scholarly journals Phylogenetic signal in extinction selectivity in Devonian terebratulide brachiopods

Paleobiology ◽  
10.1666/14006 ◽  
2014 ◽  
Vol 40 (4) ◽  
pp. 675-692 ◽  
Author(s):  
Paul G. Harnik ◽  
Paul C. Fitzgerald ◽  
Jonathan L. Payne ◽  
Sandra J. Carlson
Keyword(s):  
Body Size ◽  
Fossil Record ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Positive Association ◽  
Range Size ◽  
Biological Traits ◽  
Significant Positive Association ◽  
Extinction Selectivity

Determining which biological traits affect taxonomic durations is critical for explaining macroevolutionary patterns. Two approaches are commonly used to investigate the associations between traits and durations and/or extinction and origination rates: analyses of taxonomic occurrence patterns in the fossil record and comparative phylogenetic analyses, predominantly of extant taxa. By capitalizing upon the empirical record of past extinctions, paleontological data avoid some of the limitations of existing methods for inferring extinction and origination rates from molecular phylogenies. However, most paleontological studies of extinction selectivity have ignored phylogenetic relationships because there is a dearth of phylogenetic hypotheses for diverse non-vertebrate higher taxa in the fossil record. This omission inflates the degrees of freedom in statistical analyses and leaves open the possibility that observed associations are indirect, reflecting shared evolutionary history rather than the direct influence of particular traits on durations. Here we investigate global patterns of extinction selectivity in Devonian terebratulide brachiopods and compare the results of taxonomic vs. phylogenetic approaches. Regression models that assume independence among taxa provide support for a positive association between geographic range size and genus duration but do not indicate an association between body size and genus duration. Brownian motion models of trait evolution identify significant similarities in body size, range size, and duration among closely related terebratulide genera. We use phylogenetic regression to account for shared evolutionary history and find support for a significant positive association between range size and duration among terebratulides that is also phylogenetically structured. The estimated range size–duration relationship is moderately weaker in the phylogenetic analysis due to the down-weighting of closely related genera that were both broadly distributed and long lived; however, this change in slope is not statistically significant. These results provide evidence for the phylogenetic conservatism of organismal and emergent traits, yet also the general phylogenetic independence of the relationship between range size and duration.

A fossil record of land plant origins from charophyte algae

Science ◽  
2021 ◽  
Vol 373 (6556) ◽  
pp. 792-796 ◽  
Author(s):  
Paul K. Strother ◽  
Clinton Foster
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Land Plant ◽  
Fossil Plants ◽  
Fossil Plant ◽  
Molecular Phylogenetic ◽  
History Of ◽  
Time Gap ◽  
Evolutionary Continuity

Molecular time trees indicating that embryophytes originated around 500 million years ago (Ma) during the Cambrian are at odds with the record of fossil plants, which first appear in the mid-Silurian almost 80 million years later. This time gap has been attributed to a missing fossil plant record, but that attribution belies the case for fossil spores. Here, we describe a Tremadocian (Early Ordovician, about 480 Ma) assemblage with elements of both Cambrian and younger embryophyte spores that provides a new level of evolutionary continuity between embryophytes and their algal ancestors. This finding suggests that the molecular phylogenetic signal retains a latent evolutionary history of the acquisition of the embryophytic developmental genome, a history that perhaps began during Ediacaran-Cambrian time but was not completed until the mid-Silurian (about 430 Ma).

The first potential fossil record of a dibamid reptile (Squamata: Dibamidae): a new taxon from the early Oligocene of Central Mongolia

2019 ◽  
Vol 187 (3) ◽  
pp. 782-799 ◽  
Author(s):  
Andrej Čerňanský
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
New Taxon ◽  
Unique Combination ◽  
Central Mongolia ◽  
Squamate Reptiles ◽  
The Past ◽  
Early Oligocene ◽  
Fossil Material

Abstract Dibamid reptiles have a known current distribution on two continents (Asia and North America). Although this clade represents an early-diverging group in the Squamata and thus should have a long evolutionary history, no fossil record of these peculiar burrowing squamate reptiles has been documented so far. The fossil material described here comes from the early Oligocene of the Valley of Lakes in Central Mongolia. This material consists of jaws and is placed in the clade Dibamidae on the basis of its morphology, which is further confirmed by phylogenetic analyses. In spite of the fragmentary nature of this material, it thus forms the first, but putative, fossil evidence of this clade. If correctly interpreted, this material demonstrates the occurrence of Dibamidae in East Asia in the Palaeogene, indicating its distribution in higher latitudes than today. The preserved elements possess a unique combination of character states, and a new taxon name is therefore erected: Hoeckosaurus mongoliensis sp. nov. The dentary of Hoeckosaurus exhibits some characters of the two extant dibamid taxa. However, the open Meckel’s groove, together with other characters, show that this group was morphologically much more diverse in the past.

scholarly journals Intragenic Conflict in Phylogenomic Data Sets

2020 ◽  
Vol 37 (11) ◽  
pp. 3380-3388
Author(s):  
Stephen A Smith ◽  
Nathanael Walker-Hale ◽  
Joseph F Walker
Keyword(s):  
Data Analysis ◽  
Empirical Data ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Simulated Data ◽  
Data Sets ◽  
Alignment Error ◽  
Biological Processes ◽  
Simple Method

Abstract Most phylogenetic analyses assume that a single evolutionary history underlies one gene. However, both biological processes and errors can cause intragenic conflict. The extent to which this conflict is present in empirical data sets is not well documented, but if common, could have far-reaching implications for phylogenetic analyses. We examined several large phylogenomic data sets from diverse taxa using a fast and simple method to identify well-supported intragenic conflict. We found conflict to be highly variable between data sets, from 1% to >92% of genes investigated. We analyzed four exemplar genes in detail and analyzed simulated data under several scenarios. Our results suggest that alignment error may be one major source of conflict, but other conflicts remain unexplained and may represent biological signal or other errors. Whether as part of data analysis pipelines or to explore biologically processes, analyses of within-gene phylogenetic signal should become common.

Biotic influences on species duration: interactions between traits in marine molluscs

Paleobiology ◽  
2010 ◽  
Vol 36 (2) ◽  
pp. 204-223 ◽  
Author(s):  
James S. Crampton ◽  
Roger A. Cooper ◽  
Alan G. Beu ◽  
Michael Foote ◽  
Bruce A. Marshall
Keyword(s):  
Body Size ◽  
Large Range ◽  
Geographic Range ◽  
Range Size ◽  
Biological Traits ◽  
Data Set ◽  
Marine Molluscs ◽  
Larval Type ◽  
Feeding Type ◽  
Life Mode

We analyze relationships among a range of ecological and biological traits—geographic range size, body size, life mode, larval type, and feeding type—in order to identify those traits that are associated significantly with species duration in New Zealand Cenozoic marine molluscs, during a time of background extinction. Using log-linear modeling, we find that bivalves have only a small number of simple, two-way associations between the studied traits and duration. In contrast, gastropods display more complex interactions involving three-way associations between traits, a pattern that suggests greater macroecological complexity of gastropods. This is not an artifact caused by the larger number of gastropods than bivalves in our data set. We used stratified randomized resampling of families to test for associations between traits that might result from shared inheritance rather than ecological trait interactions; we found no evidence of phylogenetic effects in any associations examined. The relationships revealed by our study should serve to constrain the range of possible biological mechanisms that underlie these relationships. As previously observed, two-way associations are present between large geographic range and increased duration, and between large geographic range and large body size, in both bivalves and gastropods. In gastropods, planktotrophic larval type is associated with large range size through a three-way interaction that also involves duration; there is no direct association of larval type and geographic range. Gastropods also display two-way associations between duration and life mode, and duration and feeding type. We note that in gastropods, an infaunal life mode is associated with large range size, whereas in bivalves infaunality is associated with reduced range size.

scholarly journals Evolutionary patterns of range size, abundance and species richness in Amazonian trees

2016 ◽  
Author(s):  
Kyle Dexter ◽  
Jérôme Chave
Keyword(s):  
Species Richness ◽  
Phylogenetic Signal ◽  
Negative Relationship ◽  
Range Size ◽  
Biological Traits ◽  
Evolutionary Patterns ◽  
Phylogenetically Independent Contrasts ◽  
Significant Negative Relationship ◽  
The Mean ◽  
Amazonian Trees

Amazonian tree species vary enormously in their total abundance and range size, while Amazonian tree genera vary greatly in species richness. Here, we construct a phylogenetic hypothesis that represents half of Amazonian tree genera in order to analyse evolutionary patterns of range size, abundance, and species richness. We find several clear, broad-scale patterns. Firstly, there is significant phylogenetic signal for all three characteristics, i.e. closely related genera tend to have similar numbers of species and similar mean range size and abundance. Additionally, the species richness of genera shows a significant, negative relationship with the mean range size and abundance of their constituent species, while mean range size and abundance are significantly, positively correlated. These correlations are stronger in the raw data, but still significant when using phylogenetically independent contrasts. We suggest that tree stature and/or other phylogenetically related biological traits underlie these results. Lineages comprised of small-statured trees show greater species richness and smaller range sizes and abundances. Lastly, the phylogenetic signal that we evidence for range size suggests that should many small ranged species go extinct, greater phylogenetic diversity may be lost than expected if range size were distributed randomly across the phylogeny.

scholarly journals The phylogeny and systematics of Xiphosura

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10431
Author(s):  
James C. Lamsdell
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Systematic Revision ◽  
Ecological History ◽  
Living Fossils ◽  
Modern Species ◽  
The Matrix ◽  
History Of ◽  
Taxonomic Framework

Xiphosurans are aquatic chelicerates with a fossil record extending into the Early Ordovician and known from a total of 88 described species, four of which are extant. Known for their apparent morphological conservatism, for which they have gained notoriety as supposed ‘living fossils’, recent analyses have demonstrated xiphosurans to have an ecologically diverse evolutionary history, with several groups moving into non-marine environments and developing morphologies markedly different from those of the modern species. The combination of their long evolutionary and complex ecological history along with their paradoxical patterns of morphological stasis in some clades and experimentation among others has resulted in Xiphosura being of particular interest for macroevolutionary study. Phylogenetic analyses have shown the current taxonomic framework for Xiphosura—set out in the Treatise of Invertebrate Paleontology in 1955—to be outdated and in need of revision, with several common genera such as Paleolimulus Dunbar, 1923 and Limulitella Størmer, 1952 acting as wastebasket taxa. Here, an expanded xiphosuran phylogeny is presented, comprising 58 xiphosuran species as part of a 158 taxon chelicerate matrix coded for 259 characters. Analysing the matrix under both Bayesian inference and parsimony optimisation criteria retrieves a concordant tree topology that forms the basis of a genus-level systematic revision of xiphosuran taxonomy. The genera Euproops Meek, 1867, Belinurus König, 1820, Paleolimulus, Limulitella, and Limulus are demonstrated to be non-monophyletic and the previously synonymized genera Koenigiella Raymond, 1944 and Prestwichianella Cockerell, 1905 are shown to be valid. In addition, nine new genera (Andersoniella gen. nov., Macrobelinurus gen. nov., and Parabelinurus gen. nov. in Belinurina; Norilimulus gen. nov. in Paleolimulidae; Batracholimulus gen. nov. and Boeotiaspis gen. nov. in Austrolimulidae; and Allolimulus gen. nov., Keuperlimulus gen. nov., and Volanalimulus gen. nov. in Limulidae) are erected to accommodate xiphosuran species not encompassed by existing genera. One new species, Volanalimulus madagascarensis gen. et sp. nov., is also described. Three putative xiphosuran genera—Elleria Raymond, 1944, Archeolimulus Chlupáč, 1963, and Drabovaspis Chlupáč, 1963—are determined to be non-xiphosuran arthropods and as such are removed from Xiphosura. The priority of Belinurus König, 1820 over Bellinurus Pictet, 1846 is also confirmed. This work is critical for facilitating the study of the xiphosuran fossil record and is the first step in resolving longstanding questions regarding the geographic distribution of the modern horseshoe crab species and whether they truly represent ‘living fossils’. Understanding the long evolutionary history of Xiphosura is vital for interpreting how the modern species may respond to environmental change and in guiding conservation efforts.

scholarly journals A tiny ornithodiran archosaur from the Triassic of Madagascar and the role of miniaturization in dinosaur and pterosaur ancestry

2020 ◽  
Vol 117 (30) ◽  
pp. 17932-17936 ◽  
Author(s):  
Christian F. Kammerer ◽  
Sterling J. Nesbitt ◽  
John J. Flynn ◽  
Lovasoa Ranivoharimanana ◽  
André R. Wyss
Keyword(s):  
Body Size ◽  
Fossil Record ◽  
Evolutionary History ◽  
Trophic Ecology ◽  
Upper Triassic ◽  
Important Group ◽  
Size Evolution ◽  
Stem Lineage ◽  
Body Size Evolution

Early members of the dinosaur–pterosaur clade Ornithodira are very rare in the fossil record, obscuring our understanding of the origins of this important group. Here, we describe an early ornithodiran (Kongonaphon kelygen. et sp. nov.) from the Mid-to-Upper Triassic of Madagascar that represents one of the smallest nonavian ornithodirans. Although dinosaurs and gigantism are practically synonymous, an analysis of body size evolution in dinosaurs and other archosaurs in the context of this taxon and related forms demonstrates that the earliest-diverging members of the group may have been smaller than previously thought, and that a profound miniaturization event occurred near the base of the avian stem lineage. In phylogenetic analysis,Kongonaphonis recovered as a member of the Triassic ornithodiran clade Lagerpetidae, expanding the range of this group into Africa and providing data on the craniodental morphology of lagerpetids. The conical teeth ofKongonaphonexhibit pitted microwear consistent with a diet of hard-shelled insects, indicating a shift in trophic ecology to insectivory associated with diminutive body size. Small ancestral body size suggests that the extreme rarity of early ornithodirans in the fossil record owes more to taphonomic artifact than true reflection of the group’s evolutionary history.

Occupancy, range size, and phylogeny in Eurasian Pliocene to Recent large mammals

Paleobiology ◽  
2010 ◽  
Vol 36 (3) ◽  
pp. 399-414 ◽  
Author(s):  
Francesco Carotenuto ◽  
Carmela Barbera ◽  
Pasquale Raia
Keyword(s):  
Body Size ◽  
Evolutionary Ecology ◽  
Phylogenetic Signal ◽  
Geographic Range ◽  
Range Size ◽  
Mammal Species ◽  
Mean Values ◽  
Geographic Range Size ◽  
Western Eurasia ◽  
Species Occupancy

Temporal patterns in species occupancy and geographic range size are a major topic in evolutionary ecology research. Here we investigate these patterns in Pliocene to Recent large mammal species and genera in Western Eurasia. By using an extensively sampled fossil record including some 700 fossil localities, we found occupancy and range size trajectories over time to be predominantly peaked among both species and genera, meaning that occupancy and range size reached their maxima midway along taxon existence. These metrics are strongly correlated with each other and to body size, after phylogeny is accounted for by using two different phylogenetic topologies for both species and genera. Phylogenetic signal is strong in body size, and weaker but significant in both occupancy and range size mean values among genera, indicating that these variables are heritable. The intensity of phylogenetic signal is much weaker and often not significant at the species level. This suggests that within genera, occupancy and range size are somewhat variable. However, sister taxa inherit geographic position (the center of their geographic distribution). Taken together, the latter two results indicate that sister species occupy similar positions on the earth's surface, and that the expansion of the geographic range during the existence of a given genus is driven by range expansion of one or more of the species it includes, rather than simply being the summation of these species ranges.

scholarly journals Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

2015 ◽  
Vol 282 (1804) ◽  
pp. 20142953 ◽  
Author(s):  
Prashant P. Sharma ◽  
Rosa Fernández ◽  
Lauren A. Esposito ◽  
Edmundo González-Santillán ◽  
Lionel Monod
Keyword(s):  
Fossil Record ◽  
Evolutionary History ◽  
Digestive System ◽  
Sequence Data ◽  
Phylogenetic Signal ◽  
Molecular Sequence Data ◽  
Molecular Sequence ◽  
Single Origin ◽  
As Species ◽  
First Time

Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships with up to 5025 genes. Analyses of supermatrices as well as species tree approaches converged upon a robust basal topology of scorpions that is entirely at odds with traditional systematics and controverts previous understanding of scorpion evolutionary history. All analyses unanimously support a single origin of katoikogenic development, a form of parental investment wherein embryos are nurtured by direct connections to the parent's digestive system. Based on the phylogeny obtained herein, we propose the following systematic emendations: Caraboctonidae is transferred to Chactoidea new superfamilial assignment ; superfamily Bothriuroidea revalidated is resurrected and Bothriuridae transferred therein; and Chaerilida and Pseudochactida are synonymized with Buthida new parvordinal synonymies .

scholarly journals Phylogenetic non-independence in rates of trait evolution

2018 ◽  
Vol 14 (10) ◽  
pp. 20180502 ◽  
Author(s):  
Manabu Sakamoto ◽  
Chris Venditti
Keyword(s):  
Statistical Power ◽  
Evolutionary History ◽  
Phylogenetic Signal ◽  
Small Sample ◽  
Evolutionary Rates ◽  
Biological Traits ◽  
Beak Shape ◽  
Rates Of Evolution ◽  
Shared Ancestry ◽  
History Of

Statistical non-independence of species’ biological traits is recognized in most traits under selection. Yet, whether or not the evolutionary rates of such biological traits are statistically non-independent remains to be tested. Here, we test the hypothesis that phenotypic evolutionary rates are non-independent, i.e. contain phylogenetic signal, using empirical rates of evolution in three separate traits: body mass in mammals, beak shape in birds and bite force in amniotes. Specifically, we test if evolutionary rates are phylogenetically interdependent. We find evidence for phylogenetic signal in evolutionary rates in all three case studies. While phylogenetic signal diminishes deeper in time, this is reflective of statistical power owing to small sample and effect sizes. When effect size is large, e.g. owing to the presence of fossil tips, we detect high phylogenetic signals even in deeper time slices. Thus, we recommend that rates be treated as being non-independent throughout the evolutionary history of the group of organisms under study, and any summaries or analyses of rates through time—including associations of rates with traits—need to account for the undesired effects of shared ancestry.

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