Discovery of sea urchin NGFFFamide receptor unites a bilaterian neuropeptide family

Neuropeptides are ancient regulators of physiology and behaviour, but reconstruction of neuropeptide evolution is often difficult owing to lack of sequence conservation. Here, we report that the receptor for the neuropeptide NGFFFamide in the sea urchin Strongylocentrotus purpuratus (phylum Echinodermata) is an orthologue of vertebrate neuropeptide-S (NPS) receptors and crustacean cardioactive peptide (CCAP) receptors. Importantly, this has facilitated reconstruction of the evolution of two bilaterian neuropeptide signalling systems. Genes encoding the precursor of a vasopressin/oxytocin-type neuropeptide and its receptor duplicated in a common ancestor of the Bilateria. One copy of the precursor retained ancestral features, as seen in highly conserved vasopressin/oxytocin–neurophysin-type precursors. The other copy diverged, but this took different courses in protostomes and deuterostomes. In protostomes, the occurrence of a disulfide bridge in neuropeptide product(s) of the precursor was retained, as in CCAP, but with loss of the neurophysin domain. In deuterostomes, we see the opposite scenario—the neuropeptides lost the disulfide bridge, and neurophysin was retained (as in the NGFFFamide precursor) but was subsequently lost in vertebrate NPS precursors. Thus, the sea urchin NGFFFamide precursor and receptor are ‘missing links’ in the evolutionary history of neuropeptides that control ecdysis in arthropods (CCAP) and regulate anxiety in humans (NPS).

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Urbilaterian origin and evolution of sNPF-type neuropeptide signalling

10.1101/712687 ◽

2019 ◽

Cited By ~ 1

Author(s):

Luis Alfonso Yañez-Guerra ◽

Xingxing Zhong ◽

Ismail Moghul ◽

Thomas Butts ◽

Cleidiane G. Zampronio ◽

...

Keyword(s):

Evolutionary History ◽

Molecular Phylogenetics ◽

Common Ancestor ◽

Sequence Data ◽

Experimental Studies ◽

Peptide Ligands ◽

Origin And Evolution ◽

History Of ◽

Type Receptor ◽

Signalling Systems

AbstractPhysiology and behaviour are controlled by neuropeptide signalling systems comprising peptide ligands and cognate receptors. Molecular phylogenetics combined with experimental identification of neuropeptide-receptor pairs has revealed that many neuropeptide signalling systems originated in the urbilaterian common ancestor of protostomes and deuterostomes. Neuropeptide-Y/neuropeptide-F (NPY/NPF)-type signalling is one such example, whereas NPY/NPF-related short-NPF (sNPF)-type signalling has hitherto only been identified in protostomes. Here we report the discovery of a neuropeptide (pQDRSKAMQAERTGQLRRLNPRF-NH2) that is the ligand for an sNPF-type receptor in a deuterostome, the starfish Asterias rubens (Phylum Echinodermata). Informed by phylogenetic analysis of sequence data, we conclude that the paralogous NPY/NPF-type and sNPF-type signalling systems originated in Urbilateria but NPY/NPF-type signalling was lost in echinoderms. Furthermore, we present evidence that sNPF-type peptides are orthologs of vertebrate prolactin-releasing peptides. Our findings demonstrate the importance of experimental studies on echinoderms for reconstructing the evolutionary history of neuropeptide signalling systems.

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Genome sequences reveal divergence times of malaria parasite lineages

Parasitology ◽

10.1017/s0031182010001575 ◽

2010 ◽

Vol 138 (13) ◽

pp. 1737-1749 ◽

Cited By ~ 34

Author(s):

JOANA C. SILVA ◽

AMY EGAN ◽

ROBERT FRIEDMAN ◽

JAMES B. MUNRO ◽

JANE M. CARLTON ◽

...

Keyword(s):

Evolutionary History ◽

Common Ancestor ◽

Orthologous Gene ◽

The Other ◽

Divergence Times ◽

Last Common Ancestor ◽

Genome Sequences ◽

Malaria Parasites ◽

Human Malaria ◽

History Of

SUMMARYObjectiveThe evolutionary history of human malaria parasites (genus Plasmodium) has long been a subject of speculation and controversy. The complete genome sequences of the two most widespread human malaria parasites, P. falciparum and P. vivax, and of the monkey parasite P. knowlesi are now available, together with the draft genomes of the chimpanzee parasite P. reichenowi, three rodent parasites, P. yoelii yoelli, P. berghei and P. chabaudi chabaudi, and one avian parasite, P. gallinaceum.MethodsWe present here an analysis of 45 orthologous gene sequences across the eight species that resolves the relationships of major Plasmodium lineages, and provides the first comprehensive dating of the age of those groups.ResultsOur analyses support the hypothesis that the last common ancestor of P. falciparum and the chimpanzee parasite P. reichenowi occurred around the time of the human-chimpanzee divergence. P. falciparum infections of African apes are most likely derived from humans and not the other way around. On the other hand, P. vivax, split from the monkey parasite P. knowlesi in the much more distant past, during the time that encompasses the separation of the Great Apes and Old World Monkeys.ConclusionThe results support an ancient association between malaria parasites and their primate hosts, including humans.

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Evolutionary history of dimethylsulfoniopropionate (DMSP) demethylation enzyme DmdA in marine bacteria

10.1101/766360 ◽

2019 ◽

Author(s):

Laura Hernández ◽

Alberto Vicens ◽

Luis Enrique Eguiarte ◽

Valeria Souza ◽

Valerie De Anda ◽

...

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Common Ancestor ◽

Functional Divergence ◽

Gene Families ◽

Recent Common Ancestor ◽

Common Ancestry ◽

Demethylation Pathway ◽

History Of ◽

New Gene

ABSTRACTDimethylsulfoniopropionate (DMSP), an osmolyte produced by oceanic phytoplankton, is predominantly degraded by bacteria belonging to the Roseobacter lineage and other marine Alphaproteobacteria via DMSP-dependent demethylase A protein (DmdA). To date, the evolutionary history of DmdA gene family is unclear. Some studies indicate a common ancestry between DmdA and GcvT gene families and a co-evolution between Roseobacter and the DMSP-producing-phytoplankton around 250 million years ago (Mya). In this work, we analyzed the evolution of DmdA under three possible evolutionary scenarios: 1) a recent common ancestor of DmdA and GcvT, 2) a coevolution between Roseobacter and the DMSP-producing-phytoplankton, and 3) pre-adapted enzymes to DMSP prior to Roseobacter origin. Our analyses indicate that DmdA is a new gene family originated from GcvT genes by duplication and functional divergence driven by positive selection before a coevolution between Roseobacter and phytoplankton. Our data suggest that Roseobacter acquired dmdA by horizontal gene transfer prior to exposition to an environment with higher DMSP. Here, we propose that the ancestor that carried the DMSP demethylation pathway genes evolved in the Archean, and was exposed to a higher concentration of DMSP in a sulfur rich atmosphere and anoxic ocean, compared to recent Roseobacter ecoparalogs (copies performing the same function under different conditions), which should be adapted to lower concentrations of DMSP.

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An early fossil remora (Echeneoidea) reveals the evolutionary assembly of the adhesion disc

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2013.1200 ◽

2013 ◽

Vol 280 (1766) ◽

pp. 20131200 ◽

Cited By ~ 15

Author(s):

Matt Friedman ◽

Zerina Johanson ◽

Richard C. Harrington ◽

Thomas J. Near ◽

Mark R. Graham

Keyword(s):

Evolutionary History ◽

Body Plan ◽

The Other ◽

Ontogenetic Changes ◽

Dorsal Fin ◽

Early Oligocene ◽

Stem Group ◽

History Of ◽

And Migration ◽

Fin Spines

The adhesion disc of living remoras (Echeneoidea: Echeneidae) represents one of the most remarkable structural innovations within fishes. Although homology between the spinous dorsal fin of generalized acanthomorph fishes and the remora adhesion disc is widely accepted, the sequence of evolutionary—rather than developmental—transformations leading from one to the other has remained unclear. Here, we show that the early remora † Opisthomyzon (Echeneoidea: †Opisthomyzonidae), from the early Oligocene (Rupelian) of Switzerland, is a stem-group echeneid and provides unique insights into the evolutionary assembly of the unusual body plan characteristic of all living remoras. The adhesion disc of † Opisthomyzon retains ancestral features found in the spiny dorsal fins of remora outgroups, and corroborates developmental interpretations of the homology of individual skeletal components of the disc. † Opisthomyzon indicates that the adhesion disc originated in a postcranial position, and that other specializations (including the origin of pectination, subdivision of median fin spines into paired lamellae, increase in segment count and migration to a supracranial position) took place later in the evolutionary history of remoras. This phylogenetic sequence of transformation finds some parallels in the order of ontogenetic changes to the disc documented for living remoras.

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The shared evolutionary history of kinship classifications and language

Behavioral and Brain Sciences ◽

10.1017/s0140525x10001421 ◽

2010 ◽

Vol 33 (5) ◽

pp. 402-403 ◽

Cited By ~ 3

Author(s):

Robert M. Seyfarth ◽

Dorothy L. Cheney

Keyword(s):

Human Evolution ◽

Evolutionary History ◽

The Other ◽

History Of ◽

System Maps

AbstractAmong monkeys and apes, both the recognition and classification of individuals and the recognition and classification of vocalizations constitute discrete combinatorial systems. One system maps onto the other, suggesting that during human evolution kinship classifications and language shared a common cognitive precursor.

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Systematics of Senecio section Crociseris (Compositae, Senecioneae)

Phytotaxa ◽

10.11646/phytotaxa.211.1.1 ◽

2015 ◽

Vol 211 (1) ◽

pp. 1 ◽

Cited By ~ 4

Author(s):

JOEL CALVO ◽

INÉS ÁLVAREZ ◽

CARLOS AEDO

Keyword(s):

Central Asia ◽

Evolutionary History ◽

Morphological Characters ◽

The Other ◽

Distribution Maps ◽

History Of ◽

Perennial Herbs ◽

First Time ◽

Northwestern Africa ◽

Shape And Size

The complexity of the evolutionary history of Senecio is reflected in its conflicted taxonomy. Within this genus, Senecio section Crociseris (Compositae, Senecioneae), a group of perennial herbs distributed in Europe, western and Central Asia, and northwestern Africa, was not fully revised. A worldwide revision of this section recognizing 28 species and eight subspecies is presented here. The main morphological characters revealed as useful for distinguishing between species are the number and shape of supplementary and involucral bracts, synflorescence architecture, indumentum, and the shape and size of leaves and achenes. In this new taxonomic treatment S. provincialis and S. lagascanus have been segregated from S. doronicum, within which three subspecies are recognized (S. doronicum subsp. orientalis is validly published herein). On the other hand, S. ruthenensis from France and S. lusitanicus from Portugal have been synonymized to S. lagascanus, as well as S. ovatifolius, S. pisidicus, and S. tmoleus from Anatolia to S. kolenatianus, S. olympicus, and S. castagneanus respectively, S. bertramii from Lebanon to S. cilicius, and S. delbesianus from Syria to S. racemosus subsp. racemosus. Sixty eight names are lectotypified, the names S. barrelieri, S. pyrenaicus, and S. scopolii are neotypified, and one epitype is designated for the name S. perralderianus. Descriptions and distribution maps are provided for all the species included, as well as an identification key. Nine species are illustrated for the first time.

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Deep Ancestry of Orthologs and a Theoretical, Gradualist Perspective for the Formation of the LUCA’s (Last Universal Common Ancestor) Genome

10.20944/preprints201808.0330.v1 ◽

2018 ◽

Author(s):

Francisco Prosdocimi ◽

Sávio Torres de Farias

Keyword(s):

Evolutionary History ◽

Common Ancestor ◽

Deep Understanding ◽

Sister Group ◽

Recent Common Ancestor ◽

Evolutionary Relationships ◽

Universal Common Ancestor ◽

History Of ◽

Group Relationships ◽

Level Of Understanding

Genes and gene trees have been extensively used to study the evolutionary relationships among populations, species, families and higher systematic clades of organisms. This brought modern Biology into a sophisticated level of understanding about the evolutionary relationships and diversification patterns that happened along the entire history of organismal evolution in Earth. Genes however have not been placed in the center of questions when one aims to unravel the evolutionary history of genes themselves. Thus, we still ignore whether Insulin share a more recent common ancestor to Hexokinase or DNA polymerase. This brought modern Genetics into a very poor level of understanding about sister group relationships that happened along the entire evolutionary history of genes. Many conceptual challenges must be overcome to allow this broader comprehension about gene evolution. Here we aim to clear the intellectual path in order to provide a fertile research program that will help geneticists to understand the deep ancestry and sister group relationships among different gene families (or orthologs). We aim to propose methods to study gene formation starting from the establishment of the genetic code in pre-cellular organisms like the FUCA (First Universal Common Ancestor) until the formation of the highly complex genome of LUCA (Last UCA), that harbors hundreds of genes families working coordinated into a cellular organism. The deep understanding of ancestral relationships among orthologs will certainly inspire biotechnological and biomedical approaches and allow a deep understanding about how Darwinian molecular evolution operates inside cells and before the appearance of cellular organisms.

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Cereulide synthetase acquisition and loss events within the evolutionary history of Group III Bacillus cereus sensu lato facilitate the transition between emetic and diarrheal foodborne pathogen

10.1101/2020.05.12.090951 ◽

2020 ◽

Cited By ~ 1

Author(s):

Laura M. Carroll ◽

Martin Wiedmann

Keyword(s):

Bacillus Cereus ◽

Evolutionary History ◽

Common Ancestor ◽

Reference Genome ◽

Foodborne Pathogen ◽

Genomic Diversity ◽

Whole Genome ◽

Group Iii ◽

History Of ◽

Bacillus Cereus Sensu Lato

AbstractCereulide-producing members of Bacillus cereus sensu lato (B. cereus s.l.) Group III, also known as “emetic B. cereus”, possess cereulide synthetase, a plasmid-encoded, non-ribosomal peptide synthetase encoded by the ces gene cluster. Despite the documented risks that cereulide-producing strains pose to public health, the level of genomic diversity encompassed by “emetic B. cereus” has never been evaluated at a whole-genome scale. Here, we employ a phylogenomic approach to characterize Group III B. cereus s.l. genomes which possess ces (ces-positive) alongside their closely related ces-negative counterparts to (i) assess the genomic diversity encompassed by “emetic B. cereus”, and (ii) identify potential ces loss and/or gain events within the evolutionary history of the high-risk and medically relevant sequence type (ST) 26 lineage often associated with emetic foodborne illness. Using all publicly available ces-positive Group III B. cereus s.l. genomes and the ces-negative genomes interspersed among them (n = 150), we show that “emetic B. cereus” is not clonal; rather, multiple lineages within Group III harbor cereulide-producing strains, all of which share a common ancestor incapable of producing cereulide (posterior probability [PP] 0.86-0.89). The ST 26 common ancestor was predicted to have emerged as ces-negative (PP 0.60-0.93) circa 1904 (95% highest posterior density [HPD] interval 1837.1-1957.8) and first acquired the ability to produce cereulide before 1931 (95% HPD 1893.2-1959.0). Three subsequent ces loss events within ST 26 were observed, including among isolates responsible for B. cereus s.l. toxicoinfection (i.e., “diarrheal” illness).Importance“B. cereus” is responsible for thousands of cases of foodborne disease each year worldwide, causing two distinct forms of illness: (i) intoxication via cereulide (i.e., “emetic” syndrome) or (ii) toxicoinfection via multiple enterotoxins (i.e., “diarrheal” syndrome). Here, we show that “emetic B. cereus” is not a clonal, homogenous unit that resulted from a single cereulide synthetase gain event followed by subsequent proliferation; rather, cereulide synthetase acquisition and loss is a dynamic, ongoing process that occurs across lineages, allowing some Group III B. cereus s.l. populations to oscillate between diarrheal and emetic foodborne pathogen over the course of their evolutionary histories. We also highlight the care that must be taken when selecting a reference genome for whole-genome sequencing-based investigation of emetic B. cereus s.l. outbreaks, as some reference genome selections can lead to a confounding loss of resolution and potentially hinder epidemiological investigations.

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The evolutionary history of human spindle genes includes back-and-forth gene flow with Neandertals

10.1101/2021.11.29.470407 ◽

2021 ◽

Author(s):

Stéphane Peyrégne ◽

Janet Kelso ◽

Benjamin Marco Peter ◽

Svante Pääbo

Keyword(s):

Gene Flow ◽

Evolutionary History ◽

Common Ancestor ◽

Modern Human ◽

Modern Humans ◽

Ancestral Gene ◽

Cytoskeletal Structure ◽

Spindle Apparatus ◽

History Of ◽

Segregation Of Chromosomes

Proteins associated with the spindle apparatus, a cytoskeletal structure that ensures the proper segregation of chromosomes during cell division, experienced an unusual number of amino acid substitutions in modern humans after the split from the ancestors of Neandertals and Denisovans. Here, we analyze the history of these substitutions and show that some of the genes in which they occur may have been targets of positive selection. We also find that the two changes in the kinetochore scaffold 1 (KNL1) protein, previously believed to be specific to modern humans, were present in some Neandertals. We show that the KNL1 gene of these Neandertals shared a common ancestor with present-day Africans about 200,000 years ago due to gene flow from the ancestors (or relatives) of modern humans into Neandertals. Subsequently, some non-Africans inherited this modern human-like gene variant from Neandertals, but none inherited the ancestral gene variants. These results add to the growing evidence of early contacts between modern humans and archaic groups in Eurasia and illustrate the intricate relationships among these groups.

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Genomic analysis finds no evidence of canonical eukaryotic DNA processing complexes in a free-living protist

Nature Communications ◽

10.1038/s41467-021-26077-2 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Dayana E. Salas-Leiva ◽

Eelco C. Tromer ◽

Bruce A. Curtis ◽

Jon Jerlström-Hultqvist ◽

Martin Kolisko ◽

...

Keyword(s):

Evolutionary History ◽

Origin Recognition Complex ◽

Common Ancestor ◽

Genomic Analysis ◽

Free Living ◽

A Genome ◽

History Of ◽

Eukaryotic Dna ◽

Comparative Genomics Analysis ◽

Dna Processing

AbstractCells replicate and segregate their DNA with precision. Previous studies showed that these regulated cell-cycle processes were present in the last eukaryotic common ancestor and that their core molecular parts are conserved across eukaryotes. However, some metamonad parasites have secondarily lost components of the DNA processing and segregation apparatuses. To clarify the evolutionary history of these systems in these unusual eukaryotes, we generated a genome assembly for the free-living metamonad Carpediemonas membranifera and carried out a comparative genomics analysis. Here, we show that parasitic and free-living metamonads harbor an incomplete set of proteins for processing and segregating DNA. Unexpectedly, Carpediemonas species are further streamlined, lacking the origin recognition complex, Cdc6 and most structural kinetochore subunits. Carpediemonas species are thus the first known eukaryotes that appear to lack this suite of conserved complexes, suggesting that they likely rely on yet-to-be-discovered or alternative mechanisms to carry out these fundamental processes.

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