Gut bacterial communities in Atlantic bottlenose dolphins (Tursiops truncatus) throughout a disease-driven (Morbillivirus) unusual mortality event

Gut microbiomes are important determinants of animal health. In sentinel marine mammals where animal and ocean health are connected, microbiome impacts can scale to ecosystem-level importance. Mass mortality events affect cetacean populations worldwide, yet little is known about the contributory role of their gut bacterial communities to disease susceptibility and progression. Here, we characterized bacterial communities from fecal samples of common bottlenose dolphins, Tursiops truncatus, across an unusual mortality event (UME) caused by dolphin Morbillivirus (DMV). 16S rRNA gene sequence analysis revealed similar diversity and structure of bacterial communities in individuals stranding before, during, and after the 2013-2015 Mid-Atlantic Bottlenose Dolphin UME and these trends held in a subset of dolphins tested by PCR for DMV infection. Fine-scale shifts related to the UME were not common (10 of 968 bacterial taxa) though potential biomarkers for health monitoring were identified within the complex bacterial communities. Accordingly, acute DMV infection was not associated with a distinct gut bacterial community signature in T. truncatus. However, temporal stratification of DMV-positive dolphins did reveal changes in bacterial community composition between early and late outbreak periods, suggesting that gut community disruptions may be amplified by the indirect effects of accumulating health burdens associated with chronic morbidity.

Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode of the process of parallel evolution remains debated. Here, we harness the temporal resolution of paleogenomics to address these long-standing questions, by comparing genomes originating from the mid-Holocene (8610-5626 years before present, BP) to contemporary pairs of coastal-pelagic ecotypes of bottlenose dolphin. We find that the affinity of ancient samples to coastal populations increases as the age of the samples decreases. We assess the youngest genome (5626 years BP) at sites previously inferred to be under parallel selection to coastal habitats and find it contained coastal-associated genotypes. Thus, coastal-associated variants rose to detectable frequencies close to the emergence of coastal habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic and coastal populations, sharing standing genetic variation that facilitated rapid adaptation to newly emerged coastal habitats.

The longest recorded movement of an inshore common bottlenose dolphin (Tursiops truncatus)

Information on movements and connectivity among populations of animals is important for the delineation of units to conserve, so that demographic parameters, such as abundance, fecundity and mortality, can be placed in an appropriate population and conservation context. Common bottlenose dolphins (Tursiops truncatus) are often considered relatively ‘resident’ and demonstrating strong site fidelity to specific areas. However, this perception may partly be an artefact of the distribution and ‘habitat use’ of cetacean researchers, rather than animals themselves, and bottlenose dolphins have been shown to be capable of substantial movements, often in relatively short periods of time. Here, we report on two long-distance movements of a common bottlenose dolphin within the Mediterranean Sea, across the Tyrrhenian, Ionian and Adriatic Seas, and subsequently back across all three seas to Ligurian Sea, making these the two longest recorded movement for this species in the Mediterranean Sea to date and some of the longest in the world. We also review published records of long-distance movements in this species worldwide. This study highlights the utility of photo-identification and the importance of regional data sharing. We argue that photo-identification comparisons are always worthwhile and the results are informative regardless of the presence or absence of matches, especially with the ongoing advances in automated matching software.

Patterns of association and distribution of estuarine-resident common bottlenose dolphins (Tursiops truncatus) in North Carolina, USA

The social structure of estuarine-resident bottlenose dolphins is complex and varied. Residing in habitats often utilized for resource exploitation, dolphins are at risk due to anthropogenic pressures while still federally protected. Effective conservation is predicated upon accurate abundance estimates. In North Carolina, two estuarine-resident stocks (demographically independent groups) of common bottlenose dolphin have been designated using spatiotemporal criteria. Both stocks are subjected to bycatch in fishing gear. The southern North Carolina estuarine stock was estimated at <200 individuals from surveys in 2006, which is outdated per US guidelines. Thus, we conducted a new capture-mark-recapture survey in 2018, identifying 547 distinct individuals, about three times higher than the prior abundance estimate. We compared those individuals to our long-term photo-identification catalog (1995–2018, n = 2,423 individuals), matching 228 individuals. Of those 228, 65 were also included in the 2013 abundance estimate for the northern North Carolina estuarine stock. Using sighting histories for all individuals in the long-term catalog, we conducted a social network analysis, which is independent of a priori stock assignments. The three primary clusters identified were inconsistent with current stock designations and not defined by spatiotemporal distribution. All three clusters had sighting histories in the estuary and on the coast, however, that with the highest within-cluster associations appeared to use estuarine waters more often. The within-cluster association strength was low for one cluster, possibly due to only part of that cluster inhabiting the southern North Carolina estuarine system. Between-cluster differences occurred in infestation rates by the pseudostalked barnacle, Xenobalanus globicipitis, but that did not predict clusters. We suggest the need to re-evaluate the stock structure of estuarine-resident common bottlenose dolphins in North Carolina and currently have insufficient information to assign an abundance estimate to a currently designated stock.

Molecular Assessments, Statistical Effectiveness Parameters and Genetic Structure of Captive Populations of Tursiops truncatus Using 15 STRs

Simple Summary

The bottlenose dolphins are one of the most used species in entertainment, assisted therapy, education, and research on welfare. However, their maintenance in captivity requires powerful and sensitive tools for preserving their diversity. The number of genetic markers for this purpose remains controversial, restraining the marine species’ genetic diversity determination. We aimed to select 15 hypervariable molecular markers whose statistical parameters were made in 210 captive dolphins from 18 Mexican centers to support their usefulness. The proposed set of markers allowed us to obtain a genetic fingerprint of each dolphin. Additionally, we identified the structure of the captive population, analyzing the groups according to the capture location. Such characterization is key for maintaining the captive species’ biodiversity rates within conservation and reintroduction programs. However, these 15 genetic markers can also be helpful for small- isolated populations, subspecies and other genera of endangered and vulnerable species.

Abstract

Genetic analysis is a conventional way of identifying and monitoring captive and wildlife species. Knowledge of statistical parameters reinforcing their usefulness and effectiveness as powerful tools for preserving diversity is crucial. Although several studies have reported the diversity of cetaceans such as Tursiops truncatus using microsatellites, its informative degree has been poorly reported. Furthermore, the genetic structure of this cetacean has not been fully studied. In the present study, we selected 15 microsatellites with which 210 dolphins were genetically characterized using capillary electrophoresis. The genetic assertiveness of this set of hypervariable markers identified one individual in the range of 6.927e¹³ to 1.806e¹⁶, demonstrating its substantial capability in kinship relationships. The genetic structure of these 210 dolphins was also determined regarding the putative capture origin; a genetic stratification (k = 2) was found. An additional dolphin group of undetermined origin was also characterized to challenge the proficiency of our chosen markers. The set of markers proposed herein could be a helpful tool to guarantee the maintenance of the genetic diversity rates in conservation programs both in Tursiops truncatus and across other odontocetes, Mysticeti and several genera of endangered and vulnerable species.

Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins

Studying repeated adaptation can provide insights into the mechanisms allowing species to adapt to novel environments. Here, we investigate repeated evolution driven by habitat specialization in the common bottlenose dolphin. Parapatric pelagic and coastal ecotypes of common bottlenose dolphins have repeatedly formed across the oceans. Analyzing whole genomes of 57 individuals, we find that ecotype evolution involved a complex reticulated evolutionary history. We find parallel linked selection acted upon ancient alleles in geographically distant coastal populations, which were present as standing genetic variation in the pelagic populations. Candidate loci evolving under parallel linked selection were found in ancient tracts, suggesting recurrent bouts of selection through time. Therefore, despite the constraints of small effective population size and long generation time on the efficacy of selection, repeated adaptation in long-lived social species can be driven by a combination of ecological opportunities and selection acting on ancestral standing genetic variation.

Population structure associated with bioregion and seasonal prey distribution for Indo-Pacific bottlenose dolphins (Tursiops aduncus) in South Africa

Many marine species exhibit fine-scale population structure despite high mobility and a lack of physical barriers to dispersal, but the evolutionary drivers of differentiation in these systems are generally poorly understood. Here we investigate the potential role of habitat transitions and seasonal prey distributions on the evolution of population structure in the Indo-Pacific bottlenose dolphin, Tursiops aduncus, off South Africa's coast, using double-digest restriction-site associated DNA sequencing. Population structure was identified between the eastern and southern coasts and correlated with the habitat transition between the temperate Agulhas (southern) and subtropical Natal (eastern) Bioregions, suggesting differentiation driven by resource specializations. Differentiation along the Natal coast was comparatively weak, but was evident in some analyses and varied depending on whether the samples were collected during or outside the seasonal sardine (Sardinops sagax) run. This local abundance of prey could influence the ranging patterns and apparent genetic structure of T. aduncus. These findings have significant and transferable management implications, most importantly in terms of differentiating populations inhabiting distinct bioregions and seasonal structural patterns within a region associated with the movement of prey resources.

Using the otolith sulcus to aid in prey identification and improve estimates of prey size in diet studies of a piscivorous predator

Diet studies are fundamental for understanding trophic connections in marine ecosystems. In the southeastern US, the common bottlenose dolphin Tursiops truncatus is the predominant marine mammal in coastal waters, but its role as a top predator has received little attention. Diet studies of piscivorous predators, like bottlenose dolphins, start with assessing prey otoliths recovered from stomachs or feces, but digestive erosion hampers species identification and underestimates fish weight (FW). To compensate, FW is often estimated from the least affected otoliths and scaled to other otoliths, which also introduces bias. The sulcus, an otolith surface feature, has a species-specific shape of its ostium and caudal extents, which is within the otolith edge for some species. We explored whether the sulcus could improve species identification and estimation of prey size using a case study of four sciaenid species targeted by fisheries and bottlenose dolphins in North Carolina. Methods were assessed first on otoliths from a reference collection (n = 421) and applied to prey otoliths (n = 5,308) recovered from 120 stomachs of dead stranded dolphins. We demonstrated in reference-collection otoliths that cauda to sulcus length (CL:SL) could discriminate between spotted seatrout (Cynoscion nebulosus) and weakfish (Cynoscion regalis) (classification accuracy = 0.98). This method confirmed for the first time predation of spotted seatrout by bottlenose dolphins in North Carolina. Using predictive models developed from reference-collection otoliths, we provided evidence that digestion affects otolith length more than sulcus or cauda length, making the latter better predictors. Lastly, we explored scenarios of calculating total consumed biomass across degrees of digestion. A suggested approach was for the least digested otoliths to be scaled to other otoliths iteratively from within the same stomach, month, or season as samples allow. Using the otolith sulcus helped overcome challenges of species identification and fish size estimation, indicating their potential use in other diet studies.

Ecological divergence and speciation in common bottlenose dolphins in the western South Atlantic

Coastal and offshore ecotypes of common bottlenose dolphins have been recognized in the western South Atlantic, and it is possible that trophic niche divergence associated with social interactions is leading them to genetic and phenotypic differentiation. The significant morphological differentiation observed between these ecotypes suggests they represent two different subspecies. However, there is still a need to investigate whether there is congruence between morphological and genetic data to rule out the possibility of ecophenotypic variation accompanied by gene flow. Mitochondrial DNA (mtDNA) control region sequence data and 10 microsatellite loci collected from stranded and biopsied dolphins sampled in coastal and offshore waters of Brazil as well as 106 skulls for morphological analyses were used to determine whether the morphological differentiation was supported by genetic differentiation. There was congruence among the data sets, reinforcing the presence of two distinct ecotypes. The divergence may be relatively recent, however, given the moderate values of mtDNA nucleotide divergence (dA = 0.008), presence of one shared mtDNA haplotype and possibly low levels of gene flow (around 1% of migrants per generation). Results suggest the ecotypes may be in the process of speciation and reinforce they are best described as two different subspecies until the degree of nuclear genetic divergence is thoroughly evaluated: Tursiops truncatus gephyreus (coastal ecotype) and T. t. truncatus (offshore ecotype). The endemic distribution of T. t. gephyreus in the western South Atlantic and number of anthropogenic threats in the area reinforces the importance of protecting this ecotype and its habitat.

Killer whales (Orcinus orca) in Iceland show weak genetic structure among diverse isotopic signatures and observed movement patterns

Local adaption through ecological niche specialization can lead to genetic structure between and within populations. In the Northeast Pacific, killer whales (Orcinus orca) of the same population have uniform specialized diets that are non-overlapping with other sympatric, genetically divergent, and socially isolated killer whale ecotypes. However, killer whales in Iceland show intrapopulation variation of isotopic niches and observed movement patterns: some individuals appear to specialize on herring and follow it year-round while others feed upon herring only seasonally or opportunistically. We investigated genetic differentiation among Icelandic killer whales with different isotopic signatures and observed movement patterns. This information is key for management and conservation purposes but also for better understanding how niche specialization drives genetic differentiation. Photo-identified individuals (N = 61) were genotyped for 22 microsatellites and a 611 bp portion of the mitochondrial DNA (mtDNA) control region. Photo-identification of individuals allowed linkage of genetic data to existing data on individual isotopic niche, observed movement patterns, and social associations. Population subdivision into three genetic units was supported by a discriminant analysis of principal components (DAPC). Genetic clustering corresponded to the distribution of isotopic signatures, mtDNA haplotypes, and observed movement patterns, but genetic units were not socially segregated. Genetic differentiation was weak (F ST < 0.1), suggesting ongoing gene flow or recent separation of the genetic units. Our results show that killer whales in Iceland are not as genetically differentiated, ecologically discrete, or socially isolated as the Northeast Pacific prey-specialized killer whales. If any process of ecological divergence and niche specialization is taking place among killer whales in Iceland, it is likely at a very early stage and has not led to the patterns observed in the Northeast Pacific.

Quantifying dispersal between marine protected areas by a highly mobile species, the bottlenose dolphin, Tursiops truncatus

The functioning of marine protected areas (MPAs) designated for marine megafauna has been criticized due to the high mobility and dispersal potential of these taxa. However, dispersal within a network of small MPAs can be beneficial as connectivity can result in increased effective population size, maintain genetic diversity, and increase robustness to ecological and environmental changes making populations less susceptible to stochastic genetic and demographic effects (i.e., Allee effect). Here, we use both genetic and photo-identification methods to quantify gene flow and demographic dispersal between MPAs of a highly mobile marine mammal, the bottlenose dolphin Tursiops truncatus. We identify three populations in the waters of western Ireland, two of which have largely nonoverlapping core coastal home ranges and are each strongly spatially associated with specific MPAs. We find high site fidelity of individuals within each of these two coastal populations to their respective MPA. We also find low levels of demographic dispersal between the populations, but it remains unclear whether any new gametes are exchanged between populations through these migrants (genetic dispersal). The population sampled in the Shannon Estuary has a low estimated effective population size and appears to be genetically isolated. The second coastal population, sampled outside of the Shannon, may be demographically and genetically connected to other coastal subpopulations around the coastal waters of the UK. We therefore recommend that the methods applied here should be used on a broader geographically sampled dataset to better assess this connectivity.

Genetic divergence and fine scale population structure of the common bottlenose dolphin (Tursiops truncatus, Montagu) found in the Gulf of Guayaquil, Ecuador

The common bottlenose dolphin, Tursiops truncatus, is widely distributed along the western coast of South America. In Ecuador, a resident population of bottlenose dolphins inhabits the inner estuarine area of the Gulf of Guayaquil located in the southwestern part of the country and is under threat from different human activities in the area. Only one genetic study on South American common bottlenose dolphins has been carried out to date, and understanding genetic variation of wildlife populations, especially species that are identified as threatened, is crucial for defining conservation units and developing appropriate conservation strategies. In order to evaluate the evolutionary link of this population, we assessed the phylogenetic relationships, phylogeographic patterns, and population structure using mitochondrial DNA (mtDNA). The sampling comprised: (i) 31 skin samples collected from free-ranging dolphins at three locations in the Gulf of Guayaquil inner estuary, (ii) 38 samples from stranded dolphins available at the collection of the “Museo de Ballenas de Salinas,” (iii) 549 mtDNA control region (mtDNA CR) sequences from GenBank, and (iv) 66 concatenated sequences from 7-mtDNA regions (12S rRNA, 16S rRNA, NADH dehydrogenase subunit I–II, cytochrome oxidase I and II, cytochrome b, and CR) obtained from mitogenomes available in GenBank. Our analyses indicated population structure between both inner and outer estuary dolphin populations as well as with distinct populations of T. truncatus using mtDNA CR. Moreover, the inner estuary bottlenose dolphin (estuarine bottlenose dolphin) population exhibited lower levels of genetic diversity than the outer estuary dolphin population according to the mtDNA CR. Finally, the estuarine bottlenose dolphin population was genetically distinct from other T. truncatus populations based on mtDNA CR and 7-mtDNA regions. From these results, we suggest that the estuarine bottlenose dolphin population should be considered a distinct lineage. This dolphin population faces a variety of anthropogenic threats in this area; thus, we highlight its fragility and urge authorities to issue prompt management and conservation measures.

Eco-Evolutionary Processes Generating Diversity Among Bottlenose Dolphin, Tursiops truncatus, Populations off Baja California, Mexico

For highly mobile species that nevertheless show fine-scale patterns of population genetic structure, the relevant evolutionary mechanisms determining structure remain poorly understood. The bottlenose dolphin (Tursiops truncatus) is one such species, exhibiting complex patterns of genetic structure associated with local habitat dependence in various geographic regions. Here we studied bottlenose dolphin populations in the Gulf of California and Pacific Ocean off Baja California where habitat is highly structured to test associations between ecology, habitat dependence and genetic differentiation. We investigated population structure at a fine geographic scale using both stable isotope analysis (to assess feeding ecology) and molecular genetic markers (to assess population structure). Our results show that there are at least two factors affecting population structure for both genetics and feeding ecology (as indicated by stable isotope profiles). On the one hand there is a signal for the differentiation of individuals by ecotype, one foraging more offshore than the other. At the same time, there is differentiation between the Gulf of California and the west coast of Baja California, meaning that for example, nearshore ecotypes were both genetically and isotopically differentiated either side of the peninsula. We discuss these data in the context of similar studies showing fine-scale population structure for delphinid species in coastal waters, and consider possible evolutionary mechanisms.

High genetic structure and low mitochondrial diversity in bottlenose dolphins of the Archipelago of Bocas del Toro, Panama: A population at risk?

The current conservation status of the bottlenose dolphin (Tursiops truncatus) under the IUCN is ‘least concern’. However, in the Caribbean, small and localized populations of the ‘inshore form’ may be at higher risk of extinction than the ‘worldwide distributed form’ due to a combination of factors including small population size, high site fidelity, genetic isolation, and range overlap with human activities. Here, we study the population genetic structure of bottlenose dolphins from the Archipelago of Bocas del Toro in Panama. This is a small population characterized by high site fidelity and is currently heavily-impacted by the local dolphin-watching industry. We collected skin tissue samples from 25 dolphins to study the genetic diversity and structure of this population. We amplified a portion of the mitochondrial Control Region (mtDNA-CR) and nine microsatellite loci. The mtDNA-CR analyses revealed that dolphins in Bocas del Toro belong to the ‘inshore form’, grouped with the Bahamas-Colombia-Cuba-Mexico population unit. They also possess a unique haplotype new for the Caribbean. The microsatellite data indicated that the Bocas del Toro dolphin population is highly structured, likely due to restricted movement patterns. Previous abundance estimates obtained with mark-recapture methods reported a small population of 80 dolphins (95% CI = 72–87), which is similar to the contemporary effective population size estimated in this study (Ne = 73 individuals; CI = 18.0 - ∞; 0.05). The combination of small population size, high degree of genetic isolation, and intense daily interactions with dolphin-watching boats puts the Bocas del Toro dolphin to at high risk of extinction. Despite national guidelines to regulate the dolphin-watching industry in Bocas del Toro and ongoing educational programs for tour operators, only in 2012 seven animals have died due to boat collisions. Our results suggest that the conservation status of bottlenose dolphins in Bocas del Toro should be elevated to ‘endangered’ at the national level, as a precautionary measure while population and viability estimates are conducted.

Genetic divergence between two phenotypically distinct bottlenose dolphin ecotypes suggests separate evolutionary trajectories

Due to their worldwide distribution and occupancy of different types of environments, bottlenose dolphins display considerable morphological variation. Despite limited understanding about the taxonomic identity of such forms and connectivity among them at global scale, coastal (or inshore) and offshore (or oceanic) ecotypes have been widely recognized in several ocean regions. In the Southwest Atlantic Ocean (SWA), however, there are scarce records of bottlenose dolphins differing in external morphology according to habitat preferences that resemble the coastal-offshore pattern observed elsewhere. The main aim of this study was to analyze the genetic variability, and test for population structure between coastal (n = 127) and offshore (n = 45) bottlenose dolphins sampled in the SWA to assess whether their external morphological distinction is consistent with genetic differentiation. We used a combination of mtDNA control region sequences and microsatellite genotypes to infer population structure and levels of genetic diversity. Our results from both molecular marker types were congruent and revealed strong levels of structuring (microsatellites FST = 0.385, p < .001; mtDNA FST =  0.183, p < .001; ΦST = 0.385, p < .001) and much lower genetic diversity in the coastal than the offshore ecotype, supporting patterns found in previous studies elsewhere. Despite the opportunity for gene flow in potential "contact zones", we found minimal current and historical connectivity between ecotypes, suggesting they are following discrete evolutionary trajectories. Based on our molecular findings, which seem to be consistent with morphological differentiations recently described for bottlenose dolphins in our study area, we recommend recognizing the offshore bottlenose dolphin ecotype as an additional Evolutionarily Significant Unit (ESU) in the SWA. Implications of these results for the conservation of bottlenose dolphins in SWA are also discussed.

Genetic diversity of bottlenose dolphin (Tursiops sp.) populations in the western North Pacific and the conservation implications

The evolutionary processes that shape patterns of diversity in highly mobile marine species are poorly understood, but important towards transferable inference on their effective conservation. In this study, bottlenose dolphins (Tursiops sp.) are studied to address this broader question. They exhibit remarkable geographical variation for morphology, life history, and genetic diversity, and this high level of variation has made the taxonomy of the genus controversial. A significant population structure has been reported for the most widely distributed species, the common bottlenose dolphin (T. truncatus), in almost all ocean basins, though no data have been available for the western North Pacific Ocean (WNP). The genetic diversity of bottlenose dolphins in the WNP was investigated based on 20 microsatellite and one mitochondrial DNA markers for samples collected from Taiwanese, Japanese, and Philippine waters (9°-39°N, 120°-140°E) during 1986-2012. The results indicated that there are at least four genetically differentiated populations of common bottlenose dolphins in the western and central North Pacific Ocean. The pattern of differentiation appears to correspond to habitat types, resembling results seen in other populations of the same species. Our analyses also showed that there was no evident gene flow between the two "sister species", the common bottlenose dolphins, and the Indo-Pacific bottlenose dolphins (T. aduncus) occurring sympatrically in our study region.

Population genetic structure of Guiana dolphin (Sotalia guianensis) from the southwestern Atlantic coast of Brazil

Sotalia guianensis is a small dolphin that is vulnerable to anthropogenic impacts. Along the Brazilian Atlantic coast, this species is threatened with extinction. A prioritized action plan for conservation strategies relies on increased knowledge of the population. The scarcity of studies about genetic diversity and assessments of population structure for this animal have precluded effective action in the region. Here, we assessed, for the first time, the genetic differentiation at 14 microsatellite loci in 90 S. guianensis specimens stranded on the southeastern Atlantic coast of the State of Espírito Santo, Brazil. We estimated population parameters and structure, measured the significance of global gametic disequilibrium and the intensity of non-random multiallelic interallelic associations and constructed a provisional synteny map using Bos taurus, the closest terrestrial mammal with a reference genome available. All microsatellite loci were polymorphic, with at least three and a maximum of ten alleles each. Allele frequencies ranged from 0.01 to 0.97. Observed heterozygosity ranged from 0.061 to 0.701. The mean inbreeding coefficient was 0.103. Three loci were in Hardy-Weinberg disequilibrium even when missing genotypes were inferred. Although 77 of the 91 possible two-locus associations were in global gametic equilibrium, we unveiled 13 statistically significant, sign-based, non-random multiallelic interallelic associations in 10 two-locus combinations with either coupling (D' values ranging from 0.782 to 0.353) or repulsion (D' values -0.517 to -1.000) forces. Most of the interallelic associations did not involve the major alleles. Thus, for either physically or non-physically linked loci, measuring the intensity of non-random interallelic associations is important for defining the evolutionary forces at equilibrium. We uncovered a small degree of genetic differentiation (F_ST = 0.010; P-value = 0.463) with a hierarchical clustering into one segment containing members from the southern and northern coastal regions. The data thus support the scenario of little genetic structure in the population of S. guianensis in this geographic area.

Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise

The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-by-distance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.

Historical dimensions of population structure in a continuously distributed marine species: The case of the endemic Chilean dolphin

The complementarity of historical and contemporary processes contributes to understanding the genetic structure of continuously distributed marine species with high dispersal capabilities. Cephalorhynchus eutropia, has a continuous coastal distribution with strong genetic differentiation identified by nuclear DNA markers. We explored the historical dimension of this genetic differentiation between northern and southern populations to evaluate phylogeographic structure. Additionally, we conducted mtDNA and microsatellite analyses to detect past and recent demographic changes. The southern population was characterized by lower genetic diversity with a signal of population expansion, likely associated with ice retreat and habitat extension after the Last Glacial Maximum (LGM). In contrast, structure within the northern population was more consistent with stable historical population size. Approximate Bayesian Computation analyses suggested that during the LGM, C. eutropia persisted in the northern area; while the south was colonized by dispersal ~11,000 years ago followed by population expansion. This study shows that Chilean dolphin population structure is consistent with predictions from the Expansion-Contraction biogeographic model, with a poleward post-glacial shift revealed in current genetic structure. The results also confirm the validity of the population units previously identified, demonstrating their historical origin and highlighting the utility of integrating genetic markers with different temporal scale resolutions.

Partially observed epidemics in wildlife hosts: modelling an outbreak of dolphin morbillivirus in the northwestern Atlantic, June 2013-2014

Morbilliviruses cause major mortality in marine mammals, but the dynamics of transmission and persistence are ill understood compared to terrestrial counterparts such as measles; this is especially true for epidemics in cetaceans. However, the recent outbreak of dolphin morbillivirus in the northwestern Atlantic Ocean can provide new insights into the epidemiology and spatio-temporal spread of this pathogen. To deal with uncertainties surrounding the ecology of this system (only stranded animals were observed), we develop a statistical framework that can extract key information about the underlying transmission process given only sparse data. Our self-exciting Poisson process model suggests that individuals are infectious for at most 24 days and can transfer infection up to two latitude degrees (220 km) within this time. In addition, the effective reproduction number is generally below one, but reaches 2.6 during a period of heightened stranding numbers near Virginia Beach, Virginia, in summer 2013. Network analysis suggests local movements dominate spatial spread, with seasonal migration facilitating wider dissemination along the coast. Finally, a low virus transmission rate or high levels of pre-existing immunity can explain the lack of viral spread into the Gulf of Mexico. More generally, our approach illustrates novel methodologies for analysing very indirectly observed epidemics.

Comparative phylogeography of black mangroves (Avicennia germinans) and red mangroves (Rhizophora mangle) in Florida: Testing the maritime discontinuity in coastal plants

PREMISE OF THE STUDY

Previous studies of the comparative phylogeography of coastal and marine species in the southeastern United States revealed that phylogenetically diverse taxa share a phylogeographic break at the southern tip of Florida (the maritime discontinuity). These studies have focused nearly exclusively on animals; few coastal plant species in Florida have been analyzed phylogeographically. We investigated phylogeographic patterns of black mangroves (Avicennia germinans) and red mangroves (Rhizophora mangle), two coastal trees that occur on both coasts of the peninsula of Florida.

METHODS

We sampled and genotyped 150 individuals each of A. germinans and R. mangle, using eight microsatellite loci per species. We used observed and expected heterozygosity to quantify genetic diversity in each sampling location and allele frequencies to identify putative phylogeographic breaks and measure gene flow using BayesAss and Migrate-n. We tested the hypothesis that both species would exhibit a phylogeographic break at the southern tip of Florida.

KEY RESULTS

We did not find any significant phylogeographic breaks in either species. Rhizophora mangle exhibits greater genetic structure than A. germinans, contrary to expectations based on propagule dispersal capability. However, directional gene flow from the Gulf to the Atlantic was more pronounced in R. mangle, indicating that the Gulf Stream may affect genetic patterns in R. mangle more than in A. germinans.

CONCLUSIONS

The high dispersal capability of these species may lead to high genetic connectivity between sampling locations and little geographic structure. We also identified several locations that, based on genetic data, should be the focus of conservation efforts.

Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico

Cetaceans are protected worldwide but vulnerable to incidental harm from an expanding array of human activities at sea. Managing potential hazards to these highly-mobile populations increasingly requires a detailed understanding of their seasonal distributions and habitats. Pursuant to the urgent need for this knowledge for the U.S. Atlantic and Gulf of Mexico, we integrated 23 years of aerial and shipboard cetacean surveys, linked them to environmental covariates obtained from remote sensing and ocean models, and built habitat-based density models for 26 species and 3 multi-species guilds using distance sampling methodology. In the Atlantic, for 11 well-known species, model predictions resembled seasonal movement patterns previously suggested in the literature. For these we produced monthly mean density maps. For lesser-known taxa, and in the Gulf of Mexico, where seasonal movements were less well described, we produced year-round mean density maps. The results revealed high regional differences in small delphinoid densities, confirmed the importance of the continental slope to large delphinoids and of canyons and seamounts to beaked and sperm whales, and quantified seasonal shifts in the densities of migratory baleen whales. The density maps, freely available online, are the first for these regions to be published in the peer-reviewed literature.

Seasonal variation in the skin transcriptome of common bottlenose dolphins (Tursiops truncatus) from the northern Gulf of Mexico

As long-lived predators that integrate exposures across multiple trophic levels, cetaceans are recognized as sentinels for the health of marine ecosystems. Their utility as sentinels requires the establishment of baseline health parameters. Because cetaceans are protected, measurements obtained with minimal disruption to free ranging animals are highly desirable. In this study we investigated the utility of skin gene expression profiling to monitor health and contaminant exposure in common bottlenose dolphins (Tursiops truncatus). Remote integument biopsies were collected in the northern Gulf of Mexico prior to the Deepwater Horizon oil spill (May 2010) and during summer and winter for two years following oil contamination (2010-2011). A bottlenose dolphin microarray was used to characterize the skin transcriptomes of 94 individuals from three populations: Barataria Bay, Louisiana, Chandeleur Sound, Louisiana, and Mississippi Sound, Mississippi/Alabama. Skin transcriptomes did not differ significantly between populations. In contrast, season had a profound effect on gene expression, with nearly one-third of all genes on the array differing in expression between winter and the warmer seasons (moderated T-test; p<0.01, fold-change≥1.5). Persistent organic pollutants (POPs) in blubber changed concurrently, reaching >two-fold higher concentrations in summer compared to winter, due to a seasonal decrease in blubber thickness and loss of stored lipid. However, global gene expression did not correlate strongly with seasonally changing contaminant concentrations, most likely because the refractory, lipid-stored metabolites are not substrates for phase I or II xenobiotic detoxification pathways. Rather, processes related to cell proliferation, motility, and differentiation dominated the differences in expression in winter and the warmer seasons. More subtle differences were seen between spring and summer (1.5% of genes differentially expressed). However, two presumed oil-exposed animals from spring presented gene expression profiles more similar to the summer animals (presumed exposed) than to other spring animals. Seasonal effects have not previously been considered in studies assessing gene expression in cetaceans, but clearly must be taken into account when applying transcriptomic analyses to investigate their contaminant exposure or health status.

Adrenal Hormones in Common Bottlenose Dolphins (Tursiops truncatus): Influential Factors and Reference Intervals

Inshore common bottlenose dolphins (Tursiops truncatus) are exposed to a broad spectrum of natural and anthropogenic stressors. In response to these stressors, the mammalian adrenal gland releases hormones such as cortisol and aldosterone to maintain physiological and biochemical homeostasis. Consequently, adrenal gland dysfunction results in disruption of hormone secretion and an inappropriate stress response. Our objective herein was to develop diagnostic reference intervals (RIs) for adrenal hormones commonly associated with the stress response (i.e., cortisol, aldosterone) that account for the influence of intrinsic (e.g., age, sex) and extrinsic (e.g., time) factors. Ultimately, these reference intervals will be used to gauge an individual's response to chase-capture stress and could indicate adrenal abnormalities. Linear mixed models (LMMs) were used to evaluate demographic and sampling factors contributing to differences in serum cortisol and aldosterone concentrations among bottlenose dolphins sampled in Sarasota Bay, Florida, USA (2000-2012). Serum cortisol concentrations were significantly associated with elapsed time from initial stimulation to sample collection (p<0.05), and RIs were constructed using nonparametric methods based on elapsed sampling time for dolphins sampled in less than 30 minutes following net deployment (95% RI: 0.91-4.21 µg/dL) and following biological sampling aboard a research vessel (95% RI: 2.32-6.68 µg/dL). To examine the applicability of the pre-sampling cortisol RI across multiple estuarine stocks, data from three additional southeast U.S. sites were compared, revealing that all of the dolphins sampled from the other sites (N = 34) had cortisol concentrations within the 95th percentile RI. Significant associations between serum concentrations of aldosterone and variables reported in previous studies (i.e., age, elapsed sampling time) were not observed in the current project (p<0.05). Also, approximately 16% of Sarasota Bay bottlenose dolphin aldosterone concentrations were below the assay's detection limit (11 pg/mL), thus hindering the ability to derive 95th percentile RIs. Serum aldosterone concentrations from animals sampled at the three additional sites were compared to the detection limit, and the proportion of animals with low aldosterone concentrations was not significantly different than an expected prevalence of 16%. Although this study relied upon long-term, free-ranging bottlenose dolphin health data from a single site, the objective RIs can be used for future evaluation of adrenal function among individuals sampled during capture-release health assessments.

Microsatellite markers reveal strong genetic structure in the endemic Chilean dolphin

Understanding genetic differentiation and speciation processes in marine species with high dispersal capabilities is challenging. The Chilean dolphin, Cephalorhynchus eutropia, is the only endemic cetacean of Chile and is found in two different coastal habitats: a northern habitat with exposed coastlines, bays and estuaries from Valparaíso (33°02′S) to Chiloé (42°00′S), and a southern habitat with highly fragmented inshore coastline, channels and fjords between Chiloé and Navarino Island (55°14′S). With the aim of evaluating the potential existence of conservation units for this species, we analyzed the genetic diversity and population structure of the Chilean dolphin along its entire range. We genotyped 21 dinucleotide microsatellites for 53 skin samples collected between 1998 and 2012 (swab: n = 8, biopsy: n = 38, entanglement n = 7). Bayesian clustering and spatial model analyses identified two genetically distinct populations corresponding to the northern and southern habitats. Genetic diversity levels were similar in the two populations (He: 0.42 v/s 0.45 for southern and northern populations, respectively), while effective size population was higher in the southern area (Ne: 101 v/s 39). Genetic differentiation between these two populations was high and significant (F_ST = 0.15 and R_ST = 0.19), indicating little or no current gene flow. Because of the absence of evident geographical barriers between the northern and southern populations, we propose that genetic differentiation may reflect ecological adaptation to the different habitat conditions and resource uses. Therefore, the two genetic populations of this endemic and Near Threatened species should be considered as different conservation units with independent management strategies.

Cetacean morbillivirus: current knowledge and future directions

We review the molecular and epidemiological characteristics of cetacean morbillivirus (CeMV) and the diagnosis and pathogenesis of associated disease, with six different strains detected in cetaceans worldwide. CeMV has caused epidemics with high mortality in odontocetes in Europe, the USA and Australia. It represents a distinct species within the Morbillivirus genus. Although most CeMV strains are phylogenetically closely related, recent data indicate that morbilliviruses recovered from Indo-Pacific bottlenose dolphins (Tursiops aduncus), from Western Australia, and a Guiana dolphin (Sotalia guianensis), from Brazil, are divergent. The signaling lymphocyte activation molecule (SLAM) cell receptor for CeMV has been characterized in cetaceans. It shares higher amino acid identity with the ruminant SLAM than with the receptors of carnivores or humans, reflecting the evolutionary history of these mammalian taxa. In Delphinidae, three amino acid substitutions may result in a higher affinity for the virus. Infection is diagnosed by histology, immunohistochemistry, virus isolation, RT-PCR, and serology. Classical CeMV-associated lesions include bronchointerstitial pneumonia, encephalitis, syncytia, and lymphoid depletion associated with immunosuppression. Cetaceans that survive the acute disease may develop fatal secondary infections and chronic encephalitis. Endemically infected, gregarious odontocetes probably serve as reservoirs and vectors. Transmission likely occurs through the inhalation of aerosolized virus but mother to fetus transmission was also reported.

Review of historical unusual mortality events (UMEs) in the Gulf of Mexico (1990-2009): providing context for the multi-year northern Gulf of Mexico cetacean UME declared in 2010

An unusual mortality event (UME) was declared for cetaceans in the northern Gulf of Mexico (GoM) for Franklin County, Florida, west through Louisiana, USA, beginning in February 2010 and was ongoing as of September 2014. The 'Deepwater Horizon' (DWH) oil spill began on 20 April 2010 in the GoM, raising questions regarding the potential role of the oil spill in the UME. The present study reviews cetacean mortality events that occurred in the GoM prior to 2010 (n = 11), including causes, durations, and some specific test results, to provide a historical context for the current event. The average duration of GoM cetacean UMEs prior to 2010 was 6 mo, and the longest was 17 mo (2005-2006). The highest number of cetacean mortalities recorded during a previous GoM event was 344 (in 1990). In most previous events, dolphin morbillivirus or brevetoxicosis was confirmed or suspected as a causal factor. In contrast, the current northern GoM UME has lasted more than 48 mo and has had more than 1000 reported mortalities within the currently defined spatial and temporal boundaries of the event. Initial results from the current UME do not support either morbillivirus or brevetoxin as primary causes of this event. This review is the first summary of cetacean UMEs in the GoM and provides evidence that the most common causes of previous UMEs are unlikely to be associated with the current UME.

Lack of variation in voltage-gated sodium channels of common bottlenose dolphins (Tursiops truncatus) exposed to neurotoxic algal blooms

In coastal marine ecosystems, neurotoxins produced by harmful algal blooms (HABs) often result in large-scale mortality events of many marine species. Historical and frequent exposure to HABs therefore may provide a strong selective pressure for adaptations that result in toxin resistance. Neurotoxin resistance has independently evolved in a variety of terrestrial and marine species via mutations in genes encoding the toxin binding sites within the voltage-gated sodium channel gene complex. Accordingly, we tested the hypothesis that genetic variation in the putative binding site of brevetoxins in common bottlenose dolphins (Tursiops truncatus) explains differences among individuals or populations in resistance to harmful Karenia brevis blooms in the Gulf of Mexico. We found very little variation in the sodium channel exons encoding the putative brevetoxin binding site among bottlenose dolphins from central-west Florida and the Florida Panhandle. Our study included samples from several bottlenose dolphin mortality events associated with HABs, but we found no association between genetic variation and survival. We observed a significant effect of geographic region on genetic variation for some sodium channel isoforms, but this can be primarily explained by rare private alleles and is more likely a reflection of regional genetic differentiation than the cause of different levels of HAB resistance between regions. In contrast to many other previously studied neurotoxin-resistant species, we conclude that bottlenose dolphins have not evolved resistance to HABs via mutations in genes encoding the brevetoxin binding site on the voltage-gated sodium channels.

Population differentiation and hybridisation of Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins in north-western Australia

Little is known about the Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins (‘snubfin’ and ‘humpback dolphins’, hereafter) of north-western Australia. While both species are listed as ‘near threatened’ by the IUCN, data deficiencies are impeding rigorous assessment of their conservation status across Australia. Understanding the genetic structure of populations, including levels of gene flow among populations, is important for the assessment of conservation status and the effective management of a species. Using nuclear and mitochondrial DNA markers, we assessed population genetic diversity and differentiation between snubfin dolphins from Cygnet (n = 32) and Roebuck Bays (n = 25), and humpback dolphins from the Dampier Archipelago (n = 19) and the North West Cape (n = 18). All sampling locations were separated by geographic distances >200 km. For each species, we found significant genetic differentiation between sampling locations based on 12 (for snubfin dolphins) and 13 (for humpback dolphins) microsatellite loci (F_ST = 0.05–0.09; P<0.001) and a 422 bp sequence of the mitochondrial control region (F_ST = 0.50–0.70; P<0.001). The estimated proportion of migrants in a population ranged from 0.01 (95% CI 0.00–0.06) to 0.13 (0.03–0.24). These are the first estimates of genetic diversity and differentiation for snubfin and humpback dolphins in Western Australia, providing valuable information towards the assessment of their conservation status in this rapidly developing region. Our results suggest that north-western Australian snubfin and humpback dolphins may exist as metapopulations of small, largely isolated population fragments, and should be managed accordingly. Management plans should seek to maintain effective population size and gene flow. Additionally, while interactions of a socio-sexual nature between these two species have been observed previously, here we provide strong evidence for the first documented case of hybridisation between a female snubfin dolphin and a male humpback dolphin.

Patterns of population structure for inshore bottlenose dolphins along the eastern United States

Globally distributed, the bottlenose dolphin (Tursiops truncatus) is found in a range of offshore and coastal habitats. Using 15 microsatellite loci and mtDNA control region sequences, we investigated patterns of genetic differentiation among putative populations along the eastern US shoreline (the Indian River Lagoon, Florida, and Charleston Harbor, South Carolina) (microsatellite analyses: n = 125, mtDNA analyses: n = 132). We further utilized the mtDNA to compare these populations with those from the Northwest Atlantic, Gulf of Mexico, and Caribbean. Results showed strong differentiation among inshore, alongshore, and offshore habitats (ФST = 0.744). In addition, Bayesian clustering analyses revealed the presence of 2 genetic clusters (populations) within the 250 km Indian River Lagoon. Habitat heterogeneity is likely an important force diversifying bottlenose dolphin populations through its influence on social behavior and foraging strategy. We propose that the spatial pattern of genetic variation within the lagoon reflects both its steep longitudinal transition of climate and also its historical discontinuity and recent connection as part of Intracoastal Waterway development. These findings have important management implications as they emphasize the role of habitat and the consequence of its modification in shaping bottlenose dolphin population structure and highlight the possibility of multiple management units existing in discrete inshore habitats along the entire eastern US shoreline.

Spatial distribution of bottlenose dolphins (Tursiops truncatus) inferred from stable isotopes and priority organic pollutants

Differences in priority organic pollutants (POPs), analyzed by gas chromatography-mass spectrometry, and stable isotope ratios (δ(13)C, δ(34)S, and δ(15)N; analyzed by isotope ratio-mass spectrometry), divide 77 bottlenose dolphins (Tursiops truncatus) from the Florida Gulf Coast into three distinct groups. POP levels reflect human population and historical contamination along the coast. In the least disturbed site, concentrations of ΣPOP in male dolphins were 18,000 ng g(-1)±6000 (95% confidence interval here and throughout); in the intermediate bay, males had ΣPOP concentrations of 19,000 ng g(-1)±10,000. St Andrews Bay was home to dolphins with the highest ΣPOP concentrations: 44,000 ng g(-1)±10,300. δ(34)S and δ(15)N, differed significantly between St. George Sound dolphins and those frequenting each of the other two bays, but not between St. Andrews and St. Joseph Bays. ΣPOP concentrations were statistically higher in dolphins frequenting St. Andrews Bay, but were not significantly different between dolphins occupying St. Joseph Bay and St. George Sound. Thus, using either POP or isotope values alone, we would only be able to identify two dolphin groups, but when POP and isotope data are viewed cumulatively, the results clearly define three distinct communities occupying this region.

Bottlenose dolphins as indicators of persistent organic pollutants in the western North Atlantic Ocean and northern Gulf of Mexico

Persistent organic pollutants (POPs) including legacy POPs (PCBs, chlordanes, mirex, DDTs, HCB, and dieldrin) and polybrominated diphenyl ether (PBDE) flame retardants were determined in 300 blubber biopsy samples from coastal and near shore/estuarine male bottlenose dolphins (Tursiops truncatus) sampled along the U.S. East and Gulf of Mexico coasts and Bermuda. Samples were from 14 locations including urban and rural estuaries and near a Superfund site (Brunswick, Georgia) contaminated with the PCB formulation Aroclor 1268. All classes of legacy POPs in estuarine stocks varied significantly (p < 0.05) among sampling locations. POP profiles in blubber varied by location with the most characteristic profile observed in bottlenose dolphins sampled near the Brunswick and Sapelo estuaries along the Georgia coast which differed significantly (p < 0.001) from other sites. Here and in Sapelo, PCB congeners from Aroclor 1268 dominated indicating widespread food web contamination by this PCB mixture. PCB 153, which is associated with non-Aroclor 1268 PCB formulations, correlated significantly to human population indicating contamination from a general urban PCB source. Factors influencing regional differences of other POPs were less clear and warrant further study. This work puts into geographical context POP contamination in dolphins to help prioritize efforts examining health effects from POP exposure in bottlenose dolphins.

Thar she blows! A novel method for DNA collection from cetacean blow

Background

Molecular tools are now widely used to address crucial management and conservation questions. To date, dart biopsying has been the most commonly used method for collecting genetic data from cetaceans; however, this method has some drawbacks. Dart biopsying is considered inappropriate for young animals and has recently come under scrutiny from ethical boards, conservationists, and the general public. Thus, identifying alternative genetic collection techniques for cetaceans remains a priority, especially for internationally protected species.

Methodology/Principal Findings

In this study, we investigated whether blow-sampling, which involves collecting exhalations from the blowholes of cetaceans, could be developed as a new less invasive method for DNA collection. Our current methodology was developed using six bottlenose dolphins, Tursiops truncatus, housed at the National Aquarium, Baltimore (USA), from which we were able to collect both blow and blood samples. For all six individuals, we found that their mitochondrial and microsatellite DNA profile taken from blow, matched their corresponding mitochondrial and microsatellite DNA profile collected from blood. This indicates that blow-sampling is a viable alternative method for DNA collection.

Conclusion/Significance

In this study, we show that blow-sampling provides a viable and less invasive method for collection of genetic data, even for small cetaceans. In contrast to dart biopsying, the advantage of this method is that it capitalizes on the natural breathing behaviour of dolphins and can be applied to even very young dolphins. Both biopsy and blow-sampling require close proximity of the boat, but blow-sampling can be achieved when dolphins voluntarily bow-ride and involves no harmful contact.

The confounding effects of population structure, genetic diversity and the sampling scheme on the detection and quantification of population size changes

The idea that molecular data should contain information on the recent evolutionary history of populations is rather old. However, much of the work carried out today owes to the work of the statisticians and theoreticians who demonstrated that it was possible to detect departures from equilibrium conditions (e.g., panmictic population/mutation-drift equilibrium) and interpret them in terms of deviations from neutrality or stationarity. During the last 20 years the detection of population size changes has usually been carried out under the assumption that samples were obtained from populations that can be approximated by a Wright-Fisher model (i.e., assuming panmixia, demographic stationarity, etc.). However, natural populations are usually part of spatial networks and are interconnected through gene flow. Here we simulated genetic data at mutation and migration-drift equilibrium under an n-island and a stepping-stone model. The simulated populations were thus stationary and not subject to any population size change. We varied the level of gene flow between populations and the scaled mutation rate. We also used several sampling schemes. We then analyzed the simulated samples using the Bayesian method implemented in MSVAR, the Markov Chain Monte Carlo simulation program, to detect and quantify putative population size changes using microsatellite data. Our results show that all three factors (genetic differentiation/gene flow, genetic diversity, and the sampling scheme) play a role in generating false bottleneck signals. We also suggest an ad hoc method to counter this effect. The confounding effect of population structure and of the sampling scheme has practical implications for many conservation studies. Indeed, if population structure is creating "spurious" bottleneck signals, the interpretation of bottleneck signals from genetic data might be less straightforward than it would seem, and several studies may have overestimated or incorrectly detected bottlenecks in endangered species.