Historical ecology and the conservation of large, hermaphroditic fishes in Pacific Coast kelp forest ecosystems

MTaxi: A comparative tool for taxon identification of ultra low coverage ancient genomes

A major challenge in zooarchaeology is to morphologically distinguish closely related species' remains, especially using small bone fragments. Shotgun sequencing aDNA from archeological remains and comparative alignment to the candidate species' reference genomes will only apply when reference nuclear genomes of comparable quality are available, and may still fail when coverages are low. Here, we propose an alternative method, MTaxi, that uses highly accessible mitochondrial DNA (mtDNA) to distinguish between pairs of closely related species from ancient DNA sequences. MTaxi utilises mtDNA transversion-type substitutions between pairs of candidate species, assigns reads to either species, and performs a binomial test to determine the sample taxon. We tested MTaxi on sheep/goat and horse/donkey data, between which zooarchaeological classification can be challenging in ways that epitomise our case. The method performed efficiently on simulated ancient genomes down to 0.3x mitochondrial coverage for both sheep/goat and horse/donkey, with no false positives. Trials on n=18 ancient sheep/goat samples and n=10 horse/donkey samples of known species identity also yielded 100% accuracy. Overall, MTaxi provides a straightforward approach to classify closely related species that are difficult to distinguish through zooarchaeological methods using low coverage aDNA data, especially when similar quality reference genomes are unavailable. MTaxi is freely available at https://github.com/goztag/MTaxi.

El Niño frequency threshold controls coastal biotic communities

El Niño has profound influences on ecosystem dynamics. However, we know little about how it shapes vertebrate faunal community composition over centennial time scales, and this limits our ability to forecast change under projections of future El Niño events. On the basis of correlations between geological records of past El Niño frequency and the species composition of bird and fish remains from a Baja California bone deposit that spans the past 12,000 years, we documented marked faunal restructuring when major El Niño events occurred more than five times per century. This tipping point has implications for the past and future ecology of eastern Pacific coastal environments.

The potential of historical ecology to aid understanding of human-ocean interactions throughout the Anthropocene

Marine historical ecology emerged in the scholarly literature with the aim of understanding long-term dynamics in marine ecosystems and the outcomes of past human-ocean interactions. The use of historical sources, which differ in temporal scale and resolution to most scientific monitoring data, present both opportunities and challenges for informing our understanding of past marine ecosystems and the ways in which human communities made use of them. With an emphasis upon marine social-ecological changes over the past 200 years, I present an overview of the relevant historical ecology literature and summarise how this approach generates a richer understanding of human-ocean interactions and the legacies associated with human-induced ecosystem change. Marine historical ecology methodologies continue to be developed, whereas expanded inter- and multidisciplinary collaborations provide exciting avenues for future discoveries. Beyond scholarship, historical ecology presents opportunities to foster a more sustainable relationship with oceans going forward: by challenging ingrained perceptions of what is "normal" within marine ecosystems, reconnecting human communities to the oceans and providing cautionary lessons and exemplars of sustainable human-ocean interactions from the past. To leverage these opportunities, scholars must work alongside practitioners, managers and policy makers to foster mutual understanding, explore new opportunities to communicate historical findings and address the challenges of integrating historical data into modern-day frameworks.

In Support of Sustainability: The Historical Ecology of Vertebrate Biodiversity and Native American Harvest Practices in the Florida Keys, USA

The Florida Keys are currently experiencing unprecedented loss of lifeways, biodiversity, and cultural heritage due to sea-level rise, catastrophic storm events, unsustainable traditions of resource exploitation, and land development. Yet, these islands have a long history of human occupation and socioecological systems underlying their current sustainability crisis that date back at least 2500 years. Here we report early results of ongoing zooarchaeological research from Upper Matecumbe Key designed to explore anthropogenic engagement with vertebrate fauna between AD 800 and 1250, providing an approximately 500-year window on marine fisheries and terrestrial faunal harvesting for this small island archipelago. Focusing on one of the few remaining, nearly intact Native American archaeological sites in the region, our research contributes to critically needed long-term anthropogenic perspectives on harvest patterns relevant to regional biodiversity conservation and sustainability initiatives.

A palaeothermometer of ancient Indigenous fisheries reveals increases in mean temperature of the catch over five millennia

Climate change is altering the distribution and composition of marine fish populations globally, which presents substantial risks to the social and economic well-being of humanity. While deriving long-term climatic baselines is an essential step for detecting and attributing the magnitude of climate change and its impacts, these baselines tend to be limited to historical datasets and palaeoecological sediment records. Here, we develop a method for estimating the 'ancient Mean Temperature of the Catch' (aMTC) using Indigenous fisheries catch records from two archaeological sites in the northeast Pacific. Despite different catch compositions, we observe an increase in aMTC over a 5,000-year period at two contemporaneously occupied archaeological sites in southwestern British Columbia, Canada. We document cooler catches from 5,000 to 3,000 cal yr BP and comparatively warmer catches from 1,800 to 250 cal yr BP. These warmer temperatures are broadly consistent with palaeoceanographic sea surface temperature proxies from British Columbia and Alaska. Because this method requires converting measures of fish bones into estimates of fish size structure, abundance, biomass, and finally aMTC, opportunities exist to account for both variation and uncertainty at every step. Nevertheless, given that preindustrial fisheries data are ubiquitous in coastal archaeological sites, this method has the potential to be applied globally to broaden the temporal and geographic scale of ocean temperature baselines.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10641-022-01243-7.

Archaeological and Contemporary Evidence Indicates Low Sea Otter Prevalence on the Pacific Northwest Coast During the Late Holocene

The historic extirpation and subsequent recovery of sea otters (Enhydra lutris) have profoundly changed coastal social-ecological systems across the northeastern Pacific. Today, the conservation status of sea otters is informed by estimates of population carrying capacity or growth rates independent of human impacts. However, archaeological and ethnographic evidence suggests that for millennia, complex hunting and management protocols by Indigenous communities limited sea otter abundance near human settlements to reduce the negative impacts of this keystone predator on shared shellfish prey. To assess relative sea otter prevalence in the Holocene, we compared the size structure of ancient California mussels (Mytilus californianus) from six archaeological sites in two regions on the Pacific Northwest Coast, to modern California mussels at locations with and without sea otters. We also quantified modern mussel size distributions from eight locations on the Central Coast of British Columbia, Canada, varying in sea otter occupation time. Comparisons of mussel size spectra revealed that ancient mussel size distributions are consistently more similar to modern size distributions at locations with a prolonged absence of sea otters. This indicates that late Holocene sea otters were maintained well below carrying capacity near human settlements as a result of human intervention. These findings illuminate the conditions under which sea otters and humans persisted over millennia prior to the Pacific maritime fur trade and raise important questions about contemporary conservation objectives for an iconic marine mammal and the social-ecological system in which it is embedded.

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.

Improving metabarcoding taxonomic assignment: A case study of fishes in a large marine ecosystem

DNA metabarcoding is an important tool for molecular ecology. However, its effectiveness hinges on the quality of reference sequence databases and classification parameters employed. Here we evaluate the performance of MiFish 12S taxonomic assignments using a case study of California Current Large Marine Ecosystem fishes to determine best practices for metabarcoding. Specifically, we use a taxonomy cross-validation by identity framework to compare classification performance between a global database comprised of all available sequences and a curated database that only includes sequences of fishes from the California Current Large Marine Ecosystem. We demonstrate that the regional database provides higher assignment accuracy than the comprehensive global database. We also document a tradeoff between accuracy and misclassification across a range of taxonomic cutoff scores, highlighting the importance of parameter selection for taxonomic classification. Furthermore, we compared assignment accuracy with and without the inclusion of additionally generated reference sequences. To this end, we sequenced tissue from 597 species using the MiFish 12S primers, adding 252 species to GenBank's existing 550 California Current Large Marine Ecosystem fish sequences. We then compared species and reads identified from seawater environmental DNA samples using global databases with and without our generated references, and the regional database. The addition of new references allowed for the identification of 16 additional native taxa representing 17.0% of total reads from eDNA samples, including species with vast ecological and economic value. Together these results demonstrate the importance of comprehensive and curated reference databases for effective metabarcoding and the need for locus-specific validation efforts.

Island Colonization and Environmental Sustainability in the Postglacial Mediterranean

Island environments present challenges to human colonization, but we have a poor understanding of how environmental difference drives heterogeneous patterns of insular settlement. In this paper, we assess which environmental and geographic variables positively or negatively affect the long-term sustainability of human settlement on islands. Using the postglacial Mediterranean basin as a case study, we assess the impact of area, isolation index, species richness, and net primary productivity (NPP) on patterns of island occupation for both hunter-gatherer and agropastoral populations. We find that models involving area most effectively accounts for sustainability in hunter-gatherer island settlement. The agropastoral data are noisier, perhaps due to culturally specific factors responsible for the distribution of the data; nonetheless, we show that area and NPP exert profound influence over sustainability of agropastoral island settlement. We conclude by suggesting that this relates to the capacity of these variables to impact demographic robusticity directly.

Integrating fish scale and bone isotopic compositions for 'deep time' retrospective studies

Isotopic studies of archived fish scales have tremendous potential to develop long-term retrospectives that provide important insights into how humans have altered aquatic ecosystems. However, fish specimens in museum archives and other repositories typically date to time periods when the impacts of industrial societies may have already caused profound environmental changes. Archaeological fish bones offer an opportunity to bridge this key temporal gap by providing samples spanning from the recent past to as far back as the Pleistocene. Collagen is the primary protein component of both fish scale and bone, but the comparability of isotopic compositions from these tissues has not been established experimentally. To lay the framework for integrating isotopic datasets from these tissues, we compare δ¹³C and δ¹⁵N of bone and scale collagen, as well as other tissues, from fish with life-time controlled diets. Results show that while there is no difference in δ¹³C between scale and bone collagen, there may be a very slight but meaningful inter-tissue offset in δ¹⁵N (<0.3‰). We discuss potential sources of δ¹⁵N variation in scale and bone collagen measurements. Because there is no difference in scale and bone δ¹³C, and the observed offset in δ¹⁵N is very small (less than analytical uncertainty in many studies), our findings demonstrate that collagen isotopic compositions from these tissues should be directly comparable when integrating datasets from modern and ancient samples to build more powerful, millennium-scale isotopic times series. In linking isotopic compositions of collagen from modern, historical (scales), and archaeological (bones) fish, our findings open the way for more nuanced contextualization of how ecosystems functioned prior to large-scale exploitation and how they have responded to mounting anthropogenic pressures in the intervening centuries.

Predicting habitat use by the Argentine hake Merluccius hubbsi in a warmer world: inferences from the Middle Holocene

Fish skeletal remains recovered from two archaeological sites dated in the Middle Holocene of Tierra del Fuego (Argentina) were analysed to describe habitat use patterns by hake in the past and predict changes in a warmer world. Mitochondrial DNA was successfully extracted and amplified from 42 out of 45 first vertebra from ancient hake and phylogenetic analysis assigned all haplotypes to Argentine hake (Merluccius hubbsi). According to osteometry, the Argentine hake recovered from the archaeological site were likely adults ranging 37.2-58.1 cm in standard length. C and N stable isotope analysis showed that currently Argentine hake use foraging grounds deeper than those of Patagonian blenny and pink cusk-eel. Argentine hake, however, had a much broader isotopic niche during the Middle Holocene, when a large part of the population foraged much shallower than contemporary pink cusk-eel. The overall evidence suggests the presence of large numbers of Argentine hake onshore Tierra del Fuego during the Middle Holocene, which allowed exploitation by hunter-gatherer-fisher groups devoid of fishing technology. Interestingly, average SST off Tierra del Fuego during the Middle Holocene was higher than currently (11 °C vs 7 °C) and matched SST in the current southernmost onshore spawning aggregations, at latitude 47 °S. This indicates that increasing SST resulting from global warming will likely result into an increased abundance of adult Argentine hake onshore Tierra del Fuego, as during the Middle Holocene. Furthermore, stable isotope ratios from mollusc shells confirmed a much higher marine primary productivity during the Middle Holocene off Tierra del Fuego.

Back to the future? Late Holocene marine food web structure in a warm climatic phase as a predictor of trophodynamics in a warmer South-Western Atlantic Ocean

Stable carbon and nitrogen isotope ratios in the skeletal elements of both ancient and modern marine species from the Beagle Channel were used to compare the structure of Late Holocene and modern food webs, and predict potential changes as a result of a Sea Surface Temperature (SST) increase in the region. Complementary, ancient and modern shells of limpets and mussels were isotopically analysed to explore changes in the isotopic baseline and compare marine food webs through time after an appropriate correction for baseline shifts. Results confirmed a declining pattern of marine primary productivity during the Late Holocene in the Beagle Channel. In general, the isotopic niches overlapped largely in the ancient food web in comparison to the current marine one, with the exception of that of cormorants (Phalacrocorax sp.). Our data suggest that all the species that have undergone intense human exploitation (Arctocephalus australis, Otaria flavescens and Merluccius sp.) significantly increased their trophic levels. The most important finding of this work was the very high isotopic overlap between snoek (Thyrsites atun) and hake (Merluccius sp.) during the Late Holocene. Increasing SST as a result of global warming could favour the recolonization of the southern South-Western Atlantic Ocean by snoek from the South-Eastern Pacific Ocean, with a potential impact on the landings of the economically important Argentine and Austral hake. These findings highlight the relevance of using zooarchaeological remains for providing predictions about marine food webs changes in the near future.

Effects of skeletal element identity, delipidation and demineralization on the analysis of stable isotope ratios of C and N in fish bone

Stable isotope ratios of C and N in the bone tissue of three different skeletal elements (angular, cleithrum and vertebra) of three fish species from different evolutionary lineages (Clupeiformes, Atheriniformes and Notothenioidei) were determined before (δ¹³ C_bulk and δ¹⁵ N_bulk ) and after demineralization and delipidation (δ¹³ C_dml and δ¹⁵ N_dml ). One of the species had cellular bone and the other two had acellular bone. Results revealed that δ¹⁵ N and δ¹³ C values from different skeletal elements were interchangeable in species with acellular bone, but caution was needed in species with cellular bone, as δ¹⁵ N values varied among skeletal elements. Furthermore, δ¹⁵ N_bulk values were significantly lower than δ¹⁵ N_dml values in the three species, thus suggesting that they are not comparable. This difference is probably because δ¹⁵ N_bulk refers to total bone protein and δ¹⁵ N_dml to collagen only.

Long-term ecological changes in marine mammals driven by recent warming in northwestern Alaska

Carbon and nitrogen isotopes analyses were performed on marine mammal bone collagen from three archaeological sites (ad 1170-1813) on Cape Espenberg (Kotzebue Sound, northwestern Alaska) as well as modern animals harvested from the same area to examine long-term trends in foraging ecology and sea ice productivity. We observed significant and dramatic changes in ringed seal stable isotope values between the early 19th and early 21st centuries, likely due to changing sea ice productivity and reduced delivery of organic matter to the benthos driven by recent warming in the Arctic. These data highlight the importance of the archaeological record for providing a long-term perspective on environmental variation and interpreting recent changes driven by anthropogenic processes.

The Biophysical Effects of Neolithic Island Colonization: General Dynamics and Sociocultural Implications

Does anthropogenic environmental change constrain long-term sociopolitical outcomes? It is clear that human colonization of islands radically alters their biological and physical systems. Despite considerable contextual variability in local specificities of this alteration, I argue that these processes are to some extent regular, predictable, and have socio-political implications. Reviewing the data for post-colonization ecodynamics, I show that Neolithic colonization of previously insulated habitats drives biotic homogenization. I argue that we should expect such homogenization to promote regular types of change in biophysical systems, types of change that can be described in sum as environmentally convergent. Such convergence should have significant implications for human social organization over the long term, and general dynamics of this sort are relevant in the context of understanding remarkably similar social evolutionary trajectories towards wealth-inequality not only islands, but also more generally.