Palaeogenomic analysis of black rat (Rattus rattus) reveals multiple European introductions associated with human economic history.

The distribution of the black rat (Rattus rattus) has been heavily influenced by its association with humans. The dispersal history of this non-native commensal rodent across Europe, however, remains poorly understood, and different introductions may have occurred during the Roman and medieval periods. Here, in order to reconstruct the population history of European black rats, we first generate a de novo genome assembly of the black rat. We then sequence 67 ancient and three modern black rat mitogenomes, and 36 ancient and three modern nuclear genomes from archaeological sites spanning the 1st-17th centuries CE in Europe and North Africa. Analyses of our newly reported sequences, together with published mitochondrial DNA sequences, confirm that black rats were introduced into the Mediterranean and Europe from Southwest Asia. Genomic analyses of the ancient rats reveal a population turnover in temperate Europe between the 6th and 10th centuries CE, coincident with an archaeologically attested decline in the black rat population. The near disappearance and re-emergence of black rats in Europe may have been the result of the breakdown of the Roman Empire, the First Plague Pandemic, and/or post-Roman climatic cooling.

67,000 years of coastal engagement at Panga ya Saidi, eastern Africa.

The antiquity and nature of coastal resource procurement is central to understanding human evolution and adaptations to complex environments. It has become increasingly apparent in global archaeological studies that the timing, characteristics, and trajectories of coastal resource use are highly variable. Within Africa, discussions of these issues have largely been based on the archaeological record from the south and northeast of the continent, with little evidence from eastern coastal areas leaving significant spatial and temporal gaps in our knowledge. Here, we present data from Panga ya Saidi, a limestone cave complex located 15 km from the modern Kenyan coast, which represents the first long-term sequence of coastal engagement from eastern Africa. Rather than attempting to distinguish between coastal resource use and coastal adaptations, we focus on coastal engagement as a means of characterising human relationships with marine environments and resources from this inland location. We use aquatic mollusc data spanning the past 67,000 years to document shifts in the acquisition, transportation, and discard of these materials, to better understand long-term trends in coastal engagement. Our results show pulses of coastal engagement beginning with low-intensity symbolism, and culminating in the consistent low-level transport of marine and freshwater food resources, emphasising a diverse relationship through time. Panga ya Saidi has the oldest stratified evidence of marine engagement in eastern Africa, and is the only site in Africa which documents coastal resources from the Late Pleistocene through the Holocene, highlighting the potential archaeological importance of peri-coastal sites to debates about marine resource relationships.

Identifying species threatened with local extinction in tropical reef fisheries using historical reconstruction of species occurrence.

Identifying the species that are at risk of local extinction in highly diverse ecosystems is a big challenge for conservation science. Assessments of species status are costly and difficult to implement in developing countries with diverse ecosystems due to a lack of species-specific surveys, species-specific data, and other resources. Numerous techniques are devised to determine the threat status of species based on the availability of data and budgetary limits. On this basis, we developed a framework that compared occurrence data of historically exploited reef species in Kenya from existing disparate data sources. Occurrence data from archaeological remains (750-1500CE) was compared with occurrence data of these species catch assessments, and underwater surveys (1991-2014CE). This comparison indicated that only 67 species were exploited over a 750 year period, 750-1500CE, whereas 185 species were landed between 1995 and 2014CE. The first step of our framework identified 23 reef species as threatened with local extinction. The second step of the framework further evaluated the possibility of local extinction with Bayesian extinction analyses using occurrence data from naturalists' species list with the existing occurrence data sources. The Bayesian extinction analysis reduced the number of reef species threatened with local extinction from 23 to 15. We compared our findings with three methods used for assessing extinction risk. Commonly used extinction risk methods varied in their ability to identify reef species that we identified as threatened with local extinction by our comparative and Bayesian method. For example, 12 of the 15 threatened species that we identified using our framework were listed as either least concern, unevaluated, or data deficient in the International Union for the Conservation of Nature red list. Piscivores and macro-invertivores were the only functional groups found to be locally extinct. Comparing occurrence data from disparate sources revealed a large number of historically exploited reef species that are possibly locally extinct. Our framework addressed biases such as uncertainty in priors, sightings and survey effort, when estimating the probability of local extinction. Our inexpensive method showed the value and potential for disparate data to fill knowledge gaps that exist in species extinction assessments.

Reconstructing Asian faunal introductions to eastern Africa from multi-proxy biomolecular and archaeological datasets.

Human-mediated biological exchange has had global social and ecological impacts. In sub-Saharan Africa, several domestic and commensal animals were introduced from Asia in the pre-modern period; however, the timing and nature of these introductions remain contentious. One model supports introduction to the eastern African coast after the mid-first millennium CE, while another posits introduction dating back to 3000 BCE. These distinct scenarios have implications for understanding the emergence of long-distance maritime connectivity, and the ecological and economic impacts of introduced species. Resolution of this longstanding debate requires new efforts, given the lack of well-dated fauna from high-precision excavations, and ambiguous osteomorphological identifications. We analysed faunal remains from 22 eastern African sites spanning a wide geographic and chronological range, and applied biomolecular techniques to confirm identifications of two Asian taxa: domestic chicken (Gallus gallus) and black rat (Rattus rattus). Our approach included ancient DNA (aDNA) analysis aided by BLAST-based bioinformatics, Zooarchaeology by Mass Spectrometry (ZooMS) collagen fingerprinting, and direct AMS (accelerator mass spectrometry) radiocarbon dating. Our results support a late, mid-first millennium CE introduction of these species. We discuss the implications of our findings for models of biological exchange, and emphasize the applicability of our approach to tropical areas with poor bone preservation.