Status of the world's baleen whales

No global synthesis of the status of baleen whales has been published since the 2008 IUCN Red List assessments. Many populations remain at low numbers from historical commercial whaling, which had ceased for all but a few by 1989. Fishing gear entanglement and ship strikes are the most severe current threats. The acute and long‐term effects of anthropogenic noise and the cumulative effects of multiple stressors are of concern but poorly understood. The looming consequences of climate change and ocean acidification remain difficult to characterize. North Atlantic and North Pacific right whales are among the species listed as Endangered. Southern right, bowhead, and gray whales have been assessed as Least Concern but some subpopulations of these species ‐ western North Pacific gray whales, Chile‐Peru right whales, and Svalbard/Barents Sea and Sea of Okhotsk bowhead whales ‐ remain at low levels and are either Endangered or Critically Endangered. Eastern North Pacific blue whales have reportedly recovered, but Antarctic blue whales remain at about 1% of pre‐exploitation levels. Small isolated subspecies or subpopulations, such as northern Indian Ocean blue whales, Arabian Sea humpback whales, and Mediterranean Sea fin whales are threatened while most subpopulations of sei, Bryde's, and Omura's whales are inadequately monitored and difficult to assess.     

What Happened to Gray Whales during the Pleistocene? The Ecological Impact of Sea-Level Change on Benthic Feeding Areas in the North Pacific Ocean

Background

Gray whales (Eschrichtius robustus) undertake long migrations, from Baja California to Alaska, to feed on seasonally productive benthos of the Bering and Chukchi seas. The invertebrates that form their primary prey are restricted to shallow water environments, but global sea-level changes during the Pleistocene eliminated or reduced this critical habitat multiple times. Because the fossil record of gray whales is coincident with the onset of Northern Hemisphere glaciation, gray whales survived these massive changes to their feeding habitat, but it is unclear how.

Methodology/Principal Findings

We reconstructed gray whale carrying capacity fluctuations during the past 120,000 years by quantifying gray whale feeding habitat availability using bathymetric data for the North Pacific Ocean, constrained by their maximum diving depth. We calculated carrying capacity based on modern estimates of metabolic demand, prey availability, and feeding duration; we also constrained our estimates to reflect current population size and account for glaciated and non-glaciated areas in the North Pacific. Our results show that key feeding areas eliminated by sea-level lowstands were not replaced by commensurate areas. Our reconstructions show that such reductions affected carrying capacity, and harmonic means of these fluctuations do not differ dramatically from genetic estimates of carrying capacity.

Conclusions/Significance

Assuming current carrying capacity estimates, Pleistocene glacial maxima may have created multiple, weak genetic bottlenecks, although the current temporal resolution of genetic datasets does not test for such signals. Our results do not, however, falsify molecular estimates of pre-whaling population size because those abundances would have been sufficient to survive the loss of major benthic feeding areas (i.e., the majority of the Bering Shelf) during glacial maxima. We propose that gray whales survived the disappearance of their primary feeding ground by employing generalist filter-feeding modes, similar to the resident gray whales found between northern Washington State and Vancouver Island.     

Gene flow on ice: the role of sea ice and whaling in shaping Holarctic genetic diversity and population differentiation in bowhead whales (Balaena mysticetus)

Sea ice is believed to be a major factor shaping gene flow for polar marine organisms, but it remains unclear to what extent it represents a true barrier to dispersal for arctic cetaceans. Bowhead whales are highly adapted to polar sea ice and were targeted by commercial whalers throughout Arctic and subarctic seas for at least four centuries, resulting in severe reductions in most areas. Both changing ice conditions and reductions due to whaling may have affected geographic distribution and genetic diversity throughout their range, but little is known about range‐wide genetic structure or whether it differed in the past. This study represents the first examination of genetic diversity and differentiation across all five putative stocks, including Baffin Bay‐Davis Strait, Hudson Bay‐Foxe Basin, Bering‐Beaufort‐Chukchi, Okhotsk, and Spitsbergen. We also utilized ancient specimens from Prince Regent Inlet (PRI) in the Canadian Arctic and compared them with modern stocks. Results from analysis of molecular variance and demographic simulations are consistent with recent and high gene flow between Atlantic and Pacific stocks in the recent past. Significant genetic differences between ancient and modern populations suggest PRI harbored unique maternal lineages in the past that have been recently lost, possibly due to loss of habitat during the Little Ice Age and/or whaling. Unexpectedly, samples from this location show a closer genetic relationship with modern Pacific stocks than Atlantic, supporting high gene flow between the central Canadian Arctic and Beaufort Sea over the past millennium despite extremely heavy ice cover over much of this period.     

Paleodistribution modeling suggests glacial refugia in Scandinavia and out‐of‐Tibet range expansion of the Arctic fox

Quaternary glacial cycles have shaped the geographic distributions and evolution of numerous species in the Arctic. Ancient DNA suggests that the Arctic fox went extinct in Europe at the end of the Pleistocene and that Scandinavia was subsequently recolonized from Siberia, indicating inability to track its habitat through space as climate changed. Using ecological niche modeling, we found that climatically suitable conditions for Arctic fox were found in Scandinavia both during the last glacial maximum (LGM) and the mid‐Holocene. Our results are supported by fossil occurrences from the last glacial. Furthermore, the model projection for the LGM, validated with fossil records, suggested an approximate distance of 2000 km between suitable Arctic conditions and the Tibetan Plateau well within the dispersal distance of the species, supporting the recently proposed hypothesis of range expansion from an origin on the Tibetan Plateau to the rest of Eurasia. The fact that the Arctic fox disappeared from Scandinavia despite suitable conditions suggests that extant populations may be more sensitive to climate change than previously thought.     

Using pre- and postexploitation samples to assess the impact of commercial whaling on the genetic characteristics of eastern North Pacific gray and humpback whales and to compare methods used to infer historic demography

Many species of whales went through recent bottlenecks due to commercial whaling. These declines were rapid and recent relative to the life spans and generation times of these species, raising questions regarding to what degree commercial whaling influenced the genetic characteristics of these populations. We analyzed mitochondrial and nuclear DNA from pre- and postwhaling samples from two populations that have arguably shown the greatest degree of recovery: eastern North Pacific gray and humpback whales. We also compare the performance of different methods to test for historic bottlenecks and infer past demography based on genetic data. We found substantially higher levels of genetic diversity in gray than in humpback whales (for both time periods), likely due to recent connectivity between Atlantic and Pacific gray whale populations. Other than mitochondrial diversity in humpback whales, levels of diversity were not lower in contemporary samples relative to prewhaling samples, indicating that commercial whaling had a minimal impact on metrics of genetic diversity themselves. However, it did have large impacts on the patterns of diversity, as evidenced by all coalescent-based methods showing clear evidence of a bottleneck for both populations, whereas all but one method not based on the coalescent failed to detect a bottleneck.     

Historic and current habitat use by North Pacific right whales Eubalaena japonica in the Bering Sea and Gulf of Alaska

1. To help define areas and ecological parameters critical to the survival and recovery of the remnant population of North Pacific right whales, habitat use was investigated by examining all available sighting and catch records in the south-eastern Bering Sea (SEBS) and Gulf of Alaska (GOA) over the past two centuries. 2. Based on re-analyses of commercial whaling records, search effort, and resultant catches and sightings, waters of the: (i) SEBS slope and shelf, (ii) eastern Aleutian Islands and (iii) GOA slope and abyssal plain were important habitat for North Pacific right whales through the late 1960s. 3. Since 1980, the only area where right whales have been seen consistently is on the SEBS middle shelf. However, acoustic detections and single sightings have been reported in all other regions except the SEBS slope and oceanic GOA (areas where little, if any, acoustic and visual effort has occurred). 4. Sightings since 1979 were in waters < 200 m deep which may simply reflect the paucity of search effort elsewhere. From the commercial whaling era to the late 1960s, right whales were commonly seen in waters > 2000 m deep, indicating that their distribution is not restricted to shallow continental shelves. 5. North Pacific right whale sightings through the centuries have been associated with a variety of oceanic features, and there is little in common in the bathymetry of these regions. These whales appear to have a greater pelagic distribution than that observed in the North Atlantic, which may be related to the availability of larger copepods across the SEBS and GOA.     

Future recovery of baleen whales is imperiled by climate change

Historical harvesting pushed many whale species to the brink of extinction. Although most Southern Hemisphere populations are slowly recovering, the influence of future climate change on their recovery remains unknown. We investigate the impacts of two anthropogenic pressures—historical commercial whaling and future climate change—on populations of baleen whales (blue, fin, humpback, Antarctic minke, southern right) and their prey (krill and copepods) in the Southern Ocean. We use a climate–biological coupled “Model of Intermediate Complexity for Ecosystem Assessments” (MICE) that links krill and whale population dynamics with climate change drivers, including changes in ocean temperature, primary productivity and sea ice. Models predict negative future impacts of climate change on krill and all whale species, although the magnitude of impacts on whales differs among populations. Despite initial recovery from historical whaling, models predict concerning declines under climate change, even local extinctions by 2100, for Pacific populations of blue, fin and southern right whales, and Atlantic/Indian fin and humpback whales. Predicted declines were a consequence of reduced prey (copepods/krill) from warming and increasing interspecific competition between whale species. We model whale population recovery under an alternative scenario whereby whales adapt their migratory patterns to accommodate changing sea ice in the Antarctic and a shifting prey base. Plasticity in range size and migration was predicted to improve recovery for ice‐associated blue and minke whales. Our study highlights the need for ongoing protection to help depleted whale populations recover, as well as local management to ensure the krill prey base remains viable, but this may have limited success without immediate action to reduce emissions.     

Molecular insights into the historic demography of bowhead whales: understanding the evolutionary basis of contemporary management practices

Patterns of genetic variation observed within species reflect evolutionary histories that include signatures of past demography. Understanding the demographic component of species' history is fundamental to informed management because changes in effective population size affect response to environmental change and evolvability, the strength of genetic drift, and maintenance of genetic variability. Species experiencing anthropogenic population reductions provide valuable case studies for understanding the genetic response to demographic change because historic changes in the census size are often well documented. A classic example is the bowhead whale, Balaena mysticetus, which experienced dramatic population depletion due to commercial whaling in the late 19th and early 20th centuries. Consequently, we analyzed a large multi‐marker dataset of bowhead whales using a variety of analytical methods, including extended Bayesian skyline analysis and approximate Bayesian computation, to characterize genetic signatures of both ancient and contemporary demographic histories. No genetic signature of recent population depletion was recovered through any analysis incorporating realistic mutation assumptions, probably due to the combined influences of long generation time, short bottleneck duration, and the magnitude of population depletion. In contrast, a robust signal of population expansion was detected around 70,000 years ago, followed by a population decline around 15,000 years ago. The timing of these events coincides to a historic glacial period and the onset of warming at the end of the last glacial maximum, respectively. By implication, climate driven long‐term variation in Arctic Ocean productivity, rather than recent anthropogenic disturbance, appears to have been the primary driver of historic bowhead whale demography.     

A biological consequence of reducing Arctic ice cover: arrival of the Pacific diatom Neodenticula seminae in the North Atlantic for the first time in 800 000 years

The Continuous Plankton Recorder survey has monitored plankton in the Northwest Atlantic at monthly intervals since 1962, with an interegnum between 1978 and 1990. In May 1999, large numbers of the Pacific diatom Neodenticula seminae were found in Continuous Plankton Recorder (CPR) samples in the Labrador Sea as the first record in the North Atlantic for more than 800 000 years. The event coincided with modifications in Arctic hydrography and circulation, increased flows of Pacific water into the Northwest Atlantic and in the previous year the exceptional occurrence of extensive ice‐free water to the North of Canada. These observations indicate that N. seminae was carried in a pulse of Pacific water in 1998/early 1999 via the Canadian Arctic Archipelago and/or Fram Strait. The species occurred previously in the North Atlantic during the Pleistocene from∼1.2 to∼0.8 Ma as recorded in deep sea sediment cores. The reappearance of N. seminae in the North Atlantic is an indicator of the scale and speed of changes that are taking place in the Arctic and North Atlantic oceans as a consequence of regional climate warming. Because of the unusual nature of the event it appears that a threshold has been passed, marking a change in the circulation between the North Pacific and North Atlantic Oceans via the Arctic. Trans‐Arctic migrations from the Pacific into the Atlantic are likely to occur increasingly over the next 100 years as Arctic ice continues to melt affecting Atlantic biodiversity and the biological pump with consequent feedbacks to the carbon cycle.     

Mitochondrial and nuclear genetic variation across calving lagoons in Eastern North Pacific gray whales (Eschrichtius robustus)

Accurate knowledge of population structure in cetaceans is critical for preserving and managing breeding habitat, particularly when habitat is not uniformly protected. Most eastern gray whales return to their major breeding range each winter along the Pacific coast of Baja California, Mexico, concentrating in 3 major calving lagoons, but it is unknown whether genetic differences exist between lagoons. Previous photo-identification studies and genetic studies suggest that gray whales may return to their natal lagoons to breed, potentially resulting in the buildup of genetic differences. However, an earlier genetic study used only one genetic marker and did not include samples from Bahia Magdalena, a major calving lagoon not currently designated as a wildlife refuge. To expand on this previous study, we collected genetic data from the mitochondrial control region (442 bp) and 9 microsatellite markers from 112 individuals across all 3 major calving lagoons. Our data suggest that migration rates between calving lagoons are high but that a small but significant departure from panmixia exists between Bahia Magdalena and Laguna San Ignacio (Fisher's Exact test, P < 0.0001; F(ST) = 0.006, P = 0.025). Coalescent simulations show that the lack of extensive population structure may result from the disruption of structure due to whaling. Another possibility is that rates of migration have always been high (>10% per generation). In addition, microsatellite data showed evidence of a severe population bottleneck. Eastern gray whales are still recovering from the impacts of whaling on their breeding grounds, and these populations should be protected and monitored for future genetic changes.     

Spatial dynamics of Chinese Muntjac related to past and future climate fluctuations

Climate fluctuations in the past and in the future are likely to result in population expansions, shifts, or the contraction of the ecological niche of many species, and potentially leading to the changes in their geographical distributions. Prediction of suitable habitats has been developed as a useful tool for the assessment of habitat suitability and resource conservation to protect wildlife. Here, we model the ancestral demographic history of the extant modern Chinese Muntjac Muntiacus reevesi populations using approximate Bayesian computation (ABC) and used the maximum entropy model to simulate the past and predict the future spatial dynamics of the species under climate oscillations. Our results indicated that the suitable habitats for the M. reevesi shifted to the Southeast and contracted during the Last Glacial Maximum, whereas they covered a broader and more northern position in the Middle Holocene. The ABC analyses revealed that the modern M. reevesi populations diverged in the Middle Holocene coinciding with the significant contraction of the highly suitable habitat areas. Furthermore, our predictions suggest that the potentially suitable environment distribution for the species will expand under all future climate scenarios. These results indicated that the M. reevesi diverged in the recent time after the glacial period and simultaneously as its habitat’s expanded in the Middle Holocene. Furthermore, the past and future climate fluctuation triggered the change of Chinese muntjac spatial distribution, which has great influence on the Chinese muntjac’s population demographic history.     

King penguin demography since the last glaciation inferred from genome-wide data

How natural climate cycles, such as past glacial/interglacial patterns, have shaped species distributions at the high-latitude regions of the Southern Hemisphere is still largely unclear. Here, we show how the post-glacial warming following the Last Glacial Maximum (ca 18 000 years ago), allowed the (re)colonization of the fragmented sub-Antarctic habitat by an upper-level marine predator, the king penguin Aptenodytes patagonicus. Using restriction site-associated DNA sequencing and standard mitochondrial data, we tested the behaviour of subsets of anonymous nuclear loci in inferring past demography through coalescent-based and allele frequency spectrum analyses. Our results show that the king penguin population breeding on Crozet archipelago steeply increased in size, closely following the Holocene warming recorded in the Epica Dome C ice core. The following population growth can be explained by a threshold model in which the ecological requirements of this species (year-round ice-free habitat for breeding and access to a major source of food such as the Antarctic Polar Front) were met on Crozet soon after the Pleistocene/Holocene climatic transition.     

Colonization, dispersal, and hybridization influence phylogeography of North Atlantic sea urchins (Strongylocentrotus droebachiensis)

We used frequency-based and coalescent-based phylogeographic analysis of sea urchin (Strongylocentrotus droebachiensis) mitochondrial DNA (mtDNA) sequences and previously published microsatellite data to understand the relative influence of colonization and gene flow from older (north Pacific) and younger (northeast Atlantic) sea urchin populations on genetic variation in the northwest Atlantic. We found strong evidence of survival of northwestern Atlantic populations in local Pleistocene glacial refugia: most haplotypes were the same as or closely related to Pacific haplotypes, with deep gene genealogies that reflect divergence times within the northwestern Atlantic that are much older than the last glacial maximum. We detected gene flow across the North Atlantic in the form of haplotypes shared with or recently descended from European populations. We also found evidence of significant introgression of haplotypes from a closely related species (S. pallidus). The relative magnitude of gene flow estimated by coalescent methods (and the effective population size differences among oceanic regions) depended on the genetic marker used. In general, we found very small effective population size in the northeastern Atlantic and high trans-Arctic gene flow between the Pacific and northwestern Atlantic. Both analyses suggested significant back-migration to the Pacific. However, microsatellites more strongly reflected older Pacific migration (with similar effective population sizes across the Arctic), whereas mtDNA sequences appeared to be more sensitive to recent trans- Atlantic dispersal (with larger differences in effective population size). These differences across marker types might have several biological or methodological causes, and they suggest caution in interpretation of the results from a single locus or class of markers.     

THE BIOGEOGRAPHIC ORIGIN OF ARCTIC ENDEMIC SEAWEEDS: A THERMOGEOGRAPHIC VIEW1

The Arctic is geologically and biogeographically young, and the origin of its seaweed flora has been widely debated. The Arctic littoral biogeographic region dates from the latest Tertiary and Pleistocene. Following the opening of Bering Strait, about 3.5 mya, the “Great Trans‐Arctic Biotic Interchange” populated the Arctic with a fauna strongly dominated by species of North Pacific origin. The Thermogeographic Model (TM) demonstrates why climate and geography continued to support this pattern in the Pleistocene. Thus, Arctic and Atlantic subarctic species of seaweeds are likely to be evolutionarily “based” in the North Pacific, subarctic species are likely to be widespread in the warmer Arctic, and species of Atlantic Boreal or warmer origin are unlikely in the Arctic and Subarctic. Although Arctic seaweeds have been thought to have a greater affinity with the North Atlantic, we have reanalyzed the Arctic endemic algal flora, using the Thermogeographic Model and evolutionary trees based on molecular data, to demonstrate otherwise. There are 35 congeneric species of the six, abundant Arctic Rhodophyta that we treat in this paper; 32 of these species (91%) occur in the North Pacific, two species (6%) occur in the Boreal or warmer Atlantic Ocean, and a single species is panoceanic, but restricted to the Subarctic. Laminaria solidungula J. Agardh, a kelp Arctic “endemic” species, has 18 sister species. While only eleven (61%) occur in the North Pacific, this rapidly dispersing and evolving genus is a terminal member of a diverse family and order (Laminariales) widely accepted to have evolved in the North Pacific. Thus, both the physical/time‐based TM and the dominant biogeographic pattern of relatives of Arctic macrophytes suggest strong compliance with the evidence of zoology, geology, and paleoclimatology that the Arctic marine flora is largely of Pacific origin.     

Genetic signatures of a demographic collapse in a large-bodied forest dwelling primate (Mandrillus leucophaeus)

It is difficult to predict how current climate change will affect wildlife species adapted to a tropical rainforest environment. Understanding how population dynamics fluctuated in such species throughout periods of past climatic change can provide insight into this issue. The drill (Mandrillus leucophaeus) is a large-bodied rainforest adapted mammal found in West Central Africa. In the middle of this endangered monkey's geographic range is Lake Barombi Mbo, which has a well-documented palynological record of environmental change that dates to the Late Pleistocene. We used a Bayesian coalescent-based framework to analyze 2,076 base pairs of mitochondrial DNA across wild drill populations to infer past changes in female effective population size since the Late Pleistocene. Our results suggest that the drill underwent a nearly 15-fold demographic collapse in female effective population size that was most prominent during the Mid Holocene (approximately 3-5 Ka). This time period coincides with a period of increased dryness and seasonality across Africa and a dramatic reduction in forest coverage at Lake Barombi Mbo. We believe that these changes in climate and forest coverage were the driving forces behind the drill population decline. Furthermore, the warm temperatures and increased aridity of the Mid Holocene are potentially analogous to current and future conditions faced by many tropical rainforest communities. In order to prevent future declines in population size in rainforest-adapted species such as the drill, large tracts of forest should be protected to both preserve habitat and prevent forest loss through aridification.     

Evolution of the Northern Rockweed,Fucus distichus,in a Regime of Glacial Cycling: Implications for Benthic Algal Phylogenetics

Northern hemisphere rockweeds (Fucus) are thought to have evolved in the North Pacific and then spread to the North Atlantic following the opening of the Bering Strait. They have dispersed and widely speciated in the North Atlantic and its tributary seas. Fucus distichus is likely near the ancestral member of this genus, and studies have shown that there are several species/subspecies in this complex (i.e. F. evanescens and F. gardneri). We used phylogenetic and haplotype analyses to test the phylogenetic relationships and biogeography of F. distichus. Our data and subsequent analyses demonstrate that, unlike previous studies that lacked samples from an extensive geographical area of the Arctic and Subarctic, there is a distinct Arctic haplotype that is the source of subspecies in both the North Pacific and North Atlantic. Fucus distichus occupies a low tide zone habitat, and in Arctic/Subarctic regions it is adapted to the severe stress of sea ice coverage and disturbance during many months per year. We hypothesize that the very large geographic area of Arctic and Subarctic rocky shores available to this species during interglacials, supported by large Arctic/Subarctic fringe areas as well as unglaciated refugia during glacial cycles, provided a robust population and gene pool (described by the Thermogeographic Model). This gene pool dilutes that of the more fragmented and area-limited Temperate/Boreal area populations when they are brought together during glacial cycles. We suggest that similar subspecies complexes for a variety of Arctic/Subarctic shore biota should be examined further in this context, rather than arbitrarily being split up into numerous species.     

Faunal histories from Holocene ancient DNA

Recent studies using ancient DNA have been instrumental in advancing understanding of the impact of Holocene climate change on biodiversity. Ancient DNA has been used to track demography, migration and diversity, and is providing new insights into the long-term dynamics of species and population distributions. The Holocene is key to understanding how the past has impacted on the present, as it bridges the gap between contemporary phylogeographic studies and those with inference on Pleistocene patterns, based on ancient DNA studies. Here, we examine the major patterns of Holocene faunal population dynamics and connectivity; highlighting the dynamic nature of species and population responses to Holocene climatic change, thereby providing an 'analogue' for understanding potential impacts of future change.     

Cycles of trans‐Arctic dispersal and vicariance,and diversification of the amphi‐boreal marine fauna

The amphi‐boreal faunal element comprises closely related species and conspecific populations with vicarious distributions in the North Atlantic and North Pacific basins. It originated from an initial trans‐Arctic dispersal in the Pliocene after the first opening of the Bering Strait, and subsequent inter‐oceanic vicariance through the Pleistocene when the passage through the Arctic was severed by glaciations and low sea levels. Opportunities for further trans‐Arctic dispersal have risen at times, however, and molecular data now expose more complex patterns of inter‐oceanic affinities and dispersal histories. For a general view on the trans‐Arctic dynamics and of the roles of potential dispersal–vicariance cycles in generating systematic diversity, we produced new phylogeographic data sets for amphi‐boreal taxa in 21 genera of invertebrates and vertebrates, and combined them with similar published data sets of mitochondrial coding gene variation, adding up to 89 inter‐oceanic comparisons involving molluscs, crustaceans, echinoderms, polychaetes, fishes and mammals. Only 39% of the cases correspond to a simple history of Pliocene divergence; in most taxonomical groups, the range of divergence estimates implies connections through the entire Pliocene–Pleistocene–Holocene time frame. Repeated inter‐oceanic exchange was inferred for 23 taxa, and the latest connection was usually post‐glacial. Such repeated invasions have usually led to secondary contacts and occasionally to widespread hybridization between the different invasion waves. Late‐ or post‐glacial exchange was inferred in 46% of the taxa, stressing the importance of the relatively recent invasions to the current diversity in the North Atlantic. Individual taxa also showed complex idiosyncratic patterns and histories, and several instances of cryptic speciation were recognized. In contrast to a simple inter‐oceanic vicariance scenario underlying amphi‐boreal speciation, the data expose complex patterns of reinvasion and reticulation that complicate the interpretation of taxon boundaries in the region.     

Reconciling historical processes and population structure in the sooty tern Sterna fuscata

To test the influence of past vicariant events on population genetic structure of the sooty tern Sterna fuscata , we examined sequence variation in the mitochondrial control region of individuals from the Indo-Pacific and Atlantic Oceans. Our analyses indicate a rapid population expansion at a global scale during the last 100 000 years, consistent with global recolonisation during the interstade following the Pleistocene glacial maxima (125 000–175 000 years bp). We estimate islands of the Great Barrier Reef and Coral Sea were colonised no more than 16 000 years ago, most likely in association with the appearance of new breeding habitat following the final Pleistocene glacial retreat (19 000–22 000 years bp). Our results suggest that ice sheets linked to major glacial events not only impact genetic structuring in temperate seabirds, but that sea level changes in the tropics associated with these same events have also significantly impacted contemporary genetic structuring in tropical seabird species.     

Demography or selection on linked cultural traits or genes? Investigating the driver of low mtDNA diversity in the sperm whale using complementary mitochondrial and nuclear genome analyses

Mitochondrial DNA has been heavily utilized in phylogeography studies for several decades. However, underlying patterns of demography and phylogeography may be misrepresented due to coalescence stochasticity, selection, variation in mutation rates and cultural hitchhiking (linkage of genetic variation to culturally‐transmitted traits affecting fitness). Cultural hitchhiking has been suggested as an explanation for low genetic diversity in species with strong social structures, counteracting even high mobility, abundance and limited barriers to dispersal. One such species is the sperm whale, which shows very limited phylogeographic structure and low mtDNA diversity despite a worldwide distribution and large population. Here, we use analyses of 175 globally distributed mitogenomes and three nuclear genomes to evaluate hypotheses of a population bottleneck/expansion vs. a selective sweep due to cultural hitchhiking or selection on mtDNA as the mechanism contributing to low worldwide mitochondrial diversity in sperm whales. In contrast to mtDNA control region (CR) data, mitogenome haplotypes are largely ocean‐specific, with only one of 80 shared between the Atlantic and Pacific. Demographic analyses of nuclear genomes suggest low mtDNA diversity is consistent with a global reduction in population size that ended approximately 125,000 years ago, correlated with the Eemian interglacial. Phylogeographic analysis suggests that extant sperm whales descend from maternal lineages endemic to the Pacific during the period of reduced abundance and have subsequently colonized the Atlantic several times. Results highlight the apparent impact of past climate change, and suggest selection and hitchhiking are not the sole processes responsible for low mtDNA diversity in this highly social species.