scholarly journals Tempo and mode of antibat ultrasound production and sonar jamming in the diverse hawkmoth radiation

2015 ◽  
Vol 112 (20) ◽  
pp. 6407-6412 ◽  
Author(s):  
Akito Y. Kawahara ◽  
Jesse R. Barber
Keyword(s):  
Evolutionary History ◽  
Tactile Stimulation ◽  
Phylogenetic Analyses ◽  
Physical Contact ◽  
Divergence Times ◽  
Entire Group ◽  
Multigene Phylogeny ◽  
Late Oligocene ◽  
Entire Family ◽  
Big Brown Bats

The bat–moth arms race has existed for over 60 million y, with moths evolving ultrasonically sensitive ears and ultrasound-producing organs to combat bat predation. The evolution of these defenses has never been thoroughly examined because of limitations in simultaneously conducting behavioral and phylogenetic analyses across an entire group. Hawkmoths include >1,500 species worldwide, some of which produce ultrasound using genital stridulatory structures. However, the function and evolution of this behavior remain largely unknown. We built a comprehensive behavioral dataset of hawkmoth hearing and ultrasonic reply to sonar attack using high-throughput field assays. Nearly half of the species tested (57 of 124 species) produced ultrasound to tactile stimulation or playback of bat echolocation attack. To test the function of ultrasound, we pitted big brown bats (Eptesicus fuscus) against hawkmoths over multiple nights and show that hawkmoths jam bat sonar. Ultrasound production was immediately and consistently effective at thwarting attack and bats regularly performed catching behavior without capturing moths. We also constructed a fossil-calibrated, multigene phylogeny to study the evolutionary history and divergence times of these antibat strategies across the entire family. We show that ultrasound production arose in multiple groups, starting in the late Oligocene (∼26 Ma) after the emergence of insectivorous bats. Sonar jamming and bat-detecting ears arose twice, independently, in the Miocene (18–14 Ma) either from earless hawkmoths that produced ultrasound in response to physical contact only, or from species that did not respond to touch or bat echolocation attack.

scholarly journals Intrahost speciations and host switches shaped the evolution of herpesviruses

2018 ◽  
Author(s):  
Anderson F. Brito ◽  
John W. Pinney
Keyword(s):  
Early Cretaceous ◽  
Late Cretaceous ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Continental Drift ◽  
Divergence Times ◽  
Crucial Information ◽  
Host Evolution ◽  
Over Time

ABSTRACTCospeciation has been suggested to be the main force driving the evolution of herpesviruses, with viral species co-diverging with their hosts along more than 400 million years of evolutionary history. Recent studies, however, have been challenging this assumption, showing that other co-phylogenetic events, such as intrahost speciations and host switches play a central role on their evolution. Most of these studies, however, were performed with undated phylogenies, which may underestimate or overestimate the frequency of certain events. In this study we performed co-phylogenetic analyses using time-calibrated trees of herpesviruses and their hosts. This approach allowed us to (i) infer co-phylogenetic events over time, and (ii) integrate crucial information about continental drift and host biogeography to better understand virus-host evolution. We observed that cospeciations were in fact relatively rare events, taking place mostly after the Late Cretaceous (~100 Millions of years ago). Host switches were particularly common among alphaherpesviruses, where at least 10 transfers were detected. Among beta- and gammaherpesviruses, transfers were less frequent, with intrahost speciations followed by losses playing more prominent roles, especially from the Early Jurassic to the Early Cretaceous, when those viral lineages underwent several intrahost speciations. Our study reinforces the understanding that cospeciations are uncommon events in herpesvirus evolution. More than topological incongruences, mismatches in divergence times were the main disagreements between host and viral phylogenies. In most cases, host switches could not explain such disparities, highlighting the important role of losses and intrahost speciations in the evolution of herpesviruses.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

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.

scholarly journals A test statistic to quantify treelikeness in phylogenetics

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

scholarly journals A New Paralog Removal Pipeline Resolves Conflict between RAD-seq and Enrichment

2020 ◽  
Author(s):  
Wenbin Zhou ◽  
John Soghigian ◽  
Qiu-yun (Jenny) Xiang
Keyword(s):  
High Throughput Sequencing ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Disjunct Distribution ◽  
Divergence Times ◽  
Target Enrichment ◽  
Sequencing Technologies ◽  
Duplication Events ◽  
The Witch ◽  
Phylogenomic Analyses

ABSTRACTTarget enrichment and RAD-seq are well-established high throughput sequencing technologies that have been increasingly used for phylogenomic studies, and the choice between methods is a practical issue for plant systematists studying the evolutionary histories of biodiversity of relatively recent origins. However, few studies have compared the congruence and conflict between results from the two methods within the same group of organisms, especially in plants, where extensive genome duplication events may complicate phylogenomic analyses. Unfortunately, currently widely used pipelines for target enrichment data analysis do not have a vigorous procedure for remove paralogs in Hyb-Seq data. In this study, we employed RAD-seq and Hyb-Seq of Angiosperm 353 genes in phylogenomic and biogeographic studies of Hamamelis (the witch-hazels) and Castanea (chestnuts), two classic examples exhibiting the well-known eastern Asian-eastern North American disjunct distribution. We compared these two methods side by side and developed a new pipeline (PPD) with a more vigorous removal of putative paralogs from Hyb-Seq data. The new pipeline considers both sequence similarity and heterozygous sites at each locus in identification of paralogous. We used our pipeline to construct robust datasets for comparison between methods and downstream analyses on the two genera. Our results demonstrated that the PPD identified many more putative paralogs than the popular method HybPiper. Comparisons of tree topologies and divergence times showed significant differences between data from HybPiper and data from our new PPD pipeline, likely due to the error signals from the paralogous genes undetected by HybPiper, but trimmed by PPD. We found that phylogenies and divergence times estimated from our RAD-seq and Hyb-Seq-PPD were largely congruent. We highlight the importance of removal paralogs in enrichment data, and discuss the merits of RAD-seq and Hyb-Seq. Finally, phylogenetic analyses of RAD-seq and Hyb-Seq resulted in well-resolved species relationships, and revealed ancient introgression in both genera. Biogeographic analyses including fossil data revealed a complicated history of each genus involving multiple intercontinental dispersals and local extinctions in areas outside of the taxa’s modern ranges in both the Paleogene and Neogene. Our study demonstrates the value of additional steps for filtering paralogous gene content from Angiosperm 353 data, such as our new PPD pipeline described in this study. [RAD-seq, Hyb-Seq, paralogs, Castanea, Hamamelis, eastern Asia-eastern North America disjunction, biogeography, ancient introgression]

scholarly journals Morphometric and phylogenetic analyses of the Paleozoic Subulitoidea (Gastropoda)

1992 ◽  
Vol 6 ◽  
pp. 93-93
Author(s):  
Douglas H. Erwin
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Temporal Trends ◽  
Thin Sections ◽  
Middle Ordovician ◽  
Shell Form ◽  
External Shell ◽  
Morphometric Analyses ◽  
Angular Measurements ◽  
Permian Mass Extinction

The gastropod superfamily Subulitoidea first appeared during the Early-Middle Ordovician gastropod radiation, seemingly from within the pleurotomarid family Lophospiridea, and persisted with low diversity and generally low abundance through the Paleozoic. One species survived the end-Permian mass extinction, but like many other Paleozoic remnants, the clade became extinct in the mid-Triassic. Many members of the clade are homeomorphic with later ‘neogastropods' and have frequently been fingered as the ancestors of these later, predatory gastropods. There is however, no direct evidence for an ancestor-descendent relationship. Addressing this possibility and understanding of the systematics and evolutionary history of the clade has been complicated by relatively simple shell form and apparent paucity of shell characters. The strength of the morphological and probable ecologic similarities between subulitids and ‘neogastropods' raises the question why this clade was unable to capitalize on their position as perhaps the only predatory gastropods during the Paleozoic. Such questions of evolutionary history are best addressed within the context of a combination of morphometric and phylogenetic analyses which may resolve the systematic questions and reveal something of the evolutionary relationships of the clade.Morphometric analyses were performed on some 40 specimens covering the 13 described genera (and several undescribed forms). Both linear and angular measurements of external shell form and internal structure from axial thin sections were measured and apertures were analyzed using elliptical Fourier analysis (EFA). The number of specimens analyzed was intentionally limited because of difficulties obtaining specimens with sufficient preservation of the aperture. The results demonstrate the necessity, for this clade at least, of including a more complex description of apertural morphology than simple maximum length and width. Principle component analyses of the EFA data distinguishes complexity of the columellar folds along the first axis and basal rounding along the second - both biologically meaningful aspects of apertural form. Moreover, the occupation of a taxon-specific apertural space defined by the PCA increases through the Paleozoic. Further, the analyses suggest that the two traditionally recognized subfamilies of the Subulitidae (Ordovician-Devonian and Devonian-Triassic) each exhibit increased variance in the occupation of morphologic space, but additional data is required to confirm this pattern and determine if any temporal trends exist.Analyzing patterns of occupation of morphologic space requires a rigorously constructed phylogeny. A cladistic (parsimony) analysis of the superfamily was performed using 16 taxa and over 30 discrete morphologic characters. The resulting cladograms were plotted within the taxon-specific morphospaces produced by the morphometric analyses.

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

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.

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

2019 ◽  
Vol 286 (1897) ◽  
pp. 20182929 ◽  
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.

scholarly journals Systematics of the Etheostoma cinereum (Teleostei: Percidae) species complex (subgenus Allohistium)

Zootaxa ◽  
2012 ◽  
Vol 3277 (1) ◽  
pp. 43 ◽  
Author(s):  
STEVEN L. POWERS ◽  
BERNARD R. KUHAJDA ◽  
SARAH E. AHLBRAND
Keyword(s):  
Geographic Variation ◽  
Species Complex ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Species Concepts ◽  
Cyt B ◽  
Cumberland River

We examined geographic variation within the Ashy Darter, Etheostoma cinereum, of the mitochondrially enconded cyto-chrome b gene (cyt b) and nuclear recombination activation gene 1 (RAG1) as well as pigmentation, 6 meristic variables,and 20 morphometric variables for patterns indicative of speciation within the complex. Four geographically disjunct en-tities were identified by at least one of the datasets corresponding to the Cumberland, Duck, Elk, and upper Tennesseeriver systems. Monophyly of cyt b and RAG1 sequences, modal meristic differences, moderate morphometric divergence,and unique pigmentation in specimens from the Cumberland River suggest this entity represents an evolutionary speciesunder many different species concepts and is described herein as Etheostoma maydeni. Other populations exhibit varyingdegrees of divergence in the different datasets and have conflicting relationships in phylogenetic analyses using cyt b andRAG1 sequences, leaving the evolutionary history and taxonomic status of the Duck, Elk and upper Tennessee populations unclear.

The first potential fossil record of a dibamid reptile (Squamata: Dibamidae): a new taxon from the early Oligocene of Central Mongolia

2019 ◽  
Vol 187 (3) ◽  
pp. 782-799 ◽  
Author(s):  
Andrej Čerňanský
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
New Taxon ◽  
Unique Combination ◽  
Central Mongolia ◽  
Squamate Reptiles ◽  
The Past ◽  
Early Oligocene ◽  
Fossil Material

Abstract Dibamid reptiles have a known current distribution on two continents (Asia and North America). Although this clade represents an early-diverging group in the Squamata and thus should have a long evolutionary history, no fossil record of these peculiar burrowing squamate reptiles has been documented so far. The fossil material described here comes from the early Oligocene of the Valley of Lakes in Central Mongolia. This material consists of jaws and is placed in the clade Dibamidae on the basis of its morphology, which is further confirmed by phylogenetic analyses. In spite of the fragmentary nature of this material, it thus forms the first, but putative, fossil evidence of this clade. If correctly interpreted, this material demonstrates the occurrence of Dibamidae in East Asia in the Palaeogene, indicating its distribution in higher latitudes than today. The preserved elements possess a unique combination of character states, and a new taxon name is therefore erected: Hoeckosaurus mongoliensis sp. nov. The dentary of Hoeckosaurus exhibits some characters of the two extant dibamid taxa. However, the open Meckel’s groove, together with other characters, show that this group was morphologically much more diverse in the past.

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