Breed Structures of for Conservation of Middle Rare Pigs: Implications the Berkshire, Tamworth, White, Large Black, Gloucester Old Spot, British Saddleback, and British Lop

Abstract: Registration details of seven rare British breeds of pig w e studied over the period 1978–1986 inclusive. For four breeds, numbers of pigs registered have shown a slight upward trend. About 70% of males and 40% of females that breed, do so in herds other than the natal herd In the breed for which most pedigree data were analysed (the British Lop), 95–100% of recent pig crops were inbred In the rare breeds generally, mean inbreeding at around 6% signifies an inbreeding rate of about 1 % per generation, higher than has been found in commercial breeds. Breeds did not differ greatly in the ways they were structured.
About a third of herds supplied boars to other herds, a relatively high proportion, indicating that the breeds have a structure that is not completely hierarchical, and this is favorable for genetic conservation. Pigs whose parents were from different herds were significantly less inbred than those with both parents from the same herd In some breeds it was clear that pigs sharing the same bloodline name were more closely related than pigs within the same herd but with different bloodline names.
Conservation procedures applied to these pigs have been designed to conform with the customs and procedures of the British pedigree livestock industry. The most important single such procedure is the registration, with a central authority, of breeding stock.     

A Framework for Prioritizing Domestic Animal Breeds for Conservation Purposes at the National Level: a Norwegian Case Study

Abstract: Although encompassing only a handful of species, domestic animals have had profound effects on food production for humankind and on human societies. On a global basis, a large proportion of breeds are currently in danger of becoming extinct in the near future. At this critical time, resources are limited and only a selected number of breeds may be supported by concrete conservation programs. I present a framework to facilitate decision making on a national level as to which breeds to support for conservation. These decisions should be made by a national committee of experts experienced with the different breeds and species. First, they must define the species of interest. Second, they should collate as much data as possible and score each breed for key criteria: degree of endangerment, presence of traits of current economic value, presence of traits of current scientific value, agroecological value in a special landscape, cultural-historical value, and genetic uniqueness. The degree of endangerment is the most important criterion because great uncertainty about the future means that all breeds may have traits of future economic or scientific value, so the main aim should therefore be to minimize loss of breeds. To illustrate use of the framework, I considered breed prioritization in Norway. I compared and scored 45 breeds from 17 domestic animal species for these key criteria and thus identified Norwegian breeds of high priority for conservation.     

Genetic Estimates of Variability and Relatedness for Conservation of an Ozark Cave Crayfish Species Complex

Allozyme-based genetic distances were used to determine the distinctness of six species of cave crayfish from the Ozark Plateau in Missouri, Arkansas, and Oklahoma. One of the cave species is in the subgenus Erebicambarus and the others are in Jugicambarus . Four of the six species are very rare and are found in only one to three known sites each. In addition, most populations of all the species are presumed to be small; rarely are more than a few individuals observed. A chela (claw) was collected from sixty individuals representing the six species, including all known populations of the four rare species. Variability and distance estimates were based on 20 presumptive gene loci. Population samples with identical genotypes were pooled. Thirteen loci were polymorphic, but average heterozygosity was low (H= 1%) compared to epigean crayfish species. Pairwise genetic distances within Jugicambarus ranged from D = 0.051 to 0.522, and mean distance between subgenera was D = 0.676. The underground water systems in Ozark caves are defined by discreet recharge zones. Groundwater pollution threatens the stability of cave ecosystems, including the survival of cave crayfish. If restoration of threatened or extirpated populations becomes necessary, a database of genetic variability and relatedness estimates for known populations of all the species will aid decisions about numbers and sources of individuals for propagation or transfer.     

Nestmate recognition and the genetic relatedness of nests in the ant Formica pratensis

Genetic relatedness of the mound-building ant Formica pratensis was determined by means of microsatellite DNA polymorphism, and its impact on nestmate recognition was tested in a population in Southern Sweden (Oeland). Recognition between nests was measured by testing aggression levels between single pairs of workers. The genetic distances of nests (Nei's genetic distance) and the spatial distance of nests were correlated and both showed a strong relation to the aggression behavior. Multiple regression analysis revealed a stronger impact of genetic relatedness rather than spatial distances on aggression behavior. Neighbouring nests were more closely related than distant nests, which may reflect budding as a possible spreading mechanism. The genetic distance data showed that nestmate recognition was strongly genetically influenced in F. pratensis. Received: 2 October 1997 / Accepted after revision: 10 January 1998     

Comparative Population Genetic Structure of the Rare Woodland Shrub Daviesia suaveolens and Its Common Congener D. mimosoides

Genetic (allozyme) variation and population genetic structure of the rare shrub Daviesia suaveolens , found in only a few large populations on the eastern escarpment of the southern tablelands of New South Wales, were compared to those of its abundant and widespread relative D. mimosoides at both spatially equivalent and rangewide scales. We hypothesized that the rare species is genetically depauperate relative to the common one. We also generated baseline data on D. suaveolens to provide management recommendations for its conservation. Both species had high variation relative to other widespread woody angiosperms. Rangewide, the rare species exhibited lower species-level genetic variation than its common relative but a similar level of variation to that found in D. mimosoides over an equivalent spatial scale. Population-level genetic variation was similar for the two species. Over its small geographic range, D. suaveolens populations were three times as genetically differentiated as D. mimosoides over the same scale, showing a clear northsouth genetic disjunction and as much interpopulation divergence as the common species exhibited rangewide. These results confirm that not all types of rarity have the same genetic implications. Conservation strategies for D. suaveolens need not be concerned about low population-level variation unless populations become significantly smaller than is currently typical. Of more importance is to maintain the high interpopulation differentiation by conserving populations from both the north and south of the species' range.     

Microsatellite Analysis of Population Structure in the Endangered Hawaiian Monk Seal

Abstract: The endangered Hawaiian monk seal breeds at six locations in the northwestern Hawaiian Islands. To determine whether significant genetic differentiation exists among these sites, we used microsatellite loci to examine the monk seal population structure at the five largest breeding colonies. Of 27 loci isolated from other seal species, only 3 were polymorphic in an initial screening of one individual from each breeding site. Only two alleles were found at each of these 3 loci in samples of 46–108 individuals. This extremely low variation is consistent with other measures of genetic variability in this species and is probably the result of a recent severe population bottleneck, combined with a long-term history of small population sizes. Although the smallest monk seal subpopulation in this study ( Kure Atoll) showed some evidence of heterozygote deficit, possibly indicative of inbreeding, the next smallest ( Pearl and Hermes Reef) had an apparent excess of heterozygous individuals. Genetic differentiation was detected between the two subpopulations at extreme ends of the range ( Kure and French Frigate Shoals). This trend was significant only at the microsatellite locus for which we had the largest sample size ( Hg6.3: R _ST = 0.206, p = 0.002; allelic goodness of fit G _h = 15.412, p < 0.005). French Frigate Shoals is the source population for translocated animals that have been released primarily at Kure Atoll. Differentiation between these sites consisted of allele frequency differences (with the same allele predominant in each location at all three loci), rather than the preservation of alternative alleles. Although the translocations have had positive demographic effects, we recommend continued genetic monitoring of both the source and recipient populations because translocated individuals are now entering the breeding population.     

A Hierarchical View of Genetic Structure in the Rare Annual Plant Clarkia springvillensis

Genetic structure at several spatial scales was examined in the rare California annual, Clarkia springvillensis . Using seven isozyme-encoding loci as genetic markers, we assessed the amount and distribution of genetic variation among three populations and eight subpopulations. Total genetic variation was lower than in species with similar life history traits but equivalent to that of other endemic plants. Spatial autocorrelation showed some evidence for very limited differentiation within subpopulations at a scale of 1–2 m. The subpopulations, separated by tens of meters, were found to be more differentiated from each other ( F _sp = 0.084) on average than were populations ( F,pt = 0.017). This local genetic differentiation was not correlated with physical distance between subpopulations. The low F_pt estimates suggest that substantial gene flow is occurring among populations. However, the lack of correlation between genetic and geographic distances and the significant differentiation of subpopulations suggest that genetic drift is occurring within populations. Therefore, we believe the apparent homogeneity of populations is due to each population's gene frequencies' being an average of several divergent subpopulations. If drift is causing differentiation within populations, it may eventually cause differentiation between populations. The importance of using a hierarchical approach to evaluating genetic structure is clear. Patterns occurring at one spatial scale may not be evident at others. One should not necessarily conclude that gene flow is substantial and that the risk of genetic erosion via drift is negligible just because differentiation between populations is small; the system may not be at equilibrium. This lesson is particularly important when recent changes in climate or land use are apparent.     

Genetic structure of the subtidal red alga Delisea pulchra

We used random amplified polymorphic DNA (RAPDs) to examine small-scale spatial genetic structure in the red alga Delisea pulchra (Greville) Montagne at two locations near Sydney, Australia. We examined genetic structure among plants at four spatial scales ranging from 2 km apart down to <50 cm apart between locations, among sites within locations, among quadrats within sites, and among plants within quadrats. Haploid stages of D. pulchra were absent from the populations studied, suggesting that they are maintained through asexual reproduction of diploid plants. Consistent with this, we found that 19 RAPD phenotypes scored in this study had multiple individuals, indicating the presence of clones in these populations. However, there were no RAPD phenotypes common to two locations separated by only 2 km. Analysis of molecular variance revealed that strong genetic differences occurred between plants from these two locations, with 46.3% of the total genetic variation occurring at this scale, most probably reflecting limited gene flow. Within each location, <25% of the genetic variation was attributable to differences among sites or quadrats, indicating gene flow at those smaller scales. Most of the variation within each location occurred at the smallest spatial scale, among plants within 0.25 m² quadrats. Nonetheless, some pairwise genetic distances (φST) between sites or quadrats within locations were large, indicating some genetic divergence on smaller scales. Genetic distance was independent of spatial distance within both locations, suggesting that fine-scale differences within locations were most probably caused by variation in fine-scale patterns of water movement or fine-scale natural selection. We assessed the impact of one potential selective agent, grazing sea urchins, on the fine-scale genetic structure of D. pulchra. There was no evidence that grazing by sea urchins affected the genetic structure of D. pulchra. In combination with demographic data, our results indicated that local populations of D. pulchra within locations were relatively open and that fine-scale genetic structure was probably constrained by gene flow. At the larger scale however, strong genetic differentiation indicated little gene flow between locations and restricted dispersal of spores. Received: 22 April 1999 / Accepted: 29 November 1999     

Effects of Harvesting on Genetic Diversity in Old-Growth Eastern White Pine in Ontario, Canada

Genetic diversity measures at 54 isozyme loci coding for 16 enzymes in megagametophytes were compared between preharvest and postharvest gene pools of two adjacent virgin, old-growth (∼250 years) stands of eastern white pine ( Pinus strobus L.) in the Galloway Lake Old Pine Area of central Ontario. The concurrence of genetic diversity changes between the stands suggests that real and repeatable genetic erosion occurred in these gene pools as a result of harvesting. The total and mean number of alleles detected in each stand were reduced by approximately 25% after tree density reductions of 75%. The percentage of polymorphic loci dropped by about 33% from preharvest levels. About 40% of the low frequency (0.25> p ≥ 0.01) alleles and 80% of the rare ( p < 0.01) alleles were lost from each stand because of harvesting. Hypothetical multilocus gametic diversity was reduced by about 40% in each stand after harvesting. Latent genetic potential of each stand was reduced by about 50%, suggesting that the ability of these gene pools to adapt to changing environmental conditions may have been compromised. Heterozygosity estimates in the postharvest stands did not reflect reductions in allelic richness due to harvesting. Observed heterozygosity increased by 12% in one stand after harvesting, even though other genetic diversity measures decreased. Gene frequency changes due to harvesting imply that gene pools of naturally regenerated progeny stands may be quite different from the original parental stands. Silvicultural practices should ensure that the gene pools of remaining pristine old-growth stands have been reconstituted in the regenerating stands.     

Translating effects of inbreeding depression on component vital rates to overall population growth in endangered bighorn sheep

Evidence of inbreeding depression is commonly detected from the fitness traits of animals, yet its effects on population growth rates of endangered species are rarely assessed. We examined whether inbreeding depression was affecting Sierra Nevada bighorn sheep (Ovis canadensis sierrae), a subspecies listed as endangered under the U.S. Endangered Species Act. Our objectives were to characterize genetic variation in this subspecies; test whether inbreeding depression affects bighorn sheep vital rates (adult survival and female fecundity); evaluate whether inbreeding depression may limit subspecies recovery; and examine the potential for genetic management to increase population growth rates. Genetic variation in 4 populations of Sierra Nevada bighorn sheep was among the lowest reported for any wild bighorn sheep population, and our results suggest that inbreeding depression has reduced adult female fecundity. Despite this population sizes and growth rates predicted from matrix-based projection models demonstrated that inbreeding depression would not substantially inhibit the recovery of Sierra Nevada bighorn sheep populations in the next approximately 8 bighorn sheep generations (48 years). Furthermore, simulations of genetic rescue within the subspecies did not suggest that such activities would appreciably increase population sizes or growth rates during the period we modeled (10 bighorn sheep generations, 60 years). Only simulations that augmented the Mono Basin population with genetic variation from other subspecies, which is not currently a management option, predicted significant increases in population size. Although we recommend that recovery activities should minimize future losses of genetic variation, genetic effects within these endangered populations-either negative (inbreeding depression) or positive (within subspecies genetic rescue)-appear unlikely to dramatically compromise or stimulate short-term conservation efforts. The distinction between detecting the effects of inbreeding depression on a component vital rate (e.g., fecundity) and the effects of inbreeding depression on population growth underscores the importance of quantifying inbreeding costs relative to population dynamics to effectively manage endangered populations.     

Genetic variability in bloodworm (Glycera dibranchiata) populations in the Gulf of Maine

Genetic structure of eight Northwest Atlantic populations of the marine polychaeteGlycera dibranchiata Ehlers was examined with starch gel electrophoresis. Samples were collected during summer and fall 1981, and seven polymorphic and four monomorphic loci were consistently scored. Average heterozygosity (0.126) and percent polymorphic loci (59.3) were comparable to the averages reported for marine invertebrates. Minimum genetic distances between populations ranged from 0.003 to 0.093, levels typically associated with local populations of the same species in other taxa. Based on these data, inter- and intra-estuarine migration and gene flow appear to be low. Only two populations, separated by 13 km along the same river in New Brunswick, Canada, were not genetically different from each other. These findings may have relevance for management strategies in bloodworms.     

Genetic structure of dictyoceratid sponge populations on the western Coral Sea reefs

Allozyme variation at six polymorphic loci was examined in foliose dictyoceratid sponges from isolated reefs in the western Coral Sea. Four major genetic groups corresponding to the species Phyllospongia lamellosa, P. alcicornis, Carterospongia flabellifera and Collospongia auris were examined. A further two rare morphotypes from individual reefs formed genetic outliers to the P. lamellosa group, and may represent further taxa related to P. lamellosa. Gene frequencies in individual reef populations were largely in Hardy-Weinberg equilibrium, suggesting that random mating occurred in local populations of all four common species. Genetic variability was high and observed heterozygosities within populations ranged from 0.13 to 0.40. All four taxa showed significant genetic differentiation among populations (F _ST=0.05 to 0.36). Genetic distances (Nei's D) among populations within species ranged from 0 to 0.723 and increased with increasing geographical separation. There was evidence that genetic differentiation between populations to the north and to the south of the southern limit of the South Equatorial Current (SEC) divergence was greater than expected on the basis of their geographical separation. The SEC divergence may form a partial barrier to gene flow among populations of these ecologically important sponges on the submerged Queensland Plateau. Levels of migration among populations of three of the species was less than those required to prevent divergence of the populations through genetic drift (Nm<1). Restricted migration among populations may provide a mechanism to explain the occurrence of highly divergent populations of dictyoceratid sponges whose specific identity is not clear, and may allow them additionally to develop partial reproduction isolation from other populations.     

Genetic Diversity and Tests of the Hybrid Origin of the Endangered Yellow Larkspur

Abstract: Delphinium luteum ( Ranunculaceae), an endangered larkspur, is restricted to two wild populations near Bodega Bay, California. The total number of individuals in these two populations is estimated to be <100. We used allozyme and random amplified polymorphic DNA ( RAPD) markers to (1) assess levels and patterns of genetic diversity in one wild population and two cultivated populations and (2) test the hypothesis that D. luteum is of hybrid origin between D. decorum and D. nudicaule . These data will be used to aid in developing a management plan to conserve the species. The wild population maintains high levels of genetic diversity. Genetic data indicate that both cultivated populations, especially the north Sonoma population, have several allozymes and RAPD markers not found in the wild population and could be used to establish new populations of D. luteum or to enhance the diversity and size of the wild population. The allozyme data did not reveal any fixed differences between D. decorum and D. nudicaule , although allele frequencies of the putative parental populations differed. At these loci, D. luteum resembled D. nudicaule more than D. decorum  . Many unique RAPD markers distinguish each of the three species. The diagnostic markers from populations of D. nudicaule and D. decorum were not additive in the putative hybrid, and these data indicate that D. luteum is not of recent hybrid origin. Conservation of the yellow larkspur should include strategies that use the cultivated populations of D. luteum , but hybridizing D. decorum and D. nudicaule to "recreate" D. luteum is not recommended.     

Understanding origins of present-day genetic structure in marine fish: biologically or historically driven patterns?

Determining the origin of genetic structure is of wide interest because of its use in stock discrimination in marine organisms. Schematically, genetic differentiation can result from historical patterns maintained over geological time or from present-day isolation attributable to biological characteristics of the species. We used a comparative approach to population genetic analysis based on allozyme polymorphism to determine the impact of reproductive strategy (i.e. biological origin) and habitat (i.e. historical origin) on the genetic structure of individuals sampled from five isolated islands in French Polynesia. Eight species of coral reef fishes from two families (Chaetodontidae and Pomacentridae) were selected to test the impact of sea-level change (historical origin) and reproductive strategy (biological origin) on genetic structure. Seven of the eight study species showed significant divergence in allelic frequencies computed over all sites. For these seven species, multilocus F_stvalues ranged from 0.0114 to 0.0287. None of the eight species showed a significant relationship between genetic divergence and geographical distance between sites. Significant divergence (difference in allozyme frequencies) between some pairs of sites occurred but was unrelated to distances between them. These results suggest that the genetic structure of coral reef fish in French Polynesia is likely to be driven according to an island model in which migrations between populations are rare and random in space and time. Overall, none of the species showed congruent genetic structures between sites sampled. Genetic structure of the eight species did not appear significantly related either to reproductive strategy or habitat preference. Genetic diversity (heterozygosity) was significantly correlated with these two factors, with species laying benthic eggs and/or inhabiting lagoons showing significantly higher multilocus heterozygosity than species laying pelagic eggs and/or living on the outer reef slope. Overall, the absence of differences according to habitat and/or reproductive strategy did not provide any conclusive pattern regarding the origin of the genetic structure, but the limited divergence in allelic frequencies suggests recent differentiations.     

Population History, Genetic Variability, and Horn Growth in Bighorn Sheep

Bighorn sheep ( Ovis canadensis ) are restricted in distribution and numbers relative to presettlement conditions. Some populations have alledgedly suffered losses of fitness resulting from small, insular populations and a breeding system that reduces effective population size. Large horns in rams, which confer breeding superiority, are absent from some populations, and this absence may result in part from loss of genetic variability. We investigated the relationship among allozyme variability, population history, and horn growth in bighorn sheep from the Rocky Mountains. Heterozygosity was higher for bighorn sheep than has been reported for Dall sheep ( O. dalli ). Heterozygosity and allelic variability were marginally related to effective population size for the proceeding 15 years. Horn growth was significantly higher in more heterozygous than in less heterozygous rams for years 6, 7, and 8 of life. By the end of year 8, more heterozygous rams had 13% higher horn volumes than less heterozygous rams. Most hunting of bighorn sheep involves selective removal of large-horned rams, which we hypothesize may reduce genetic variability of these populations and contribute to losses in fitness.     

Genetic Diversity and Population Size in Four Rare Southern Appalachian Plant Species

Allozyme diversity was examined in four rare, high-montane plant species from the Appalachian Mountains of southeastern North America. These species may represent relictual members or descendants of an alpine community that was more widespread during the late Pleistocene. We sampled five populations of Geum radiatum (Rosaceae), Carex misera (Cyperaceae), Trichophorum cespitosum (Cyperaceae), and the four known populations of Calamagrostis cainii (Poaceae). Genetic diversity was low for all species but was typical of that found for plant species with limited ranges. Low genetic diversity may reflect historical events associated with changes in the species' biogeography. As the Pleistocene climate warmed, suitable habitat decreased in areal extent and became fragmented, probably resulting in smaller, more-isolated populations. In recent times these species, which co-occur in fragile rock outcrop habitats, have been adversely affected by human activities. Genetic analyses revealed reduced diversity in populations of decreasing size for three species. Estimates of gene flow were low ( Nm < 1.0) in all four species. Positive associations between genetic diversity and population size, evidence of recent population declines, and the low estimates of gene flow suggest that genetic drift may play a prominent role in shaping the present-day genetic composition of these species. Furthermore, these data suggest that the genetically depauperate populations are unlikely to regain genetic variation without human intervention.     

Genetic Diversity, Population Size, and Fitness in Central and Peripheral Populations of a Rare Plant Lychnis viscaria

Abstract: Genetic diversity is expected to decrease in small and isolated populations as a consequence of bottlenecks, founder effects, inbreeding, and genetic drift. The genetics and ecology of the rare perennial plant Lychnis viscaria (Caryophyllaceae) were studied in both peripheral and central populations within its distribution area. We aimed to investigate the overall level of genetic diversity, its spatial distribution, and possible differences between peripheral and central populations by examining several populations with electrophoresis. Our results showed that the level of genetic diversity varied substantially among populations (  H _exp = 0.000–0.116) and that the total level of genetic diversity (mean H _exp = 0.056) was low compared to that of other species with similar life-history attributes. The peripheral populations of L. viscaria had less genetic variation (mean H _exp = 0.034) than the central ones (0.114). Analysis of genetic structure suggested limited gene flow (mean F _ST = 0.430) and high differentiation among populations, emphasizing the role of genetic drift (  N _e m = 0.33). Isolation was even higher than expected based on the physical distance among populations. We also focused on the association between population size and genetic diversity and possible effects on fitness of these factors. Population size was positively correlated with genetic diversity. Population size and genetic diversity, however, were not associated with fitness components such as germination rate, seedling mass, or seed yield. There were no differences in the measured fitness components between peripheral and central populations. Even though small and peripheral populations had lower levels of genetic variation, they were as viable as larger populations, which emphasizes their potential value for conservation.     

Seasonal changes in population of some selected earthworm species and soil nutrients in cultivated agroecosystem

Studies were conducted on population dynamics of Metaphire posthuma, Lampito mauritii and Dichogaster bolaui in cultivated pedoecosystem of desert region of Rajasthan. The populations of aclitellate and clitellate M. posthuma, L. mauritii and D. bolaui were maximum in rainy season and minimum in summer season. The abundant population of these worms were found during the months of July to October. The species M. posthuma breed throughout the year except in extreme summer but L. mauritii breed twice in a year in the field. However, D. bolaui breed once in a year. Among these earthworm species D. bolaui with relative density of 44.2% was the most dominant species in cultivated land while L. mauritii and M. posthuma contributed 33.3% and 22.5% of density, respectively. The total population of earthworms showed significant positive correlation with different soil nutrients.     

Conservation Genetics in the Management of Desert Fishes

Abstract: The status and security of fishes in North American deserts have steadily declined in this century due to man's activities in this naturally fragile region. We address genetic aspects of the population structure of desert fishes as applicable to conservation and recovery programs by developing two zoogeographic models of isolation and gene flow. In the Death Valley model populations are isolated, with no chance of natural gene flow among them. Genetic diversity within populations tends to be low, but genetic divergence among populations within a species is high. In the Stream Hierarchy model, a complicated hierarchical genetic structure exists and is a function of geographic proximity and connectivity of habitats. Within-habitat genetic diversity tends to be higher, and among-habitat differentiation lower, than in the Death Valley model. These two systems must be recognized as distinct and managed differently. We also suggest three areas of experimentation needed to better understand and manage genetic stocks of desert fishes: relationships between heterozygosity and fitness, experimental mixing of similar stocks to examine effects of increased heterozygosity, and analysis of the relative roles of genetic adaptation and phenotypic plasticity in local differentiation.     

Investigating stock structure and trophic relationships among island-associated dolphins in the oceanic waters of the North Atlantic using fatty acid and stable isotope analyses

Short-beaked common dolphins (Delphinus delphis) and Atlantic spotted dolphins (Stenella frontalis) are the two most abundant cetacean species in the oceanic waters of Madeira and the Azores. They are of similar size, occur in similar habitats and are regularly observed in mixed-species groups to forage together. Genetic analyses suggested that, within each species, dolphins ranging around both archipelagos belong to the same panmictic population. We tested the hypotheses that (1) within each species, individuals from the two archipelagos belong to a single ecological stock; (2) between species, common and spotted dolphins have distinct trophic niches; using fatty acid (FA) and stable isotope (SI) analyses. Fatty acids and stable isotopes were analysed from 86 blubber and 150 skin samples of free-ranging dolphins, respectively. Sex-related differences were not significant, except for common dolphin FA profiles. In S. frontalis, FA and SI differences between archipelagos suggested that individuals belonged to different ecological stocks, despite the existence of gene flow between the two archipelagos. In D. delphis, differences were more pronounced, but it was not possible to distinguish between stock structure and a seasonal effect, due to differential sampling periods in the Azores and Madeira. Inter-specific comparisons were restricted to the Azores where all samples were collected during summer. Differences in FA proportions, noticeably for FA of dietary origin, as well as in nitrogen SI profiles, confirmed that both species feed on distinct resources. This study emphasizes the need for an integrated approach including both genetic and biochemical analyses for stock assessment, especially in wide-ranging marine top predators.