scholarly journals Carybdea alata auct. (Cubozoa): rediscovery of the Alatina grandis type

Zootaxa ◽  
2019 ◽  
Vol 2713 (1) ◽  
pp. 52 ◽  
Author(s):  
BASTIAN BENTLAGE
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Smithsonian Institution ◽  
Type Specimen ◽  
Nominal Species ◽  
Separate Species ◽  
Future Studies ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Morphological Differences

Numerous nominal species have been considered synonymous with Carybdea alata Reynaud, 1830 (cf. Gershwin 2005). A recent revision concluded that several of the species collectively referred to as C. alata are valid and indeed separate species (Gershwin 2005; but see also Bentlage et al. 2010). Additionally, these species (including C. alata) were moved into the genus Alatina Gershwin 2005 (family Alatinidae Gershwin, 2005) because of stark morphological differences they display compared to the other species of Carybdea. In particular, Alatina species possess crescentic phacellae and a rhopaliar niche ostium that is covered by a single upper and two lateral scales (t-shaped sensu Gershwin 2005; cf. Bigelow 1938) compared to a single upper covering scale (heart-shaped sensu Gershwin 2005; cf. Bigelow 1938) and epaulette-like or linear phacellae in the corners of the stomach in Carybdea species. Recent molecular phylogenetic analyses support the separation of Carybdea and Alatina (Bentlage et al. 2010). Alatina grandis posed a problem in Gershwin's (2005) revision, as the type of this species appeared to be lost to science, preventing a closer investigation of its identity. I located a type specimen of the species in the collections of the National Museum of Natural History, Smithsonian Institution (USNM). The purpose of this letter is to draw attention to this important specimen, and highlight directions for future studies on the evolutionary history of the genus Alatina.

scholarly journals Diversification of African Tree Legumes in Miombo–Mopane Woodlands

Plants ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 182 ◽  
Author(s):  
Ivete Maquia ◽  
Silvia Catarino ◽  
Ana R. Pena ◽  
Denise R.A. Brito ◽  
Natasha. S. Ribeiro ◽  
...  
Keyword(s):  
Species Diversity ◽  
Plant Diversity ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Conservation Status ◽  
Conservation Areas ◽  
Future Studies ◽  
Tree Legumes ◽  
Key Species ◽  
History Of

The southern African Miombo and Mopane ecoregions constitute a unique repository of plant diversity whose diversification and evolutionary history is still understudied. In this work, we assessed the diversity, distribution, and conservation status of Miombo and Mopane tree legumes within the Zambezian phytoregion. Data were retrieved from several plant and gene databases and phylogenetic analyses were performed based on genetic barcodes. Seventy-eight species (74 from Miombo and 23 from Mopane, 19 common to both ecoregions) have been scored. Species diversity was high within both ecoregions, but information about the actual conservation status is scarce and available only for ca. 15% of the species. Results of phylogenetic analyses were consistent with current legume classification but did not allow us to draw any conclusion regarding the evolutionary history of Miombo and Mopane tree legumes. Future studies are proposed to dissect the diversity and structure of key species in order to consolidate the network of conservation areas.

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 Morphological and molecular phylogenetic analyses of Zepedanulus ishikawai (Arachnida: Opiliones: Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago

2021 ◽  
pp. 1-28
Author(s):  
Yoshimasa Kumekawa ◽  
Haruka Fujimoto ◽  
Osamu Miura ◽  
Ryo Arakawa ◽  
Jun Yokoyama ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Analyses ◽  
Divergence Time ◽  
Morphological Characters ◽  
Ryukyu Archipelago ◽  
Divergence Time Estimates ◽  
Time Estimates ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Polymerase Chain

Abstract Harvestmen (Arachnida: Opiliones) are soil animals with extremely low dispersal abilities that experienced allopatric differentiation. To clarify the morphological and phylogenetic differentiation of the endemic harvestman Zepedanulus ishikawai (Suzuki, 1971) (Laniatores: Epedanidae) in the southern part of the Ryukyu Archipelago, we conducted molecular phylogenetic analyses and divergence time estimates based on CO1 and 16S rRNA sequences of mtDNA, the 28S rRNA sequence of nrDNA, and the external morphology. A phylogenetic tree based on mtDNA sequences indicated that individuals of Z. ishikawai were monophyletic and were divided into clade I and clade II. This was supported by the nrDNA phylogenetic tree. Although clades I and II were distributed sympatrically on all three islands examined (Ishigaki, Iriomote, and Yonaguni), heterogeneity could not be detected by polymerase chain reaction–restriction fragment length polymorphism of nrDNA, indicating that clades I and II do not have a history of hybridisation. Also, several morphological characters differed significantly between individuals of clade I and clade II. The longstanding isolation of the southern Ryukyus from the surrounding islands enabled estimation of the original morphological characters of both clades of Z. ishikawai.

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 The dynamic evolutionary history of genome size in North American woodland salamanders

Genome ◽  
2017 ◽  
Vol 60 (4) ◽  
pp. 285-292 ◽  
Author(s):  
Catherine E. Newman ◽  
T. Ryan Gregory ◽  
Christopher C. Austin
Keyword(s):  
Genome Size ◽  
Evolutionary History ◽  
Future Studies ◽  
Plethodontid Salamanders ◽  
Genome Size Evolution ◽  
Size Evolution ◽  
History Of ◽  
Large Genome Size ◽  
Uncertain Future ◽  
Phylogeographic Study

The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5–20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders.

Molecular phylogenetic position of Haplometroides intercaecalis (Digenea, Plagiorchiidae)

2018 ◽  
Vol 63 (3) ◽  
pp. 522-526 ◽  
Author(s):  
Maria Isabel Müller ◽  
Drausio Honorio Morais ◽  
Reinaldo José da Silva
Keyword(s):  
Dna Sequences ◽  
Additional Data ◽  
Ribosomal Gene ◽  
Valid Species ◽  
Phylogenetic Position ◽  
Systematic Analysis ◽  
Future Studies ◽  
New Family ◽  
Molecular Phylogenetic ◽  
Morphological Differences

Abstract Three valid species of Haplometroides Odhner, 1910 parasitise snakes and amphisbaenians from South America. This study provides additional data on morphometric and molecular phylogenetic position inferred from the nuclear ribosomal gene 28S (partial). DNA sequences were isolated from Haplometroides intercaecalis Silva, Ferreira and Strüssmann, 2007 found in one specimen of Phalotris matogrossensis Lema, D’Agostini and Cappellari, 2005. Five digenean specimens were recovered from the esophagus of this snake, and four specimens were used for morphometrical studies and one specimen for molecular analysis. Phylogenetic analysis using maximum likelihood and Bayesian methods was conducted with sequences available for the order Plagiorchiida and its phylogenetic position places H. intercaecalis among the brachycoeliids Brachycoelium (Dujardin, 1845) Stiles and Hassall, 1898 and Parabrachycoelium Pérez-Ponce de León, Mendoza-Garfias, Razo-Mendivil and Parra-Olea, 2011, and the mesocoeliid Mesocoelium Odhner, 1910, not closely related to plagiorchids as expected. Due to morphological differences among these families, it may be necessary to create a new family to accommodate Haplometroides spp. However, more genera/taxa as well as other molecular markers should be added in future studies to confirm our results and resolve this matter. This is the first phylogenetic positioning of digeneans of the genus Haplometroides, contributing to the systematic analysis of the helminthological biodiversity of Neotropical snakes.

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 Molecular forms of Anopheles subpictus and Anopheles sundaicus in the Indian subcontinent

2020 ◽  
Vol 19 (1) ◽  
Author(s):  
Ankita Sindhania ◽  
Manoj K. Das ◽  
Gunjan Sharma ◽  
Sinnathamby N. Surendran ◽  
B. R. Kaushal ◽  
...  
Keyword(s):  
Sibling Species ◽  
Molecular Form ◽  
Indian Subcontinent ◽  
Phylogenetic Analyses ◽  
Coastal Areas ◽  
Molecular Forms ◽  
Nominal Species ◽  
Anopheles Subpictus ◽  
Species Complexes ◽  
Molecular Phylogenetic

Abstract Background Anopheles subpictus and Anopheles sundaicus are closely related species, each comprising several sibling species. Ambiguities exist in the classification of these two nominal species and the specific status of members of these species complexes. Identifying fixed molecular forms and mapping their spatial distribution will help in resolving the taxonomic ambiguities and understanding their relative epidemiological significance. Methods DNA sequencing of Internal Transcribed Spacer-2 (ITS2), 28S-rDNA (D1-to-D3 domains) and cytochrome oxidase-II (COII) of morphologically identified specimens of two nominal species, An. subpictus sensu lato (s.l.) and An. sundaicus s.l., collected from the Indian subcontinent, was performed and subjected to genetic distance and molecular phylogenetic analyses. Results Molecular characterization of mosquitoes for rDNA revealed the presence of two molecular forms of An. sundaicus s.l. and three molecular forms of An. subpictus s.l. (provisionally designated as Form A, B and C) in the Indian subcontinent. Phylogenetic analyses revealed two distinct clades: (i) subpictus clade, with a single molecular form of An. subpictus (Form A) prevalent in mainland India and Sri Lanka, and (ii) sundaicus clade, comprising of members of Sundaicus Complex, two molecular forms of An. subpictus s.l. (Form B and C), prevalent in coastal areas or islands in Indian subcontinent, and molecular forms of An. subpictus s.l. reported from Thailand and Indonesia. Based on the number of float-ridges on eggs, all An. subpictus molecular Form B were classified as Species B whereas majority (80%) of the molecular Form A were classified as sibling species C. Fixed intragenomic sequence variation in ITS2 with the presence of two haplotypes was found in molecular Form A throughout its distribution. Conclusion A total of three molecular forms of An. subpictus s.l. and two molecular forms of An. sundaicus s.l. were recorded in the Indian subcontinent. Phylogenetically, two forms of An. subpictus s.l. (Form B and C) prevalent in coastal areas or islands in the Indian subcontinent and molecular forms reported from Southeast Asia are members of Sundaicus Complex. Molecular Form A of An. subpictus is distantly related to all other forms and deserve a distinct specific status.

scholarly journals Fungia fungites (Linnaeus, 1758) (Scleractinia, Fungiidae) is a species complex that conceals large phenotypic variation and a previously unrecognized genus

2020 ◽  
Vol 89 (2) ◽  
pp. 188-209
Author(s):  
Yutaro Oku ◽  
Kenji Iwao ◽  
Bert W. Hoeksema ◽  
Naoko Dewa ◽  
Hiroyuki Tachikawa ◽  
...  
Keyword(s):  
Species Complex ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Scleractinian Corals ◽  
Type Specimens ◽  
Mitochondrial Coi ◽  
Clade B ◽  
Unknown Species ◽  
Molecular Phylogenetic ◽  
Morphological Differences

Recent molecular phylogenetic analyses of scleractinian corals have resulted in the discovery of cryptic lineages. To understand species diversity in corals, these lineages need to be taxonomically defined. In the present study, we report the discovery of a distinct lineage obscured by the traditional morphological variation of Fungia fungites. This taxon exists as two distinct morphs: attached and unattached. Molecular phylogenetic analyses using mitochondrial COI and nuclear ITS markers as well as morphological comparisons were performed to clarify their phylogenetic relationships and taxonomic positions. Molecular data revealed that F. fungites consists of two genetically distinct clades (A and B). Clade A is sister to a lineage including Danafungia scruposa and Halomitra pileus, while clade B formed an independent lineage genetically distant from these three species. The two morphs were also found to be included in both clades, although the attached morph was predominantly found in clade A. Morphologically, both clades were statistically different in density of septal dentation, septal number, and septal teeth shape. These results indicate that F. fungites as presently recognized is actually a species complex including at least two species. After checking type specimens, we conclude that specimens in clade A represent true F. fungites with two morphs (unattached and attached) and that all of those in clade B represent an unknown species and genus comprising an unattached morph with only one exception. These findings suggest that more unrecognized taxa with hitherto unnoticed morphological differences can be present among scleractinian corals.

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