scholarly journals The phylogeny and systematics of Xiphosura

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10431
Author(s):  
James C. Lamsdell
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Systematic Revision ◽  
Ecological History ◽  
Living Fossils ◽  
Modern Species ◽  
The Matrix ◽  
History Of ◽  
Taxonomic Framework

Xiphosurans are aquatic chelicerates with a fossil record extending into the Early Ordovician and known from a total of 88 described species, four of which are extant. Known for their apparent morphological conservatism, for which they have gained notoriety as supposed ‘living fossils’, recent analyses have demonstrated xiphosurans to have an ecologically diverse evolutionary history, with several groups moving into non-marine environments and developing morphologies markedly different from those of the modern species. The combination of their long evolutionary and complex ecological history along with their paradoxical patterns of morphological stasis in some clades and experimentation among others has resulted in Xiphosura being of particular interest for macroevolutionary study. Phylogenetic analyses have shown the current taxonomic framework for Xiphosura—set out in the Treatise of Invertebrate Paleontology in 1955—to be outdated and in need of revision, with several common genera such as Paleolimulus Dunbar, 1923 and Limulitella Størmer, 1952 acting as wastebasket taxa. Here, an expanded xiphosuran phylogeny is presented, comprising 58 xiphosuran species as part of a 158 taxon chelicerate matrix coded for 259 characters. Analysing the matrix under both Bayesian inference and parsimony optimisation criteria retrieves a concordant tree topology that forms the basis of a genus-level systematic revision of xiphosuran taxonomy. The genera Euproops Meek, 1867, Belinurus König, 1820, Paleolimulus, Limulitella, and Limulus are demonstrated to be non-monophyletic and the previously synonymized genera Koenigiella Raymond, 1944 and Prestwichianella Cockerell, 1905 are shown to be valid. In addition, nine new genera (Andersoniella gen. nov., Macrobelinurus gen. nov., and Parabelinurus gen. nov. in Belinurina; Norilimulus gen. nov. in Paleolimulidae; Batracholimulus gen. nov. and Boeotiaspis gen. nov. in Austrolimulidae; and Allolimulus gen. nov., Keuperlimulus gen. nov., and Volanalimulus gen. nov. in Limulidae) are erected to accommodate xiphosuran species not encompassed by existing genera. One new species, Volanalimulus madagascarensis gen. et sp. nov., is also described. Three putative xiphosuran genera—Elleria Raymond, 1944, Archeolimulus Chlupáč, 1963, and Drabovaspis Chlupáč, 1963—are determined to be non-xiphosuran arthropods and as such are removed from Xiphosura. The priority of Belinurus König, 1820 over Bellinurus Pictet, 1846 is also confirmed. This work is critical for facilitating the study of the xiphosuran fossil record and is the first step in resolving longstanding questions regarding the geographic distribution of the modern horseshoe crab species and whether they truly represent ‘living fossils’. Understanding the long evolutionary history of Xiphosura is vital for interpreting how the modern species may respond to environmental change and in guiding conservation efforts.

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.

A fossil record of land plant origins from charophyte algae

Science ◽  
2021 ◽  
Vol 373 (6556) ◽  
pp. 792-796 ◽  
Author(s):  
Paul K. Strother ◽  
Clinton Foster
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Land Plant ◽  
Fossil Plants ◽  
Fossil Plant ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Time Gap ◽  
Evolutionary Continuity

Molecular time trees indicating that embryophytes originated around 500 million years ago (Ma) during the Cambrian are at odds with the record of fossil plants, which first appear in the mid-Silurian almost 80 million years later. This time gap has been attributed to a missing fossil plant record, but that attribution belies the case for fossil spores. Here, we describe a Tremadocian (Early Ordovician, about 480 Ma) assemblage with elements of both Cambrian and younger embryophyte spores that provides a new level of evolutionary continuity between embryophytes and their algal ancestors. This finding suggests that the molecular phylogenetic signal retains a latent evolutionary history of the acquisition of the embryophytic developmental genome, a history that perhaps began during Ediacaran-Cambrian time but was not completed until the mid-Silurian (about 430 Ma).

scholarly journals Experimental degradation of helicoidal photonic nanostructures in scarab beetles (Coleoptera: Scarabaeidae): implications for the identification of circularly polarizing cuticle in the fossil record

2018 ◽  
Vol 15 (148) ◽  
pp. 20180560 ◽  
Author(s):  
Giliane P. Odin ◽  
Maria E. McNamara ◽  
Hans Arwin ◽  
Kenneth Järrendahl
Keyword(s):  
Uric Acid ◽  
Fossil Record ◽  
Evolutionary History ◽  
Polarized Light ◽  
Circularly Polarized Light ◽  
Circularly Polarized ◽  
Alkaline Conditions ◽  
History Of ◽  
Diagenetic History ◽  
Scarab Beetles

Scarab beetles (Coleoptera: Scarabaeidae) can exhibit striking colours produced by pigments and/or nanostructures. The latter include helicoidal (Bouligand) structures that can generate circularly polarized light. These have a cryptic evolutionary history in part because fossil examples are unknown. This suggests either a real biological signal, i.e. that Bouligand structures did not evolve until recently, or a taphonomic signal, i.e. that conditions during the fossilization process were not conducive to their preservation. We address this issue by experimentally degrading circularly polarizing cuticle of modern scarab beetles to test the relative roles of decay, maturation and taxonomy in controlling preservation. The results reveal that Bouligand structures have the potential to survive fossilization, but preservation is controlled by taxonomy and the diagenetic history of specimens. Further, cuticle of specific genus ( Chrysina ) is particularly decay-prone in alkaline conditions; this may relate to the presence of certain compounds, e.g. uric acid, in the cuticle of these taxa.

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

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.

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.

scholarly journals A comparative atlas of the skull osteology of European lizards (Reptilia: Squamata)

2019 ◽  
Vol 187 (3) ◽  
pp. 829-928 ◽  
Author(s):  
Andrea Villa ◽  
Massimo Delfino
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
European Species ◽  
History Of ◽  
Diagnostic Key ◽  
Single Bone ◽  
Fossil Lizards ◽  
Bone Remains ◽  
Comparative Osteology ◽  
Broad Scale

Abstract The fossil record provides evidence of a long evolutionary history of European lizards. Since fossil lizards are regularly represented by bone remains, the knowledge of the origins of extant taxa and their distribution in time and space is hindered by the fact that their comparative osteology is not yet completely and adequately known. In spite of a rising interest in this topic since the end of the 20th century, a gap in our knowledge is still evident. We here report the first broad-scale comparative osteological analysis of the skulls of extant European lizards, highlighting significant differences that can be used in identification. This comparative study, including as many European species as possible, leads to the creation of a detailed diagnostic key for each single bone. Also, our data significantly improve the recognizability of extant European non-snake squamates, with 54% of the current diversity to be recognized based on the new results contra the previously estimated 31%. This recognizability is expected to further increase in the future, with new studies focusing on species that are either missing or poorly represented here, or applying promising advanced methodologies.

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

2002 ◽  
Vol 93 (4) ◽  
pp. 333-353 ◽  
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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