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Food availability modulates survival, reproduction and thereby population size. In addition to direct effects, food availability has indirect effects through density of conspecifics and predators. We tested the prediction that food availability in isolation affects reproductive success by experimentally manipulating food availability continuously for 3 years in zebra finches (Taeniopygia guttata) housed in outdoor aviaries. To this end, we applied a technique that mimics natural variation in food availability: increasing the effort required per food reward without affecting diet. Lower food availability resulted in a slight delay of start of laying and fewer clutches per season, but did not affect clutch size or number of offspring reared per annum. However, increasing foraging costs substantially reduced offspring growth. Thus, food availability in isolation did not impact the quantity of offspring reared, at the expense of offspring quality. Growth declined strongly with brood size, and we interpret the lack of response with respect to offspring number as an adaptation to environments with low predictability, at the time of egg laying, of food availability during the period of peak food demand, typically weeks later. Manipulated natal brood size of the parents did not affect reproductive success. Individuals that were more successful reproducers were more likely to survive to the next breeding season, as frequently found in natural populations. We conclude that the causal mechanisms underlying associations between food availability and reproductive success in natural conditions may be more complex than usually assumed. Experiments in semi-natural meso-populations can contribute to further unravelling these mechanisms.

Pleistocene environmental changes are generally assumed to have dramatically affected species’ demography via changes in habitat availability, but this is challenging to investigate due to our limited knowledge of how Pleistocene ecosystems changed through time. Here, we tracked changes in shallow marine habitat availability resulting from Pleistocene sea level fluctuations throughout the last glacial cycle (120–14 thousand years ago; kya) and assessed correlations with past changes in genetic diversity inferred from genome-wide SNPs, obtained via ddRAD sequencing, in Caribbean hawksbill turtles, which feed in coral reefs commonly found in shallow tropical waters. We found sea level regression resulted in an average 75% reduction in shallow marine habitat availability during the last glacial cycle. Changes in shallow marine habitat availability correlated strongly with past changes in hawksbill turtle genetic diversity, which gradually declined to ~1/4th of present-day levels during the Last Glacial Maximum (LGM; 26–19 kya). Shallow marine habitat availability and genetic diversity rapidly increased after the LGM, signifying a population expansion in response to warming environmental conditions. Our results suggest a positive correlation between Pleistocene environmental changes, habitat availability and species’ demography, and that demographic changes in hawksbill turtles were potentially driven by feeding habitat availability. However, we also identified challenges associated with disentangling the potential environmental drivers of past demographic changes, which highlights the need for integrative approaches. Our conclusions underline the role of habitat availability on species’ demography and biodiversity, and that the consequences of ongoing habitat loss should not be underestimated.

Assessing environmental changes in Southern Ocean ecosystems is difficult due to its remoteness and data sparsity. Monitoring marine predators that respond rapidly to environmental variation may enable us to track anthropogenic effects on ecosystems. Yet, many long-term datasets of marine predators are incomplete because they are spatially constrained and/or track ecosystems already modified by industrial fishing and whaling in the latter half of the 20th century. Here, we assess the contemporary offshore distribution of a wide-ranging marine predator, the southern right whale (SRW, Eubalaena australis ), that forages on copepods and krill from ~30°S to the Antarctic ice edge (>60°S). We analyzed carbon and nitrogen isotope values of 1,002 skin samples from six genetically distinct SRW populations using a customized assignment approach that accounts for temporal and spatial variation in the Southern Ocean phytoplankton isoscape. Over the past three decades, SRWs increased their use of mid-latitude foraging grounds in the south Atlantic and southwest (SW) Indian oceans in the late austral summer and autumn and slightly increased their use of high-latitude (>60°S) foraging grounds in the SW Pacific, coincident with observed changes in prey distribution and abundance on a circumpolar scale. Comparing foraging assignments with whaling records since the 18th century showed remarkable stability in use of mid-latitude foraging areas. We attribute this consistency across four centuries to the physical stability of ocean fronts and resulting productivity in mid-latitude ecosystems of the Southern Ocean compared with polar regions that may be more influenced by recent climate change.

Large grazers (megaherbivores) have a profound impact on ecosystem functioning. However, how ecosystem multifunctionality is affected by changes in megaherbivore populations remains poorly understood. Understanding the total impact on ecosystem multifunctionality requires an integrative ecosystem approach, which is especially challenging to obtain in marine systems. We assessed the effects of experimentally simulated grazing intensity scenarios on ecosystem functions and multifunctionality in a tropical Caribbean seagrass ecosystem. As a model, we selected a key marine megaherbivore, the green turtle, whose ecological role is rapidly unfolding in numerous foraging areas where populations are recovering through conservation after centuries of decline, with an increase in recorded overgrazing episodes. To quantify the effects, we employed a novel integrated index of seagrass ecosystem multifunctionality based upon multiple, well-recognized measures of seagrass ecosystem functions that reflect ecosystem services. Experiments revealed that intermediate turtle grazing resulted in the highest rates of nutrient cycling and carbon storage, while sediment stabilization, decomposition rates, epifauna richness, and fish biomass are highest in the absence of turtle grazing. In contrast, intense grazing resulted in disproportionally large effects on ecosystem functions and a collapse of multifunctionality. These results imply that (i) the return of a megaherbivore can exert strong effects on coastal ecosystem functions and multifunctionality, (ii) conservation efforts that are skewed toward megaherbivores, but ignore their key drivers like predators or habitat, will likely result in overgrazing-induced loss of multifunctionality, and (iii) the multifunctionality index shows great potential as a quantitative tool to assess ecosystem performance. Considerable and rapid alterations in megaherbivore abundance (both through extinction and conservation) cause an imbalance in ecosystem functioning and substantially alter or even compromise ecosystem services that help to negate global change effects. An integrative ecosystem approach in environmental management is urgently required to protect and enhance ecosystem multifunctionality.

This thesis examines ancient sea turtles from the Levant and more recent archaeological sea turtle bones from the Netherlands. The research investigates foraging ecology, DNA preservation, provenance, and trade. Only two sea turtle species, green turtles and loggerhead turtles, breed and nest in the Mediterranean. Understanding the historical ecology of ancient Mediterranean sea turtle populations hunted in the Bronze and Iron ages was the main goal of the thesis. The Netherlands also participated in large-scale exploitation during colonial times, but sea turtle bones are rare in the archaeological record. By studying archaeological sea turtle bones, the research sheds light on the biological characteristics of archaeological sea turtle populations. The thesis statistically assigns ancient Mediterranean green turtles to modern foraging grounds using palaeoproteomics and stable isotope analysis. Sea turtle trade by the Netherlands is also explored. The possibilities of ancient DNA analysis of archaeological sea turtle remains is investigated, with a focus on DNA preservation. This research integrates marine biology and zooarchaeology to better understand ancient and historical sea turtle exploitation and ecology. The results contribute to nature preservation discussions and emphasise learning from the past for present conservation efforts.

Our goal was to understand the mechanisms behind the impact of nutrient enrichment at intermediate distances from aquaculture on the interactions of a subtidal macroalgae community with its main grazer, the sea urchin Paracentrotus lividus. We assessed the diversity and cover of the macroalgal community, the abundance and biometrics of the sea urchins, the carbon and nitrogen elemental and isotopic compositions, and their metabolome in two stations, at an intermediate distance (station A) and away (station B) from a fish cage facility in the Aegean Sea (Greece), during the warm and cold seasons. The nutrient input at station A favored a shift to a macroalgal assemblage dominated by turf-forming species, depleted of native-erected species and with a higher abundance of invasive algae. A stable isotope analysis showed fish-farm-associated nitrogen enrichment of the macroalgae and trophic transfer to P. lividus. A decrease in metabolites related to grazing, reproduction, and energy reserves was found in P. lividus at station A. Furthermore, the metabolomic analysis was able to pinpoint stress in P. lividus at an intermediate distance from aquaculture. The chosen combination of traditional ecology with omics technology could be used to uncover not only the sublethal effects of nutrient loading but also the pathways for species interactions.

Studies of cetacean evolution using genetics and other biomolecules have come a long way—from the use of allozymes and short sequences of mitochondrial or nuclear DNA to the assembly of full nuclear genomes and characterization of proteins and lipids. Cetacean research has also advanced from using only contemporary samples to analyzing samples dating back thousands of years, and to retrieving data from indirect environmental sources, including water or sediments. Combined, these studies have profoundly deepened our understanding of the origin of cetaceans; their adaptation and speciation processes; and of the past population change, migration, and admixture events that gave rise to the diversity of cetaceans found today.

The occasional westward transport of warm water of the Agulhas Current, ‘Agulhas leakage’, around southern Africa has been suggested to facilitate tropical marine connectivity between the Atlantic and Indian oceans, but the ‘Agulhas leakage’ hypothesis doesn’t explain the signatures of eastward gene flow observed in many tropical marine fauna. We investigated an alternative hypothesis: the establishment of a warm-water corridor during comparatively warm interglacial periods. The ‘warm-water corridor’ hypothesis was investigated by studying the population genomic structure of Atlantic and Southwest Indian Ocean green turtles (N = 27) using 12,035 genome-wide single nucleotide polymorphisms (SNPs) obtained via ddRAD sequencing. Model-based and multivariate clustering suggested a hierarchical population structure with two main Atlantic and Southwest Indian Ocean clusters, and a Caribbean and East Atlantic sub-cluster nested within the Atlantic cluster. Coalescent-based model selection supported an ancestral position of the East Atlantic from which the Southwest Indian Ocean and Caribbean populations diverged during the transition from the last interglacial period (130 – 115 thousand years ago; kya) to the last glacial period (115 – 90 kya). The onset of the last glaciation appeared to isolate Atlantic and Southwest Indian Ocean green turtles into three refugia, which subsequently came into secondary contact in the Caribbean and Southwest Indian Ocean when global temperatures increased after the Last Glacial Maximum. Our findings support the establishment of a warm-water corridor facilitating tropical marine connectivity between the Atlantic and Southwest Indian Ocean during warm interglacials.

1. Historical abundance estimates are important for establishing baselines fromwhich trends can be determined using more recent data. Long-term studies basedon photo-identification were merged and used to estimate population size,survival rate and sex ratio (biopsy sampling) of fin whales in the North-westernMediterranean.2. Merging four existing photo-id catalogues yielded a Mediterranean cataloguewith 507 individually identified fin whales. Ninety-five (18.7%) individuals wereresighted at least once during the study period (1990–2007): 71 whales wereresighted in different years, 24 within the same season and 13 both in the sameseason and in different years. The number of resightings within-season rangedfrom one to four, over periods from 1 to 90 days.3. Capture histories from these individuals were used in the capture–recaptureanalyses. Estimates of the animals present in the area each year between 1991and 1995 through different modelling approaches were consistent: 900–1,000from a POPAN open population model; 1,200 from a multi-sample closedpopulation model; and 900–1,100 from simple two-sample closed populationmodels for pairs of consecutive years, all with heavily overlapping 95%confidence intervals.4. The estimated apparent survival rate of 0.916 (95% CI=0.773–0.972) was lowerthan expected, which may be linked to temporary or permanent emigration, ormortality possibly owing to ship strikes.5. Conservation and mitigation measures such as Important Marine Mammal Areasand Particularly Sensitive Sea Areas are presented and discussed.

Several previous studies have described epigenetic clocks for whale and dolphin species. Here we present a novel and highly robust epigenetic clock for the humpback whale based on methylation levels measured using the Mammalian Methylation Array platform. Skin samples were obtained from 76 individuals that had been studied since their birth year and known to range in age from

Full mitochondrial genomes were assembled for 12 recently sampled animals from the Svalbard bowhead whale (Balaena mysticetus) stock via high-throughput sequencing data, facilitating analysis of the demographic history of the population for the first time. The Svalbard population has retained noticeable amounts of mitochondrial genome diversity despite extreme historical harvest levels. Haplotype and nucleotide diversities were similar to those estimated earlier for other bowhead whale populations. The reconstructed demographic history was in accordance with a boom–bust scenario, combining a slight Pleistocene population growth 25 000–35 000 years ago and a Holocene decline. Employing a mutation rate of 3.418 × 10–8 substitutions per site per year, the time to the most recent common ancestor for the mitochondrial genomes of the contemporary Svalbard bowhead whales was estimated to be 68 782 (54 353–83 216) years before the present. Based on 370 bp fragments of the D-loop region, significant genetic differentiation was detected between all extant bowhead whale populations across the circumpolar Arctic. Thus, the Svalbard bowhead whales can be regarded as a population with its own genetic legacy.

Funding: The aerial part of the study in 2018 and 2019 was funded by DFO. Entanglement in fishing gear is a significant threat to many cetaceans. For the 2 largest species, the blue whale Balaenoptera musculus and the fin whale B. physalus, reports of entangled individuals are rare, leading to the assumption that entanglements are not common. Studies of interaction with fisheries in other species often rely on the presence of scars from previous entanglements. Here, scar detection rates were first examined in humpback Megaptera novaeangliae, fin and blue whales using standard vessel-based photo-identification photographs collected between 2009 and 2016 in the Gulf of St. Lawrence, Canada. We then examined aerial images of fin whales collected with a drone in 2018 and 2019 and compared both methods. Entanglement rates were 6.5% for fin and 13.1% for blue whales using photo-identification images of individuals. Prominent scarring was observed around the tail and caudal peduncle, visible only when animals lifted those body sections above water when diving. For the small subset of pictures which captured the entire caudal peduncle, entanglement rates ranged between 60% for blue and 80% for fin whales. This result was similar to the 85% entanglement rate estimated in humpback whales. The assessment of aerial-based photography yielded an entanglement rate of 44.1 to 54.7% in fin whales. Scars were always around the peduncle, often the tail, rarely the dorsal fin and never around the pectoral fins, while the mouth cannot be examined from above. Thus, in species that do not regularly expose their tail or peduncle, aerial imagery is the preferred method to quantify entanglement rates by assessment of scars. Publisher PDF

DNA metabarcoding methods have been implemented in studies aimed at detecting and quantifying marine benthic biodiversity. In such surveys, universal barcodes are amplified and sequenced from environmental DNA. To quantify biodiversity with DNA metabarcoding, a relation between the number of DNA sequences of a species and its biomass and/or the abundance is required. However, this relationship is complicated by many factors, and it is often unknown. In this study, we validate estimates of biomass and abundance from molecular approaches with those from the traditional morphological approach. Abundance and biomass were quantified from 126 samples of benthic intertidal mudflat using traditional morphological approaches and compared with frequency of occurrence and relative read abundance estimates from a molecular approach. A relationship between biomass and relative read abundance was found for two widely dispersed annelid taxa (Pygospio and Scoloplos). None of the other taxons, however, showed such a relationship. We discuss how quantification of abundance and biomass using molecular approaches are hampered by the ecology of DNA i.e. all the processes that determine the amount of DNA in the environment, including the ecology of the benthic species as well as the compositional nature of sequencing data.

To learn more about the occurrence and behaviour of a recently discovered population of blue whales, passive acoustic data were collected between January 2012 and April 2013 in the Chiloense ecoregion of southern Chile. Automatic detectors and manual auditing were used to detect blue whale songs (SEP calls) and D calls, which were then analysed to gain insights into temporal calling patterns. We found that D call rates were extremely low during winter (June–August) but gradually increased in spring and summer, decreasing again later during fall. SEP calls were absent for most winter and spring months (July–November) but increased in summer and fall, peaking between March and April. Thus, our results support previous studies documenting the austral summer residency of blue whales in this region, while suggesting that some individuals stay longer, highlighting the importance of this area as a blue whale habitat. We also investigated the daily occurrence of each call type and found that D calls occurred more frequently during dusk and night hours compared to dawn and day periods, whereas SEP calls did not show any significant diel patterns. Overall, these findings help to understand the occurrence and behaviour of endangered Chilean blue whales, enhancing our ability to develop conservation strategies in this important Southern Hemisphere habitat.

Progress in genome sequencing now enables the large-scale generation of reference genomes. Various international initiatives aim to generate reference genomes representing global biodiversity. These genomes provide unique insights into genomic diversity and architecture, thereby enabling comprehensive analyses of population and functional genomics, and are expected to revolutionize conservation genomics., Trends in Ecology & Evolution, 37 (3), ISSN:0169-5347, ISSN:1872-8383

Global warming is affecting the population dynamics and trophic interactions across a wide range of ecosystems and habitats. Translating these real-time effects into their long-term consequences remains a challenge. The rapid and extreme warming period that occurred after the Last Glacial Maximum (LGM) during the Pleistocene-Holocene transition (7-12 thousand years ago) provides an opportunity to gain insights into the long-term responses of natural populations to periods with global warming. The effects of this post-LGM warming period have been assessed in many terrestrial taxa, whereas insights into the impacts of rapid global warming on marine taxa remain limited, especially for megafauna. In order to understand how large-scale climate fluctuations during the post-LGM affected baleen whales and their prey, we conducted an extensive, large-scale analysis of the long-term effects of the post-LGM warming on abundance and inter-ocean connectivity in eight baleen whale and seven prey (fish and invertebrates) species across the Southern and the North Atlantic Ocean; two ocean basins that differ in key oceanographic features. The analysis was based upon 7032 mitochondrial DNA sequences as well as genome-wide DNA sequence variation in 100 individuals. The estimated temporal changes in genetic diversity during the last 30,000 years indicated that most baleen whale populations underwent post-LGM expansions in both ocean basins. The increase in baleen whale abundance during the Holocene was associated with simultaneous changes in their prey and climate. Highly correlated, synchronized and exponential increases in abundance in both baleen whales and their prey in the Southern Ocean were indicative of a dramatic increase in ocean productivity. In contrast, the demographic fluctuations observed in baleen whales and their prey in the North Atlantic Ocean were subtle, varying across taxa and time. Perhaps most important was the observation that the ocean-wide expansions and decreases in abundance that were initiated by the post-LGM global warming, continued for millennia after global temperatures stabilized, reflecting persistent, long-lasting impacts of global warming on marine fauna.

The gene Clock is a key part of the Core Circadian Oscillator, and the length of the polyglutamine (poly-Q) repeat sequence in Clock (ClkpolyQcds) has been proposed to be associated with the timing of annual cycle events in birds. We tested whether variation in ClkpolyQcds corresponds to variation in migration timing in the bar-tailed godwit (Limosa lapponica baueri), a species in which individuals show strong annual consistency in their migration timing despite the New Zealand population migrating across a 5-week period. We describe allelic variation of the ClkpolyQcds in 135 godwits over-wintering in New Zealand (N.Z.) and investigate whether polymorphism in this region is associated with northward migration timing (chronophenotype) from N.Z. or (for 32 birds tracked by geolocator) after the primary stopover in Asia. Six Clock alleles were detected (Q(7)-Q(12)) and there was substantial variation between individuals (heterozygosity of 0.79). There was no association between ClkpolyQcds polymorphism and migration timing from N.Z. The length of the shorter Clock allele was related to migration timing from Asia, though this relationship arose largely from just a few northern-breeding birds with longer alleles. Other studies show no consistent associations between ClkpolyQcds and migration timing in birds, although Clock may be associated with breeding latitude in some species (as an adaptation to photoperiodic regime). Apparent relationships with migration timing could reflect latitude-related variation in migration timing, rather than Clock directly affecting migration timing. On current evidence, ClkpolyQcds is not a strong candidate for driving migration timing in migratory birds generally.

Current research on anthropogenic impacts on marine ecosystems often relies on the concept of a “baseline,” which aims to describe ecosystems prior to human contact. Recent research is increasingly showing that humans have been involved in marine ecosystems for much longer than previously understood. We propose a theoretical framework oriented around a system of “thresholds” referring to system-wide changes in human culture, ecosystem dynamics, and molecular evolution. The concept of the threshold allows conceptual space to account for the fluid nature of ecosystems throughout time while providing a critical framework for understanding drivers of ecosystem change. We highlight practical research approaches for exploring thresholds in the past and provide key insights for future adaptation to a changing world. To ensure ecological and societal goals for the future are met, it is critical that research efforts are contextualized into a framework that incorporates human society as integral to ecology and evolution.

Coral reefs are important ecosystems in terms of their biodiversity and ecosystem functions. Particularly at local scales, coral reefs are vulnerable to natural and anthropogenic disturbances, leading to the degradation of reef health. Here, we employed two different methods to monitor reef health. First, we conducted line transect surveys to record the benthic community structure to infer ecological reef health. Secondly, trace metal concentrations in sediment samples and a bioindicator sponge species, Haliclona fascigera, were compared among sites to detect cryptic degradation and unknown sources of pollution. The study area comprised six reefs situated along the coast of Zanzibar’s main agglomeration, Stone Town, and subject to different types of disturbances and conservation management schemes. Overall, coral reef health was found to decrease with increasing proximity to Stone Town, with living hard coral cover being particularly low on reefs closest to Stone Town, which coincided with greater fishing, tourism, and pollution pressures. Reef assessments based on trace metal analyses differed from the community structure surveys. All sites showed high levels of arsenic and cadmium contamination, with some samples revealing concerning levels of chromium, copper and zinc. The reefs differed significantly between each other in terms of trace metal concentration for both sediments (p = 0.031, PERMANOVA) and sponge samples (p = 0.001, PERMANOVA). Trace metal concentrations were not correlated with distance to Stone Town, highlighting the downstream effects of industrial and urban sewage on even remote reefs. Coral reef health assessment was found to be dependent on the survey method employed, which is why we recommend the combination of complementary methods.

Humpback whales are thought to undertake annual migrations between their low latitude breeding grounds and high latitude feeding grounds. However, under specific conditions, humpback whales sometimes change their migratory destination or skip migration overall. Here we document the surprising persistent presence of humpback whales in the Atlantic sector of the Southern Ocean during five years (2011, 2012, 2013, 2017, and 2018) using passive acoustic data. However, in the El Niño years 2015 and 2016, humpback whales were virtually absent. Our data show that humpback whales are systematically present in the Atlantic sector of the Southern Ocean and suggest that these whales are particularly sensitive to climate oscillations which have profound effects on winds, sea ice extent, primary production, and especially krill productivity., Schall et al. use passive acoustic recordings of humpback whale calls to report the presence of humpback whales in the Atlantic sector of the Southern Ocean between 2011 and 2018. This serves as the first long-term report of humpback whales on a Southern Ocean feeding ground, and their notable absence during the El Niño years of 2015 and 2016 indicates that the inter-annual variability in their acoustic presence is driven by large-scale climate variability.

Background Mangroves are tropical and subtropical intertidal forests colonising sheltered coasts across the world. They host a unique faunal community, dominated by brachyuran crabs and gastropods. These invertebrates strongly contribute to the functionality of the entire forest. The reliable assessment of mangrove faunal diversity is, thus, a crucial step for efficient management and conservation plans, but it is hindered by difficulties in species identification. Here we provide a verified DNA barcode library for brachyuran crabs and gastropods inhabiting the mangroves of the Greater Bay Area, Southern China. In particular, we collected and morphologically identified 1100 specimens of mangrove associated brachyuran crabs and gastropods. The partial sequences of the mtDNA cytochrome oxidase subunit I gene were obtained from 275 specimens. Barcode sequences were then used to delineate Molecular Operational Taxonomic Units (MOTUs), employing three different delimitation methods: the automatic barcode gap discovery (ABGD) method, the general mixed Yule coalescent (GMYC) model and a Bayesian implementation of the Poisson tree processes (bPTP) model. Results By integrating DNA barcodes with morphology, we identified 44 gastropod species and 58 brachyuran species associated with Hong Kong mangroves, with five and seven new records, for gastropods and crabs, respectively, for the Greater Bay Area. The delineation of MOTUs based on barcode sequences revealed a strong congruence between morphological and molecular identification for both taxa, showing the high reliability of the barcode library. Conclusions This study provides the first reference barcode library for mangrove-associated macrobenthic fauna in the Greater Bay Area and represents a reliable tool to management and conservation plans. Our molecular analyses resolved long lasting taxonomic misidentifications and inconsistencies and updated the knowledge on the geographical distribution of Asian mangrove associated fauna, ultimately highlighting a level of biodiversity higher than previously thought for Southern China.

Fecal hormone analysis shows high potential for noninvasive assessment of population-level patterns in stress and reproduction of marine mammals. However, the marine environment presents unique challenges for fecal sample collection. Data are still lacking on collection methodology and assay validations for most species, particularly for those mysticete whales that have variable diets. In this study we tested collection techniques for fecal samples of free-swimming humpback whales (Megaptera novaeangliae), and validated immunoassays for five steroid and thyroid hormones. Resulting data were used for preliminary physiological validations, i.e., comparisons to independently confirmed sex and reproductive state. Pregnant females had significantly higher fecal progestins and glucocorticoids than did other demographic categories of whales. Two possible cases of previously undetected pregnancies were noted. Males had significantly higher fecal testosterone metabolites than nonpregnant females. Fecal glucocorticoids were significantly elevated in pregnant females and mature males compared to nonpregnant females. Calf fecal samples had elevated concentrations of all fecal hormones. Fecal thyroid hormones showed a significant seasonal decline from spring to summer. Though sample sizes were small, and sampling was necessarily opportunistic, these patterns indicate that noninvasive fecal hormone analysis may facilitate studies of reproduction, stress and potentially energetics in humpback whales.

The Gulf of California, Mexico is home to many cetacean species, including a presumed resident population of fin whales, Balaenoptera physalus. Past studies reported very low levels of genetic diversity among Gulf of California fin whales and a significant level of genetic differentiation from con-specifics in the eastern North Pacific. The aim of the present study was to assess the degree and timing of the isolation of Gulf of California fin whales in a population genetic analysis of 18 nuclear microsatellite genotypes from 402 samples and 565 mitochondrial control region DNA sequences (including mitochondrial sequences retrieved from NCBI). The analyses revealed that the Gulf of California fin whale population was founded ~2.3 thousand years ago and has since remained at a low effective population size (~360) and isolated from the eastern North Pacific (Nem between 0.89–1.4). The low effective population size and high degree of isolation implied that Gulf of California fin whales are vulnerable to the negative effects of genetic drift, human-caused mortality and habitat change.

The auditory frequency weighted daily sound exposure level (SEL) is used in many jurisdictions to assess possible injury to the hearing of marine life. Therefore, using daily SEL to describe soundscapes would provide baseline information about the environment using the same tools used to measure injury. Here, the daily SEL from 12 recordings with durations of 18-97days are analyzed to: (1) identify natural soundscapes versus environments affected by human activity, (2) demonstrate how SEL accumulates from different types of sources, (3) show the effects of recorder duty cycling on daily SEL, (4) make recommendations on collecting data for daily SEL analysis, and (5) discuss the use of the daily SEL as an indicator of cumulative effects. The autocorrelation of the one-minute sound exposure is used to help identify soundscapes not affected by human activity. Human sound sources reduce the autocorrelation and add low-frequency energy to the soundscapes. To measure the daily SEL for all marine mammal auditory frequency weighting groups, data should be sampled at 64kHz or higher, for at least 1min out of every 30min. The daily autocorrelation of the one-minute SEL provides a confidence interval for the daily SEL computed with duty-cycled data. (C) 2019 Acoustical Society of America.

1. Our knowledge of the functional role of large herbivores is rapidly expanding, and the impact of grazing on species coexistence and nonnative species expansion has been studied across ecosystems. However, experimental data on large grazer impacts on plant invasion in aquatic ecosystems are lacking.2. Since its introduction in 2002, the seagrass species Halophila stipulacea has rapidly expanded across the Eastern Caribbean, forming dense meadows in green turtle (Chelonia mydas)-foraging areas. We investigate the changes in seagrass species coexistence and the impacts of leaf grazing by green turtles on nonnative seagrass expansion in Lac Bay (Bonaire, Caribbean Netherlands).3. Green turtle grazing behaviour changed after the introduction of nonnative seagrass to Lac Bay in 2010. Field observations, together with time-lapse satellite images over the last four decades, showed initiation of new grazing patches (65 ha, an increase of 72%). The sharp border between grazed and ungrazed seagrass patches moved in the direction of shallower areas with native seagrass species that had previously (1970-2010) been ungrazed. Green turtles deployed with Fastloc-GPS transmitters confirmed high site fidelity to these newly cropped patches. In addition, cafeteria experiments indicated selective grazing by green turtles on native species. These native seagrass species had significantly higher nutritional values compared to the nonnative species. In parallel, exclosure experiments showed that nonnative seagrass expanded more rapidly in grazed canopies compared to ungrazed canopies. Finally, in 6 years from 2011 to 2017, H. stipulacea underwent a significant expansion, invading 20-49 fixed monitoring locations in Lac Bay, increasing from 6% to 20% in total occurrence. During the same period, native seagrass Thalassia testudinum occurrence decreased by 33%.4. Synthesis. Our results provide first-time evidence of large-scale replacement of native seagrasses by rapidly colonizing Halophila stipulacea in the Caribbean and add a mechanistic explanation for this invasiveness. We conclude that green turtle leaf grazing may modify the rate and spatial extent of this invasive species' expansion, due to grazing preferences, and increased space for settlement. This work shows how large herbivores play an important but unrecognized role in species coexistence and plant invasions of aquatic ecosystems.

A. Schleimer was supported by the Luxembourg National Research Fund (FNR; AFR/11256673). Significant ecosystem changes in the Gulf of St. Lawrence (GSL) have had far-reaching effects at all trophic levels. The abundance of fin whales (Balaenoptera physalus) has declined significantly in the northern GSL over the past decade. This study aimed to test the hypothesis that the observed decline was correlated to changing environmental conditions. Cetacean sighting data from 292 surveys, resulting in 2986 fin whale encounters from 2007 to 2013, were used to fit two separate generalised additive models in terms of (1) bathymetric and oceanographic variables (the proxy model) and (2) modelled krill biomass (the prey model). The concept of “handling time” was introduced to correct for time off search effort, applicable to other studies relying on opportunistically sampled data. While a positive correlation between krill biomass and fin whale numbers was found, the performance of the proxy model (24.2 % deviance explained) was overall better than the prey model (11.8 %). Annual predictive maps derived from the final proxy model highlighted two key areas with recurrently high relative fin whale abundance and a significant overlap with shipping lanes. While both models provided evidence for an annual decline in relative fin whale abundance, static bathymetric features were the most important predictors of habitat use and no correlation between dynamic variables and the decline was found. High resolution prey data and a better understanding of the feeding ecology of fin whales are proposed to further investigate the predator-prey relationship and decline of fin whales in the GSL. Postprint

Humans have been exploiting marine resources along the Levantine coast for millennia. Advances in biomolecular archaeology present novel opportunities to understand the exploitation of these taxa in antiquity. We discuss the potential insights generated by applying collagen peptide fingerprinting, ancient DNA analysis, and stable isotope analysis to groupers (Serranidae) and sea turtles (Chelonia mydas and Caretta caretta) in the Levant. When combined with traditional zooarchaeological techniques, biomolecular archaeology offers utility to further investigate human impacts on marine ecosystems.

This study sought to estimate the effect of an anthropogenic and climate-driven change in prey availability on the degree of individual and population specialization of a large marine predator, the fin whale (Balaenoptera physalus). We examined skin biopsies from 99 fin whales sampled in the St. Lawrence Estuary (Canada) over a nine year period (1998–2006) during which environmental change was documented. We analyzed stable isotope ratios in skin and fatty acid signatures in blubber samples of whales, as well as in seven potential prey species, and diet was quantitatively assessed using Bayesian isotopic models. An abrupt change in fin whale dietary niche coincided with a decrease in biomass of their predominant prey, Arctic krill (Thysanoessa spp.). This dietary niche widening toward generalist diets occurred in nearly 60% of sampled individuals. The fin whale population, typically composed of specialists of either krill or lipid-rich pelagic fishes, shifted toward one composed either of krill specialists or true generalists feeding on various zooplankton and fish prey. This change likely reduced intraspecific competition. In the context of the current “Atlantification” of northern water masses, our findings emphasize the importance of considering individual-specific foraging tactics and not only population or group average responses when assessing population resilience or when implementing conservation measures.

Owing to the intensified domestication process with artificial trait selection, introgressive hybridisation between domestic and wild species poses a management problem. Traditional free-range livestock husbandry, as practiced in Corsica and Sardinia, is known to facilitate hybridisation between wild boars and domestic pigs (Sus scrofa). Here, we assessed the genetic distinctness and genome-wide domestic pig ancestry levels of the Corsican wild boar subspecies S. s. meridionalis, with reference to its Sardinian conspecifics, employing a genome-wide single nucleotide polymorphism (SNP) assay and mitochondrial control region (mtCR) haplotypes. We also assessed the reliance of morphological criteria and the melanocortin-1 receptor (MC1R) coat colour gene to identify individuals with domestic introgression. While Corsican wild boars showed closest affinity to Sardinian and Italian wild boars compared to other European populations based on principal component analysis, the observation of previously undescribed mtCR haplotypes and high levels of nuclear divergence (Weir’s θ > 0.14) highlighted the genetic distinctness of Corsican S. s. meridionalis. Across three complementary analyses of mixed ancestry (i.e., STRUCTURE, PCADMIX, and ELAI), proportions of domestic pig ancestry were estimated at 9.5% in Corsican wild boars, which was significantly higher than in wild boars in Sardinia, where free-range pig keeping was banned in 2012. Comparison of morphologically pure- and hybrid-looking Corsican wild boars suggested a weak correlation between morphological criteria and genome-wide domestic pig ancestry. The study highlights the usefulness of molecular markers to assess the direct impacts of management practices on gene flow between domestic and wild species.

Rapid anthropogenic environmental change is expected to impact a host of ecological parameters in Southern Ocean ecosystems. Of critical concern are the consequences of these changes on the range of species that show fidelity to migratory destinations, as philopatry is hypothesized to help or hinder adaptation to climate change depending on the circumstances. Many baleen whales show philopatry to feeding grounds and are also capital breeders that meet migratory and reproductive costs through seasonal energy intake. Southern right whales (Eubalaena australis, SRWs) are capital breeders that have a strong relationship between reproductive output and foraging success. The population dynamics of South Africa's population of SRWs are characterized by two distinct periods: the 1990s, a period of high calving rates; and the late 2010s, a period associated with lowered calving rates. Here we use analyses of stable carbon (δ13C) and nitrogen (δ15N) isotope values from SRW biopsy samples (n = 122) collected during these two distinct periods to investigate foraging ecology of the South African population of SRWs over a time period coincident with the demographic shift. We show that South African SRWs underwent a dramatic northward shift, and diversification, in foraging strategy from 1990s to 2010s. Bayesian mixing model results suggest that during the 1990s, South African SRWs foraged on prey isotopically similar to South Georgia/Islas Georgias del Sur krill. In contrast, in the 2010s, South African SRWs foraged on prey isotopically consistent with the waters of the Subtropical Convergence, Polar Front and Marion Island. We hypothesize that this shift represents a response to changes in preferred habitat or prey, for example, the decrease in abundance and southward range contraction of Antarctic krill. By linking reproductive decline to changing foraging strategies for the first time in SRWs, we show that altering foraging strategies may not be sufficient to adapt to a changing ocean.

Offshore Exploration and Production (E&P) activities, such as seismic surveys and drilling, generate sound that can affect marine mammals in different ways. These effects range from permanent or temporary auditory impacts to disturbance or behavioral changes, and communication masking. Depending on the intensity and duration of these effects, and without implementation of appropriate mitigation measures, this can result in population-level consequences. The overarching objective of this study was to advance the protection of marine mammals during the implementation of E&P activities through the following themes: (1) enhancement of the state of knowledge of risk management, (2) efficacy of mitigation, (3) advanced monitoring technology, (4) implementation of advanced industry monitoring and mitigation measures and (5) measurement of heretofore unassessed E&P activities. In this study several marine mammal monitoring and mitigation programs associated with E&P projects are presented to further advance these themes. Topics being addressed include the use of autonomous camera systems for aerial monitoring of a narwhal population, long-term photo-identification studies of western gray whales to better understand site fidelity to their summer feeding grounds, mitigation of gray whales’ behavioral responses to a seismic survey near these feeding grounds and use of Passive Acoustic Monitoring to characterize seismic pulses and drilling activity as well as marine mammal presence in remote arctic areas. A synthesis of the main findings is provided that includes identification of future research needs. Conclusions and specific recommendations are made that will contribute to our ability to assess and mitigate risks of E&P sound to marine mammals.

Fin whales are the second largest mammals to roam across the oceans, often returning to the same feeding grounds every summer. In this PhD thesis, I used a different approach in each chapter to gain insight into how numbers, distribution, and connectivity of fin whales have changed over time. One approach to track fin whales over time is through the use of photo-identification, which identifies individuals based on unique pigmentation patterns and dorsal fin shapes. Based on the number of photographic recaptures, I detected a decline in the number of fin whales in the Gulf of St. Lawrence in eastern Canada from 2004 to 2016. This decline was likely the result of increased mortality or a shift in distribution. Another useful method to evaluate the extent of mixing among different groups of fin whales is the analysis of genetic profiles. For that purpose, over 1,500 genetic profiles from fin whales across the North Atlantic and Mediterranean Sea were compared. I found that differences in genetic profiles of fin whales increased with distance, suggesting that fin whales preferably mate with individuals from the same or neighbouring areas (albeit with exceptions). The composition of genetic profiles is also affected by historic events. Using this feature of genetic profiles, I described how past periods of extreme climatic fluctuations (e.g., during glaciation periods) influenced the amount of connectivity among fin whales from the Atlantic, Pacific, and Southern Ocean. Overall, this research highlighted the complex interplay between fin whale population trends and environmental conditions.

DNA can teach us many things about natural populations, for example, where they come from and how many there are, which is important for studying endangered species like sea turtles. Thanks to our DNA research on sea turtles, we learned that there is an increasing number of sea turtles in the sea near Bonaire that come from nesting colonies where nesting numbers are increasing thanks to succesful conservation. We also saw that sea currents near Madagascar had an important influence on the migration of young sea turtles: they move with the currents. We could also look in the past using DNA, at the evolution of sea turtles. Apparently, the ice ages had a major influence on sea turtles. When the earth started to cool down around 115 thousand years ago, sea turtles in the Atlantic Ocean became separated from their neighbors in the Southwest Indian Ocean. Because of this, their DNA slowly became more different over time during the previous ice age. The ice ages also influenced sea levels. The formation of land ice caused sea levels to drop. Sea levels were almost 120 meters lower than the present level during the peak of the previous ice age. Many shallow seas became exposed, wich resulted in less areas where sea turtles could feed. Less food apparently resulted in fewer sea turtles, because in their DNA we see, using mathematical models, a reduction in diversity during the last ice age!

The Western North-Pacific (WNP) gray whale feeding grounds are off the northeastern coast of Sakhalin Island, Russia and is comprised of a nearshore and offshore component that can be distinguished by both depth and location. Spatial movements of gray whales within their foraging grounds were examined based on 13 years of opportunistic vessel and shore-based photo-identification surveys. Site fidelity was assessed by examining annual return and resighting rates. Lagged Identification Rates (LIR) analyses were conducted to estimate the residency and transitional movement patterns within the two components of their feeding grounds. In total 243 individuals were identified from 2002-2014, among these were 94 calves. The annual return rate over the period 2002-2014 was 72%, excluding 35 calves only seen one year. Approximately 20% of the individuals identified from 2002-2010 were seen every year after their initial sighting (including eight individuals that returned for 13 consecutive years). The majority (239) of the WNP whales were observed in the nearshore area while only half (122) were found in the deeper offshore area. Within a foraging season, there was a significantly higher probability of gray whales moving from the nearshore to the offshore area. No mother-calf pairs, calves or yearlings were observed in the offshore area, which was increasingly used by mature animals. The annual return rates, and population growth rates that are primarily a result of calf production with little evidence of immigration, suggest that this population is demographically self-contained and that both the nearshore and offshore Sakhalin feeding grounds are critically important areas for their summer annual foraging activities. The nearshore habitat is also important for mother-calf pairs, younger individuals, and recently weaned calves. Nearshore feeding could also be energetically less costly compared to foraging in the deeper offshore habitat and provide more protection from predators, such as killer whales.

Sperm whales communicate using codas (stereotyped click sequences). Females and juveniles live in long‐term social units, and units with similar coda repertoires share vocal clan membership. Vocal clans exhibit culturally defined differences in their multilevel social structure. Here, we aimed to identify different social units among sperm whales in Mauritius in the southwestern Indian Ocean, and to describe and compare their coda repertoires to investigate the presence of different vocal clans. We conducted six boat‐based surveys between 2008 and 2013, during which 101 different individuals were photo‐identified. Analysis of associations between 22 resighted individuals divided them into four candidate social units, but a lack of resightings impedes solid delineation of social units. Based on number and rhythm of clicks, at least 24 discrete coda types were detected among 4,767 analyzed codas using two different classification methods. Comparison of coda repertoires recorded from seven sperm whale groupings revealed the possible existence of two sympatric vocal clans, but the size differences of recorded repertoires warrant caution of interpretation. To further evaluate social structuring and the presence of different vocal clans in this region, future surveys should aim at obtaining long‐term sighting and acoustic data, and cover a more extensive area.

Seafloor massive sulfide (SMS) deposits are commonly found at hydrothermal vents and recently gained the special interest of mining industries. These deposits contain valuable metals and methods are currently developed to mine deep sea SMS deposits. However, excavation of SMS deposits potentially pose a threat to benthic life at the mining site itself, and also in the surrounding environment with plumes of suspended sediment and fine-grained SMS debris created during deep sea mining activities being highlighted as one of the major threats to deep-sea benthic fauna. The benthic communities surrounding the vents are, however, poorly known. As they are often exposed to natural plumes studying such communities could provide valuable information on their resilience toward mining related plumes. The Rainbow hydrothermal vent site at the Mid-Atlantic Ridge is a site characterized by one of the largest continuous natural plumes, which is found persisting over an extensive area. Sediment and water samples were taken both upstream and downstream of the Rainbow hydrothermal vent. Approximately 25 km away from the vent reference sites were samples as well. In addition to detecting the plume itself, concentrations of major and trace-metals in the sediments were used as tracers for long time sustained plume influence. At all sites, we assessed benthic species composition and detected larvae. Metabarcoding methods were used to determine species composition. Benthic species composition in the sediment was shown to differ between all locations and was highly influenced by the plume's fall out. Arthropoda were more dominant closer to the vent whereas Annelida and Nematoda were more dominant at the reference locations. Conservation and restoration of all these communities after a deep sea mining event will be difficult due to the spatial variation of these benthic communities.

Marien benthische biodiversiteit, de diversiteit aan soorten die in de zeebodem leven, is van grote waarde voor het mariene ecosysteem. Echter, deze benthische biodiversiteit wordt bedreigd door anthropogene invloeden zoals habitatsveranderingen, vervuiling en (over-)bevissing. Om te kunnen anticiperen op zulke invloeden is het belangrijk om verandering in de benthische biodiversiteit te kunnen meten. Traditionele methodes, gebaseerd op morphologische taxonomie zijn vaak tijd-rovend en vereist een uitgebreide taxonomische kennis. In het afgelopen decennium zijn moleculaire methodes, zoals DNA metabarcoding, ontwikkelend tot een alternatieve methode. In mijn proefschrift heb ik onderzoek gedaan naar de toepassing van zulke metabarcoding methodes om de mariene bentische biodiversiteit te analyseren en menselijke invloeden op dit ecosysteem te kunnen meten. De resultaten in mijn proefschrift laten zien dat de metabarcoding methode een waardevolle methode is om antropogene effecten op de benthische biodiversiteit te bepalen. Vergeleken met traditionele morfologische werden met de metabarcoding methode dezelfde conclusies getrokken omtrent het antropogene effect. Met de metabarcoding methode was het bovendien mogelijk om dit effect voor een grotere groep soorten te laten zien. Echter, de metabarcoding methode heeft ook een aantal nadelen ten opzichte van de traditionele morfologische methode. Zo is het bijvoorbeeld lastig om soortgroepen te kwantificeren op zowel abundantie als biomassa en kunnen door hiaten in de referentie databank niet altijd alle DNA-sequenties worden vertaald in een taxonomische groep. De methode ontwikkeld zich nog altijd erg snel, en deze snelle ontwikkelingen zullen hopelijk in de toekomst huidige limiteringen overkomen en de methode een nog waardevolle aanvulling in het werkveld maken., The marine ecosystem is one of Earth’s most valuable natural resources and marine benthic communities are a crucial component of this ecosystem. However, benthic communities are under stress due to anthropogenic influences such as habitat alterations, overexploitation and pollution. To be able to anticipate on such changes, monitoring the benthic diversity in a consistent and reliable way is essential. Traditional methods for measuring biodiversity, using morphological taxonomy of individual specimens, is time-consuming and requires specialized taxonomic knowledge. In the past decade, molecular tools and more specific DNA metabarcoding has emerged as an alternative method for species identification. In this thesis I explored the application of metabarcoding methods to assess marine benthic biodiversity.The work I presented in this thesis showed that metabarcoding is a valuable approach to assess anthropogenic effects on marine benthic communities. Compared to traditional morphological taxonomy, the metabarcoding approach gave comparable outcomes regarding the impact of anthropogenic influences. Moreover, the metabarcoding approach was able to include more taxa in the assessment and hence increase the power of the analysis. However, the metabarcoding approach also has limitations compared to the traditional approach. For instance, quantitative analyses are limited and gaps in the reference library can lead to misidentifications of taxa. Nonetheless, rapid developments are still made for the metabarcoding approach and molecular approaches in general. These developments may soon overcome many of the limitations and will probably increase the value of this approach even further.

Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.

Heteroplasmy is defined as the presence of two or more different mitochondrial DNA (mtDNA) genomes in one individual. Heteroplasmy can arise from insertions or deletions (length heteroplasmy) or single nucleotide substitutions (point heteroplasmy). The phenomenon has been widely studied in humans and model species; however, reports from non-model species are rare, possibly because heteroplasmy was undetected or ignored during sequencing. Among cetaceans, a few studies have reported heteroplasmy and speculated on its possible effects, suggesting that heteroplasmy could be rare or simply ignored. The aim of the present study was to assess and confirm point heteroplasmies, as well as to determine their frequency in five baleen whale species. We analyzed 10,748 mtDNA sequence electropherograms of the mitochondrial control region obtained by Sanger sequencing. A pipeline was developed to detect potential heteroplasmy by analyzing chromatogram peak heights. Potential heteroplasmies were subsequently verified experimentally. A total of 7,882 samples were assessed, among which 326 (4,1%) presented potential point heteroplasmy at more than 35 different nucleotide positions. These results indicated that heteroplasmy is more frequent than previously reported. Several heteroplasmies were tracked across multiple generations, providing insights into the introduction of new mtDNA haplotypes. Ignoring heteroplasmy might bias relatedness analyses as well as estimates of genetic diversity and mtDNA mutation rates. Thus, it is extremely important to develop efficient ways to detect and verify heteroplasmy.

Currently, three stocks of sei whales (Balaenoptera borealis) are defined in the North Atlantic; the Nova Scotian, Iceland-Denmark Strait and Eastern North Atlantic stocks, which are mainly based upon historical catch and sighting data. We analyzed mitochondrial control region DNA (mtDNA) sequences and genotypes from 7 to 11 microsatellite loci in 87 samples from three sites in the North Atlantic; Iceland, the Gulf of Maine and the Azores, and compared against the North Pacific using 489 previously published samples. No statistically significant deviations from homogeneity were detected among the North Atlantic samples at mtDNA or microsatellite loci. The genealogy estimated from the mtDNA sequences revealed a clear division of the haplotypes into a North Atlantic and a North Pacific clade, with the exception of one haplotype detected in a single sample from the Azores, which was included in the North Pacific clade. Significant genetic divergence between the North Atlantic and North Pacific Oceans was detected (mtDNA ΦST = 0.72, microsatellite Weir and Cockerham’s ϴ = 0.20; p

Understanding how habitat quality in heterogeneous landscapes governs the distribution and fitness of individuals is a fundamental aspect of ecology. While mean individual fitness is generally considered a key to assessing habitat quality, a comprehensive understanding of habitat quality in heterogeneous landscapes requires estimates of dispersal rates among habitat types. The increasing accessibility of genomic approaches, combined with field-based demographic methods, provides novel opportunities for incorporating dispersal estimation into assessments of habitat quality. In this study, we integrated genomic kinship approaches with field-based estimates of fitness components and Approximate Bayesian Computation (ABC) procedures to estimate habitat-specific dispersal rates and characterize habitat quality in two-toed sloths (Choloepus hoffmanni) occurring in a Costa Rican agricultural ecosystem. Field-based observations indicated that birth and survival rates were similar in a sparsely-shaded cacao farm and adjacent cattle pasture-forest mosaic. Sloth density was threefold higher in pasture compared to cacao, whereas home range size and overlap were greater in cacao compared to pasture. Dispersal rates were similar between the two habitats, as estimated using ABC procedures applied to the spatial distribution of pairs of related individuals identified using 3,431 SNP and 11 microsatellite locus genotypes. Our results indicate that crops produced under a sparse overstory can, in some cases, constitute lower quality habitat than pasture-forest mosaics for sloths, perhaps because of differences in food resources or predator communities. Finally, our study demonstrates that integrating field-based demographic approaches with genomic methods can provide a powerful means for characterizing habitat quality for animal populations occurring in heterogeneous landscapes. This article is protected by copyright. All rights reserved.

SummaryThe Numeniini is a tribe of 13 wader species (Scolopacidae, Charadriiformes) of which seven are Near Threatened or globally threatened, including two Critically Endangered. To help inform conservation management and policy responses, we present the results of an expert assessment of the threats that members of this taxonomic group face across migratory flyways. Most threats are increasing in intensity, particularly in non-breeding areas, where habitat loss resulting from residential and commercial development, aquaculture, mining, transport, disturbance, problematic invasive species, pollution and climate change were regarded as having the greatest detrimental impact. Fewer threats (mining, disturbance, problematic native species and climate change) were identified as widely affecting breeding areas. Numeniini populations face the greatest number of non-breeding threats in the East Asian-Australasian Flyway, especially those associated with coastal reclamation; related threats were also identified across the Central and Atlantic Americas, and East Atlantic flyways. Threats on the breeding grounds were greatest in Central and Atlantic Americas, East Atlantic and West Asian flyways. Three priority actions were associated with monitoring and research: to monitor breeding population trends (which for species breeding in remote areas may best be achieved through surveys at key non-breeding sites), to deploy tracking technologies to identify migratory connectivity, and to monitor land-cover change across breeding and non-breeding areas. Two priority actions were focused on conservation and policy responses: to identify and effectively protect key non-breeding sites across all flyways (particularly in the East Asian- Australasian Flyway), and to implement successful conservation interventions at a sufficient scale across human-dominated landscapes for species’ recovery to be achieved. If implemented urgently, these measures in combination have the potential to alter the current population declines of many Numeniini species and provide a template for the conservation of other groups of threatened species.

From 25 to 30 August 2014 a double-observer line-transect survey was conducted over Melville Bay, home to one of two summering populations of narwhal (Monodon monoceros) off West Greenland. A total of 1,932 linear kilometers was surveyed along 33 transects. In addition to using observers, the aircraft was equipped with two oblique cameras to capture a comparable data set. Analysts reviewed the images for narwhal sightings, which were then matched to the observer sightings. The objectives of the study were to determine advantages and disadvantages of the detection capabilities of both methodologies, and to conduct a comparative analysis of population abundance estimates. Correcting for the truncated detection distance of the images (500 m), the image analysts recorded more sightings (62) and a lower mean group size (2.2) compared to aerial observers (36 and 3.5, respectively), resulting in comparable numbers of individuals detected by both platforms (135 vs. 126). The abundance estimate based on the image sightings was 2,536 (CV = 0.51, 95% CI: 1,003-6,406), which was not significantly different from the aerial observers estimate of 2,596 individuals (CV = 0.51; 95% CI: 961-7,008). This study supports the potential of using UAS for marine mammal abundance studies.

Knowing the migratory movements and behaviour of baleen whales is fundamental to understanding their ecology. We compared δ 15 N and δ 13 C values in the skin of blue ( Balaenoptera musculus ), fin ( Balaenoptera physalus ) and sei ( Balaenoptera borealis ) whales sighted in the Azores in spring with the values of potential prey from different regions within the North Atlantic using Bayesian mixing models to investigate their trophic ecology and migration patterns. Fin whale δ 15 N values were higher than those recorded in blue and sei whales, reflecting feeding at higher trophic levels. Whales' skin δ 15 N and δ 13 C values did not reflect prey from high-latitude summer foraging grounds; instead mixing models identified tropical or subtropical regions as the most likely feeding areas for all species during winter and spring. Yet, differences in δ 13 C values among whale species suggest use of different regions within this range. Blue and sei whales primarily used resources from the Northwest African upwelling and pelagic tropical/subtropical regions, while fin whales fed off Iberia. However, determining feeding habitats from stable isotope values remains difficult. In conclusion, winter feeding appears common among North Atlantic blue, fin and sei whales, and may play a crucial role in determining their winter distribution. A better understanding of winter feeding behaviour is therefore fundamental for the effective conservation of these species.

HighlightsMitochondrial monophyly is commonly employed to define evolutionary significant units.Monophyly may be caused by insufficient sampling or a recent common ancestor.Mitogenomic studies are generally based on few samples and prone to sampling issues.Expanded mitogenome sampling negates previous monophyly in fin whales.AbstractThe advent of massive parallel sequencing technologies has resulted in an increase of studies based upon complete mitochondrial genome DNA sequences that revisit the taxonomic status within and among species. Spatially distinct monophyly in mitogenomic genealogies, i.e., the sharing of a recent common ancestor among con-specific samples collected in the same region has been viewed as evidence for subspecies. Several recent studies in cetaceans have employed this criterion to suggest subsequent intraspecific taxonomic revisions. We reason that employing intra-specific, spatially distinct monophyly at non-recombining, clonally inherited genomes is an unsatisfactory criterion for defining subspecies based upon theoretical (genetic drift) and practical (sampling effort) arguments. This point is illustrated by a re-analysis of a global mitogenomic assessment of fin whales,Balaenoptera physalusspp., published by Archer et al. (2013) which proposed to further subdivide the Northern Hemisphere fin whale subspecies,B. p. physalus. The proposed revision was based upon the detection of spatially distinct monophyly among North Atlantic and North Pacific fin whales in a genealogy based upon complete mitochondrial genome DNA sequences. The extended analysis conducted in this study (1,676 mitochondrial control region, 162 complete mitochondrial genome DNA sequences and 20 microsatellite loci genotyped in 358 samples) revealed that the apparent monophyly among North Atlantic fin whales reported by Archer et al. (2013) to be due to low sample sizes. In conclusion, defining sub-species from monophyly (i.e., the absence of para-or polyphyly) can lead to erroneous conclusions due to relatively “trivial” aspects, such as sampling. Basic population genetic processes (i.e., genetic drift and migration) also affect the time to most recent common ancestor and hence the probability that individuals in a sample are monophyletic.

The interplay between environmental selection and available variation within a population are central in the adaptation of populations to changing environments, for seemingly all levels of complexity in life. In order to investigate properties and mode of actions of the two counterplayers, more and more studies have started to conduct experiments, that expose populations to different, non-optimal conditions and describe changes in phenotypic traits and genotypes observed. Whereas the extrinsic selection regimes surrounding the populations can easily be changed at will by the investigators and hereby serves the elucidation of the properties of selection, modifying the intrinsic genetic variation of the individuals remains challenging and less of an experimental subject so far. In order to investigate mechanisms that cause genetic mutations, we constructed bacterial strains, that harbour mutator genes on plasmids with an inducible expression system. We present results of the characterization of the mutator strains, as a first step towards understanding mutation mechanisms and their influence on standing genetic variation and subsequent adaptation, in order to complement the investigations on selection for a full picture of the driving forces in evolution.

A. Schleimer was supported by the Luxembourg National Research Fund (FNR; AFR/11256673). Estimates of abundance and survivorship provide quantifiable measures to monitor populations and to define and understand their conservation status. This study investigated changes in abundance and survival rates of fin whales (Balaenoptera physalus) in the northern Gulf of St. Lawrence in the context of anthropogenic pressures and changing environmental conditions. A long‐term data set, consisting of 35 years of photo‐identification surveys and comprising more than 5,000 identifications of 507 individuals, formed the basis of this mark–recapture study. Based on model selection using corrected Akaike Information Criterion, the most parsimonious Cormack–Jolly–Seber model included a linear temporal trend in noncalf apparent survival rates with a sharp decline in the last 5 years of the study and a median survival rate of 0.946 (95% confidence interval (CI) 0.910–0.967). To account for capture heterogeneity due to divergent patterns of site fidelity, agglomerative hierarchical cluster analysis was employed to categorize individuals based on their annual and survey site fidelity indices. However, the negative trend in survivorship remained and was corroborated by a significant decline in the estimated super‐population size from 335 (95% CI 321–348) individuals in 2004–2010 to 291 (95% CI 270–312) individuals in 2010–2016. Concurrently, a negative trend was estimated in recruitment to the population, supported by a sharp decrease in the number of observed calves. Ship strikes and changes in prey availability are potential drivers of the observed decline in fin whale abundance. The combination of clustering methods with mark–recapture represents a flexible way to investigate the effects of site fidelity on demographic variables and is broadly applicable to other individual‐based studies. Publisher PDF

Kubelka et al. (Reports, 9 November 2018, p. 680) claim that climate change has disrupted patterns of nest predation in shorebirds. They report that predation rates have increased since the 1950s, especially in the Arctic. We describe methodological problems with their analyses and argue that there is no solid statistical support for their claims. Fil: Bulla, Martin. Nioz Royal Netherlands Institute For Sea Research; Países Bajos. Max Planck Institute For Ornithology; Alemania. Czech University of Life Sciences; República Checa Fil: Reneerkens, Jeroen. Nioz Royal Netherlands Institute For Sea Research; Países Bajos. University of Groningen; Países Bajos Fil: Weiser, Emily L.. Upper Midwest Environmental Sciences Center; Estados Unidos Fil: Sokolov, Aleksandr. Institute Of Plant And Animal Ecology; Rusia Fil: Taylor, Audrey R.. University of Alaska; Estados Unidos Fil: Sittler, Benoît. Albert Ludwigs University of Freiburg; Alemania. Arctic Ecology Research Group; Francia Fil: McCaffery, Brian J.. U.S. Fish and Wildlife Service; Estados Unidos Fil: Ruthrauff, Dan R.. U.S. Geological Survey; Estados Unidos Fil: Catlin, Daniel H.. Virginia Tech University; Estados Unidos Fil: Payer, David C.. National Park Service; Estados Unidos Fil: Ward, David H.. U.S. Geological Survey; Estados Unidos Fil: Solovyeva, Diana V.. Institute of Biological Problems of the North; Rusia Fil: Santos, Eduardo S. A.. Universidade de São Paulo; Brasil Fil: Rakhimberdiev, Eldar. Lomonosov Moscow State University; Rusia. University of Groningen; Países Bajos Fil: Nol, Erica. Trent University; Canadá Fil: Kwon, Eunbi. Virginia Tech; Estados Unidos Fil: Brown, Glen S.. Ministry of Natural Resources and Forestry; Canadá Fil: Hevia, Glenda Denise. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; Argentina Fil: Gates, H. River. National Audubon Society; Estados Unidos Fil: Johnson, James A.. Fish and Wildlife Service; Estados Unidos Fil: van Gils, Jan A.. Department of Coastal Systems and Utrecht University; Países Bajos Fil: Hansen, Jannik. Aarhus University. Aarhus Institute Of Advanced Studies.; Dinamarca Fil: Lamarre, Jean-François. Polar Knowledge Canada; Canadá Fil: Rausch, Jennie. Environment and Climate Change Canada; Canadá Fil: Conklin, Jesse R.. University of Groningen; Países Bajos Fil: Liebezeit, Joe. Audubon Society of Portland; Estados Unidos Fil: Bêty, Joël. University of Quebec; Canadá Fil: Lang, Johannes. Arctic Ecology Research Group ; Francia. Giessen University; Alemania Fil: Alves, José A.. University of Aveiro; Portugal. University of Iceland; Islandia Fil: Fernández-Elipe, Juan. No especifíca; Fil: Exo, Klaus-Michael. Institute of Avian Research “Vogelwarte Helgoland"; Alemania Fil: Bollache, Loïc. Universite de Franche-Comte; Francia Fil: Bertellotti, Néstor Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; Argentina Fil: Giroux, Marie-Andrée. Université de Moncton; Canadá Fil: van de Pol, Martijn. Netherlands Institute of Ecology ; Países Bajos Fil: Johnson, Matthew. USDA Forest Service; Estados Unidos Fil: Boldenow, Megan L.. University of Alaska; Estados Unidos Fil: Valcu, Mihai. Max Planck Institute für Ornithologie; Alemania Fil: Soloviev, Mikhail. Lomonosov Moscow State University; Alemania Fil: Sokolova, Natalya. Arctic Research Station; Rusia Fil: Senner, Nathan R.. University of South Carolina; Estados Unidos Fil: Lecomte, Nicolas. Université de Moncton; Canadá Fil: Meyer, Nicolas. Universite de Franche-Comte; Francia. Arctic Ecology Research Group; Francia Fil: Schmidt, Niels Martin. Aarhus University. Department of Bioscience; Dinamarca Fil: Gilg, Olivier. Arctic Ecology Research Group; Francia. Universite de Franche-Comte; Francia Fil: Smith, Paul A.. Environment and Climate Change Canada; Canadá Fil: Machín, Paula. No especifíca; Fil: McGuire, Rebecca L.. Wildlife Conservation Society; Estados Unidos Fil: Cerboncini, Ricardo A. S.. Universidade Federal do Paraná; Brasil Fil: Ottvall, Richard. No especifíca; Fil: van Bemmelen, Rob S. A.. Wageningen Marine Research; Países Bajos Fil: Swift, Rose J.. Cornell University; Estados Unidos Fil: Saalfeld, Sarah T.. No especifíca; Fil: Jamieson,Sarah E.. Simon Fraser University; Canadá Fil: Brown, Stephen. No especifíca; Fil: Piersma, Theunis. NIOZ Royal Netherlands Institute for Sea Research; Países Bajos. Conservation Ecology Group; Países Bajos Fil: Albrecht, Tomas. Czech Academy of Sciences; República Checa. Charles University; República Checa Fil: D’Amico, Verónica. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Centro para el Estudio de Sistemas Marinos; Argentina Fil: Lanctot, Richard B.. U.S. Fish and Wildlife Service; Estados Unidos Fil: Kempenaers, Bart. Max Planck Institute für Ornithologie; Alemania

Metabarcoding of genetic material in environmental samples has increasingly been employed as a means to assess biodiversity, also of marine benthic communities. Current protocols employed to extract DNA from benthic samples and subsequent bioinformatics pipelines differ considerably. The present study compares three commonly deployed metabarcoding approaches against a morphological approach to assess benthic biodiversity in an intertidal bay in the Dutch Wadden Sea. Environmental DNA was extracted using three different approaches; extraction of extracellular DNA, extraction preceded by cell lysis of a sieved fraction of the sediment, and extraction of DNA directly from small amounts of sediment. DNA extractions after lysis of sieved sediment fractions best recovered the macrofauna diversity whereas direct DNA extraction of small amounts of sediment best recovered the meiofauna diversity. Extractions of extracellular DNA yielded the lowest number of OTUs per sample and hence an incomplete view of benthic biodiversity. An assessment of different bioinformatic pipelines and parameters was conducted using a mock sample with a known species composition. The RDP classifier performed better than BLAST for taxonomic assignment of the samples in this study. Novel metabarcodes obtained from local specimens were added to the SILVA 18S rRNA database to improve taxonomic assignment. This study provides recommendations for a general metabarcoding protocol for marine benthic surveys in the Wadden Sea.