Species-level phylogenetic analysis of pterocephaliids (Trilobita, Cambrian) from the Great Basin, western USA

2011 ◽  
Vol 85 (6) ◽  
pp. 1128-1153 ◽  
Author(s):  
Melanie J. Hopkins
Keyword(s):  
Phylogenetic Analysis ◽  
Great Basin ◽  
Species Level ◽  
Character State ◽  
State Transformation ◽  
Late Cambrian ◽  
The Family ◽  
Composite Section ◽  
Tree Topologies ◽  
Direct Ancestor

Considerable systematic work devoted to late Cambrian trilobites includes very little species-level phylogenetic analysis. This paper presents the phylogenetic analysis of 36 species representing eight genera assigned to the Family Pterocephaliidae that occur in the Great Basin of the western United States during the Steptoean stage (Furongian). Continuous characters are treated in four different ways: discretization using finite mixture coding, discretization using gap-weighting, “as such” using ranges of values as implemented in the phylogeny program TNT, and exclusion altogether. Results indicate that even the inclusion of only a few continuous characters dramatically increases the resolution of nodes. Despite the different treatments of continuous characters, major features of the trees are shared across all results. The subfamily Pterocephaliinae is restricted to genera which possess a concave anterior border. Relative stratigraphic placement was estimated using a composite section built in CONOP and used to scale the tree topologies and to assess stratigraphic consistency. Although previously hypothesized multispecies evolutionary series are not supported by the results, tree topology, stratigraphic distribution, and optimized character state transformation support the interpretation of several sister taxa as direct ancestor-descendent pairs.

Phylogeny accurately predicts behaviour in Indian Ocean Clitaetra spiders (Araneae:Nephilidae)

2009 ◽  
Vol 23 (3) ◽  
pp. 193 ◽  
Author(s):  
Matjaž Kuntner ◽  
Ingi Agnarsson
Keyword(s):  
South Africa ◽  
Phylogenetic Analysis ◽  
Indian Ocean ◽  
Species Level ◽  
Web Architecture ◽  
Evolutionarily Conserved ◽  
The Family ◽  
Behavioural Biology

Phylogenies are underutilised, powerful predictors of traits in unstudied species. We tested phylogenetic predictions of web-related behaviour in Clitaetra Simon, 1889, an Afro-Indian spider genus of the family Nephilidae. Clitaetra is phylogenetically sister to all other nephilids and thus important for understanding ancestral traits. Behavioural information on Clitaetra has been limited to only C. irenae Kuntner, 2006 from South Africa which constructs ladder webs. A resolved species-level phylogeny unambiguously optimised Clitaetra behavioural biology and predicted web traits in five unstudied species and a uniform intrageneric nephilid web biology. We tested these predictions by studying the ecology and web biology of C. perroti Simon, 1894 on Madagascar and C. episinoides Simon, 1889 on Mayotte. We confirm predicted arboricolous web architecture in these species. The expected ontogenetic allometric transition from orbs in juveniles to elongate ladder webs in adults was statistically significant in C. perroti, whereas marginally not significant in C. episinoides. We demonstrate the persistence of the temporary spiral in finished Clitaetra webs. A morphological and behavioural phylogenetic analysis resulted in unchanged topology and persisting unambiguous behavioural synapomorphies. Our results support the homology of Clitaetra hub reinforcement with the nephilid hub-cup. In Clitaetra, behaviour was highly predictable and remained consistent with new observations. Our results confirm that nephilid web biology is evolutionarily conserved within genera.

scholarly journals The challenges and potential utility of phenotypic specimen-level phylogeny based on maximum parsimony

2018 ◽  
Vol 109 (1-2) ◽  
pp. 301-323 ◽  
Author(s):  
Emanuel TSCHOPP ◽  
Paul UPCHURCH
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Parsimony ◽  
Large Scale ◽  
Intraspecific Variability ◽  
Species Level ◽  
A Posteriori ◽  
Operational Taxonomic Units ◽  
Vertebrate Palaeontology ◽  
Tree Topologies ◽  
Parsimony Criterion

ABSTRACTSpecimen-level phylogenetic approaches are widely used in molecular biology for taxonomic and systematic purposes. However, they have been largely ignored in analyses based on morphological traits, where phylogeneticists mostly resort to species-level analyses. Recently, a number of specimen-level studies have been published in vertebrate palaeontology. These studies indicate that specimen-level phylogeny may be a very useful tool for systematic reassessments at low taxonomic levels. Herein, we review the challenges when working with individual organisms as operational taxonomic units in a palaeontological context, and propose guidelines of how best to perform a specimen-level phylogenetic analysis using the maximum parsimony criterion. Given that no single methodology appears to be perfectly suited to resolve relationships among individuals, and that different taxa probably require different approaches to assess their systematics, we advocate the use of a number of methodologies. In particular, we recommend the inclusion of as many specimens and characters as feasible, and the analysis of relationships using an extended implied weighting approach with different downweighting functions. Resulting polytomies should be explored using a posteriori pruning of unstable specimens, and conflicting tree topologies between different iterations of the analysis should be evaluated by a combination of support values such as jackknifing and symmetric resampling. Species delimitation should be consistent among the ingroup and based on a reproducible approach. Although time-consuming and methodologically challenging, specimen-level phylogenetic analysis is a highly useful tool to assess intraspecific variability and provide the basis for a more informed and accurate creation of species-level operational taxonomic units in large-scale systematic studies. It also has the potential to inform us about past speciation processes, morphological trait evolution, and their potential intrinsic and extrinsic drivers in pre-eminent detail.

The Late Cambrian (Steptoean; Furongian) trilobite Pseudokingstonia Palmer, 1965 in North America

2009 ◽  
Vol 46 (5) ◽  
pp. 355-360
Author(s):  
Stephen R. Westrop ◽  
Jonathan M. Adrain
Keyword(s):  
North America ◽  
Great Basin ◽  
Anterior Margin ◽  
Lower Half ◽  
Anterior Border ◽  
Late Cambrian ◽  
Type Area ◽  
The Family ◽  
New Material ◽  
High Degree

The poorly known Late Cambrian (Steptoean; Furongian) genus Pseudokingstonia Palmer is revised using new material from the type area in west-central Utah. Previously undocumented features of pygidial morphology, including patterns of segmentation of the axis and pleural fields, and articulating flanges on the anterior margin, confirm that the genus is closely related to the dameselloidean Cheilocephalus Berkey and that together they constitute the family Cheilocephalidae Shaw. Pseudokingstonia is diagnosed by a high degree of cranidial and, especially, pygidial effacement, an exceedingly short anterior border on the cranidium, and steeply sloping pygidial borders. In addition to the Great Basin of Nevada and Utah, the genus is also known from Alberta, Arkansas, and Pennsylvania, and all occurrences are confined to the lower half of the late Steptoean Elvinia Zone.

Systematics of the Gondwanan pseudoscorpion family Hyidae (Pseudoscorpiones:Neobisioidea): new data and a revised phylogenetic hypothesis

2007 ◽  
Vol 21 (4) ◽  
pp. 365 ◽  
Author(s):  
Mark S. Harvey ◽  
Erich S. Volschenk
Keyword(s):  
Phylogenetic Analysis ◽  
Type Species ◽  
Short Range ◽  
Phylogenetic Position ◽  
Central Position ◽  
Phylogenetic Hypothesis ◽  
Biogeographic Patterns ◽  
The Family ◽  
Tree Topologies ◽  
The Indian Ocean

The neobisioid pseudoscorpion family Hyidae has a distribution spanning the margins of the Indian Ocean and its phylogenetic position has been suggested to lie midway between a clade containing the Bochidae and Ideoroncidae, and a clade containing the remaining neobisioid families, Gymnobisiidae, Neobisiidae, Parahyidae and Syarinidae. Their central position within the Neobisioidea, and their biogeographic patterns, have prompted the present study, which is designed to test the monophyly of the family, deduce the phylogeny of all known hyids and to describe several newly discovered species. The phylogenetic analysis of the 14 species of the pseudoscorpion family Hyidae along with 20 other species of Neobisioidea demonstrates the monophyly of the family and its distinctness from all other neobisioid families. Two genera, Hya Chamberlin and Indohya Beier, are recognised, even though the phylogenetic analysis did not consistently recover the monophyly of Indohya. The effect of outgroup selection was tested on the Hyidae and revealed markedly different tree topologies. Hyella Harvey, with the type species H. humphreysi Harvey, is newly synonymised with Indohya owing to similarities between the previously described species and some new troglobitic species. The Indohyinae Harvey is synonymised with Hyidae. Two new epigean species and three new troglobitic species of Indohya are described: I. damocles, sp. nov., I. gollum, sp. nov., I. haroldi, sp. nov. and I. napierensis, sp. nov. from northern Western Australia, and I. jacquelinae, sp. nov. from Madagascar. All species of Indohya are short-range endemics, having very small distributional ranges. New data are presented for Indohya humphreysi (Harvey), including the first description of the male. The first protonymphs of the family Hyidae are described, including those of Hya minuta (Tullgren) and Indohya gollum, sp. nov.

scholarly journals Two new Lophoturus species (Diplopoda, Polyxenida, Lophoproctidae) from Queensland, Australia

ZooKeys ◽  
2018 ◽  
Vol 741 ◽  
pp. 133-154 ◽  
Author(s):  
Cuong Huynh ◽  
Anneke A. Veenstra
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Analysis ◽  
Morphological Characters ◽  
Species Level ◽  
Tropical Region ◽  
Undescribed Species ◽  
Body Colour ◽  
Body Form ◽  
The Family ◽  
Two New Species

Lophoturus queenslandicus Verhoeff, 1924 was the first penicillate millipede in the family Lophoproctidae collected from Cairns, a tropical region in Queensland, Australia, to be formally described. Specimens collected from this region in a recent study had the morphological characters known to define this genus. However, their body form and length, as well as dorsal colouration proved to be different, suggesting the possibility of more than one Lophoturus species. This assertion was supported by the results of a phylogenetic analysis of DNA extracted and sequenced using 18S and COI regions from L. queenslandicus and two undescribed species from this genus. Specimens preserved in ethanol can prove difficult to confidently identify to species level because their colour gradually fades. Examination of live specimens with their body colour visible, together with morphological characters and DNA analysis is the most reliable way of correctly distinguishing between these three species. Two new species, L. boondallus sp. n. and L. molloyensis sp. n. collected in Queensland, Australia are described.

Phylogeny, taxonomy and distribution of the Neotropical lizard genus Echinosaura (Squamata: Gymnophthalmidae), with the recognition of two new genera in Cercosaurinae

2019 ◽  
Vol 189 (1) ◽  
pp. 287-314
Author(s):  
Juan D Vásquez-Restrepo ◽  
Roberto Ibáñez ◽  
Santiago J Sánchez-Pacheco ◽  
Juan M Daza
Keyword(s):  
Phylogenetic Analysis ◽  
Central America ◽  
Species Level ◽  
New Genera ◽  
The Family ◽  
Taxonomic Changes ◽  
Molecular Dataset ◽  
Northern South America ◽  
Taxonomic Studies ◽  
First Time

Abstract The family Gymnophthalmidae is a highly diverse Neotropical lizard clade. Although multiple phylogenetic and taxonomic studies have reshaped our understanding of gymnophthalmid systematics and diversity, many groups remain understudied. This is the case for the cercosaurine genus Echinosaura, which includes eight species of small riparian lizards distributed across lower Central America and northern South America. Here, we present a comprehensive phylogenetic analysis of Echinosaura, including DNA data for all species of the genus for the first time. To rigorously test the relationships of all Echinosaura, we have assembled the largest molecular dataset of cercosaurine lizards to date. Our analysis refutes the monophyly of Echinosaura, with E. apodema and E. sulcarostrum not closely related to the remaining species. To remedy the polyphyly of Echinosaura, we describe two new genera for E. apodema and E. sulcarostrum. Morphological distinctiveness and biogeography further support these taxonomic changes. In light of our phylogenetic results, we review the species-level taxonomy of the redefined Echinosaura based on morphological and genetic variation. We resurrect E. centralis and designate a neotype given the absence of type and topotypic material. In addition, we provide taxonomic accounts for each species and analyse their patterns of geographic distribution.

LINGULIFORM BRACHIOPODS ACROSS THE STEPTOEAN/SUNWAPTAN (LATE CAMBRIAN) “BIOMERE” BOUNDARY IN THE GREAT BASIN, USA

2017 ◽  
Author(s):  
Rebecca L. Freeman ◽  
◽  
James F. Miller ◽  
Kevin R. Evans ◽  
Damon J. Bassett
Keyword(s):  
Great Basin ◽  
Late Cambrian

scholarly journals Extensive Phylogenetic Analysis of Piscine Orthoreovirus Genomic Sequences Shows the Robustness of Subgenotype Classification

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 41
Author(s):  
Marcos Godoy ◽  
Daniel A. Medina ◽  
Rudy Suarez ◽  
Sandro Valenzuela ◽  
Jaime Romero ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Genetic Variation ◽  
Sequence Analysis ◽  
Molecular Phylogeny ◽  
Phylogenetic Trees ◽  
Genomic Segment ◽  
Double Stranded Rna ◽  
The Family ◽  
Original Classification

Piscine orthoreovirus (PRV) belongs to the family Reoviridae and has been described mainly in association with salmonid infections. The genome of PRV consists of about 23,600 bp, with 10 segments of double-stranded RNA, classified as small (S1 to S4), medium (M1, M2 and M3) and large (L1, L2 and L3); these range approximately from 1000 bp (segment S4) to 4000 bp (segment L1). How the genetic variation among PRV strains affects the virulence for salmonids is still poorly understood. The aim of this study was to describe the molecular phylogeny of PRV based on an extensive sequence analysis of the S1 and M2 segments of PRV available in the GenBank database to date (May 2020). The analysis was extended to include new PRV sequences for S1 and M2 segments. In addition, subgenotype classifications were assigned to previously published unclassified sequences. It was concluded that the phylogenetic trees are consistent with the original classification using the PRV genomic segment S1, which differentiates PRV into two major genotypes, I and II, and each of these into two subgenotypes, designated as Ia and Ib, and IIa and IIb, respectively. Moreover, some clusters of country- and host-specific PRV subgenotypes were observed in the subset of sequences used. This work strengthens the subgenotype classification of PRV based on the S1 segment and can be used to enhance research on the virulence of PRV.

A REVISED GENERIC SYNOPSIS OF HYACINTHACEAE IN SUB-SAHARAN AFRICA, BASED ON MOLECULAR EVIDENCE, INCLUDING NEW COMBINATIONS AND THE NEW TRIBE PSEUDOPROSPEREAE

2003 ◽  
Vol 60 (3) ◽  
pp. 533-568 ◽  
Author(s):  
J. C. MANNING ◽  
P. GOLDBLATT ◽  
M. F. FAY
Keyword(s):  
Phylogenetic Analysis ◽  
Sub Saharan Africa ◽  
Molecular Evidence ◽  
New Combinations ◽  
Generic Level ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Single Genus ◽  
New Tribe ◽  
Sub Saharan

A revised generic synopsis of sub-Saharan Hyacinthaceae is presented, based on a molecular phylogenetic analysis of the family. Generic rank is accorded only to reciprocally monophyletic clades that can be distinguished by recognizable morphological discontinuities, thereby permitting an appropriate generic assignment of species not included in the analysis. Three subfamilies are recognized within the region. Subfamily Ornithogaloideae, characterized by flattened or angular seeds with tightly adhering testa, is considered to include the single genus Ornithogalum, which is expanded to include the genera Albuca, Dipcadi, Galtonia, Neopatersonia and Pseudogaltonia. Recognizing any of these segregates at generic level renders the genus Ornithogalum polyphyletic, while subdivision of Ornithogalum into smaller, morphologically distinguishable segregates in order to preserve the monophyly of each is not possible. Subfamily Urgineoideae, characterized by flattened or winged seeds with brittle, loosely adhering testa, comprises the two mainland African genera Bowiea and Drimia. The latter is well circumscribed by its deciduous, short-lived perianth and includes the previously recognized genera Litanthus, Rhadamanthus, Schizobasis and Tenicroa. The monotypic Madagascan Igidia is provisionally included in the subfamily as a third genus on the basis of its seeds, pending molecular confirmation of its relationships. Subfamily Hyacinthoideae resolves into three clades, distinguished as tribes Hyacintheae (strictly northern hemisphere and not treated further), Massonieae and Pseudoprospereae tribus nov. Full descriptions and a key to their identification are provided for all genera. New combinations reflecting the generic circumscriptions adopted here are made for most African and all Indian and Madagascan species.

A Family of Genes Clustered at the Triplo-lethal Locus of Drosophila melanogaster Has an Unusual Evolutionary History and Significant Synteny With Anopheles gambiae

Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 613-621 ◽  
Author(s):  
Douglas R Dorer ◽  
Jamie A Rudnick ◽  
Etsuko N Moriyama ◽  
Alan C Christensen
Keyword(s):  
Phylogenetic Analysis ◽  
Drosophila Melanogaster ◽  
Anopheles Gambiae ◽  
Evolutionary History ◽  
Codon Bias ◽  
Good Target ◽  
The Family ◽  
Genes Encoding ◽  
And Function ◽  
Gambiae Genome

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.

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