scholarly journals Congruence, fossils and the evolutionary tree of rodents and lagomorphs

2019 ◽  
Vol 6 (7) ◽  
pp. 190387 ◽  
Author(s):  
Robert J. Asher ◽  
Martin R. Smith ◽  
Aime Rankin ◽  
Robert J. Emry
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Signal ◽  
Phylogenetic Analyses ◽  
Evolutionary Process ◽  
Morphological Characters ◽  
Evolutionary Tree ◽  
Locomotor Pattern ◽  
Living Species ◽  
The Common ◽  
Common Ancestors

Given an evolutionary process, we expect distinct categories of heritable data, sampled in ever larger amounts, to converge on a single tree of historical relationships. We tested this assertion by undertaking phylogenetic analyses of a new morphology-DNA dataset for mammals, focusing on Glires and including the oldest known skeletons of geomyoid and Ischyromys rodents. Our results support geomyoids in the mouse-related clade (Myomorpha) and a ricochetal locomotor pattern for the common ancestor of geomyoid rodents. They also support Ischyromys in the squirrel-related clade (Sciuromorpha) and the evolution of sciurids and Aplodontia from extinct, ‘protrogomorph’-grade rodents. Moreover, ever larger samples of characters from our dataset increased congruence with an independent, well-corroborated tree. Addition of morphology from fossils increased congruence to a greater extent than addition of morphology from extant taxa, consistent with fossils' temporal proximity to the common ancestors of living species, reflecting the historical, phylogenetic signal present in our data, particularly in morphological characters from fossils. Our results support the widely held but poorly tested intuition that fossils resemble the common ancestors shared by living species, and that fossilizable hard tissues (i.e. bones and teeth) help to reconstruct the evolutionary tree of life.

scholarly journals Morphology-based phylogenetic analysis of the treehopper tribe Smiliini (Hemiptera: Membracidae: Smiliinae), with reinstatement of the tribe Telamonini

Zootaxa ◽  
2011 ◽  
Vol 3047 (1) ◽  
pp. 1 ◽  
Author(s):  
MATTHEW S. WALLACE
Keyword(s):  
Phylogenetic Analysis ◽  
Common Ancestor ◽  
Hind Wing ◽  
Morphological Characters ◽  
Dorsal Margin ◽  
Incertae Sedis ◽  
Plant Associations ◽  
Original Dataset ◽  
The Common ◽  
Morphological Differences

Members of the Smiliini, the nominotypical tribe of the large New World subfamily Smiliinae, are predominately Nearctic in distribution. This tribe included 169 mostly tree-feeding species in 23 genera. A parsimony-based phylogenetic analysis of an original dataset comprising 89 traditional and newly discovered morphological characters for 69 species, including representatives of 22 of the 23 described genera of Smiliini and five other previously recognized tribes of the subfamily, resulted in a single most parsimonious tree with three major clades. The broad recent concept of Smiliini (including Telamonini as a junior synonym) was not recovered as monophyletic by the analysis. Instead, the analysis supported narrower definitions of both Telamonini, here reinstated from synonymy, and Smiliini. A key and diagnoses are given to define these tribes, along with discussions of their phylogeny, biogeography, and host plant associations. The genera Antianthe Fowler, Hemicardiacus Plummer, Smilirhexia McKamey, and Tropidarnis Fowler are placed as Smiliinae, incertae sedis. Based on the phylogeny, several genera from both tribes including Atymna Stål, Cyrtolobus Goding, Heliria Stål, and Telamona Fitch are not monophyletic. Diagnostic characters emphasizing the morphological differences between the Smiliini and Telamonini include the dorsal margin of the head, the shape of the pronotum, the size of the pronotal humeral angles, the presence or absence of pronotal longitudinal rugae, the size of forewing cells, variations in the fusion of veins R and M apically in both the foreand hind wing, and the shape of the apex of the female second valvulae. Mapping geographic distribution onto the phylogeny suggests that the common ancestor of the ingroup (all three clades) occurred in Central America and Mexico, with multiple dispersals to temperate North America. Many Smiliini and Telamonini feed on various species of oak (Quercus) and the close evolutionary association between these insects and their hosts is discussed.

scholarly journals Placenta-Specific Protein 1 Is Conserved throughout the Placentalia under Purifying Selection

2014 ◽  
Vol 2014 ◽  
pp. 1-5 ◽  
Author(s):  
Eric J. Devor
Keyword(s):  
Phylogenetic Analysis ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Mammalian Species ◽  
Purifying Selection ◽  
Specific Protein ◽  
Mammal Species ◽  
Crucial Component ◽  
Successful Group ◽  
The Common

Placental mammals (Placentalia) are a very successful group that, today, comprise 94% of all mammalian species. Recent phylogenetic analyses, coupled with new, quite complete fossils, suggest that the crown orders were all established rapidly from a common ancestor just after the Cretaceous/Tertiary (K/T) boundary 65 million years ago. Extensive molecular and morphologic evidence has led to a description of the common ancestor of all Placentalia in which a two-horned uterus and a hemochorial placenta are present. Thus, the process of placentation in which the placenta invades and anchors to the uterine epithelium was already established. One factor that has been suggested as a crucial component of this process is placenta-specific protein 1 (PLAC1). A phylogenetic analysis of the PLAC1 protein in 25 placental mammal species, representing nine of the sixteen crown orders of the Placentalia, suggests that this protein was present in the placental common ancestor in the form we see it today, that it evolved in the Placentalia and has been subject to the effects of purifying selection since its appearance.

scholarly journals Intact rDNA arrays of Potentilla-origin detected in Erythronium nucleus suggest recent eudicot-to-monocot horizontal transfer

2021 ◽  
Author(s):  
Laszlo Bartha ◽  
Terezie Mandakova ◽  
Ales Kovarik ◽  
Paul Adrian Bulzu ◽  
Nathalie Rodde ◽  
...  
Keyword(s):  
Southern Blotting ◽  
Common Ancestor ◽  
Phylogenetic Signal ◽  
Molecular Cytogenetics ◽  
Nuclear Genome ◽  
Phylogenetic Distance ◽  
Bac Clone ◽  
Intimate Association ◽  
The Common ◽  
Naturally Transgenic Plants

The occurrence of horizontal gene transfer (HGT) in Eukarya is increasingly gaining recognition. Nuclear-to-nuclear jump of DNA between plant species at high phylogenetic distance and devoid of intimate association (e.g., parasitism) is still scarcely reported. Within eukaryotes, components of ribosomal DNA (rDNA) multigene family have been found to be horizontally transferred in protists, fungi and grasses. However, in neither case HGT occurred between phylogenetic families, nor the transferred rDNA remained tandemly arrayed and transcriptionally active in the recipient organism. This study aimed to characterize an alien eudicot-type of 45S nuclear rDNA, assumingly transferred horizontally to the genome of monocot European Erythronium (Liliaceae). Genome skimming coupled by PacBio HiFi sequencing of a BAC clone were applied to determine DNA sequence of the alien rDNA. A clear phylogenetic signal traced the origin of the alien rDNA of Erythronium back to the Argentea clade of Potentilla (Rosaceae) and deemed the transfer to have occurred in the common ancestor of E. dens-canis and E. caucasicum. Though being discontinuous, transferred rDNA preserved its general tandemly arrayed feature in the host organism. Southern blotting, molecular cytogenetics, and sequencing of a BAC clone derived from flow-sorted nuclei indicated integration of the alien rDNA into the recipient's nuclear genome. Unprecedently, dicot-type alien rDNA was found to be transcribed in the monocot Erythronium albeit much less efficiently than the native counterpart. This study adds a new example to the growing list of naturally transgenic plants while holding the scientific community continually in suspense about the mode of DNA transfer.

scholarly journals The Common Ancestor of Archaea and Eukarya Was Not an Archaeon

Archaea ◽  
2013 ◽  
Vol 2013 ◽  
pp. 1-18 ◽  
Author(s):  
Patrick Forterre
Keyword(s):  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Critical Role ◽  
Last Common Ancestor ◽  
Dna Viruses ◽  
The Common ◽  
Basic Features ◽  
Origin Of Eukaryotes ◽  
Archaeal Ancestor ◽  
Selection Of

It is often assumed that eukarya originated from archaea. This view has been recently supported by phylogenetic analyses in which eukarya are nested within archaea. Here, I argue that these analyses are not reliable, and I critically discuss archaeal ancestor scenarios, as well as fusion scenarios for the origin of eukaryotes. Based on recognized evolutionary trends toward reduction in archaea and toward complexity in eukarya, I suggest that their last common ancestor was more complex than modern archaea but simpler than modern eukaryotes (the bug in-between scenario). I propose that the ancestors of archaea (and bacteria) escaped protoeukaryotic predators by invading high temperature biotopes, triggering their reductive evolution toward the “prokaryotic” phenotype (the thermoreduction hypothesis). Intriguingly, whereas archaea and eukarya share many basic features at the molecular level, the archaeal mobilome resembles more the bacterial than the eukaryotic one. I suggest that selection of different parts of the ancestral virosphere at the onset of the three domains played a critical role in shaping their respective biology. Eukarya probably evolved toward complexity with the help of retroviruses and large DNA viruses, whereas similar selection pressure (thermoreduction) could explain why the archaeal and bacterial mobilomes somehow resemble each other.

scholarly journals The molecular evolution of Dabie bandavirus (Phenuiviridae: Bandavirus: Dabie bandavirus), the agent of severe fever with thrombocytopenia syndrome

2022 ◽  
Vol 66 (6) ◽  
pp. 409-416
Author(s):  
T. E. Sizikova ◽  
V. N. Lebedev ◽  
S. V. Borisevich
Keyword(s):  
Molecular Evolution ◽  
Phylogenetic Trees ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Virus Transmission ◽  
Infectious Agent ◽  
Global Public Health ◽  
The Common ◽  
Epidemiological Characteristics ◽  
Severe Fever

Since the Dabie bandavirus (DBV; former SFTS virus, SFTSV) was identified, the epidemics of severe fever with thrombocytopenic syndrome (SFTS) caused by this virus have occurred in several countries in East Asia. The rapid increase in incidence indicates that this infectious agent has a pandemic potential and poses an imminent global public health threat.The analysis of molecular evolution of SFTS agent that includes its variants isolated in China, Japan and South Korea was performed in this review. The evolution rate of DBV and the estimated dates of existence of the common ancestor were ascertained, and the possibility of reassortation was demonstrated.The evolutionary rates of DBV genome segments were estimated to be 2.28 × 10-4 nucleotides/site/year for S-segment, 2.42 × 10-4 for M-segment, and 1.19 × 10-4 for L-segment. The positions of positive selection were detected in the viral genome.Phylogenetic analyses showed that virus may be divided into two clades, containing six different genotypes. The structures of phylogenetic trees for S-, M- and L-segments showed that all genotypes originate from the common ancestor.Data of sequence analysis suggest that DBV use several mechanisms to maintain the high level of its genetic diversity. Understanding the phylogenetic factors that determine the virus transmission is important for assessing the epidemiological characteristics of the disease and predicting its possible outbreaks.

Preliminary reconstructions of nasal chemosensory evolution in Squamata

1996 ◽  
Vol 17 (4) ◽  
pp. 395-415 ◽  
Author(s):  
William E. Cooper
Keyword(s):  
Olfactory Receptor ◽  
Common Ancestor ◽  
Chemical Senses ◽  
Squamate Reptiles ◽  
Olfactory Development ◽  
Olfactory Systems ◽  
The Common ◽  
Common Ancestors

AbstractSquamate reptiles are known for using vomerolfaction, the sense associated with the vomeronasal organs, to detect prey, predators, and conspecifies. By comparison, olfaction has been relatively neglected, yet many squamates have highly developed olfactory systems. Data from the literature were used to make preliminary reconstructions of the evolution of the vomeronasal and olfactory systems in Squamata. Vomerolfaction is highly developed in nearly all squamates, and was enhanced progressively in the common ancestors of Scleroglossa, Autarchoglossa, and Anguimorpha, reaching peaks in two autarchoglossan clades, Varanoidea, and Lacertiformes. Olfaction also improved in the common ancestor of Scleroglossa. Olfactory receptor abundance peaked in Gekkota and Lacertoidea, but declined in Anguimorpha, with some increase in snakes. Five major clades of lizards differ in development of chemical senses. Iguanians have the least developed vomerolfaction and olfaction. Gekkotans and lacertoideans have the greatest olfactory development, with greater vomerolfactory development in Lacertoidea. Scincoideans have intermediate olfaction and vomerolfaction. Anguimorphans have the most specialized vomerolfaction coupled in snakes with apparently greater olfactory powers than in varanids.

THE CYTOGENETIC POSITION OF AVENA PROSTRATA AMONG THE DIPLOID OATS

1973 ◽  
Vol 15 (3) ◽  
pp. 443-450 ◽  
Author(s):  
Gideon Ladizinsky
Keyword(s):  
Chromosome Pairing ◽  
Common Ancestor ◽  
Morphological Characters ◽  
Chromosome Architecture ◽  
Evolutionary Step ◽  
The Common ◽  
Restoration Of Fertility

The chromosome architecture of the newly discovered diploid oat A. prostrata is similar to that of A. longiglumis. The hybrids involving these oats had many PMC's with seven bivalents and were partially fertile. Considerable restoration of fertility in the F2 was coupled with improvement of chromosome pairing and usually linked to the diagnostic morphological characters of either parent. The hybrids involving A. prostrata and A. strigosa were characterized by multivalent associations in meiosis, indicating at least five translocation differences between the two species. By combining the cytogenetical, morphological and the ecological evidence, it was suggested that A. prostrata is either the first evolutionary step from A. longiglumis toward A. damascena and A. strigosa or, more probably, the common ancestor of these three diploid oats.

scholarly journals Phylogeny of Stenopodidea (Crustacea : Decapoda) shrimps inferred from nuclear and mitochondrial genes reveals non-monophyly of the families Spongicolidae and Stenopididae and most of their composite genera

2016 ◽  
Vol 30 (5) ◽  
pp. 479 ◽  
Author(s):  
Chien-Lin Chen ◽  
Joseph W. Goy ◽  
Heather D. Bracken-Grissom ◽  
Darryl L. Felder ◽  
Ling Ming Tsang ◽  
...  
Keyword(s):  
Deep Sea ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Characters ◽  
12S Rrna ◽  
Reciprocal Monophyly ◽  
Sodium Potassium ◽  
Α Subunit ◽  
Molecular Phylogenetic ◽  
Living Species

The infraorder Stenopodidea is a relatively small group of marine decapod crustaceans including the well known cleaner shrimps, but their higher taxonomy has been rather controversial. This study provides the most comprehensive molecular phylogenetic analyses of Stenopodidea using sequence data from two mitochondrial (16S and 12S rRNA) and two nuclear (histone H3 and sodium–potassium ATPase α-subunit (NaK)) genes. We included all 12 nominal genera from the three stenopodidean families in order to test the proposed evolutionary hypothesis and taxonomic scheme of the group. The inferred phylogeny did not support the familial ranking of Macromaxillocarididae and rejected the reciprocal monophyly of Spongicolidae and Stenopididae. The genera Stenopus, Richardina, Spongiocaris, Odontozona, Spongicola and Spongicoloides are showed to be poly- or paraphyletic, with monophyly of only the latter three genera strongly rejected in the analysis. The present results only strongly support the monophyly of Microprosthema and suggest that Paraspongiola should be synonymised with Spongicola. The three remaining genera, Engystenopus, Juxtastenopus and Globospongicola, may need to be expanded to include species from other genera if their statuses are maintained. All findings suggest that the morphological characters currently adopted to define genera are mostly invalid and substantial taxonomic revisions are required. As the intergeneric relationships were largely unresolved in the present attempt, the hypothesis of evolution of deep-sea sponge-associated taxa from shallow-water free-living species could not be verified here. The present molecular phylogeny, nevertheless, provides some support that stenopoididean shrimps colonised the deep sea in multiple circumstances.

Stratocladistic analysis of blastoid phylogeny

2001 ◽  
Vol 75 (2) ◽  
pp. 351-369 ◽  
Author(s):  
Brian E. Bodenbender ◽  
Daniel C. Fisher
Keyword(s):  
Ad Hoc ◽  
Common Ancestor ◽  
Phylogenetic Analyses ◽  
Cladistic Analysis ◽  
Morphological Characters ◽  
Accurate Estimation ◽  
Evolutionary Relationships ◽  
Temporal Data ◽  
Stratigraphic Record ◽  
Different Sources

Stratocladistics combines morphological and stratigraphic data in a parsimony-based analysis of evolutionary relationships. We use stratocladistics here to provide an overview of the phylogeny of the extinct echinoderm class Blastoidea. Both cladistic and stratocladistic methods evaluate alternative phylogenies by comparing the number of ad hoc hypotheses needed to reconcile each alternative to observed data. Minimization of ad hoc hypotheses selects the phylogeny best supported by data and enables phylogenetic analyses to incorporate data from different sources. Cladistics treats ad hoc hypotheses of homoplasy, whereas stratocladistics additionally considers ad hoc hypotheses of differential preservation probability of lineages in the stratigraphic record.The blastoid phylogeny derived using stratocladistics is more resolved than hypotheses selected by cladistics. Although the morphological characters are relatively homoplasious, in this instance the stratigraphic ordering of fossils provides both structure and altered polarity for the stratocladistic hypothesis. The stratocladistic phylogeny supports previous paleontological conclusions of convergence among blastoid lineages and facilitates evaluation of specific hypotheses of character transformation that are integral to recent systematic revisions. Additionally, consideration of temporal data makes some hypotheses of ancestor-descendant relationships more parsimonious than hypotheses of derivation from a common ancestor. The ability to recognize sequential members within single lineages allows more accurate estimation of faunal diversities and more specific reconstruction of evolutionary histories. Chief among possible confounding factors in stratocladistics are instances where preservation potential shows significant geographic variation, although problems of preservation are more tractable than the difficulties homoplasy presents for cladistic analysis.

scholarly journals The Deep(er) Roots of Eukaryotes and Akaryotes

2020 ◽  
Author(s):  
Ajith Harish ◽  
David A. Morrison
Keyword(s):  
Evolutionary History ◽  
Common Ancestor ◽  
Phylogenetic Signal ◽  
The Other ◽  
Root Node ◽  
Molecular Features ◽  
Universal Common Ancestor ◽  
Evolutionary Relatedness ◽  
The Common ◽  
Phylogenetic Character

AbstractLocating the root-node of the “tree of life” (ToL) is one of the hardest problems in phylogenetics1. The root-node or the universal common ancestor (UCA) divides the descendants into organismal domains2. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently3,4, though, Williams and colleagues (W&C)4 claim that one is better supported than the other. Here, we argue that important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data were overlooked4. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. It is well-known that different character-types present different perspectives on evolutionary history that relate to different phylogenetic depths5–7. Which of the 2D-ToL2,4 hypotheses is better supported depends on which kind of molecular features – protein-domains or their component amino-acids – are better for resolving the common ancestors (CA) at the roots of clades. In practice, this involves reconstructing character compositions of the ancestral nodes all the way back to the UCA2,3.

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