Danielle Buss

Introduction: Sperm whales (Physeter macrocephalus) are deep-diving apex predators whose offshore ecology limits direct observation. Stable isotope analysis is widely used to infer cetacean diet and habitat use, but its application to archaeological whale remains remains rare despite the regular occurrence of sperm whales in zooarchaeological assemblages. Here, we combine stable carbon (δ¹³C) and nitrogen (δ ¹⁵ N) isotope analysis with zooarchaeological and palaeontological data to investigate the long-term foraging ecology of sperm whales in the North Atlantic. Methods: Bone specimens identified as P. macrocephalus using morphological and palaeoproteomic methods, including Zooarchaeology by Mass Spectrometry (ZooMS), were sampled from Late Holocene contexts across northern and western Europe. Stable isotope values of bone collagen were measured using EA-IRMS. Three known-age specimens were used to calculate an empirically based, eastern North Atlantic sperm-whale-specific marine reservoir correction, which was applied when comparing the Late Holocene specimens with previously published radiocarbon-dated Late Glacial material. Published modern isotope data were corrected for the Suess effect before comparison. Results: The three known-age specimens produced a provisional ΔR₂₀ estimate of −192 ± 40 ¹⁴C years. Within the Late Holocene, δ¹³C values showed modest temporal variation, including more depleted values during some earlier periods and relatively enriched values from the Medieval Climate Anomaly onward, whereas δ¹⁵N values showed no directional temporal trend. Late Glacial specimens had significantly higher δ¹⁵N values than Late Holocene specimens, by approximately 2.3‰, while δ¹³C values did not differ significantly between the periods. After Suess correction, modern oceanic North Atlantic sperm whales were isotopically similar to Late Holocene North Atlantic specimens, whereas Mediterranean sperm whales were isotopically distinct regardless of time period. Discussion: The results suggest broad long-term stability in carbon isotope baselines or habitat use, alongside substantial reorganisation of nitrogen cycling or deep-pelagic food-web structure between the Late Glacial and Late Holocene. The distinct Mediterranean isotope values are also consistent with the known demographic separation of Mediterranean sperm whales from the wider North Atlantic population. These results provide rare historical isotopic baselines for sperm whales in the eastern North Atlantic and demonstrate that apparent stability in predator trophic ecology can coexist with substantial changes in underlying ocean biogeochemistry. Such baselines are essential for evaluating future responses of this deep-diving predator to anthropogenic pressures and climate-driven reorganisation of deep-ocean food webs.

Animal bones from archaeological contexts can reveal the interplay between past environments and human societies. Resource acquisition shaped many aspects of past societies and influenced the development of trade networks and migration. Fish have been a cornerstone of human subsistence for millennia, yet the rise of commercial fishing and trade was complex. Here, we synthesised a database of ∼1.9 million zooarchaeological fish records spanning 2000 years across Europe. Using machine-learning of catch compositions alongside fish thermal tolerances, we show that fisheries became less local over time, with homogenisation coinciding with Little Ice Age-associated cooling, a period of documented resource scarcity, concurring with growing trade. Moreover, increased proportions of marine taxa and more specialist marine fisheries were observed in the preceding Medieval Climate Anomaly, to sustain concurrent urban and population growth. Enhanced use of marine protein buffered food insecurity, whilst signalling the transition from localised to trans-regional trade networks.

Baleen whales are key marine predators that were heavily exploited throughout the 20th century, resulting in reductions in population size for many species. Whilst population recovery is evident for some species, baseline information on ecological niches is still unknown, rendering it difficult to forecast the manner in which baleen whales will reoccupy their former ecological niches as they recover. Biogeochemical analyses of bone fragments from 20th century whaling provide invaluable information on the foraging ecology and trophic niches of whale populations in the past, and provide a baseline for assessing recovery. Here, we combined Zooarchaeology by Mass Spectrometry (ZooMS) and DNA barcoding to assign bone specimens to species from 3 former whaling sites in the western South Atlantic, and used stable isotope analysis of carbon and nitrogen to infer differences in the long-term foraging preferences of baleen whales utilising western South Atlantic feeding grounds. These data sets indicate that baleen whale species partitioned prey resources with slight overlap in isotopic niches for 3 of the 4 species, with sei whales Balaenoptera borealis likely to be foraging predominantly on different feeding grounds relative to Antarctic blue B. musculus, fin B. physalus, and humpback Megaptera novaeangliae whales. Niche sizes reveal that Antarctic blue and sei whales are specialist feeders at the population level, suggesting that they are less likely to adapt to continuing climate change relative to more generalist fin and humpback whales. Characterising historical foraging baselines such as these are essential for assessing the ecological implications of changing oceans for recovering whale populations.

Archaeological faunal remains provide key insights into human societies in the past, alongside information on previous resource utilisation and exploitation of wildlife populations. The great whales (Mysticete and sperm whales) were hunted unsustainably throughout the 16th - 20th centuries (herein defined as the modern period) leading to large population declines and variable recovery patterns among species. Humans have utilised whales as a resource through carcass scavenging for millennia; however, increasing local and regional ethnographic and archaeological evidence suggests that, prior to the modern period, hunting of the great whales was more common than previously thought; impacts of earlier hunting pressures on the population ecology of many whale species remains relatively unknown. Hunting guided by traditional ecological knowledge may have been sustainable and likely originated in societies that also incorporated opportunistic use of stranded individuals. The collation of georeferenced zooarchaeological data of the great whales between the 1st - 20th centuries CE worldwide will provide insight into the timescale and distribution of resource utilisation of the great whales and how this varied within and between societies, and may have changed over time. By comparing regions of known resource utilisation and breeding and feeding grounds of current-day whale populations, this information will subsequently be used to infer regions where whale populations were possibly lost or extirpated prior to detailed historical records. This systematic review protocol also provides a template for archaeologists, ecologists, and historians interested in using faunal remains to infer historical ecology and resource use of wild animal populations. The transparency of our data collection approach provides opportunities for reproducibility and comparability with future datasets.

The 20 ^th century commercial whaling industry severely reduced populations of great whales throughout the Southern Hemisphere. The effect of this exploitation on genetic diversity and population structure remains largely undescribed. Here, we compare pre- and post-whaling diversity of mitochondrial DNA (mtDNA) control region sequences for three great whales in the South Atlantic, the blue, humpback and fin whale. Pre-whaling diversity is described from mtDNA extracted from bones collected near abandoned whaling stations, primarily from the South Atlantic island of South Georgia. These bones are known to represent the first stage of 20 ^th century whaling and thus pre-whaling diversity of these populations. Post-whaling diversity is described from previously published studies reporting large-scale sampling of living whales in the Southern Hemisphere. Despite relatively high levels of surviving genetic diversity in the post-whaling populations, we found evidence of a probable loss of mtDNA lineages in all three species. This is evidenced by the detection of a large number of haplotypes found in the pre-whaling samples that are not present in the post-whaling samples. A rarefaction analysis further supports a loss of haplotypes in the South Atlantic humpback and Antarctic blue whale populations. The bones from former whaling stations in the South Atlantic represent a remarkable molecular archive for further investigation of the decline and ongoing recovery in the great whales of the Southern Hemisphere.

Stage‐based demographic methods, such as matrix population models (MPMs), are powerful tools used to address a broad range of fundamental questions in ecology, evolutionary biology and conservation science. Accordingly, MPMs now exist for over 3000 species worldwide. These data are being digitised as an ongoing process and periodically released into two large open‐access online repositories: the COMPADRE Plant Matrix Database and the COMADRE Animal Matrix Database. During the last decade, data archiving and curation of COMPADRE and COMADRE, and subsequent comparative research, have revealed pronounced variation in how MPMs are parameterized and reported. Here, we summarise current issues related to the parameterisation and reporting of MPMs that arise most frequently and outline how they affect MPM construction, analysis, and interpretation. To quantify variation in how MPMs are reported, we present results from a survey identifying key aspects of MPMs that are frequently unreported in manuscripts. We then screen COMPADRE and COMADRE to quantify how often key pieces of information are omitted from manuscripts using MPMs. Over 80% of surveyed researchers (n = 60) state a clear benefit to adopting more standardised methodologies for reporting MPMs. Furthermore, over 85% of the 300 MPMs assessed from COMPADRE and COMADRE omitted one or more elements that are key to their accurate interpretation. Based on these insights, we identify fundamental issues that can arise from MPM construction and communication and provide suggestions to improve clarity, reproducibility and future research utilising MPMs and their required metadata. To fortify reproducibility and empower researchers to take full advantage of their demographic data, we introduce a standardised protocol to present MPMs in publications. This standard is linked to www.compadre‐db.org, so that authors wishing to archive their MPMs can do so prior to submission of publications, following examples from other open‐access repositories such as DRYAD, Figshare and Zenodo. Combining and standardising MPMs parameterized from populations around the globe and across the tree of life opens up powerful research opportunities in evolutionary biology, ecology and conservation research. However, this potential can only be fully realised by adopting standardised methods to ensure reproducibility.

Healthy insect populations are vital for maintaining natural ecosystems and essential to global food security. The ongoing dramatic loss of insect species and biomass is thus a global cause for concern, with much focus on this topic in the media. Yet, determining the mechanism behind these declines remains difficult, particularly when attempting to differentiate between anthropogenic drivers of biodiversity loss and long‐term natural fluctuations. In a From the Cover manuscript in this issue of Molecular Ecology, Crossley et al. (2022) examined the long‐term impact of land use change on freshwater insects by estimating levels of genetic diversity with publicly available data for the cytochrome c oxidase subunit 1 (CO1) mitochondrial locus from >700 aquatic insect species across the United States. Contemporary genetic diversity measures reflect both current and past demography and therefore are related to both past and present habitat change. Crossley et al. found that environments with greater cropland extent over the last 200 years were associated with lower genetic diversity in contemporary aquatic insect populations. This indicates that historical land use is an important factor in contemporary population dynamics. Most critically, in regions of historical cropland cover that have been converted towards other uses (such as urban environments) more recently, aquatic insect populations exhibited higher levels of genetic diversity, indicating a possible rebound in insect populations after cessation of agricultural activity. This study highlights the power of using publicly available data to answer crucial questions regarding the current biospheric emergency.

Fin whales Balaenoptera physalus were hunted unsustainably across the globe in the 19th and 20th centuries, leading to vast reductions in population size. Whaling catch records indicate the importance of the Southern Ocean for this species; approximately 730,000 fin whales were harvested during the 20th century in the Southern Hemisphere (SH) alone, 94% of which were at high latitudes. Genetic samples from contemporary whales can provide a window to past population size changes, but the challenges of sampling in remote Antarctic waters limit the availability of data. Here, we take advantage of historical samples in the form of bones and baleen available from ex-whaling stations and museums to assess the pre-whaling diversity of this once abundant species. We sequenced 27 historical mitogenomes and 50 historical mitochondrial control region sequences of fin whales to gain insight into the population structure and genetic diversity of Southern Hemisphere fin whales (SHFWs) before and after the whaling. Our data, both independently and when combined with mitogenomes from the literature, suggest SHFWs are highly diverse and may represent a single panmictic population that is genetically differentiated from Northern Hemisphere populations. These are the first historic mitogenomes available for SHFWs, providing a unique time series of genetic data for this species.