Dataset Information

Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone.

ABSTRACT: Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incomplete lineage sorting. The positions of Eulipotyphla and Chiroptera as the first and second earliest divergences were consistent across the approaches. However, the phylogenetic relationships of Perissodactyla, Cetartiodactyla, and Ferae, were contradictory. While retrotransposon insertion analyses suggest a clade with Cetartiodactyla and Ferae, the exon dataset favoured Cetartiodactyla and Perissodactyla. Future analyses of hitherto unsampled laurasiatherian lineages and synergistic analyses of retrotransposon insertions, exon and conserved intron/intergenic sequences might unravel the conflicting patterns of relationships in this major mammalian clade.

SUBMITTER: Doronina L

PROVIDER: S-EPMC9141728 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

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Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone.

Doronina Liliya L Hughes Graham M GM Moreno-Santillan Diana D Lawless Colleen C Lonergan Tadhg T Ryan Louise L Jebb David D Kirilenko Bogdan M BM Korstian Jennifer M JM Dávalos Liliana M LM Vernes Sonja C SC Myers Eugene W EW Teeling Emma C EC Hiller Michael M Jermiin Lars S LS Schmitz Jürgen J Springer Mark S MS Ray David A DA

Genes 20220426 5

Relationships among laurasiatherian clades represent one of the most highly disputed topics in mammalian phylogeny. In this study, we attempt to disentangle laurasiatherian interordinal relationships using two independent genome-level approaches: (1) quantifying retrotransposon presence/absence patterns, and (2) comparisons of exon datasets at the levels of nucleotides and amino acids. The two approaches revealed contradictory phylogenetic signals, possibly due to a high level of ancestral incom ...[more]

PMID: 35627151

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Project description:Motivation. Anomaly EEG detection is a long-standing problem in analysis of EEG signals. The basic premise of this problem is consideration of the similarity between two nonstationary EEG recordings. A well-established scheme is based on sequence matching, typically including three steps: feature extraction, similarity measure, and decision-making. Current approaches mainly focus on EEG feature extraction and decision-making, and few of them involve the similarity measure/quantification. Generally, to design an appropriate similarity metric, that is compatible with the considered problem/data, is also an important issue in the design of such detection systems. It is however impossible to directly apply those existing metrics to anomaly EEG detection without any consideration of domain specificity. Methodology. The main objective of this work is to investigate the impacts of different similarity metrics on anomaly EEG detection. A few metrics that are potentially available for the EEG analysis have been collected from other areas by a careful review of related works. The so-called power spectrum is extracted as features of EEG signals, and a null hypothesis testing is employed to make the final decision. Two indicators have been used to evaluate the detection performance. One is to reflect the level of measured similarity between two compared EEG signals, and the other is to quantify the detection accuracy. Results. Experiments were conducted on two data sets, respectively. The results demonstrate the positive impacts of different similarity metrics on anomaly EEG detection. The Hellinger distance (HD) and Bhattacharyya distance (BD) metrics show excellent performances: an accuracy of 0.9167 for our data set and an accuracy of 0.9667 for the Bern-Barcelona EEG data set. Both of HD and BD metrics are constructed based on the Bhattacharyya coefficient, implying the priority of the Bhattacharyya coefficient when dealing with the highly noisy EEG signals. In future work, we will exploit an integrated metric that combines HD and BD for the similarity measure of EEG signals.

Project description:Background and aimsGymnosperms are either wind-pollinated (anemophilous) or both wind- and insect-pollinated (ambophilous). Regardless of pollination mode, ovular secretions play a key role in pollen capture, germination and growth; they are likely also involved in pollinator reward. Little is known about the broad-scale diversity of ovular secretions across gymnosperms, and how these may relate to various reproductive functions. This study analyses the sugar and amino acid profiles of ovular secretions across a range of ambophilous (cycads and Gnetales) and anemophilous gymnosperms (conifers) to place them in an evolutionary context of their possible functions during reproduction.MethodsOvular secretions from 13 species representing all five main lineages of extant gymnosperms were sampled. High-performance liquid chromatography techniques were used to measure sugar and amino acid content. Multivariate statistics were applied to assess whether there are significant differences in the chemical profiles of anemophilous and ambophilous species. Data were compared with published chemical profiles of angiosperm nectar. Chemical profiles were placed in the context of phylogenetic relationships.Key resultsTotal sugar concentrations were significantly higher in ovular secretions of ambophilous species than wind-pollinated taxa such as Pinaceae and Cupressophyta. Ambophilous species had lower amounts of total amino acids, and a higher proportion of non-protein amino acids compared with anemophilous lineages, and were also comparable to angiosperm nectar. Results suggest that early gymnosperms likely had ovular secretion profiles that were a mosaic of those associated with modern anemophilous and ambophilous species. Ginkgo, thought to be anemophilous, had a profile typical of ambophilous taxa, suggesting that insect pollination either exists in Gingko, but is undocumented, or that its ancestral populations were insect-pollinated.ConclusionsChemical profiles of ovular secretions of ambophilous gymnosperms show a clear signal of pollinator-driven selection, including higher levels of carbohydrates than anemophilous taxa, lower levels of amino acids, and the presence of specific amino acids, such as β-alanine, that are known to influence insect feeding behaviour and physiology.

Dataset Information

Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone.

Publications

Contradictory Phylogenetic Signals in the Laurasiatheria Anomaly Zone.

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