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"Cladistic analysis."
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Deep time : cladistics, the revolution in evolution
\"For a long time, popular scientists have told us that by looking at a fossilised bone we could tell whether it belonged to our ancestors. This is not true. A fossil cannot answer scientific questions of ascent and descent. Following this logic. Henry Gee shows us that the stories we have told ourselves about the history of life are pure imagination.\" \"Real scientists have put aside such popular bedtime stories about ancestry for decades. Instead, they have adopted a method called cladistics. This simple technique of comparison makes no unsustainable assumptions about ancestry and descent. Cladistics is the true, scientific heart of palaeontology.\" \"Henry Gee shows how cladistics has punctured holes in our cherished view of evolution as progressive, culminating in humanity. He shows how fish evolved legs not to crawl onto land, but to get back underwater as quickly as possible. He shows how dinosaurs evolved feathers long before they became birds - so whatever feathers were used for, it wasn't for flying. Cladistics shows that birds and dinosaurs are intimate relations, and offers the startling suggestion that some dinosaurs could have been the dragons that fell to Earth. In the age-old debate over what came first, the chicken or the egg, cladistics has the definitive answer - the egg.\"--Jacket.
Discovery of the pincer wasp Thaumatodryininae (Hymenoptera, Dryinidae) in Burmese amber, with description of a new genus and the first phylogenetic analysis of the subfamily
Thaumatodryininae is a small subfamily of Dryinidae, known to attack nymphs of auchenorrhynchous Flatidae (Hemiptera). Only one genus is recognized, Thaumatodryinus Perkins, with 35 species including fossil and extant taxa. Currently, the oldest record for the genus is from Baltic amber. Here, we present the first record of Thaumatodryininae from mid-Cretaceous Burmese amber with the description of † Thaumatorrhinos athrix gen. et sp. nov. , derived from the first phylogeny for this subfamily based on morphological characters. The placement of † Thaumatorrhinos gen. nov. in Thaumatodryininae and the phylogenetic relationships of this subfamily within Dryinidae are discussed.
Journal Article
Oneirosaurus caballeroi gen. et sp. nov., a nev., mosasaur from Colombia/Oneirosaurus caballeroi gen. et sp. nov., un nuevo mosasaurio de Colombia
A new mosasaur specimen found in the Coniacian beds of Lebrija, Santander, Central Colombia, is here described. The new specimen represents a new genus and species of plioplatecarpine mosasaurid that we name Oneirosaurus caballeroi gen. et sp. nov. Oneirosaurus is a plioplatecarpine characterized by one character unknown in any other plioplatecarpine: the presence of two external foramina for the exit of nerves X, XI, and XII. It is also distinguished by a combination of characters that includes among others: prefrontal and postorbitofrontal separated at the roof of the orbit; broad frontal, with short triangular surface anterior to the orbits; triangular and broad anterodorsal surface of the parietal contacting the postorbital for a short distance; infrastapedial process of the quadrate robust without being fused to the suprastapedial process; small otosphenoidal crest of prootic not covering the exit of nerve VII; basioccipital canal opening into the floor of the braincase through two large foramina separated by a medial septum; lingual alveolar parapet of dentary lower than labial; marginal teeth crown with subcircular cross-section at base and with two carinae arranged at 180[degrees]; and presence of a notch in anterior border of the atlas neural arch. The morphological comparisons and the cladistic analysis show the new taxon as an intermedium plioplatecarpine with phylogenetic proximity to the Colombian species Yaguarasaurus columbianus from the lower Turonian and to the species Ectenosaurus clidastoides from the Santonian-Campanian of the USA. Our phylogenetic results shows tethysaurines and halisaurines as plesio-pelvic and plesiopedal groups separated from the hydropelvic and hydropedal derived groups Tylosaurinae, Plioplatecarpinae, and Mosasaurinae.
Journal Article
Cladistic analysis of the genus Bruggmanniella Tavares
In this study, we present a phylogenetic analysis of the genus Bruggmanniella Tavares based on morphological features. Cladistic analyses were conducted using 57 characters from 26 species. All species of Bruggmanniella except for B. byrsonimae were selected as ingroup and the genera Asphondylia Loew, Bruggmannia Tavares, Illiciomyia Tokuda, Parazalepidota Maia, Pseudasphondylia Monzen, Schizomyia Kieffer, and Lopesia Rübsaamen as outgroup. We used characters from larvae, pupae, adults, and galls. The results of this study supported Bruggmanniella as the sister group of Pseudasphondylia. Bruggmanniella actinodaphnes Tokuda and Yukawa and B. cinnamomi Tokuda and Yukawa have been moved to genus Pseudasphondylia (Pseudasphondylia actinodaphnes (Tokuda and Yukawa) comb. nov. and Pseudasphondylia cinnamomi (Tokuda and Yukawa) comb. nov.). The new genus Odontokeros gen. nov. has been erected for the single species Odontokeros brevipes (Lin, Yang & Tokuda) comb. nov. In addition, we described a new Brazilian species, Bruggmanniella miconia Garcia, Lamas and Urso-Guimarães sp. nov. Identification keys to the New World species of Bruggmanniella are presented.
Journal Article
The oldest species of Peltoperleidus of China, with phylogenetic and biogeographic implications
The previously alleged 'perleidid' genus Peltoperleidus is a stem-neopterygian fish taxon with two or three horizontal rows of notably deepened flank scales. Until recently, members of this genus were known only from the Ladinian (late Middle Triassic) or near the Anisian/Ladinian boundary (~242 Ma) in southern Switzerland and northern Italy. Here, I report the discovery of a new species of the genus, Peltoperleidus asiaticus sp. nov., based on three well-preserved specimens from the Anisian (early Middle Triassic, ~244 Ma) of Luoping, eastern Yunnan, China. The discovery extends the geological range of Peltoperleidus by approximately two million years and documents the first record of the genus in Asia. Similar to its relatives (represented by P. macrodontus) from Europe, P. asiaticus sp. nov. is likely a small-sized durophagous predator with dentition combining grasping and crushing morphologies. Results of a cladistic analysis unite four species of Peltoperleidus as a monophyletic group within the Louwoichthyiformes, and suggest that the presence of two horizontal rows of notably deepened scales was independently evolved in Peltoperleidus and another stem-neopterygian taxon Altisolepis. P. asiaticus sp. nov. is nested at the base of Peltoperleidus, and a new family Peltoperleididae is proposed for the genus, contrasting the previous placement of Peltoperleidus in the poorly defined, paraphyletic 'Perleididae'. Comparative studies of the basal peltoperleidid from China with its younger relatives from Europe provide new insights into the evolutionary origin and paleogeographic distribution of this clade.
Journal Article
Close relatives of Mediterranean endemo-relict hoverflies
An ongoing study of the genus Merodon Meigen, 1803 in the Republic of South Africa (RSA) has revealed the existence of new species related to M. melanocerus Bezzi, 1915. The M. melanocerus subgroup belongs to the Afrotropical lineage of the M. desuturinus group. Revision of all available material from museums and detailed analyses of newly -collected specimens from our own expeditions to RSA resulted in delimitation of five species: M. capensis Hurkmans sp. n., M. commutabilis Radenkovic et Vujic sp. n., M. drakonis Vujic et Radenkovic sp. n., M. flavocerus Hurkmans sp. n. and M. melanocerus. In addition to classical morphological characters, sequences of the mitochondrial COI gene are provided for four related taxa. Results of molecular phylogenetic analyses supports monophyly of the M. desuturinus group and confirmed delimitation between species. Links between Palaearctic and Afrotropical faunas of this group, as well as possible evolutionary paths, are discussed. Based on phylogenetic analyses, four lineages (putative subgenera) have been recognized within the genus Merodon; besides the three previously established ones, albifrons+desuturinus, aureus (sensu lato) and avidus-nigritarsis, one new lineage named natans is distinguished.
Journal Article
Helen’s twins in the Balkans: discovery of two new Paraptychoptera Tonnoir, 1919 species closely related to P. helena Peus, 1958, with systematic revision of the “lacustris” group (Diptera, Ptychopteridae)
Ptychoptera castor Keresztes & Klappert, sp. nov. and P. pollux Keresztes & Török, sp. nov. both belong to the subgenus Ptychoptera (Paraptychoptera)Tonnoir (1919) and are described from boggy headwaters in the south Balkan area. These new species are closely related to the range-restricted P. helena Peus, 1958, which is known only from Oiti village, Mount Oeta, Phthioitis region, Greece and, together with P. lacustris , forms a morphologically well-defined unit in the subgenus Paraptychoptera. Based on cladistic analyses of 53 different morphological characters using the male antenna, wing, and genital structures, a general revision of the “lacustris” group is proposed with a dichotomous key of Paraptychoptera species.
Journal Article
TreeTime: Maximum-likelihood phylodynamic analysis
Abstract
Mutations that accumulate in the genome of cells or viruses can be used to infer their evolutionary history. In the case of rapidly evolving organisms, genomes can reveal their detailed spatiotemporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidly evolving viral pathogens. As the number of genome sequences available for different pathogens has increased dramatically over the last years, phylodynamic analysis with traditional methods becomes challenging as these methods scale poorly with growing datasets. Here, we present TreeTime, a Python-based framework for phylodynamic analysis using an approximate Maximum Likelihood approach. TreeTime can estimate ancestral states, infer evolution models, reroot trees to maximize temporal signals, estimate molecular clock phylogenies and population size histories. The runtime of TreeTime scales linearly with dataset size.
Journal Article
Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10
The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses.
Journal Article