العنوان البديل: Actualizando divisiones, agrupamientos y reorganizaciones: reconciliando nombres de GenBank con taxonomías aviares estandarizadas. (Spanish)

المؤلفون: Hosner, Peter A., Min Zhao, Kimball, Rebecca T., Braun, Edward L., Burleigh, J. Gordon

المصدر: Ornithology (Oxford University Press); 10/6/2022, Vol. 139 Issue 4, p1-15, 15p

مصطلحات موضوعية: GENE libraries, BIRD ecology, DNA sequencing, NUCLEOTIDE sequence, BIG data

الملخص (بالإنجليزية): Biodiversity research has advanced by testing expectations of ecological and evolutionary hypotheses through the linking of large-scale genetic, distributional, and trait datasets. The rise of molecular systematics over the past 30 years has resulted in a wealth of DNA sequences from around the globe. Yet, advances in molecular systematics also have created taxonomic instability, as new estimates of evolutionary relationships and interpretations of species limits have required widespread scientific name changes. Taxonomic instability, colloquially "splits, lumps, and shuffles," presents logistical challenges to large-scale biodiversity research because (1) the same species or sets of populations may be listed under different names in different data sources, or (2) the same name may apply to different sets of populations representing different taxonomic concepts. Consequently, distributional and trait data are often difficult to link directly to primary DNA sequence data without extensive and time-consuming curation. Here, we present RANT: Reconciliation of Avian NCBI Taxonomy. RANT applies taxonomic reconciliation to standardize avian taxon names in use in NCBI GenBank, a primary source of genetic data, to a widely used and regularly updated avian taxonomy: eBird/Clements. Of 14,341 avian species/subspecies names in GenBank, 11,031 directly matched an eBird/Clements; these link to more than 6 million nucleotide sequences. For the remaining unmatched avian names in GenBank, we used Avibase's system of taxonomic concepts, taxonomic descriptions in Cornell's Birds of the World, and DNA sequence metadata to identify corresponding eBird/Clements names. Reconciled names linked to more than 600,000 nucleotide sequences, ~9% of all avian sequences on GenBank. Nearly 10% of eBird/Clements names had nucleotide sequences listed under 2 or more GenBank names. Our taxonomic reconciliation is a first step towards rigorous and open-source curation of avian GenBank sequences and is available at GitHub, where it can be updated to correspond to future annual eBird/Clements taxonomic updates. [ABSTRACT FROM AUTHOR]

Abstract (Spanish): La investigación sobre biodiversidad ha avanzado al evaluar las expectativas de las hipótesis ecológicas y evolutivas a través de la vinculación de bases de datos genéticos, de distribución y de rasgos a gran escala. El auge de la sistemática molecular en los últimos 30 años ha dado como resultado una gran cantidad de secuencias de ADN de todo el mundo. Sin embargo, los avances en la sistemática molecular también han creado inestabilidad taxonómica, ya que las nuevas estimaciones de las relaciones evolutivas y las interpretaciones de los límites de las especies han requerido cambios generalizados en los nombres científicos. La inestabilidad taxonómica, coloquialmente llamada "divisiones, agrupamientos y reorganizaciones," presenta desafíos logísticos para la investigación de la biodiversidad a gran escala porque (1) las mismas especies o conjuntos de poblaciones pueden estar listados con diferentes nombres en diferentes fuentes de datos, o (2) el mismo nombre puede aplicarse a diferentes conjuntos de poblaciones representando diferentes conceptos taxonómicos. En consecuencia, los datos de distribución y rasgos a menudo son difíciles de vincular directamente a los datos primarios de secuencias de ADN sin una curación extensa y demandante de tiempo. Aquí, presentamos RANT (por sus siglas en inglés): reconciliación de la taxonomía aviar del Centro Nacional para la Información Biotecnológica (CNIB). RANT aplica la reconciliación taxonómica para estandarizar los nombres de taxones aviares en uso en el GenBank de CNIB, una fuente principal de datos genéticos, con la taxonomía aviar ampliamente utilizada y actualizada periódicamente de eBird/Clements. De los 14.341 nombres de especies/subespecies de aves en GenBank, 11.031 coincidieron directamente con eBird/Clements; estos se vinculan a más de 6 millones de secuencias de nucleótidos. Para los restantes nombres de aves no coincidentes en GenBank, utilizamos el sistema de conceptos taxonómicos de Avibase, descripciones taxonómicas en Aves del Mundo de Cornell y metadatos de secuencias de ADN para identificar los nombres correspondientes de eBird/Clements. Los nombres reconciliados vincularon a más de 600.000 secuencias de nucleótidos, ~9% de todas las secuencias de aves en GenBank. Casi el 10% de los nombres de eBird/Clements tuvieron secuencias de nucleótidos enumeradas bajo dos o más nombres en GenBank. Nuestra reconciliación taxonómica es un primer paso hacia la curación rigurosa y de código abierto de las secuencias aviares de GenBank y está disponible en GitHub, donde se puede actualizar para que corresponda con las futuras actualizaciones taxonómicas anuales de eBird/Clements. [ABSTRACT FROM AUTHOR]

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المؤلفون: Hosner, Peter A., Owens, Hannah L., Braun, Edward L., Kimball, Rebecca T.

المصدر: Zoologica Scripta; Sep2020, Vol. 49 Issue 5, p549-562, 14p

مصطلحات موضوعية: GALLIFORMES, PHYLOGENY, NUCLEOTIDE sequence, BIRDS, INTRONS

مستخلص: The gallopheasants comprise a clade of 22 species including some of the most elaborately plumaged and highly ornamented birds in the world. They also occupy a remarkable breath of environments and habitats, ranging from lowland rainforests to high grasslands and steppes of the Tibetan plateau. Here, we provide the first well‐resolved species phylogeny of this charismatic group, inferred from ultraconserved elements, nuclear introns and mitochondrial DNA sequences. Unlike previous studies which found unresolvable relationships and suggested a rapid initial burst of diversification, we identified a well‐resolved phylogeny supported in both concatenated and coalescent analytical frameworks, and a steady accrual of lineages through time. Morphological trait reconstructions demonstrated strong phylogenetic signal, not only for highly ornamented males, but also in more cryptically plumaged females. Environmental niche similarly exhibited strong phylogenetic signal. Moreover, evolution of male traits, female traits and environmental niche were all significantly correlated, making it difficult to disentangle their individual roles in gallopheasant diversification. [ABSTRACT FROM AUTHOR]

: Copyright of Zoologica Scripta is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

المؤلفون: KIN-LAN HAN^1,2,3 hankin@ul.edu, BRAUN, EDWARD L.^1,3, KIMBALL, REBECCA T.¹, REDDY, SUSHMA^4,5, BOWIE, RAURI C. K.^6,7, BRAUN, MICHAEL J.², CHOJNOWSKI, JENA L.¹, HACKETT, SHANNON J.⁵, Harshman, John⁵, Huddleston, Christopher J.², Marks, Ben D.⁸, Miglia, Kathleen J.⁹, Moore, William S.⁹, Sheldon, Frederick H.⁸, Steadman, David W.¹⁰, Witt, Christopher C.^11,12, Yuri, Tamaki^1,2,13

المصدر: Systematic Biology. May2011, Vol. 60 Issue 3, p375-386. 12p. 2 Charts, 3 Graphs.

مصطلحات موضوعية: *TRANSPOSONS, *HOMOPLASY, *NUCLEOTIDE sequence, *GENETICS, *GENETIC code

مستخلص: This article examines whether transposable element (TE) insertions as an example of rare genomic changes (RGC) exhibit little or no homoplasy. Data suggest that TE insertion sites reduce state space for such RGC, that precise deletion of these TE can occur or that both phenomena contribute to homoplasy in avian TE. The importance of sequencing TE insertions is emphasized. It is also recommended to develop methods that can integrate data from TE insertions into large-scale analyses of nucleotide sequences, along with information about other RGC types.

المؤلفون: Braun, Edward L.¹ ebraun68@ufl.edu, Kimball, Rebecca T.¹, Kin-Lan Han¹, Iuhasz-Velez, Naomi R.², Bonilla, Amber J.¹, Chojnowski, Jena L.¹, Smith, Jordan V.¹, Bowie, Rauri C. K.^3,4, Braun, Michael J.^5,6, Hackett, Shannon J.³, Harshman, John³, Huddleston, Christopher J.⁵, Marks, Ben D.⁷, Miglia, Kathleen J.⁸, Moore, William S.⁸, Reddy, Sushma^3,9, Sheldon, Frederick H.⁷, Witt, Christopher C.^8,10, Yuri, Tamaki^1,5,11

المصدر: BMC Evolutionary Biology. 2011, Vol. 11 Issue 1, p141-150. 10p.

مصطلحات موضوعية: *GENETICS, *GENOMES, *NUCLEOTIDE sequence, *BIOLOGICAL evolution, *PHYLOGENY

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

المؤلفون: Houde, Peter¹ (AUTHOR) lzhou@nmsu.edu, Braun, Edward L.² (AUTHOR) phoude@nmsu.edu, Zhou, Lawrence¹ (AUTHOR)

المصدر: Diversity (14242818). Apr2020, Vol. 12 Issue 4, p164-164. 1p.

مصطلحات موضوعية: *CRETACEOUS-Paleogene boundary, *NUCLEOTIDE sequence, *GENETIC speciation, *ADAPTIVE radiation

مستخلص: Assessing the applicability of theory to major adaptive radiations in deep time represents an extremely difficult problem in evolutionary biology. Neoaves, which includes 95% of living birds, is believed to have undergone a period of rapid diversification roughly coincident with the Cretaceous–Paleogene (K-Pg) boundary. We investigate whether basal neoavian lineages experienced an ecological release in response to ecological opportunity, as evidenced by density compensation. We estimated effective population sizes (Ne) of basal neoavian lineages by combining coalescent branch lengths (CBLs) and the numbers of generations between successive divergences. We used a modified version of Accurate Species TRee Algorithm (ASTRAL) to estimate CBLs directly from insertion–deletion (indel) data, as well as from gene trees using DNA sequence and/or indel data. We found that some divergences near the K-Pg boundary involved unexpectedly high gene tree discordance relative to the estimated number of generations between speciation events. The simplest explanation for this result is an increase in Ne, despite the caveats discussed herein. It appears that at least some early neoavian lineages, similar to the ancestor of the clade comprising doves, mesites, and sandgrouse, experienced ecological release near the time of the K-Pg mass extinction. [ABSTRACT FROM AUTHOR]

العنوان البديل: Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist.

المؤلفون: Cox, W. Andrew¹, Kimball, Rebecca T.¹ rkimball@zoo.ufl.edu, Braun, Edward L.¹

المصدر: Auk (American Ornithologists Union). Jan2007, Vol. 124 Issue 1, p71-84. 14p.

مصطلحات موضوعية: *QUAILS, *GALLIFORMES, *GUINEAFOWL, *NUCLEOTIDE sequence, *PHASIANIDAE

الملخص (بالإنجليزية): The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. [ABSTRACT FROM AUTHOR]

Abstract (Spanish): La relación evolutiva entre las codornices del Nuevo Mundo (Odontophoridae) y otros grupos de Galliformes ha sido un área de debate. En particular, la relación entre Odontophoridae y Numidinae ha resultado difícil de resolver. Analizamos >8 kb de datos de secuencias de ADN de 16 taxa que representan todos los linajes principales de Galliformes para resolver la posición filogenética de Odontophoridae. Un conjunto de datos combinado de ocho loci nucleares y tres regiones mitocondriales analizado con métodos de máxima parsimonia, de máxima verosimilitud y Bayesianos apoya fuertemente la posición basal de Odontophoridae en un clado de fasiánidos que no incluye a los Numidinae. En contraste, las tres regiones mitocondriales presentan incongruencias modestas entre sí. Esto se refleja en los análisis de datos mitocondriales combinados, los cuales apoyan débilmente la topología de Sibley y Ahlquist, en la que Odontophoridae ocupaba una posición basal con respecto a Numidinae y llevó a la decisión de reconocer a Odontophoridae como una familia aparte, hermana de Phasianidae. Sin embargo, pruebas de topología basadas en simulaciones hechas empleando los datos mitocondriales no pudieron rechazar la topología sugerida por nuestro conjunto de datos mitocondriales y nucleares combinados. En cambio, pruebas similares hechas utilizando nuestra topología más verosímil y nuestros datos nucleares y mitocondriales combinados nos permitieron rechazar fuertemente la topología de Sibley y Ahlquist y una topologia basada en datos morfológicos que agrupa alas codornices del Viejo y del Nuevo Mundo. [ABSTRACT FROM AUTHOR]

المؤلفون: Persons, Nicholas W.¹, Hosner, Peter A.¹, Meiklejohn, Kelly A.¹, Braun, Edward L.^1,2, Kimball, Rebecca T.¹ rkimball@ufl.edu

المصدر: Molecular Phylogenetics & Evolution. May2016, Vol. 98, p123-132. 10p.

مصطلحات موضوعية: *PTARMIGANS, *INTRONS, *GROUSE, *MITOCHONDRIAL DNA, *NUCLEOTIDE sequence, *SEXUAL behavior in birds

مستخلص: The Holarctic phasianid clade of the grouse and ptarmigan has received substantial attention in areas such as evolution of mating systems, display behavior, and population ecology related to their conservation and management as wild game species. There are multiple molecular phylogenetic studies that focus on grouse and ptarmigan. In spite of this, there is little consensus regarding historical relationships, particularly among genera, which has led to unstable and partial taxonomic revisions. We estimated the phylogeny of all currently recognized species using a combination of novel data from seven nuclear loci (largely intron sequences) and published data from one additional autosomal locus, two W-linked loci, and four mitochondrial regions. To explore relationships among genera and assess paraphyly of one genus more rigorously, we then added over 3000 ultra-conserved element (UCE) loci (over 1.7 million bp) gathered using Illumina sequencing. The UCE topology agreed with that of the combined nuclear intron and previously published sequence data with 100% bootstrap support for all relationships. These data strongly support previous studies separating Bonasa from Tetrastes and Dendragapus from Falcipennis . However, the placement of Lagopus differed from previous studies, and we found no support for Falcipennis monophyly. Biogeographic analysis suggests that the ancestors of grouse and ptarmigan were distributed in the New World and subsequently underwent at least four dispersal events between the Old and New Worlds. Divergence time estimates from maternally-inherited and autosomal markers show stark differences across this clade, with divergence time estimates from maternally-inherited markers being nearly half that of the autosomal markers at some nodes, and nearly twice that at other nodes. [ABSTRACT FROM AUTHOR]

المؤلفون: Kimball, Rebecca T.¹ (AUTHOR) rkimball@ufl.edu, Guido, Marisa^1,2 (AUTHOR), Hosner, Peter A.^1,3 (AUTHOR), Braun, Edward L.¹ (AUTHOR)

المصدر: Gene. Oct2021, Vol. 801, pN.PAG-N.PAG. 1p.

مصطلحات موضوعية: *GALLIFORMES, *DNA sequencing, *MITOCHONDRIA, *NUCLEOTIDE sequence, *PHYLOGENY, *PLANT mitochondria

مستخلص: • Discordance between mitochondrial and nuclear phylogenies is common. • Mitonuclear discordance can reflect biological processes or analytical artifacts. • Examination of sites supporting alternative topologies may be informative. • Analysis of mitogenomes found well-supported conflicts with a nuclear topology. • The sites supporting alternative topologies suggest conflicts are biological. 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. [ABSTRACT FROM AUTHOR]

المؤلفون: Hackett, Shannon J., Kimball, Rebecca T., Reddy, Sushma, Bowie, Rauri C. K.^1,2, Braun, Edward L.³, Braun, Michael J., Chojnowski, Jena L., Cox, W. Andrew, Kin-Lan Han³, Harshman, John, Huddleston, Christopher J., Marks, Ben D.⁴, Miglia, Kathleen J.⁵, Moore, William S.⁵, Sheldon, Frederick H.⁴, Steadman, David W.⁶, Witt, Christopher C.^4,7, Yuri, Tamaki

المصدر: Science. 6/27/2008, Vol. 320 Issue 5884, p1763-1768. 6p. 4 Diagrams.

مصطلحات موضوعية: *NUCLEIC acids, *NUCLEOTIDE sequence, *BIRD evolution, *PHYLOGENY, *BIOLOGICAL evolution, *IMMUNOTAXONOMY, *CLADISTIC analysis, *DNA, *BIRD watching

مستخلص: Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds. [ABSTRACT FROM AUTHOR]