Publications by authors named "Edward L Braun"

83 Publications

A novel exome probe set captures phototransduction genes across birds (Aves) enabling efficient analysis of vision evolution.

Mol Ecol Resour 2021 Oct 15. Epub 2021 Oct 15.

Neurobiology Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA.

The diversity of avian visual phenotypes provides a framework for studying mechanisms of trait diversification generally, and the evolution of vertebrate vision, specifically. Previous research has focused on opsins, but to fully understand visual adaptation, we must study the complete phototransduction cascade (PTC). Here, we developed a probe set that captures exonic regions of 46 genes representing the PTC and other light responses. For a subset of species, we directly compared gene capture between our probe set and low-coverage whole genome sequencing (WGS), and we discuss considerations for choosing between these methods. Finally, we developed a unique strategy to avoid chimeric assembly by using "decoy" reference sequences. We successfully captured an average of 64% of our targeted exome in 46 species across 14 orders using the probe set and had similar recovery using the WGS data. Compared to WGS or transcriptomes, our probe set: (1) reduces sequencing requirements by efficiently capturing vision genes, (2) employs a simpler bioinformatic pipeline by limiting required assembly and negating annotation, and (3) eliminates the need for fresh tissues, enabling researchers to leverage existing museum collections. We then utilized our vision exome data to identify positively selected genes in two evolutionary scenarios-evolution of night vision in nocturnal birds and evolution of high-speed vision specific to manakins (Pipridae). We found parallel positive selection of SLC24A1 in both scenarios, implicating the alteration of rod response kinetics, which could improve color discrimination in dim light conditions and/or facilitate higher temporal resolution.
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http://dx.doi.org/10.1111/1755-0998.13496DOI Listing
October 2021

When good mitochondria go bad: Cyto-nuclear discordance in landfowl (Aves: Galliformes).

Gene 2021 Oct 16;801:145841. Epub 2021 Jul 16.

Department of Biology, University of Florida, Gainesville, FL, USA.

Mitochondrial sequences were among the first molecular data collected for phylogenetic studies and they are plentiful in DNA sequence archives. However, the future value of mitogenomic data in phylogenetics is uncertain, because its phylogenetic signal sometimes conflicts with that of the nuclear genome. A thorough understanding of the causes and prevalence of cyto-nuclear discordance would aid in reconciling different results owing to sequence data type, and provide a framework for interpreting megaphylogenies when taxa which lack substantial nuclear data are placed using mitochondrial data. Here, we examine the prevalence and possible causes of cyto-nuclear discordance in the landfowl (Aves: Galliformes), leveraging 47 new mitogenomes assembled from off-target reads recovered as part of a target-capture study. We evaluated two hypotheses, that cyto-nuclear discordance is "genuine" and a result of biological processes such as incomplete lineage sorting or introgression, and that cyto-nuclear discordance is an artifact of inaccurate mitochondrial tree estimation (the "inaccurate estimation" hypothesis). We identified seven well-supported topological differences between the mitogenomic tree and trees based on nuclear data. These well-supported topological differences were robust to model selection. An examination of sites suggests these differences were driven by small number of sites, particularly from third-codon positions, suggesting that they were not confounded by convergent directional selection. Hence, the hypothesis of genuine discordance was supported.
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http://dx.doi.org/10.1016/j.gene.2021.145841DOI Listing
October 2021

Complete vertebrate mitogenomes reveal widespread repeats and gene duplications.

Genome Biol 2021 04 29;22(1):120. Epub 2021 Apr 29.

Oxford Nanopore Technologies Ltd, Oxford Science Park, Oxford, UK.

Background: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.

Results: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization.

Conclusions: Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.
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http://dx.doi.org/10.1186/s13059-021-02336-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8082918PMC
April 2021

A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths.

Mol Phylogenet Evol 2021 05 2;158:107091. Epub 2021 Feb 2.

Department of Biology, University of Florida, Gainesville, FL 32607, USA.

Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology ("legacy" markers, such as mitochondrial data and small numbers of nuclear loci). However, incorporating phylogenomic studies into supermatrices allows problem nodes to be targeted and resolved with considerable amounts of data, while improving taxon sampling with legacy data. Here we estimate phylogeny from a galliform supermatrix which includes well-known model and agricultural species such as the chicken and turkey. We assembled a supermatrix comprising 4500 ultra-conserved elements (UCEs) collected as part of recent phylogenomic studies in this group and legacy mitochondrial and nuclear (intron and exon) sequences. Our resulting phylogeny included 88% of extant species and recovered well-accepted relationships with strong support. However, branch lengths, which are particularly important in down-stream macroevolutionary studies, appeared vastly skewed. Taxa represented only by rapidly evolving mitochondrial data had high proportions of missing data and exhibited long terminal branches. Conversely, taxa sampled for slowly evolving UCEs with low proportions of missing data exhibited substantially shorter terminal branches. We explored several branch length re-estimation methods with particular attention to terminal branches and conclude that re-estimation using well-sampled mitochondrial sequences may be a pragmatic approach to obtain trees suitable for macroevolutionary analysis.
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http://dx.doi.org/10.1016/j.ympev.2021.107091DOI Listing
May 2021

The mitochondrial genome of the Maltese honey bee, (Insecta: Hymenoptera: Apidae).

Mitochondrial DNA B Resour 2020 Jan 27;5(1):877-878. Epub 2020 Jan 27.

Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, FL, USA.

The mitochondrial genome of consisted of 13 protein-coding genes, two rRNAs, 22 tRNAs, an AT-rich control region, and was 16,577 bp long. The phylogenetic analyses suggested that was closely related to two North African subspecies: and .
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http://dx.doi.org/10.1080/23802359.2020.1717384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7748607PMC
January 2020

The complete mitochondrial genome of (Insecta: Hymenoptera: Apidae), the Arabian honey bee.

Mitochondrial DNA B Resour 2020 Jan 27;5(1):875-876. Epub 2020 Jan 27.

Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, FL, USA.

The mitochondrial genome of a worker was 16,623 bp. It consisted of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs and a control region. Phylogenetic analyses suggest a close relationship between , and .
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http://dx.doi.org/10.1080/23802359.2020.1717383DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7748573PMC
January 2020

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

Mol Phylogenet Evol 2021 02 17;155:107013. Epub 2020 Nov 17.

Department of Ornithology, American Museum of Natural History, New York, NY, USA. Electronic address:

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 clade was an exception to the generally high support we observed; the topology of this clade 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.
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http://dx.doi.org/10.1016/j.ympev.2020.107013DOI Listing
February 2021

Dense sampling of bird diversity increases power of comparative genomics.

Nature 2020 11 11;587(7833):252-257. Epub 2020 Nov 11.

Centre for Zoo and Wild Animal Health, Copenhagen Zoo, Frederiksberg, Denmark.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity. Sparse taxon sampling has previously been proposed to confound phylogenetic inference, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.
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http://dx.doi.org/10.1038/s41586-020-2873-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7759463PMC
November 2020

Tempo and Pattern of Avian Brain Size Evolution.

Curr Biol 2020 06 23;30(11):2026-2036.e3. Epub 2020 Apr 23.

Department of Otorhinolaryngology, University Medical Center, Groningen 9713, the Netherlands.

Relative brain sizes in birds can rival those of primates, but large-scale patterns and drivers of avian brain evolution remain elusive. Here, we explore the evolution of the fundamental brain-body scaling relationship across the origin and evolution of birds. Using a comprehensive dataset sampling> 2,000 modern birds, fossil birds, and theropod dinosaurs, we infer patterns of brain-body co-variation in deep time. Our study confirms that no significant increase in relative brain size accompanied the trend toward miniaturization or evolution of flight during the theropod-bird transition. Critically, however, theropods and basal birds show weaker integration between brain size and body size, allowing for rapid changes in the brain-body relationship that set the stage for dramatic shifts in early crown birds. We infer that major shifts occurred rapidly in the aftermath of the Cretaceous-Paleogene mass extinction within Neoaves, in which multiple clades achieved higher relative brain sizes because of a reduction in body size. Parrots and corvids achieved the largest brains observed in birds via markedly different patterns. Parrots primarily reduced their body size, whereas corvids increased body and brain size simultaneously (with rates of brain size evolution outpacing rates of body size evolution). Collectively, these patterns suggest that an early adaptive radiation in brain size laid the foundation for subsequent selection and stabilization.
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http://dx.doi.org/10.1016/j.cub.2020.03.060DOI Listing
June 2020

Phylogenetic Analyses of Sites in Different Protein Structural Environments Result in Distinct Placements of the Metazoan Root.

Biology (Basel) 2020 Mar 28;9(4). Epub 2020 Mar 28.

Department of Biology, University of Florida.

Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life; this could reflect, at least in part, the poor-fit of the models used to analyze heterogeneous datasets. Some of the heterogeneity may reflect the different patterns of selection on proteins based on their structures. To test that hypothesis, we developed a pipeline to divide phylogenomic protein datasets into subsets based on secondary structure and relative solvent accessibility. We then tested whether amino acids in different structural environments had distinct signals for the topology of the deepest branches in the metazoan tree. We focused on a dataset that appeared to have a mixture of signals and we found that the most striking difference in phylogenetic signal reflected relative solvent accessibility. Analyses of exposed sites (residues located on the surface of proteins) yielded a tree that placed ctenophores sister to all other animals whereas sites buried inside proteins yielded a tree with a sponge+ctenophore clade. These differences in phylogenetic signal were not ameliorated when we conducted analyses using a set of maximum-likelihood profile mixture models. These models are very similar to the Bayesian CAT model, which has been used in many analyses of deep metazoan phylogeny. In contrast, analyses conducted after recoding amino acids to limit the impact of deviations from compositional stationarity increased the congruence in the estimates of phylogeny for exposed and buried sites; after recoding amino acid trees estimated using the exposed and buried site both supported placement of ctenophores sister to all other animals. Although the central conclusion of our analyses is that sites in different structural environments yield distinct trees when analyzed using models of protein evolution, our amino acid recoding analyses also have implications for metazoan evolution. Specifically, our results add to the evidence that ctenophores are the sister group of all other animals and they further suggest that the placozoa+cnidaria clade found in some other studies deserves more attention. Taken as a whole, these results provide striking evidence that it is necessary to achieve a better understanding of the constraints due to protein structure to improve phylogenetic estimation.
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http://dx.doi.org/10.3390/biology9040064DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7235752PMC
March 2020

The mitochondrial genome of the Carniolan honey bee, (Insecta: Hymenoptera: Apidae).

Mitochondrial DNA B Resour 2019 Sep 30;4(2):3288-3290. Epub 2019 Sep 30.

Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, FL, USA.

Sequencing the mitochondrial genome of the Carniolan honey bee, revealed 16,358 bp, consisting of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and a control region. Phylogenetic analysis supported a close relationship to another south-eastern European (C-lineage) honey bee, .
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http://dx.doi.org/10.1080/23802359.2019.1671250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7707220PMC
September 2019

The complete mitochondrial genome of (Insecta: Hymenoptera: Apidae), the Malagasy honey bee.

Mitochondrial DNA B Resour 2019 Sep 30;4(2):3286-3287. Epub 2019 Sep 30.

Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, FL, USA.

The complete mitochondrial genome of the endemic Malagasy honey bee is 16,373 bp and comprises 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region. The mitochondrial genome closely resembles mitogenomes of other published subspecies, and the phylogenetic analysis suggests that is distinct from other African (A) lineage honey bees but is most closely related to the honey bees from southern African: and .
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http://dx.doi.org/10.1080/23802359.2019.1671247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7707310PMC
September 2019

Earth history and the passerine superradiation.

Proc Natl Acad Sci U S A 2019 04 1;116(16):7916-7925. Epub 2019 Apr 1.

Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013-7012.

Avian diversification has been influenced by global climate change, plate tectonic movements, and mass extinction events. However, the impact of these factors on the diversification of the hyperdiverse perching birds (passerines) is unclear because family level relationships are unresolved and the timing of splitting events among lineages is uncertain. We analyzed DNA data from 4,060 nuclear loci and 137 passerine families using concatenation and coalescent approaches to infer a comprehensive phylogenetic hypothesis that clarifies relationships among all passerine families. Then, we calibrated this phylogeny using 13 fossils to examine the effects of different events in Earth history on the timing and rate of passerine diversification. Our analyses reconcile passerine diversification with the fossil and geological records; suggest that passerines originated on the Australian landmass ∼47 Ma; and show that subsequent dispersal and diversification of passerines was affected by a number of climatological and geological events, such as Oligocene glaciation and inundation of the New Zealand landmass. Although passerine diversification rates fluctuated throughout the Cenozoic, we find no link between the rate of passerine diversification and Cenozoic global temperature, and our analyses show that the increases in passerine diversification rate we observe are disconnected from the colonization of new continents. Taken together, these results suggest more complex mechanisms than temperature change or ecological opportunity have controlled macroscale patterns of passerine speciation.
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http://dx.doi.org/10.1073/pnas.1813206116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6475423PMC
April 2019

What are the roles of taxon sampling and model fit in tests of cyto-nuclear discordance using avian mitogenomic data?

Mol Phylogenet Evol 2019 01 12;130:132-142. Epub 2018 Oct 12.

Department of Biology, University of Florida, Gainesville, FL 32611, USA. Electronic address:

Conflicts between nuclear and mitochondrial phylogenies have led to uncertainty for some relationships within the tree of life. These conflicts have led some to question the value of mitochondrial DNA in phylogenetics now that genome-scale nuclear data can be readily obtained. However, since mitochondrial DNA is maternally inherited and does not recombine, its phylogeny should be closer to the species tree. Additionally, its rapid evolutionary rate may drive accumulation of mutations along short internodes where relevant information from nuclear loci may be limited. In this study, we examine the mitochondrial phylogeny of Cavitaves to elucidate its congruence with recently published nuclear phylogenies of this group of birds. Cavitaves includes the orders Trogoniformes (trogons), Bucerotiformes (hornbills), Coraciiformes (kingfishers and allies), and Piciformes (woodpeckers and allies). We hypothesized that sparse taxon sampling in previously published mitochondrial trees was responsible for apparent cyto-nuclear discordance. To test this hypothesis, we assembled 27 additional Cavitaves mitogenomes and estimated phylogenies using seven different taxon sampling schemes ranging from five to 42 ingroup species. We also tested the role that partitioning and model choice played in the observed discordance. Our analyses demonstrated that improved taxon sampling could resolve many of the disagreements. Similarly, partitioning was valuable in improving congruence with the topology from nuclear phylogenies, though the model used to generate the mitochondrial phylogenies had less influence. Overall, our results suggest that the mitochondrial tree is trustworthy when partitioning is used with suitable taxon sampling.
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http://dx.doi.org/10.1016/j.ympev.2018.10.008DOI Listing
January 2019

A simple strategy for recovering ultraconserved elements, exons, and introns from low coverage shotgun sequencing of museum specimens: Placement of the partridge genus Tropicoperdix within the galliformes.

Mol Phylogenet Evol 2018 12 7;129:304-314. Epub 2018 Sep 7.

MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing 100875, China.

Next-generation DNA sequencing (NGS) offers a promising way to obtain massive numbers of orthologous loci to understand phylogenetic relationships among organisms. Of particular interest are old museum specimens and other samples with degraded DNA, where traditional sequencing methods have proven to be challenging. Low coverage shotgun sequencing and sequence capture are two widely used NGS approaches for degraded DNA. Sequence capture can yield sequence data for large numbers of orthologous loci, but it can only be used to sequence genomic regions near conserved sequences that can be used as probes. Low coverage shotgun sequencing has the potential to yield different data types throughout the genome. However, many studies using this method have often generated mitochondrial sequences, and few nuclear sequences, suggesting orthologous nuclear sequences are likely harder to recover. To determine the phylogenetic position of the galliform genus Tropicoperdix, whose phylogenetic position is currently uncertain, we explored two strategies to maximize data extraction from low coverage shotgun sequencing from approximately 100-year-old museum specimens from two species of Tropicoperdix. One approach, a simple read mapping strategy, outperformed the other (a reduced complexity assembly approach), and allowed us to obtain a large number of ultraconserved element (UCE) loci, relatively conserved exons, more variable introns, as well as mitochondrial genomes. Additionally, we demonstrated some simple approaches to explore possible artifacts that may result from the use of degraded DNA. Our data placed Tropicoperdix within a clade that includes many taxa characterized with ornamental eyespots (peafowl, argus pheasants, and peacock pheasants), and established relationships among species within the genus. Therefore, our study demonstrated that low coverage shotgun sequencing can easily be leveraged to yield substantial amounts and varying types of data, which opens the door for many research questions that might require information from different data types from museum specimens.
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http://dx.doi.org/10.1016/j.ympev.2018.09.005DOI Listing
December 2018

An evolutionary model motivated by physicochemical properties of amino acids reveals variation among proteins.

Authors:
Edward L Braun

Bioinformatics 2018 07;34(13):i350-i356

Department of Biology and Genetics Institute, University of Florida, Gainesville, FL, USA.

Motivation: The relative rates of amino acid interchanges over evolutionary time are likely to vary among proteins. Variation in those rates has the potential to reveal information about constraints on proteins. However, the most straightforward model that could be used to estimate relative rates of amino acid substitution is parameter-rich and it is therefore impractical to use for this purpose.

Results: A six-parameter model of amino acid substitution that incorporates information about the physicochemical properties of amino acids was developed. It showed that amino acid side chain volume, polarity and aromaticity have major impacts on protein evolution. It also revealed variation among proteins in the relative importance of those properties. The same general approach can be used to improve the fit of empirical models such as the commonly used PAM and LG models.

Availability And Implementation: Perl code and test data are available from https://github.com/ebraun68/sixparam.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty261DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022633PMC
July 2018

Comparative Genomics Reveals a Burst of Homoplasy-Free Numt Insertions.

Mol Biol Evol 2018 08;35(8):2060-2064

Department of Biology, University of Florida, Gainesville, FL.

Mitochondrial DNA sequences are frequently transferred into the nuclear genome, giving rise to numts (nuclear mitochondrial DNA segments). In the absence of whole genomes, avian numts have been suggested to be rare and relatively short. We examined 64 bird genomes to test hypotheses regarding numt frequency, distribution among taxa, and likelihood of homoplasy. We discovered 100-fold variation in numt number across species. Two songbirds, Geospiza fortis (Darwin's finch) and Zonotrichia albicollis (white-throated sparrow) had the largest number of numts. Ancestral state reconstruction of 957 numt insertions in these two species and their close relatives indicated a remarkable acceleration of numt insertion in the ancestor of Geospiza and Zonotrichia followed by slower, continued accumulation in each lineage. These numts appear to result primarily from de novo insertion with the duplication of existing numts representing a secondary pathway. Insertion events were essentially homoplasy-free and numts appear to represent perfect rare genomic changes.
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http://dx.doi.org/10.1093/molbev/msy112DOI Listing
August 2018

Mitochondrial genome diversity and population structure of two western honey bee subspecies in the Republic of South Africa.

Sci Rep 2018 01 22;8(1):1333. Epub 2018 Jan 22.

Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, Florida, 32611-0620, USA.

Apis mellifera capensis Eschscholtz and A.m. scutellata Lepeletier are subspecies of western honey bees that are indigenous to the Republic of South Africa (RSA). Both subspecies have invasive potential and are organisms of concern for areas outside their native range, though they are important bees to beekeepers, agriculture, and the environment where they are native. The aim of the present study was to examine genetic differentiation among these subspecies and estimate their phylogenetic relationships using complete mitochondrial genomes sequences. We used 25 individuals that were either assigned to one of the subspecies or designated hybrids using morphometric analyses. Phylogenetic analyses of mitogenome sequences by maximum likelihood (ML) and Bayesian inference identified a monophyletic RSA clade, subdivided into two clades. A haplotype network was consistent with the phylogenetic trees. However, members of both subspecies occurred in both clades, indicating that A.m. capensis and A.m. scutellata are neither reciprocally monophyletic nor do they exhibit paraphyly with one subspecies nested within the other subspecies. Furthermore, no mitogenomic features were diagnostic to either subspecies. All bees analyzed from the RSA expressed a substantial level of haplotype diversity (most samples had unique haplotypes) but limited nucleotide diversity. The number of variable codons across protein-coding genes (PCGs) differed among loci, with CO3 exhibiting the most variation and ATP6 the least.
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http://dx.doi.org/10.1038/s41598-018-19759-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5778041PMC
January 2018

The complete mitochondrial genome of an east African honey bee, Smith (Insecta: Hymenoptera: Apidae).

Mitochondrial DNA B Resour 2017 Sep 1;2(2):589-590. Epub 2017 Sep 1.

Entomology and Nematology Department, Honey Bee Research and Extension Laboratory, University of Florida, Gainesville, FL, USA.

The complete mitochondrial genome of was sequenced and annotated. The genome is 16,343 bp in length and encodes all 37 mitochondrial genes with an A + T content of 84.8%. Gene directions and arrangements are identical to those of other sequenced mitogenomes in . Most genes initiated with ATT, though ATG, ATA, and ATC also were used as start codons. All genes terminated with TAA. Four PCG genes, eight tRNAs and both rRNAs are encoded on the heavy strand while all others are coded on the light strand (nine PCGs and 14 tRNAs). Overall, the GC content composed 15.2% of the mitogenome. All of the 22 tRNA genes, ranging from 63 to 78 bp, have a typical cloverleaf structure. A phylogenetic tree showed that clusters with other African subspecies.
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http://dx.doi.org/10.1080/23802359.2017.1372722DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799518PMC
September 2017

The complete mitochondrial genome of Tingek, an Asian honey bee (Insecta: Hymenoptera: Apidae).

Mitochondrial DNA B Resour 2017 Aug 17;2(2):552-553. Epub 2017 Aug 17.

Entomology and Nematology Department, Honey Bee Research and Extension Laboratory, University of Florida, Gainesville, FL, USA.

The complete mitochondrial genome of Tingek was sequenced. The mitochondrial genome was 15,843 bp in length, with 37 classical eukaryotic mitochondrial genes and an A + T-rich region. Gene directions and arrangements were similar to those of other mitogenomes. Most genes initiate with ATT (though ATG and ATC also were used) and all genes terminated with TAA. Nine genes were encoded on the light strand while four were encoded on the heavy strand. All 22 tRNA genes have a typical cloverleaf structure. The most likely phylogenetic tree showed clustering with . The complete mitogenome of completes the sequencing of all mitogenomes of the currently accepted species of .
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http://dx.doi.org/10.1080/23802359.2017.1365655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799457PMC
August 2017

Phylogenomic analysis supports multiple instances of polyphyly in the oomycete peronosporalean lineage.

Mol Phylogenet Evol 2017 09 20;114:199-211. Epub 2017 Jun 20.

Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Department of Plant Pathology, University of Florida, Gainesville, FL, USA. Electronic address:

The study of biological diversification of oomycetes has been a difficult task for more than a century. Pioneer researchers used morphological characters to describe this heterogeneous group, and physiological and genetic tools expanded knowledge of these microorganisms. However, research on oomycete diversification is limited by conflicting phylogenies. Using whole genomic data from 17 oomycete taxa, we obtained a dataset of 277 core orthologous genes shared among these genomes. Analyses of this dataset resulted in highly congruent and strongly supported estimates of oomycete phylogeny when we used concatenated maximum likelihood and coalescent-based methods; the one important exception was the position of Albugo. Our results supported the position of Phytopythium vexans (formerly in Pythium clade K) as a sister clade to the Phytophthora-Hyaloperonospora clade. The remaining clades comprising Pythium sensu lato formed two monophyletic groups. One group was composed of three taxa that correspond to Pythium clades A, B and C, and the other group contained taxa representing clades F, G and I, in agreement with previous Pythium phylogenies. However, the group containing Pythium clades F, G and I was placed as sister to the Phytophthora-Hyaloperonospora-Phytopythium clade, thus confirming the lack of monophyly of Pythium sensu lato. Multispecies coalescent methods revealed that the white blister rust, Albugo laibachii, could not be placed with a high degree of confidence. Our analyses show that genomic data can resolve the oomycete phylogeny and provide a phylogenetic framework to study the evolution of oomycete lifestyles.
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http://dx.doi.org/10.1016/j.ympev.2017.06.013DOI Listing
September 2017

The complete mitochondrial genome of the Egyptian honey bee, (Insecta: Hymenoptera: Apidae).

Mitochondrial DNA B Resour 2017 May 12;2(1):270-272. Epub 2017 May 12.

Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, FL, USA.

The complete mitochondrial genome of the western honey bee subspecies was sequenced. This mitochondrial genome is 16,589 bp in length with 37 classical eukaryotic mitochondrial genes and an A + T-rich region. Gene directions and arrangements are similar to those of other mitogenomes. Seven genes begin with ATT, four with ATG, and two with ATA (none with ATC) and all genes terminate with TAA. Four genes are encoded on the heavy strand and nine are encoded on light strand. All of the 22 tRNA genes, ranging from 66 to 80 bp, have a typical cloverleaf structure. A phylogenetic tree showed that clusters with other subspecies, as expected.
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http://dx.doi.org/10.1080/23802359.2017.1325343DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799828PMC
May 2017

The complete mitochondrial genome of (Insecta: Hymenoptera: Apidae).

Mitochondrial DNA B Resour 2017 May 12;2(1):268-269. Epub 2017 May 12.

Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, FL, USA.

The complete mitochondrial genome of the western honey bee subspecies was sequenced. This mitochondrial genome is 16,248 bp in length, with 37 classical eukaryotic mitochondrial genes and an A + T-rich region. Gene direction and arrangement are similar to those of other mitogenomes. All genes initiate with ATT (six genes), ATG (four genes), ATA (two genes), and ATC (one gene) start codons and terminate with a TAA stop codon. Four genes are encoded on the heavy and nine on the light strands, respectively. All of the 22 tRNA genes, ranging from 66 to 78 bp, have a typical cloverleaf structure. The complete mitogenome of provides information on the biogeography and evolution of subspecies.
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http://dx.doi.org/10.1080/23802359.2017.1325342DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800517PMC
May 2017

How do seemingly non-vagile clades accomplish trans-marine dispersal? Trait and dispersal evolution in the landfowl (Aves: Galliformes).

Proc Biol Sci 2017 May;284(1854)

Department of Biology, University of Florida, Gainesville, FL, USA.

Dispersal ability is a key factor in determining insular distributions and island community composition, yet non-vagile terrestrial organisms widely occur on oceanic islands. The landfowl (pheasants, partridges, grouse, turkeys, quails and relatives) are generally poor dispersers, but the Old World quail () are a notable exception. These birds evolved small body sizes and high-aspect-ratio wing shapes, and hence are capable of trans-continental migrations and trans-oceanic colonization. Two monotypic partridge genera, of Madagascar and of alpine New Guinea, may represent additional examples of trans-marine dispersal in landfowl, but their body size and wing shape are typical of poorly dispersive continental species. Here, we estimate historical relationships of quail and their relatives using phylogenomics, and infer body size and wing shape evolution in relation to trans-marine dispersal events. Our results show that and are nested within the quail, and are each 'island giants' that independently evolved from dispersive, -like ancestral populations that colonized and were subsequently isolated on Madagascar and New Guinea. This evolutionary cycle of gain and loss of dispersal ability, coupled with extinction of dispersive taxa, can result in the false appearance that non-vagile taxa somehow underwent rare oceanic dispersal.
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http://dx.doi.org/10.1098/rspb.2017.0210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5443944PMC
May 2017

Evolution of the 3R-MYB Gene Family in Plants.

Genome Biol Evol 2017 Apr;9(4):1013-1029

Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL.

Plant 3R-MYB transcription factors are an important subgroup of the MYB super family in plants; however, their evolutionary history and functions remain poorly understood. We identified 225 3R-MYB proteins from 65 plant species, including algae and all major lineages of land plants. Two segmental duplication events preceding the common ancestor of angiosperms have given rise to three subgroups of the 3R-MYB proteins. Five conserved introns in the domain region of the 3R-MYB genes were identified, which arose through a step-wise pattern of intron gain during plant evolution. Alternative splicing (AS) analysis of selected species revealed that transcripts from more than 60% of 3R-MYB genes undergo AS. AS could regulate transcriptional activity for some of the plant 3R-MYBs by generating different regulatory motifs. The 3R-MYB genes of all subgroups appear to be enriched for Mitosis-Specific Activator element core sequences within their upstream promoter region, which suggests a functional involvement in cell cycle. Notably, expression of 3R-MYB genes from different species exhibits differential regulation under various abiotic stresses. These data suggest that the plant 3R-MYBs function in both cell cycle regulation and abiotic stress response, which may contribute to the adaptation of plants to a sessile lifestyle.
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http://dx.doi.org/10.1093/gbe/evx056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405339PMC
April 2017

The complete mitochondrial genome and phylogenetic placement of Smith (Insecta: Hymenoptera: Apidae), an Asian, cavity-nesting honey bee.

Mitochondrial DNA B Resour 2017 Apr 25;2(1):249-250. Epub 2017 Apr 25.

Honey Bee Research and Extension Laboratory, Entomology and Nematology Department, University of Florida, Gainesville, FL, USA.

The complete mitochondrial genome of was sequenced. The mitochondrial genome is a circular molecule of 15,855 bp, including 37 classical eukaryotic mitochondrial regions and an A + T-rich region. Gene directions and arrangements are similar to those of other mitogenomes. Most genes initiated with ATT, though ATG and ATA were also used as start codons. Twelve of 13 protein-coding genes terminated with TAA, though ND2 terminated with TAG. Four PCG genes, eight tRNAs and both rRNAs were encoded on the heavy strand while all others were encoded on the light strand (9 PCGs and 14 tRNAs). Overall, the GC content composed 15.6% of the mitogenome. All of the 22 tRNA genes, ranging from 66 to 114 bp, have a typical cloverleaf structure. A phylogenetic tree showed that clustered closest to . The complete mitogenome of provides essential information on the biogeography and evolution of this Asian honey bee species.
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http://dx.doi.org/10.1080/23802359.2017.1318683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7799737PMC
April 2017

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling.

Syst Biol 2017 Sep;66(5):857-879

Department of Biology, University of Florida, Gainesville, FL 32607, USA.

Phylogenomics, the use of large-scale data matrices in phylogenetic analyses, has been viewed as the ultimate solution to the problem of resolving difficult nodes in the tree of life. However, it has become clear that analyses of these large genomic data sets can also result in conflicting estimates of phylogeny. Here, we use the early divergences in Neoaves, the largest clade of extant birds, as a "model system" to understand the basis for incongruence among phylogenomic trees. We were motivated by the observation that trees from two recent avian phylogenomic studies exhibit conflicts. Those studies used different strategies: 1) collecting many characters [$\sim$ 42 mega base pairs (Mbp) of sequence data] from 48 birds, sometimes including only one taxon for each major clade; and 2) collecting fewer characters ($\sim$ 0.4 Mbp) from 198 birds, selected to subdivide long branches. However, the studies also used different data types: the taxon-poor data matrix comprised 68% non-coding sequences whereas coding exons dominated the taxon-rich data matrix. This difference raises the question of whether the primary reason for incongruence is the number of sites, the number of taxa, or the data type. To test among these alternative hypotheses we assembled a novel, large-scale data matrix comprising 90% non-coding sequences from 235 bird species. Although increased taxon sampling appeared to have a positive impact on phylogenetic analyses the most important variable was data type. Indeed, by analyzing different subsets of the taxa in our data matrix we found that increased taxon sampling actually resulted in increased congruence with the tree from the previous taxon-poor study (which had a majority of non-coding data) instead of the taxon-rich study (which largely used coding data). We suggest that the observed differences in the estimates of topology for these studies reflect data-type effects due to violations of the models used in phylogenetic analyses, some of which may be difficult to detect. If incongruence among trees estimated using phylogenomic methods largely reflects problems with model fit developing more "biologically-realistic" models is likely to be critical for efforts to reconstruct the tree of life. [Birds; coding exons; GTR model; model fit; Neoaves; non-coding DNA; phylogenomics; taxon sampling.].
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http://dx.doi.org/10.1093/sysbio/syx041DOI Listing
September 2017

Historical relationships of three enigmatic phasianid genera (Aves: Galliformes) inferred using phylogenomic and mitogenomic data.

Mol Phylogenet Evol 2017 04 11;109:217-225. Epub 2017 Jan 11.

Department of Biology, University of Florida, Gainesville, FL 32611, USA. Electronic address:

The phylogeny of the Phasianidae (pheasants, partridges, and allies) has been studied extensively. However, these studies have largely ignored three enigmatic genera because of scarce DNA source material and limited overlapping phylogenetic data: blood pheasants (Ithaginis), snow partridges (Lerwa), and long-billed partridges (Rhizothera). Thus, phylogenetic positions of these three genera remain uncertain in what is otherwise a well-resolved phylogeny. Previous studies using different data types place Lerwa and Ithaginis in similar positions, but the absence of overlapping data means the relationship between them could not be inferred. Rhizothera was originally described in the genus Perdix (true partridges), although a partial cytochrome b (CYB) sequence suggests it is sister to Pucrasia (koklass pheasant). To identify robust relationships among Ithaginis, Lerwa, Rhizothera, and their phasianid relatives, we used 3692 ultra-conserved element (UCE) loci and complete mitogenomes from 19 species including previously hypothesized relatives of the three focal genera and representatives from all major phasianid clades. We used DNA extracted from historical specimen toepads for species that lacked fresh tissue in museum collections. Maximum likelihood and multispecies coalescent UCE analyses strongly supported Lerwa sister to a large clade which included Ithaginis at its base, and also including turkey, grouse, typical pheasants, tragopans, Pucrasia, and Perdix. Rhizothera was also in this clade, sister to a diverse group comprising Perdix, typical pheasants, Pucrasia, turkey and grouse. Mitogenomic genealogies differed from UCEs topologies, supporting a sister relationship between Ithaginis and Lerwa rather than a grade. The position of Rhizothera using mitogenomes depended on analytical choices. Unpartitioned and codon-based analyses placed Rhizothera sister to a tragopan clade, whereas a partitioned DNA model of the mitogenome was congruent with UCE results. In all mitogenome analyses, Pucrasia was sister to a clade including Perdix and the typical pheasants with high support, in contrast to UCEs and published nuclear intron data. Due to the strong support and consistent topology provided by all UCE analyses, we have identified phylogenetic relationships of these three enigmatic, poorly-studied, phasianid taxa.
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http://dx.doi.org/10.1016/j.ympev.2017.01.006DOI Listing
April 2017

The complete mitochondrial genome of the Cape honey bee, Esch. (Insecta: hymenoptera: apidae).

Mitochondrial DNA B Resour 2016 Nov 12;1(1):817-819. Epub 2016 Nov 12.

Honey Bee Research and Extension Laboratory, Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA.

We characterized the complete mitogenome sequence of the Cape honey bee, , from South Africa. The circle genome is 16,470 bp in length, with the base composition of 43.2% A, 9.6% C, 5.6% G, and 41.5% T. The assembled mitogenome has 13 protein-coding genes (PCGs), 22 transfer RNAs, two ribosomal RNA genes, and one control region. All protein-coding genes are initiated by ATT, ATC, ATG or ATA codons and are terminated by the typical stop codon TAA. The heavy strand encodes four protein-coding genes, eight tRNAs, and two rRNAs. The light strand encodes nine protein-coding genes and 14 tRNAs. The complete mitogenome sequence of is identical to the gene arrangement found in other mitogenomes and it provides essential and important DNA molecular data for further phylogenetic and evolutionary analysis of members of the genus .
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http://dx.doi.org/10.1080/23802359.2016.1241682DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7800515PMC
November 2016
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