Hasil untuk "Human evolution"

P. Perelman, W. Johnson, C. Roos et al.

Comparative genomic analyses of primates offer considerable potential to define and understand the processes that mold, shape, and transform the human genome. However, primate taxonomy is both complex and controversial, with marginal unifying consensus of the evolutionary hierarchy of extant primate species. Here we provide new genomic sequence (∼8 Mb) from 186 primates representing 61 (∼90%) of the described genera, and we include outgroup species from Dermoptera, Scandentia, and Lagomorpha. The resultant phylogeny is exceptionally robust and illuminates events in primate evolution from ancient to recent, clarifying numerous taxonomic controversies and providing new data on human evolution. Ongoing speciation, reticulate evolution, ancient relic lineages, unequal rates of evolution, and disparate distributions of insertions/deletions among the reconstructed primate lineages are uncovered. Our resolution of the primate phylogeny provides an essential evolutionary framework with far-reaching applications including: human selection and adaptation, global emergence of zoonotic diseases, mammalian comparative genomics, primate taxonomy, and conservation of endangered species.

P. Hastings, J. Lupski, J. Lupski et al.

K. Bussey, A. Bandura

D. Haraway

K. Laland, J. Odling-Smee, M. Feldman

Brian Hare, M. Tomasello

F. Malavasi, S. Deaglio, A. Funaro et al.

J. Rilling, M. Glasser, T. Preuss et al.

The International HapMap Consortium

D. Nettle

D. Behar, M. van Oven, Saharon Rosset et al.

B. Mecozzi, F. Bona, J. Conti et al.

Since the beginning of the XIX century, Grotta Romanelli gained recognition in European stratigraphy as an important site for the Late Pleistocene, due to the attribution of its basal sediments to the Last Interglacial (MIS 5e). Its abundant archaeological and paleontological findings made the cave a key reference point for the study of human evolution and faunal dynamics in the larger Mediterranean area over approximately the last 130,000 years. After a century, a new chronostratigraphic reassessment of Grotta Romanelli revised the timeframe of its lower levels, predating them to the late Middle Pleistocene.In this study, we re-evaluate selected historical museum collections from the so-called “lower complex” of Grotta Romanelli and examine the new fossils excavated between 2015 and 2022. We identify three main mammal assemblages associated with three different interglacial periods spanning the last 350,000 years. Our findings offer new insights into terrestrial ecosystems in Mediterranean Europe from the late Middle Pleistocene to early Late Pleistocene. Additionally, they provide valuable information to the biochronological framework of the European large mammal faunas.

PETRA TONAROVÁ, THOMAS J. SUTTNER, OLLE HINTS et al.

The end of the Ordovician witnessed major perturbations in the ecosystem, seriously affecting global marine biodiversity. Nevertheless, some marine organism groups and their crisis-bound palaeogeographic distribution are still understudied. Among the outliers are eunicid polychaetes, even though they flourished and diversified extensively during the Ordovician. A collection of seven genera of jaw-bearing polychaetes, including the new ramphoprionid genus Spitiprion Tonarová, Suttner, & Hints, with type new species of Spitiprion khannai Tonarová, Suttner, & Hints, is described here from Katian (Upper Ordovician) deposits of Spiti, northern India. The new species is preserved as isolated maxillae and a jaw cluster, and 3D models of the maxillary apparatus are reconstructed based on submicron-CT. Along with the scolecodonts, a low-diversity assemblage of chitinozoans was recovered, comprising five genera. The most common chitinozoan species are Acanthochitina cf. cancellata and Spinachitina suecica.

Victor Lundström, David Simpson, Peter Yaworsky

At the end of the Pleistocene as temperatures warmed, new habitats opened up to human occupation as the Fennoscandian Ice Sheet receded. Along the west coast of modern-day Norway, human populations of coastal foragers slowly transitioned from short-term settlement patterns in the Early Mesolithic (ca. 11,500–10,000 cal BP), to more lasting ones during the Late Mesolithic (8500-6000 BP) and Early Neolithic (ca. 6000–5200 BP) as climatic conditions improved and stabilized. Here, using spatially and temporally resolved archaeological observations, paleoclimate data, and a spatiotemporal species distribution model, we test whether a) improvements in climate resulted in expansion of the available human niche space allowing for human population growth, and b) whether increasing population densities and ensuing deprecation of habitat suitability pushed people into occupying successively lower ranked habitats as predicted by the Ideal Free Distribution model. We find that a) climate gradually improved and stabilized during the Holocene, with the effect of improving general habitat suitability, which in turn led to an increase in human population size, b) that immediate proximity to sheltered coastal areas was central to settlement decisions but that c) increasing populations did not drive dispersal patterns into lower ranked habitats. The latter is likely attributable to the general improvements in habitat suitability due to the warming climate and the relative abundance of coastal habitats found in Norway.

GABRIELA SOBRAL

Prolacerta broomi is one of the most important of fossil reptiles. First considered as one of the earliest members of squamates, this basal archosauromorph has been used as a model for diapsid morphological evolution ever since its discovery, playing a pivotal role in hypotheses on the origin of diapsid reptiles. The holotype of Prolacerta broomi (UCMZ 2003.41R) is known from a mostly complete skull, but the original description is limited to the superficial features of the skull roof and palate. Since then, many other specimens of Prolacerta broomi have been recovered that potentially account for this limited access to anatomical information, but it remains unclear whether these aspects correspond well to the known material of the holotype. Here, the skull morphology of the holotype of Prolacerta broomi is revisited through the use of µCT scans. The identifications of some cranial elements have been corrected, such as the left prefrontal and lacrimal, and several new elements are revealed, including the epi- and ectopterygoids, prearticular, coronoid, and braincase bones. The orbitonasal region is described in detail and significantly shows a contribution of the lacrimal to the dorsal alveolar canal. Finally, the addition of the holotype as an independent OTU in recently published analyses indicate conflicts with the current knowledge on Prolacerta broomi phylogenetic affinity and taxonomy. First, it points to potential taxonomic inconsistency since the holotype does not form a monophyletic group with other Prolacerta broomi OTUs in any of the analyses and, second, it suggests a more basal position for the holotype than that recovered in some studies, more basal than rhynchosaurs and close to the origin of Crocopoda. Together, these findings indicate areas of future research interest in the study of early evolving archosauromorphs.

Mathieu Decloquement, Marzia Tindara Venuto, Virginie Cogez et al.

Abstract The human polysialyltransferases ST8Sia II and ST8Sia IV catalyze the transfer of several Neu5Ac residues onto glycoproteins forming homopolymers with essential roles during different physiological processes. In salmonids, heterogeneous set of sialic acids polymers have been described in ovary and on eggs cell surface and three genes st8sia4, st8sia2-r1 and st8sia2-r2 were identified that could be implicated in these heteropolymers. The three polysialyltransferases from the salmonid Coregonus maraena were cloned, recombinantly expressed in HEK293 cells and the ST8Sia IV was biochemically characterized. The MicroPlate Sialyltransferase Assay and the non-natural donor substrate CMP-SiaNAl were used to demonstrate enzyme activity and optimize polysialylation reactions. Polysialylation was also carried out with natural donor substrates CMP-Neu5Ac, CMP-Neu5Gc and CMP-Kdn in cell-free and cell-based assays and structural analyses of polysialylated products using the anti-polySia monoclonal antibody 735 and endoneuraminidase N and HPLC approaches. Our data highlighted distinct specificities of human and salmonid polysialyltransferases with notable differences in donor substrates use and the capacity of fish enzymes to generate heteropolymers. This study further suggested an evolution of the biological functions of polySia. C. maraena ST8Sia IV of particular interest to modify glycoproteins with a variety of polySia chains.

Vassilena Sharlandjieva, Alexander G. Beristain, Alexander G. Beristain et al.

IntroductionBacteria derived from the maternal circulation have been suggested to seed the human placenta during development leading to an intrinsic placental microbiome. This concept has become controversial as numerous studies suggest that the apparent placental microbiome is mostly, if not completely, comprised of contaminants. If the maternal circulation seeds the placenta then there should be an increase in abundance and diversity of detectable bacteria with onset of maternal perfusion of the placenta around 10 weeks gestational age; however, if only contaminants are present then there should be no significant evolution of the placental microbiome with increasing gestational age. This pilot study addresses whether bacterial abundance and diversity increase in human placenta and whether there is an associated shift in the immunophenotype of the decidual immune cell complement before and after initiation of placental perfusion.MethodsHuman placental and decidual tissue from 5 to 19 weeks gestational age, handled aseptically to minimize contamination, is assessed by quantitative 16S polymerase chain reaction (PCR), 16S gene sequencing, and immunological flow cytometry studies.ResultsA weak positive correlation between placental bacterial abundance and gestational age is identified but is not statistically significant. No significant changes in bacterial diversity are found with increasing gestational age. The proportion of decidual activated memory T helper cells increases with gestational age but no change was observed in other lymphocyte subsets.DiscussionThis pilot study does not strongly support bacterial colonization of the placenta after initiation of maternal perfusion; however, the minor trends towards increases in bacterial abundance and activated memory T helper cells may represent an early stage of this process. Additional investigations in larger cohorts are warranted.

Sherry L. Haller, Chen Peng, G. McFadden et al.

Wen Zhang, Zhen Zhang, Xiaobing Wei et al.

Study region: Han River mainstream, China. Study focus: Human activities and climate change are synergistically impacting on the spatiotemporal features of Han River surface water, which affects the ecological environment evolution and economic development of the basin. However, the long-term changes of the area and spatial characteristics of Han River surface water have not been well quantified for lack of sufficient data and data processing powers. The study produced the annual surface water products of Han River mainstream from 1986 to 2020 based on Google Earth Engine and Landsat images, and then analyzed the long-term spatiotemporal dynamics of surface water and the influence of climatic factor and water conservancy projects construction. New hydrological insights for the region: During the past 35 years, the surface water area of Han River mainstream has shown a fluctuating upward trend overall, and the dynamic changes have obvious regional and phased differences. Precipitation is the main climatic factor affecting the surface water area changes. With precipitation changes and the implementation of water conservancy projects in Han River, the surface water area has increased significantly and many reaches have gradually widened in upstream, while the surface water area has slowly decreased and many reaches have gradually narrowed in mid-downstream. The latest information about the spatiotemporal dynamics of Han River surface water provided by the research can be used for the optimal allocation and management of the river’s water resources.

Perumal Arumugam Desingu, T. P. Rubeni, Nagalingam R. Sundaresan

Monkeypox virus (MPXV) causing multi-country outbreak-2022 is related to viruses caused outbreak-2017–2018 in West Africa. Still not fully understood which proteins of the MPXV discovered in Nigeria in 2017 have mutated through different lineages to the extent that it could cause a multi-country outbreak in 2022; similarly, codon usage bias, host adaptation indices, and the role of selection or mutation pressure in the mutated genes are also not fully studied. Here we report that according to the available sequence data this monkeypox virus acquires point mutations in multiple proteins in each period, and these point mutations accumulate and become a virus that can root outbreak-2022. Viruses exported from Nigeria to Singapore, Israel, and the United Kingdom in 2018–2019 were developed as evolutionary ancestors to B.1 viruses (MPXVs causing multi-country outbreak-2022) through MPXV/United States/2021/MD virus. Although these exported viruses have different amino acid mutations in different proteins, amino acid mutations in 10 proteins are common among them. The MPXV-United Kingdom-P2 virus evolved with only mutations in these 10 proteins and further evolved into MPXV/United States/2021/MD with amino acid mutations in 26 (including amino acid mutations in 10 proteins of the MPXV-United States-P2) proteins. It is noteworthy that specific amino acid mutations in these 22/26 (presence in MPXV/United States/2021/MD) proteins are present in B.1 viruses. Further, analysis of Relative Synonymous Codon Usage (RSCU), Synonymous Codon Usage Fraction (SCUF), and Effective Number of Codons (ENc) revealed codon usage bias in genes that exhibited nucleotide mutations in lineage B.1. Also, host adaptation indices analyzes such as Codon Adaptation Index (CAI), Expected-CAI (eCAI), Relative Codon Deoptimization Index (RCDI) and Expected value for the RCDI (eRCDI) analyzes reveal that the genes that demonstrated nucleotide mutations in lineage B.1 are favorable for human adaptation. Similarly, ENc-GC3s plot, Neutrality plot, and Parity Rule 2 (PR2)-bias plot analyzes suggest a major role of selection pressure than mutation pressure in the evolution of genes displaying nucleotide mutations in lineage B.1. Overall, from 2017 to 2022, MPXV’s mutation and spread suggests that this virus continues to evolve through point mutation in the genes according to the available sequence data.