Phylogenetic analyses of morphological evolution in the gametophyte and sporophyte generations of the moss order Hookeriales (Bryopsida)

2012 ◽  
Vol 63 (2) ◽  
pp. 351-364 ◽  
Author(s):  
L. Pokorny ◽  
B.-C. Ho ◽  
J.-P. Frahm ◽  
D. Quandt ◽  
A.J. Shaw
Keyword(s):  
Morphological Evolution ◽  
Phylogenetic Analyses

scholarly journals A Short-Snouted, Middle Triassic Phytosaur and its Implications for the Morphological Evolution and Biogeography of Phytosauria

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Michelle R. Stocker ◽  
Li-Jun Zhao ◽  
Sterling J. Nesbitt ◽  
Xiao-Chun Wu ◽  
Chun Li
Keyword(s):  
Middle Triassic ◽  
Prey Capture ◽  
General Trend ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Late Triassic ◽  
Early Triassic ◽  
Terrestrial Vertebrate ◽  
Nearshore Environments ◽  
Permian Extinction

Abstract Following the end-Permian extinction, terrestrial vertebrate diversity recovered by the Middle Triassic, and that diversity was now dominated by reptiles. However, those reptilian clades, including archosaurs and their closest relatives, are not commonly found until ~30 million years post-extinction in Late Triassic deposits despite time-calibrated phylogenetic analyses predicting an Early Triassic divergence for those clades. One of these groups from the Late Triassic, Phytosauria, is well known from a near-Pangean distribution, and this easily recognized clade bears an elongated rostrum with posteriorly retracted nares and numerous postcranial synapomorphies that are unique compared with all other contemporary reptiles. Here, we recognize the exquisitely preserved, nearly complete skeleton of Diandongosuchus fuyuanensis from the Middle Triassic of China as the oldest and basalmost phytosaur. The Middle Triassic age and lack of the characteristically-elongated rostrum fill a critical morphological and temporal gap in phytosaur evolution, indicating that the characteristic elongated rostrum of phytosaurs appeared subsequent to cranial and postcranial modifications associated with enhanced prey capture, predating that general trend of morphological evolution observed within Crocodyliformes. Additionally, Diandongosuchus supports that the clade was present across Pangea, suggesting early ecosystem exploration for Archosauriformes through nearshore environments and leading to ease of dispersal across the Tethys.

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.

Phylogeny, ancestors and anagenesis in the hominin fossil record

2018 ◽  
Author(s):  
Caroline Parins-Fukuchi ◽  
Elliot Greiner ◽  
Laura M. MacLatchy ◽  
Daniel C. Fisher
Keyword(s):  
Probabilistic Models ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Probabilistic Methods ◽  
Evolutionary Divergence ◽  
Temporal Data ◽  
Evolutionary Pattern ◽  
Phylogenetic Methods ◽  
Competing Models ◽  
Fossil Preservation

AbstractProbabilistic approaches to phylogenetic inference have recently gained traction in paleontological studies. Because they directly model processes of evolutionary change, probabilistic methods facilitate a deeper assessment of variability in evolutionary pattern by weighing evidence for competing models. Although phylogenetic methods used in paleontological studies have generally assumed that evolution proceeds by splitting cladogenesis, extensions to previous models help explore the potential for morphological and temporal data to provide differential support for contrasting modes of evolutionary divergence. Recent methodological developments have integrated ancestral relationships into probabilistic phylogenetic methods. These new approaches rely on parameter-rich models and sophisticated inferential methods, potentially obscuring the respective contributions of data and models. In this study, we describe a simple likelihoodist approach that combines probabilistic models of morphological evolution and fossil preservation to reconstruct both cladogenetic and anagenetic relationships. By applying this approach to a dataset of fossil hominins, we demonstrate the capability of existing models to unveil evidence for anagenesis presented by morphological and temporal data. This evidence was previously recognized by qualitative assessments, but largely ignored by quantitative phylogenetic analyses. For example, we find support for directly ancestral relationships in multiple lineages: Sahelanthropus is ancestral to later hominins; Australopithecus anamensis is ancestral to Au. afarensis; Au. garhi is ancestral to Homo; H. antecessor is ancestral to H. heidelbergensis, which in turn is ancestral to both H. sapiens and H. neanderthalensis. These results show a benefit of accommodating direct ancestry in phylogenetics. By so doing, quantitative results align more closely with previous qualitative expectations.

scholarly journals First Phylogeny of Bitterbush Family, Picramniaceae (Picramniales)

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 284
Author(s):  
Alexey Shipunov ◽  
Shyla Carr ◽  
Spencer Furniss ◽  
Kyle Pay ◽  
José Rubens Pirani
Keyword(s):  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Nuclear Markers ◽  
Molecular Phylogenetic Tree ◽  
Plant Group ◽  
The Family ◽  
Molecular Phylogenetic ◽  
Recent Addition ◽  
The Subject ◽  
American Tropics

Picramniaceae is the only member of Picramniales which is sister to the clade (Sapindales (Huerteales (Malvales, Brassicales))) in the rosidsmalvids. Not much is known about most aspects of their ecology, geography, and morphology. The family is restricted to American tropics. Picramniaceae representatives are rich in secondary metabolites; some species are known to be important for pharmaceutical purposes. Traditionally, Picramniaceae was classified as a subfamily of Simaroubaceae, but from 1995 on, it has been segregated containing two genera, Picramnia and Alvaradoa, with the recent addition of a third genus, Nothotalisia, described in 2011. Only a few species of the family have been the subject of DNA-related research, and fewer than half of the species have been included in morphological phylogenetic analyses. It is clear that Picramniaceae remains a largely under-researched plant group. Here we present the first molecular phylogenetic tree of the group, based on both chloroplast and nuclear markers, widely adopted in the plant DNA barcoding. The main findings are: The family and its genera are monophyletic and Picramnia is sister to two other genera; some clades corroborate previous assumptions of relationships made on a morphological or geographical basis, while most parts of the molecular topology suggest high levels of homoplasy in the morphological evolution of Picramnia.

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.

Using phylogeny and ultrastructure to study cystidia of two Psathyrella species: reciprocal illumination

Botany ◽  
2008 ◽  
Vol 86 (11) ◽  
pp. 1334-1342 ◽  
Author(s):  
Mahajabeen Padamsee ◽  
Gail J. Celio ◽  
David J. McLaughlin
Keyword(s):  
Electron Microscopy ◽  
Smooth Endoplasmic Reticulum ◽  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Freeze Substitution ◽  
Calcium Oxalate Crystals ◽  
Closely Related Species ◽  
Transmission Electron ◽  
First Time ◽  
Crystalline Matrix

Ultrastructure of the cystidia of Psathyrella aff. nolitangere (Fr.) A. Pearson & Dennis and Psathyrella rhodospora Weaver & Smith (Agaricales) was examined primarily using freeze substitution, with the goal of evaluating whether these cells could provide phylogenetically informative characters with which to study morphological evolution. Within the Agaricales, the diversity of cystidial form coupled with the limited number of studies makes accurate character coding for use in phylogenetic analyses problematic. This study revealed many common cystidial characteristics between the two closely related species examined, including well-formed apical crystals, abundant free ribosomes, and scattered smooth endoplasmic reticulum. Transmission electron microscopy was used for the first time to examine calcium oxalate crystals in cystidia, and demonstrated the formation of a pre-crystalline matrix at the apex of each cell that possibly disrupts the wall as the crystals form. The shared subcellular traits suggest that ultrastructural details of cystidia may provide additional characters for and signal in phylogenetic analyses.

scholarly journals 40 new specimens of Ichthyornis provide unprecedented insight into the postcranial morphology of crownward stem group birds.

2022 ◽  
Author(s):  
Juan Benito ◽  
Albert Chen ◽  
Laura E. Wilson ◽  
Bhart-Anjan S. Bhullar ◽  
David Burnham ◽  
...  
Keyword(s):  
Morphological Evolution ◽  
Phylogenetic Analyses ◽  
Three Dimensional ◽  
Ontogenetic Changes ◽  
Crown Group ◽  
Postcranial Morphology ◽  
Stem Group ◽  
New Information ◽  
The 19Th Century ◽  
Future Work

Ichthyornis has long been recognized as a pivotally important fossil taxon for understanding the latest stages of the dinosaur-bird transition, but little significant new postcranial material has been brought to light since initial descriptions of partial skeletons in the 19th Century. Here, we present new information on the postcranial morphology of Ichthyornis from 40 previously undescribed specimens, providing the most detailed morphological assessment of Ichthyornis to date. The new material includes four partially complete skeletons and numerous well-preserved isolated elements, enabling new anatomical observations such as muscle attachments previously undescribed for Mesozoic euornitheans. Among the elements that were previously unknown or poorly represented for Ichthyornis, the new specimens include an almost-complete axial series, a hypocleideum-bearing furcula, radial carpal bones, fibulae, a complete tarsometatarsus bearing a rudimentary hypotarsus, and one of the first-known nearly complete three-dimensional sterna from a Mesozoic avialan. Several pedal phalanges are preserved, revealing a remarkably enlarged pes presumably related to foot-propelled swimming. Although diagnosable as Ichthyornis, the new specimens exhibit a substantial degree of morphological variation, some of which may relate to ontogenetic changes. Phylogenetic analyses incorporating our new data and employing alternative morphological datasets recover Ichthyornis stemward of Hesperornithes and Iaceornis, in line with some recent hypotheses regarding the topology of the crownward-most portion of the avian stem group, and we establish phylogenetically-defined clade names for relevant avialan subclades to help facilitate consistent discourse in future work. The new information provided by these specimens improves our understanding of morphological evolution among the crownward-most non-neornithine avialans immediately preceding the origin of crown group birds.

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 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.

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