scholarly journals A higher‐level nuclear phylogenomic study of the carrot family (Apiaceae)

2021 ◽  
Author(s):  
James J. Clarkson ◽  
Alexandre R. Zuntini ◽  
Olivier Maurin ◽  
Stephen R. Downie ◽  
Gregory M. Plunkett ◽  
...  
Keyword(s):  
Phylogenomic Study

Phylogenomic study of the subfamily Caprinae by cross-species chromosome painting with Chinese muntjac paints

2005 ◽  
Vol 13 (4) ◽  
pp. 389-399 ◽  
Author(s):  
Ling Huang ◽  
Wenhui Nie ◽  
Jinhuan Wang ◽  
Weiting Su ◽  
Fengtang Yang
Keyword(s):  
Chromosome Painting ◽  
Cross Species Chromosome Painting ◽  
Phylogenomic Study

scholarly journals Tetraconatan phylogeny with special focus on Malacostraca and Branchiopoda: highlighting the strength of taxon-specific matrices in phylogenomics

2018 ◽  
Vol 285 (1885) ◽  
pp. 20181524 ◽  
Author(s):  
Martin Schwentner ◽  
Stefan Richter ◽  
D. Christopher Rogers ◽  
Gonzalo Giribet
Keyword(s):  
Amino Acid ◽  
Analytical Methods ◽  
Special Focus ◽  
Evolutionary Models ◽  
Phylogenomic Analyses ◽  
New Generation ◽  
Analytical Approaches ◽  
Internal Relationships ◽  
Complete Matrix ◽  
Phylogenomic Study

Understanding the evolution of Tetraconata or Pancrustacea—the clade that includes crustaceans and insects—requires a well-resolved hypothesis regarding the relationships within and among its constituent taxa. Here, we assembled a taxon-rich phylogenomic dataset focusing on crustacean lineages based solely on genomes and new-generation Illumina-generated transcriptomes, including 89 representatives of Tetraconata. This constitutes, to our knowledge, the first phylogenomic study specifically addressing internal relationships of Malacostraca (with 26 species included) and Branchiopoda (36 species). Seven matrices comprising 81–684 orthogroups and 17 690–242 530 amino acid positions were assembled and analysed under five different analytical approaches. To maximize gene occupancy and to improve resolution, taxon-specific matrices were designed for Malacostraca and Branchiopoda. Key tetraconatan taxa (i.e. Oligostraca, Multicrustacea, Branchiopoda, Malacostraca, Thecostraca, Copepoda and Hexapoda) were monophyletic and well supported. Within Branchiopoda, Phyllopoda, Diplostraca, Cladoceromorpha and Cladocera were monophyletic. Within Malacostraca, the clades Eumalacostraca, Decapoda and Reptantia were well supported. Recovery of Caridoida or Peracarida was highly dependent on the analysis for the complete matrix, but it was consistently monophyletic in the malacostracan-specific matrices. From such examples, we demonstrate that taxon-specific matrices and particular evolutionary models and analytical methods, namely CAT-GTR and Dayhoff recoding, outperform other approaches in resolving certain recalcitrant nodes in phylogenomic analyses.

Phylogenomics and Historical Biogeography of Seahorses, Dragonets, Goatfishes, and Allies (Teleostei: Syngnatharia): Assessing Factors Driving Uncertainty in Biogeographic Inferences

2021 ◽  
Author(s):  
Aintzane Santaquiteria ◽  
Alexandre C Siqueira ◽  
Emanuell Duarte-Ribeiro ◽  
Giorgio Carnevale ◽  
William White ◽  
...  
Keyword(s):  
Species Diversity ◽  
Great Proportion ◽  
Long Range ◽  
Late Cretaceous ◽  
Tree Topology ◽  
Divergence Times ◽  
Center Of Origin ◽  
Tethys Sea ◽  
Warm Temperate ◽  
Phylogenomic Study

Abstract The charismatic trumpetfishes, goatfishes, dragonets, flying gurnards, seahorses, and pipefishes encompass a recently defined yet extraordinarily diverse clade of percomorph fishes—the series Syngnatharia. This group is widely distributed in tropical and warm-temperate regions, with a great proportion of its extant diversity occurring in the Indo-Pacific. Because most syngnatharians feature long-range dispersal capabilities, tracing their biogeographic origins is challenging. Here, we applied an integrative phylogenomic approach to elucidate the evolutionary biogeography of syngnatharians. We built upon a recently published phylogenomic study that examined ultraconserved elements by adding 62 species (total 169 species) and one family (Draconettidae), to cover ca. 25% of the species diversity and all 10 families in the group. We inferred a set of time-calibrated trees and conducted ancestral range estimations. We also examined the sensitivity of these analyses to phylogenetic uncertainty (estimated from multiple genomic subsets), area delimitation, and biogeographic models that include or exclude the jump-dispersal parameter (j). Of the three factors examined, we found that the j parameter has the strongest effect in ancestral range estimates, followed by number of areas defined, and tree topology and divergence times. After accounting for these uncertainties, our results reveal that syngnatharians originated in the ancient Tethys Sea ca. 87 Ma (84–94 Ma; Late Cretaceous) and subsequently occupied the Indo-Pacific. Throughout syngnatharian history, multiple independent lineages colonized the eastern Pacific (6–8 times) and the Atlantic (6–14 times) from their center of origin, with most events taking place following an east-to-west route prior to the closure of the Tethys Seaway ca. 12–18 Ma. Ultimately, our study highlights the importance of accounting for different factors generating uncertainty in macroevolutionary and biogeographic inferences.

A Global Phylogenomic Study of the Thelypteridaceae

2021 ◽  
Vol 46 (4) ◽  
pp. 891-915
Author(s):  
Susan Fawcett ◽  
Alan R. Smith ◽  
Michael Sundue ◽  
J. Gordon Burleigh ◽  
Emily B. Sessa ◽  
...  
Keyword(s):  
Morphological Characters ◽  
Morphological Evidence ◽  
Phylogenetic Studies ◽  
The Family ◽  
Likelihood Analysis ◽  
Single Genus ◽  
The Subject ◽  
Recent Classification ◽  
Phylogenomic Study

Abstract— The generic classification of the Thelypteridaceae has been the subject of much controversy. Proposed taxonomic systems have varied from recognizing the approximately 1200 species in the family within the single genus Thelypteris, to systems favoring upwards of 30 genera. Insights on intrafamilial relationships, especially for neotropical taxa, have been gained from recent phylogenetic studies; however, in the most recent classification, 10 of 30 recognized genera are either non-monophyletic or untested. We sequenced 407 nuclear loci for 621 samples, representing all recognized genera and approximately half the known species diversity. These were analyzed using both maximum likelihood analysis of a concatenated matrix and multi-species coalescent methods. Our phylogenomic results, informed by recently published morphological evidence, provide the foundation for a generic classification which recircumscribed 14 genera and recognized seven new genera. The 37 monophyletic genera sampled demonstrate greater geographic coherence than previous taxonomic concepts suggested. Additionally, our results demonstrate that certain morphological characters, such as frond division, are evolutionarily labile and are thus inadequate for defining genera.

scholarly journals A phylogenomic study of DNA repair genes, proteins, and processes

1999 ◽  
Vol 435 (3) ◽  
pp. 171-213 ◽  
Author(s):  
Jonathan A Eisen ◽  
Philip C Hanawalt
Keyword(s):  
Dna Repair ◽  
Dna Repair Genes ◽  
Repair Genes ◽  
Phylogenomic Study

scholarly journals Gene markers for exon capture and phylogenomics in ray-finned fishes

2017 ◽  
Author(s):  
Jiamei Jiang ◽  
Hao Yuan ◽  
Xin Zheng ◽  
Qian Wang ◽  
Ting Kuang ◽  
...  
Keyword(s):  
Target Gene ◽  
Single Copy ◽  
A Posteriori ◽  
Protein Coding ◽  
Gene Markers ◽  
Taxonomic Level ◽  
Exon Capture ◽  
Phylogenomic Study ◽  
Generation Sequencing ◽  
Selection Of

AbstractGene capture coupled with the next generation sequencing has become one of the favorable methods in subsampling genomes for phylogenomic studies. Many target gene markers have been developed in plants, sharks, frogs, reptiles and others, but few have been reported in the ray-finned fishes. Here, we identified a suite of “single-copy” protein coding sequence (CDS) markers through comparing eight fish genomes, and tested them empirically in 83 species (33 families and 11 orders) of ray-finned fishes. Sorting through the markers according to their completeness and phylogenetic decisiveness in taxa tested resulted in a selection of 4,434 markers, which were proven to be useful in reconstructing phylogenies of the ray-finned fishes at different taxonomic level. We also proposed a strategy of refining baits (probes) design a posteriori based on empirical data. The markers that we have developed may fill a gap in the tool kit of phylogenomic study in vertebrates.

scholarly journals The Opiliones Tree of Life: shedding light on harvestmen relationships through transcriptomics

2016 ◽  
Author(s):  
Rosa Fernándeza ◽  
Prashant Sharma ◽  
Ana L.M. Tourinho ◽  
Gonzalo Giribet
Keyword(s):  
Phylogenetic Analyses ◽  
Tree Of Life ◽  
Molecular Techniques ◽  
Evolutionary Patterns ◽  
Factors Affecting ◽  
Biogeographic Patterns ◽  
The Family ◽  
The Times ◽  
Phylogenomic Study ◽  
Data Matrices

AbstractOpiliones are iconic arachnids with a Paleozoic origin and a diversity that reflects ancient biogeographical patterns dating back at least to the times of Pangea. Due to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to systematics. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here we analyze a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing ca. 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families are precisely placed. Our dating analyses also using alternative calibration points, methods, and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as a general overview of the general biogeographic patterns of this ancient arthropod group.

scholarly journals New Insights on Lilium Phylogeny Based on a Comparative Phylogenomic Study Using Complete Plastome Sequences

Plants ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 547 ◽  
Author(s):  
Hyoung Tae Kim ◽  
Ki-Byung Lim ◽  
Jung Sung Kim
Keyword(s):  
Species Tree ◽  
Long Distance ◽  
Plant Groups ◽  
Lilium Species ◽  
Molecular Phylogenetic ◽  
Group A ◽  
Sectional Classification ◽  
Natural Characteristics ◽  
Phylogenomic Study

The genus Lilium L. is widely distributed in the cold and temperate regions of the Northern Hemisphere and is one of the most valuable plant groups in the world. Regarding the classification of the genus Lilium, Comber’s sectional classification, based on the natural characteristics, has been primarily used to recognize species and circumscribe the sections within the genus. Although molecular phylogenetic approaches have been attempted using different markers to elucidate their phylogenetic relationships, there still are unresolved clades within the genus. In this study, we constructed the species tree for the genus using 28 Lilium species plastomes, including three currently determined species (L. candidum, L. formosanum, and L. leichtlinii var. maximowiczii). We also sought to verify Comber’s classification and to evaluate all loci for phylogenetic molecular markers. Based on the results, the genus was divided into two major lineages, group A and B, consisting of eastern Asia + Europe species and Hengduan Mountains + North America species, respectively. Sectional relationships revealed that the ancestor Martagon diverged from Sinomartagon species and that Pseudolirium and Leucolirion are polyphyletic. Out of all loci in that Lilium plastome, ycf1, trnF-ndhJ, and trnT-psbD regions are suggested as evaluated markers with high coincidence with the species tree. We also discussed the biogeographical diversification and long-distance dispersal event of the genus.

Plastid phylogenomic study of species within the genus Zea: rates and patterns of three classes of microstructural changes

2016 ◽  
Vol 63 (2) ◽  
pp. 311-323 ◽  
Author(s):  
Lauren M. Orton ◽  
Sean V. Burke ◽  
William P. Wysocki ◽  
Melvin R. Duvall
Keyword(s):  
Microstructural Changes ◽  
Phylogenomic Study

scholarly journals Four myriapod relatives – but who are sisters? No end to debates on relationships among the four major myriapod subgroups

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Nikolaus U. Szucsich ◽  
Daniela Bartel ◽  
Alexander Blanke ◽  
Alexander Böhm ◽  
Alexander Donath ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Morphological Characters ◽  
Morphological Evidence ◽  
Taxon Sampling ◽  
Transcriptome Data ◽  
Data Types ◽  
Data Set ◽  
Phylogenomic Study ◽  
Quartet Topology

Abstract Background Phylogenetic relationships among the myriapod subgroups Chilopoda, Diplopoda, Symphyla and Pauropoda are still not robustly resolved. The first phylogenomic study covering all subgroups resolved phylogenetic relationships congruently to morphological evidence but is in conflict with most previously published phylogenetic trees based on diverse molecular data. Outgroup choice and long-branch attraction effects were stated as possible explanations for these incongruencies. In this study, we addressed these issues by extending the myriapod and outgroup taxon sampling using transcriptome data. Results We generated new transcriptome data of 42 panarthropod species, including all four myriapod subgroups and additional outgroup taxa. Our taxon sampling was complemented by published transcriptome and genome data resulting in a supermatrix covering 59 species. We compiled two data sets, the first with a full coverage of genes per species (292 single-copy protein-coding genes), the second with a less stringent coverage (988 genes). We inferred phylogenetic relationships among myriapods using different data types, tree inference, and quartet computation approaches. Our results unambiguously support monophyletic Mandibulata and Myriapoda. Our analyses clearly showed that there is strong signal for a single unrooted topology, but a sensitivity of the position of the internal root on the choice of outgroups. However, we observe strong evidence for a clade Pauropoda+Symphyla, as well as for a clade Chilopoda+Diplopoda. Conclusions Our best quartet topology is incongruent with current morphological phylogenies which were supported in another phylogenomic study. AU tests and quartet mapping reject the quartet topology congruent to trees inferred with morphological characters. Moreover, quartet mapping shows that confounding signal present in the data set is sufficient to explain the weak signal for the quartet topology derived from morphological characters. Although outgroup choice affects results, our study could narrow possible trees to derivatives of a single quartet topology. For highly disputed relationships, we propose to apply a series of tests (AU and quartet mapping), since results of such tests allow to narrow down possible relationships and to rule out confounding signal.

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