scholarly journals ­Comparative spigot ontogeny across the spider tree of life

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4233 ◽  
Author(s):  
Rachael E. Alfaro ◽  
Charles E. Griswold ◽  
Kelly B. Miller
Keyword(s):  
Phylogenetic Signal ◽  
Correlation Coefficients ◽  
Generalized Least Squares ◽  
Tree Of Life ◽  
Morphological Data ◽  
Singular Fiber ◽  
Rigorous Testing ◽  
Ancestral Character Estimation ◽  
First Time ◽  
Hogna Carolinensis

Spiders are well known for their silk and its varying use across taxa. Very few studies have examined the silk spigot ontogeny of the entire spinning field of a spider. Historically the spider phylogeny was based on morphological data and behavioral data associated with silk. Recent phylogenomics studies have shifted major paradigms in our understanding of silk use evolution, reordering phylogenetic relationships that were once thought to be monophyletic. Considering this, we explored spigot ontogeny in 22 species, including Dolomedes tenebrosus and Hogna carolinensis, reported here for the first time. This is the first study of its kind and the first to incorporate the Araneae Tree of Life. After rigorous testing for phylogenetic signal and model fit, we performed 60 phylogenetic generalized least squares analyses on adult female and second instar spigot morphology. Six analyses had significant correlation coefficients, suggesting that instar, strategy, and spigot variety are good predictors of spigot number in spiders, after correcting for bias of shared evolutionary history. We performed ancestral character estimation of singular, fiber producing spigots on the posterior lateral spinneret whose potential homology has long been debated. We found that the ancestral root of our phylogram of 22 species, with the addition of five additional cribellate and ecribellate lineages, was more likely to have either none or a modified spigot rather than a pseudoflagelliform gland spigot or a flagelliform spigot. This spigot ontogeny approach is novel and we can build on our efforts from this study by growing the dataset to include deeper taxon sampling and working towards the capability to incorporate full ontogeny in the analysis.

scholarly journals Phylogenetic Signal and Bias in Paleontology

2021 ◽  
Author(s):  
Robert J Asher ◽  
Martin R Smith
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Signal ◽  
Morphological Characters ◽  
Tree Of Life ◽  
Morphological Data ◽  
Phylogenetic Resolution ◽  
Phylogeny Estimation ◽  
Better Than

Abstract An unprecedented amount of evidence now illuminates the phylogeny of living mammals and birds on the Tree of Life. We use this tree to measure phylogenetic value of data typically used in paleontology (bones and teeth) from six datasets derived from five published studies. We ask three interrelated questions: 1) Can these data adequately reconstruct known parts of the Tree of Life? 2) Is accuracy generally similar for studies using morphology, or do some morphological datasets perform better than others? 3) Does the loss of non-fossilizable data cause taxa to occur in misleadingly basal positions? Adding morphology to DNA datasets usually increases congruence of resulting topologies to the well corroborated tree, but this varies among morphological datasets. Extant taxa with a high proportion of missing morphological characters can greatly reduce phylogenetic resolution when analyzed together with fossils. Attempts to ameliorate this by deleting extant taxa missing morphology are prone to decreased accuracy due to long-branch artefacts. We find no evidence that fossilization causes extinct taxa to incorrectly appear at or near topologically basal branches. Morphology comprises the evidence held in common by living taxa and fossils, and phylogenetic analysis of fossils greatly benefits from inclusion of molecular and morphological data sampled for living taxa, whatever methods are used for phylogeny estimation.

scholarly journals A phylogenomic resolution of the sea urchin tree of life

2018 ◽  
Author(s):  
Nicolás Mongiardino Koch ◽  
Simon E. Coppard ◽  
Harilaos A. Lessios ◽  
Derek E. G. Briggs ◽  
Rich Mooi ◽  
...  
Keyword(s):  
De Novo ◽  
Sea Urchins ◽  
Phylogenetic Signal ◽  
Gene Tree ◽  
Tree Of Life ◽  
Morphological Data ◽  
Morphological Evidence ◽  
Phylogenomic Analysis ◽  
Marine Animals ◽  
Sand Dollars

AbstractBackgroundEchinoidea is a clade of marine animals including sea urchins, heart urchins, sand dollars and sea biscuits. Found in benthic habitats across all latitudes, echinoids are key components of marine communities such as coral reefs and kelp forests. A little over 1,000 species inhabit the oceans today, a diversity that traces its roots back at least to the Permian. Although much effort has been devoted to elucidating the echinoid tree of life using a variety of morphological data, molecular attempts have relied on only a handful of genes. Both of these approaches have had limited success at resolving the deepest nodes of the tree, and their disagreement over the positions of a number of clades remains unresolved.ResultsWe performed de novo sequencing and assembly of 17 transcriptomes to complement available genomic resources of sea urchins and produce the first phylogenomic analysis of the clade. Multiple methods of probabilistic inference recovered identical topologies, with virtually all nodes showing maximum support. In contrast, the coalescent-based method ASTRAL-II resolved one node differently, a result apparently driven by gene tree error induced by evolutionary rate heterogeneity. Regardless of the method employed, our phylogenetic structure deviates from the currently accepted classification of echinoids, with neither Acroechinoidea (all euechinoids except echinothurioids), nor Clypeasteroida (sand dollars and sea biscuits) being monophyletic as currently defined. We demonstrate the strength and distribution of phylogenetic signal throughout the genome for novel resolutions of these lineages and rule out systematic biases as possible explanations.ConclusionsOur investigation substantially augments the molecular resources available for sea urchins, providing the first transcriptomes for many of its main lineages. Using this expanded genomic dataset, we resolve the position of several clades in agreement with early molecular analyses but in disagreement with morphological data. Our efforts settle multiple phylogenetic uncertainties, including the position of the enigmatic deep-sea echinothurioids and the identity of the sister clade to sand dollars. We offer a detailed assessment of evolutionary scenarios that could reconcile our findings with morphological evidence, opening up new lines of research into the development and evolutionary history of this ancient clade.

First Records of Bufo luchunnicus (Yang et Rao, 2008) and Amolops wenshanensis Yuan, Jin, Li, Stuart et Wu, 2018 (Anura: Bufonidae, Ranidae) from Vietnam

2020 ◽  
Vol 27 (2) ◽  
pp. 81-86
Author(s):  
Cuong The Pham ◽  
Minh Duc Le ◽  
Chung Van Hoang ◽  
Anh Van Pham ◽  
Thomas Ziegler ◽  
...  
Keyword(s):  
Natural History ◽  
Genetic Divergence ◽  
Morphological Data ◽  
Type Series ◽  
Lao Cai ◽  
First Time ◽  
Nd2 Gene ◽  
Quang Ninh

We record two species of amphibians for the first time from Vietnam: Bufo luchunnicus from Lao Cai and Son La provinces and Amolops wenshanensis from Quang Ninh Province. Morphologically, the Vietnamese representatives of B. luchunnicus resemble the type series from China. The specimen of A. wenshanensis from Vietnam slightly differs from the type series from China by having a smaller size (SVL 33.2 mm vs. 35.7 – 39.9 mm in males) and the presence of distinct transverse bands on the dorsal surfaces of limbs. Genetic divergence between the sequence of the Vietnamese specimen and those of A. wenshanensis from China available from GenBank is 1.2 – 1.6% (ND2 gene). In addition, morphological data and natural history notes of aforementioned species are provided from Vietnam.

scholarly journals Prediction of local geomagnetic activity on the example of data of “Lviv” Magnetic Observatory

2021 ◽  
Vol 27 (1) ◽  
pp. 78-84
Author(s):  
D.I. Vlasov ◽  
◽  
A.S. Parnowski ◽  
Keyword(s):  
Predictive Models ◽  
Lead Time ◽  
Measurement Data ◽  
Correlation Coefficients ◽  
Skill Score ◽  
Magnetic Observatory ◽  
Using Data ◽  
First Time ◽  
Prediction Efficiency ◽  
Main Center

For the first time in world practice, predictive models were constructed for X, Y, Z geomagnetic elements. Based on these models, the prediction was made with 3 hours lead time using data of the “Lviv” magnetic observatory. The properties of models are as follows: observatory — LVV, рredicted values — XYZ; lead time — 3 hours; correlation coefficients’ averaged measurement data — 0.824 (X), 0.811 (Y), 0.804 (Z); prediction efficiency — 0.816 (X), 0.803 (Y), 0.801 (Z); skill score — 0.115 (X), 0.095 (Y), 0.099 (Z). The developed models were tested in the Main Center of Special Monitoring, and they were found to meet the Basic Requirements for operational predictive models.

scholarly journals Comparative Cladistics: Fossils, Morphological Data Partitions and Lost Branches in the Fossil Tree of Life

2017 ◽  
Author(s):  
Ross Mounce
Keyword(s):  
Large Scale ◽  
Phylogenetic Signal ◽  
Scientific Progress ◽  
Molecular Data ◽  
Morphological Data ◽  
Data Sets ◽  
Phylogenetic Groups ◽  
Use Of Data ◽  
Wide Range ◽  
Cladistic Analyses

In this thesis I attempt to gather together a wide range of cladistic analyses of fossil and extant taxa representing a diverse array of phylogenetic groups. I use this data to quantitatively compare the effect of fossil taxa relative to extant taxa in terms of support for relationships, number of most parsimonious trees (MPTs) and leaf stability. In line with previous studies I find that the effects of fossil taxa are seldom different to extant taxa – although I highlight some interesting exceptions. I also use this data to compare the phylogenetic signal within vertebrate morphological data sets, by choosing to compare cranial data to postcranial data. Comparisons between molecular data and morphological data have been previously well explored, as have signals between different molecular loci. But comparative signal within morphological data sets is much less commonly characterized and certainly not across a wide array of clades. With this analysis I show that there are many studies in which the evidence provided by cranial data appears to be be significantly incongruent with the postcranial data – more than one would expect to see just by the effect of chance and noise alone. I devise and implement a modification to a rarely used measure of homoplasy that will hopefully encourage its wider usage. Previously it had some undesirable bias associated with the distribution of missing data in a dataset, but my modification controls for this. I also take an in-depth and extensive review of the ILD test, noting it is often misused or reported poorly, even in recent studies. Finally, in attempting to collect data and metadata on a large scale, I uncovered inefficiencies in the research publication system that obstruct re-use of data and scientific progress. I highlight the importance of replication and reproducibility – even simple reanalysis of high profile papers can turn up some very different results. Data is highly valuable and thus it must be retained and made available for further re-use to maximize the overall return on research investment.

scholarly journals Importance of the postcranial skeleton in eusuchian phylogeny: Reassessing the systematics of allodaposuchid crocodylians

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251900
Author(s):  
Alejandro Blanco
Keyword(s):  
Current Knowledge ◽  
Phylogenetic Signal ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Postcranial Skeleton ◽  
Skull Morphology ◽  
Taxonomic Descriptions ◽  
The Family ◽  
Phylogenetic Hypotheses ◽  
Internal Relationships

Our current knowledge on the crocodyliform evolution is strongly biased towards the skull morphology, and the postcranial skeleton is usually neglected in many taxonomic descriptions. However, it is logical to expect that it can contribute with its own phylogenetic signal. In this paper, the changes in the tree topology caused by the addition of the postcranial information are analysed for the family Allodaposuchidae, the most representative eusuchians in the latest Cretaceous of Europe. At present, different phylogenetic hypotheses have been proposed for this group without reaching a consensus. The results of this paper evidence a shift in the phylogenetic position when the postcranium is included in the dataset, pointing to a relevant phylogenetic signal in the postcranial elements. Finally, the phylogenetic relationships of allodaposuchids within Eusuchia are reassessed; and the internal relationships within Allodaposuchidae are also reconsidered after an exhaustive revision of the morphological data. New and improved diagnoses for each species are here provided.

scholarly journals Establishment of six new Rhabdoblatta species (Blattodea, Blaberidae, Epilamprinae) from China

ZooKeys ◽  
2019 ◽  
Vol 851 ◽  
pp. 27-69
Author(s):  
Rong Yang ◽  
Zhenzhen Wang ◽  
Yanshuang Zhou ◽  
Zongqing Wang ◽  
Yanli Che
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Molecular Species ◽  
Species Delimitation ◽  
Female Genitalia ◽  
Morphological Data ◽  
Coi Sequences ◽  
First Time

This study examined 504 Rhabdoblatta specimens sampled from China, of which, 86 Rhabdoblatta specimens were used for COI sequencing. A phylogenetic analysis using the ML method and MOTUs estimations by ABGD and GMYC based on COI sequences was performed. Eighteen Rhabdoblatta species were identified when these data were combined with morphological data. Six new species were established among these samples, i.e., Rh.similsinuatasp. n., Rh.densimaculatasp. n., Rh.gyroflexasp. n., Rh.chaulformissp. n., Rh.maculatasp. n., and Rh.ecarinatasp. n. For the first time, females including female genitalia of 14 known Rhabdoblatta species are described worldwide. Our study shows that combining molecular species delimitation methods with morphological data helps to delimit species and understand cockroach biodiversity.

Feather morphological predictors of angle-dependent color changes in parrot plumage

2020 ◽  
Vol 13 (4) ◽  
pp. 108-117
Author(s):  
Steven Reed ◽  
Richard K Simpson ◽  
Kevin J McGraw
Keyword(s):  
Phylogenetic Signal ◽  
Interspecific Variation ◽  
Plumage Color ◽  
Color Changes ◽  
Structural Colors ◽  
Angle Dependence ◽  
Novel Approach ◽  
Euclidean Distances ◽  
Parrot Species ◽  
First Time

Among the most ornate animal traits in nature are the angle-dependent (e.g. iridescent) structural colors of many fishes, damselflies, birds, beetles, and butterflies. Though we now have a solid understanding of the mechanisms that create angle-dependent coloration in several groups, we know little about whether pigmentary colors reflect light in an angle-dependent fashion or if similar or different mechanisms govern angle-dependent reflectance from pigmentary versus structural colors. Here for the first time we describe non-iridescent angle-dependent coloration from the tail and wing feathers of several parrot species (Aves: Psittaciformes). We employed a novel approach—by calculating chromatic and achromatic contrasts (in just noticeable differences, JNDs) of straight and angled measurements of the same feather patch—to test for perceptually relevant angle-dependent changes in coloration on dorsal and ventral feather surfaces. We found, among the 15 parrot species studied, significant angle dependence for seven of our eight feather JND parameters. We then measured micro-scale features on each side of feathers, including size and color of barbs and barbules, to attempt to predict interspecific variation in degree of angle-dependent reflectance. We found that barb height, plumage-color type (e.g. melanin, structural), and differences between barb-barbule coloration (measured using Euclidean distances) were the strongest predictors of angle-dependent coloration. Interestingly, there was no significant phylogenetic signal in any of the angle-dependence models tested. These findings deepen our views on the importance of microscopic feather features in the production of directional animal coloration, especially in tissues that are colored predominantly by pigments and appear to be statically colored.

scholarly journals The Immature Stages, Biology, and Phylogenetic Relationships of Rotunda rotundapex (Lepidoptera: Bombycidae)

2019 ◽  
Vol 19 (2) ◽  
Author(s):  
Rung-Juen Lin ◽  
Michael F Braby ◽  
Yu-Feng Hsu
Keyword(s):  
Phylogenetic Relationships ◽  
Host Plants ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Immature Stages ◽  
Systematic Classification ◽  
Separate Genus ◽  
Young Leaves ◽  
Segment 8 ◽  
First Time

Abstract The life history, morphology, and biology of the immature stages and phylogenetic relationships of Rotunda rotundapex (Miyata & Kishida, 1990) are described and illustrated for the first time. The species is univoltine: eggs hatch in spring (March or April) and the life cycle from egg to adult is completed in about 3 wk, with larvae developing rapidly on young leaves of the host plants, Morus australis and to a lesser extent Broussonetia monoica (Moraceae), and adults emerging in April–May. Eggs are laid in clusters on twigs of the host plant, are covered by scales during female oviposition, and remain in diapause for the remainder of the year (i.e., for 10–11 mo). Larvae (all instars) are unique among the Bombycidae in that they lack a horn on abdominal segment 8. A strongly supported molecular phylogeny based on six genes (5.0 Kbp: COI, EF-1α, RpS5, CAD, GAPDH, and wgl) representing seven genera of Bombycinae from the Old World revealed that Rotunda is a distinct monotypic lineage sister to Bombyx. This phylogenetic position, together with morphological data of the immature stages (egg and larval chaetotaxy), supports the current systematic classification in which the species rotundapex has been placed in a separate genus (Rotunda) from Bombyx in which it was previously classified.

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