Exploring the legacy of African and Indigenous Caribbean admixture in Puerto Rico

Objectives

From an anthropological genetic perspective, little is known about the ethnogenesis of African descendants in Puerto Rico. Furthermore, historical interactions between Indigenous Caribbean and African descendant peoples that may be reflected in the ancestry of contemporary populations are understudied. Given this dearth of genetic research and the precedence for Afro-Indigenous interactions documented by historical, archeological, and other lines of evidence, we sought to assess the biogeographic origins of African descendant Puerto Ricans and to query the potential for Indigenous ancestry within this community.

Materials and Methods

Saliva samples were collected from 58 self-identified African descendant Puerto Ricans residing in Puerto Rico. We sequenced whole mitochondrial genomes and genotyped Y chromosome haplogroups for each male individual (n = 25). Summary statistics, comparative analyses, and network analysis were used to assess diversity and variation in haplogroup distribution between the sample and comparative populations.

Results

As indicated by mitochondrial haplogroups, 66% had African, 5% had European, and 29% had Indigenous American matrilines. Along the Y chromosome, 52% had African, 28% had Western European, 16% had Eurasian, and, notably, 4% had Indigenous American patrilines. Both mitochondrial and Y chromosome haplogroup frequencies were significantly different from several comparative populations.

Discussion

Biogeographic origins are consistent with historical accounts of African, Indigenous American, and European ancestry. However, this first report of Indigenous American paternal ancestry in Puerto Rico suggests distinctive features within African descendant communities on the island. Future studies expanding sampling and incorporating higher resolution genetic markers are necessary to more fully understand African descendant history in Puerto Rico.     

Towards an ethical and legal framework in archeogenomics: A local case in the Atlantic coast of central Patagonia

Ethical discussions around ancient DNA (aDNA) research predate the technological breakthroughs that led to the accelerated generation of ancient genomic data, revealing a long-due need to address these aspects in the field. Given the diverse conflicts that genomics has raised towards the communities associated with the Non-living Human Ancestors under study, it has been suggested that the ethical and legal implications of genetically studying present-day and ancient human populations should be considered case-by-case. Nevertheless, the discussions have focused on US and European perspectives. To contribute from a local and Latin American position to the problem, we present the history of consensus and disagreement of the relationships between scientists and Indigenous communities of the Atlantic coast of the central Argentinian Patagonia. We describe how these relationships resulted in the approval of a groundbreaking provincial law that acknowledges the Indigenous community's right to be involved in decision-making concerning their Ancestors. In addition, we emphasize how these established relationships allowed the development of aDNA studies. With this background, we address the main ethical concerns of genomic studies of Ancestors identified in the reference literature and commit to applying some of the recommendations suggested in those ethical guidelines. Then, we reflect on possible negative consequences of ongoing research and propose some suggestions based on personal experiences that will contribute to moving the ethical field towards a more contextualized science with a local perspective.     

Testing different 3D techniques using geometric morphometrics: Implications for cranial fluctuating asymmetry in humans

This study aimed to test the performance of 3D digitizer, CT scanner, and surface scanner in detecting cranial fluctuating asymmetry. Sets of 32 landmarks (6 in the midline and 13 bilateral) were acquired from 14 archeological crania using a 3D digitizer, and from 3D models generated from a CT scanner and surface scanner using Viewbox 4. Levels of shape variation were analyzed in MorphoJ using Procrustes analysis of variance and Principal component analysis. Intra-observer error accounted for 1.7%, 1.8%, and 4.5% of total shape variation for 3D digitizer, CT scanner, and surface scanner respectively. Fluctuating asymmetry accounted for 15%–16% of total shape variation. Variation between techniques accounted for 18% of total shape variation. We found a higher level of missing landmarks in our surface scan data than for both 3D digitizer and CT scanner data, and both 3D model-based techniques sometimes obscured taphonomic damage. All three 3D techniques are appropriate for measuring cranial fluctuating asymmetry. We advise against combining data collected with different techniques.     

Changing patterns of nest predation and predator communities along a tropical elevation gradient

Tropical montane communities host the world's highest beta diversity of birds, a phenomenon usually attributed to community turnover caused by changes in biotic and abiotic factors along elevation gradients. Yet, empirical data on most biotic factors are lacking. Nest predation is thought to be especially important because it appears to be common and can change selective pressures underlying life history traits, which can alter competitive interactions. We monitored 2538 nests, 338 of which had known nest predators, to evaluate if nest predation changes along a tropical elevational gradient. We found that nest predation decreased with elevation, reflecting the loss of lowland predators that do not tolerate colder climates. We found different “super” nest predators at each elevation that accounted for a high percentage of events, suggesting that selection pressures exerted by nest predator communities may be less diffuse than has been hypothesized, at least for birds nesting in the understory.     

Subarctic forest-tundra vegetation gradients: The sigmoid wave hypothesis

Abstract. Spatial changes in tree and upland tundra cover in response to a complex environmental gradient and to landscape factors were investigated in the high subarctic forest-tundra of NW Canada. Vegetation and terrain studies provided ground truth for a grid of 1314 air photos which covered 24 % of the Canadian high subarctic and some of the adjacent low subarctic and low arctic. Across the high subarctic, gradual spatial change in % cover of tree and upland tundra vegetation is typical at both high and low cover values, with more rapid change occurring at intermediate cover. Cover gradients of zonal tree and tundra vegetation in the forest-tundra region in general follow a sigmoid pattern. Tundra and tree patch sizes increase in area and variability with higher tundra and tree cover, respectively.     

Environmental vibrio phage–bacteria interaction networks reflect the genetic structure of host populations

Phages depend on their bacterial hosts to replicate. The habitat, density and genetic diversity of host populations are therefore key factors in phage ecology, but our ability to explore their biology depends on the isolation of a diverse and representative collection of phages from different sources. Here, we compared two populations of marine bacterial hosts and their phages collected during a time series sampling program in an oyster farm. The population of Vibrio crassostreae, a species associated specifically to oysters, was genetically structured into clades of near clonal strains, leading to the isolation of closely related phages forming large modules in phage–bacterial infection networks. For Vibrio chagasii, which blooms in the water column, a lower number of closely related hosts and a higher diversity of isolated phages resulted in small modules in the phage–bacterial infection network. Over time, phage load was correlated with V. chagasii abundance, indicating a role of host blooms in driving phage abundance. Genetic experiments further demonstrated that these phage blooms can generate epigenetic and genetic variability that can counteract host defence systems. These results highlight the importance of considering both the environmental dynamics and the genetic structure of the host when interpreting phage–bacteria networks.     

Combined effect of ambient temperature and solar radiation on maned sloths' behaviour and detectability

Changes in ambient temperature and solar radiation may affect sloths' metabolic rate and body temperature, with consequent changes in activities, postures and microhabitat selection. Although the separate effect of temperature and solar radiation on sloth's behaviour have been previously studied, the combined effect of these climatic factors on behavioural aspects of sloths has never been systematically evaluated in field conditions. Here we evaluated the influence of hourly ambient temperature variation on maned sloth (Bradypus torquatus) activities, postures and tree crown positions, under sunny and cloudy conditions; and tested if any of the animal posture and position increase their exposure to human detection. We performed 350 h of visual observation on eight maned sloths, equipped with radio-backpacks, in northern Bahia, Brazil, recording their activities, and their resting postures and positions on tree crowns. We also recorded the time taken to visualize the sloths on 58 days to analyse if sloths' detection is affected by posture and position. Higher ambient temperature, within a range of 21–33°C, increased the sloths' activity levels in cloudy conditions but reduced their activity in sunny conditions. Increasing ambient temperature also reduced the frequency of huddled posture and increased the frequency of extended posture and permanence in the inner tree crown. Lastly, the postures and positions did not influence sloths' detectability. Thus, the direction of the temperature–activity relationship depends on climatic conditions (sunny/cloudy), and individuals rely on resting postures and positions to thermoregulate. The warmer and drier future climate, expected to occur in the northern Atlantic Forest, may impose change in the diurnal activity levels and postural pattern for this threatened species, leading maned sloths to reduce its activity on sunny and warmer days and adopting an extended posture.