Nuclear and mtDNA phylogenetic analyses clarify the evolutionary history of two species of native Hawaiian bats and the taxonomy of Lasiurini (Mammalia: Chiroptera)

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

Download Full-text

A test statistic to quantify treelikeness in phylogenetics

10.1101/2021.02.16.431544 ◽

2021 ◽

Author(s):

Caitlin Cherryh ◽

Bui Quang Minh ◽

Rob Lanfear

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Phylogenetic Network ◽

Parametric Bootstrap ◽

Lineage Sorting ◽

Test Statistic ◽

Sequence Alignments ◽

Wide Range ◽

History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

Download Full-text

Adaptive convergent evolution of genome proofreading in SARS-CoV2: insights into the Eigen’s paradox

10.1101/2021.09.11.459886 ◽

2021 ◽

Author(s):

Keerthic Aswin ◽

Srinivasan Ramachandran ◽

Vivek T Natarajan

Keyword(s):

Convergent Evolution ◽

Genome Stability ◽

Evolutionary History ◽

Rna Binding ◽

Phylogenetic Analyses ◽

Comparative Genome Analysis ◽

The Family ◽

History Of ◽

Key Residues

AbstractEvolutionary history of coronaviruses holds the key to understand mutational behavior and prepare for possible future outbreaks. By performing comparative genome analysis of nidovirales that contain the family of coronaviruses, we traced the origin of proofreading, surprisingly to the eukaryotic antiviral component ZNFX1. This common recent ancestor contributes two zinc finger (ZnF) motifs that are unique to viral exonuclease, segregating them from DNA proof-readers. Phylogenetic analyses indicate that following acquisition, genomes of coronaviruses retained and further fine-tuned proofreading exonuclease, whereas related families harbor substitution of key residues in ZnF1 motif concomitant to a reduction in their genome sizes. Structural modelling followed by simulation suggests the role of ZnF in RNA binding. Key ZnF residues strongly coevolve with replicase, and the helicase involved in duplex RNA unwinding. Hence, fidelity of replication in coronaviruses is a result of convergent evolution, that enables maintenance of genome stability akin to cellular proofreading systems.

Download Full-text

Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2018.2929 ◽

2019 ◽

Vol 286 (1897) ◽

pp. 20182929 ◽

Cited By ~ 2

Author(s):

Elena A. Ritschard ◽

Robert R. Fitak ◽

Oleg Simakov ◽

Sönke Johnsen

Keyword(s):

Signal Transduction ◽

Positive Selection ◽

G Protein ◽

Evolutionary History ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Genomic Signatures ◽

History Of ◽

G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

Download Full-text

Evolutionary relationships of the Sparidae (Teleostei: Percoidei): integrating fossil and Recent data

Transactions of the Royal Society of Edinburgh Earth Sciences ◽

10.1017/s0263593300000468 ◽

2002 ◽

Vol 93 (4) ◽

pp. 333-353 ◽

Cited By ~ 3

Author(s):

Julia J. Day

Keyword(s):

Evolutionary History ◽

Phylogenetic Analyses ◽

Successive Approximations ◽

Feeding Strategies ◽

New Genera ◽

Minimum Age ◽

Character Weighting ◽

History Of ◽

London Clay ◽

Fossil Data

ABSTRACTThe Eocene sparid fauna (Teleostei: Percoidei) from Monte Bolca, Italy and from the London Clay, U.K. is revised based on re-examination of the type material and phylogenetic analyses of primarily osteological data. Two phylogenetic analyses, one of the Eocene taxa and a combined analysis of fossil and extant taxa, were performed. The addition of fossils to the extant data greatly increased numbers of most parsimonious trees, destabilising and obscuring basal relationships within the Sparidae. Combination of the data from fossil and extant data also affected relationships among the fossil taxa, changing some from those recovered using fossil data alone and destabilising others. Successive approximations character weighting supported the inclusion of the Eocene taxa within a monophyletic Sparidae. The genus Sparnodus, as previously conceived, is paraphyletic and is partitioned to remove the paraphyly. Five monotypic genera are recognised, including three new genera, Abromasta, Ellaserrata and Pseudosparnodus. Inclusion of the fossils in the phylogenetic analysis implies a minimum age of origin for the Sparidae of 55 Ma with most Recent sparid fauna in place no later than the Miocene, and provides further evidence that the diversification of feeding strategies occurred early on in the evolutionary history of the group.

Download Full-text

Morphology, songs and genetics identify two new cicada species from Morocco: Tettigettalna afroamissa sp. nov. and Berberigetta dimelodica gen. nov. & sp. nov. (Hemiptera: Cicadettini)

Zootaxa ◽

10.11646/zootaxa.4237.3.4 ◽

2017 ◽

Vol 4237 (3) ◽

pp. 517

Author(s):

GONÇALO JOÃO COSTA ◽

VERA L. NUNES ◽

EDUARDO MARABUTO ◽

RAQUEL MENDES ◽

TELMA G. LAURENTINO ◽

...

Keyword(s):

Evolutionary History ◽

New Genus ◽

Acoustic Analysis ◽

Phylogenetic Analyses ◽

Habitat Preferences ◽

Dna Barcode ◽

Genetic Data ◽

North African ◽

History Of ◽

The Subject

Morocco has been the subject of very few expeditions on the last century with the objective of studying small cicadas. In the summer of 2014 an expedition was carried out to Morocco to update our knowledge with acoustic recordings and genetic data of these poorly known species. We describe here two new small-sized cicadas that could not be directly assigned to any species of North African cicadas: Tettigettalna afroamissa sp. nov. and Berberigetta dimelodica gen. nov. & sp. nov. In respect to T. afroamissa it is the first species of the genus to be found outside Europe and we frame this taxon within the evolutionary history of the genus. Acoustic analysis of this species allows us to confidently separate T. afroamissa from its congeners. With B. dimelodica, a small species showing a remarkable calling song characterized by an abrupt frequency modulation, a new genus had to be erected. Bayesian inference and maximum likelihood phylogenetic analyses with DNA-barcode sequences of Cytochrome C Oxidase 1 support the monophyly of both species, their distinctness and revealed genetic structure within B. dimelodica. Alongside the descriptions we also provide GPS coordinates of collection points, distributions and habitat preferences.

Download Full-text

Ancient DNA forces reconsideration of evolutionary history of Mediterranean pygmy elephantids

Biology Letters ◽

10.1098/rsbl.2006.0467 ◽

2006 ◽

Vol 2 (3) ◽

pp. 451-454 ◽

Cited By ~ 23

Author(s):

Nikos Poulakakis ◽

Aris Parmakelis ◽

Petros Lymberakis ◽

Moysis Mylonas ◽

Eleftherios Zouros ◽

...

Keyword(s):

Dna Sequence ◽

Ancient Dna ◽

Evolutionary History ◽

Eastern Mediterranean ◽

Multiple Displacement Amplification ◽

Phylogenetic Analyses ◽

Molecular Data ◽

Mediterranean Islands ◽

Amplification Method ◽

History Of

During the Pleistocene pygmy elephantids, some only a quarter of their ancestors' size, were present on Mediterranean islands until about 10 000 years ago (y.a.). Using a new methodology for ancient DNA (aDNA) studies, the whole genomic multiple displacement amplification method, we were able to retrieve cytochrome b (cyt b ) DNA fragments from 4200 to 800 000 y.a. specimens from island and mainland samples, including pygmy and normal-sized forms. The short DNA sequence (43 bp) retrieved from the 800 000 y.a. sample is one of the oldest DNA fragment ever retrieved. Duplication of the experiments in two laboratories, the occurrence of three diagnostic sites and the results of the phylogenetic analyses strongly support its authenticity. Our results challenge the prevailing view that pygmy elephantids of the eastern Mediterranean originated exclusively from Elephas , suggesting independent histories of dwarfism and the presence of both pygmy mammoths and elephant-like taxa on these islands. Based on our molecular data, the origin of the Tilos and Cyprus elephantids from a lineage within the genus Elephas is confirmed, while the DNA sequence from the Cretan sample falls clearly within the mammoth clade. Thus, the name Mammuthus creticus rather than Elephas creticus , seems to be justified for this form. Our findings also suggest a need to re-evaluate the evolutionary history of the Sicilian/Maltese species, traditionally included in the genus Elephas .

Download Full-text

Evolutionary history of phycoerythrin pigmentation in the water bloom-forming cyanobacteriumMicrocystis aeruginosa

10.1101/485508 ◽

2018 ◽

Cited By ~ 2

Author(s):

Yuuhiko Tanabe ◽

Haruyo Yamaguchi

Keyword(s):

Evolutionary History ◽

Core Genome ◽

Genomic Organization ◽

Phylogenetic Analyses ◽

Green Light ◽

Water Bloom ◽

Phylogenetic Groups ◽

Genome Phylogeny ◽

History Of ◽

Genomic Basis

AbstractMicrocystis aeruginosais a bloom-forming cyanobacterium found in eutrophic fresh-and brackish water bodies worldwide. As typical for cyanobacteria, mostM. aeruginosastrains are blue-green in color owing to the concomitance of two photosynthetic pigments, phycocyanin (PC) and chlorophylla. Although less common,M. aeruginosastrains that are brownish in color owing to the presence of another pigment phycoerythrin (PE) have been documented. However, the genomic basis, phylogeny, and evolutionary origin of PE pigmentation inM. aeruginosahave only been poorly characterized until date. In the present study, we sequenced and characterized the genomes of five PE-containingM. aeruginosastrains. Putative PE synthesis and regulation genes (thecpecluster) were identified in all five sequenced genomes as well as in three previously publishedM. aeruginosagenomes. Of note, Absorption spectra indicated that the PE content, but not PC content, was markedly altered in response to availability of red/green light in all PE-containing strains. This was consistent with the presence ofccaS/ccaR, a hallmark of type II chromatic adapter, in thecpecluster. Phylogenetic analyses of core genome genes indicated that PE-containing genotypes were located in three different phylogenetic groups. In contrast, the genomic organization of thecpecluster was mostly conserved regardless of genomic background. Additionally, the phylogenies of PE genes were found to be congruent, consistent with the core genome phylogeny. A comparison of core genome and PE genes showed a similar level of genetic divergence between two PE-containing groups. These results suggest that genes responsible for PE pigmentation were introduced intoM. aeruginosaearly during evolution and were repeatedly lost thereafter possibly due to ecological adaptation. Additional horizontal gene transfer (HGT) later during evolution also contributed to the present phylogenetic distribution of PE inM. aeruginosa.

Download Full-text

Evolutionary history of inversions in the direction of architecture-driven mutational pressures in crustacean mitochondrial genomes

10.1101/2020.05.09.085712 ◽

2020 ◽

Author(s):

Dong Zhang ◽

Hong Zou ◽

Jin Zhang ◽

Gui-Tang Wang ◽

Ivan Jakovlić

Keyword(s):

Evolutionary History ◽

Phylogenetic Analyses ◽

Branch Length ◽

Mitochondrial Genomes ◽

Close Attention ◽

Mtdna Sequences ◽

Mitochondrial Data ◽

Gc Skew ◽

History Of ◽

Taxonomic Approach

AbstractInversions of the origin of replication (ORI) of mitochondrial genomes produce asymmetrical mutational pressures that can cause artefactual clustering in phylogenetic analyses. It is therefore an absolute prerequisite for all molecular evolution studies that use mitochondrial data to account for ORI events in the evolutionary history of their dataset. The number of ORI events in crustaceans remains unknown; several studies reported ORI events in some crustacean lineages on the basis of fully inversed (e.g. negative vs. positive) GC skew patterns, but studies of isolated lineages could have easily overlooked ORI events that produced merely a reduction in the skew magnitude. In this study, we used a comprehensive taxonomic approach to systematically study the evolutionary history of ORI events in crustaceans using all available mitogenomes and combining signals from lineage-specific skew magnitude and direction (+ or -), cumulative skew diagrams, and gene rearrangements. We inferred 24 putative ORI events (14 of which have not been proposed before): 17 with relative confidence, and 7 speculative. Most of these were located at lower taxonomic levels, but there are indications of ORIs that occurred at or above the order-level: Copepoda, Isopoda, and putatively in Branchiopoda and Poecilostomatida+Cyclopoida. Several putative ORI events did not result in fully inversed skews. In many lineages skew plots were not informative for the prediction of replication origin and direction of mutational pressures, but inversions of the mitogenome fragment comprising the ancestral CR (rrnS-CR-trnI) were rather good predictors of skew inversions. We also found that skew plots can be a useful tool to indirectly infer the relative strengths of mutational/purifying pressures in some crustacean lineages: when purifying pressures outweigh mutational, GC skew plots are strongly affected by the strand distribution of genes, and when mutational > purifying, GC skew plots can be even completely (apparently) unaffected by the strand distribution of genes. This observation has very important repercussions for phylogenetic and evolutionary studies, as it implies that not only the relatively rare ORI events, but also much more common gene strand switches and same-strand rearrangements can produce mutational bursts, which in turn affect phylogenetic and evolutionary analyses. We argue that such compositional biases may produce misleading signals not only in phylogenetic but also in other types of evolutionary analyses (dN/dS ratios, codon usage bias, base composition, branch length comparison, etc.), and discuss several such examples. Therefore, all studies aiming to study the evolution of mtDNA sequences should pay close attention to architectural rearrangements.

Download Full-text

The complex evolution of the HSP70 gene family

10.1101/2020.09.21.307264 ◽

2020 ◽

Author(s):

Er-meng Yu ◽

Tatsuki Yoshinaga ◽

Frank L. Jalufka ◽

Hashimul Ehsan ◽

David B. Mark Welch ◽

...

Keyword(s):

Heat Shock ◽

Evolutionary History ◽

Brachionus Plicatilis ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Evolutionary Genetics ◽

Purifying Selection ◽

Hsp70 Family ◽

History Of ◽

Species Specific

AbstractThe 70-kDa heat shock protein (HSP70) family contains several isoforms localized in different subcellular compartments. The cytosolic isoforms have been classified into stress-inducible HSP70s and constitutive heat shock cognates (HSC70s), but occasional reports of “constitutive HSP70s” and the lack of cross-phylum comparisons have been a source of confusion in the evolution of the metazoan HSP70 family. Here we provide novel insights into the evolutionary history of this important molecular chaperone. We first cloned two HSP70 genes from the rotifer Brachionus plicatilis, an emerging model in evolutionary genetics, and confirmed their stress inducibility. Subsequent phylogenetic analyses of 100 full-length HSP70 family member genes revealed an ancient duplication that gave rise to two lineages from which all metazoan cytosolic HSP70s descend. One lineage contains a relatively small number of Lophotrochozoan and Ecdysozoan genes, none of which have been shown to be constitutively expressed. The second included both inducible and constitutive genes from diverse phyla. Species-specific duplications are present in both lineages, and in the second there are well-supported phylum-specific clades for Rotifera, Nematoda, and Chordata. Some genes in this lineage have likely independently acquired stress inducibility, which may explain the sporadic distribution of genes designated as “HSP70” or “HSC70” in previous analyses. Consistent with the history of diversification within each group, stress-inducible members of the second lineage show lower purifying selection pressure compared to constitutive members. These results illustrate the evolutionary history of the HSP70 family independent from their expression patterns, encouraging the development of new nomenclature based on evolutionary history.

Download Full-text