The ratting of North America: A 350-year retrospective on Rattus species compositions and competition.

While the impacts of black (Rattus rattus) and brown (Rattus norvegicus) rats on human society are well documented-including the spread of disease, broad-scale environmental destruction, and billions spent annually on animal control-little is known about their ecology and behavior in urban areas due to the challenges of studying animals in city environments. We use isotopic and ZooMS analysis of archaeological (1550s-1900 CE) rat remains from eastern North America to provide a large-scale framework for species arrival, interspecific competition, and dietary ecology. Brown rats arrived earlier than expected and rapidly outcompeted black rats in coastal urban areas. This replacement happened despite evidence that the two species occupy different trophic positions. Findings include the earliest molecularly confirmed brown rat in the Americas and show a deep ecological structure to how rats exploit human-structured areas, with implications for understanding urban zoonosis, rat management, and ecosystem planning as well as broader themes of rat dispersal, phylogeny, evolutionary ecology, and climate impacts.

Why aquatic scientists should use sulfur stable isotope ratios (ẟ34S) more often.

Over the last few decades, measurements of light stable isotope ratios have been increasingly used to answer questions across physiology, biology, ecology, and archaeology. The vast majority analyse carbon (δ13C) and nitrogen (δ15N) stable isotopes as the 'default' isotopes, omitting sulfur (δ34S) due to time, cost, or perceived lack of benefits and instrumentation capabilities. Using just carbon and nitrogen isotopic ratios can produce results that are inconclusive, uncertain, or in the worst cases, even misleading, especially for scientists that are new to the use and interpretation of stable isotope data. Using sulfur isotope values more regularly has the potential to mitigate these issues, especially given recent advancements that have lowered measurement barriers. Here we provide a review documenting case studies with real-world data, re-analysing different biological topics (i.e. niche, physiology, diet, movement and bioarchaeology) with and without sulfur isotopes to highlight the various strengths of this stable isotope for various applications. We also include a preliminary meta-analysis of the trophic discrimination factor (TDF) for sulfur isotopes, which suggest small (mean -0.4 ± 1.7 ‰ SD) but taxa-dependent mean trophic discrimination. Each case study demonstrates how the exclusion of sulfur comes at the detriment of the results, often leading to very different outputs, or missing valuable discoveries entirely. Given that studies relying on carbon and nitrogen stable isotopes currently underpin most of our understanding of various ecological processes, this has concerning implications. Collectively, these examples strongly suggest that researchers planning to use carbon and nitrogen stable isotopes for their research should incorporate sulfur where possible, and that the new 'default' isotope systems for aquatic science should now be carbon, nitrogen, and sulfur.

Impact of Holocene environmental change on the evolutionary ecology of an Arctic top predator.

The Arctic is among the most climatically sensitive environments on Earth, and the disappearance of multiyear sea ice in the Arctic Ocean is predicted within decades. As apex predators, polar bears are sentinel species for addressing the impact of environmental variability on Arctic marine ecosystems. By integrating genomics, isotopic analysis, morphometrics, and ecological modeling, we investigate how Holocene environmental changes affected polar bears around Greenland. We uncover reductions in effective population size coinciding with increases in annual mean sea surface temperature, reduction in sea ice cover, declines in suitable habitat, and shifts in suitable habitat northward. Furthermore, we show that west and east Greenlandic polar bears are morphologically, and ecologically distinct, putatively driven by regional biotic and genetic differences. Together, we provide insights into the vulnerability of polar bears to environmental change and how the Arctic marine ecosystem plays a vital role in shaping the evolutionary and ecological trajectories of its inhabitants.

Holocene deglaciation drove rapid genetic diversification of Atlantic walrus.

Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations was initially shaped by the last glacial maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.

Ancient Mongolian aurochs genomes reveal sustained introgression and management in East Asia.

Societies in East Asia have utilized domesticated cattle for over 5000 years, but the genetic history of cattle in East Asia remains understudied. Genome-wide analyses of 23 ancient Mongolian cattle reveal that East Asian aurochs and ancient East Asian taurine cattle are closely related, but neither are closely related to any modern East Asian breeds. We observe binary variation in aurochs diet throughout the early Neolithic, and genomic evidence shows millennia of sustained male-dominated introgression. We identify a unique connection between ancient Mongolian aurochs and the European Hereford breed. These results point to the likelihood of human management of aurochs in Northeast Asia prior to and during the initial adoption of taurine cattle pastoralism.

Combining δ13C and δ15N from bone and dentine in marine mammal palaeoecological research: insights from toothed whales.

Stable carbon (δ13C) and nitrogen (δ15N) isotopic compositions of bone and dentine collagen extracted from museum specimens have been widely used to study the paleoecology of past populations. Due to possible systematic differences in stable isotope values between bone and dentine, dentine values need to be transformed into bone-collagen equivalent using a correction factor to allow comparisons between the two collagen sources. Here, we provide correction factors to transform dentine δ13C and δ15N values into bone-collagen equivalent for two toothed whales: narwhal and beluga. We sampled bone and dentine from the skulls of 11 narwhals and 26 belugas. In narwhals, dentine was sampled from tusk and embedded tooth; in belugas, dentine was sampled from tooth. δ13C and δ15N were measured, and intra-individual bone and dentine isotopic compositions were used to calculate correction factors for each species. We detected differences in δ13C and δ15N. In both narwhals and belugas, we found lower average δ13C and δ15N in bone compared with dentine. The correction factors provided by the study enable the combined analysis of stable isotope data from bone and dentine in these species.

Skull ecomorphological variation of narwhals (Monodon monoceros, Linnaeus 1758) and belugas (Delphinapterus leucas, Pallas 1776) reveals phenotype of their hybrids.

Narwhals and belugas are toothed whales belonging to the Monodontidae. Belugas have a circumpolar Arctic and sub-Artic distribution while narwhals are restricted to the Atlantic Arctic. Their geographical ranges overlap during winter migrations in the Baffin Bay area (Canada/West Greenland) and successful interbreeding may occur. Here, we employed geometric morphometrics on museum specimens to explore the cranium and mandible morphology of a known hybrid (NHMD MCE 1356) and the cranium morphology of a putative hybrid (NHMD 1963.44.1.4) relative to skull morphological variation in the parental species. Specifically, we used 3D models of skulls from 69 belugas, 86 narwhals, and the two known/putative hybrids and 2D left hemi-mandibles from 20 belugas, 64 narwhals and the known hybrid. Skull shape analyses allowed clear discrimination between species. Narwhals are characterised by a relatively short rostrum and wide neurocranium while belugas show a more elongated and narrower cranium. Sexual size dimorphism was detected in narwhals, with males larger than females, but no sexual shape dimorphism was detected in either species (excluding presence/absence of tusks in narwhals). Morphological skull variation was also dependent on different allometric slopes between species and sexes in narwhals. Our analyses showed that the cranium of the known hybrid was phenotypically close to belugas but its 2D hemi-mandible had a narwhal shape and size morphology. Both cranium and mandible were strongly correlated, with the pattern of covariation being similar to belugas. The putative hybrid was a pure male narwhal with extruded teeth. Comparison of genomic DNA supported this result, and stable carbon and nitrogen isotope values suggested that the putative hybrid had a more benthic foraging strategy compared to narwhals. This work demonstrates that although the known hybrid could be discriminated from narwhals and belugas, detection of its affinities with these parental species was dependent on the part of the skull analysed.

The evolution of dog diet and foraging: Insights from archaeological canids in Siberia.

Research on the evolution of dog foraging and diet has largely focused on scavenging during their initial domestication and genetic adaptations to starch-rich food environments following the advent of agriculture. The Siberian archaeological record evidences other critical shifts in dog foraging and diet that likely characterize Holocene dogs globally. By the Middle Holocene, body size reconstruction for Siberia dogs indicates that most were far smaller than Pleistocene wolves. This contributed to dogs' tendencies to scavenge, feed on small prey, and reduce social foraging. Stable carbon and nitrogen isotope analysis of Siberian dogs reveals that their diets were more diverse than those of Pleistocene wolves. This included habitual consumption of marine and freshwater foods by the Middle Holocene and reliance on C4 foods by the Late Holocene. Feeding on such foods and anthropogenic waste increased dogs' exposure to microbes, affected their gut microbiomes, and shaped long-term dog population history.

Acidification does not alter the stable isotope composition of bone collagen.

In this study, we compared the elemental and isotopic composition of modern and ancient bone samples pre-treated using different demineralization agents with acidic and neutral pH. The purpose of our research was to examine if demineralization using a mineral acid such as hydrochloric acid (HCl) significantly alters the δ 15N and δ 13C values of bone collagen. Evidence from the elemental and amino acid composition of the samples were incorporated alongside isotopic compositions to provide a holistic view of the effect of demineralization agents on the composition of bone collagen. The stable isotope compositions of collagen extracts were also compared against equivalent whole bone samples to assess whether whole bone has a stable isotope composition that is comparable to collagen demineralized with a neutral agent. Our results demonstrate that bone demineralization using either ethylenediaminetetraacetic acid (EDTA) or HCl yields collagen extracts with stable isotope compositions that are not significantly different, indicating that mineral acid does not alter δ 15N and δ 13C values of bone collagen. The results comparing whole bone and extracted collagen stable isotope compositions indicate that whole bone cannot be used as an effective replacement for bone collagen due to the significantly different stable isotope compositions between these sample materials. In ecological and archaeological studies performing stable isotope analysis on bone, sample pre-treatment to isolate collagen is a necessity to obtain the most reliable and reproducible isotopic measurements.

Early evidence for historical overfishing in the Gulf of Mexico.

Fisheries encompass complex interplays between social, economic, and environmental factors, but limitations on historical fisheries data can hamper efforts to identify and contextualize the long-term spatiotemporal patterns that shape them. We integrate 2500 years of stable isotope (δ34S, δ13C, and δ15N) and zooarchaeological evidence from Gulf of Mexico fisheries to assess cultural, demographic, and technological changes affecting sheepshead (Archosargus probatocephalus) populations and fishing practices in Louisiana, USA. Concurrent with human population growth, average sizes of sheepshead caught decreased from the 1720s to 1830s. The size of fish caught after the 1830s increased to pre-1720 levels at the same time that isotopic compositions of fish bone collagen show that fish were being caught from a more diverse range of ecosystems, including distant seagrass beds. Our findings provide the first evidence for large-scale depressions of historical sheepshead populations and the processes driving them, including rapid human population growth and sustained harvesting pressure.

Zinc isotopes from archaeological bones provide reliable tropic level information for marine mammals.

In marine ecology, dietary interpretations of faunal assemblages often rely on nitrogen isotopes as the main or only applicable trophic level tracer. We investigate the geographic variability and trophic level isotopic discrimination factors of bone zinc 66Zn/64Zn ratios (δ66Zn value) and compared it to collagen nitrogen and carbon stable isotope (δ15N and δ13C) values. Focusing on ringed seals (Pusa hispida) and polar bears (Ursus maritimus) from multiple Arctic archaeological sites, we investigate trophic interactions between predator and prey over a broad geographic area. All proxies show variability among sites, influenced by the regional food web baselines. However, δ66Zn shows a significantly higher homogeneity among different sites. We observe a clear trophic spacing for δ15N and δ66Zn values in all locations, yet δ66Zn analysis allows a more direct dietary comparability between spatially and temporally distinct locations than what is possible by δ15N and δ13C analysis alone. When combining all three proxies, a more detailed and refined dietary analysis is possible.

Population-specific sex and size variation in long-term foraging ecology of belugas and narwhals.

Intraspecific variation in resource use by individuals of different age, sex or size may reflect differing energetic requirements and physiological constraints. Males and females often show differences in diet owing to sexual size dimorphism, different life histories and/or habitat use. Here, we investigate how sex and size influence the long-term foraging ecology of belugas and narwhals in Greenland, using stable isotopes of carbon and nitrogen from bone collagen. We show that males have a higher trophic level and a larger ecological niche than females in West Greenland belugas and in East Greenland narwhals. In addition, for these two populations, we find that δ 15N increases with size, particularly in males. We hypothesize that sexual size dimorphism together with strong maternal investment drive these differences. By contrast, we find no differences in foraging ecology between sexes in West Greenland narwhals and observe no influence of size on trophic level. This may reflect the influence of interspecific competition in West Greenland, where the distributions of belugas and narwhals overlap, and/or geographical resource partitioning among different summer aggregations of narwhals. Our results suggest that sex and size variations in diet are population dependent, and probably the result of varying ecological interactions.

Migration and maize in the Virú Valley: Understanding life histories through multi-tissue carbon, nitrogen, sulfur, and strontium isotope analyses.

OBJECTIVES: Stable isotope analysis can provide crucial insight into the function and development of early state-level societies on the north coast of Peru. MATERIALS AND METHODS: Multi-tissue (bone collagen, tooth enamel, hair, nail, skin, and tendon) stable isotope analyses (carbon, nitrogen, sulfur, and strontium) were conducted for 13 individuals from the lower Virú Valley. RESULTS: Non-seasonal changes in a predominantly C4 -based terrestrial diet, with minimal inputs of marine foods were identified. One individual (Burial 5), however, had a stable isotope signature unlike any previously found on the north coast of Peru, indicating both a large contribution of C3 -terrestrial resources to their diet and an 87 Sr/86 Sr value suggestive of highland residence during childhood. DISCUSSION: This research provides the first strong stable isotope evidence of a highland individual within a coastal burial in northern Peru, new insight into the ritual killing event at Huaca Santa Clara during the late middle horizon and supporting evidence of the importance of C4 terrestrial resources to the developing Virú polity during the early intermediate period.

Predicting sample success for large-scale ancient DNA studies on marine mammals.

In recent years, nonhuman ancient DNA studies have begun to focus on larger sample sizes and whole genomes, offering the potential to reveal exciting and hitherto unknown answers to ongoing biological and archaeological questions. However, one major limitation to such studies is the substantial financial and time investments still required during sample screening, due to uncertainty regarding successful sample selection. This study investigates the effect of a wide range of sample properties including latitude, sample age, skeletal element, collagen preservation, and context on endogenous content and DNA damage profiles for 317 ancient and historic pinniped samples collected from across the North Atlantic and surrounding regions. Using generalised linear and mixed-effect models, we found that a range of factors affected DNA preservation within each of the species under consideration. The most important findings were that endogenous content varied significantly within species according to context, the type of skeletal element, the collagen content and collection year. There also appears to be an effect of the sample's geographic origin, with samples from the Arctic generally showing higher endogenous content and lower damage rates. Both latitude and sample age were found to have significant relationships with damage levels, but only for walrus samples. Sex, ontogenetic age and extraction material preparation were not found to have any significant relationship with DNA preservation. Overall, skeletal element and sample context were found to be the most influential factors and should therefore be considered when selecting samples for large-scale ancient genome studies.

Storing fish?: a dog's isotopic biography provides insight into Iron Age food preservation strategies in the Russian Arctic.

Analysis of individual animal bodies can provide numerous useful insights in archeology, including how humans provisioned such animals, which in turn informs on a variety of other past behaviors such as human dietary patterns. In this study, we conducted stable carbon (δ 13C) and nitrogen (δ 15N) isotope analysis of collagen and keratin from four types of tissues from a dog burial at the Ust'-Polui site in the Iamal region of Arctic Russia. Ust'-Polui is an Iron Age site located on the Lower Ob River, a major northern fishery characterized by extreme seasonal shifts in fish presence. During a 6-month period stretching over the coldest months of the year, fish are nearly entirely absent in the Lower Ob River. Despite this, the stable isotope compositions of the dog's bone and dentine collagen and hair and nail keratin all indicate a monotonous diet focusing on local fish. This pattern indicates the dog was provisioned year-round with fish. This was likely accomplished by mass harvesting of fish using nets or traps. Such fish were then processed and frozen for consumption during the non-fishing season. These findings suggest that people in the Ust'-Polui region also relied to some extent on fish throughout the year. Stored fish likely provided a dietary buffer for uneven returns from reindeer and bird hunting, both of which also are well-evidenced at the site.

Seaweed-eating sheep show that δ34 S evidence for marine diets can be fully masked by sea spray effects.

RATIONALE: Stable sulfur isotope compositions (δ34 S values) are a useful marker of terrestrial (lower δ34 S) versus marine (higher δ34 S) diets. In coastal areas, 34 S-enriched sea spray can obscure these marine/terrestrial differences. We sought to establish whether δ34 S values of sea spray-affected terrestrial fauna can be distinguished from those of marine-feeding terrestrial fauna. METHODS: We measured bone and dentine collagen δ34 S values, as well as stable carbon (δ13 C) and nitrogen (δ15 N) isotope compositions via continuous flow elemental analysis/isotope ratio mass spectrometry of 21 sheep (Ovis aries) raised on an island (North Ronaldsay, UK) of <7 km2 that had widely divergent access to marine (seaweed) and heavily sea spray-affected terrestrial (grass) food sources. We also analyzed the bone collagen of marine and terrestrial fauna from this island. RESULTS: Sheep bone collagen showed well-defined trends with highly significant correlations between δ13 C and δ15 N values indicative of feeding along a continuum of fully terrestrial to fully marine diets, consistent with other modern baseline data from marine and terrestrial animals in the same area. In contrast, δ34 S values were generally elevated for all sheep and were not significantly correlated with either δ13 C or δ15 N values. CONCLUSIONS: Our findings demonstrate that δ34 S values are poorly suited for differentiating marine and terrestrial diets in terrestrial animals in areas with pronounced sea spray effects. Care must be taken to characterize the isotopic compositions of potential food items before δ34 S values are used as a marker for reliance on marine protein in modern and ancient contexts.

Differentiating salmonid migratory ecotypes through stable isotope analysis of collagen: Archaeological and ecological applications.

The ability to distinguish between different migratory behaviours (e.g., anadromy and potamodromy) in fish can provide important insights into the ecology, evolution, and conservation of many aquatic species. We present a simple stable carbon isotope (δ13C) approach for distinguishing between sockeye (anadromous ocean migrants) and kokanee (potamodromous freshwater residents), two migratory ecotypes of Oncorhynchus nerka (Salmonidae) that is applicable throughout most of their range across coastal regions of the North Pacific Ocean. Analyses of kokanee (n = 239) and sockeye (n = 417) from 87 sites spanning the North Pacific (Russia to California) show that anadromous and potamodromous ecotypes are broadly distinguishable on the basis of the δ13C values of their scale and bone collagen. We present three case studies demonstrating how this approach can address questions in archaeology, archival, and conservation research. Relative to conventional methods for determining migratory status, which typically apply chemical analyses to otoliths or involve genetic analyses of tissues, the δ13C approach outlined here has the benefit of being non-lethal (when applied to scales), cost-effective, widely available commercially, and should be much more broadly accessible for addressing archaeological questions since the recovery of otoliths at archaeological sites is rare.

Camelid husbandry in the Atacama Desert? A stable isotope study of camelid bone collagen and textiles from the Lluta and Camarones Valleys, northern Chile.

Management of camelids in the coastal valleys of the Andes has generated much debate in recent years. Zooarchaeological and isotopic studies have demonstrated that in the coastal valleys of northern and southern Peru there were locally maintained camelid herds. Because of the hyperarid conditions of the northern coast of Chile, this region has been assumed to be unsuitable for the raising of camelids. In this study we report stable carbon and nitrogen isotopic compositions of camelid bone collagen and textiles made from camelid fiber from Late Intermediate Period (LIP) and Late Horizon (LH) occupations in northern Chilean river valleys. The camelid bone collagen isotopic compositions are consistent with these animals originating in the highlands, although there is a significant difference in the camelids dating to the LIP and LH, possibly because of changes made to distribution and exchange networks by the Inca in the LH. There were no differences between the isotopic compositions of the camelid fibers sampled from textiles in the LIP and LH, suggesting that either the production of camelid fiber was unchanged by the Inca or the changes that were made do not present visible isotopic evidence. Several camelid fiber samples from both the LIP and LH present very high δ13C and δ15N values, comparable to human hair samples from one site (Huancarane) in the Camarones Valley. These data suggest that people in the northern valleys of Chile may have kept small numbers of animals specifically for fiber production. Overall, however, the vast majority of the textile samples have isotopic compositions that are consistent with an origin in the highlands. These data suggest that the hyperarid coastal river valleys of northern Chile did not support substantial camelid herds as has been interpreted for northern Peru.