Constraints on the timescale of animal evolutionary history

Benton, Michael J.; Donoghue, Philip C. J.; Asher, Robert J.; Friedman, Matt; Near, Thomas J.; Vinther, Jakob

doi:10.26879/424

Cited by 200 publications

(343 citation statements)

References 639 publications

(922 reference statements)

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“…Based on the mean estimate from the 95 genes using a strict molecular clock with a 450-Mya root age (the divergence between Latimeria and Protopterus; ref. 59), the prior for the overall substitution rate (rgene gamma) was set at G (1, 11.96, 1). The prior for the rate-drift parameter (sigma2 gamma) was set at G (1, 4.5, 1).…”

Section: Methodsmentioning

confidence: 99%

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

Feng

Blackburn

Liang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

318

362

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Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous-Paleogene (K-Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K-Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation. amphibia | Anura | nuclear genes | phylogeny | divergence time

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Section: Methodsmentioning

confidence: 99%

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

Feng

Blackburn

Liang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

318

362

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“…The maximumlikelihood tree obtained using the 11 lophotrochozoan species was used to provide a reference tree topology, and the WAG + Γ protein substitution model was employed on each site. The tree was calibrated with the following time frames to constrain the age of the nodes between the species: minimum = 305.5 Ma and soft maximum = 581 Ma, for C. teleta and H. robusta 44 ; minimum = 168.6 Ma and soft 44 ; minimum = 532 Ma and soft maximum = 549 Ma, for the first appearance of mollusks 45 ; and minimum = 550.25 Ma and soft maximum = 636.1 Ma, for the first appearance of Lophotrochozoa 45 .…”

Section: Phylogenomics Protein Sequences Of the Nine Published Or Pumentioning

confidence: 99%

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

et al. 2017

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Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialized macro benthos such as mussels. But the lack of genome information hinders the understanding of the adaptation of these animals to such inhospitable environments. Here we report the genomes of a deep-sea vent/seep mussel (Bathymodiolus platifrons) and a shallow-water mussel (Modiolus philippinarum). Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilizing protein structures and removing toxic substances from cells, are highly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The innate immune system of B. platifrons is considerably more complex than that of other lophotrochozoan species, including M. philippinarum, with substantial expansion and high expression levels of gene families that are related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons shows methanotrophy, assimilatory sulfate reduction and ammonia metabolic pathways in the symbionts, providing energy and nutrients, which allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.

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“…THB is sandwiched between the active-site cap and lower lip of the enzyme and is adjacent to the pore through which acceptors must pass to enter the active site. The sequences of SULT1A3 and SULT1A1 differ by 21 amino acids, 11 of which are clustered into two spatially separate, functionally related regions-the allosteric and active sites-that have coevolved since the evolutionary inception of SULT1A3, ∼60 Mya (50).…”

Section: Resultsmentioning

confidence: 99%

Tetrahydrobiopterin regulates monoamine neurotransmitter sulfonation

Cook

Wang

Leyh

2017

Proc. Natl. Acad. Sci. U.S.A.

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Monoamine neurotransmitters are among the hundreds of signaling small molecules whose target interactions are switched "on" and "off" via transfer of the sulfuryl-moiety (-SO 3 ) from PAPS (3′-phosphoadenosine 5′-phosphosulfate) to the hydroxyls and amines of their scaffolds. These transfer reactions are catalyzed by a small family of broad-specificity enzymes-the human cytosolic sulfotransferases (SULTs). The first structure of a SULT allosteric-binding site (that of SULT1A1) has recently come to light. The site is conserved among SULT1 family members and is promiscuous-it binds catechins, a naturally occurring family of flavanols. Here, the catechin-binding site of SULT1A3, which sulfonates monoamine neurotransmitters, is modeled on that of 1A1 and used to screen in silico for endogenous metabolite 1A3 allosteres. Screening predicted a single high-affinity allostere, tetrahydrobiopterin (THB), an essential cofactor in monoamine neurotransmitter biosynthesis. THB is shown to bind and inhibit SULT1A3 with high affinity, 23 (±2) nM, and to bind weakly, if at all, to the four other major SULTs found in brain and liver. The structure of the THB-bound binding site is determined and confirms that THB binds the catechin site. A structural comparison of SULT1A3 with SULT1A1 (its immediate evolutionary progenitor) reveals how SULT1A3 acquired high affinity for THB and that the majority of residue changes needed to transform 1A1 into 1A3 are clustered at the allosteric and active sites. Finally, sequence records reveal that the coevolution of these sites played an essential role in the evolution of simian neurotransmitter metabolism.sulfotransferase | tetrahydrobiopterin | neurotransmitter | allostery | evolution H uman cytosolic sulfotransferases (SULTs) regulate the activities of thousands of endogenous small-molecule metabolites and xenobiotics via transfer of the sulfuryl-moiety (-SO 3 ) to and from the hydroxyl-and amine-moieties of these acceptors. The 13 full-length SULT isoforms encoded in the human genome are expressed in tissue-and developmentally specific patterns (1-3). SULT substrate specificities are typically broad, overlapping, and centered on different areas of metabolism. The diversity of function across SULT isoforms results in a remarkably broad range of metabolic functions including potent regulation of steroids (4), thyroid (5) and peptide hormones (6), oxysterols (7), pheromones (8), selectins (9), and neurotransmitters (10, 11).Although recent work has deepened our understanding of SULT small-molecule allosteric regulation, the topic remains largely unexplored (12-16). The catechin-binding site is the most well-characterized SULT allosteric site (12). Catechins, a complex biomorphic family of SULT allosteric inhibitors, are found at high levels in tea leaves, cocoa, and coffee (17-19). The binding site is promiscuous in that it binds numerous catechins (15, 20) and related structures. The structure of the SULT1A1 catechin-binding site, the only published SULT allosteric-site structure, has recentl...

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Constraints on the timescale of animal evolutionary history

Cited by 200 publications

References 639 publications

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

Phylogenomics reveals rapid, simultaneous diversification of three major clades of Gondwanan frogs at the Cretaceous–Paleogene boundary

Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

Tetrahydrobiopterin regulates monoamine neurotransmitter sulfonation

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