Subjects: Biology >> Biological Evolution submitted time 2024-03-21
Abstract： The affinity of ‘Dongfangaspis qujingensis’, initially assigned to Dongfangaspis but later to Laxaspis, has long been controversial. However, the taxonomical revision raises a new problem of junior homonym since the type species of Laxaspis is L. qujingensis. Here, we describe some new materials of ‘Dongfangaspis qujingensis’ and Damaspis vartus from the Xishancun Formation (early Lochkovian, Early Devonian) in Qujing, Yunnan Province. ‘Dongfangaspis qujingensis’ strikingly resembles Damaspis vartus in the slightly longer headshield, bifurcated ends of the lateral transverse canals, unconnected V-shaped posterior supraorbital canals, and at least seven pairs of lateral transverse canals issuing from the lateral dorsal canal. These similarities indicate that ‘D. qujingensis’ is more suggestive of Damaspis than
Dongfangaspis and Laxaspis. Therefore, we propose to remove ‘Dongfangaspis qujingensis’ from Laxaspis to Damaspis. The new specimens of Damaspis vartus reveal five long lateral transverse
canals on the right side, corroborating that the asymmetric sensory canal system in the holotype is
the intraspecific variation.
Subjects: Biology >> Biological Evolution submitted time 2024-03-20
Abstract： Here we report a new form of amphicyonid from an uncertain locality in the Linxia Basin. The derived dental traits imply an affinity to Magericyon, previously known from Europe and possibly southern Asia. The specimen suggests a higher diversity of amphicyonids in eastern Asia than previously thought, and more discovery with stratigraphic information will be needed to elucidate the evolution of Amphicyonidae in eastern Asia.
Subjects: Biology >> Biological Evolution submitted time 2024-03-15
Abstract： The previously alleged ‘eugnathid amiiform’ Sinoeugnathus kueichowensis is a small-sized halecomorph from the Middle Triassic (Ladinian) marine deposits of Guizhou and Yunnan, China. A morphological redescription and taxonomic revision of this taxon are provided based on a detailed examination of 15 new specimens. Among them, IVPP V24315 (standard length = 64 mm) is appointed as the neotype, given that the holotype is missing. Studies of these specimens revealed some morphological details previously undescribed or misidentified for this taxon, including a hatchet-shaped antorbital, two broad suborbitals, a sensory canal in the maxilla, and three pairs of extrascapulars. For the first time, Sinoeugnathus was incorporated into an analysis of halecomorph phylogeny, and the results recover it as the sister taxon of the Anisian Subortichthys from Luoping, Yunnan, and both are grouped with two Ladinian genera Allolepidotus and Eoeugnathus from the Monte San Giorgio area into a monophyletic group (namely Subortichthyidae fam. nov. herein) at the base of Ionoscopiformes. This taxonomic reassessment of Subortichthys provides new insights into the phylogeny and paleogeographic evolution of Ionoscopiformes.
Subjects: Biology >> Biological Evolution submitted time 2024-03-15
Abstract： All the extant rhino species belong to Rhinocerotini and either have one horn (a nasal horn) or two horns (a nasal horn and frontal horn). So far, the earliest Rhinocerotini to have been identified in China is the “Dicerorhinus” cixianensis, which was based on a juvenile skull with an associated mandible from the Middle Miocene locality of Jiulongkou in Cixian County, Hebei Province of northern China. Our analyses suggest that there are similarities between this specimen and the modern genus, Dicerorhinus, but it differs in several cranial traits and therefore cannot be assigned to the modern genus. Instead, it is closer to the Middle Miocene Lartetotherium from Europe, especially the specimen from La Retama in Spain and should be assigned to that genus, indicating the presence of intracontinental dispersal at this time. The Jiulongkou fauna is the only Middle Miocene fauna with Rhinocerotini in China, and, together with the faunal composition, this implies a more humid and closed environment, in contrast to those found in western China. We suggest that the position of the posterior border of the nasal notch is a good indication of the specimen’s evolutionary level in Rhinocerotini. The anterior position of the nasal notch as seen in modern Dicerorhinus, together with its certain similarities to L. cixianensis as well as its differences with more specialized species of the Dihoplus-Pliorhinus-Stephanorhinus -Coelodonta lineage, supports the conclusion that Dicerorhinus experienced little change during a nearly 10 Myr evolutionary history, possibly due to the low selection pressure seen in the tropical/subtropical forests in southeastern Asia.
Subjects: Information Science and Systems Science >> Basic Disciplines of Information Science and Systems Science Subjects: Biology >> Biological Evolution Subjects: Biology >> Biomathematics Subjects: Physics >> Interdisciplinary Physics and Related Areas of Science and Technology Subjects: Biology >> Genetics submitted time 2023-10-15
Zhang, Zecheng
Liu, Chunxiuzi
Zhu, Yingjun
Peng, Lu
Qiu, Weiyi
Tang, Qianyuan
Liu, He
Zhang, Ke
Di, Zengru
Liu, Yu
Abstract： Background: In bioinformatics, tools like multiple sequence alignment and entropy methods probe sequence information and evolutionary relationships between species. Although powerful, they might miss crucial hierarchical relationships formed by the reuse of repetitive subsequences like duplicons and transposable elements. Such relationships are governed by “evolutionary tinkering'', as described by Fran c{c}ois Jacob. The newly developed Ladderpath theory provides a quantitative framework to describe these hierarchical relationships.
Results: Based on this theory, we introduce two indicators: order-rate $ eta$, characterizing sequence pattern repetitions and regularities, and ladderpath-complexity $ kappa$, characterizing hierarchical richness within sequences, considering sequence length. Statistical analyses on real amino acid sequences showed: (1) Among the typical species analyzed, humans possess relatively more sequences with large $ kappa$ values. (2) Proteins with a significant proportion of intrinsically disordered regions exhibit increased $ eta$ values. (3) There are almost no super long sequences with low $ eta$. We hypothesize that this arises from varied duplication and mutation frequencies across different evolutionary stages, which in turn suggests a zigzag pattern for the evolution of protein complexity. This is supported by our simulations and examples from protein families such as Ubiquitin and NBPF.
Conclusions: Our method emphasizes “how objects are generated'', capturing the essence of evolutionary tinkering and reuse. The findings hint at a connection between sequence orderliness and structural uncertainty, and suggest that different species or those in varied environments might adopt distinct protein elongation strategies. These insights highlight our method's value for further in-depth evolutionary biology applications.
Peer Review Status:
Awaiting Review
Subjects: Biology >> Virology Subjects: Biology >> Biological Evolution Subjects: Biology >> Genetics submitted time 2020-02-21
Abstract： Background. The outbreak of COVID-19 started in mid-December 2019 in Wuhan, Central China. Up to February 18, 2020, SARS-CoV-2 has infected more than 70,000 people in China, and another 25 countries across five continents. In this study, we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFluTM database to decode the evolution and human-to-human transmissions of SARS-CoV-2 in the recent two months. Methods. Alignment of coding-regions was conducted haplotype analyses using DnaSP. Substitution sites were analyzed in codon. Evolutionary analysis of haplotypes used NETWORK. Population size changes were estimated using both DnaSP and Arlequin. Expansion date of population size was calculated based on the expansion parameter tau (τ) using the formula t=τ/2u. Findings. Eight coding-regions have 120 substitution sites, including 79 non-synonymous and 40 synonymous substitutions. Forty-two non-synonymous substitutions changed the biochemical property of amino acids. No evident combination was found. Fifty-eight haplotypes were classified as five groups, and 31 haplotypes were found in samples from both China and other countries, respectively. The rooted network suggested H13 and H35 to be ancestral haplotypes, and H1 (and its descendent haplotypes including all samples from the Hua Nan market) was derived H3 haplotype. Population size of SARS-CoV-2 were estimated to have a recent expansion on 6 January 2020, and an early expansion on 8 December 2019. Interpretation. Genomic variations of SARS-CoV-2 are still low in comparisons with published genomes of SARS-CoV and MERS-CoV. Phyloepidemiologic analyses indicated the SARS-CoV-2 source at the Hua Nan market should be imported from other places. The crowded market boosted SARS-CoV-2 rapid circulations in the market and spread it to the whole city in early December 2019. Furthermore, phyloepidemiologic approaches have recovered specific direction of human-to-human transmissions, and the import sources of international infectious cases.
Peer Review Status:Awaiting Review
Subjects: Biology >> Biological Evolution submitted time 2018-04-20
Abstract： Archaeanthus is a famous Cretaceous angiosperm from the Albian-Cenomanian of Kansas, USA documented by Dilcher and Crane in 1984. Its seeds/ovules were interpreted as arranged along the adaxial (ventral) suture of the fruits. This interpretation used to be plausible, especially under the light of then-dominating doctrine of angiosperm evolution. However, Dilcher and Crane’s interpretation of ovule insertion was not fully supported even by their own evidence. Considering the early age, importance and influence of Archaeanthus in palaeobotany and angiosperm systematics, it is necessary to double check the ovule insertion in Archaeanthus and its implications for homology of carpel as well as origin of angiosperms. New observation on the type materials of Archaeanthus indicates that, besides adaxial(ventral) arrangement of ovule/seed as assumed formerly, at least some ovules/seeds in Archaeanthus are attached to the abaxial(dorsal) margin of the fruit. This information undermines the former assumed Magnoliaceous affinity of Archaeanthus, and falsifies its support to the influencing speculation of carpel homology and origin of angiosperms. Analysis of the common reason underlying the misinterpretations of early fossil angiosperms (including Archaeanthus, Archaefructus, and others) indicates that the speculation of Arber and Parkin is groundless and the major culprit inflicting botany in the past century.
Peer Review Status:Awaiting Review
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