Ancient mtDNA Analysis of Early 16th Century Caribbean Cattle Provides Insight into Founding Populations of New World Creole Cattle Breeds

The Columbian Exchange resulted in a widespread movement of humans, plants and animals between the Old and New Worlds. The late 15th to early 16th century transfer of cattle from the Iberian Peninsula and Canary Islands to the Caribbean laid the foundation for the development of American creole cattle (Bos taurus) breeds. Genetic analyses of modern cattle from the Americas reveal a mixed ancestry of European, African and Indian origins. Recent debate in the genetic literature centers on the ‘African’ haplogroup T1 and its subhaplogroups, alternatively tying their origins to the initial Spanish herds, and/or from subsequent movements of taurine cattle through the African slave trade. We examine this problem through ancient DNA analysis of early 16th century cattle bone from Sevilla la Nueva, the first Spanish colony in Jamaica. In spite of poor DNA preservation, both T3 and T1 haplogroups were identified in the cattle remains, confirming the presence of T1 in the earliest Spanish herds. The absence, however, of “African-derived American” haplotypes (AA/T1c1a1) in the Sevilla la Nueva sample, leaves open the origins of this sub-haplogroup in contemporary Caribbean cattle

Early Cessation of Ceramic Production for Ancestral Polynesian Society in Tonga

Ancestral Polynesian society is the formative base for development of the Polynesian cultural template and proto-Polynesian linguistic stage. Emerging in western Polynesia ca 2700 cal BP, it is correlated in the archaeological record of Tonga with the Polynesian Plainware ceramic phase presently thought to be of approximately 800 years duration or longer. Here we re-establish the upper boundary for this phase to no more than 2350 cal BP employing a suite of 44 new and existing radiocarbon dates from 13 Polynesian Plainware site occupations across the extent of Tonga. The implications of this boundary, the abruptness of ceramic loss, and the shortening of duration to 350 years have substantive implications for archaeological interpretations in the ancestral Polynesian homeland

Digital Bridges Across Disciplinary, Practical and Pedagogical Divides: An Online Professional Master’s Program in Heritage Resource Management

Growth and diversification in heritage resource management (HRM) archaeology since the 1960s have created new demands for training the next generations of HRM leaders and for addressing persistent and counterproductive divisions between academic and applied archaeologies. The Simon Fraser University Department of Archaeology (SFU) has responded to these demands with an all-new, cohort-based, thesis-focused graduate program created by and for HRM professionals. The program’s target audience is HRM practitioners who hold Bachelor’s credentials, have initiated promising careers in HRM, and desire advanced, research-focused degrees to enable their professional capacity and upward mobility. The SFU program is structured and focused to provide intensive, predominantly online training in the four essential dimensions of HRM: law and policy, ethics and practice, business management, and research design and methods. The program has been successful through initial cohort cycles and in attracting HRM industry interest in collaboration. Industry-academic partnerships in cognate disciplines have proved effective in comparable circumstances but remain underdeveloped as bases for planning and delivering state-of-the-art training in applied archaeology and the broader field of HRM. Critical next steps in program development entail the identification of attributes of HRM futures desired by all or most HRM stakeholders and the collaborative pursuit of those desired futures

"The End of Immortality!" Eternal Life and the Makropulos Debate

Responding to a well-known essay by Bernard Williams, philosophers (and a few theologians) have engaged in what I call “the Makropulos debate,” a debate over whether immortality—“living forever”—would be desirable for beings like us. Lacking a firm conceptual grounding in the religious contexts from which terms such as “immortality” and “eternal life” gain much of their sense, the debate has consisted chiefly in a battle of speculative fantasies. Having presented my four main reasons for this assessment, I examine an alternative and neglected conception, the idea of eternal life as a present possession, derived in large part from Johannine Christianity. Without claiming to argue for the truth of this conception, I present its investigation as exemplifying a conceptually fruitful direction of inquiry into immortality or eternal life, one which takes seriously the religious and ethical surroundings of these concepts

Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

Structural classifications of proteins assume the existence of the fold, which is an intrinsic equivalence class of protein domains. Here, we test in which conditions such an equivalence class is compatible with objective similarity measures. We base our analysis on the transitive property of the equivalence relationship, requiring that similarity of A with B and B with C implies that A and C are also similar. Divergent gene evolution leads us to expect that the transitive property should approximately hold. However, if protein domains are a combination of recurrent short polypeptide fragments, as proposed by several authors, then similarity of partial fragments may violate the transitive property, favouring the continuous view of the protein structure space. We propose a measure to quantify the violations of the transitive property when a clustering algorithm joins elements into clusters, and we find out that such violations present a well defined and detectable cross-over point, from an approximately transitive regime at high structure similarity to a regime with large transitivity violations and large differences in length at low similarity. We argue that protein structure space is discrete and hierarchic classification is justified up to this cross-over point, whereas at lower similarities the structure space is continuous and it should be represented as a network. We have tested the qualitative behaviour of this measure, varying all the choices involved in the automatic classification procedure, i.e., domain decomposition, alignment algorithm, similarity score, and clustering algorithm, and we have found out that this behaviour is quite robust. The final classification depends on the chosen algorithms. We used the values of the clustering coefficient and the transitivity violations to select the optimal choices among those that we tested. Interestingly, this criterion also favours the agreement between automatic and expert classifications. As a domain set, we have selected a consensus set of 2,890 domains decomposed very similarly in SCOP and CATH. As an alignment algorithm, we used a global version of MAMMOTH developed in our group, which is both rapid and accurate. As a similarity measure, we used the size-normalized contact overlap, and as a clustering algorithm, we used average linkage. The resulting automatic classification at the cross-over point was more consistent than expert ones with respect to the structure similarity measure, with 86% of the clusters corresponding to subsets of either SCOP or CATH superfamilies and fewer than 5% containing domains in distinct folds according to both SCOP and CATH. Almost 15% of SCOP superfamilies and 10% of CATH superfamilies were split, consistent with the notion of fold change in protein evolution. These results were qualitatively robust for all choices that we tested, although we did not try to use alignment algorithms developed by other groups. Folds defined in SCOP and CATH would be completely joined in the regime of large transitivity violations where clustering is more arbitrary. Consistently, the agreement between SCOP and CATH at fold level was lower than their agreement with the automatic classification obtained using as a clustering algorithm, respectively, average linkage (for SCOP) or single linkage (for CATH). The networks representing significant evolutionary and structural relationships between clusters beyond the cross-over point may allow us to perform evolutionary, structural, or functional analyses beyond the limits of classification schemes. These networks and the underlying clusters are available at http://ub.cbm.uam.es/research/ProtNet.ph

Variability of Female Responses to Conspecific vs. Heterospecific Male Mating Calls in Polygynous Deer: An Open Door to Hybridization?

Males of all polygynous deer species (Cervinae) give conspicuous calls during the reproductive season. The extreme interspecific diversity that characterizes these vocalizations suggests that they play a strong role in species discrimination. However, interbreeding between several species of Cervinae indicates permeable interspecific reproductive barriers. This study examines the contribution of vocal behavior to female species discrimination and mating preferences in two closely related polygynous deer species known to hybridize in the wild after introductions. Specifically, we investigate the reaction of estrous female red deer (Cervus elaphus) to playbacks of red deer vs. sika deer (Cervus nippon) male mating calls, with the prediction that females will prefer conspecific calls. While on average female red deer preferred male red deer roars, two out of twenty females spent more time in close proximity to the speaker broadcasting male sika deer moans. We suggest that this absence of strict vocal preference for species-specific mating calls may contribute to the permeability of pre-zygotic reproductive barriers observed between these species. Our results also highlight the importance of examining inter-individual variation when studying the role of female preferences in species discrimination and intraspecific mate selection

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods

Cross Correlation of IceCube Neutrinos with Tracers of Large Scale Structure

The origin of most astrophysical neutrinos is unknown, but extragalactic neutrino sources may follow the spatial distribution of the large-scale structure of the universe. Galaxies also follow the same large scale distribution, so establishing a correlation between galaxies and IceCube neutrinos could help identify the origins of the diffuse neutrinos observed by IceCube. Following a preliminary study based on the WISE and 2MASS catalogs, we will investigate an updated galaxy catalog with improved redshift measurements and reduced stellar contamination. Our IceCube data sample consists of track-like muon neutrinos selected from the Northern sky. The excellent angular resolution of track-like events and low contamination with atmospheric muons is necessary for the sensitivity of the analysis. Unlike a point source stacking analysis, the calculation of the cross correlation does not scale with the number of entries in the catalog, making the work tractable for catalogs with millions of objects. We present the development and performance of a two-point cross correlation of IceCube neutrinos with a tracer of the large scale structure