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Mitogenomic insights into a recently described and rarely observed killer whale morphotype
Abstract
Identifying evolutionary divergent taxonomic units, e.g. species and subspecies, is important for conservation and evolutionary biology. The ‘type D’ killer whale, Orcinus orca, is a rarely observed morphotype with a pelagic, circumpolar subantarctic distribution, making dedicated research and therefore taxonomic study extremely difficult to date. In this study, we used DNA target enrichment hybridisation capture coupled to high throughput sequencing, to obtain the first DNA sequence from the only known museum specimen of this recently described morphotype. The high coverage, complete mitogenome sequence was compared to a previously published global dataset of 139 individuals, indicating that this type is highly divergent to all previously genetically sequenced killer whale forms. The estimated divergence time (390,000 years ago) from its most recent common ancestor with other extant killer whale lineages was the second oldest split within the killer whale phylogeny. This study provides the first genetic support of type D potentially being a distinct subspecies or species of killer whale, although further samples are needed to identify whether there is monophyly of mitogenome sequences and whether nuclear DNA also indicates reproductive isolation. These findings also highlight the value of natural history museum collections and new technologies to investigate the taxonomy of rare, cryptic or difficult to access species.
... Top photo is of the 1955 New Zealand stranding, (provided by A. van Helden); middle photos compare type A (photo credit: R. Pitman) and type D killer whales (photo credit: P. Tixier); lower photo is of one of the type D killer whales biopsy sampled in 2019 from which the genomes used in this study were sequenced (photo credit: J. Totterdell). specimen #1077 from the Museum of New Zealand-Te Papa Tongarewa, Wellington originated from the 1955 mass stranding of type D killer whales (Foote et al. 2013). Sequencing of nuclear genomic DNA from the New Zealand stranded specimen offers the opportunity to compare 2 social groups of type D killer whale. ...
... DNA was extracted from a piece of dried soft tissue on the skull and from approximately 0.5 g of powdered tooth from the New Zealand stranded specimen. DNA extraction and purification from powdered tooth followed the protocols set out in Foote et al. (2013). Extraction and purification of DNA from the dried tissue was conducted using the Qiagen DNeasy kit following the manufacturer's guidelines. ...
... Additionally, reads were mapped using BWA-MEM to the previously generated mitogenome sequence of the New Zealand type D specimen (accession KF164610; Foote et al. 2013). In a previous study of 139 killer whale mitogenome sequences (Morin et al. 2010), the inclusion of intra-and interlab PCR, library build, and sequencing replicates identified inconsistencies in the assembly of polynucleotide repeat regions: one of between 9 and 14 Cs in a row (positions 1130 to 1144 in the original alignment), and another region of 7 to 8 As in a row (positions 5210 to 5217). ...
Genome sequences can reveal the extent of inbreeding in small populations. Here, we present the first genomic characterization of type D killer whales, a distinctive eco/morphotype with a circumpolar, subantarctic distribution. Effective population size is the lowest estimated from any killer whale genome and indicates a severe population bottleneck. Consequently, type D genomes show among the highest level of inbreeding reported for any mammalian species (FROH ≥ 0.65). Detected recombination cross-over events of different haplotypes are up to an order of magnitude rarer than in other killer whale genomes studied to date. Comparison of genomic data from a museum specimen of a type D killer whale that stranded in New Zealand in 1955, with 3 modern genomes from the Cape Horn area, reveals high covariance and identity-by-state of alleles, suggesting these genomic characteristics and demographic history are shared among geographically dispersed social groups within this morphotype. Limitations to the insights gained in this study stem from the nonindependence of the 3 closely related modern genomes, the recent coalescence time of most variation within the genomes, and the nonequilibrium population history which violates the assumptions of many model-based methods. Long-range linkage disequilibrium and extensive runs of homozygosity found in type D genomes provide the potential basis for both the distinctive morphology, and the coupling of genetic barriers to gene flow with other killer whale populations.
... Differences among the four forms is supported by historical (Mikhalev et al. 1981; Berzin & Vladimirov 1983 New Zealand Journal of Marine and Freshwater Research, 2013 http://dx.doi.org/10.1080/00288330.2013.844721 and contemporary (Pitman et al. 2007 ) morphological data, diet specialisation (Berzin & Vladimirov 1983) and genetic analysis (LeDuc et al. 2008; Morin et al. 2010; Foote et al. 2013). New Zealand is the only place in the southern hemisphere where three out of the four forms of killer whales have been reported (Visser 1999b; Pitman & Ensor 2003; Pitman et al. 2011; Foote et al. 2013). ...
... and contemporary (Pitman et al. 2007 ) morphological data, diet specialisation (Berzin & Vladimirov 1983) and genetic analysis (LeDuc et al. 2008; Morin et al. 2010; Foote et al. 2013). New Zealand is the only place in the southern hemisphere where three out of the four forms of killer whales have been reported (Visser 1999b; Pitman & Ensor 2003; Pitman et al. 2011; Foote et al. 2013). As these southern hemisphere forms have been described only recently, little is known about their distribution or movements. ...
... Benthic foraging of stingrays by killer whales has been reported to occur commonly in New Zealand, but seems uncommon elsewhere (Visser 1999a; Duignan et al. 2000). Previous genetic analyses have included a small number (n = 5) of New Zealand killer whale samples for worldwide phylogeography studies, identification of putative forms/species and estimation of divergence times among types (Hoelzel et al. 2002b; Morin et al. 2010; Foote et al. 2013). Here, we report the genetic diversity of killer whales around New Zealand, and compare samples collected in this region with larger geographic databases (Hoelzel et al. 2002b; Morin et al. 2010; Foote et al. 2013) to investigate the relationship of the New Zealand killer whales with more distant populations/ecotypes. ...
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... Separate species status has been suggested for different forms found in the Southern Ocean, based on substantial morphological and ecological divergence and habitat segregation (Pitman and Ensor 2003;Pitman et al. 2011;Durban et al. 2016). There is morphological and genetic support for a separate status particularly for the distinctively looking type D killer whales, found in subantarctic waters (Pitman et al. 2011;Foote et al. 2013a). ...
... were also recognized by the same committee. Recent genetic evidence supported the division of subspecies or even different species, however the taxonomy has not yet been fully resolved (Leduc et al. 2008;Foote et al. 2009Foote et al. , 2013aMorin et al. 2010). Forms of killer whales in the North Pacific, North Atlantic, and Antarctic Ocean may warrant future recognition as separate subspecies or even species, as further genetic evidence is compiled. ...
... emblematic species such as the killer whale (Orcinus orca, Linnaeus 1758), despite the fact that the phylogenetic relationships among different lineages of this species have been studied in depth (Foote et al., 2013;Morin et al., 2010). Moreover, subfamilies and the species they comprise within Delphinidae also remain unclear , though they probably could be Delphininae, Stenoninae, Globicephalinae or Lissodelphininae (Cunha et al., 2011;McGowen, 2011;McGowen, Spaulding, & Gatesy, 2009). ...
... Delphinidae (Cunha et al., 2011;May-Collado & Agnarsson, 2006;McGowen, 2011;McGowen et al., 2009 same intra species topology to that of Morin et al. (2010) andFoote et al. (2013), who included the newly discovered type D killer whales. ...
The phylogenetic relationships of oceanic dolphins (family Delphinidae) remain un- clear. Several works using mitochondrial and/or nuclear DNA on different genera and species have been published, though no consensus exists regarding even the sub- families that conform the family. Here, a new phylogeny for the family Delphinidae, including 36 different complete mitochondrial genomes (plus two outgroups), was constructed under Bayesian and maximum likelihood approaches. Results indicate identical tree topology in both cases, with almost all nodes fully supported indepen- dently of the reconstruction approach. This topology is different from those previ- ously published and proposes new phylogenetic relationships among subfamilies, genera and species of the family. These findings are critically important for the study of oceanic dolphin taxonomy, ecology, evolution and conservation, and highlight the importance of revisiting and resolving uncertain phylogenies.
... Mitogenome sequences were combined from previous publications (N = 169) and newly generated data (N = 283 excluding replicates; see Results). A subset (n=36) of the samples was sequenced at the Centre for GeoGenetics, Natural History Museum of Denmark, using methods describe in Foote et al. (2013b;2013c). The remaining 247 ...
... Haplotypes were assigned sequences with missing data by construction of a neighbor joining tree and comparison to the most similar sequences. We identified 150 unique haplotypes, including previously identified haplotypes from 169 individuals in Morin et al. (2010) and Foote et al. (2013b;2013c;2011c), plus eight sequences with missing data that prevented unambiguous assignment to an existing or unique haplotype. All 158 unique sequences representing 452 individual killer whales (after removal of duplicate sequences from three individuals that were sampled twice; see nuclear SNP analysis below) were used for phylogenetic analysis (Table S1). ...
Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global dataset of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from the ice edge to the tropics, often exhibiting ecological, behavioral and morphological variation suggestive of local adaptation accompanied by reproductive isolation. Results suggest a rapid global radiation occurred over the last 350,000 years. Based on habitat models, we estimated there was only a 15% global contraction of core suitable habitat during the Last Glacial Maximum, and the resources appeared to sustain a constant global effective female population size throughout the Late Pleistocene. Reconstruction of the ancestral phylogeography highlighted the high mobility of this species, identifying 22 strongly supported long-range dispersal events including inter-oceanic and inter-hemispheric movement. Despite this propensity for geographic dispersal, the increased sampling of this study uncovered very few potential examples of ancestral dispersal among ecotypes. Concordance of nuclear and mitochondrial data further confirm genetic cohesiveness, with little or no current gene flow among sympatric ecotypes. Taken as a whole, our data suggest that the glacial cycles influenced local populations in different ways, with no clear global pattern, but with secondary contact among lineages following long-range dispersal as a potential mechanism driving ecological diversification. This article is protected by copyright. All rights reserved.
This article is protected by copyright. All rights reserved.
... Tom's mitogenome sequence was a novel haplotype in the dataset. The mitogenome sequence of the Kattegat sample was identical to that previously generated for this individual (GenBank accession: KF418373; Foote et al. 2013). The effective depth of coverage (i.e. ...
Cooperative hunting between humans and killer whales (Orcinus orca) targeting baleen whales was reported in Eden, New South Wales, Australia, for almost a century. By 1928, whaling operations had ceased, and local killer whale sightings became scarce. A killer whale from the group, known as "Old Tom, " washed up dead in 1930 and his skeleton was preserved. How these killer whales from Eden relate to other populations globally and whether their genetic descendants persist today remains unknown. We extracted and sequenced DNA from Old Tom using ancient DNA techniques. Genomic sequences were then compared with a global dataset of mitochondrial and nuclear genomes. Old Tom shared a most recent common ancestor with killer whales from Australasia, the North Atlantic, and the North Pacific, having the highest genetic similarity with contemporary New Zealand killer whales. However, much of the variation found in Old Tom's genome was not shared with these widespread populations, suggesting ancestral rather than ongoing gene flow. Our genetic comparisons also failed to find any clear descendants of Tom, raising the possibility of local extinction of this group. We integrated Traditional Custodian knowledge to recapture the events in Eden and recognize that Indigenous Australians initiated the relationship with the killer whales before European colonization and the advent of commercial whaling locally. This study rectifies discrepancies in local records and provides new insight into the origins of the killer whales in Eden and the history of Australasian killer whales.
... Between 2003 and 2020 there were sightings of type D killer whales in South Georgia, in waters of the Southeast Atlantic, near Campbell Island, in the Drake Passage (Pitman et al. 2011(Pitman et al. , 2019Foote et al. 2023) and associated with a toothfish (Dissostichus eleginoides) fishery in the Crozet Islands (Tixier et al. 2014(Tixier et al. , 2016Amelot et al. 2022). By sequencing mitochondrial DNA obtained from the skull of an individual preserved from the 1955 stranding, Foote et al. (2013) reported that type D killer whales are the most divergent ecotype, suggesting that type D is potentially a subspecies or a distinct species of killer whale. Subsequently it was indicated that type D is genetically intermediate between Southern Ocean and North Atlantic populations (Foote et al. 2019). ...
There are different ecotypes of killer whales (Orcinus orca) worldwide; type D killer whales are the least known. These killer whales have a globose head, an extremely small post-ocular patch and a falcate dorsal fin. We report the first stranding event of type D killer whales recorded in southern South America, in the Magellan Strait, Chile. The group consisted of four adult females, two juvenile females, and two females and one male of indeterminate age class. Total length of adult females averaged 572.8 ± 23.6 cm and juvenile females averaged 397.0 ± 24.0 cm. Dorsal fin height of adult females averaged 57.3 ± 8.5 cm and in juvenile females 30.5 ± 19.1 cm. No obvious signs of anthropogenic intervention were observed. The characteristic small post-ocular white eye patch of this killer whale ecotype measured 21.8 cm long and 5.9 cm wide in the freshest carcass found. All animals presented backswept dorsal fins and a dental formula of 11 to 13 maxillary and mandibular teeth. The length of the largest tooth in each individual ranged from 8.0 to 10.2 cm, suggesting that type D killer whales have smaller teeth. We suggest that the total length of type D killer whales is shorter than other killer whale ecotypes. After 67 years, we report the second known stranding of type D killer whales worldwide and we report for the first time body measurements, size, and number of teeth of this ecotype of killer whales.
... This suggests that during the Pleistocene, prior to the evolution of larger-bodied killer whales that evolved to eat other odontocetes (Berta et al., 2022), there may have been a lack of large oceanic predators of odontocetes. The split between the ancestors of modern killer whales and their closest living relatives, the false killer whales, occurred around 1.9 million years ago with a large margin of error (range of 700,000 to 3.5 Mya) (Foote et al., 2013). Fusiform body shape in odontocetes appears to have evolved recently, with extremes in body shape associated with speed emerging during the Pleistocene (< 2.5 Mya), a period characterized by repeated glaciations (Fig. 1). ...
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A widespread pattern in vertebrate life-history evolution is for species to evolve towards either fast or slow life histories; however, the underlying causes of this pattern remain unclear. Toothed whales (Odontoceti) are a diverse group with a range of body sizes and life histories, making them an ideal model to investigate potential drivers of this dichotomy. Using ancestral reconstruction, we identified that certain groups of odontocetes evolved more-streamlined, presumably faster, body shapes around the same time that killer whales (Orcinus orca) evolved into whale predators approximately 1 Mya during the Pleistocene. This suggests that the evolution of a streamlined body shape may have been an adaptation to escape killer whale predation, leading to longer life-history events. To test this hypothesis, we performed a cluster analysis of odontocete whales and confirmed the dual pattern of life-history traits, with one group referred to as 'reproducers' characterized by early age of maturity, short gestation, short interbirth interval, and short lifespan, and the other group referred to as 'bet-hedgers' exhibiting the opposite pattern. However, we found that life history grouping was relatively unrelated to whale shape (i.e., more streamlined or less streamlined). Therefore, we incorporated principal component results into mixed effects models, and the model results indicated that body shape was positively related to neonate length (a measure of investment in progeny), but not significantly related to the temporal life-history traits. Thus, whale body shape is not a sufficient explanation for the evolution of fast-slow life histories in odontocete whales.
Supplementary information:
The online version contains supplementary material available at 10.1007/s11692-023-09605-4.
... Ford et al., 1998;de Bruyn et al., 2012). Indeed, the reliance on alternative prey sources, and the ability to switch between these, is likely a major driver of killer whale population connectivity in the entire eastern North Atlantic, with movements between Norway, Iceland, East Greenland and the North Sea, as also indicated by analysis of genetic, isotopic and photo-ID data (Bolt et al., 2009;Foote et al., 2010;Foote et al., 2013;Vongraven and Bisther, 2013). Thus, although herring constitute a major part of their diet, killer whales in the eastern North Atlantic appear to adopt a broad range of feeding strategies, and may not fit into the strict dietary ecotype classifications used for other populations. ...
Assessing the migratory behaviour of individual and groups of animals is key to understand the function of migration, its evolution, and how it is affected by environment and human activities. In the eastern North Atlantic, killer whales (Orcinus orca) presumably track herring stocks as they migrate between across the region. However, the detailed migratory and foraging behaviour of eastern North Atlantic killer whales is poorly understood. We report on the behaviour of 15 adult male killer whales equipped with Argos satellite transmitters during the winter of 2015-2016 along the coast of Troms, northern Norway. The animals were tracked for 8-104 days (mean: 41 days), during which they migrated 302-7608 Km (mean: 2646 Km). The observed movement of killer whales south to 64.2°N along the Norwegian coast following NSS-herring to their spawning grounds is in agreement with previous studies. However, our study is the first to also document northern migration of three of the Norwegian killer whales into the Barents Sea region towards Novaya Zemlya Island about 900 km from the Norwegian coast approaching 77.0°N. Importantly, using a Bayesian state-space model, we offer new insights on killer whale searching and transit movements, as well as diurnal patterns in swimming speed, preferred foraging habitat and feeding behaviour. The 15 tagged killer whales spend 75.0% of the time in an area restricted search (ARS) mode (range: 55.2-95.2%), 3.9% of the time in a transit mode (range: 0.0-16.1%) and 21.1% (range: 4.8-36.3%) in uncertain mode. The restricted search behaviour peaked at the end of January and beginning of February, after which the killer whales gradually performed transit behaviour as they followed the migrating herring out of the region, or shifted to other prey items.
... Finally, Type D, also known as subantarctic killer whales, have a circumpolar distribution in deep, oceanic waters between 40 S and 60 S (Pitman et al. 2011). It is very distinctive in appearance and highly divergent genetically from other ecotypes (Foote et al. 2013). ...
The killer whale—the largest of the dolphins and the top marine predator––has a cosmopolitan distribution throughout the world’s oceans. Although globally it could be considered a generalist predator with a diverse diet, it is deeply divided into ecotypes, many of which have distinct foraging strategies involving only a narrow range of prey species. These ecotypes, which often exist in sympatry, are believed to arise from culturally driven dietary specializations that develop within matrilineal social groups and are transmitted among matriline members and across generations by social learning. Specializations are maintained by behavioral conformity and social insularity of lineages, which result in reproductive isolation and, ultimately, genetic divergence of ecotypes. Ecotypes have distinct patterns of seasonal distribution, group size, social organization, foraging behavior, and acoustic activity that are related to the type of prey being sought. Sophisticated cooperative foraging tactics have evolved in some ecotypes, and prey sharing within matrilineal social groups is common. Remarkable behavioral and demographic attributes have been documented in one well-studied ecotype, including lifelong natal philopatry without dispersal of either sex from the social group, vocal dialects that encode genealogical relatedness within lineages, and multi-decade long post-reproductive periods of females. Cultural traditions of killer whales, including foraging specializations, can be deeply rooted and resistant to change, which may limit the ability of ecotypes to adapt to sudden environmental variability.
... A large and diverse community of killer whales (Orcinus orca, Types A, B1, and B2) are important top predators in this region (see Ainley et al. 2007Ainley et al. , 2010, but there are currently no data on their abundance or trends. These killer whale types are phenotypically, genetically, and culturally distinct, and may represent different species (Pitman and Ensor 2003;LeDuc et al. 2008;Morin et al. 2010Morin et al. , 2015Durban 2010, 2012;Foote et al. 2011Foote et al. , 2013Foote et al. , 2016Durban et al. 2017). To date, most research has focused on the pagophilic Type B killer whales, which are rarely observed away from Antarctica and show evidence of physiological adaptations to living in these frigid waters (Foote et al. 2011(Foote et al. , 2016. ...
A diverse community of phenotypically, genetically, and culturally distinct killer whales (Orcinus orca; Types B1, B2, and A) are important top predators in the coastal waters off the western Antarctic Peninsula (WAP), but there are currently no data on their abundance or trends. Most research to date has focused on the distinctive and pagophilic Type B killer whales and much less is known about the Type A killer whale, an open-water form that is more typical in appearance. Here, we integrate satellite telemetry (n = 10 tags, median duration = 57 days) and photo-identifications (13 years, 15,828 photographs) collected during austral summers from 2004/2005 to 2016/2017 to describe the movement patterns of Type A killer whales and estimate their abundance and trends in the coastal waters of the WAP. Tagged whales typically ranged widely on the continental shelf in the austral summer, but also moved over long distances into the Southern Ocean and beyond off both sides of South America (up to 3048 km from tagging site). Photographic re-sightings within this core summer range were common across years (up to 13 years), and a Bayesian Mark–recapture analysis estimated high average annual survival (posterior median = 0.98, 95% probability interval 0.74–1), and an average annual abundance that increased from a low of 91 (95% probability interval 58–147) in 2009/2010 to a high of 149 (95% PI 101–226) in 2016/2017. This increase may be a response to changing ice conditions that increased access to new feeding areas, and/or an increasing local abundance of marine mammal prey species in the WAP.
... A large and diverse community of killer whales (Orcinus orca, Types A, B1, and B2) are important top predators in this region (see Ainley et al. 2007Ainley et al. , 2010, but there are currently no data on their abundance or trends. These killer whale types are phenotypically, genetically, and culturally distinct, and may represent different species (Pitman and Ensor 2003;LeDuc et al. 2008;Morin et al. 2010Morin et al. , 2015Durban 2010, 2012;Foote et al. 2011Foote et al. , 2013Foote et al. , 2016Durban et al. 2017). To date, most research has focused on the pagophilic Type B killer whales, which are rarely observed away from Antarctica and show evidence of physiological adaptations to living in these frigid waters (Foote et al. 2011(Foote et al. , 2016. ...
A diverse community of phenotypically, genetically, and culturally distinct killer whales (Orcinus orca; Types B1, B2, and A) are important top predators in the coastal waters off the western Antarctic Peninsula (WAP), but there are currently no data on their abundance or trends. Most research to date has focused on the distinctive and pagophilic Type B killer whales and much less is known about the Type A killer whale, an open-water form that is more typical in appearance. Here, we integrate satellite telemetry (n = 10 tags, median duration = 57 days) and photo-identifications (13 years, 15,828 photographs) collected during austral summers from 2004/2005 to 2016/2017 to describe the movement patterns of Type A killer whales and estimate their abundance and trends in the coastal waters of the WAP. Tagged whales typically ranged widely on the continental shelf in the austral summer, but also moved over long distances into the Southern Ocean and beyond off both sides of South America (up to 3048 km from tagging site). Photographic re-sightings within this core summer range were common across years (up to 13 years), and a Bayesian Mark–recapture analysis estimated high average annual survival (posterior median = 0.98, 95% probability interval 0.74–1), and an average annual abundance that increased from a low of 91 (95% probability interval 58–147) in 2009/2010 to a high of 149 (95% PI 101–226) in 2016/2017. This increase may be a response to changing ice conditions that increased access to new feeding areas, and/or an increasing local abundance of marine mammal prey species in the WAP.
... Although broadly sympatric, these forms are morphologically distinct (i.e., readily field-identifiable). They also show consistent differences in habitat preferences, prey specialization, foraging behaviors, and mean group sizes, and evidence from molecular genetic analyses suggests that they could comprise different species (LeDuc et al. 2008;Morin et al. 2010Morin et al. , 2015Foote et al. 2013). Two Antarctic killer whale ecotypes are known to occur in McMurdo Sound (McM) in the southwestern Ross Sea, Antarctica ( Fig. 1): type B (presumably B1), a mammal-eating form that preys primarily on ice seals, and type C, a dwarf form currently known to feed only on fish (Pitman and Ensor 2003;Ballard and Ainley 2005;Pitman et al. 2007;Ainley and Ballard 2012;Pitman 2014;Eisert et al. 2015). ...
For over a century, the Ross Sea killer whale (RSKW; Orcinus orca, Antarctic type C), a fish-eating ecotype, has been commonly reported in McMurdo Sound (McM), Ross Sea, Antarctica. However, a significant population decline reported at Ross Island after 2006 has been linked to a commercial fishery that began in the Ross Sea in 1996–1997 and targets large Antarctic toothfish (Dissostichus mawsoni)—the presumed primary prey of RSKW. We assessed RSKW population abundance and trends using photo-identification data collected in McM during seven summers from 2001–2002 to 2014–2015. We identified 352 individual RSKWs and estimated an average annual population of 470 distinctly marked whales. Using a Bayesian mark–recapture model, we identified two population clusters: ‘regulars’ showed strong inter- and intra-annual site fidelity and an average annual abundance of 73 distinctive individuals (95% probability: 57–88); ‘irregulars’ were less frequently encountered but comprised a larger population with an annual estimate of 397 distinctive individuals (287–609). The number of seasonally resident regulars appeared to be stable over the period of purported RSKW decline, with the estimated annual number of deaths (6; 95% probability: 1–22) offset by the number of recruits (6; 2–19). As an alternative to the decline-due-to-fishery hypothesis, we suggest that the presence of mega-iceberg B-15 at Ross Island during the “iceberg years” (2000–2001 to 2005–2006) could have temporarily disrupted normal RSKW movement patterns, resulting in an apparent decline. Continued population monitoring of toothfish and their predators will be important for assessing ecosystem impacts of commercial fishing in the Ross Sea.
... In the NE Atlantic there is evidence for two partially sympatric populations that may specialize on different prey (herring and mackerel), and one parapatric population in lower latitudes . Long-term studies in the Southern Hemisphere have led to the discovery of further populations and ecotypes (e.g, Antarctic: Pitman & Ensor, 2003;Pitman et al., 2007Pitman et al., , 2011Foote et al., 2013;Argentina: Iñiguez, 2001;Crozet Islands: Guinet & Bouvier, 1995;New Zealand: Constantine et al., 1998;Visser, 1999;Visser et al., 2000). ...
Cultural evolution is a powerful process shaping behavioural phenotypes of many species including our own. Killer whales are one of the species with relatively well-studied vocal culture. Pods have distinct dialects comprising a mix of unique and shared call types; calves adopt the call repertoire of their matriline through social learning. We review different aspects of killer whale acoustic communication to provide insights into the cultural transmission and gene-culture co-evolution processes that produce the extreme diversity of group and population repertoires. We argue that the cultural evolution of killer whale calls is not a random process driven by steady error accumulation alone: temporal change occurs at different speeds in different components of killer whale repertoires, and constraints in call structure and horizontal transmission often degrade the phylogenetic signal. We discuss the implications from bird song and human linguistic studies, and propose several hypotheses of killer whale dialect evolution.
... Haplotypes were assigned sequences with missing data by construction of a neighbour joining tree and comparison to the most similar sequences. We identified 150 unique haplotypes, including previously identified haplotypes from 169 individuals in Morin et al. (2010) and Foote et al. (2011cFoote et al. ( , 2013b, plus eight sequences with missing data that prevented unambiguous assignment to an existing or unique haplotype. All 158 unique sequences representing 452 individual killer whales (after removal of duplicate sequences from three individuals that were sampled twice; see nuclear SNP analysis below) were used for phylogenetic analysis (Table S1, Supporting information). ...
... However, all social units are thought to all belong to the same population as they associate with each other (Tixier, 2012). Two distinct and genetically segregated morphotypes (Foote et al., 2013) are observed in Crozet waters the type D killer whales (Pitman et al., 2011;Tixier et al., 2014a) and the 'Crozet killer whales' (Tixier et al., 2014b) more similar to type A Antarctic killer whales (Pitman et al., 2011). Type D killer whales were uncommonly observed interacting with the fishery in Crozet waters and the two morphotypes were never observed to associate with each other. ...
This paper provides a synthesis of results obtained as part of a long-term collaborative study involving biologists, fishers, and resource managers—centring on the occurrence of killer whales in the Crozet Archipelago before and after the implementation of a demersal longline fishery for Patagonian toothfish. Depredation behaviour was reported as soon as the fishery was initiated, with dramatic effects on both the demographic trajectories of the killer whales and on the amount of fish lost by the fishers. Killer whales interacting with the fishery exhibited very high mortality rates when illegal fishing took place, while killer whales not interacting were unaffected. However, after illegal fishing ended, killer whales interacting with the fishery exhibited both higher fecundity and survival rates compared with killer whales not interacting. Since whales typically removed fish entirely from the hooks, an adapted methodology that did not rely on determining the number of damaged fish was developed to estimate depredation rates. In the Crozet EEZ over a 10-year period, 33.9% of the total amount of Patagonian toothfish caught, representing a total of 28 million €, was estimated to be lost due to the combined effects of killer whale and sperm whale depredation. In an effort to reduce depredation losses, modifications to fishing methods, such as changing the fishing season, changing fishing areas when exposed to depredation and changing longline length and hauling speed were successfully tested. Acoustic deterrent devices were ineffective in deterring killer whales from depredating longlines. Alternative fishing gears, such as fish pots, were also tested. However, while providing encouraging results regarding the suppression of depredation and seabird bycatch, fish pots were not efficient enough to sustain an economically viable fishery. In conclusion, we discuss how the findings of this comprehensive study can be used elsewhere in fisheries confronted with depredation.
... Two distinct morphotypes exist in the area: type-D killer whales (Pitman et al., 2010) and the 'Crozet killer whales'. They both interact with fisheries, but are genetically segregated (Foote et al., 2013). This study focused on the Crozet killer whales, which are genetically closer to type-A Antarctic killer whales. ...
Prey availability is a critical factor influencing demographic trajectories of long-lived, top predators, which may therefore be strongly affected by artificial food provisioning. In the Crozet archipelago, killer whales feed on a wide range of species including birds, marine mammals and fish. Following the development of the Patagonian toothfish fisheries in 1996, killer whales began to also depredate longlines. Social groups, hereafter referred to as matrilines, exhibited different levels of interaction; some were involved in most of the depredation events, while others were never observed interacting with fisheries. These differences in interaction levels influenced reproduction. An extensive photo-identification effort from 2003 to 2012 allowed us to estimate the probability of calving for 21 reproductive females. Using multi-model inference, we found a positive effect of depredation on female calving rate. These results suggest an effect of artificial food provisioning on female reproductive output with potentially far-reaching consequences on the demography of the Crozet killer whale population. Our findings evidence the need to account for both intra-population heterogeneity and level of interaction with fisheries when assessing conservation strategies of long-lived marine predators involved in similar depredation worldwide.
... Paired with recent studies on genetics, which showed that the two types are from very distant lineages (Foote et al., 2013), the social seggregation as well as the observed differences in morphology and likely foraging ecology suggest the sympatry of the Type-D and the Crozet killer whales. ...
... Killer whales (Orcinus orca) are found in all the world's oceans (Forney and Wade 2006), and this wide distribution results in a variety of morphological and behavioural patterns among populations (De Bruyn et al. 2013). In the Southern Ocean, 5 types of killer whales have been proposed (types A, B (2 forms), C, and D) based on differences in their diets, behaviour, morphology, habitat preferences, and genetic characteristics (Pitman and Ensor 2003;Morin et al. 2010;Pitman 2011;Foote et al. 2013). In southern South America, the species has been studied in detail in northern Patagonia (Argentina) (López and López 1985;Hoelzel 1991) and sightings have been compiled for southern Chile (Capella et al. 1999;Häussermann et al. 2013). ...
Killer whales occur in Chilean waters, but their seasonality, diets, and overall distribution are poorly known. Here, we present data on group composition, site fidelity, and prey species of individual killer whales recorded in 63 sightings between 2004 and 2012 in the Chilean Patagonian fjords. Group sizes were small (mean = 5, SD = 2.5 for calf groups; mean = 3, SD = 1.5 for non-calf groups), and occurrence was significantly lower in summer months. Photographs enabled identification of 55 individuals from natural markings, and all resembled Southern Ocean type A killer whales. The species was transient in the area; the average presence was 1.7 days with 60 % of individuals seen only once. Occupancy was 3–44 days, and low levels of site fidelity were recorded (64 % of individuals were seen in only 1 year). Group composition at short time scales (3 months) remained stable, but we detected changes at longer time scales. Prey included fish, otariids, and seabirds. Twelve individual killer whales showed a broad dietary spectrum: 3 ate otariids and fish, 2 ate birds and otariids, and 7 ate otariids, birds, and possibly fish. Further research is needed to increase basic biological knowledge of these killer whales and to determine the relationship with type A killer whales from the Southern Ocean.
... The ranges of these morphotypes can overlap or they may occur sympatrically, and while some are specialist feeders others are more generalist and can feed at different trophic levels. The systematic relationship between these different morphotypes is still not fully resolved, but complete mitochondrial genome analysis suggests that three (North Pacific transients, Southern Ocean Type B and Type C) could each be elevated to full species and others to subspecies pending additional data (Morin et al. 2010), while Type D could be either a distinct species or subspecies (Foote et al. 2013). The concept of killer whale ecotypes outside the North Pacific has been criticised by De Bruyn et al. (2013) who argue that there has been insufficient long-term behavioural/ecological research to establish whether morphotypes indeed correspond to ecotypes. ...
Killer whales Orcinus orca occur worldwide in a number of morphotypes that differ in size, pigmentation, acoustic behaviour, food type and genetics – some may indeed warrant subspecific or even specific status. Until recently, all killer whales in South African waters were referred to a single morphotype, Type A, but three individuals (two males and one female) that have stranded since 1969 differ in several respects from other killer whales examined from the region. Adult length is some 1–1.5 m smaller, appendages such as dorsal fin and flippers tend to be relatively larger, and tooth wear is excessive. Although dietary information is scant, one stomach contained the remains of several elasmobranchs, identified from a DNA subsample as blue sharks Prionace glauca, a dietary item that, if habitual, might account for the tooth wear. This morphotype, referred to here as ‘flat-toothed’ and which in several respects resembles the offshore form in the North Pacific and the Type 1 form in the North Atlantic, does not seem to have been recorded previously from the Southern Hemisphere.
... Recently, several ecotypes or distinguishable populations have been identified in the north-western Pacific Ocean, north-eastern Atlantic Ocean, New Zealand and Antarctica, differing in morphology, prey preference, social structure and distribution pattern (Ford et al. 1998, Baird 2000, Pitman & Ensor 2003, Taylor et al. 2008, Pitman et al. 2011. Recent molecular genetics and phylogeographic studies support the view that several ecotypes and populations have unique evolutionary histories, and some may qualify as full species or subspecies (LeDuc et al. 2008, Morin et al. 2010, Anonymous 2011, Foote et al. 2013a. The killer whale, as a single taxonomic unit, is classed as data deficient by the International Union for Conservation of Nature (Taylor et al. 2008). ...
Killer whales O rcinus orca are found in all oceans of the world, but most of our knowledge on the species comes from studies conducted at higher latitudes. Studies on killer whales in the C aribbean have been scarce.
We compiled 176 records of killer whales from the C aribbean, including 95 previously unreported records and 81 records recovered from the literature, consisting of 27 capture or kill records, 4 stranding records and 145 sighting records.
Our results indicate that killer whales are widespread in the C aribbean S ea and can be found year‐round in the region. Mean group size was 3.7 animals. A diversity of prey items was recorded, including sea turtles and marine mammals and possibly fish. We cannot exclude ecotype or morphotype‐specific dietary specialization in the C aribbean population. A preliminary morphological analysis of 10 characters in 52 individuals from 21 different groups suggests that C aribbean killer whales do not represent any of the four A ntarctic and subantarctic types, type 1 from the northwest A tlantic, or ‘resident’ and ‘transient’ killer whales from the northwest P acific. Some C aribbean killer whales share a combination of characters typical of type 2 in the N orth A tlantic, whereas others share those typical of ‘offshore’ killer whales in the northwest P acific. The significance of this is unclear. Comparison of C aribbean killer whales to previously described morphotypes and ecotypes is hampered by the lack of detailed, quantitative data on variation within other types, as well as by the lack of comparisons of genetic diversity.
Our study adds to the growing knowledge of the diversity of killer whales worldwide but underscores that additional research is warranted in the tropics.
The superorder Cetartiodactyla has expanded to occupy a wide range of terrestrial and marine niches with very different energy requirements. As mitochondria are the primary site of energy production, we hypothesized that the structure and evolutionary rate of Cetartiodactyla mitochondrial DNA (mtDNA) have been influenced by the metabolic requirements of different ecological niches. In this study, we constructed full-length mtDNA sequences for four Cetartiodactyla species: Babyrousa babyrussa, Stenella clymene, Stenella frontalis, and Cephalorhynchus commersonii. We performed comparative mitochondrial genome analysis, selection pressure analyses, and phylogenetic independent contrasts (PIC) analysis to detect the structure and evolutionary rate of mitogenomes from Cetartiodactyla native to plain, plateau, and marine niches. We found that the structure of Cetartiodactyla mtDNA was consistent across three niches. However, selection pressure analyses showed that the evolutionary rate of mtDNA protein-coding genes (PCGs) was significantly different between niches. The marine Cetartiodactyla had the highest rate of PCG evolution, while in terrestrial species, the evolutionary rate of all PCGs except ND3 and ND6 was faster in plateau Cetartiodactyla than in plain Cetartiodactyla. PIC analysis also demonstrated that PCG evolutionary rates were positively correlated with niche type (R2 = 0.1226, p = 0.04239). This study suggests divergent mechanisms for the evolution of mtDNA PCGs, prompting the adaptation of Cetartiodactyla to diverse niches.
The Antarctic Peninsula (AP) is rapidly warming and empirical data on abundance trends of marine organisms are required to understand the impact of these physical changes, and interacting anthropogenic impacts, on the ecosystem. Recent estimates inferred increasing abundance of Type A killer whales at the top of this food chain, and here we provide new data on the abundance of Type B1 and B2 killer whales using photographic mark‐recaptures collected during austral summers from 2008/2009 to 2017/2018. Both ecotypes were regularly photographed around the AP coastline, particularly off the west side, and individuals of both showed site fidelity across years. B1s had a higher re‐identification rate (58% photographed in multiple years, range: 1–7 years) compared to B2s (31%, 1–4 years). We fit mark‐recapture models that allowed temporary emigration beyond the study area, to effectively monitor the size of wide‐ranging populations and documented contrasting trends for B1s and B2s. A smaller population size (~102) of B1s was estimated to use the area, with a declining trend in abundance (−4.7% per year) and reduced apparent survival in recent years. In contrast, a much larger population size (~740) of B2s was estimated to be generally stable in abundance and apparent survival over the past decade.
In 1955, 17 killer whales (Orcinus orca) stranded on a beach in Paraparaumu, New Zealand. From the grainy, black and white photographs (Fig. 1), it was clear that they were not typical killer whales: they were small, with narrow, pointy dorsal fins, a bulbous head, and the prominent white eyepatch normally found on killer whales was reduced to a tiny slip. Nothing like them had ever been reported – either before the stranding or for decades afterward.
Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global dataset of killer whale genomes in a rare attempt to elucidate global population structure in a non-human species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during post-glacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.
Obtaining the representative morphological data required for traditional taxonomy is difficult, and sometimes impossible, for cetaceans, especially large ones. As a result, three quarters of the 88 currently recognized extant species have no subspecies and 40 taxa likely have additional unnamed taxa. Conservation needs give urgency to improving taxonomy because unnamed taxa are unlikely to receive protection equivalent to that received by named taxa. Genetic data can improve efforts to delimit subspecies, but the markers and methods used have varied and the magnitude of genetic difference used to justify subspecies distinctions across studies has also varied. Here, we define the concepts of populations, subspecies, and species to establish a foundation for developing guidelines (data to include and analyses to conduct) and quantitative standards (the magnitude of differentiation expected at different taxonomic levels) for using genetic data to support taxonomic recognition. Our definition is particularly applicable to data-poor groups because it allows for naming a subspecies when there is uncertainty about whether lineages have diverged sufficiently for species-level recognition. This allows a species that lacks convincing data for lineage divergence to be recognized as a subspecies while sufficient data are accrued, which could take decades for some cetaceans.
Sympatric forms of ecologically distinctive killer whales (Orcinus orca) have been documented worldwide. This study focused on a new case of such sympatric occurrence of the “Crozet” type and the recently described “type D” killer whales off the Crozet Islands. The two ecotypes are morphologically and genetically distinct, but they both depredate the same local longline fishery. We used observational, photo-identification, and fishing data, collected between 2003 and 2015, to examine differences in their patterns of depredation. Of the 828 sets where ecotype could be confirmed, type D killer whales interacted with 82 (11%) of the sets, including 9 (1%) sets that were simultaneously depredated by both ecotypes. Associations between the two types were never observed. Type D killer whales typically occurred in larger groups and both ecotypes preferentially depredated Patagonian toothfish (Dissostichus eleginoides). GLMM modeling revealed that the probability of type D depredation significantly increased throughout the study period, especially in deep waters, and photo-identification data suggested that a subset of all individuals were habituating to depredation. This study documents the partitioning of resources between two distinct ecotypes of killer whales and provides preliminary insight into the feeding ecology of the rare type D killer whale.
This paper provides field descriptions and biological observations of three different forms of killer whale (Orcinus orca) that occur in Antarctica based on field observations and a review of available photographs. Identifications were based on the relative size and orientation of the white eyepatch and the presence or absence of a dorsal cape. Type A (presumably the nominate form) has a medium-sized eyepatch oriented parallel to the body axis, no dorsal cape, it occurs mainly off-shore in ice-free water, has a circumpolar distribution and apparently preys mainly upon Antarctic minke whales (Balaenoptera bonaerensis). Type B also has an eyepatch oriented parallel to the body axis, but the eyepatch is at least twice as large as in Type A, it has a dorsal cape, mainly inhabits inshore waters, regularly occurs in pack-ice, is distributed around the continent and is regularly sighted in the Antarctic Peninsula area. Although it may also prey upon Antarctic minke whales and possibly humpback whales (Megaptera novaeangliae), seals seem to be the most important prey item. Type C has a small, forward-slanted eyepatch, a dorsal cape, inhabits inshore waters and lives mainly in the pack-ice; it occurs mostly off East Antarctica, and to date it has been recorded feeding only on Antarctic toothfish (Dissostichus mawsoni). Type C appears to be referable to Orcinus glacialis as described by Berzin and Vladimirov (1983). Although similar ecological specialisations have been reported for sympatric killer whale populations in the Northeast Pacific (i.e. an inshore mammal-eater, an inshore fish-eater and an offshore form), the extent of morphological divergence, habitat segregation and, perhaps, reproductive isolation, appears to be more pronounced among Antarctic populations. Although under a Biological Species Concept these forms appear to warrant separate species status, it will be important to show that this interpretation is consistent with results of molecular genetic analyses and additional morphological studies.
To understand the impact of a possibly warmer future climate, geologists are searching the past for warmer-than-present interglacial intervals — examples of what we may expect in a world with more greenhouse gases than ours1. A common tactic is to look at the last interglacial (around 120,000 years ago), but a period 423,000 to 362,000 years ago may fit the bill better, because the Earth's orbital geometry has been similar during the Holocene (the present interglacial period) to what it was then. This period is known to palaeoclimatologists as stage 11 or 'MIS 11', according to a numbering system for glacial advances and retreats marked in the marine oxygen isotope record (Fig. 1). At a recent symposium*, evidence emerged of extreme climatic variation and peculiar interplays between ocean temperature, thermohaline circulation, plankton ecology, sea level and reef growth during MIS 11, all of which may provide insight into the response of the natural carbon cycle to future climate change.
Background: Empirical and theoretical studies suggest that individual specialization can be an important force in evolutionary diversification. However, few studies of natural populations have explicitly considered the impact of individual specialization on adaptive divergence.
Questions: To what extent do individuals within a bimodal Darwin’s finch population specialize on different resources? Is this individual specialization likely to enhance adaptive divergence?
Field site: El Garrapatero, Santa Cruz Island, Galápagos, Ecuador.
Organism: A population of the medium ground finch, Geospiza fortis, showing large – and bimodal – morphological and genetic variation resulting from ecologically based adaptive divergence.
Methods: We described the diets of individual G. fortis through feeding observations in the wild. We calculated several indices of individual specialization. We then examined the relationship between individual specialization, adaptive morphological traits (beak and head dimensions), and neutral genetic variation (microsatellites). We also performed a cluster analysis on the basis of individual foraging observations and asked whether the clusters were morphologically and genetically divergent.
Results: We found significant levels of individual specialization and expected, but weak, associations between individual diet differences, morphological traits, and neutral genetic variation. The cluster analysis yielded two distinct diet-clusters of individuals that differed in morphological traits but not in neutral genetic markers. In the early stages of adaptive radiation, individual specialization appears to be associated with morphological divergence but not neutral genetic divergence.
Ecological speciation occurs when adaptation to different environments or resources causes the evolution of reproductive isolation. This process is now thought to be very important in the evolution of biological diversity. Indeed, support for ecological speciation is so often asserted in the literature that one can get the impression of ubiquity. Eager to ride on the coattails of this exciting work, my own research has investigated ecological speciation in guppies, sticklebacks, and Darwin’s finches. Much to my initial dismay, I failed to find simple and strong signatures of ecological speciation in the first two of these systems. Setting aside the possibility of personal incompetence, my apparent deviation from ubiquity might simply reflect an existing literature bias. This bias seems obvious in retrospect given that essentially all published studies of ecological speciation purport to be confirmatory, whereas many cases of divergent selection and adaptive divergence are associated with only weak to modest levels of reproductive isolation. In short, different populations can be arrayed along a continuum from panmixia to complete reproductive isolation. Variation along this continuum might profitably be used for studying factors, outlined herein, that can promote or constrain “progress” toward ecological speciation.
The persistence and size of social groups can be plastic and governed by ecological selection or be under greater genetic control and constrained by phylogenetic inertia. Comparing sociality of phylogenetically divergent populations under the same ecolog-ical conditions or between groups within a population under different ecological conditions can identify the relative influence of ecological selection on group formation. Here, we compare the size and persistence of social groups within a community of Atlantic killer whales, comparing between data collected from an area around Scotland where the whales have mainly been seen to hunt seals and data collected from an area around Iceland where the whales have mainly been seen to hunt herring. Additionally, we compare the observed social structure with that of previously studied Pacific ecotypes. Atlantic killer whale groups in both locations had a stable long-term primary social tier (association index level . 0.8) similar to that of Pacific killer whales. However, associations between these groups were much lower when hunting for seals than for fish in both the Atlantic and the Pacific. The occurrence of these differences in sociality between Atlantic groups, which are linked in a single social network, suggests that ecological selection partially determines sociality in this species. Furthermore, if sociality was constrained by phylogenetic inertia, then the Atlantic killer whales would all be expected to be more similar to the Pacific fish-eating ecotype than the more phylogenetically distant Pacific mammal-eating ecotype. Our study suggests that sociality in killer whales is to some extent plastic and can be adapted to the local ecological conditions.
Two forms of killer whale (Orcinus orca), resident and transient, occur sympatrically in coastal waters of British Columbia, Washington State, and southeastern Alaska. The two forms do not mix, and differ in seasonal distribution, social structure, and behaviour. These distinctions have been attributed to apparent differences in diet, although no comprehensive comparative analysis of the diets of the two forms had been undertaken. Here we present such an analysis, based on field observations of predation and on the stomach contents of stranded killer whales collected over a 20-year period. In total, 22 species of fish and 1 species of squid were documented in the diet of resident-type killer whales; 12 of these are previously unrecorded as prey of O. orca. Despite the diversity of fish species taken, resident whales have a clear preference for salmon prey. In field observations of feeding, 96% of fish taken were salmonids. Six species of salmonids were identified from prey fragments, with chinook salmon (Oncorhynchus tshawytscha ) being the most common. The stomach contents of stranded residents also indicated a preference for chinook salmon. On rare occasions, resident whales were seen to harass marine mammals, but no kills were confirmed and no mammalian remains were found in the stomachs of stranded residents. Transient killer whales were observed to prey only on pinnipeds, cetaceans, and seabirds. Six mammal species were taken, with over half of observed attacks involving harbour seals (Phoca vitulina). Seabirds do not appear to represent a significant prey resource. This study thus reveals the existence of strikingly divergent prey preferences of resident and transient killer whales, which are reflected in distinctive foraging strategies and related sociobiological traits of these sympatric populations. 1471
Metabolically inert, accretionary structures such as the dentin growth layers in teeth provide a life history record of individual diet with near-annual resolution. We constructed ontogenetic δ13C and δ15N profiles by analyzing tooth dentin growth layers from 13 individual killer whales Orcinus orca collected in the eastern northeast Pacific Ocean between 1961 and 2003. The individuals sampled were 6 to 52 yr old, representing 2 ecotypes-resident and transient - collected across ∼25° of latitude. The average isotopic values of transient individuals (n = 10) are consistent with a reliance on mammalian prey, while the average isotopic values of residents (n = 3) are consistent with piscivory. Regardless of ecotype, most individuals show a decrease in δ15N values of ∼2.5% through the first 3 yr of life, roughly equivalent to a decrease of one trophic level. We interpret this as evidence of gradual weaning, after which, ontogenetic shifts in isotopic values are highly variable. A few individuals (n = 2) maintained relatively stable δ15N and δ13C values throughout the remainder of their lives, whereas δ15N values of most (n = 11) increased by ∼1.5%, suggestive of an ontogenetic increase in trophic level. Significant differences in mean δ13C and δ15N values among transients collected off California suggest that individuality in prey preferences may be prevalent within this ecotype. Our approach provides retrospective individual life history and dietary information that cannot be obtained through traditional field observations of free-ranging and elusive species such as killer whales, including unique historic ecological information that pre-dates modern studies. By providing insights into individual diet composition, stable isotope analysis of teeth and/or bones may be the only means of evaluating a number of hypothesized historical dietary shifts in killer whales of the northeast Pacific Ocean.
The vast expanses of the South Pacific Ocean have, until recently, concealed the identity of the world's rarest whale, the spade-toothed beaked whale (Mesoplodon traversii). Based on the scarcity of records and the total absence of previous sightings, this species is the least known species of whale and one of the world's rarest living mammals. Two individuals of this species, previously known from only two skull fragments and a mandible, were recently discovered beach-cast in New Zealand. Although initially misidentified, we have used DNA analysis to reveal their true identity. We provide the first morphological description and images of this enigmatic species. This study highlights the importance of DNA typing and reference collections for the identification of rare species.
This paper provides field descriptions and biological observations of three different forms of killer whale (Orcinus orca) that occur in Antarctica based on field observations and a review of available photographs. Identifications were based on the relative size and orientation of the white eyepatch and the presence or absence of a dorsal cape. Type A (presumably the nominate form) has a medium-sized eyepatch oriented parallel to the body axis, no dorsal cape, it occurs mainly off-shore in ice-free water, has a circumpolar distribution and apparently preys mainly upon Antarctic minke whales (Balaenoptera bonaerensis). Type B also has an eyepatch oriented parallel to the body axis, but the eyepatch is at least twice as large as in Type A, it has a dorsal cape, mainly inhabits inshore waters, regularly occurs in pack-ice, is distributed around the continent and is regularly sighted in the Antarctic Peninsula area. Although it may also prey upon Antarctic minke whales and possibly humpback whales (Megaptera novaeangliae), seals seem to be the most important prey item. Type C has a small, forward-slanted eyepatch, a dorsal cape, inhabits inshore waters and lives mainly in the pack-ice; it occurs mostly off East Antarctica, and to date it has been recorded feeding only on Antarctic toothfish (Dissostichus mawsoni). Type C appears to be referable to Orcinus glacialis as described by Berzin and Vladimirov (1983). Although similar ecological specialisations have been reported for sympatric killer whale populations in the Northeast Pacific (i.e. an inshore mammal-eater, an inshore fish-eater and an offshore form), the extent of morphological divergence, habitat segregation and, perhaps, reproductive isolation, appears to be more pronounced among Antarctic populations. Although under a Biological Species Concept these forms appear to warrant separate species status, it will be important to show that this interpretation is consistent with results of molecular genetic analyses and additional morphological studies.
Background
With the advent of next-generation sequencing there is an increased demand for tools to pre-process and handle the vast amounts of data generated. One recurring problem is adapter contamination in the reads, i.e. the partial or complete sequencing of adapter sequences. These adapter sequences have to be removed as they can hinder correct mapping of the reads and influence SNP calling and other downstream analyses.
Findings
We present a tool called AdapterRemoval which is able to pre-process both single and paired-end data. The program locates and removes adapter residues from the reads, it is able to combine paired reads if they overlap, and it can optionally trim low-quality nucleotides. Furthermore, it can look for adapter sequence in both the 5’ and 3’ ends of the reads. This is a flexible tool that can be tuned to accommodate different experimental settings and sequencing platforms producing FASTQ files. AdapterRemoval is shown to be good at trimming adapters from both single-end and paired-end data.
Conclusions
AdapterRemoval is a comprehensive tool for analyzing next-generation sequencing data. It exhibits good performance both in terms of sensitivity and specificity. AdapterRemoval has already been used in various large projects and it is possible to extend it further to accommodate application-specific biases in the data.
A bstract
Killer whales ( Orcinus orca ) feed on a wide variety of fish, cephalopods, and marine mammals throughout their cosmopolitan range; however, the dietary breadth that characterizes the species is not reflected in all populations. Here, we present the findings of a 14‐yr study of the diet and feeding habits of killer whales in Prince William Sound, Alaska. Two non‐associating forms of killer whale, termed resident and transient (Bigg et al. 1987), were identified. All prey seen taken by transients were marine mammals, including harbor seals ( Phoca vitulina ), Dall's porpoises ( Phocoenoides dalli ), Steller sea lions ( Eumetopias jubatus ), and harbor porpoises ( Phocoena phocoena ). Resident killer whales appeared to prey principally on salmon ( Oncorhynchus spp.), preferring coho salmon ( O. kisutch ) over other, more abundant salmon species. Pacific herring ( Clupea pallasi ) and Pacific halibut ( Hippocampus stenolepis ) were also taken. Resident killer whales frequently were seen to interact in non‐predatory ways with Steller sea lions and Dall's porpoises, while transients were not. Differences in the social organization and behavior of the resident and transient killer whales in Prince William Sound are discussed in the light of the dietary differences documented here.
Studies have shown that killer whale (Orcinus orca) communities in high latitudes regularly comprise assemblages of sympatric ‘ecotypes’—forms that differ in morphology, behavior,
and prey preferences. Although they can appear superficially similar, recent genetic evidence suggests that breeding is assortative
among ecotypes within individual communities, and species-level divergences are inferred in some cases. Here, we provide information
on a recently recognized ‘type D’ killer whale based on photographs of a 1955 mass stranding in New Zealand and our own six
at-sea sightings since 2004. It is the most distinctive-looking form of killer whale that we know of, immediately recognizable
by its extremely small white eye patch. Its geographic range appears to be circumglobal in subantarctic waters between latitudes
40°S and 60°S. School sizes are relatively large (mean 17.6; range 9–35; n=7), and although nothing is known about the type D diet, it is suspected to include fish because groups have been photographed
around longline vessels where they reportedly depredate Patagonian toothfish (Dissostichus eleginoides).
KeywordsKiller whale–
Orcinus orca
–Subantarctic–Type D
Evidence from North Atlantic deep sea cores reveals that abrupt shifts punctuated what is conventionally thought to have been
a relatively stable Holocene climate. During each of these episodes, cool, ice-bearing waters from north of Iceland were advected
as far south as the latitude of Britain. At about the same times, the atmospheric circulation above Greenland changed abruptly.
Pacings of the Holocene events and of abrupt climate shifts during the last glaciation are statistically the same; together,
they make up a series of climate shifts with a cyclicity close to 1470 ± 500 years. The Holocene events, therefore, appear
to be the most recent manifestation of a pervasive millennial-scale climate cycle operating independently of the glacial-interglacial
climate state. Amplification of the cycle during the last glaciation may have been linked to the North Atlantic's thermohaline
circulation.
The harbour porpoise Phocoena phocoena, grey seal Halichoerus grypus, harbour seal Phoca vitulina and white-beaked dolphin Lagenorhynchus albirostris are regularly found stranded along southern North Sea coasts. Occasionally, offshore species such as the fin whale Balaenoptera physalus, the white-sided dolphin L. acutus and the sperm whale Physeter macrocephalus are also found stranded. In order to trace their diet, we measured delta(13)C and delta(15)N in their muscles as well as in 49 invertebrate and fish species collected from the southern North Sea. The delta(15)N data indicate that the harbour seal, grey seal and white-beaked dolphin occupy the highest trophic position, along with ichtyophageous fishes such as the cod Gadus morhua (mean muscle values of 18.7, 17.9, 18.8 and 19.2parts per thousand respectively). The harbour porpoise occupies a slightly lower trophic position (mean delta(15)N value of 16.2parts per thousand), reflecting a higher amount of zooplanktivorous fishes in its diet (mean delta(15)N of 14.7parts per thousand); 2 suckling harbour porpoises displayed a significant delta(15)N enrichment of 2.2parts per thousand compared to adult females. Adult females are delta(15)N-enriched compared to adult male harbour porpoises. Fin whales, sperm whales and white-sided dolphins are C-13-depleted compared to southern North Sea particulate organic matter and species, suggesting that despite regular sightings, they do not feed within the southern North Sea area.
The availability of mitochondrial genome sequences is growing as a result of recent technological advances in molecular biology. In phylogenetic analyses, the complete mitogenome is increasingly becoming the marker of choice, usually providing better phylogenetic resolution and precision relative to traditional markers such as cytochrome b (CYTB) and the control region (CR). In some cases, the differences in phylogenetic estimates between mitogenomic and single-gene markers have yielded incongruent conclusions. By comparing phylogenetic estimates made from different genes, we identified the most informative mitochondrial regions and evaluated the minimum amount of data necessary to reproduce the same results as the mitogenome. We compared results among individual genes and the mitogenome for recently published complete mitogenome datasets of selected delphinids (Delphinidae) and killer whales (genus Orcinus). Using Bayesian phylogenetic methods, we investigated differences in estimation of topologies, divergence dates, and clock-like behavior among genes for both datasets. Although the most informative regions were not the same for each taxonomic group (COX1, CYTB, ND3 and ATP6 for Orcinus, and ND1, COX1 and ND4 for Delphinidae), in both cases they were equivalent to less than a quarter of the complete mitogenome. This suggests that gene information content can vary among groups, but can be adequately represented by a portion of the complete sequence. Although our results indicate that complete mitogenomes provide the highest phylogenetic resolution and most precise date estimates, a minimum amount of data can be selected using our approach when the complete sequence is unavailable. Studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates similar to those obtained using the entire mitogenome.
To utilize the power of high-throughput sequencers, target enrichment methods have been developed. The majority of these require reagents and equipment that are only available from commercial vendors and are not suitable for the targets that are a few kilobases in length.
We describe a novel and economical method in which custom made long-range PCR products are used to capture complete human mitochondrial genomes from complex DNA mixtures. We use the method to capture 46 complete mitochondrial genomes in parallel and we sequence them on a single lane of an Illumina GA(II) instrument.
This method is economical and simple and particularly suitable for targets that can be amplified by PCR and do not contain highly repetitive sequences such as mtDNA. It has applications in population genetics and forensics, as well as studies of ancient DNA.
Mitochondria produce up to 95 per cent of the eukaryotic cell's energy. The coding genes of the mitochondrial DNA may therefore evolve under selection owing to metabolic requirements. The killer whale, Orcinus orca, is polymorphic, has a global distribution and occupies a range of ecological niches. It is therefore a suitable organism for testing this hypothesis. We compared a global dataset of the complete mitochondrial genomes of 139 individuals for amino acid changes that were associated with radical physico-chemical property changes and were influenced by positive selection. Two such selected non-synonymous amino acid changes were found; one in each of two ecotypes that inhabit the Antarctic pack ice. Both substitutions were associated with changes in local polarity, increased steric constraints and α-helical tendencies that could influence overall metabolic performance, suggesting a functional change.
INTRODUCTION
The large amount of DNA sequence data generated by high-throughput sequencing technologies often allows multiple samples to be sequenced in parallel on a single sequencing run. This is particularly true if subsets of the genome are studied rather than complete genomes. In recent years, target capture from sequencing libraries has largely replaced polymerase chain reaction (PCR) as the preferred method of target enrichment. Parallelizing target capture and sequencing for multiple samples requires the incorporation of sample-specific barcodes into sequencing libraries, which is necessary to trace back the sample source of each sequence. This protocol describes a fast and reliable method for the preparation of barcoded (“indexed”) sequencing libraries for Illumina’s Genome Analyzer platform. The protocol avoids expensive commercial library preparation kits and can be performed in a 96-well plate setup using multi-channel pipettes, requiring not more than two or three days of lab work. Libraries can be prepared from any type of double-stranded DNA, even if present in subnanogram quantity.
Killer whales (Orcinus orca) currently comprise a single, cosmopolitan species with a diverse diet. However, studies over the last 30 yr have revealed populations of sympatric "ecotypes" with discrete prey preferences, morphology, and behaviors. Although these ecotypes avoid social interactions and are not known to interbreed, genetic studies to date have found extremely low levels of diversity in the mitochondrial control region, and few clear phylogeographic patterns worldwide. This low level of diversity is likely due to low mitochondrial mutation rates that are common to cetaceans. Using killer whales as a case study, we have developed a method to readily sequence, assemble, and analyze complete mitochondrial genomes from large numbers of samples to more accurately assess phylogeography and estimate divergence times. This represents an important tool for wildlife management, not only for killer whales but for many marine taxa. We used high-throughput sequencing to survey whole mitochondrial genome variation of 139 samples from the North Pacific, North Atlantic, and southern oceans. Phylogenetic analysis indicated that each of the known ecotypes represents a strongly supported clade with divergence times ranging from approximately 150,000 to 700,000 yr ago. We recommend that three named ecotypes be elevated to full species, and that the remaining types be recognized as subspecies pending additional data. Establishing appropriate taxonomic designations will greatly aid in understanding the ecological impacts and conservation needs of these important marine predators. We predict that phylogeographic mitogenomics will become an important tool for improved statistical phylogeography and more precise estimates of divergence times.
Individual variation in resource use has often been ignored in ecological studies, but closer examination of individual patterns through time may reveal significant intrapopulation differences. Adult loggerhead sea turtles (Caretta caretta) are generalist carnivores with a wide geographical range, resulting in a broad isotopic niche. We microsampled scute, a persistent and continuously growing tissue, to examine long-term variation in resource use (up to 12 years) in 15 nesting loggerhead turtles. Using stable isotopes of nitrogen and carbon, we examined the resource use patterns (integration of diet, habitat and geographical location) and demonstrate that individual loggerheads are long-term specialists within a generalist population. We present our results in the context of a conceptual model comparing isotopic niches in specialist and generalist populations. Individual consistency may have important ecological, evolutionary and conservation consequences, such as the reduction of intraspecific competition.
1. Although conceptually robust, it has proven difficult to find practical measures of niche width that are simple to obtain, yet provide an adequate descriptor of the ecological position of the population examined. 2. Trophic niche has proven more tractable than other niche dimensions. However, indices used as a proxy for trophic niche width often suffer from the following difficulties. Such indices rarely lie along a single scale making comparisons between populations or species difficult; have difficulty in combining dietary prey diversity and evenness in an ecologically meaningful way; and fail to integrate diet over ecological time-scales thus usually only comprise single snapshots of niche width. 3. We propose an alternative novel method for the comparison of trophic niche width: the use of variance of tissue stable isotope ratios, especially those of nitrogen and carbon. 4. This approach is a potentially powerful method of measuring trophic niche width, particularly if combined with conventional approaches, because: it provides a single measure on a continuous axis that is common to all species; it integrates information on only assimilated prey over time; the integration period changes with choice of tissue sampled; and data production is theoretically fast and testing among populations simple. 5. Empirical studies are now required to test the benefits of using isotopic variance as a measure of niche width, and in doing so help refine this approach.
1. Inter-individual differences in trophic behaviour are considered important in the disruptive selection process for resource specialization and may represent an early phase in the evolution of polymorphism and adaptive radiation. Here, we provide evidence of high stability of individual trophic niches of a fish predator from a 15-year study.
2. Individual resource specialization was investigated by combining data from analyses of stomach contents (recent trophic niche), trophically transmitted parasites (long-term niche) and trophic morphology (niche adaptations) from single specimens of a postglacial fish (Arctic charr) population sampled from contrasting pelagic and littoral habitats.
3. Based on the relationships between morphology, parasites and diet, high inter-individual temporal consistency of narrow niches (zooplanktivorous vs. benthivorous) was evident through the ontogeny of the charr, indicating low degree of switching both in habitat utilization and feeding strategy of individual fish. Co-occurrence of differently specialized behavioural phenotypes was sustained over multiple generations.
4. The stable long-term habitat and feeding specializations may represent an important initial step in an adaptive radiation process, and our findings suggest a case of sympatric speciation into two incipient forms diverging along the littoral–pelagic resource axis.
We used mtDNA sequence data to confirm that the controversial 100-year-old holotype of the Bogotá sunangel (Heliangelus zusii) represents a valid species. We demonstrate that H. zusii is genetically well differentiated from taxa previously hypothesized to have given rise to the specimen via hybridization. Phylogenetic analyses place H. zusii as sister to a clade of mid- to high-elevation Andean species currently placed in the genera Taphrolesbia and Aglaiocercus. Heliangelus zusii, presumed extinct, has never been observed in nature by biologists. We infer that the species occupied a restricted distribution between the upper tropical and temperate zones of the northern Andes and that it was most probably driven to extinction by deforestation that accompanied human population growth during the nineteenth and early twentieth centuries. We demonstrate the feasibility of obtaining DNA from nearly microscopic tissue samples from old hummingbird specimens and suggest that these methods could be used to resolve the taxonomy of dozens of avian taxa known only from type specimens.
Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress
has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence
retrieval that greatly reduces sample destruction and sequencing demands and use this method to reconstruct the complete mitochondrial
DNA (mtDNA) genomes of five Neandertals from across their geographic range. We find that mtDNA genetic diversity in Neandertals
that lived 38,000 to 70,000 years ago was approximately one-third of that in contemporary modern humans. Together with analyses
of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than
that of modern humans and extant great apes.
The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Availability: http://samtools.sourceforge.net
Contact: rd@sanger.ac.uk
The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals.
We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is approximately 10-20x faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package.
http://maq.sourceforge.net.
Natural selection commonly drives the origin of species, as Darwin initially claimed. Mechanisms of speciation by selection fall into two broad categories: ecological and mutation-order. Under ecological speciation, divergence is driven by divergent natural selection between environments, whereas under mutation-order speciation, divergence occurs when different mutations arise and are fixed in separate populations adapting to similar selection pressures. Tests of parallel evolution of reproductive isolation, trait-based assortative mating, and reproductive isolation by active selection have demonstrated that ecological speciation is a common means by which new species arise. Evidence for mutation-order speciation by natural selection is more limited and has been best documented by instances of reproductive isolation resulting from intragenomic conflict. However, we still have not identified all aspects of selection, and identifying the underlying genes for reproductive isolation remains challenging.
Forty-nine species of cetaceans have been recorded in the literature with cookie cutter shark (Isistius sp.) bites. The first record of a cookie cutter shark bite mark on orca (Orcinus orca) was from New Zealand waters in 1955. We present 37 unpublished records of cookie cutter shark bite marks on orca in tropical to cold waters; a further six published records were collated, and additionally 35 individuals with bite marks were noted in photo-identification catalogues. A total of 120 individuals and 198 bite marks were recorded, with the northernmost at 70° 44' N and the southernmost at 77° 14' S. We provide the first heal- ing rate of a cookie cutter shark bite mark on an orca in New Zealand waters, with a maximum of 150 d between open wound and healed scar. Longevity of scars is considered, with one particular bite mark still visible as a dark grey oval/elliptic mark 1,158 d post photographing the open wound. Open cookie cutter shark bite marks were not observed on orca photo- graphed in Antarctic waters, despite the majority of bite marks being recorded on Antarctic orca. This sug- gests a high level of movement outside the Antarctic cold water regions as the known distribution of cookie cutter sharks is in warm temperate to tropical waters. Supporting evidence for these movements is given by records of Antarctic orca in New Zealand waters with open cookie cutter shark bite marks.
Our objectives were to investigate the seasonal occurrence of photoidentified killer whale pods in relation to the distribution of Norwegian spring-spawning herring and whether or not pod-specific differences in the occurrence or diet of killer whales could be demonstrated. In a 4-year study, the killer whales occurred in different areas during the summer and the fall-winter, and these areas coincided with the distribution areas of herring. Killer whales were encountered most frequently during October-January when the whole adult and part of the adolescent stock of spring-spawning herring wintered in the study area. Thirty-nine killer whale pods were identified, and generally the same pods were encountered each year of the study. Differences in the timing and areas of occurrence of pods could be demonstrated. Adult and adolescent herring seemed to be the main prey of the killer whales during both fall-winter and summer. Six new species were added to the list of known prey species of Norwegian killer whales. The present pattern of seasonal occurrence of killer whales in the coastal waters of northern Norway is expected to change as a result of growth in the Norwegian spring-spawning herring stock.
In six bird species convenient for study, niches are known to be broader on some islands than on the mainland. In every case there is also greater variation in a bill measurement on the islands, except for one species in which the niche on the Canary Islands is narrower than that on the mainland. The adjusted variances average about twice as great in the broader niche. These and other results suggest that continuous variation within local populations is often adaptive in itself and is not part of the genetic or phenotypic load.
Speciation is a process that occurs over time and, as such, can only be fully understood in an explicitly temporal context.
Here we discuss three major consequences of speciation’s extended duration. First, the dynamism of environmental change indicates
that nascent species may experience repeated changes in population size, genetic diversity, and geographic distribution during
their evolution. The present characteristics of species therefore represents a static snapshot of a single time point in a
species’ highly dynamic history, and impedes inferences about the strength of selection or the geography of speciation. Second,
the process of speciation is open ended—ecological divergence may evolve in the space of a few generations while the fixation
of genetic differences and traits that limit outcrossing may require thousands to millions of years to occur. As a result,
speciation is only fully recognized long after it occurs, and short-lived species are difficult to discern. Third, the extinction
of species or of clades provides a simple, under-appreciated, mechanism for the genetic, biogeographic, and behavioral ‘gaps’
between extant species. Extinction also leads to the systematic underestimation of the frequency of speciation and the overestimation
of the duration of species formation. Hence, it is no surprise that a full understanding of speciation has been difficult
to achieve. The modern synthesis—which united genetics, development, ecology, biogeography, and paleontology—greatly advanced
the study of evolution. Here we argue that a similarly synthetic approach must be taken to further our understanding of the
origin of species.
Epidermal skin samples from eastern North Atlantic killer whales, Orcinus orca, were analyzed for carbon and nitrogen stable isotope ratios. From those, comparisons within a data set of 17 samples collected from Tysfjord, Norway, in November suggested that diet is relatively specialized during this time period at this location. There were significant differences between a small set of samples from Iceland and those collected from Norway, which had all been assigned to the same population by a previous population genetics study. The results would be consistent with matrilines feeding on either the Norwegian or Icelandic stocks of Atlantic herring (Clupea harengus). There was no significant difference within Icelandic samples between those assigned to the population known to feed upon herring and those assigned to a population hypothesized to follow Atlantic mackerel (Scomber scombrus). The greatest differences were between the epidermal samples analyzed in this study and tooth and bone collagen samples from the North Sea that were analyzed previously, which also showed significantly more variation in isotopic ratios than found for skin samples. These differences could reflect differences in turnover rate, differences in diet-tissue fractionation and discrimination due to the amino acid composition of the different tissues, and/or greater competition promoting dietary variation between groups in the North Sea.
Stable isotope analysis (SIA) has emerged as a common tool in ecology and has proven especially useful in the study of animal diet, habitat use, movement, and physiology. SIA has been vigorously applied to the study of marine mammals, because most species live in habitats or undergo large migrations/movements that make them difficult to observe. Our review supplies a complete list of published SIA contributions to marine mammal science and highlights informative case examples in four general research areas: (1) physiology and fractionation, (2) foraging ecology and habitat use, (3) ecotoxicology, and (4) historic ecology and paleoecology. We also provide a condensed background of isotopic nomenclature, highlight several physiological considerations important for accurate interpretation of isotopic data, and identify research areas ripe for future growth. Because it is impossible to conduct controlled laboratory experiments on most marine mammal species, future studies in marine mammal ecology must draw on isotopic data collected from other organisms and be cognizant of key assumptions often made in the application of SIA to the study of animal ecology. The review is designed to be accessible to all audiences, from students unfamiliar with SIA to those who have utilized it in published studies.
Longitudinal records of prey selection by 10 adult female sea otters on the Monterey Peninsula, California, from 1983 to 1990 demonstrate extreme inter‐individual variation in diet. Variation in prey availability cannot explain these differences as the data were obtained from a common spatial‐temporal area.
Individual dietary patterns persisted throughout our study, thus indicating that they are life‐long characteristics.
Individual dietary patterns in sea otters appear to be transmitted along matrilines, probably by way of learning during the period of mother–young association.
Efficient utilization of different prey types probably requires radically different sensory/motor skills, each of which is difficult to acquire and all of which may exceed the learning and performance capacities of any single individual. This would explain the absence of generalists and inertia against switching, but not the existence of alternative specialists.
Such individual variation might arise in a constant environment from frequency‐dependent effects, whereby the relative benefit of a given prey specialization depends on the number of other individuals utilizing that prey. Additionally, many of the sea otter's prey fluctuate substantially in abundance through time. This temporal variation, in conjunction with matrilineal transmission of foraging skills, may act to mediate the temporal dynamics of prey specializations.
Regardless of the exact cause, such extreme individual variation in diet has broad ramifications for population and community ecology.
The published literature indicates that similar patterns occur in many other species.
Movement, site fidelity and connectivity have important consequences for the evolution of population structure and therefore
the conservation and management of a species. In this study photographs of naturally marked killer whales collected from sites
across the Northeast Atlantic are used to estimate fidelity to sampling locations and movement between locations, expressed
as transition probabilities, pt, using maximum likelihood methods. High transition probabilities suggest there is high inter-annual
site fidelity to all locations, and large-scale movement between the spawning and wintering grounds of both Norwegian and
Iceland stocks of Atlantic herring. There was no evidence of movement between the Norwegian herring grounds and Icelandic
herring grounds, or between the mackerel fishing grounds and the herring fishing grounds. Thus the movement of predictable
and abundant prey resources can lead to intrinsic isolation in this species We also find movement between the Northern Isles,
Scotland and East Iceland. An association network indicates that killer whales predating seals around the Northern Isles,
Scotland are linked to the community of killer whales that follow the Icelandic summer-spawning herring. This adds support
to existing evidence of a broad niche width in some populations.
KeywordsPopulation structure-Spatial dynamics-
Orcinus orca
-Connectivity
New experiments were performed with three-dimensional thermomechanical models of the Greenland and Antarctic ice sheets to simulate their behaviour during the glacial cycles, to reconstruct their thickness and extent at the Last Glacial Maximum (LGM), and to estimate their glacio-eustatic contribution to the global sea-level stand. The calculations used improved ice-dynamic and isostatic treatments, updated datasets on higher grid resolutions, and refined climatic treatments based on newly calibrated transfer functions between ice core records and climatic perturbations. Results are discussed from a reference run with standard parameters that is compared with available glacial-geological observations, and from a series of sensitivity experiments focusing on isostatic adjustment, thermomechanical coupling, climatic forcing, mass-balance changes, and basal melting rates and viscosity changes of Antarctic ice shelves. For the Antarctic ice sheet, we find that volume changes are closely linked with grounding line changes of the West Antarctic ice sheet. At the LGM, the grounding line extended close to the continental shelf break almost everywhere. Ice over central East Antarctica was generally thinner than today and varied mainly in accordance with accumulation fluctuations. For the Greenland ice sheet, melting is important only during interglacial periods and the most sensitive period concerns the size of the ice sheet during the Eemian. At the LGM, the Greenland ice sheet extended beyond the present coastline to cover at least the inner continental shelf and thinned by up to several hundred meters in central areas. For a plausible range of parameters, the experiments indicate that at the time of maximum sea-level depression (21 kyr BP), the Antarctic ice sheet contributed 14–18 m to the sea-level lowering, and the Greenland ice sheet 2–3 m, significantly less than the older CLIMAP reconstructions. Whereas both ice sheets were at 21 kyr BP close to their maximum extent, the experiments also indicate that their maximum volumes were reached only by 16.5 kyr BP (Greenland) and 10 kyr BP (Antarctica), equal to an additional sea-level lowering of, respectively, 0.4 and 3.7 m. Holocene retreat was essentially complete by 5 kyr BP in Greenland, but is found to still continue today in West Antarctica before reversing to growth during the next millenium. The models were found to reproduce gross features of the ice sheet's history since the LGM in reasonably good agreement with available glacial-geological data, although observational control on ice thickness changes remains very limited.
There are many sources of natural selection that can favour the evolution of ecological specialization in diet, habitat use or physiological tolerance. This review includes discussion of the ecological bases of such an evolution: environmental constancy, foraging theory, interspecific interactions, and mating rendezvous. Trade-offs and constraints are noted, and macroevolutionary aspects are outlined. Clades may be distinguished in which a particular specialization is phylogenetically conservative; in other clades species have different specializations. In the former case, trade-offs in morphological and physiological traits may enforce commitment to a historically acquired particular specialization; in the latter, selection for specialization per se may be imposed by ecological factors, eg competition or mating success. -P.J.Jarvis
1. The use of stable isotope data to infer characteristics of community structure and niche width of community members has become increasingly common. Although these developments have provided ecologists with new perspectives, their full impact has been hampered by an inability to statistically compare individual communities using descriptive metrics. 2. We solve these issues by reformulating the metrics in a Bayesian framework. This reformulation takes account of uncertainty in the sampled data and naturally incorporates error arising from the sampling process, propagating it through to the derived metrics. 3. Furthermore, we develop novel multivariate ellipse-based metrics as an alternative to the currently employed Convex Hull methods when applied to single community members. We show that unlike Convex Hulls, the ellipses are unbiased with respect to sample size, and their estimation via Bayesian inference allows robust comparison to be made among data sets comprising different sample sizes. 4. These new metrics, which we call SIBER (Stable Isotope Bayesian Ellipses in R), open up more avenues for direct comparison of isotopic niches across communities. The computational code to calculate the new metrics is implemented in the free-to-download package Stable Isotope Analysis for the R statistical environment.
Population genetic structure of North Atlantic killer whale samples was resolved from differences in allele frequencies of 17 microsatellite loci, mtDNA control region haplotype frequencies and for a subset of samples, using complete mitogenome sequences. Three significantly differentiated populations were identified. Differentiation based on microsatellite allele frequencies was greater between the two allopatric populations than between the two pairs of partially sympatric populations. Spatial clustering of individuals within each of these populations overlaps with the distribution of particular prey resources: herring, mackerel and tuna, which each population has been seen predating. Phylogenetic analyses using complete mitogenomes suggested two populations could have resulted from single founding events and subsequent matrilineal expansion. The third population, which was sampled at lower latitudes and lower density, consisted of maternal lineages from three highly divergent clades. Pairwise population differentiation was greater for estimates based on mtDNA control region haplotype frequencies than for estimates based on microsatellite allele frequencies, and there were no mitogenome haplotypes shared among populations. This suggests low or no female migration and that gene flow was primarily male mediated when populations spatially and temporally overlap. These results demonstrate that genetic differentiation can arise through resource specialization in the absence of physical barriers to gene flow.
Ecological divergence has a central role in speciation and is therefore an important source of biodiversity. Studying the micro-evolutionary processes of ecological diversification at its early stages provides an opportunity for investigating the causative mechanisms and ecological conditions promoting divergence. Here we use morphological traits, nitrogen stable isotope ratios and tooth wear to characterize two disparate types of North Atlantic killer whale. We find a highly specialist type, which reaches up to 8.5 m in length and a generalist type which reaches up to 6.6 m in length. There is a single fixed genetic difference in the mtDNA control region between these types, indicating integrity of groupings and a shallow divergence. Phylogenetic analysis indicates this divergence is independent of similar ecological divergences in the Pacific and Antarctic. Niche-width in the generalist type is more strongly influenced by between-individual variation rather than within-individual variation in the composition of the diet. This first step to divergent specialization on different ecological resources provides a rare example of the ecological conditions at the early stages of adaptive radiation.
Divergent natural selection has been shown to promote speciation in many taxa. However, although divergent selection often initiates the process of speciation, it often fails to complete it. Several time-based, geographic and genetic factors have been recognized to explain this variability in how far speciation proceeds. We review here recent evidence indicating that variability in the completeness of speciation can also be associated with the nature of divergent selection itself, with speciation being greatly promoted by (i) stronger selection on a given, single trait (the 'stronger selection' hypothesis) and (ii) selection on a greater number of traits (the 'multifarious selection' hypothesis). However, evidence for each selective hypothesis is still scarce, and further work is required to determine their relative importance.