Recommendations for improving photo quality in close range photogrammetry, exemplified in hand bones of chimpanzees and gorillas / Recomendaciones para mejorar la calidad de las fotos en fotogrametría de corto alcance, ejemplificado en huesos de las manos de chimpancés y gorillas

SUMMARY: Photogrammetry is becoming increasingly popular in morphological research and teaching due to its portability, ability to reliably render 3D models, and quality-to-price relationship relative to some popular surface scanners. Compared to surface scanners, however, the learning process in photogrammetry can be very time consuming. Here we describe common mistakes of photo capture in close-range photogrammetry that greatly affect 3D output and tips to improve them. Problems were identified after the 3D model construction of 780 hand bones of chimpanzees and gorillas from museum collections. Their hands are composed of 27 bones which vary in length and complexity. We show how lighting, object position and orientation, camera angle, and background affect the 3D output. By taking these factors into account, time and error rates for beginners can be greatly reduced and 3D model quality can be considerably improved.

RESUMEN: La fotogrametría está siendo cada vez más popular en la investigación y enseñanza morfológica. Esto debido a su portabilidad, confiabilidad de los modelos 3D y buena relación calidadprecio. Comparada con los escáneres de superficie, sin embargo, el proceso de aprendizaje de la fotogrametría puede llevar mucho tiempo. Aquí se describen errores comunes en la toma de fotos para fotogrametería que afectan de manera importante la creación de los modelos 3D, así como consejos para superarlos. Los problemas descritos fueron identificados luego de la construcción de 780 modelos 3D de huesos de la mano de chimpancés y gorillas depositados en distintas colecciones de museos. Las manos de estas especies están compuestas por 27 huesos que varían en tamaño y complejidad. En este artículo mostramos como la luz, la posición y orientación del objeto, el ángulo de la cámara y el fondo de la imagen afectan el resultado en 3D. Considerando estos factores, personas que están aprendiendo esta técnica pueden reducir de manera importante el tiempo y la probabilidad de error, y mejorar considerablemente la calidad de los modelos 3D.

Phylogenetics applied to the human immunodeficiency virus type 1 (HIV-1): from the cross-species transmissions to the contact network inferences

Phylogenetic analyses were crucial to elucidate the origin and spread of the pandemic human immunodeficiency virus type 1 (HIV-1) group M virus, both during the pre-epidemic period of cryptic dissemination in human populations as well as during the epidemic phase of spread. The use of phylogenetics and phylodynamics approaches has provided important insights to track the founder events that resulted in the spread of HIV-1 strains across vast geographic areas, specific countries and within geographically restricted communities. In the recent years, the use of phylogenetic analysis combined with the huge availability of HIV sequences has become an increasingly important approach to reconstruct HIV transmission networks and understand transmission dynamics in concentrated and generalised epidemics. Significant efforts to obtain viral sequences from newly HIV-infected individuals could certainly contribute to detect rapidly expanding HIV-1 lineages, identify key populations at high-risk and understand what public health interventions should be prioritised in different scenarios.

Mental rotation of anthropoid hands: a chronometric study

It has been shown that mental rotation of objects and human body parts is processed differently in the human brain. But what about body parts belonging to other primates? Does our brain process this information like any other object or does it instead maximize the structural similarities with our homologous body parts? We tried to answer this question by measuring the manual reaction time (MRT) of human participants discriminating the handedness of drawings representing the hands of four anthropoid primates (orangutan, chimpanzee, gorilla, and human). Twenty-four right-handed volunteers (13 males and 11 females) were instructed to judge the handedness of a hand drawing in palm view by pressing a left/right key. The orientation of hand drawings varied from 0° (fingers upwards) to 90° lateral (fingers pointing away from the midline), 180° (fingers downwards) and 90° medial (finger towards the midline). The results showed an effect of rotation angle (F(3, 69) = 19.57, P < 0.001), but not of hand identity, on MRTs. Moreover, for all hand drawings, a medial rotation elicited shorter MRTs than a lateral rotation (960 and 1169 ms, respectively, P < 0.05). This result has been previously observed for drawings of the human hand and related to biomechanical constraints of movement performance. Our findings indicate that anthropoid hands are essentially equivalent stimuli for handedness recognition. Since the task involves mentally simulating the posture and rotation of the hands, we wondered if "mirror neurons" could be involved in establishing the motor equivalence between the stimuli and the participants' own hands.

Recent integrations of mammalian Hmg retropseudogenes.

We propose that select retropseudogenes of the high mobility group nonhistone chromosomal protein genes have recently integrated into mammalian genomes on the basis of the high sequence identity of the copies to the cDNA sequences derived from the original genes. These include the Hmg1 gene family in mice and the Hmgn2 family in humans. We investigated orthologous loci of several strains and species of Mus for presence or absence of apparently young Hmg1 retropseudogenes. Three of four analysed elements were specific to Mus musculus, two of which were not fixed, indicative of recent evolutionary origins. Additionally, we datamined a presumptive subfamily (Hmgz) of mouse Hmg1, but only identified one true element in the GenBank database, which is not consistent with a separate subfamily status. Two of four analysed Hmgn2 retropseudogenes were specific for the human genome, whereas a third was identified in human, chimpanzee and gorilla genomes, and a fourth additionally found in orangutan but absent in African green monkey. Flanking target-site duplications were consistent with LINE integration sites supporting LINE machinery for their mechanism of amplification. The human Hmgn2 retropseudogenes were full length, whereas the mouse Hmg1 elements were either full length or 3'-truncated at specific positions, most plausibly the result of use of alternative polyadenylation sites. The nature of their recent amplification success in relation to other retropseudogenes is unclear, although availability of a large number of transcripts during gametogenesis may be a reason. It is apparent that retropseudogenes continue to shape mammalian genomes, and may provide insight into the process of retrotransposition, as well as offer potential use as phylogenetic markers.

Evidencia parasitológica sobre la filogenia de los homínidos y los cébidos / Parasitological evidence about the phylogeny of the hominoids and the ceboids

A systematic revision of the ectoparasites (lice) of the hominids and ceboids supports the Trogloditian hypothesis, according to which the genus Homo is the sister of Pan, and the genus Gorilla the sister group of both. The phylogenetic analysis of this matrix derived from the study of primate lice shows an C.I. of 0.71 for the Trogloditian hypothesis including the ceboids in the analysis

Evolution and the origins of man: clues from complete sequences of hominoid mitochondrial DNA.

Dating the origins of Homo sapiens sapiens is a central problem in human population genetics and anthropology. Do we descend from a single recent ancestral population in Africa, or from multiple ancestral populations in various regions of the world which one million years ago simultaneously began developing into H.s.sapiens? The high substitution rate of mitochondrial DNA (mtDNA) makes this molecule suitable for genealogical and chronological research on closely related hominoid species. We have analyzed the complete mtDNA sequences of three humans (African, European and Japanese) and two African apes (common chimpanzee and gorilla) in an attempt to estimate more accurately the substitution rates and divergence times of hominoid mtDNAs. Nonsynonymous substitutions and substitutions in RNA genes have accumulated at an approximately constant rate. Under the assumption, supported by the fossil record, that the orangutan and African apes diverged 13 million years ago, we have previously obtained 4.7 million years as the divergence time between humans and chimpanzees. Using this date, we calibrated the substitution rates at synonymous sites and in the displacement-loop region as 4.03 and 7.25 x 10(-8)/site/year, respectively. Based on these rates together with the observation that the African sequence presented here is most diverged from all other human sequences, we inferred the age of the last common ancestor of the human mtDNAs as 140,000 +/- 18,000 years. The result strongly supports the recent African origin of modern humans, H.s. sapiens.