scholarly journals Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)

IMA Fungus ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Claudio G. Ametrano ◽  
Felix Grewe ◽  
Pedro W. Crous ◽  
Stephen B. Goodwin ◽  
Chen Liang ◽  
...  
Keyword(s):  
Character State ◽  
Ancestral Character State ◽  
Wide Range ◽  
Tree Inference ◽  
Ancestral Character State Reconstruction ◽  
Inference Methods ◽  
Genome Scale ◽  
The Impact ◽  
Rock Inhabiting Fungi ◽  
Scale Data

Abstract Dothideomycetes is the most diverse fungal class in Ascomycota and includes species with a wide range of lifestyles. Previous multilocus studies have investigated the taxonomic and evolutionary relationships of these taxa but often failed to resolve early diverging nodes and frequently generated inconsistent placements of some clades. Here, we use a phylogenomic approach to resolve relationships in Dothideomycetes, focusing on two genera of melanized, extremotolerant rock-inhabiting fungi, Lichenothelia and Saxomyces, that have been suggested to be early diverging lineages. We assembled phylogenomic datasets from newly sequenced (4) and previously available genomes (238) of 242 taxa. We explored the influence of tree inference methods, supermatrix vs. coalescent-based species tree, and the impact of varying amounts of genomic data. Overall, our phylogenetic reconstructions provide consistent and well-supported topologies for Dothideomycetes, recovering Lichenothelia and Saxomyces among the earliest diverging lineages in the class. In addition, many of the major lineages within Dothideomycetes are recovered as monophyletic, and the phylogenomic approach implemented strongly supports their relationships. Ancestral character state reconstruction suggest that the rock-inhabiting lifestyle is ancestral within the class.

Convergence to the tiniest detail: vocal sac structure in torrent-dwelling frogs

2019 ◽  
Author(s):  
Agustín J Elias-Costa ◽  
Julián Faivovich
Keyword(s):  
Background Noise ◽  
Evolutionary History ◽  
Visual Display ◽  
Character State ◽  
Visual Displays ◽  
State Reconstruction ◽  
Ancestral Character State ◽  
History Of ◽  
Ancestral Character State Reconstruction ◽  
Detection And Recognition

Abstract Cascades and fast-flowing streams impose severe restrictions on acoustic communication, with loud broadband background noise hampering signal detection and recognition. In this context, diverse behavioural features, such as ultrasound production and visual displays, have arisen in the evolutionary history of torrent-dwelling amphibians. The importance of the vocal sac in multimodal communication is being increasingly recognized, and recently a new vocal sac visual display has been discovered: unilateral inflation of paired vocal sacs. In the diurnal stream-breeding Hylodidae from the Atlantic forest, where it was first described, this behaviour is likely to be enabled by a unique anatomical configuration of the vocal sacs. To assess whether other taxa share this exceptional structure, we surveyed torrent-dwelling species with paired vocal sacs across the anuran tree of life and examined the vocal sac anatomy of exemplar species across 18 families. We found striking anatomical convergence among hylodids and species of the distantly related basal ranid genera Staurois, Huia, Meristogenys and Amolops. Ancestral character state reconstruction identified three new synapomorphies for Ranidae. Furthermore, we surveyed the vocal sac configuration of other anuran species that perform visual displays and report observations on what appears to be unilateral inflation of paired vocal sacs, in Staurois guttatus – an extremely rare behaviour in anurans.

scholarly journals Bipedalism in Mexican Albian lizard (Squamata) and the locomotion type in other Cretaceous lizards

2021 ◽  
Author(s):  
Damián Villaseñor-Amador ◽  
José Alberto Cruz ◽  
Nut Xanat Suárez
Keyword(s):  
North America ◽  
Lower Cretaceous ◽  
Evolutionary History ◽  
Quantitative Methods ◽  
Character State ◽  
State Reconstruction ◽  
Ancestral Character State ◽  
Extant Species ◽  
Ancestral Character State Reconstruction ◽  
Locomotion Type

Representative locomotion types in lizards include terrestrial, arboreal, grass swimmer, sand swimmer and bipedal. Few studies explain the locomotion habit of extinct lizards, and even less asses those of bipedal ones. Here, we use quantitative methods to infer the type of locomotion of two Albian Mexican lizards (Lower Cretaceous) and three Cretaceous lizards from Brazil, North America and Spain, assessing the similarities of the hindlimb-forelimb length ratio amongst extinct and extant species. Additionally, an ancestral character state reconstruction analysis was performed, to evaluate the evolution of lizard locomotion habits. The species Huehuecuetzpalli mixtecus was bipedal while Tijubina pontei was facultative bipedal, Hoyalacerta sanzi, Tepexisaurus tepexii and Polyglyphanodon sternbergi cannot be differentiated amongst terrestrial or arboreal with the approach used in this work. The ancestral character state reconstruction analysis showed a terrestrial ancestral locomotion type, with a basal character state of hindlimbs longer than forelimbs. Equal length between hind and forelimbs appear to be a derivate state that evolved multiple times in lizard evolutionary history.

Mucron morphology in male entomopathogenic nematodes of the Steinernematidae (Nematoda)

Nematology ◽  
2018 ◽  
Vol 20 (8) ◽  
pp. 769-779
Author(s):  
Zdeněk Mráček ◽  
Jiří Nermuť ◽  
Vladimír Půža
Keyword(s):  
Entomopathogenic Nematodes ◽  
Second Generation ◽  
Published Data ◽  
Character State ◽  
Taxonomic Significance ◽  
Phylogenetic Groups ◽  
State Reconstruction ◽  
Ancestral Character State ◽  
Variable Shape ◽  
Ancestral Character State Reconstruction

Summary The mucron in male steinernematid nematodes may be missing or present either in the first or second generation, or missing in both generations, with variable shape. However, for many species, the information on mucron morphology is incomplete and its taxonomic significance and distribution remain unclear. The present study assessed mucron morphology in males of 26 species using LM and SEM microscopy. For other species we summarised the published data. Furthermore, ancestral character state reconstruction analysis was performed to assess the distribution of mucron morphology within steinernematid phylogeny. In most species, papilla/spine-like or filamentous mucrons occur at least in the second generation. The species gathered in single phylogenetic groups have a similar mucron morphology. Generally, species with a prominent filamentous mucron belong to the ‘kraussei/feltiae’ and ‘carpocapsae’ groups, whereas mostly non-mucronated species occur in ‘glaseri’ and ‘riobrave’ groups. For future descriptions a precise mucron characterisation in both generations of the male is recommended.

Phylogenetic inference and trait evolution of the psychedelic mushroom genus Psilocybe sensu lato (Agaricales)

Botany ◽  
2013 ◽  
Vol 91 (9) ◽  
pp. 573-591 ◽  
Author(s):  
Virginia Ramírez-Cruz ◽  
Gastón Guzmán ◽  
Alma Rosa Villalobos-Arámbula ◽  
Aarón Rodríguez ◽  
P. Brandon Matheny ◽  
...  
Keyword(s):  
Phylogenetic Inference ◽  
Sensu Stricto ◽  
Spore Wall ◽  
Character State ◽  
Multigene Phylogeny ◽  
Frontal View ◽  
Nuclear Markers ◽  
Ancestral Character State ◽  
5.8S Rrna ◽  
Ancestral Character State Reconstruction

The genus Psilocybe contains iconic species of fungi renowned for their hallucinogenic properties. Recently, Psilocybe also included non-hallucinogenic species that have since been shifted to the genus Deconica. Here, we reconstruct a multigene phylogeny for Psilocybe, Deconica, and other exemplars of the families Hymenogastraceae and Strophariaceae sensu stricto (s. str.), using three nuclear markers (nLSU-rRNA, 5.8S rRNA, and rpb1). Our results confirm the monophyly of Deconica within Strophariaceae s. str., as well as numerous robust infrageneric relationships. Psilocybe is also recovered as a monophyletic group in the Hymenogastraceae, in which two principal lineages are recognized, including several nested subgroups. Most sections of Psilocybe following classifications based on morphological features are not supported in these analyses. Ancestral character state reconstruction analyses suggest that basidiospore shape in frontal view and spore wall thickness, commonly used to characterize sections in Deconica and Psilocybe, are homoplastic. Chrysocystidia, sterile cells located in the hymenium, evolved on at least two occasions in the Strophariaceae s. str., including in a novel lineage of Deconica.

scholarly journals Disentangling biological and analytical factors that give rise to outlier genes in phylogenomic matrices

2020 ◽  
Author(s):  
Joseph F. Walker ◽  
Xing-Xing Shen ◽  
Antonis Rokas ◽  
Stephen A. Smith ◽  
Edwige Moyroud
Keyword(s):  
Large Scale ◽  
Simulated Data ◽  
Tree Of Life ◽  
Rate Of Molecular Evolution ◽  
History Of ◽  
Patterns And Processes ◽  
Genome Scale ◽  
The Impact ◽  
Alignment Length ◽  
Scale Data

AbstractThe genomic data revolution has enabled biologists to develop innovative ways to infer key episodes in the history of life. Whether genome-scale data will eventually resolve all branches of the Tree of Life remains uncertain. However, through novel means of interrogating data, some explanations for why evolutionary relationships remain recalcitrant are emerging. Here, we provide four biological and analytical factors that explain why certain genes may exhibit “outlier” behavior, namely, rate of molecular evolution, alignment length, misidentified orthology, and errors in modeling. Using empirical and simulated data we show how excluding genes based on their likelihood or inferring processes from the topology they support in a supermatrix can mislead biological inference of conflict. We next show alignment length accounts for the high influence of two genes reported in empirical datasets. Finally, we also reiterate the impact misidentified orthology and short alignments have on likelihoods in large scale phylogenetics. We suggest that researchers should systematically investigate and describe the source of influential genes, as opposed to discarding them as outliers. Disentangling whether analytical or biological factors are the source of outliers will help uncover new patterns and processes that are shaping the Tree of Life.

scholarly journals Genome Warehouse: A Public Repository Housing Genome-scale Data

2021 ◽  
Author(s):  
Meili Chen ◽  
Yingke Ma ◽  
Song Wu ◽  
Xinchang Zheng ◽  
Hongen Kang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Public Repository ◽  
Genome Sequences ◽  
Link Type ◽  
Genome Data ◽  
Research Activities ◽  
Wide Range ◽  
Genome Assemblies ◽  
Genome Scale ◽  
Scale Data

AbstractThe Genome Warehouse (GWH) is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission, storage, release, and sharing. As one of the core resources in the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB, https://bigd.big.ac.cn/), GWH accepts both full genome and partial genome (chloroplast, mitochondrion, and plasmid) sequences with different assembly levels, as well as an update of existing genome assemblies. For each assembly, GWH collects detailed genome-related metadata including biological project and sample, and genome assembly information, in addition to genome sequence and annotation. To archive high-quality genome sequences and annotations, GWH is equipped with a uniform and standardized procedure for quality control. Besides basic browse and search functionalities, all released genome sequences and annotations can be visualized with JBrowse. By December 2020, GWH has received 17,264 direct submissions covering a diversity of 949 species, and has released 3370 of them. Collectively, GWH serves as an important resource for genome-scale data management and provides free and publicly accessible data to support research activities throughout the world. GWH is publicly accessible at https://bigd.big.ac.cn/gwh/.

Sign in / Sign up

Export Citation Format

Share Document