scholarly journals Cladistics and rates of morphological evolution: computation and comparison

1992 ◽  
Vol 6 ◽  
pp. 61-61
Author(s):  
Richard Cloutier ◽  
Timothy Rowe
Keyword(s):  
Morphological Evolution ◽  
Average Rate ◽  
Relative Rate ◽  
Phylogenetic Analyses ◽  
Evolutionary Rates ◽  
Data Matrix ◽  
Morphological Data ◽  
Geological Time Scale ◽  
Rates Of Evolution ◽  
Wide Range

For the part fifty years, the concept of evolutionary rates has been developed largely in an evolutionary or phenetic framework. Many authors discussed rates, but under previous systematic paradigms no standardized methods developed to provide a uniform and general framework in which temporal properties of different lineages could be objectively measured and compared.We review recently developed methods for measuring rate-related properties of lineages that are based on phylogenetic analyses. Rate measurements are made directly from phylogenetic data matrices and cladograms. Because they benefit from the standardized procedures required to compile a data matrix, these methods are potentially exportable to a wide range of phylogenetic studies. Four potential factors relevant to the study of evolutionary rates in a cladistic framework have been analyzed with these methods: (1) morphological changes, (2) age and duration, (3) cladogenesis, and (4) species-diversity. We investigate interactions among these factors.Underlying assumptions in using a cladogram to calculate rates of evolution are: (1) the tree reflects the history of the group, and (2) the distributions of character states on the tree reflects the true distribution of character states during the evolution of the group. The calculation of rates from a cladogram requires that: (1) the cladograms are derived from parsimony analysis (e.g., PAUP, HENNIG86) of species coded for discrete character states; (2) the phylogenetic pattern (or branching sequence) is superimposed on a geological time scale in which each species is mapped according to its geological age (temporal cladogram); (3) phylogenetic pathways (unidirectional series of consecutive cladogenetic events) are determined in such a manner that the selected origin is a hypothetical ancestor to the terminal taxa selected; and (4) rates are calculated along selected phylogenetic pathways.Rates may be calculated as the number of changes—including autapomorphies, synapomorphies, and homoplasies—per unit of time. Alternatively, relative measures of rate may be obtained by comparing the average number of changes for an entire data matrix with changes in data subsets within the matrix. Five types of rates of morphological evolution can be determined and quantified along a phylogenetic pathway: (1) rate between two consecutive cladogenetic events, (2) rate during a geological period, (3) rate during a fixed period of time in millions of years, (4) relative rates of change for different morphological data subsets, such as dentition versus skeleton, and (5) relative rate along a selected segment of the cladogram, compared to the average rate measured for the cladogram as a whole. Various methods for comparing rates are investigated, such as Spearman Rank correlation, Fourier analysis, time series, and homoplasy index.Classic examples of rates of morphological evolution were previously taken from bivalves, echinoderms, lungfishes, coelacanths, and mammals. In the present study, rates of evolution within and/or between the Dipnoi (lungfishes), the Actinistia (coelacanths), and the Mammalia are calculated and compared.

scholarly journals Morphological and molecular rates of evolution in post-Paleozoic echinoids

1992 ◽  
Vol 6 ◽  
pp. 273-273
Author(s):  
Andrew B. Smith ◽  
R. Christen
Keyword(s):  
Morphological Evolution ◽  
Large Subunit ◽  
Rank Correlation ◽  
Great Majority ◽  
Data Matrix ◽  
Time Interval ◽  
28S Rrna ◽  
Geological Time ◽  
Molecular Change ◽  
Rates Of Evolution

Phylogenetic analysis of a data matrix of 86 skeletal characteristics, and of the first 400 bases of the 5’ end of the large subunit ribosomal RNA gene produce congruent cladograms for 11 extant echinoids. Based on these cladistic analyses the great majority of morphologic and molecular apomorphies can be placed in one of 18 independent geological time intervals. When the cladogram is calibrated using the fossil record of post-Paleozoic echinoids, rates of molecular change in 28S rRNA can be calculated and compared with estimated rates of morphological evolution.Morphological and molecular apomorphies acquired in each time interval both correlate moderately strongly with time elapsed, but less strongly with one another. As expected, morphological rates vary considerably over time and between sister groups, but so too do molecular rates. When averaged over all echinoids studied, the number of morphological apomorphies accrued yields a slightly higher Spearman Rank correlation coefficient with time elapsed than does the number of molecular apomorphies accrued. This is because there is a three-fold difference in the rate of molecular change amongst the echinoid lineages studied.

scholarly journals Host Switching in Lyssavirus History from the Chiroptera to the Carnivora Orders

2001 ◽  
Vol 75 (17) ◽  
pp. 8096-8104 ◽  
Author(s):  
Hassan Badrane ◽  
Noël Tordo
Keyword(s):  
Average Rate ◽  
Relative Rate ◽  
Phylogenetic Reconstruction ◽  
Surface Glycoprotein ◽  
Host Switching ◽  
Virulence Determinants ◽  
Rates Of Evolution ◽  
Tests Of Neutrality ◽  
Genes Encoding ◽  
History Of

ABSTRACT Lyssaviruses are unsegmented RNA viruses causing rabies. Their vectors belong to the Carnivora and Chiroptera orders. We studied 36 carnivoran and 17 chiropteran lyssaviruses representing the main genotypes and variants. We compared their genes encoding the surface glycoprotein, which is responsible for receptor recognition and membrane fusion. The glycoprotein is the main protecting antigen and bears virulence determinants. Point mutation is the main force in lyssavirus evolution, as Sawyer's test and phylogenetic analysis showed no evidence of recombination. Tests of neutrality indicated a neutral model of evolution, also supported by globally high ratios of synonymous substitutions (dS ) to nonsynonymous substitutions (dN ) (>7). Relative-rate tests suggested similar rates of evolution for all lyssavirus lineages. Therefore, the absence of recombination and similar evolutionary rates make phylogeny-based conclusions reliable. Phylogenetic reconstruction strongly supported the hypothesis that host switching occurred in the history of lyssaviruses. Indeed, lyssaviruses evolved in chiropters long before the emergence of carnivoran rabies, very likely following spillovers from bats. Using dated isolates, the average rate of evolution was estimated to be roughly 4.3 × 10−4 dS /site/year. Consequently, the emergence of carnivoran rabies from chiropteran lyssaviruses was determined to have occurred 888 to 1,459 years ago. Glycoprotein segments accumulating more dN than dS were distinctly detected in carnivoran and chiropteran lyssaviruses. They may have contributed to the adaptation of the virus to the two distinct mammal orders. In carnivoran lyssaviruses they overlapped the main antigenic sites, II and III, whereas in chiropteran lyssaviruses they were located in regions of unknown functions.

scholarly journals Evaluating species in Botryosphaeriales

2021 ◽  
Author(s):  
W. Zhang ◽  
J.Z. Groenewald ◽  
L. Lombard ◽  
R.K. Schumacher ◽  
A.J.L. Phillips ◽  
...  
Keyword(s):  
South Africa ◽  
Woody Plants ◽  
Phylogenetic Analyses ◽  
Culture Collection ◽  
Morphological Data ◽  
Culture Collections ◽  
Future Studies ◽  
The Past ◽  
Wide Range ◽  
Solid Foundation

The Botryosphaeriales (Dothideomycetes) includes numerous endophytic, saprobic, and plant pathogenic species associated with a wide range of symptoms, most commonly on woody plants. In a recent phylogenetic treatment of 499 isolates in the culture collection (CBS) of the Westerdijk Institute, we evaluated the families and genera accommodated in this order of important fungi. The present study presents multigene phylogenetic analyses for an additional 230 isolates, using ITS, tef1, tub2, LSU and rpb2 loci, in combination with morphological data. Based on these data, 58 species are reduced to synonymy, and eight novel species are described. They include Diplodia afrocarpi (Afrocarpus, South Africa), Dothiorella diospyricola (Diospyros, South Africa), Lasiodiplodia acaciae (Acacia, Indonesia), Neofusicoccum podocarpi (Podocarpus, South Africa), N. rapaneae (Rapanea, South Africa), Phaeobotryon ulmi (Ulmus, Germany), Saccharata grevilleae (Grevillea, Australia) and S. hakeiphila (Hakea, Australia). The results have clarified the identity of numerous isolates that lacked Latin binomials or had been deposited under incorrect names in the CBS collection in the past. They also provide a solid foundation for more in-depth future studies on taxa in the order. Sequences of the tef1, tub2 and rpb2 genes proved to be the most reliable markers. At the species level, results showed that the most informative genes were inconsistent, but that a combination of four candidate barcodes (ITS, tef1, tub2 and rpb2) provided reliable resolution. Furthermore, given the large number of additional isolates included in this study, and newly generated multigene DNA datasets, several species could also be reduced to synonymy. The study illustrates the value of reassessing the identity of older collections in culture collections utilising modern taxonomic frameworks and methods.

scholarly journals Rapid morphological evolution in placental mammals post-dates the origin of the crown group

2019 ◽  
Vol 286 (1898) ◽  
pp. 20182418 ◽  
Author(s):  
Thomas J. D. Halliday ◽  
Mario dos Reis ◽  
Asif U. Tamuri ◽  
Henry Ferguson-Gow ◽  
Ziheng Yang ◽  
...  
Keyword(s):  
Fossil Record ◽  
Morphological Evolution ◽  
Relative Rate ◽  
Molecular Data ◽  
Placental Mammal ◽  
Dental Morphology ◽  
Crown Group ◽  
Rates Of Evolution ◽  
Early Paleocene ◽  
Molecular Evolutionary Rates

Resolving the timing and pattern of early placental mammal evolution has been confounded by conflict among divergence date estimates from interpretation of the fossil record and from molecular-clock dating studies. Despite both fossil occurrences and molecular sequences favouring a Cretaceous origin for Placentalia, no unambiguous Cretaceous placental mammal has been discovered. Investigating the differing patterns of evolution in morphological and molecular data reveals a possible explanation for this conflict. Here, we quantified the relationship between morphological and molecular rates of evolution. We show that, independent of divergence dates, morphological rates of evolution were slow relative to molecular evolution during the initial divergence of Placentalia, but substantially increased during the origination of the extant orders. The rapid radiation of placentals into a highly morphologically disparate Cenozoic fauna is thus not associated with the origin of Placentalia, but post-dates superordinal origins. These findings predict that early members of major placental groups may not be easily distinguishable from one another or from stem eutherians on the basis of skeleto-dental morphology. This result supports a Late Cretaceous origin of crown placentals with an ordinal-level adaptive radiation in the early Paleocene, with the high relative rate permitting rapid anatomical change without requiring unreasonably fast molecular evolutionary rates. The lack of definitive Cretaceous placental mammals may be a result of morphological similarity among stem and early crown eutherians, providing an avenue for reconciling the fossil record with molecular divergence estimates for Placentalia.

scholarly journals Total-Evidence Framework Reveals Complex Morphological Evolution in Nightbirds (Strisores)

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 143 ◽  
Author(s):  
Albert Chen ◽  
Noor D. White ◽  
Roger B.J. Benson ◽  
Michael J. Braun ◽  
Daniel J. Field
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Sequence Data ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Anatomical Data ◽  
Evidence Framework

Strisores is a clade of neoavian birds that include diurnal aerial specialists such as swifts and hummingbirds, as well as several predominantly nocturnal lineages such as nightjars and potoos. Despite the use of genome-scale molecular datasets, the phylogenetic interrelationships among major strisorean groups remain controversial. Given the availability of next-generation sequence data for Strisores and the clade’s rich fossil record, we reassessed the phylogeny of Strisores by incorporating a large-scale sequence dataset with anatomical data from living and fossil strisoreans within a Bayesian total-evidence framework. Combined analyses of molecular and morphological data resulted in a phylogenetic topology for Strisores that is congruent with the findings of two recent molecular phylogenomic studies, supporting nightjars (Caprimulgidae) as the extant sister group of the remainder of Strisores. This total-evidence framework allowed us to identify morphological synapomorphies for strisorean clades previously recovered using molecular-only datasets. However, a combined analysis of molecular and morphological data highlighted strong signal conflict between sequence and anatomical data in Strisores. Furthermore, simultaneous analysis of molecular and morphological data recovered differing placements for some fossil taxa compared with analyses of morphological data under a molecular scaffold, highlighting the importance of analytical decisions when conducting morphological phylogenetic analyses of taxa with molecular phylogenetic data. We suggest that multiple strisorean lineages have experienced convergent evolution across the skeleton, obfuscating the phylogenetic position of certain fossils, and that many distinctive specializations of strisorean subclades were acquired early in their evolutionary history. Despite this apparent complexity in the evolutionary history of Strisores, our results provide fossil support for aerial foraging as the ancestral ecological strategy of Strisores, as implied by recent phylogenetic topologies derived from molecular data.

scholarly journals Tip dating supports novel resolutions of controversial relationships among early mammals

2020 ◽  
Vol 287 (1928) ◽  
pp. 20200943
Author(s):  
Benedict King ◽  
Robin M. D. Beck
Keyword(s):  
Early Cretaceous ◽  
Late Jurassic ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Late Triassic ◽  
Crown Group ◽  
Jehol Biota ◽  
Rates Of Evolution ◽  
Mammal Evolution ◽  
Minimum Divergence

The estimation of the timing of major divergences in early mammal evolution is challenging owing to conflicting interpretations of key fossil taxa. One contentious group is Haramiyida, the earliest members of which are from the Late Triassic. Many phylogenetic analyses have placed haramiyidans in a clade with multituberculates within crown Mammalia, thus extending the minimum divergence date for the crown group deep into the Triassic. A second taxon of interest is the eutherian Juramaia from the Middle–Late Jurassic Yanliao Biota, which is morphologically very similar to eutherians from the Early Cretaceous Jehol Biota and implies a very early origin for therian mammals. Here, we apply Bayesian tip-dated phylogenetic methods to investigate these issues. Tip dating firmly rejects a monophyletic Allotheria (multituberculates and haramiyidans), which are split into three separate clades, a result not found in any previous analysis. Most notably, the Late Triassic Haramiyavia and Thomasia are separate from the Middle Jurassic euharamiyidans. We also test whether the Middle–Late Jurassic age of Juramaia is ‘expected’ given its known morphology by assigning an age prior without hard bounds. Strikingly, this analysis supports an Early Cretaceous age for Juramaia , but similar analyses on 12 other mammaliaforms from the Yanliao Biota return the correct, Jurassic age. Our results show that analyses incorporating stratigraphic data can produce results very different from other methods. Early mammal evolution may have involved multiple instances of convergent morphological evolution (e.g. in the dentition), and tip dating may be a method uniquely suitable to recognizing this owing to the incorporation of stratigraphic data. Our results also confirm that Juramaia is anomalous in exhibiting a much more derived morphology than expected given its age, which in turn implies very high rates of evolution at the base of therian mammals.

scholarly journals Comparative Morphology, Phylogeny, Classification and Evolution of Interstitial Habits in Microcambevine Catfishes (Siluriformes: Trichomycteridae)

Taxonomy ◽  
2021 ◽  
Vol 1 (4) ◽  
pp. 313-344
Author(s):  
Wilson J. E. M. Costa ◽  
Axel M. Katz
Keyword(s):  
Morphological Traits ◽  
Phylogenetic Trees ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Morphological Diversity ◽  
Comparative Morphology ◽  
Morphological Characters ◽  
Morphological Data ◽  
High Level ◽  
Available Information

The Microcambevinae are a catfish subfamily endemic to the Brazilian Atlantic Forest, comprising rare species with interstitial habits. Microcambevines have been classified in two genera, Listrura and Microcambeva, but the relationships among included intrageneric lineages are still poorly understood. The objectives of this study are to conduct a phylogenetic analysis integrating morphological characters and a multigene dataset, and to propose a classification better reflecting morphological diversity and phylogenetic relationships. Phylogenetic analyses combining 57 morphological characters and a 2563 bp molecular dataset generated similar phylogenetic trees with high support values for most clades, including the two genera and some intrageneric groups. Six morphologically distinctive infrageneric lineages, three in Listrura and three in Microcambeva, are classified as subgenera, as well as two new species are described. The morphological diversity here recorded integrated to available information about habitat indicate high level of divergent specialisation among lineages. The analyses indicate a series of convergent morphological traits between Listrura and other teleosts sharing a fossorial lifestyle, as well as specialised traits independently occurring within Listrura lineages. Similarly, a great diversity of morphological traits occurs convergently in Microcambeva lineages and other teleosts sharing psammophilic habits. This study shows that combining molecular and morphological data yields well-supported phylogenies, making possible to unambiguously diagnose clades and to establish evolutionary hypothesis on morphological evolution.

scholarly journals Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54

2021 ◽  
Vol 12 ◽  
Author(s):  
Julien Andreani ◽  
Frederik Schulz ◽  
Fabrizio Di Pinto ◽  
Anthony Levasseur ◽  
Tanja Woyke ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Experimental Studies ◽  
Morphological Data ◽  
Metagenomic Data ◽  
Translation System ◽  
Proton Pumps ◽  
Dna Viruses ◽  
Successful Isolation ◽  
Wide Range ◽  
Nucleocytoplasmic Large Dna Viruses

Since the discovery of Mimivirus, viruses with large genomes encoding components of the translation machinery and other cellular processes have been described as belonging to the nucleocytoplasmic large DNA viruses. Recently, genome-resolved metagenomics led to the discovery of more than 40 viruses that have been grouped together in a proposed viral subfamily named Klosneuvirinae. Members of this group had genomes of up to 2.4Mb in size and featured an expanded array of translation system genes. Yet, despite the large diversity of the Klosneuvirinae in metagenomic data, there are currently only two isolates available. Here, we report the isolation of a novel giant virus known as Fadolivirus from an Algerian sewage site and provide morphological data throughout its replication cycle in amoeba and a detailed genomic characterization. The Fadolivirus genome, which is more than 1.5Mb in size, encodes 1,452 predicted proteins and phylogenetic analyses place this viral isolate as a near relative of the metagenome assembled Klosneuvirus and Indivirus. The genome encodes for 66 tRNAs, 23 aminoacyl-tRNA synthetases and a wide range of transcription factors, surpassing Klosneuvirus and other giant viruses. The Fadolivirus genome also encodes putative vacuolar-type proton pumps with the domains D and A, potentially constituting a virus-derived system for energy generation. The successful isolation of Fadolivirus will enable future hypothesis-driven experimental studies providing deeper insights into the biology of the Klosneuvirinae.

scholarly journals Ancient dates or accelerated rates? Morphological clocks and the antiquity of placental mammals

2014 ◽  
Vol 281 (1793) ◽  
pp. 20141278 ◽  
Author(s):  
Robin M. D. Beck ◽  
Michael S. Y. Lee
Keyword(s):  
Morphological Evolution ◽  
Fold Increase ◽  
Evolutionary Rates ◽  
Total Evidence ◽  
Morphological Data ◽  
Slight Reduction ◽  
Crown Group ◽  
Divergence Dates ◽  
Clock Models ◽  
Relaxed Clock

Analyses of a comprehensive morphological character matrix of mammals using ‘relaxed’ clock models (which simultaneously estimate topology, divergence dates and evolutionary rates), either alone or in combination with an 8.5 kb nuclear sequence dataset, retrieve implausibly ancient, Late Jurassic–Early Cretaceous estimates for the initial diversification of Placentalia (crown-group Eutheria). These dates are much older than all recent molecular and palaeontological estimates. They are recovered using two very different clock models, and regardless of whether the tree topology is freely estimated or constrained using scaffolds to match the current consensus placental phylogeny. This raises the possibility that divergence dates have been overestimated in previous analyses that have applied such clock models to morphological and total evidence datasets. Enforcing additional age constraints on selected internal divergences results in only a slight reduction of the age of Placentalia. Constraining Placentalia to less than 93.8 Ma, congruent with recent molecular estimates, does not require major changes in morphological or molecular evolutionary rates. Even constraining Placentalia to less than 66 Ma to match the ‘explosive’ palaeontological model results in only a 10- to 20-fold increase in maximum evolutionary rate for morphology, and fivefold for molecules. The large discrepancies between clock- and fossil-based estimates for divergence dates might therefore be attributable to relatively small changes in evolutionary rates through time, although other explanations (such as overly simplistic models of morphological evolution) need to be investigated. Conversely, dates inferred using relaxed clock models (especially with discrete morphological data and M r B ayes ) should be treated cautiously, as relatively minor deviations in rate patterns can generate large effects on estimated divergence dates.

Telaprocera (Araneae: Araneidae), a new genus of Australian orb-web spiders with highly elongated webs

Zootaxa ◽  
2008 ◽  
Vol 1956 (1) ◽  
pp. 59-80 ◽  
Author(s):  
AARON M. T. HARMER ◽  
VOLKER W. FRAMENAU
Keyword(s):  
New Genus ◽  
Phylogenetic Analyses ◽  
Data Matrix ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
South Wales ◽  
Closed Canopy ◽  
Orb Web ◽  
Orb Web Spiders ◽  
Far Eastern

A new genus of orb-web spider (Araneidae Simon), Telaprocera gen. nov., including two new species, T. maudae sp. nov. (type species) and T. joanae sp. nov., are described. Telaprocera gen. nov. differs from all other araneid genera by the presence of a dorsal keel on the male cymbium. The known range of Telaprocera maudae sp. nov. is limited to the east coast of Australia, from far northern Queensland to central New South Wales. The spiders are found in closed canopy rainforest and adults can be found year round. Telaprocera joanae sp. nov. has been found from central coastal Queensland to far eastern Victoria. They occur in similar habitats, with similar phenology, as T. maudae sp. nov. Both species build highly elongated orb-webs known as ladder-webs. A variety of phylogenetic analyses based on an updated morphological data matrix for orb-web spiders did not provide a conclusive placement of Telaprocera gen. nov. within the Araneidae. Equally weighted analysis placed the genus as sister to Kaira O. P.-Cambridge and Metepeira F. O. P.Cambridge combined. Strong downweighting of homoplasious characters placed the genus as sister taxon to the traditional Argiopinae Simon. The uncertain phylogenetic position of Telaprocera gen. nov. may reflect the insufficient knowledge of the morphology of Australian taxa—taxa that may possess characters previously not considered in phylogenetic analyses of the Araneidae.

Sign in / Sign up

Export Citation Format

Share Document