gady-i-płazy: Evidence of common descent

Evidence: 59 • authority: 92

The Evolution of Molecular Clocks: Concepts, Calibrations, and Challenges.. Molecular clocks use the accumulation of genetic changes to estimate the timing of evolutionary and demographic events. Since their formulation in the 1960s, molecular clocks have evolved from relatively simple strict-rate assumptions into a diverse set of statistical frameworks that include strict, relaxed, local and time-dependent models. In this review, we examine the conceptual basis of molecular-clock inference and the biological, demographic and methodological factors that influence clock estimates. We distinguish mutation rates from substitution rates and discuss how molecular, genomic, life-history, environm…

Evidence: 54 • authority: 92

A timetree of Fungi dated with fossils and horizontal gene transfers.. Dating the tree of Fungi has been challenging due to a paucity of fossil calibrations and high taxonomic diversity of the group. Here we reconstructed and dated a comprehensive phylogeny comprising 110 fungal species, utilizing 225 phylogenetic markers and accounting for across-site compositional heterogeneity in amino acid sequences. To address uncertainties in fungal dating, we sampled chronograms from four relaxed molecular clock analyses, each integrating distinct sets of calibrations and relative time-order constraints. The first analysis used a core set of 27 calibrations alongside 17 relative constraints derived f…

Evidence: 54 • authority: 92

Phylogenetic reconciliation provides new insights into the evolutionary diversification of the glutamine synthetase gene family in seed plants.. Glutamine synthetase (GS) catalyzes the incorporation of ammonium into glutamate, a crucial reaction in nitrogen metabolism. Despite advances in plant genomics, the evolutionary relationships among GS isoforms in seed plants remain incompletely understood. In this study, we selected 155 GS genes from 45 phylogenetically well-characterized seed plant species. Our analyses consistently support the existence of three distinct evolutionary lineages of GS genes in seed plants: GS2 (chloroplastic), and GS1a and GS1b (cytosolic). Using a Bayesian molecula…

Evidence: 54 • authority: 72

Molecular paleontology refers to the recovery and analysis of DNA, proteins, carbohydrates, or lipids, and their diagenetic products from ancient human, animal, and plant remains. The field of molecular paleontology has yielded important insights into evolutionary events, species' diasporas, and the discovery and characterization of extinct species. In shallow time, advancements in the field of molecular paleontology have allowed scientists to pursue evolutionary questions on a genetic level rather than relying on phenotypic variation alone. By applying molecular analytical techniques to DNA in recent animal remains, one can quantify the level of relatedness between any two organisms for wh…

Evidence: 47 • authority: 92

Cretaceous Connections Among Camel Cricket Lineages in the Himalaya Revealed Through Fossil-Calibrated Mitogenomic Phylogenetics.. The nocturnal, flightless camel crickets (Rhaphidophoridae) have a global distribution and are believed to have originated prior to the breakup of Pangea. We investigated the phylogeny and the timing of the radiation of East Asian species with mitogenomic data. Initially we analyzed a large taxon dataset (n = 117) using available partial mitochondrial and nuclear DNA sequences to confirm the monophyly of subfamilies and current taxonomy. Our findings support the monophyly of each genus within the subfamily Aemodogryllinae, with a minor inconsistency between taxo…

Evidence: 47 • authority: 72

The chimpanzee–human last common ancestor (CHLCA) is the last common ancestor shared by the extant Homo (human) and Pan (chimpanzee and bonobo) genera of Hominini. Estimates of the divergence date vary widely from thirteen to five million years ago. In human genetic studies, the CHLCA is useful as an anchor point for calculating single-nucleotide polymorphism (SNP) rates in human populations where chimpanzees are used as an outgroup, that is, as the extant species most genetically similar to Homo sapiens. Despite extensive research, no direct fossil evidence of the CHLCA has been discovered. Fossil candidates like Sahelanthropus tchadensis, Orrorin tugenensis, and Ardipithecus ramidus have…

Evidence: 45 • authority: 88

Sub‐Paratethyan origin and Middle to Late Miocene principal diversification of the Lactucinae (Compositae: Cichorieae) inferred from molecular phylogenetics, divergence‐dating and biogeographic analysis. Abstract The Lactucinae or Lactuca alliance include approximately 200 species distributed across the Northern Hemisphere and Africa. They were not recognised as a separate lineage until the late 20th century and their circumscription is still not fully settled. The generic classification of no other group of the Cichorieae has faced as many controversies as the Lactuca alliance and competing taxonomies coexist. This paper provides the first molecular phylogeny of the subtribe on a global sc…

Evidence: 39 • authority: 80

Molecular clock for dating of divergence between animal phyla

Evidence: 39 • authority: 80

Taxon sampling effects in molecular clock dating: An example from the African Restionaceae

Evidence: 39 • authority: 72

Molecular phylogenetics () is the branch of phylogeny that analyzes genetic, hereditary molecular differences, predominantly in DNA sequences, to gain information on an organism's evolutionary relationships. From these analyses, it is possible to determine the processes by which diversity among species has been achieved. The result of a molecular phylogenetic analysis is expressed in a phylogenetic tree. Molecular phylogenetics is one aspect of molecular systematics, a broader term that also includes the use of molecular data in taxonomy and biogeography. Molecular phylogenetics and molecular evolution correlate. Molecular evolution is the process of selective changes (mutations) at a molec…

Evidence: 38 • authority: 92

A High-quality Reference Genome and Tissue Expression Atlas for the European Lobster (Homarus gammarus).. Homarid lobsters are notable for their remarkable immunity and longevity, with lifespans reaching up to 80 years in the wild. A reference genome is available for the American lobster (Homarus americanus), but not for the European lobster (H. gammarus), despite its ecological significance and importance to fisheries and aquaculture. Here, we present a high-quality genome assembly and annotation for the European lobster. The assembly spans 1.76 Gb, with a scaffold N50 of 1.82 Mb and a BUSCO completeness of 97.6% (96.8% single-copy, 0.8% duplicated). As observed in the American lobster, th…

Evidence: — • authority: 65