Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial

Anthropogenic factors have impacted the diversity and evolutionary trajectory of various species. This can be through factors such as pressure on population size or range, habitat fragmentation, or extensive manipulation and translocation. Here we use time-calibrated data to better understand the pattern and processes of evolution in the heavily manipulated European fallow deer (Dama dama). During the Pleistocene, fallow deer had a broad distribution across Europe and were found as far north as Britain during the Eemian interglacial. The last glacial period saw fallow deer retreat to southern refugia and they did not disperse north afterwards. Their recolonisation was mediated by people and, from northern Europe and the British Isles, fallow deer were transported around the world. We use ancient and modern mitochondrial DNA (mtDNA) and mitogenomic data from Eemian Britain to assess the pattern of change in distribution and lineage structure across Europe over time. We find founder effects and mixed lineages in the northern populations, and stability over time for populations in southern Europe. The Eemian sample was most similar to a lineage currently in Italy, suggesting an early establishment of the relevant refuge. We consider the implications for the integration of anthropogenic and natural processes towards a better understanding of the evolution of fallow deer in Europe.

Marine mammal conservation: over the horizon

Marine mammals can play important ecological roles in aquatic ecosystems, and their presence can be key to community structure and function. Consequently, marine mammals are often considered indicators of ecosystem health and flagship species. Yet, historical population declines caused by exploitation, and additional current threats, such as climate change, fisheries bycatch, pollution and maritime development, continue to impact many marine mammal species, and at least 25% are classified as threatened (Critically Endangered, Endangered or Vulnerable) on the IUCN Red List. Conversely, some species have experienced population increases/recoveries in recent decades, reflecting management interventions, and are heralded as conservation successes. To continue these successes and reverse the downward trajectories of at-risk species, it is necessary to evaluate the threats faced by marine mammals and the conservation mechanisms available to address them. Additionally, there is a need to identify evidence-based priorities of both research and conservation needs across a range of settings and taxa. To that effect we: (1) outline the key threats to marine mammals and their impacts, identify the associated knowledge gaps and recommend actions needed; (2) discuss the merits and downfalls of established and emerging conservation mechanisms; (3) outline the application of research and monitoring techniques; and (4) highlight particular taxa/populations that are in urgent need of focus.

A global cline in a colour polymorphism suggests a limited contribution of gene flow towards the recovery of a heavily exploited marine mammal

Evaluating how populations are connected by migration is important for understanding species resilience because gene flow can facilitate recovery from demographic declines. We therefore investigated the extent to which migration may have contributed to the global recovery of the Antarctic fur seal (Arctocephalus gazella), a circumpolar distributed marine mammal that was brought to the brink of extinction by the sealing industry in the eighteenth and nineteenth centuries. It is widely believed that animals emigrating from South Georgia, where a relict population escaped sealing, contributed to the re-establishment of formerly occupied breeding colonies across the geographical range of the species. To investigate this, we interrogated a genetic polymorphism (S291F) in the melanocortin 1 receptor gene, which is responsible for a cream-coloured phenotype that is relatively abundant at South Georgia and which appears to have recently spread to localities as far afield as Marion Island in the sub-Antarctic Indian Ocean. By sequencing a short region of this gene in 1492 pups from eight breeding colonies, we showed that S291F frequency rapidly declines with increasing geographical distance from South Georgia, consistent with locally restricted gene flow from South Georgia mainly to the South Shetland Islands and Bouvetøya. The S291F allele was not detected farther afield, suggesting that although emigrants from South Georgia may have been locally important, they are unlikely to have played a major role in the recovery of geographically more distant populations.

Hybridization in bottlenose dolphins-A case study of Tursiops aduncus × T. truncatus hybrids and successful backcross hybridization events

The bottlenose dolphin, genus Tursiops is one of the best studied of all the Cetacea with a minimum of two species widely recognised. Common bottlenose dolphins (T. truncatus), are the cetacean species most frequently held in captivity and are known to hybridize with species from at least 6 different genera. In this study, we document several intra-generic hybridization events between T. truncatus and T. aduncus held in captivity. We demonstrate that the F1 hybrids are fertile and can backcross producing apparently healthy offspring, thereby showing introgressive inter-specific hybridization within the genus. We document that female F1 hybrids can reach sexual maturity at 4 yr and 3 mo of age, and can become pregnant and give birth before being fully weaned. The information presented has implications for understanding hybrid reticulation among cetacean species and practical implications for captive facilities housing either Tursiops species or hybrids thereof.

Strong population structure in a species manipulated by humans since the Neolithic: the European fallow deer (Dama dama dama)

Species that have been translocated and otherwise manipulated by humans may show patterns of population structure that reflect those interactions. At the same time, natural processes shape populations, including behavioural characteristics like dispersal potential and breeding system. In Europe, a key factor is the geography and history of climate change through the Pleistocene. During glacial maxima throughout that period, species in Europe with temperate distributions were forced south, becoming distributed among the isolated peninsulas represented by Anatolia, Italy and Iberia. Understanding modern patterns of diversity depends on understanding these historical population dynamics. Traditionally, European fallow deer (Dama dama dama) are thought to have been restricted to refugia in Anatolia and possibly Sicily and the Balkans. However, the distribution of this species was also greatly influenced by human-mediated translocations. We focus on fallow deer to better understand the relative influence of these natural and anthropogenic processes. We compared modern fallow deer putative populations across a broad geographic range using microsatellite and mitochondrial DNA loci. The results revealed highly insular populations, depauperate of genetic variation and significantly differentiated from each other. This is consistent with the expectations of drift acting on populations founded by small numbers of individuals, and reflects known founder populations in the north. However, there was also evidence for differentiation among (but not within) physically isolated regions in the south, including Iberia. In those regions we find evidence for a stronger influence from natural processes than may be expected for a species with such strong, known anthropogenic influence.

Post-glacial habitat release and incipient speciation in the genus Delphinus

The role of ecological and changing environmental factors in the radiation of species diversity is a fundamental question in evolutionary biology. Of particular interest is the potential for these factors to determine the boundary between what we would consider differentiation among populations and incipient speciation. Dolphins in the genus Delphinus provide a useful test case, exhibiting morphological variation in beak length, coloration and body size across their wide geographic distribution, and in particular among coastal and more pelagic habitats. Two species have been proposed, D. delphis and D. capensis, but morphologically similar allopatric populations are not monophyletic, indicating that the mostly coastal 'long-beaked' D. capensis form is not a single globally distributed species. However, the sympatric populations in the Eastern North Pacific currently designated as these two species are both morphologically and genetically differentiated. Here we use microsatellite DNA and mitochondrial DNA markers to investigate the evolutionary mechanisms that led to this incipient speciation event. We used coalescent and assignment methods to investigate the timing and extent of reproductive isolation. Our data indicate that although there is some level of on-going gene flow, the putative species found in the Eastern North Pacific are reciprocally monophyletic. The timing of isolation appears to be associated with regional changes in paleoceanographic conditions within the Holocene timeframe.

Phylogenomics of the killer whale indicates ecotype divergence in sympatry

For many highly mobile species, the marine environment presents few obvious barriers to gene flow. Even so, there is considerable diversity within and among species, referred to by some as the 'marine speciation paradox'. The recent and diverse radiation of delphinid cetaceans (dolphins) represents a good example of this. Delphinids are capable of extensive dispersion and yet many show fine-scale genetic differentiation among populations. Proposed mechanisms include the division and isolation of populations based on habitat dependence and resource specializations, and habitat release or changing dispersal corridors during glacial cycles. Here we use a phylogenomic approach to investigate the origin of differentiated sympatric populations of killer whales (Orcinus orca). Killer whales show strong specialization on prey choice in populations of stable matrifocal social groups (ecotypes), associated with genetic and phenotypic differentiation. Our data suggest evolution in sympatry among populations of resource specialists.

Influence of Holocene environmental change and anthropogenic impact on the diversity and distribution of roe deer

Extant patterns of population structure and levels of diversity are a consequence of factors that vary in both space and time. Our objective in this study is to investigate a species that has responded to both natural and anthropogenic changes in ways that have shaped modern populations and provide insight into the key processes. The roe deer (Capreolus capreolus) is one of the two species of deer native to Britain. During the last glacial maximum (LGM), the British habitat was largely under ice and there was a land bridge to mainland Europe. As the Earth warmed during the early Holocene, the land bridge was lost. Subsequent hunting on the British mainland left the southern region extirpated of roe deer, whereas a refugial population remained in the north. Later reintroductions from Europe led to population expansion, especially in southern United Kingdom. Here, we combine data from ancient and modern DNA to track population dynamics and patterns of connectivity, and test hypotheses about the influence of natural and anthropogenic environmental change. We find that past expansion and divergence events coincided with a warming environment and the subsequent closure of the land bridge between Europe and the United Kingdom. We also find turnover in British roe deer haplotypes between the late-Holocene and modern day that have likely resulted from recent human disturbance activities such as habitat perturbation, overhunting and restocking.

Atypical panmixia in a European dolphin species (Delphinus delphis): implications for the evolution of diversity across oceanic boundaries

Despite the scarcity of geographical barriers in the ocean environment, delphinid cetaceans often exhibit marked patterns of population structure on a regional scale. The European coastline is a prime example, with species exhibiting population structure across well-defined environmental boundaries. Here we undertake a comprehensive population genetic study on the European common dolphin (Delphinus delphis, based on 492 samples and 15 loci) and establish that this species shows exceptional panmixia across most of the study range. We found differentiation only between the eastern and western Mediterranean, consistent with earlier studies, and here use approximate Bayesian computations to explore different scenarios to explain the observed pattern. Our results suggest that a recent population bottleneck likely contributed significantly to the differentiation of the Eastern Mediterranean population (in Greek waters). This interpretation is consistent with independent census data that suggest a sharp population decline in the recent past. The implication is that an unperturbed population may currently show panmixia across the full study range. This exception to the more typical pattern of population structure seen for other regional dolphin species (and for common dolphin populations elsewhere in the world) suggests particular ecological or life-history traits distinct to this species in European waters.

Genetic panmixia and demographic dependence across the North Atlantic in the deep-sea fish, blue hake (Antimora rostrata)

The efficient investment of resources and effort into conservation strategies depends on the accurate identification of management units. At the same time, understanding the processes by which population structure evolves requires an understanding of the conditions under which panmixia may exist. Here, we study a species with an unusual, apparently sex-biased pattern of distribution, and test the hypothesis that distribution processes associated with this pattern (for example, congregating at a single dominant spawning site or periodic mixing during reproduction) could lead to panmixia over a large geographic range. Using 13 microsatellite markers, we compared 393 blue hake (Antimora rostrata) from 11 sample sites across a geographic range of over 3000 km, and found no evidence of population structure. We estimated current effective population size and found it to be large (~15,000) across the sampled area. In addition, we used simulation models to test expectations about demographic correlation among populations and our ability to detect relevant levels of gene flow. All data were consistent with the interpretation of long-range panmixia.

Social cohesion among kin, gene flow without dispersal and the evolution of population genetic structure in the killer whale (Orcinus orca)

In social species, breeding system and gregarious behavior are key factors influencing the evolution of large-scale population genetic structure. The killer whale is a highly social apex predator showing genetic differentiation in sympatry between populations of foraging specialists (ecotypes), and low levels of genetic diversity overall. Our comparative assessments of kinship, parentage and dispersal reveal high levels of kinship within local populations and ongoing male-mediated gene flow among them, including among ecotypes that are maximally divergent within the mtDNA phylogeny. Dispersal from natal populations was rare, implying that gene flow occurs without dispersal, as a result of reproduction during temporary interactions. Discordance between nuclear and mitochondrial phylogenies was consistent with earlier studies suggesting a stochastic basis for the magnitude of mtDNA differentiation between matrilines. Taken together our results show how the killer whale breeding system, coupled with social, dispersal and foraging behaviour, contributes to the evolution of population genetic structure.

Development of 10 microsatellite loci in the ling (Molva molva)

We developed primers for two dinucleotide and eight tetranucleotide microsatellite loci in a marine fish, the ling (Molva molva). All markers were obtained from partial genomic DNA libraries and characterized in 55 unrelated individuals from one putative population. The number of alleles ranged from five to 24 (average 10.5) per locus, and the observed heterozygosity ranged from 0.218 to 0.981 (average 0.643). No loci amplified in two other gadoid species tested, the Atlantic cod (Gadus morhua) and the tusk (Brosme brosme).

Phylogeography and alpha taxonomy of the common dolphin (Delphinus sp.)

The resolution of taxonomic classifications for delphinid cetaceans has been problematic, especially for species in the genera Delphinus, Tursiops and Stenella. The frequent lack of correspondence between morphological and genetic differentiation in these species raises questions about the mechanisms responsible for their evolution. In this study we focus on the genus Delphinus, and use molecular markers to address questions about speciation and the evolution of population structure. Delphinus species have a worldwide distribution and show a high degree of morphological variation. Two distinct morphotypes, long-beaked and short-beaked, have been considered different species named D. capensis and D. delphis, respectively. However, genetic differentiation between these two forms has only been demonstrated in the Pacific. We analysed samples from eight different geographical regions, including two morphologically defined long-beaked form populations, and compared these with the eastern North Pacific populations. We found high differentiation among the populations described as long-beaked instead of the expected monophyly, suggesting that these populations may have evolved from independent events converging on the same morphotype. We observed low genetic differentiation among the short-beaked populations across a large geographical scale. We interpret these phylogeographical patterns in the context of life history and population structure in related species.

Holocene elephant seal distribution implies warmer-than-present climate in the Ross Sea

We show that southern elephant seal (Mirounga leonina) colonies existed proximate to the Ross Ice Shelf during the Holocene, well south of their core sub-Antarctic breeding and molting grounds. We propose that this was due to warming (including a previously unrecognized period from approximately 1,100 to 2,300 (14)C yr B.P.) that decreased coastal sea ice and allowed penetration of warmer-than-present climate conditions into the Ross Embayment. If, as proposed in the literature, the ice shelf survived this period, it would have been exposed to environments substantially warmer than present.

Tracing the phylogeography of human populations in Britain based on 4th-11th century mtDNA genotypes

Some of the transitional periods of Britain during the first millennium A.D. are traditionally associated with the movement of people from continental Europe, composed largely of invading armies (e.g., the Roman, Saxon, and Viking invasions). However, the extent to which these were migrations (as opposed to cultural exchange) remains controversial. We investigated the history of migration by women by amplifying mitochondrial DNA (mtDNA) from ancient Britons who lived between approximately A.D. 300-1,000 and compared these with 3,549 modern mtDNA database genotypes from England, Europe, and the Middle East. The objective was to assess the dynamics of the historical population composition by comparing genotypes in a temporal context. Towards this objective we test and calibrate the use of rho statistics to identify relationships between founder and source populations. We find evidence for shared ancestry between the earliest sites (predating Viking invasions) with modern populations across the north of Europe from Norway to Estonia, possibly reflecting common ancestors dating back to the last glacial epoch. This is in contrast with a late Saxon site in Norwich, where the genetic signature is consistent with more recent immigrations from the south, possibly as part of the Saxon invasions.

Population genetics of an invasive species, Heracleum mantegazzianum: implications for the role of life history, demographics and independent introductions

The population genetic structure of an invasive, nonindigenous riparian weed (Heracleum mantegazzianum) in the northeast of England was investigated using microsatellite DNA markers. Data were used to assess the size and frequency of introductions into three catchments and the subsequent spread. We sampled 13 populations, including a remote population (Perivale, London) for comparison. Five loci were screened and considerable variation was found. Results revealed greater overall variation between populations from different catchments than those in the same catchment, and suggested the generation of population structure in the relatively short time since the initial introduction. Between-catchment variation may reflect population structure generated by local founders as the species spread and may indicate a large initial founder population at the time of the introduction into Britain, or multiple introductions. Within-catchment variation was consistent with expectations based on the water-borne dispersal of seeds in this species, and the relatively small dispersal range of likely pollinators. Independent introductions stand out in some cases as exceptions to the general pattern. Taken together the results are consistent with a relatively large initial founder population, and the subsequent spread of the species in local founder populations, followed by some level of inbreeding within local populations and novel introductions in some localities.

Phylogenetic relationships within the eared seals (Otariidae: Carnivora): implications for the historical biogeography of the family

Phylogenetic relationships within the family Otariidae were investigated using two regions of the mitochondrial genome. A 360-bp region of the cytochrome b gene was employed for the primary phylogenetic analysis, while a 356-bp segment of the control region was used to enhance resolution of the terminal nodes. Traditional classification of the family into the subfamilies Arctocephalinae (fur seals) and Otariinae (sea lions) is not supported, with the fur seal Callorhinus ursinus having a basal relationship relative to the rest of the family. This is consistent with the fossil record which suggests that this genus diverged from the line leading to the remaining fur seals and sea lions about 6 million years ago (mya). There is also little evidence to support or refute the monophyly of sea lions. Four sea lion clades and five fur seal clades were observed, but relationships among these clades are unclear. Similar genetic divergences between the sea lion clades (D(a) = 0.054-0.078), as well as between the major Arctocephalus fur seal clades (D(a) = 0.040-0.069) suggest that these groups underwent periods of rapid radiation at about the time they diverged from each other. Rapid radiations of this type make the resolution of relationships between the resulting species difficult and indicate the requirement for additional molecular data from both nuclear and mitochondrial genes. The phylogenetic relationships within the family and the genetic distances among some taxa highlight inconsistencies in the current taxonomic classification of the family.

Characterization of major histocompatibility complex DRB diversity in the endemic South African antelope Damaliscus pygargus: a comparison in two subspecies with different demographic histories

Major histocompatibility complex (MHC) class II locus DRB was investigated by single-strand conformation polymorphism analysis (SSCP) and sequence analysis in the endemic South African antelope, Damaliscus pygargus, of which there are two subspecies. Greater polymorphism was found in the blesbok (D. p. phillipsi) subspecies (n = 44; 22 alleles) than in the bontebok (D. p. pygargus) subspecies (n = 45; 6 alleles). Erosion of allelic diversity in bontebok was most likely the result of two severe bottleneck events caused by hunting pressure and parasitic infection. A majority of the polymorphism observed was found within the peptide binding region (PBR) where dN/dS ratios were higher than for the non-PBR region. This, and the apparent trans-species relationship among alleles in a bovid phylogeny, suggest the evolution of diversity by heterosis or frequency-dependent selection.

Genetic and morphometric differentiation between island and mainland southern elephant seal populations

We compare genetic (both nuclear and mitochondrial) and morphometric measures between two putative populations of southern elephant seal (Mirounga leonina), and interpret the results in the context of data from mark-recapture and satellite-telemetric studies. One population is on the Argentine mainland, while the other is 2,400 km away on South Georgia island. We found pronounced differentiation at the mitochondrial DNA (mtDNA) control region that was distinct from the pattern of variation seen among island rookeries. Some morphometric characters and seven out of ten nuclear-DNA markers also showed differentiation between the island and mainland sites. Diversity at nuclear markers was high in both populations but mtDNA diversity was low in the mainland population, suggesting a founder event and little subsequent immigration of females. Morphological differences may suggest different selective environments at the two sites.

Molecular genetic diversity and evolution at the MHC DQB locus in four species of pinnipeds

Variation was investigated at exon 2 (including part of the putative peptide-binding region) of the class II major histocompatibility complex (MHC) DQB locus for two congeneric phocid seal species and two congeneric otariid seal species. Polymorphism in one phocid species, the southern elephant seal (Mirounga leonina), was comparable to that seen in human populations, while the other phocid, the northern elephant seal (Mirounga angustirostris), has been through a severe population bottleneck and exhibited much less variation at this locus. A phylogenetic comparison of the four species was consistent with the trans-specific pattern of evolution described for other taxa at this locus, and relative nonsynonymous and synonymous substitution rates suggest the maintenance of polymorphisms by natural selection. A comparison of sequence patterns also suggested that some variation could have been generated through recombinational events, primarily within genera. These results suggest a pattern of evolution of the immune response in pinnipeds similar to that in terrestrial mammal species.

Molecular population genetics of the southern elephant seal Mirounga leonina

Southern elephant seals breed on sub-Antarctic islands and have a circumpolar distribution. We assayed mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) variation in the three main populations in the south Atlantic, south Indian, and south Pacific oceans, and a smaller continental population in South America. Population structure of mtDNA was strong and not consistent with isolation by distance. The nDNA loci, although less informative, were consistent with the mtDNA results. Geographic structure appears to be dominated by historical processes, not contemporary gene flow. Uncorrected levels of nucleotide diversity for mtDNA control region I (2.86%) and nDNA (0.09%) were similar to those in humans and mice. Mutation rates for control region I (75 x 10(-9) substitutions per site per year) and nDNA (1.23 x 10(-9)) were similar to those in other mammals. Female effective population size and total effective population size were roughly equal at approximately 4 x 10(4), indicating a twofold greater rate of drift for mtDNA. Effective breeding sex ratio of four to five females per male was estimated from nucleotide diversity and mutation rates for mtDNA and nDNA, and was much less than behavioral observations would suggest. There was no evidence for selection at any of the assayed loci.

Genetic differentiation between parapatric 'nearshore' and 'offshore' populations of the bottlenose dolphin

The existence of nearshore and offshore populations of the bottlenose dolphin has been documented throughout its range. In several cases the two regional forms have been shown to be morphologically distinct, although there is considerable overlap for most characters. The populations off the eastern coast of North America have been the subject of a long-term programme of research on their distribution and movements. In this study, we compare mitochondrial and nuclear genetic markers between dolphins classified as either nearshore or offshore type. These putative populations were found to be distinct at both nuclear and mitochondrial genetic markers. Further, the level of variation among the nearshore dolphins was reduced compared with the offshore population. A broader geographical comparison suggests a shared lineage between offshore dolphins from the western North Atlantic and both offshore and nearshore dolphins from the eastern Atlantic. These results are consistent with local differentiation based on habitat or resource specialization in the western North Atlantic, and suggest differences in the character of the nearshore/offshore distinction in different parts of the world.

Low genetic variation among killer whales (Orcinus orca) in the eastern north Pacific and genetic differentiation between foraging specialists

Killer whales from the coastal waters off California through Alaska were compared for genetic variation at three nuclear DNA markers and sequenced for a total of 520 bp from the mitochondrial control region. Two putative sympatric populations that range throughout this region were compared. They can be distinguished by social and foraging behavior and are known as "residents" and "transients". We found low levels of variation within populations compared to other cetacean species. Comparisons between fish (resident) versus marine mammal (transient) foraging specialists indicated highly significant genetic differentiation at both nuclear and mitochondrial loci. This differentiation is at a level consistent with intraspecific variation. A comparison between two parapatric resident populations showed a small but fixed mtDNA haplotype difference. Together these data suggest low levels of genetic dispersal between foraging specialists and a pattern of genetic differentiation consistent with matrifocal population structure and small effective population size.

Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores

We describe a repetitive DNA region at the 3' end of the mitochondrial DNA (mtDNA) control region and compare it in 21 carnivore species representing eight carnivore families. The sequence and organization of the repetitive motifs can differ extensively between arrays; however, all motifs appear to be derived from the core motif "ACGT." Sequence data and Southern blot analysis demonstrate extensive heteroplasmy. The general form of the array is similar between heteroplasmic variants within an individual and between individuals within a species (varying primarily in the length of the array, though two clones from the northern elephant seal are exceptional). Within certain families, notably ursids, the array structure is also similar between species. Similarity between species was not apparent in other carnivore families, such as the mustelids, suggesting rapid changes in the organization and sequence of some arrays. The pattern of change seen within and between species suggests that a dominant mechanism involved in the evolution of these arrays is DNA slippage. A comparative analysis shows that the motifs that are being reiterated or deleted vary within and between arrays, suggesting a varying rate of DNA turnover. We discuss the evolutionary implications of the observed patterns of variation and extreme levels of heteroplasmy.

Improved resolution of (CAC)n DNA fingerprints

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Evolution by DNA turnover in the control region of vertebrate mitochondrial DNA

The control region of animal mitochondrial DNA is heterogeneous, including both highly conserved and highly variable sequences. Within the variable regions, variable number tandem repeat sequences have been described for numerous species. Repeats at one location, just upstream of the origin of replication, show an unprecedented level of length variation in somatic tissue. Recent comparison of these sequences in different species indicates a pattern of DNA turnover acting at different rates and over motifs of various sizes.

Elephant seal genetic variation and the use of simulation models to investigate historical population bottlenecks

Because the northern elephant seal (Mirounga angustirostrus) was heavily exploited during the 19th century, it experienced an extreme population bottleneck. Since then, under legislative protection in the United States and Mexico, northern elephant seals have recovered dramatically in number, although their genomic diversity was greatly reduced, apparently as a consequence of the bottleneck. In this study we investigated DNA sequence diversity in two mtDNA regions (the control region and 16S RNA) and found low genetic variation in the northern elephant seal: there were only two control region haplotypes (sequence difference = 1%), which was consistent with an extreme founder event in the recent history of the northern species. We also reaffirmed the lack of allozyme diversity in this species. In contrast, the southern elephant seal (M. leonina), which though similarly exploited never fell below 1,000 animals, had 23 control region mtDNA haplotypes (average sequence difference = 2.3%). To investigate the extent of the founder event in the northern elephant seal we devised a simulation model based on extensive demographic data. This allowed a statistical analysis of the likely outcome of bottlenecks of different size and duration. Given these historical data, our results indicate (within 95% confidence) a bottleneck of less than 30 seals and 20-year duration, or, if hunting was the primary pressure on the population, a single-year bottleneck of less than 20 seals.

Generation of VNTRs and heteroplasmy by sequence turnover in the mitochondrial control region of two elephant seal species

We describe an unusual repetitive DNA region located in the 3' end of the light (L)-strand in the mitochondrial control region of two elephant seal species. The array of tandem repeats shows both VNTR (variable-number tandem repeat) and sequence variation and is absent from 12 compared mammalian species, except for the occurrence in the same location of a distinct repetitive region in rabbit mtDNA and a similar repeat in the harbor seal. The sequence composition and arrangement of the repeats differ considerably between the northern elephant seal (Mirounga angustirostris) and the southern species (M. leonina) despite an estimated divergence time of 1 MY (based on an mtDNA-RNA gene and the nonrepetitive control region). Analysis of repeat sequence relationships within and between species indicate that divergence in sequence and structure of repeats has involved both slippage-like and unequal crossingover processes of turnover, generating very high levels of divergence and heteroplasmy.

Conservation genetics of whales and dolphins

Whales and dolphins (cetaceans) are found in all the world's oceans and in some of the major rivers, yet little is known about the distribution and behaviour of many species. At the same time, cetaceans are under threat from a variety of pressures including direct and indirect takes, pollution, and competition for habitat and prey. To ensure their long-term survival it will be necessary to preserve genetic diversity through the identification and protection of differentiated populations, the assessment of variation within local populations, and through a better understanding of reproductive and dispersal behaviour. The application of molecular genetic techniques is helping to provide answers to some of these previously intractable questions. Early results suggest few consistent patterns. Obvious geographic boundaries correlate to genetic distance in some species, and not in others. Furthermore, morphological variation within species can be fairly extensive without correlating to genetic distance, or relatively minor between morphotypes that are as genetically distinct as some species. These examples emphasize the need for further study.

Evolution of the cetacean mitochondrial D-loop region

We sequenced the mitochondrial DNA D-loop regions from two cetacean species and compared these with the published D-loop sequences of several other mammalian species, including one other cetacean. Nucleotide substitution rates, DNA sequence simplicity, possible open reading frames (ORFs), and potential RNA secondary structure were investigated. The substitution rate is an order of magnitude lower than would be expected on the basis of reports on human sequence variation in this region but are consistent with interspecific primate and rodent D-loop sequence variation and with estimates of substitution rates from whole mitochondrial genomes. Deletions/insertions are less common in the cetacean D-loop than in other vertebrate species. Areas of high sequence simplicity (clusters of short repetitive motifs) across the region correspond to areas of high sequence divergence. Three regions predicted to form secondary structures are homologous to such putative structures in other species; however, the presumptive structures most conserved in cetaceans are different from those reported for other taxa. While all three species have possible long ORFs, only a short sequence of seven amino acids is shared with other mammalian species, and those changes that had occurred within it are all nonsynonymous. We conclude that DNA slippage, in addition to point mutation, contributes to the evolution of the D-loop and that regions of conserved secondary structure in cetaceans and an ORF are unlikely to contribute significantly to the conservation of the central region.