scholarly journals Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates

BMC Biology ◽  
2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Tiago R. Simões ◽  
Michael W. Caldwell ◽  
Stephanie E. Pierce
Keyword(s):  
Evolutionary History ◽  
Evolutionary Rates ◽  
Morphological Data ◽  
Divergence Times ◽  
Evolutionary Trees ◽  
Model Choice ◽  
Rates Of Evolution ◽  
History Of ◽  
Living Species ◽  
The Impact

Abstract Background The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored. Results Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group. Conclusions We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

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.

scholarly journals Phylogenetic non-independence in rates of trait evolution

2018 ◽  
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 whether rates are non-independent throughout the evolutionary history of each tree. 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 account for the undesired effects of shared ancestry.

scholarly journals Evolutionary history of field mice (Murinae: Apodemus), with emphasis on morphological variation among species in China and description of a new species

2019 ◽  
Vol 187 (2) ◽  
pp. 518-534 ◽  
Author(s):  
Deyan Ge ◽  
Anderson Feijó ◽  
Jilong Cheng ◽  
Liang Lu ◽  
Rongrong Liu ◽  
...  
Keyword(s):  
New Species ◽  
Evolutionary History ◽  
Eastern China ◽  
Guizhou Province ◽  
Morphological Data ◽  
Ancestral Area ◽  
History Of ◽  
Living Species ◽  
Field Mice ◽  
A New Species

AbstractMice of the genus Apodemus are widely distributed across Eurasia. Several species of this genus are hosts of important zoonotic diseases and parasites. The evolutionary history and dispersal routes of these mice remain unclear and the distribution of these species in China was poorly explored in previous studies. We here investigate the divergence times and historical geographical evolution of Apodemus and study the taxonomy of species in China by integrating molecular and morphological data. The crown age of this genus is dated to the Late Miocene, approximately 9.84 Mya. Western and Central Asia were inferred as the most likely ancestral area of this genus. Moreover, we recognize nine living species of Apodemus in China: Apodemus uralensis, A. agrarius, A. chevrieri, A. latronum, A. peninsulae, A. draco, A. ilex, A. semotus and A. nigrus sp. nov., the last from the highlands (elevation > 1984 m) of Fanjing Mountain in Guizhou Province and Jinfo Mountain in Chongqing Province. This new species diverged from A. draco, A. semotus and A. ilex approximately 4.53 Mya. The discovery of A. nigrus highlights the importance of high mountains as refugia and ‘isolated ecological islands’ for temperate species in south-eastern China.

scholarly journals The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data

2014 ◽  
Vol 14 (1) ◽  
pp. 52 ◽  
Author(s):  
Ralph S Peters ◽  
Karen Meusemann ◽  
Malte Petersen ◽  
Christoph Mayer ◽  
Jeanne Wilbrandt ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Morphological Data ◽  
History Of

scholarly journals Three new Cenomanian conifers from El Chango (Chiapas, Mexico) offer a snapshot of the geographic mosaic of the Mesozoic conifer decline

2021 ◽  
Author(s):  
Ixchel Gonzalez-Ramirez ◽  
Sergio RS Cevallos-Ferriz ◽  
Carl Rothfels
Keyword(s):  
Evolutionary History ◽  
Mixed Forest ◽  
Freshwater Ecosystems ◽  
Total Evidence ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Dominant Group ◽  
Geographic Mosaic ◽  
History Of ◽  
Rare Opportunity

Premise of study: El Chango is a recently discovered quarry that contains extremely well preserved fossils. The Cenomanian age of the locality corresponds to a time when the global flora was transitioning from gymnosperm- to angiosperm-dominated, yet conifers predominate in this locality. These fossils thus provide a rare opportunity to understand the replacement of conifers by angiosperms as the dominant group of plants. Methods: We collected material from El Chango in annual expeditions (2010 to 2014). We selected the three most abundant and best preserved conifer morphotypes and conducted a total-evidence (i.e., including molecular and morphological data) phylogenetic analysis of a sample of 72 extant conifer species plus the three fossils. We use these results to inform our taxonomic decisions. Results: We obtained four equally most-parsimonious trees (consistency index = 44.1%, retention index = 78.8%). Despite ambiguous relationships among some extant taxa, the three fossil conifers had the same phylogenetic position in all four most parsimonious trees; we describe these species as new: Sequoiadendron helicalancifolium sp. nov. (Cupressaceae), and Microcachrys rhomboidea sp. nov. and Dacrydium bifoliosus sp. nov (Podocarpaceae). The ecosystem is interpreted as a coastal humid mixed forest. Conclusions: Our findings contribute to the understanding of Cenomanian equatorialregions, and support the hypothesis of a geographically and ecologically structured rise of angiosperms, with conifers remaining dominant in brackish-water and angiosperms becoming dominant in freshwater-ecosystems. These fossils fill in gaps in the evolutionary history of lineages like Microcachrys, which we demonstrate occurred in the Northern hemisphere before becoming restricted to its current range (Tasmania).

Human Evolution

1984 ◽  
Vol 8 ◽  
pp. 182-198
Author(s):  
Catherine Badgley
Keyword(s):  
Human Evolution ◽  
Evolutionary History ◽  
Pan Paniscus ◽  
Homo Sapiens ◽  
Great Apes ◽  
Sister Group ◽  
The Family ◽  
History Of ◽  
Living Species ◽  
Single Living

The evolutionary history of humans is well understood in outline, compared to that of many other groups of mammals. But human evolution remains enigmatic in its details, and these are compelling both scientifically and personally because they relate to the biological uniqueness of humans. Humans are placed in the primate family Hominidae, which, in traditional classifications, contains a single living species, Homo sapiens. The closest living relatives of humans are great apes: the chimpanzees Pan paniscus and Pan troglodytes, the gorilla Gorilla gorilla, and the orangutan Pongo pygmaeus. These apes have traditionally been placed in the family Pongidae as the sister group of Hominidae. Living Hominidae and Pongidae, together with Hylobatidae (gibbons) comprise the modern representatives of the primate suborder Hominoidea.

scholarly journals Ancient origins and multiple appearances of carotenoid-pigmented feathers in birds

2014 ◽  
Vol 281 (1788) ◽  
pp. 20140806 ◽  
Author(s):  
Daniel B. Thomas ◽  
Kevin J. McGraw ◽  
Michael W. Butler ◽  
Matthew T. Carrano ◽  
Odile Madden ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
High Performance ◽  
Evolutionary History ◽  
Carotenoid Pigments ◽  
Biological Functions ◽  
The Family ◽  
Family Level ◽  
History Of ◽  
Living Species ◽  
Insight Into

The broad palette of feather colours displayed by birds serves diverse biological functions, including communication and camouflage. Fossil feathers provide evidence that some avian colours, like black and brown melanins, have existed for at least 160 million years (Myr), but no traces of bright carotenoid pigments in ancient feathers have been reported. Insight into the evolutionary history of plumage carotenoids may instead be gained from living species. We visually surveyed modern birds for carotenoid-consistent plumage colours (present in 2956 of 9993 species). We then used high-performance liquid chromatography and Raman spectroscopy to chemically assess the family-level distribution of plumage carotenoids, confirming their presence in 95 of 236 extant bird families (only 36 family-level occurrences had been confirmed previously). Using our data for all modern birds, we modelled the evolutionary history of carotenoid-consistent plumage colours on recent supertrees. Results support multiple independent origins of carotenoid plumage pigmentation in 13 orders, including six orders without previous reports of plumage carotenoids. Based on time calibrations from the supertree, the number of avian families displaying plumage carotenoids increased throughout the Cenozoic, and most plumage carotenoid originations occurred after the Miocene Epoch (23 Myr). The earliest origination of plumage carotenoids was reconstructed within Passeriformes, during the Palaeocene Epoch (66–56 Myr), and not at the base of crown-lineage birds.

scholarly journals Assessment of available anatomical characters for linking living mammals to fossil taxa in phylogenetic analyses

2016 ◽  
Vol 12 (5) ◽  
pp. 20151003 ◽  
Author(s):  
Thomas Guillerme ◽  
Natalie Cooper
Keyword(s):  
Data Collection ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Total Evidence ◽  
Morphological Data ◽  
Living Species ◽  
Anatomical Characters ◽  
The Impact

Analyses of living and fossil taxa are crucial for understanding biodiversity through time. The total evidence method allows living and fossil taxa to be combined in phylogenies, using molecular data for living taxa and morphological data for living and fossil taxa. With this method, substantial overlap of coded anatomical characters among living and fossil taxa is vital for accurately inferring topology. However, although molecular data for living species are widely available, scientists generating morphological data mainly focus on fossils. Therefore, there are fewer coded anatomical characters in living taxa, even in well-studied groups such as mammals. We investigated the number of coded anatomical characters available in phylogenetic matrices for living mammals and how these were phylogenetically distributed across orders. Eleven of 28 mammalian orders have less than 25% species with available characters; this has implications for the accurate placement of fossils, although the issue is less pronounced at higher taxonomic levels. In most orders, species with available characters are randomly distributed across the phylogeny, which may reduce the impact of the problem. We suggest that increased morphological data collection efforts for living taxa are needed to produce accurate total evidence phylogenies.

Where Fossils Dare and Males Matter: combined morphological and molecular analysis untangles the evolutionary history of the spider ant genus Leptomyrmex Mayr (Hymenoptera : Dolichoderinae)

2017 ◽  
Vol 31 (6) ◽  
pp. 765 ◽  
Author(s):  
Phillip Barden ◽  
Brendon Boudinot ◽  
Andrea Lucky
Keyword(s):  
Evolutionary History ◽  
Morphological Evolution ◽  
Sister Group ◽  
Morphological Characters ◽  
Fossil Material ◽  
First Case ◽  
History Of ◽  
The Impact ◽  
Surprising Discovery

The distinctive ant genus Leptomyrmex Mayr, 1862 had been thought to be endemic to Australasia for over 150 years, but enigmatic Neotropical fossils have challenged this view for decades. The present study responds to a recent and surprising discovery of extant Leptomyrmex species in Brazil with a thorough evaluation of the Dominican Republic fossil material, which dates to the Miocene. In the first case study of direct fossil inclusion within Formicidae Latreille, 1809, we incorporated both living and the extinct Leptomyrmex species. Through simultaneous analysis of molecular and morphological characters in both Bayesian and parsimony frameworks, we recovered the fossil taxon as sister-group to extant Leptomyrmex in Brazil while considering the influence of taxonomic and character sampling on inferred hypotheses relating to tree topology, biogeography and morphological evolution. We also identified potential loss of signal in the binning of morphological characters and tested the impact of parameterisation on divergence date estimation. Our results highlight the importance of securing sufficient taxon sampling for extant lineages when incorporating fossils and underscore the utility of diverse character sources in accurate placement of fossil terminals. Specifically, we find that fossil placement in this group is influenced by the inclusion of male-based characters and the newly discovered Neotropical ‘Lazarus taxon’.

scholarly journals Evolutionary history of the MTG gene family in vertebrates

2019 ◽  
Vol 64 (4) ◽  
pp. 391-402
Author(s):  
A. I. Kavaleuskaya ◽  
T. V. Ramanouskaya
Keyword(s):  
Gene Family ◽  
Evolutionary History ◽  
Protein Sequences ◽  
Stem Cell Differentiation ◽  
Gene Products ◽  
Functional Diversification ◽  
Rates Of Evolution ◽  
Different Types ◽  
History Of ◽  
Transcriptional Corepressors

The highly conserved MTG gene family includes three homologs in vertebrates (MTG8, MTGR1, MTG16) encoding transcriptional corepressors, which are important in haemopoiesis, neurogenesis and epithelial stem cell differentiation. These genes are of particular interest because they are involved in translocations, associated with different types of cancer. Looking at how this gene family evolved might provide insights into history of its structural and functional diversification. We have performed a phylogenetic analysis of MTG nucleotide and protein sequences to examine the evolutionary events. The domain organization of MTG gene products was clarified, the mechanism of appearance of the first MTG gene was revealed and the ancestor taxon was determined. Also the mechanism of MTG gene family emergence was established. In addition, analysis of the rates of evolution acting on individual domains was made, and conservative positions within each gene of MTG family were determined.

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