Interspecies variation of larval locomotion kinematics in the genus Drosophila and its relation to habitat temperature

Abstract Background Speed and trajectory of locomotion are the characteristic traits of individual species. Locomotion kinematics may have been shaped during evolution towards increased survival in the habitats of each species. Although kinematics of locomotion is thought to be influenced by habitats, the quantitative relation between the kinematics and environmental factors has not been fully revealed. Here, we performed comparative analyses of larval locomotion in 11 Drosophila species. Results We found that larval locomotion kinematics are divergent among the species. The diversity is not correlated to the body length but is correlated instead to the habitat temperature of the species. Phylogenetic analyses using Bayesian inference suggest that the evolutionary rate of the kinematics is diverse among phylogenetic tree branches. Conclusions The results of this study imply that the kinematics of larval locomotion has diverged in the evolutionary history of the genus Drosophila and evolved under the effects of the ambient temperature of habitats.

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Interspecies variation of larval locomotion kinematics in the genus Drosophila and its relation to habitat temperature

10.1101/2020.11.06.371120 ◽

2020 ◽

Author(s):

Yuji Matsuo ◽

Akinao Nose ◽

Hiroshi Kohsaka

Keyword(s):

Bayesian Inference ◽

Phylogenetic Trees ◽

Evolutionary History ◽

Evolutionary Rate ◽

Phylogenetic Analyses ◽

The Body ◽

Quantitative Relation ◽

Individual Species ◽

Habitat Temperature ◽

History Of

AbstractSpeed and trajectory of locomotion are characteristic traits of individual species. During evolution, locomotion kinematics is likely to have been tuned for survival in the habitats of each species. Although kinematics of locomotion is thought to be influenced by habitats, the quantitative relation between the kinematics and environmental factors has not been fully revealed. Here, we performed comparative analyses of larval locomotion in 11 Drosophila species. We found that larval locomotion kinematics are divergent among the species. The diversity is not correlated to the body length but is correlated instead to the minimum habitat temperature of the species. Phylogenetic analyses using Bayesian inference suggest that the evolutionary rate of the kinematics is diverse among phylogenetic trees. The results of this study imply that the kinematics of larval locomotion has diverged in the evolutionary history of the genus Drosophila and evolved under the effects of the minimum ambient temperature of habitats.

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

Genome Biology and Evolution ◽

10.1093/gbe/evz155 ◽

2019 ◽

Cited By ~ 4

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.

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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

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Waptia fieldensis Walcott, a mandibulate arthropod from the middle Cambrian Burgess Shale

Royal Society Open Science ◽

10.1098/rsos.172206 ◽

2018 ◽

Vol 5 (6) ◽

pp. 172206 ◽

Cited By ~ 19

Author(s):

Jean Vannier ◽

Cédric Aria ◽

Rod S. Taylor ◽

Jean-Bernard Caron

Keyword(s):

Evolutionary History ◽

The Body ◽

Formal Description ◽

Front Part ◽

Burgess Shale ◽

Middle Cambrian ◽

History Of ◽

Ellipsoid Bodies ◽

Active Swimming ◽

Prey Items

Waptia fieldensis Walcott, 1912 is one of the iconic animals from the middle Cambrian Burgess Shale biota that had lacked a formal description since its discovery at the beginning of the twentieth century. This study, based on over 1800 specimens, finds that W. fieldensis shares general characteristics with pancrustaceans, as previous authors had suggested based mostly on its overall aspect. The cephalothorax is covered by a flexible, bivalved carapace and houses a pair of long multisegmented antennules, palp-bearing mandibles, maxillules, and four pairs of appendages with five-segmented endopods—the anterior three pairs with long and robust enditic basipods, the fourth pair with proximal annulations and lamellae. The post-cephalothorax has six pairs of lamellate and fully annulated appendages which appear to be extensively modified basipods rather than exopods. The front part of the body bears a pair of stalked eyes with the first ommatidia preserved in a Burgess Shale arthropod, and a median ‘labral’ complex flanked by lobate projections with possible affinities to hemi-ellipsoid bodies. Waptia confirms the mandibulate affinity of hymenocarines, retrieved here as part of an expanded Pancrustacea, thereby providing a novel perspective on the evolutionary history of this hyperdiverse group. We construe that Waptia was an active swimming predator of soft prey items, using its anterior appendages for food capture and manipulation, and also potentially for clinging to epibenthic substrates.

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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.

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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.

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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.

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

PLoS ONE ◽

10.1371/journal.pone.0186085 ◽

2017 ◽

Vol 12 (10) ◽

pp. e0186085 ◽

Cited By ~ 10

Author(s):

Amy B. Baird ◽

Janet K. Braun ◽

Mark D. Engstrom ◽

Ashlyn C. Holbert ◽

Maritza G. Huerta ◽

...

Keyword(s):

Evolutionary History ◽

Native Hawaiian ◽

Phylogenetic Analyses ◽

History Of

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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.

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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 .

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