Comparative phylogeography of eastern chipmunks and white-footed mice in relation to the individualistic nature of species

Palaeoecological studies have demonstrated that ecological communities as a whole did not remain stable throughout the climatic fluctuations of the Quaternary. The result is that long-term associations of species cannot be inferred by contemporary associations in ecological communities. Therefore, the evolutionary significance of any contemporary ecological interactions among species and of the biotic community within which species have evolved also cannot be assumed from contemporary conditions. Comparative phylogeographic data provide a method to identify species within ecological communities that have shared biogeographic histories. We present an example of a long-term association between populations of two mammalian species, eastern chipmunks (Tamias striatus) and white-footed mice (Peromyscus leucopus), which are commonly associated with deciduous forest habitats. The distribution of mitochondrial DNA variation in T. striatus and P. leucopus from previously glaciated regions of the eastern United States support the hypothesis that, in at least part of their range, genetic lineages of the two species have expanded from similar population sources since the Last Glacial Maximum. In addition, the spatial concordance of genetic lineages of T. striatus and P. leucopus with the oak-savannah forest formations of Wisconsin and Illinois, suggest that populations associated with this community colonized the area in association with a set of arboreal species that comprise their deciduous forest habitat.     

Patterned cell development in the secondary phloem of dicotyledonous trees: a review and a hypothesis

The secondary phloem of dicotyledonous trees and shrubs is constructed of sieve tube cells (S) and their companion cells, as well as parenchyma (P) and fibre (F) cells. Different species have characteristic sequences of these S, P and F cells within the radial files of their phloem. The sequences are recurrent, and are evidence of rhythmic cell determination and differentiation. A model was devised to account for the sequences found in various dicot tree species. It is based on the pattern of radial displacement of cells through a gradient of morphogen which supports secondary phloem development. According to this model, each tree species shows a particular pattern of post-mitotic cellular displacement along each radial file as a result of a corresponding sequence of periclinal division in the cambial initial and its descendents. The divisions and displacements ensure that at each timestep (equivalent to an interdivisional interval) each cell resides in a specific location within the morphogenic gradient. Cells then emerge from the post-mitotic zone of cell determination, having acquired different final positional values. These values lie above a series of thresholds that permit the respective determination and subsequent differentiation of one or other of the three cell types S, P and F. The recurrent nature of the sequences of the three cell types within each radial cell file, as well as their tangential banding, are a consequence of a shared rhythmic spatio-temporal pattern of periclinal cambial divisions. With a single set of morphogen parameters required for cell determination, and using three positions for cambial cell divisions, all the cellular sequences of secondary phloem illustrated in the literature can be accounted for.This is an invited article.     

Multilocus phylogeography reveals nested endemism in a gecko across the monsoonal tropics of Australia

Multilocus phylogeography can uncover taxonomically unrecognized lineage diversity across complex biomes. The Australian monsoonal tropics include vast, ecologically intact savanna‐woodland plains interspersed with ancient sandstone uplands. Although recognized in general for its high species richness and endemism, the biodiversity of the region remains underexplored due to its remoteness. This is despite a high rate of ongoing species discovery, especially in wetter regions and for rock‐restricted taxa. To provide a baseline for ongoing comparative analyses, we tested for phylogeographic structure in an ecologically generalized and widespread taxon, the gecko Heteronotia binoei. We apply coalescent analyses to multilocus sequence data (mitochondrial DNA and eight nuclear DNA introns) from individuals sampled extensively and at fine scale across the region. The results demonstrate surprisingly deep and geographically nested lineage diversity. Several intra‐specific clades previously shown to be endemic to the region were themselves found to contain multiple, short‐range lineages. To infer landscapes with concentrations of unique phylogeographic diversity, we probabilistically estimate the ranges of lineages from point data and then, combining these estimates with the nDNA species tree, estimate phyloendemism across the region. Highest levels of phyloendemism occur in northern Top End, especially on islands, across the topographically complex Arnhem escarpment, and across the sandstone ranges of the western Gulf region. These results drive home that deep phylogeographic structure is prevalent in tropical low‐dispersal taxa, even ones that are ubiquitous across geography and habitats.     

Phylogeography of Southern Water Vole (Arvicola sapidus): evidence for refugia within the Iberian glacial refugium?

The role of Southern European peninsulas as glacial refugia for temperate species has been widely established, but phylogeographic patterns within refugia are being only recently addressed. Here we describe the phylogeographic patterns for Southern water vole ( Arvicola sapidus ) in its whole distribution across Iberia and France. Control region and cytochrome b sequences were obtained for 228 samples from 130 localities across Iberia and France. Eighty-five haplotypes were found in total yielding a high overall mitochondrial diversity (π = 0.027; H  = 0.974). Phylogeographic structure was relatively shallow (3.1% average intraspecific divergence) with few supported clades and 95% and 90% maximum parsimony unconnected networks, but significant, as reflected in increased pairwise nucleotide divergences with distance ( r  = 0.197, P  = 0.03) and significant autocorrelation up to ∼500 km. Spatial analysis of molecular variance analysis detected seven geographical groups explaining 43.73% of the total mitochondrial variation. We detected demographic expansions in three of these groups. A recent colonization of France from Iberia was suggested and estimated around 62 000 years bp by an isolation-with-migration model. Our results suggest the contribution of episodes of isolation in glacial subrefugia in Iberia, but seem to exclude a long-term isolation over successive glacial cycles. Phylogeographic divergence was probably tempered by relatively large population sizes and rapid and extensive mixing among subrefugia during interglacials, that might have eroded the phylogeographic structure accumulated at glacial peaks. Phenotypic differences in A. sapidus do not delineate historically isolated intraspecific divisions and do not warrant subspecific delimitations. Our results do support the existence of subrefugia within Iberia and their role in promoting intraspecific divergences.     

Highly divergent actins from karyorelictean, heterotrich, and litostome ciliates

We have cloned, sequenced, and characterized cDNA of actins from five ciliate species of three different classes of the phylum Ciliophora: Karyorelictea (Loxodes striatus), Heterotrichea (Blepharisma japonicum, Blepharisma musculus), and Litostomatea (Didinium nasutum, Dileptus margaritifer). Loxodes striatus uses UGA as the stop codon and has numerous in-frame UAA and UAG, which are translated into glutamine. The other four species use UAA as the stop codon and have no in-frame UAG nor UGA. The putative amino acid sequences of the newly determined actin genes were found to be highly divergent as expected from previous findings of other ciliate actins. These sequences were also highly divergent from other ciliate actins, indicating that actin genes are highly diverse even within the phylum Ciliophora. Phylogenetic analysis showed high evolutionary rate of ciliate actins. Our results suggest that the evolutionary rate was accelerated because of the differences in molecular interactions.     

Molecular phylogenetic relationships of Xiphidiopicus percussus, Melanerpes, and Sphyrapicus (Aves: Picidae) based on cytochrome B sequence

The endemic woodpecker, Xiphidiopicus percussus, from Cuba has been postulated as the sister taxon to the Hispaniolan woodpecker (Melanerpes striatus) and its relationships to the genera Sphyrapicus and Melanerpes have been speculated. We used mitochondrial cytochrome b sequences from a collection of New World picids to investigate the phylogenetic relationships among these species using maximum parsimony and maximum likelihood approaches. Our data suggest that X. percussus is the sister taxon to the Melanerpes woodpeckers, which appear to group into a single distinct clade. Xiphidiopicus percussus is not the sister taxon to M. striatus as has been postulated [Olson, S., 1972. The generic distinction of the Hispaniolan Woodpecker, Chryserpes striatus (Aves: Picidae). Proc. Biol. Soc. Wash. 85, 499-508]. The genus Sphyrapicus appears to have diverged earlier than Xiphidiopicus. Divergence estimates from the cytochrome b sequences indicate that Xiphidiopicus probably diverged sometime in the late Miocene-early Pliocene, and the endemic contemporary species X. percussus on Cuba may be a relict from a group that originated in Central America or North America.     

Phylogeographic incongruence of codistributed amphibian species based on small differences in geographic distribution

Codistributed species may display either congruent phylogeographic patterns, indicating similar responses to a series of shared climatic and geologic events, or discordant patterns, indicating independent responses. This study compares the phylogeographic patterns of two similarly distributed salamander species within the Pacific Northwest of the United States: Cope's giant salamander (Dicamptodon copei) and Van Dyke's salamander (Plethodon vandykei). Previous studies of P. vandykei support two reciprocally monophyletic lineages corresponding to coastal populations, located from the Olympic Mountains to the mouth of the Columbia River, and inland populations within the Cascade Mountains. We hypothesized that D. copei would have a congruent phylogeographic pattern to P. vandykei due to similarity in distribution and dependence upon similar stream and stream-side habitats. We test this hypothesis by estimating the phylogeny of D. copei using approximately 1800bp of mitochondrial DNA and comparing it to that of P. vandykei. Sympatric populations of D. copei and of P. vandykei display an identical phylogeographic pattern, suggesting similar responses within their shared distribution. Populations of D. copei occurring outside the range of P. vandykei displayed high levels of genetic divergence from those sympatric to P. vandykei. Overall, phylogeographic patterns between the two species were ultimately incongruent due to the high divergence of these allopatric populations. These results provide an example of codistributed species displaying overall incongruent phylogeographic patterns while simultaneously displaying congruent patterns within portions of their shared geographic distribution. This pattern demonstrates that a simple dichotomy of congruent and incongruent phylogeographic patterns of codistributed species may be too simplistic and that more complex intermediate patterns can result even from minor differences in species' ranges.     

Ghost mtDNA haplotypes generated by fortuitous NUMTs can deeply disturb infra‐specific genetic diversity and phylogeographic pattern

Nuclear copies of mitochondrial DNA (NUMTs or mitochondrial pseudogenes) are known to impede the detection of interspecific genetic diversity. But the effect of these artifacts on phylogeographic reconstruction remains under evaluated. In this study, we analysed a set of 115 sequences of a fragment of the cytochrome c oxidase subunit I gene (COI) of Monochamus galloprovincialis (Coleoptera, Cerambycidae) for which overlapping signals in sequencing electropherograms were observed. Comparison of full and corrected ‘ambiguities‐free’ data sets reveals the prevalence of numerous supernumerary haplotypes that deeply affect genetic diversity indices and phylogeographic patterns of this species. Slightly divergent pseudogenes were recovered in 49 of the 115 sequences. These results highlight the potential misdetection of NUMTs using current control methods and the consequences on phylogeographic structure. To test the frequency of unintended amplification of NUMTs, a cloning was performed on 15 individuals. An average of 3.72 and a maximum of six paralogous sequences with different levels of divergence were identified among individual cloned. Within individual pairwise distance between paralogs raised 1.4%. This work calls for awareness to the presence of undetected NUMTs within mitochondrial data sets, especially at infra‐specific level.     

Wolbachia Infections Mimic Cryptic Speciation in Two Parasitic Butterfly Species,Phengaris teleius and P. nausithous (Lepidoptera: Lycaenidae)

Deep mitochondrial divergence within species may result from cryptic speciation, from phylogeographic isolation or from endosymbiotic bacteria like Wolbachia that manipulate host reproduction. Phengaris butterflies are social parasites that spend most of their life in close relationship with ants. Previously, cryptic speciation has been hypothesised for two Phengaris species based on divergent mtDNA sequences. Since Phengaris species are highly endangered, the existence of cryptic species would have drastic consequences for conservation and management. We tested for cryptic speciation and alternative scenarios in P. teleius and P. nausithous based on a comprehensive sample across their Palaearctic ranges using COI gene sequences, nuclear microsatellites and tests for Wolbachia. In both species a deep mitochondrial split occurring 0.65–1.97 myrs ago was observed that did not correspond with microsatellite data but was concordant with Wolbachia infection. Haplotypes previously attributed to cryptic species were part of the Wolbachia-infected clades. In both species remaining phylogeographic structure was largely consistent between mitochondrial and nuclear genomes. In P. teleius several mitochondrial and nuclear groups were observed in East Asia while a single haplogroup and nuclear cluster prevailed across continental Eurasia. Neutrality tests suggested rapid demographic expansion into that area. In contrast, P. nausithous had several mitochondrial and nuclear groups in Europe, suggesting a complex phylogeographic history in the western part of the species range. We conclude that deep intraspecific divergences found in DNA barcode studies do not necessarily need to represent cryptic speciation but instead can be due to both infection by Wolbachia and phylogeographic structure.     

Conservation of phylogeographic lineages under climate change

Aim We address the unexplored question of whether the lack of information on intra‐specific diversity inherent in species‐level niche modelling might bias evaluation of the conservation requirements of species and phylogeographic lineages under changing climates. We test for directional biases that might arise due to these methodological differences in ways of assessing risks from climate change. Location The African continent. Methods We identified from peer‐reviewed studies that used both nuclear and plastid markers the distribution of deep phylogeographic divisions within nine species of African mammals and their phylogeographic lineages. We fitted ecological niche models to describe currently suitable, occupied climates and to project the shift of suitable climate to two future time slices. We applied gap analysis to reveal potential changes in the protection of phylogeographic diversity owing to climatic shifts. Results We found that, within species, most phylogeographic lineages differ in the climates they experience and have substantial geographic separation. Models that do not distinguish these subspecific units often fail to identify potential risks of climate change to lineages. Modelled potential effects of climate change on the geographic extent of suitable climate vary in both direction and magnitude. Predictions of the persistence of suitable climate in current protected areas for the resident lineages differ on average by factor of 2 between species and lineage models. Main conclusions Our study develops an original synthetic approach by combining niche modelling, projected climate change, phylogeographic information and gap analysis. We clearly identify the potential benefits of using the new approach to evaluate risks to the conservation of intra‐specific genetic diversity that are posed by climate change. Our results suggest that prudent conservation strategies need to incorporate potential differences in climate tolerance among lineages when planning conservation measures for species confronted with environmental change.     

Phylogeography of Potamon ibericum (Brachyura: Potamidae) identifies Quaternary glacial refugia within the Caucasus biodiversity hot spot

Refugia are critical for the maintenance of biodiversity during the periods of Quaternary climatic oscillations. The long‐term persistence of refugial populations in a large continuous refugium has resulted in a homogenous pattern of genetic structure among populations, while highly structured evolutionary lineages characterize the restriction of refugial populations to smaller subrefugia. These mechanisms have resulted in the identification of hot spots of biodiversity within putative glacial refugia. We studied phylogeography of Potamon ibericum (Brachyura: Potamidae) in the drainages of the western Caucasus biodiversity hot spot (i.e., Colchis and the Caucasus) to infer spatial genetic structure and potential refugia for a freshwater crab in this region. These areas have traditionally considered as a refugium due to the presence of Tertiary relict species. We integrated population genetic data and historical demographic analysis from cytochrome oxidase subunit I sequences and paleoclimatic data from species distribution modeling (SDM). The results revealed the lack of phylogeographic structure and provided evidence for demographic expansion. The SDM presented a rather homogenous and large refugium that extended from northeast Turkey to Colchis during the last glacial period. In contrast to these findings, previous phylogeographic study on P. ibericum of the eastern Caucasus biodiversity hot spot (i.e., Hyrcania) identified multiple independent refugia. By combining these results, we explain the significance of this important western Palearctic hot spot of biological diversity in shaping the geographic distribution of intraspecific genetic diversity in a freshwater taxon.     

Phylogeography of Iris missouriensis (Iridaceae) based on nuclear and chloroplast markers

We investigated the phylogeography of Iris missouriensis (Iridaceae), which is widely distributed in western North America. We utilized transposon display and DNA sequencing to quantify nuclear and chloroplast genetic structure. Our objectives were (i) to characterize the geographic structure of genetic variation throughout the species range, (ii) to test whether both margins of the range show reduced genetic diversity as predicted by north-south expansion and contraction associated with climate change, and (iii) to determine whether the subspecies Iris missouriensis ssp. longipetala is genetically distinct. We found that genetic diversity was significantly lower in the northern part of the range but was not significantly different between the central and southern regions, indicating greater stability of the southern margin vs. the northern. Among-population differentiation was high (PhiPT=0.52). The largest divisions in each marker set were concordant and separated the southern Rocky Mountains and Basin and Range provinces from the remainder of the range. The boundaries of this phylogeographic break do not coincide with gaps in present-day distributions or phylogeographic breaks identified in other species, and may indicate a measure of reproductive isolation. Consistent with current treatments, we did not find support for the taxonomic placement of I. missourienis ssp. longipetala as a distinct species. Although transposon display has been used to investigate relationships among crop accessions and their wild relatives, to our knowledge, this is the first use of these markers for population-level phylogeography of a nonmodel species and further demonstrates their utility in species recalcitrant to amplified fragment length polymorphism protocols.     

Mitochondrial DNA hypervariable region-1 sequence variation and phylogeny of the concolor gibbons, Nomascus

The still little known concolor gibbons are represented by 14 taxa (five species, nine subspecies) distributed parapatrically in China, Myanmar, Vietnam, Laos and Cambodia. To set the stage for a phylogeographic study of the genus we examined DNA sequences from the highly variable mitochondrial hypervariable region-1 (HVR-1 or control region) in 51 animals, mostly of unknown geographic provenance. We developed gibbon-specific primers to amplify mtDNA noninvasively and obtained >477 bp sequences from 38 gibbons in North American and European zoos and >159 bp sequences from ten Chinese museum skins. In hindsight, we believe these animals represent eight of the nine nominal subspecies and four of the five nominal species. Bayesian, maximum likelihood and maximum parsimony haplotype network analyses gave concordant results and show Nomascus to be monophyletic. Significant intraspecific variation within N. leucogenys (17 haplotypes) is comparable with that reported earlier in Hylobates lar and less than half the known interspecific pairwise distances in gibbons. Sequence data support the recognition of five species (concolor, leucogenys, nasutus, gabriellae and probably hainanus) and suggest that nasutus is the oldest and leucogenys, the youngest taxon. In contrast, the subspecies N. c. furvogaster, N. c. jingdongensis, and N. leucogenys siki, are not recognizable at this otherwise informative genetic locus. These results show that HVR-1 sequence is variable enough to define evolutionarily significant units in Nomascus and, if coupled with multilocus microsatellite or SNP genotyping, more than adequate to characterize their phylogeographic history. There is an urgent need to obtain DNA from gibbons of known geographic provenance before they are extirpated to facilitate the conservation genetic management of the surviving animals.     

Phylogeographic inferences from chloroplast DNA: quantifying the effects of mutations in repetitive and non-repetitive sequences

Phylogeographic inference can be a powerful tool in reconstructing species’ evolutionary histories; however, although inferred phylogeographic patterns should depend in part on the underlying types and rates of mutations, the effects of different types of mutations have seldom been quantified. In this study we identified two chloroplast minisatellites in the common reed Phragmites australis, and showed that these are more variable than chloroplast microsatellites. We then recreated parsimony networks of the global phylogeography of P. australis based on data that either included or excluded repetitive sequences (minisatellites and microsatellites), thereby illustrating the influence that these repetitive sequences can have on large‐scale phylogeographic inference. The resulting networks differed in the numbers of mutational steps, degrees of uncertainty, and total numbers of haplotypes. In addition, the suggested ancestor‐descendant relationships among lineages changed substantially depending on whether repetitive sequences were included. We therefore caution against the inclusion of repetitive sequences in large‐scale networks because of their high potential for homoplasy. Nevertheless, we advocate the inclusion of repetitive sequences in other analyses: specifically, we show that the ratio of mutations in repetitive vs. non‐repetitive regions can provide insight into the relative ages of lineages.     

Comparative phylogeographies of six species of hinged terrapins (Pelusios spp.) reveal discordant patterns and unexpected differentiation in the P. castaneus/P. chapini complex and P. rhodesianus

Using up to 2117 bp of mitochondrial DNA and up to 2012 bp of nuclear DNA, we analysed phylogeographic differentiation of six widely distributed species of African hinged terrapins (Pelusios spp.) representing different habitat types. Two taxa each live in savannahs or in forests and mesic savannahs, respectively, and the remaining two species occur in intermediate habitats. The species living in forests and mesic savannahs do not enter dry savannahs, whereas the savannah species may occur in dry and wet savannahs and even in semi‐arid steppe regions. We found no obvious correlation between habitat type and phylogeographic pattern: one savannah species (P. rhodesianus) shows phylogeographic structure, i.e. pronounced genetic differences among geographically distinct populations, and the other (P. nanus) not. One species inhabiting forests and mesic savannahs (P. carinatus) has phylogeographic structure, the other (P. gabonensis) not. The same pattern is true for the two ecologically intermediate species, with phylogeographic structure present in P. castaneus and absent in P. chapini. Nuclear evidence suggests that the latter two taxa with abutting and partially overlapping ranges are distinct, while mtDNA is only weakly differentiated. Pelusios castaneus shows pronounced phylogeographic structure, which could reflect Pleistocene range interruptions correlated with the fluctuating forest cover in West and Central Africa. Our results do not support the recognition of an extinct subspecies of P. castaneus for the Seychelles. Pelusios carinatus contains two well supported clades, which are separated by the Congo River. This species is closely related to P. rhodesianus, a taxon consisting of two deeply divergent mitochondrial clades. One of these clades is paraphyletic with respect to P. carinatus, but the two clades of P. rhodesianus are not differentiated in the studied nuclear markers and, again, paraphyletic with respect to P. carinatus. Using mtDNA sequences from the type material of P. rhodesianus, we were able to allocate this name to one of the two clades. However, owing to the confusing relationships of P. rhodesianus and P. carinatus, we refrain from taxonomic decisions.     

Low Phylogeographic Structure in a Wide Spread Endangered Australian Frog <Emphasis Type="Italic">Litoria aurea</Emphasis> (Anura: Hylidae)

The green and golden bell frog (Litoria aurea) has a widespread distribution along the south-east coast of Australia. The species range, however, is highly fragmented and remaining populations are predominately isolated and restricted to the coastline. Previously, the range extended further inland and the species was considered common. Here we report a study designed to identify the phylogeographic and conservation genetic parameters of L. aurea. Mitochondrial DNA sequences were examined from 263 individuals sampled from 26 locations using both phylogenetic and population analyses. Despite a general consensus that amphibians are highly structured we found no phylogeographic divisions within the species, however, there was significant structure amongst extant populations (F _ST=0.385). Patterns of haplotype relatedness, high haplotypic diversity (mean h=0.547) relative to low nucleotide diversity (mean π=0.003) and mismatch distribution analysis supported a Pleistocene expansion hypothesis with continued restricted dispersal and gene flow. We conclude that the genetic structure of the species may permit ‘well managed’ intervention to mediate gene flow amongst isolated populations and provide some guidelines for the implementation of such conservation strategies.     

Computational and comparative analyses of 150 full-length cDNA sequences from the oomycete plant pathogen Phytophthora infestans

Phytophthora infestans is a devastating phytopathogenic oomycete that causes late blight on tomato and potato. Recent genome sequencing efforts of P. infestans and other Phytophthora species are generating vast amounts of sequence data providing opportunities to unlock the complex nature of pathogenesis. However, accurate annotation of Phytophthora genomes will be a significant challenge. Most of the information about gene structure in these species was gathered from a handful of genes resulting in significant limitations for development of ab initio gene-calling programs. In this study, we collected a total of 150 bioinformatically determined near full-length cDNA (FLcDNA) sequences of P. infestans that were predicted to contain full open reading frame sequences. We performed detailed computational analyses of these FLcDNA sequences to obtain a snapshot of P. infestans gene structure, gauge the degree of sequence conservation between P. infestans genes and those of Phytophthora sojae and Phytophthora ramorum, and identify patterns of gene conservation between P. infestans and various eukaryotes, particularly fungi, for which genome-wide translated protein sequences are available. These analyses helped us to define the structural characteristics of P. infestans genes using a validated data set. We also determined the degree of sequence conservation within the genus Phytophthora and identified a set of fast evolving genes. Finally, we identified a set of genes that are shared between Phytophthora and fungal phytopathogens but absent in animal fungal pathogens. These results confirm that plant pathogenic oomycetes and fungi share virulence components, and suggest that eukaryotic microbial pathogens that share similar lifestyles also share a similar set of genes independently of their phylogenetic relatedness.     

Spatial and temporal patterns of genetic variation in the widespread antitropical deep‐sea coral Paragorgia arborea

Numerous deep‐sea species have apparent widespread and discontinuous distributions. Many of these are important foundation species, structuring hard‐bottom benthic ecosystems. Theoretically, differences in the genetic composition of their populations vary geographically and with depth. Previous studies have examined the genetic diversity of some of these taxa in a regional context, suggesting that genetic differentiation does not occur at scales of discrete features such as seamounts or canyons, but at larger scales (e.g. ocean basins). However, to date, few studies have evaluated such diversity throughout the known distribution of a putative deep‐sea species. We utilized sequences from seven mitochondrial gene regions and nuclear genetic variants of the deep‐sea coral Paragorgia arborea in a phylogeographic context to examine the global patterns of genetic variation and their possible correlation with the spatial variables of geographic position and depth. We also examined the compatibility of this morphospecies with the genealogical‐phylospecies concept by examining specimens collected worldwide. We show that the morphospecies P. arborea can be defined as a genealogical‐phylospecies, in contrast to the hypothesis that P. arborea represents a cryptic species complex. Genetic variation is correlated with geographic location at the basin‐scale level, but not with depth. Additionally, we present a phylogeographic hypothesis in which P. arborea originates from the North Pacific, followed by colonization of the Southern Hemisphere prior to migration to the North Atlantic. This hypothesis is consistent with the latest ocean circulation model for the Miocene.