Trans‐Pacific and trans‐Arctic pathways of the intertidal macroalga Fucus distichus L. reveal multiple glacial refugia and colonizations from the North Pacific to the North Atlantic

Aim We examined the phylogeography of the cold‐temperate macroalgal species Fucus distichus L., a key foundation species in rocky intertidal shores and the only Fucus species to occur naturally in both the North Pacific and the North Atlantic. Location North Pacific and North Atlantic oceans (42° to 77° N). Methods We genotyped individuals from 23 populations for a mitochondrial DNA (mtDNA) intergenic spacer (IGS) (n = 608) and the cytochrome c oxidase subunit I (COI) region (n = 276), as well as for six nuclear microsatellite loci (n = 592). Phylogeographic structure and connectivity were assessed using population genetic and phylogenetic network analyses. Results IGS mtDNA haplotype diversity was highest in the North Pacific, and divergence between Pacific haplotypes was much older than that of the single cluster of Atlantic haplotypes. Two ancestral Pacific IGS/COI clusters led to a widespread Atlantic cluster. High mtDNA and microsatellite diversities were observed in Prince William Sound, Alaska, 11 years after severe disturbance by the 1989 Exxon Valdez oil spill. Main conclusions At least two colonizations occurred from the older North Pacific populations to the North Atlantic between the opening of the Bering Strait and the onset of the Last Glacial Maximum. One colonization event was from the Japanese Archipelago/eastern Aleutians, and a second was from the Alaskan mainland around the Gulf of Alaska. Japanese populations probably arose from a single recolonization event from the eastern Aleutian Islands before the North Pacific–North Atlantic colonization. In the North Atlantic, the Last Glacial Maximum forced the species into at least two known glacial refugia: the Nova Scotia/Newfoundland (Canada) region and Andøya (northern Norway). The presence of two private haplotypes in the central Atlantic suggests the possibility of colonization from other refugia that are now too warm to support F. distichus. With the continuing decline in Arctic ice cover as a result of global climate change, renewed contact between North Pacific and North Atlantic populations of Fucus species is expected.     

THE BIOGEOGRAPHIC ORIGIN OF ARCTIC ENDEMIC SEAWEEDS: A THERMOGEOGRAPHIC VIEW1

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

Weak population genetic differentiation in the most numerous Arctic seabird,the little auk

Quantifying patterns of genetic diversity and differentiation among populations of Arctic birds is fundamental for understanding past and ongoing population processes in the Arctic. However, the genetic differentiation of many important Arctic species remains uninvestigated. Here, phylogeography and population genetics were examined in the worldwide population of a small seabird, the little auk (dovekie, Alle alle)—the most numerous avian species of the Arctic ecosystem. Blood samples or feathers were collected from 328 little auks (325 from the nominate subspecies and 3 from the A. a. polaris) in nine main breeding aggregations in the northern Atlantic and one location from the Pacific Ocean. The mtDNA haplotypes of the two subspecies were not segregated into separate groups. Also, no genetic structure was found within the nominate race based on microsatellite markers. The level of genetic differentiation among populations was low yet significant (mean F _ST = 0.005). Some pairwise F _ST comparisons revealed significant differences, including those involving the most distant Pacific colony as well as among some Atlantic populations. Weak population differentiation following the model of isolation by distance in the little auk is similar to the patterns reported in other high-Arctic bird species, indicating that a lack of distinct genetic structure is a common phenomenon in the Arctic avifauna.     

The fate of the Arctic seaweed Fucus distichus under climate change: an ecological niche modeling approach

Rising temperatures are predicted to melt all perennial ice cover in the Arctic by the end of this century, thus opening up suitable habitat for temperate and subarctic species. Canopy‐forming seaweeds provide an ideal system to predict the potential impact of climate‐change on rocky‐shore ecosystems, given their direct dependence on temperature and their key role in the ecological system. Our primary objective was to predict the climate‐change induced range‐shift of Fucus distichus, the dominant canopy‐forming macroalga in the Arctic and subarctic rocky intertidal. More specifically, we asked: which Arctic/subarctic and cold‐temperate shores of the northern hemisphere will display the greatest distributional change of F. distichus and how will this affect niche overlap with seaweeds from temperate regions? We used the program MAXENT to develop correlative ecological niche models with dominant range‐limiting factors and 169 occurrence records. Using three climate‐change scenarios, we projected habitat suitability of F. distichus – and its niche overlap with three dominant temperate macroalgae – until year 2200. Maximum sea surface temperature was identified as the most important factor in limiting the fundamental niche of F. distichus. Rising temperatures were predicted to have low impact on the species' southern distribution limits, but to shift its northern distribution limits poleward into the high Arctic. In cold‐temperate to subarctic regions, new areas of niche overlap were predicted between F. distichus and intertidal macroalgae immigrating from the south. While climate‐change threatens intertidal seaweeds in warm‐temperate regions, seaweed meadows will likely flourish in the Arctic intertidal. Although this enriches biodiversity and opens up new seaweed‐harvesting grounds, it will also trigger unpredictable changes in the structure and functioning of the Arctic intertidal ecosystem.     

The growth,reproductive phenology,and longevity of non-tide-pool Fucus distichus (L.) powell in New England

The growth, reproductive phenology, and longevity of in situ populations of Fucus distichus L. ssp. edentatus (De la Pylaie) Powell and F. distichus L. ssp. evanescens (C. Agardh) Powell were evaluated in New England. Both subspecies exhibited maximum growth during early summer, a slight decline in late summer, and a brief resurgence in the early fall. The maximum growth rates (in terms of elongation) for F. distichus ssp. edentatus and ssp. evanescens were 3.5 and 3.7 cm/28 days, respectively. Populations of both subspecies showed a distinct bimodal reproductive periodicity, with maxima in the spring and fall. Even so, individuals were either reproductive in the spring or fall but never in both seasons. After reproduction, receptacles dehisced and plants either became vegetative or died. Higher rates of plant attrition were observed during periods of reproduction than during non-reproductive periods.     

Origins of the Greenland shark (Somniosus microcephalus): Impacts of ice‐olation and introgression

Herein, we use genetic data from 277 sleeper sharks to perform coalescent‐based modeling to test the hypothesis of early Quaternary emergence of the Greenland shark (Somniosus microcephalus) from ancestral sleeper sharks in the Canadian Arctic‐Subarctic region. Our results show that morphologically cryptic somniosids S. microcephalus and Somniosus pacificus can be genetically distinguished using combined mitochondrial and nuclear DNA markers. Our data confirm the presence of genetically admixed individuals in the Canadian Arctic and sub‐Arctic, and temperate Eastern Atlantic regions, suggesting introgressive hybridization upon secondary contact following the initial species divergence. Conservative substitution rates fitted to an Isolation with Migration (IM) model indicate a likely species divergence time of 2.34 Ma, using the mitochondrial sequence DNA, which in conjunction with the geographic distribution of admixtures and Pacific signatures likely indicates speciation associated with processes other than the closing of the Isthmus of Panama. This time span coincides with further planetary cooling in the early Quaternary period followed by the onset of oscillating glacial‐interglacial cycles. We propose that the initial S. microcephalus–S. pacificus split, and subsequent hybridization events, were likely associated with the onset of Pleistocene glacial oscillations, whereby fluctuating sea levels constrained connectivity among Arctic oceanic basins, Arctic marginal seas, and the North Atlantic Ocean. Our data demonstrates support for the evolutionary consequences of oscillatory vicariance via transient oceanic isolation with subsequent secondary contact associated with fluctuating sea levels throughout the Quaternary period—which may serve as a model for the origins of Arctic marine fauna on a broad taxonomic scale.     

A mtDNA-based phylogeny of the brown algal genus Fucus (Heterokontophyta; Phaeophyta)

Species of Fucus are among the dominant seaweeds along Northern Hemisphere shores, but taxonomic designations often are confounded by significant intraspecific morphological variability. We analyzed intra- and inter-specific phylogenetic relationships within the genus (275 individuals representing 16 taxa) using two regions of the mitochondrion: a variable intergenic spacer and a conserved portion of the 23S subunit. Bayesian ML and MP analyses verified a shallow phylogeny with two major lineages (previously reported) and resolved some intra-lineage relationships. Significant species-level paraphyly/polyphyly was observed within lineages 1A and 2. Despite higher species richness in the North Atlantic, a North Pacific origin of the genus is supported by a gradient of decreasing haplotype and nucleotide diversities in F. distichus from the North Pacific to the East Atlantic.     

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

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

<Emphasis Type="Italic">Pseudoscopelus sagamianus</Emphasis> Tanaka, 1908 (Chiasmodontidae): Designation of the neotype,morphological characteristics of the North Pacific population,and species variation within its whole area

North Pacific Pseudoscopelus sagamianus (from the Kuroshio zone) are characterized morphologically in detail. The neotype is established. The North Pacific population and the group of populations from the Atlantic and Indian oceans are compared in detail, significant differences are found between them in coloration of the orobranchial cavity and in the pattern of photophores of series trf and prcf. In the author’s opinion, these differences are of the subspecies level. Potential areas of subspecies are discussed, and the area of the whole species is verified. A possibility of validity of the name P. pierbartus Spitz et al., 2007, for the group of populations from the Atlantic and Indian oceans is considered. Additions and changes to methods of investigations of Pseudoscopelus suggested by Melo et al. (2007) are critically discussed.     

The Bering Strait connection: dispersal and speciation in boreal macroalgae

A large number of boreal seaweeds have either sibling species or conspecific populations of a single species in the North Pacific and North Atlantic Oceans. This pattern is thought to have arisen from the dispersal between the two oceans through the Arctic Ocean after the opening of the Bering Strait in the mid-to-late Miocene or earliest Pliocene and from subsequent vicariant speciation as the Arctic Ocean froze and Bering Strait closed intermittently during glacial periods. Recent molecular studies of species in all three major seaweed phyla reveal patterns of vicariance. However, a number of lines of evidence point to differences in origins of these clades; some appear to be Pacific in origin whereas others appear to be derived from Atlantic stock. Different origins can be explained by recent stratigraphic finds that push the first Cenozoic opening of the Bering Strait back from 3.1–4.1 to 4.8–7.4 Ma (million years ago). Northern hemisphere ocean circulation models suggest that water flow would have been from the North Atlantic–Arctic south through the Bering Strait prior to the closure of the Panamanian Isthmus c. 3.5 Ma in contrast to the northward flow from the Pacific into the Arctic and North Atlantic, which developed after the closing of the Isthmus. Despite these differences in timing of the two invasions, there are no significant differences in levels of relationships among species with a North Atlantic origin compared with species with a North Pacific origin based on currently available data. More work is required to understand vicariance in seaweeds, especially in deciphering when a speciation event has occurred.     

Multilocus phylogeography and population structure of common eiders breeding in North America and Scandinavia

Aim Glacial refugia during the Pleistocene had major impacts on the levels and spatial apportionment of genetic diversity of species in northern latitude ecosystems. We characterized patterns of population subdivision, and tested hypotheses associated with locations of potential Pleistocene refugia and the relative contribution of these refugia to the post‐glacial colonization of North America and Scandinavia by common eiders (Somateria mollissima). Specifically, we evaluated localities hypothesized as ice‐free areas or glacial refugia for other Arctic vertebrates, including Beringia, the High Arctic Canadian Archipelago, Newfoundland Bank, Spitsbergen Bank and north‐west Norway. Location Alaska, Canada, Norway and Sweden. Methods Molecular data from 12 microsatellite loci, the mitochondrial DNA (mtDNA) control region, and two nuclear introns were collected and analysed for 15 populations of common eiders (n = 716) breeding throughout North America and Scandinavia. Population genetic structure, historical population fluctuations and gene flow were inferred using F‐statistics, analyses of molecular variance, and multilocus coalescent analyses. Results Significant inter‐population variation in allelic and haplotypic frequencies were observed (nuclear DNA F_ST = 0.004–0.290; mtDNA Φ_ST = 0.051–0.927). Whereas spatial differentiation in nuclear genes was concordant with subspecific designations, geographic proximity was more predictive of inter‐population variance in mitochondrial DNA haplotype frequency. Inferences of historical population demography were consistent with restriction of common eiders to four geographic areas during the Last Glacial Maximum: Belcher Islands, Newfoundland Bank, northern Alaska and Svalbard. Three of these areas coincide with previously identified glacial refugia: Newfoundland Bank, Beringia and Spitsbergen Bank. Gene‐flow and clustering analyses indicated that the Beringian refugium contributed little to common eider post‐glacial colonization of North America, whereas Canadian, Scandinavian and southern Alaskan post‐glacial colonization is likely to have occurred in a stepwise fashion from the same glacial refugium. Main conclusions Concordance of proposed glacial refugia used by common eiders and other Arctic species indicates that Arctic and subarctic refugia were important reservoirs of genetic diversity during the Pleistocene. Furthermore, suture zones identified at MacKenzie River, western Alaska/Aleutians and Scandinavia coincide with those identified for other Arctic vertebrates, suggesting that these regions were strong geographic barriers limiting dispersal from Pleistocene refugia.     

Diversity and distribution of foliose Bangiales (Rhodophyta) in West Greenland: a link between the North Atlantic and North Pacific

Greenland is a continental island in the northern part of the North Atlantic where the foliose Bangiales flora is poorly known. It is an important area for the study of algal biogeography because of the region’s glacial history, in which Greenland has been alternately exposed to or isolated from the North Pacific via the Bering Strait. A molecular study using 3′ rbcL + 5′ rbcL–S sequences was undertaken to assess the diversity of foliose Bangiales on the west coast of Greenland and rbcL sequences were used to study the Greenland flora in a larger phylogenetic and floristic context. New and historic collections document seven species in four genera from the west coast of Greenland. All species had a close link to North Pacific species, being either conspecific with them or North Atlantic–North Pacific vicariant counterparts.     

A new deep-sea hydroid (Cnidaria: Hydrozoa) from the Bering Sea Basin reveals high genetic relevance to Arctic and adjacent shallow-water species

The marine benthic fauna in Arctic shallow-water is reported to be a relatively young assemblage by species of either Pacific or Atlantic affinity. Whether current deep-sea Pacific species are included in the affinity or not is unknown. Combining morphological comparisons and genetic analyses, a new deep-sea hydroid to science, Sertularia xuelongi sp. nov. (Cnidaria: Hydrozoa: Sertulariidae), is described from the northern margin of the Bering Sea Basin at depths of 800–1570 m collected in 2010. It is characterized by slender and zigzag-shaped hydrocauli, alternately arranged hydrothecae and the absence of distal-lateral horns in fully matured female gonothecae. Its distribution, currently known only from Bering Sea Basin, suggests that it could not be an Arctic species with Pacific affinity. However, phylogenetic analyses based on the mitochondrial 16S rRNA gene show that it is clustered into a distinctive clade with four closely related species recorded from shallow-water of Northwest France, Iceland, Chukchi Sea and/or Bering Sea. In addition, its sequence similarity is highly relevant to these four species: Sertularia argentea (98.6 %), S. cupressina (98.8 %), S. plumosa (98.8 %) and S. robusta (99.4 %). All these provide a new insight into the relevance of North Pacific deep-sea species to the benthic fauna in Arctic and adjacent shallow-water. The taxonomic restriction of the genus Sertularia and the re-validation of the genus Polyserias are discussed. Future researches on more deep-sea species from Pacific and/or Atlantic are required to understand the evolution and speciation pattern involved in polar relevance.     

The microbiota of intertidal macroalgae Fucus distichus is site-specific and resistant to change following transplant

It is unclear how host-associated microbial communities will be affected by future environmental change. Characterizing how microbiota differ across sites with varying environmental conditions and assessing the stability of the microbiota in response to abiotic variation are critical steps towards predicting outcomes of environmental change. Intertidal organisms are valuable study systems because they experience extreme variation in environmental conditions on tractable timescales such as tide cycles and across small spatial gradients in the intertidal zone. Here we show a widespread intertidal macroalgae, Fucus distichus, hosts site-specific microbiota over small (meters to kilometres) spatial scales. We demonstrate stability of site-specific microbial associations by manipulating the host environment and microbial species pool with common garden and reciprocal transplant experiments. We hypothesized that F. distichus microbiota would readily shift to reflect the contemporary environment due to selective filtering by abiotic conditions and/or colonization by microbes from the new environment or nearby hosts. Instead, F. distichus microbiota was stable for days after transplantation in both the laboratory and field. Our findings expand the current understanding of microbiota dynamics on an intertidal foundation species. These results may also point to adaptations for withstanding short-term environmental variation, in hosts and/or microbes, facilitating stable host–microbial associations.     

Population genetic structure and evolutionary history of North Atlantic beluga whales (Delphinapterus leucas) from West Greenland, Svalbard and the White Sea

Population structure in many Arctic marine mammal species reflects a dynamic interplay between physical isolating mechanisms and the extent to which dispersal opportunities are met. We examined variation within mtDNA and eight microsatellite markers to investigate population structure and demographic history in beluga whales in the North Atlantic. Genetic heterogeneity was observed between Svalbard and West Greenland that reveals limited gene flow over ecological time scales. Differentiation was also recorded between Atlantic belugas and two previously studied populations in the North Pacific, the Beaufort Sea and Gulf of Alaska. However, Bayesian cluster analysis of the nDNA data identified two population clusters that did not correspond to the respective ocean basins, as predicted, but to: (1) Arctic (Svalbard–White Sea–Greenland–Beaufort Sea) and (2) Subarctic (Gulf of Alaska) regions. Similarly, the deepest phylogeographic signal was between the Arctic populations and the Gulf of Alaska. Fitting an isolation-with-migration model yielded genetic abundance estimates that match census estimates and revealed that Svalbard and the Beaufort Sea likely diverged 7,600–35,400 years ago but have experienced recurrent periods with gene flow since then, most likely via the Russian Arctic during subsequent warm periods. Considering current projections of continued sea ice losses in the Arctic, this study identified likely routes of future contact among extant beluga populations, and other mobile marine species, which have implications for genetic introgression, health, ecology and behavior.     

A molecular analysis of relationships and biogeography within a species complex of Holarctic fish (genus Osmerus)

Episodes of trans-Arctic faunal exchange and isolation between the north Pacific and Atlantic ocean basins have been implicated as important historic geological events contributing to extant patterns of genetic diversity and structure in Holarctic faunas. We made a further test of the significance of such biogeographic events by examining mitochondrial DNA (mtDNA) restriction fragment length and cytochrome b sequence polymorphism among north Pacific and Arctic, north-western Atlantic (north-eastern North American), and north-eastern Atlantic (European) regional forms of the boreal smelt, genus Osmerus. Our analyses also assessed whether the regional forms within this ‘species complex’: (i) represent a single widely distributed and polytypic species, or is composed of three geographically distinct species, and (ii) resulted from a single split from north Pacific ancestral Osmerus or two independent Pacific-Atlantic divergences. MtDNA sequence divergence estimates among forms ranged from 5.6–8.9% and from 6.1–8.5% based on restriction fragment and 300 base pairs of cytochrome b sequencing, respectively. Divergence within forms averaged less than 0.5% for fragment analysis and no differences were detected from sequence analysis. Provisional dating of lineage separations in Osmerus based on our sequence divergence estimates suggested a mid-Pliocene to early Pleistocene time frame for diversification among the forms. These estimated lineage separation dates support the idea that geological events in ‘Beringia’ and the surrounding trans-Arctic area (e.g. opening of the Bering Seaway, Pleistocene glacial advances), occurring over a similar time frame, have influenced radiation in Osmerus. Phenetic and parsimony analyses of the sequence divergence estimates and of sequence polymorphisms suggested that the north Pacific/Arctic form and the northwestern Atlantic form shared a common ancestor more recently than either has with the north-eastern Atlantic form, thus supporting the hypothesis that the species complex has arisen from two independent Pacific-Atlantic divergences probably beginning during the mid-Pliocene.     

Environmental confirmation of multiple ice age refugia for Pacific cod, Gadus macrocephalus

The concept of species surviving through quaternary climatic extremes by retreating to glacial refugia, and then evolving genetically during re-population movements of the following interglacial, has been in the literature for over 40 years. Recently, advances in genetic analysis have enabled this concept to be validated and theories regarding population expansions and contractions to be built. For the major Northern Hemisphere species of cod, Gadus morhua (Atlantic cod) and Gadus macrocephalus (Pacific cod), genetic analysis has suggested retreat to separate refugia on both sides of their respective ocean basins during the last glacial period. Ecosystem niche modelling has previously confirmed that environmental conditions during the last glacial were compatible with the existence of these separate refugia for Atlantic cod. Here it is shown that such modelling also confirms a reduced core glacial distribution for G. macrocephalus, but probable refugia on either side of the Pacific. Existing mitochondrial DNA analyses suggest two separate glacial populations in the northwest Pacific, which modelling confirms, with predicted separate marine refugia in the land-locked Sea of Japan basin and the Sea of Okhotsk. Existing mitochondrial DNA for the northeast Pacific populations is less conclusive regarding whether there were one or two separate refugia off this coast, and their location. Using environmental niche models this study shows the glacial NE Pacific environment could support two marine refugia, one centred in the Aleutians/Gulf of Alaska and the other off British Columbia. The intervening Cordilleran Ice Sheet, and the glacially sub-aerial and ice-free Queen Charlotte Islands shelf, is hypothesised to have constrained exchange between glacial stocks either side of the Islands. The postulated southern marine refugium is off-shore from an established terrestrial refugium, suggesting greater dependence of species and ecosystems during environmental change. An earth system approach to evolutionary change could enhance understanding of past and future ecosystems.     

Phylogeography and phylogeny of the epineritic cosmopolitan bonitos of the genus Sarda (Cuvier): inferred patterns of intra‐ and inter‐oceanic connectivity derived from nuclear and mitochondrial DNA data

Aim To reconstruct the phylogenetic relationships of the four species of the genus Sarda (Sarda sarda, Sarda orientalis, Sarda australis and Sarda chilensis) and their phylogeographic history in the context of historical and ecological biogeography. Also, to reconstruct within‐species phylogenetic relationships to test whether the North Atlantic and Mediterranean populations of Atlantic bonito (S. sarda) warrant subspecies status, and the validity of the allopatric northern and southern populations of eastern Pacific bonito (S. chiliensis), recognized as S. chiliensis lineolata and S. chiliensis chiliensis. Location Representative samples of all four Sarda species collected world‐wide were analysed. Methods Phylogenetic inference was carried out with neighbour‐joining, maximum parsimony and maximum likelihood, employing nucleotide sequences of the mitochondrial DNA (mtDNA) control region I (CR‐I) and of the single‐copy nuclear DNA (nDNA) Tmo‐4c4 gene. Analysis of molecular variance was used on the mtDNA data to estimate the extent of geographic population structuring. Results Gene trees derived from mtDNA and nDNA data yielded concordant phylogenies that support the monophyly of the genus Sarda. The following sibling pairs received strong statistical support: striped bonito (S. orientalis) with Australian bonito (S. australis), and Atlantic bonito (S. sarda) with eastern Pacific bonito (S. chiliensis). Furthermore, the origin of S. sarda mtDNA is paraphyletic with respect to S. chiliensis, and these results are indicative of introgression. The analysis of Tmo‐4c4 sequences corroborates the ancestral hybridization between these allopatric species. Comparisons of north‐west Atlantic and Mediterranean populations of S. sarda using mtDNA CR‐I data revealed substantial genetic differentiation. By contrast, no differences between the putative northern and southern allopatric subspecies of S. chiliensis were detected. Main conclusions The monophyly of the genus Sarda as indicated by morphology is corroborated using both molecular markers. However, molecular phylogenies depicted a paraphyletic relationship between S. sarda and S. chiliensis. This phylogeographical relationship is better explained by an ancestral introgression facilitated by trans‐Arctic contact during the Pleistocene. The pronounced genetic differentiation between S. sarda samples from the north‐west Atlantic and the Mediterranean is consistent with the differentiation of these two regions, but not with the amphi‐Atlantic speciation hypothesis. Finally, the S. chiliensis lineolata and S. chiliensis chiliensis subspecies status is not supported by the molecular data.