentia (treeshrews) + Glires (rabbits, rodents) clade, contradicting one of the three primary systematic conclusions of Song et al. (2012). Robust support for a Perissodactyla + Carnivora clade within Laurasiatheria is also lost, contradicting a second major conclusion of this study. Song et al.'s (2012) MP-EST species tree provided the basis for circular simulations that led these authors to conclude that the multispecies coalescent accounts for 77% of the gene tree conflicts in their dataset, but many internal branches of their MP-EST tree are stunted by an order of magnitude or more due to wholesale gene tree reconstruction errors. An independent assessment of branch lengths suggests the multispecies coalescent accounts for ≥15% of the conflicts among Song et al.'s (2012) 447 gene trees. Unfortunately, Song et al.'s (2012) flawed phylogenomic dataset has been used as a model for additional simulation work that suggests the superiority of shortcut coalescence methods relative to concatenation. Investigator error was passed on to the subsequent simulation studies, which also incorporated further logical errors that should be avoided in future simulation studies. Illegitimate branch length switches in the simulation routines unfairly protected coalescence methods from their Achilles' heel, high gene tree reconstruction error at short internodes. These simulations therefore provide no evidence that shortcut coalescence methods out-compete concatenation at deep timescales. In summary, the long c-genes that are required for accurate reconstruction of species trees using shortcut coalescence methods do not exist and are a delusion. Coalescence approaches based on SNPs that are widely spaced in the genome avoid problems with the recombination ratchet and merit further pursuit in both empirical systematic research and simulations. [ABSTRACT FROM AUTHOR]

Golden moles (Chrysochloridae) and marsupial moles (Notoryctidae) are textbook examples of convergent evolution. Both taxa are highly adapted to subterranean lifestyles and have powerful limbs for digging through the soil/sand, ears that are adapted for low-frequency hearing, vestigial eyes that are covered by skin and fur, and the absence of optic nerve connections between the eyes and the brain. The eyes of marsupial moles also lack a lens as well as retinal rods and cones. Two hypotheses have been proposed to account for the greater degeneracy of the eyes of marsupial moles than golden moles. First, marsupial moles may have had more time to adapt to their underground habitat than other moles. Second, the eyes of marsupial moles may have been rapidly and recently vestigialized to (1) reduce the injurious effects of sand getting into the eyes and (2) accommodate the enlargement of lacrimal glands that keep the nasal cavity moist and prevent the entry of sand into the nasal passages during burrowing. Here, we employ molecular evolutionary methods on DNA sequences for 38 eye genes, most of which are eye-specific, to investigate the timing of relaxed selection (=neutral evolution) for different groups of eye-specific genes that serve as proxies for distinct functional components of the eye (rod phototransduction, cone phototransduction, lens/cornea). Our taxon sampling included 12 afrothere species, of which two are golden moles (Amblysomus hottentotus, Chrysochloris asiatica), and 28 marsupial species including two individuals of the southern marsupial mole (Notoryctes typhlops). Most of the sequences were mined from databases, but we also provide new genome data for A. hottentotus and one of the two N. typhlops individuals. Even though the eyes of golden moles are less degenerate than the eyes of marsupial moles, there are more inactivating mutations (e.g., frameshift indels, premature stop codons) in their cone phototransduction and lens/cornea genes than in orthologous genes of the marsupial mole. We estimate that cone phototransduction recovery genes were inactivated first in each group, followed by lens/cornea genes and then cone phototransduction activation genes. All three groups of genes were inactivated earlier in golden moles than in marsupial moles. For the latter, we estimate that lens/cornea genes were inactivated ~17.8 million years ago (MYA) when stem notoryctids were burrowing in the soft soils of Australian rainforests. Selection on phototransduction activation genes was relaxed much later (5.38 MYA), during the early stages of Australia's aridification that produced coastal sand plains and eventually sand dunes. Unlike cone phototransduction activation genes, rod phototransduction activation genes are intact in both golden moles and one of the two individuals of N. typhlops. A second marsupial mole individual has just a single inactivating mutation in one of the rod phototransduction activation genes (PDE6B). One explanation for this result is that some rod phototransduction activation genes are pleiotropic and are expressed in extraocular tissues, possibly in conjunction with sperm thermotaxis. [ABSTRACT FROM AUTHOR]

It has recently been concluded that phylogenomic data from 310 nuclear genes support the clade of (Amborellales, Nymphaeales) as sister to the remaining angiosperms and that shortcut coalescent phylogenetic methods outperformed concatenation for these data. We falsify both of those conclusions here by demonstrating that discrepant results between the coalescent and concatenation analyses are primarily caused by the coalescent methods applied (MP-EST and STAR) not being robust to the highly divergent and often mis-rooted gene trees that were used. This result reinforces the expectation that low amounts of phylogenetic signal and methodological artifacts in gene-tree reconstruction can be more problematic for shortcut coalescent methods than is the assumption of a single hierarchy for all genes by concatenation methods when these approaches are applied to ancient divergences in empirical studies. We also demonstrate that a third coalescent method, ASTRAL, is more robust to mis-rooted gene trees than MP-EST or STAR, and that both Observed Variability (OV) and Tree Independent Generation of Evolutionary Rates (TIGER), which are two character subsampling procedures, are biased in favor of characters with highly asymmetrical distributions of character states when applied to this dataset. We conclude that enthusiastic application of novel tools is not a substitute for rigorous application of first principles, and that trending methods (e.g., shortcut coalescent methods applied to ancient divergences, tree-independent character subsampling), may be novel sources of previously under-appreciated, systematic errors. [ABSTRACT FROM AUTHOR]

[Display omitted] • Mutations in tooth genes were used to assess the timing of tooth loss in Mysticeti. • Inactivating mutations support the sequential loss of enamel and teeth in Mysticeti. • Enamel was lost very early on the stem Mysticeti branch. • Dentin loss occurred independently in Balaenidae and Plicogulae. • Odontocetes with degenerative enamel also exhibit mutations in enamel genes. The loss of teeth and evolution of baleen racks in Mysticeti was a profound transformation that permitted baleen whales to radiate and diversify into a previously underutilized ecological niche of bulk filter-feeding on zooplankton and other small prey. Ancestral state reconstructions suggest that postnatal teeth were lost in the common ancestor of crown Mysticeti. Genomic studies provide some support for this hypothesis and suggest that the genetic toolkit for enamel production was inactivated in the common ancestor of living baleen whales. However, molecular studies to date have not provided direct evidence for the complete loss of teeth, including their dentin component, on the stem mysticete branch. Given these results, several questions remain unanswered: (1) Were teeth lost in a single step or did enamel loss precede dentin loss? (2) Was enamel lost early or late on the stem mysticete branch? (3) If enamel and dentin/tooth loss were decoupled in the ancestry of baleen whales, did dentin loss occur on the stem mysticete branch or independently in different crown mysticete lineages? To address these outstanding questions, we compiled and analyzed complete protein-coding sequences for nine tooth-related genes from cetaceans with available genome data. Seven of these genes are associated with enamel formation (ACP4 , AMBN , AMELX , AMTN, ENAM , KLK4 , MMP20) whereas two other genes are either dentin-specific (DSPP) or tooth-specific (ODAPH) but not enamel-specific. Molecular evolutionary analyses indicate that all seven enamel-specific genes have inactivating mutations that are scattered across branches of the mysticete tree. Three of the enamel genes (ACP4 , KLK4 , MMP20) have inactivating mutations that are shared by all mysticetes. The two genes that are dentin-specific (DSPP) or tooth-specific (ODAPH) do not have any inactivating mutations that are shared by all mysticetes, but there are shared mutations in Balaenidae as well as in Plicogulae (Neobalaenidae + Balaenopteroidea). These shared mutations suggest that teeth were lost at most two times. Shared inactivating mutations and dN/dS analyses, in combination with cetacean divergence times, were used to estimate inactivation times of genes and by proxy enamel and tooth phenotypes at ancestral nodes. The results of these analyses are most compatible with a two-step model for the loss of teeth in the ancestry of living baleen whales: enamel was lost very early on the stem Mysticeti branch followed by the independent loss of dentin (and teeth) in the common ancestors of Balaenidae and Plicogulae, respectively. These results imply that some stem mysticetes, and even early crown mysticetes, may have had vestigial teeth comprised of dentin with no enamel. Our results also demonstrate that all odontocete species (in our study) with absent or degenerative enamel have inactivating mutations in one or more of their enamel genes. [ABSTRACT FROM AUTHOR]

Large datasets are required to solve difficult phylogenetic problems that are deep in the Tree of Life. Currently, two divergent systematic methods are commonly applied to such datasets: the traditional supermatrix approach (= concatenation) and “shortcut” coalescence (= coalescence methods wherein gene trees and the species tree are not co-estimated). When applied to ancient clades, these contrasting frameworks often produce congruent results, but in recent phylogenetic analyses of Placentalia (placental mammals), this is not the case. A recent series of papers has alternatively disputed and defended the utility of shortcut coalescence methods at deep phylogenetic scales. Here, we examine this exchange in the context of published phylogenomic data from Mammalia; in particular we explore two critical issues – the delimitation of data partitions (“genes”) in coalescence analysis and hidden support that emerges with the combination of such partitions in phylogenetic studies. Hidden support – increased support for a clade in combined analysis of all data partitions relative to the support evident in separate analyses of the various data partitions, is a hallmark of the supermatrix approach and a primary rationale for concatenating all characters into a single matrix. In the most extreme cases of hidden support, relationships that are contradicted by all gene trees are supported when all of the genes are analyzed together. A valid fear is that shortcut coalescence methods might bypass or distort character support that is hidden in individual loci because small gene fragments are analyzed in isolation. Given the extensive systematic database for Mammalia, the assumptions and applicability of shortcut coalescence methods can be assessed with rigor to complement a small but growing body of simulation work that has directly compared these methods to concatenation. We document several remarkable cases of hidden support in both supermatrix and coalescence paradigms and argue that in most instances, the emergent support in the shortcut coalescence analyses is an artifact. By referencing rigorous molecular clock studies of Mammalia, we suggest that inaccurate gene trees that imply unrealistically deep coalescences debilitate shortcut coalescence analyses of the placental dataset. We document contradictory coalescence results for Placentalia, and outline a critical conundrum that challenges the general utility of shortcut coalescence methods at deep phylogenetic scales. In particular, the basic unit of analysis in coalescence analysis, the coalescence-gene, is expected to shrink in size as more taxa are analyzed, but as the amount of data for reconstruction of a gene tree ratchets downward, the number of nodes in the gene tree that need to be resolved ratchets upward. Some advocates of shortcut coalescence methods have attempted to address problems with inaccurate gene trees by concatenating multiple coalescence-genes to yield "gene trees" that better match the species tree. However, this hybrid concatenation/coalescence approach, “concatalescence,” contradicts the most basic biological rationale for performing a coalescence analysis in the first place. We discuss this reality in the context of recent simulation work that also suggests inaccurate reconstruction of gene trees is more problematic for shortcut coalescence methods than deep coalescence of independently segregating loci is for concatenation methods. [ABSTRACT FROM AUTHOR]

Highlights: [•] Cetacea (whales, dolphins, and porpoises) is a model group for investigating the molecular signature of macroevolutionary transitions. [•] Recent research has documented the remarkable convergence between echolocating bats and odontocetes across six genes related to auditory physiology. [•] Cetaceans are a premier model of wholesale sensory evolution, in which anatomical changes related to sensory perception dovetail nicely with molecular evolutionary patterns, including the pseudogenization of some visual opsins, olfactory receptors, vomeronasal receptors, and taste receptors. [•] Modifications in myoglobin also show that the net surface charge of myoglobin in cetaceans correlates with depth of dive, and these changes have also occurred in other aquatic lineages, such as pinnipeds. [ABSTRACT FROM AUTHOR]

Cetaceans have a long history of commitment to a fully aquatic lifestyle that extends back to the Eocene. Extant species have evolved a spectacular array of adaptations in conjunction with their deployment into a diverse array of aquatic habitats. Sensory systems are among those that have experienced radical transformations in the evolutionary history of this clade. In the case of vision, previous studies have demonstrated important changes in the genes encoding rod opsin (RH1), short-wavelength sensitive opsin 1 (SWS1), and long-wavelength sensitive opsin (LWS) in selected cetaceans, but have not examined the full complement of opsin genes across the complete range of cetacean families. Here, we report proteincoding sequences for RH1 and both color opsin genes (SWS1, LWS) from representatives of all extant cetacean families. We examine competing hypotheses pertaining to the timing of blue shifts in RH1 relative to SWS1 inactivation in the early history of Cetacea, and we test the hypothesis that some cetaceans are rod monochomats. Molecular evolutionary analyses contradict the "coastal" hypothesis, wherein SWS1 was pseudogenized in the common ancestor of Cetacea, and instead suggest that RH1 was blue-shifted in the common ancestor of Cetacea before SWS1 was independently knocked out in baleen whales (Mysticeti) and in toothed whales (Odontoceti). Further, molecular evidence implies that LWS was inactivated convergently on at least five occasions in Cetacea: (1) Balaenidae (bowhead and right whales), (2) Balaenopteroidea (rorquals plus gray whale), (3) Mesoplodon bidens (Sowerby's beaked whale), (4) Physeter macrocephalus (giant sperm whale), and (5) Kogia breviceps (pygmy sperm whale). All of these cetaceans are known to dive to depths of at least 100 m where the underwater light field is dim and dominated by blue light. The knockout of both SWS1 and LWS in multiple cetacean lineages renders these taxa rod monochromats, a condition previously unknown among mammalian species. [ABSTRACT FROM AUTHOR]

Background: Secondary edentulism (toothlessness) has evolved on multiple occasions in amniotes including several mammalian lineages (pangolins, anteaters, baleen whales), birds, and turtles. All edentulous amniote clades have evolved from ancestors with enamel-capped teeth. Previous studies have documented the molecular decay of tooth-specific genes in edentulous mammals, all of which lost their teeth in the Cenozoic, and birds, which lost their teeth in the Cretaceous. By contrast with mammals and birds, tooth loss in turtles occurred in the Jurassic (201.6-145.5 Ma), providing an extended time window for tooth gene degradation in this clade. The release of the painted turtle and Chinese softshell turtle genomes provides an opportunity to recover the decayed remains of tooth-specific genes in Testudines. Results: We queried available genomes of Testudines (Chrysemys picta [painted turtle], Pelodiscus sinensis [Chinese softshell turtle]), Aves (Anas platyrhynchos [duck], Gallus gallus [chicken], Meleagris gallopavo [turkey], Melopsittacus undulatus [budgerigar], Taeniopygia guttata [zebra finch]), and enamelless mammals (Orycteropus afer [aardvark], Choloepus hoffmanni [Hoffmann's two-toed sloth], Dasypus novemcinctus [nine-banded armadillo]) for remnants of three enamel matrix protein (EMP) genes with putative enamel-specific functions. Remnants of the AMBN and ENAM genes were recovered in Chrysemys and retain their original synteny. Remnants of AMEL were recovered in both testudines, although there are no shared frameshifts. We also show that there are inactivated copies of AMBN, AMEL and ENAM in representatives of divergent avian lineages including Galloanserae, Passeriformes, and Psittaciformes, and that there are shared frameshift mutations in all three genes that predate the basal split in Neognathae. Among enamelless mammals, all three EMP genes exhibit inactivating mutations in Orycteropus and Choloepus. Conclusions: Our results highlight the power of combining fossil and genomic evidence to decipher macroevolutionary transitions and characterize the functional range of different loci involved in tooth development. The fossil record and phylogenetics combine to predict the occurrence of molecular fossils of tooth-specific genes in the genomes of edentulous amniotes, and in every case these molecular fossils have been discovered. The widespread occurrence of EMP pseudogenes in turtles, birds, and edentulous/enamelless mammals also provides compelling evidence that in amniotes, the only unique, non-redundant function of these genes is in enamel formation. [ABSTRACT FROM AUTHOR]

Abstract: The emergence of Cetacea in the Paleogene represents one of the most profound macroevolutionary transitions within Mammalia. The move from a terrestrial habitat to a committed aquatic lifestyle engendered wholesale changes in anatomy, physiology, and behavior. The results of this remarkable transformation are extant whales that include the largest, biggest brained, fastest swimming, loudest, deepest diving mammals, some of which can detect prey with a sophisticated echolocation system (Odontoceti – toothed whales), and others that batch feed using racks of baleen (Mysticeti – baleen whales). A broad-scale reconstruction of the evolutionary remodeling that culminated in extant cetaceans has not yet been based on integration of genomic and paleontological information. Here, we first place Cetacea relative to extant mammalian diversity, and assess the distribution of support among molecular datasets for relationships within Artiodactyla (even-toed ungulates, including Cetacea). We then merge trees derived from three large concatenations of molecular and fossil data to yield a composite hypothesis that encompasses many critical events in the evolutionary history of Cetacea. By combining diverse evidence, we infer a phylogenetic blueprint that outlines the stepwise evolutionary development of modern whales. This hypothesis represents a starting point for more detailed, comprehensive phylogenetic reconstructions in the future, and also highlights the synergistic interaction between modern (genomic) and traditional (morphological+paleontological) approaches that ultimately must be exploited to provide a rich understanding of evolutionary history across the entire tree of Life. [Copyright &y& Elsevier]

Vestigial structures occur at both the anatomical and molecular levels, but studies documenting the co-occurrence of morphological degeneration in the fossil record and molecular decay in the genome are rare. Here, we use morphology, the fossil record, and phylogenetics to predict the occurrence of ''molecular fossils'' of the enamelin (ENAM) gene in four different orders of placental mammals (Tubulidentata, Pholidota, Cetacea, Xenarthra) with toothless and/or enamelless taxa. Our results support the ''molecular fossil'' hypothesis and demonstrate the occurrence of frameshift mutations and/or stop codons in all toothless and enamelless taxa. We then use a novel method based on selection intensity estimates for codons (ω) to calculate the timing of iterated enamel loss in the fossil record of aardvarks and pangolins, and further show that the molecular evolutionary history of ENAM predicts the occurrence of enamel in basal representatives of Xenarthra (sloths, anteaters, armadillos) even though frameshift mutations are ubiquitous in ENAM sequences of living xenarthrans. The molecular decay of ENAM parallels the morphological degeneration of enamel in the fossil record of placental mammals and provides manifest evidence for the predictive power of Darwin's theory. [ABSTRACT FROM AUTHOR]

The phylogenetic position of Cetacea (whales, dolphins and porpoises) is an important exemplar problem for combined data parsimony analyses because the clade is ancient and includes many well-known and relatively complete fossil species. We combined data for 71 terminal taxa (43 extinct/28 extant) to test where Cetacea fits within Cetartiodactyla, and where various fossil hoofed mammals (e.g., †entelodonts, “†anthracotheriids” and †mesonychians) are positioned. We scored 635 phenotypic characters (osteology, dentition, soft tissue, behavior), approximately three times the number of characters in the last major analysis of this clade, and combined these with > 40 000 molecular characters, including new data from 10 genes. The analysis supported a topology consistent with the majority of recently published molecular studies. Cetacea was the extant sister taxon of Hippopotamidae, followed successively by Ruminantia, Suina and Camelidae. Several extinct taxa were phylogenetically unstable, upsetting resolution of the strict consensus and limiting branch support, but the positions of several key fossils were consistently resolved. The wholly extinct †Mesonychia was more closely related to Cetacea than was any “artiodactylan.”“†Anthracotheriids” were paraphyletic, and, with the exception of one species, were more closely related to Hippopotamidae than to any other living taxon. The total evidence analysis overturned a highly nested position for Moschus supported by molecular data alone. The character partition that could be scored for the fossil taxa (osteological and dental characters) included more informative characters than most molecular partitions in our analysis, and had the fewest missing data. The osteological–dental data alone, however, did not support inclusion of cetaceans within crown “Artiodactyla.” Recently discovered ankle bones from fossil whales reinforced the monophyly of Cetartiodactyla but provided no particular evidence of derived similarities between hippopotamids and fossil cetaceans that were not shared with other “artiodactylans”. © The Willi Hennig Society 2007. [ABSTRACT FROM AUTHOR]

Many genes involved in reproduction have evolved at a rapid rate in diverse taxonomic groups. We use new data for the mammalian reproductive gene that encodes acrosin to document patterns of adaptive evolution and rapid divergence. Likelihood scores for neutral and selection models indicate that molecular evolution of the Act gene is driven by positive selection. Comparisons of Act sequences to mitochondrial genes and a nuclear intron show that reproductive genes can be informative phylogenetic markers. In bovid artiodactyls (cattle, sheep, goats, and antelopes), exon 5 of Acr is highly variable, is characterized by a low level of homoplasy, and has a fairly even spread of substitutions across the 3 codon positions. Impressive congruence with independent DNA data sets suggests that Acr, and perhaps additional rapidly evolving reproductive molecules, show promise for resolving evolutionary radiations of mammals. [ABSTRACT FROM AUTHOR]

Recent reviews of the construction of large phylogenies have focused on supertree methods that involve separate analyses of data sets and subsequent integration of the resulting trees. Here, we consider the alternative method of analyzing all character data simultaneously. Such ‘supermatrix’ analyses use information from each character directly and enable straightforward incorporation of diverse kinds of data, including characters from fossils. The approach has been extended by the development of new methods, including model-based techniques for analyzing heterogeneous data and hierarchical methods for constructing extremely large trees. Recent work also suggests that the problem of missing data in supermatrix analyses has been overstated. Although the supermatrix approach is not suited for all cases, we suggest that its inherent strengths will ensure that it will continue to have a central role in inferring large phylogenetic trees from diverse data. [Copyright &y& Elsevier]

Combined analysis of multiple phylogenetic data sets can reveal emergent character support that is not evident in separate analyses of individual data sets. Previous parsimony analyses have shown that this hidden support often accounts for a large percentage of the overall phylogenetic signal in cladistic studies. Here, reanalysis of a large comparative genomic data set for yeast (genus Saccharomyces ) demonstrates that hidden support can be an important factor in maximum likelihood analyses of multiple data sets as well. Emergent signal in a concatenation of 106 genes was responsible for up to 64% of the likelihood support at a particular node (the difference in log likelihood scores between optimal topologies that included and excluded a supported clade). A grouping of four yeast species ( S. cerevisiae , S. paradoxus , S. mikatae , and S. kudriavzevii ) was robustly supported by combined analysis of all 106 genes, but separate analyses of individual genes suggested numerous conflicts. Forty-eight genes strictly contradicted S. cerevisiae + S. paradoxus + S. mikatae + S. kudriavzevii in separate analyses, but combined likelihood analyses that included up to 45 of the “wrong” data sets supported this group. Extensive hidden support also emerged in a combined likelihood analysis of 41 genes that each recovered the exact same topology in separate analyses of the individual genes. These results show that isolated analyses of individual data sets can mask congruence and distort interpretations of clade stability, even in strictly model-based phylogenetic methods. Consensus and supertree procedures that ignore hidden phylogenetic signals are, at best, incomplete. [Character partitions; combined analysis; hidden support; maximum likelihood; phylogenomics; yeast.] [ABSTRACT FROM AUTHOR]

Focuses on empirical comparison of supertree and supermatrix approaches for identical sets of characters and taxa to highlight basic differences between the two competing methods. Methods used in phylogenetic relationships of well-studied taxa; major challenge in the field of systemics; Context of supertree analysis of mammals.

Critiques an interpretation of the pattern of evolution of dental characters presented in a re-analysis of morphological and molecular data for whale phylogeny. Logical and empirical mistakes made by Naylor and Adams; Total evidence and simultaneous analyses of morphological, behavior and molecular data; Naylor and Adams' statistical test to expose incongruent classes of data.

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]

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.

Over the past 10 years, the phylogenetic relationships among higher-level artiodactyl taxa have been examined with multiple data sets. Many of these data sets suggest that Artiodactyla (even-toed ungulates) is paraphyletic and that Cetacea (whales) represents a highly derived ''artiodactyl" subgroup. In this report, phylogenetic relationships between Cetacea and artiodactyls are tested with a combination of 15 published data sets plus new DNA sequence data from two nuclear loci, interphotoreceptor retinoid-binding protein (IRBP) and von Willebrand factor (vWF). The addition of the IRBP and vWF character sets disrupts none of the relationships supported by recent cladistic analyses of the other 15 data sets. Simultaneous analyses support three critical clades: (Cetacea + Hippopotamidae), (Cetacea + Hippopotamidae + Ruminantia), and (Cetacea + Hippopotamidae + Ruminantia + Suina). Perturbations of the combined matrix show that the above clades are stable to a variety of disturbances. A chronicle of phylogenetic results over the past 3 years suggests that cladistic relationships between Cetacea and artiodactyls have been stable to increased taxonomic sampling and to the addition of more than 1,400 informative characters from 15 data sets.[Artiodactyla, Cetacea, cladogram, stability.]. [ABSTRACT FROM AUTHOR]

Determines the minimum and maximum rates of stem-pair evolution in two clades of antelopes. Analysis on the mitochondrial ribosomal DNA of antelopes; Distinction between maximum and minimum compensation lag time; Rates of compensation in antelope mtrDNA.

Presents a study in which DNA was extracted from the fossil termite Mastotermes electrodominicus preserved in Oligo-Miocene amber (25 million to 30 million years old). Phylogenetic analysis of fossil and extant 18S rDNA; Morphological cladistic analyses of living dictyopterans (termites, cockroaches, and mantids); Molecular phylogenetic hypotheses of termites.

• Up to 86% of internal gene-tree branches are dubiously or arbitrarily resolved. • Collapsing branches increased species-tree coalescent branch lengths by up to 455%. • Severe and clearly justified collapsing method for likelihood: 0% SH-like aLRT. • Severe and clearly justified collapsing method for parsimony: strict consensus. • Collapsing can improve congruence between coalescent and concatenation analyses. In two-step coalescent analyses of phylogenomic data, gene-tree topologies are treated as fixed prior to species-tree inference. Although all gene-tree conflict is assumed to be caused by lineage sorting when applying these methods, in empirical datasets much of the conflict can be caused by estimation error. Weakly supported and even arbitrarily resolved clades are important sources of this estimation error for gene trees inferred from few informative characters relative to the number of sampled terminals, and the resulting extraneous conflict among gene trees can negatively impact species-tree inference. In this study, we quantified the relative severity of alternative methods for collapsing gene-tree branches for seven empirical datasets and quantified their effects on species-tree inference. The branch-collapsing methods that we employed were based on the strict consensus of optimal topologies, various bootstrap thresholds, and 0% approximate likelihood ratio test (SH-like aLRT) support. Up to 86% of internal gene-tree branches are dubiously or arbitrarily resolved in reanalyses of these published phylogenomic datasets, and collapsing these branches increased inferred species-tree coalescent branch lengths by up to 455%. For two datasets, the longer inferred branch lengths sometimes impacted inference of anomaly-zone conditions. Although branch-collapsing methods did not consistently affect the species-tree topology, they often increased branch support. The more severe and clearly justified gene-tree branch-collapsing methods, which we recommend be broadly applied for two-step coalescent analyses, are use of the strict consensus in parsimony analyses and the collapse clades with 0% SH-like aLRT support in likelihood analyses. Collapsing dubiously or arbitrarily resolved branches in gene trees sometimes improved congruence between coalescent-based results and concatenation trees. In such cases, we contend that the resolution provided by concatenation should be preferred and that incomplete lineage sorting is a poor explanation for the initial conflict between phylogenetic approaches. [ABSTRACT FROM AUTHOR]

Studies the diversity, conservation, and convergence of spider silk fibroin sequences. Amino acid motifs that comprise orb weaver fibroins; DNA sequences in weaved spider silk; Mechanical properties of araneoid fibroins found in structural proteins.

• Partitioned coalescence support (PCS) is automated for genome-scale datasets. • PCS summarizes the support and conflict among gene trees in coalescence analyses. • PCS detects biases in phylogenomic support provided by outlier gene trees. • PCS quantifies the effects of missing taxa in gene trees. • PCS reveals the instability of clades with high bootstrap or Bayesian support. Genomic datasets sometimes support conflicting phylogenetic relationships when different tree-building methods are applied. Coherent interpretations of such results are enabled by partitioning support for controversial relationships among the constituent genes of a phylogenomic dataset. For the supermatrix (=concatenation) approach, several methods that measure the distribution of support and conflict among loci were introduced over 15 years ago. More recently, partitioned coalescence support (PCS) was developed for phylogenetic coalescence methods that account for incomplete lineage sorting and use the summed fits of gene trees to estimate the species tree. Here, we automate computation of PCS to permit application of this index to genome-scale matrices that include hundreds of loci. Reanalyses of four phylogenomic datasets for amniotes, land plants, skinks, and angiosperms demonstrate how PCS scores can be used to: (1) compare conflicting results favored by alternative coalescence methods, (2) identify outlier gene trees that have a disproportionate influence on the resolution of contentious relationships, (3) assess the effects of missing data in species-tree analysis, and (4) clarify biases in commonly-implemented coalescence methods and support indices. We show that key phylogenomic conclusions from these analyses often hinge on just a few gene trees and that results can be driven by specific biases of a particular coalescence method and/or the differential weight placed on gene trees with high versus low taxon sampling. The attribution of exceptionally high weight to some gene trees and very low weight to other gene trees counters the basic logic of phylogenomic coalescence analysis; even clades in species trees with high support according to commonly used indices (likelihood-ratio test, bootstrap, Bayesian local posterior probability) can be unstable to the removal of only one or two gene trees with high PCS. Computer simulations cannot adequately describe all of the contingencies and complexities of empirical genetic data. PCS scores complement simulation work by providing specific insights into a particular dataset given the assumptions of the phylogenetic coalescence method that is applied. In combination with standard measures of nodal support, PCS provides a more complete understanding of the overall genomic evidence for contested evolutionary relationships in species trees. [ABSTRACT FROM AUTHOR]

Background: The gene for odontogenic ameloblast-associated (ODAM) is a member of the secretory calcium-binding phosphoprotein gene family. ODAM is primarily expressed in dental tissues including the enamel organ and the junctional epithelium, and may also have pleiotropic functions that are unrelated to teeth. Here, we leverage the power of natural selection to test competing hypotheses that ODAM is tooth-specific versus pleiotropic. Specifically, we compiled and screened complete protein-coding sequences, plus sequences for flanking intronic regions, for ODAM in 165 placental mammals to determine if this gene contains inactivating mutations in lineages that either lack teeth (baleen whales, pangolins, anteaters) or lack enamel on their teeth (aardvarks, sloths, armadillos), as would be expected if the only essential functions of ODAM are related to tooth development and the adhesion of the gingival junctional epithelium to the enamel tooth surface. Results: We discovered inactivating mutations in all species of placental mammals that either lack teeth or lack enamel on their teeth. A surprising result is that ODAM is also inactivated in a few additional lineages including all toothed whales that were examined. We hypothesize that ODAM inactivation is related to the simplified outer enamel surface of toothed whales. An alternate hypothesis is that ODAM inactivation in toothed whales may be related to altered antimicrobial functions of the junctional epithelium in aquatic habitats. Selection analyses on ODAM sequences revealed that the composite dN/dS value for pseudogenic branches is close to 1.0 as expected for a neutrally evolving pseudogene. DN/dS values on transitional branches were used to estimate ODAM inactivation times. In the case of pangolins, ODAM was inactivated ~ 65 million years ago, which is older than the oldest pangolin fossil (Eomanis, 47 Ma) and suggests an even more ancient loss or simplification of teeth in this lineage. Conclusion: Our results validate the hypothesis that the only essential functions of ODAM that are maintained by natural selection are related to tooth development and/or the maintenance of a healthy junctional epithelium that attaches to the enamel surface of teeth. [ABSTRACT FROM AUTHOR]

Gene‐tree‐inference error can cause species‐tree‐inference artefacts in summary phylogenomic coalescent analyses. Here we integrate two ways of accommodating these inference errors: collapsing arbitrarily or dubiously resolved gene‐tree branches, and subsampling gene trees based on their pairwise congruence. We tested the effect of collapsing gene‐tree branches with 0% approximate‐likelihood‐ratio‐test (SH‐like aLRT) support in likelihood analyses and strict consensus trees for parsimony, and then subsampled those partially resolved trees based on congruence measures that do not penalize polytomies. For this purpose we developed a new TNT script for congruence sorting (congsort), and used it to calculate topological incongruence for eight phylogenomic datasets using three distance measures: standard Robinson–Foulds (RF) distances; overall success of resolution (OSR), which is based on counting both matching and contradicting clades; and RF contradictions, which only counts contradictory clades. As expected, we found that gene‐tree incongruence was often concentrated in clades that are arbitrarily or dubiously resolved and that there was greater congruence between the partially collapsed gene trees and the coalescent and concatenation topologies inferred from those genes. Coalescent branch lengths typically increased as the most incongruent gene trees were excluded, although branch supports typically did not. We investigated two successful and complementary approaches to prioritizing genes for investigation of alignment or homology errors. Coalescent‐tree clades that contradicted concatenation‐tree clades were generally less robust to gene‐tree subsampling than congruent clades. Our preferred approach to collapsing likelihood gene‐tree clades (0% SH‐like aLRT support) and subsampling those trees (OSR) generally outperformed competing approaches for a large fungal dataset with respect to branch lengths, support and congruence. We recommend widespread application of this approach (and strict consensus trees for parsimony‐based analyses) for improving quantification of gene‐tree congruence/conflict, estimating coalescent branch lengths, testing robustness of coalescent analyses to gene‐tree‐estimation error, and improving topological robustness of summary coalescent analyses. This approach is quick and easy to implement, even for huge datasets. [ABSTRACT FROM AUTHOR]

Abstract.— The saola, Pseudoryx nghetinhensis , was unknown to science until its formal description in 1993. This endangered species is a member of the ruminant artiodactyl family Bovidae (cattle, sheep, goats, and antelopes). However, given its puzzling combination of morphological traits, the specific affinities of Pseudoryx within Bovidae are controversial. A preliminary genetic investigation suggested that Pseudoryx should be placed in the subfamily Bovinae (cattle, buffaloes, spiral-horned antelopes, and nilgai), but a recent cladistic analysis of skeletal and dental characters allied Pseudoryx with caprine bovids (sheep, goats, musk oxen, goat antelopes, and Pantholops ). The morphological and molecular hypotheses differ in assigning the saola to either of the two most divergent clades of Bovidae. In this report, phylogenetic analyses of DNA sequences from five genes are used to test these alternatives. Protein coding regions, introns, and ribosomal DNAs from the nuclear and mitochondrial genomes discount the hypothesis that Pseudoryx is a close relative of Caprinae. Instead, combined analyses of the DNA data and published morphological evidence place Pseudoryx with Bovini (cattle and buffaloes), a subclade of Bovinae. In a separate analysis, the matrix of morphological characters links Pseudoryx with caprine bovids, but in the context of the molecular data, the gross anatomical evidence strongly supports a grouping of Pseudoryx with Bovinae. Surprisingly, the morphological partition provides the most character support in the combined analysis. This striking result is obscured by separate analyses of the individual data sets and the taxonomic congruence approach. [Bovidae; hidden support; Pseudoryx ; saola; Vu Quang.] [ABSTRACT FROM AUTHOR]

Gene-tree-estimation error is a major concern for coalescent methods of phylogenetic inference. We sampled eight empirical studies of ancient lineages with diverse numbers of taxa and genes for which the original authors applied one or more coalescent methods. We found that the average pairwise congruence among gene trees varied greatly both between studies and also often within a study. We recommend that presenting plots of pairwise congruence among gene trees in a dataset be treated as a standard practice for empirical coalescent studies so that readers can readily assess the extent and distribution of incongruence among gene trees. ASTRAL-based coalescent analyses generally outperformed MP-EST and STAR with respect to both internal consistency (congruence between analyses of subsamples of genes with the complete dataset of all genes) and congruence with the concatenation-based topology. We evaluated the approach of subsampling gene trees that are, on average, more congruent with other gene trees as a method to reduce artifacts caused by gene-tree-estimation errors on coalescent analyses. We suggest that this method is well suited to testing whether gene-tree-estimation error is a primary cause of incongruence between concatenation- and coalescent-based results, to reconciling conflicting phylogenetic results based on different coalescent methods, and to identifying genes affected by artifacts that may then be targeted for reciprocal illumination. We provide scripts that automate the process of calculating pairwise gene-tree incongruence and subsampling trees while accounting for differential taxon sampling among genes. Finally, we assert that multiple tree-search replicates should be implemented as a standard practice for empirical coalescent studies that apply MP-EST. [ABSTRACT FROM AUTHOR]

Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71-63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event ("Grande Coupure") at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts. [ABSTRACT FROM AUTHOR]

Previous analyses of relations, divergence times, and diversification patterns among extant mammalian families have relied on supertree methods and local molecular clocks. We constructed a molecular supermatrix for mammalian families and analyzed these data with likelihood-based methods and relaxed molecular clocks. Phylogenetic analyses resulted in a robust phylogeny with better resolution than phylogenies from supertree methods. Relaxed clock analyses support the long-fuse model of diversification and highlight the importance of including multiple fossil calibrations that are spread across the tree. Molecular time trees and diversification analyses suggest important roles for the Cretaceous Terrestrial Revolution and Cretaceous-Paleogene (KPg) mass extinction in opening up ecospace that promoted interordinal and intraordinal diversification, respectively. By contrast, diversification analyses provide no support for the hypothesis concerning the delayed rise of present-day mammals during the Eocene Period. [ABSTRACT FROM AUTHOR]

Abstract: Cetaceans are remarkable among mammals for their numerous adaptations to an entirely aquatic existence, yet many aspects of their phylogeny remain unresolved. Here we merged 37 new sequences from the nuclear genes RAG1 and PRM1 with most published molecular data for the group (45 nuclear loci, transposons, mitochondrial genomes), and generated a supermatrix consisting of 42,335 characters. The great majority of these data have never been combined. Model-based analyses of the supermatrix produced a solid, consistent phylogenetic hypothesis for 87 cetacean species. Bayesian analyses corroborated odontocete (toothed whale) monophyly, stabilized basal odontocete relationships, and completely resolved branching events within Mysticeti (baleen whales) as well as the problematic speciose clade Delphinidae (oceanic dolphins). Only limited conflicts relative to maximum likelihood results were recorded, and discrepancies found in parsimony trees were very weakly supported. We utilized the Bayesian supermatrix tree to estimate divergence dates among lineages using relaxed-clock methods. Divergence estimates revealed rapid branching of basal odontocete lineages near the Eocene–Oligocene boundary, the antiquity of river dolphin lineages, a Late Miocene radiation of balaenopteroid mysticetes, and a recent rapid radiation of Delphinidae beginning ∼10 million years ago. Our comprehensive, time-calibrated tree provides a powerful evolutionary tool for broad-scale comparative studies of Cetacea. [Copyright &y& Elsevier]

Background: Integration of diverse data (molecules, fossils) provides the most robust test of the phylogeny of cetaceans. Positioning key fossils is critical for reconstructing the character change from life on land to life in the water. Methodology/Principal Findings: We reexamine relationships of critical extinct taxa that impact our understanding of the origin of Cetacea. We do this in the context of the largest total evidence analysis of morphological and molecular information for Artiodactyla (661 phenotypic characters and 46,587 molecular characters, coded for 33 extant and 48 extinct taxa). We score morphological data for Carnivoramorpha, {Creodonta, Lipotyphla, and the {raoellid artiodactylan {Indohyus and concentrate on determining which fossils are positioned along stem lineages to major artiodactylan crown clades. Shortest trees place Cetacea within Artiodactyla and close to {Indohyus, with {Mesonychia outside of Artiodactyla. The relationships of {Mesonychia and {Indohyus are highly unstable, however - in trees only two steps longer than minimum length, {Mesonychia falls inside Artiodactyla and displaces {Indohyus from a position close to Cetacea. Trees based only on data that fossilize continue to show the classic arrangement of relationships within Artiodactyla with Cetacea grouping outside the clade, a signal incongruent with the molecular data that dominate the total evidence result. Conclusions/Significance: Integration of new fossil material of {Indohyus impacts placement of another extinct clade {Mesonychia, pushing it much farther down the tree. The phylogenetic position of {Indohyus suggests that the cetacean stem lineage included herbivorous and carnivorous aquatic species. We also conclude that extinct members of Cetancodonta (whales + hippopotamids) shared a derived ability to hear underwater sounds, even though several cetancodontans lack a pachyostotic auditory bulla. We revise the taxonomy of living and extinct artiodactylans and propose explicit node and stem-based definitions for the ingroup. [ABSTRACT FROM AUTHOR]