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  • Section: Paleontology ; Topics: Evolution, Paleontology, Anthropology

    OH 89: A newly described ~1.8-million-year-old hominid clavicle from Olduvai Gorge

    10.24072/pcjournal.372 - Peer Community Journal, Volume 4 (2024), article no. e34.

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    Objectives Here, we describe the morphology and geologic context of OH 89, a ∼1.8million-year-old partial hominid clavicle from Olduvai (Oldupai) Gorge, Tanzania. We compare the morphology and clavicular curvature of OH 89 to modern humans, extant apes, and a sample of other hominid fossil clavicles. Materials and Methods Comparative samples include 25 modern human clavicles, 30 Gorilla, 31 Pan, 7 Papio, and five hominid clavicles. Length regression on midshaft size using the extant comparative samples is used to estimate the total length of OH 89. A set of 9 linear measurements are taken from each individual. We also describe a new methodology for measuring clavicular curvature using measurements of sternal and acromial curvature, from which an overall curvature measurement is calculated. A principal component analysis (PCA) and a t-distributed stochastic neighbor embedding (tSNE) analysis are used to compare the morphology of OH 89 with the extant and fossil comparative samples. Results Our new method of measuring clavicular curvature successfully separates the different genera of the extant clavicles. The length estimate and sternal and acromial curve measurements for OH 89 falls within the larger male humans. The PCA shows OH 89 and most of the fossil hominids falling between the modern human and Pan groups, while the t-SNE suggests that OH 89, KSD-VP-1/1, KNM-ER 1808, and OH 48 are more similar to each other than to any of the other groups. This analysis also plots KNM-WT 15000 with the modern humans and Krapina 158 with the Pan individuals. Discussion The OH 89 clavicle derives from an individual of unknown hominid species with a shoulder breadth similar to that of a large human male. The curvature of OH 89 is relatively human-like relative to its length. Our new methodology for measuring clavicular curvature, combined with the utilization of t-SNE analyses and comparison of t-SNE results to PCA results, provides greater separation of genera than previously used methods, and wider use of t-SNE may be useful in paleoanthropological work.

  • Section: Evolutionary Biology ; Topics: Evolution, Genetics/genomics, Computer sciences

    Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent

    10.24072/pcjournal.397 - Peer Community Journal, Volume 4 (2024), article no. e33.

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    The reproductive mechanism of a species is a key driver of genome evolution. The standard Wright-Fisher model for the reproduction of individuals in a population assumes that each individual produces a number of offspring negligible compared to the total population size. Yet many species of plants, invertebrates, prokaryotes or fish exhibit neutrally skewed offspring distribution or strong selection events yielding few individuals to produce a number of offspring of up to the same magnitude as the population size. As a result, the genealogy of a sample is characterized by multiple individuals (more than two) coalescing simultaneously to the same common ancestor. The current methods developed to detect such multiple merger events do not account for complex demographic scenarios or recombination, and require large sample sizes. We tackle these limitations by developing two novel and different approaches to infer multiple merger events from sequence data or the ancestral recombination graph (ARG): a sequentially Markovian coalescent (SMβC) and a graph neural network (GNNcoal). We first give proof of the accuracy of our methods to estimate the multiple merger parameter and past demographic history using simulated data under the β-coalescent model. Secondly, we show that our approaches can also recover the effect of positive selective sweeps along the genome. Finally, we are able to distinguish skewed offspring distribution from selection while simultaneously inferring the past variation of population size. Our findings stress the aptitude of neural networks to leverage information from the ARG for inference but also the urgent need for more accurate ARG inference approaches.

  • Nematomorpha, also known as Gordiacea or Gordian worms, are a phylum of parasitic organisms that belong to the Ecdysozoa, a clade of invertebrate animals characterized by molting. They are one of the less scientifically studied animal phyla, and many aspects of their biology and evolution are still unknown, partially due to the lack of genomic resources for this phylum. As part of the European Reference Genome Atlas pilot effort to generate reference genomes for European biodiversity, we present the taxonomic description and chromosome-level genome assembly of a newly described species of Nematomorpha (Gordionus montsenyensis Schmidt-Rhaesa & Fernández sp. nov.). The final assembly has a total length of 288 Mb in 396 scaffolds with an N50 of 64.4 Mb, 97% of which is scaffolded into 5 pseudochromosomes. The circular mitochondrial genome was also assembled into a 15-kilobases sequence. Gene annotation predicted 10,320 protein-coding genes in the nuclear genome. In this study, we contribute a key genomic resource to not only explore the evolution of Ecdysozoa, but also to further our understanding on the genomic basis of parasitic lifestyles. In addition, we describe a species new to science from this enigmatic animal phyla.

  • Section: Health & Movement Sciences ; Topics: Health sciences, Neuroscience

    Interlimb coordination in Parkinson’s Disease is minimally affected by a visuospatial dual task

    10.24072/pcjournal.387 - Peer Community Journal, Volume 4 (2024), article no. e31.

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    Parkinson’s disease (PD) leads to reduced spatial and temporal interlimb coordination during gait as well as reduced coordination in the upper or lower limbs. Multi-tasking when walking is common during real-world activities, and affects some gait characteristics, like gait speed and variability. However, the impact of a dual task (DT) on intra and interlimb coordination of both lower and upper limbs when walking in people with PD remains unknown. Seventeen volunteers with mild to moderate PD (11 males, 65 ± 8 years, 173 ± 8 cm, 74 ± 20 kg, Unified Parkinson’s Disease Rating Scale motor section 10 ± 5) participated in gait trials in an Extended-CAREN system, which includes a treadmill, 12-camera Vicon motion capture system, and a 180° field-of-view virtual reality projection screen. Participants completed a 3 min walking trial and a 2 min visuospatial word recognition DT trial at their preferred walking pace. Single and DT were compared with a paired t-test, and the less and more affected (LA, MA) sides were tested for equivalence in sensitivity to the DT. During the DT, we found the LA shoulder ROM decreased by 1.5°, and the LA shoulder peak flexion decreased by 1.1° (p<.028, gav>.12). The LA and MA hip ROM were differently affected by the dual task (p=.023), and intralimb coordination was affected by dual tasking equivalently between sides (p=.004). These results suggest that during normal single-task gait, people with PD use attentional resources to compensate for reduced arm swing. Furthermore, our results indicate that any effect of DT on lower intralimb coordination is not meaningfully different between the LA and MA sides.

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