Distribution and feeding ecology of the Greenland shark (Somniosus microcephalus) in Greenland waters

Greenland sharks are widely distributed and most likely a highly abundant predator in arctic waters. Greenland sharks have previously been considered scavengers, but recent studies suggest that Greenland sharks also predate on live prey. In this study, distribution and feeding ecology in Greenland waters were investigated. Based on data from 25 years of surveys, Greenland sharks were usually caught at 400–700 m but were found at all depths between 100 and 1,200 m. Based on examination of stomachs from 30 Greenland sharks (total length of 258–460 cm), the most important prey items were Atlantic cod (65.6 % IRI), harp seal (9.9 % IRI), skates (5.2 % IRI) and wolffish (4.4 % IRI), but large geographical variations were observed. Prey composition and qualitative observations support the hypothesis of active predation. Consistent with other studies, the results of this work support the notion that the Greenland shark is an apex predator with the potential to influence trophic dynamics in the Arctic.     

Distribution, reproduction and feeding of the Greenland shark Somniosus (Somniosus) microcephalus, with notes on two other sleeper sharks, Somniosus (Somniosus) pacificus and Somniosus (Somniosus) antarcticus

The size and depth distribution, stomach contents and reproductive status of Somniosus ( Somniosus ) microcephalus, Somniosus ( Somniosus ) pacificus and Somniosus ( Somniosus ) antarcticus were examined from specimens collected from the North and South Atlantic, North and South Pacific, and the Southern Ocean. Specimens ranged in size from 42 to 480 cm total length, L _T, and were taken from depths of 35–1280 m. Stomach contents included coelenterates, gastropods, cephalopods, echinoderms, crustaceans, elasmobranchs, teleosts, penguins, marine mammals and human waste. Female S. ( S. ) microcephalus mature at c . 450 cm and S. ( S. ) antarcticus at c . 435 cm L _T; a female S. ( S. ) pacificus of 430 cm was mature. Male S. ( S. ) microcephalus mature at c . 300 cm, but male S. ( S. ) antarcticus may not mature until c . 400 cm L _T. The size at birth in these three species of Somniosus is c . 40 cm L _T.     

Hybridization and introgression among three Aconitum (Ranunculaceae) species of different ploidy levels in the Tatra Mountains (Western Carpathians)

Hybridization among species of A conitum effects their morphology and ecology. In this study the hybridization between the diploid 2n(2x) = 16 ( A . lasiocarpum and A . variegatum) and tetraploid 2n(4x) = 32 ( A . firmum) species was documented in the Tatra Mountains (Western Carpathians) in a small, local population in a semi‐natural site. The hybrid species were: homoploid A . × pawlowskii ( A . lasiocarpum × A . variegatum), and triploid A . × berdaui ( A . firmum × A . variegatum, 2n(3x) = 24). Chloroplast DNA (cpDNA) alleles formed two distinct haplotypes, one typical for the tetraploid and another for diploid lines, shared between the tetraploid, triploid and diploid groups, indicating introgressive hybridization. The presumed gene flow was from the tetraploid to diploid species via the triploid bridge. The only two specimens of A . × pawlowskii that harbored tetraploid ( A . firmum) type cpDNA possessed bracteoles of A . firmum‐type. The remaining introgressed (cpDNA and Inter Simple Sequence Repeats (ISSR)) specimens ( A . variegatum) were morphologically pure, implying cryptic introgression. ISSR loci shared between the tetraploid A . firmum and diploid A . variegatum support the hypothesis of an ancient allopolyploid origin of A . firmum and the diploid species of A . variegatum‐type as one of its parent.     

Multilocus analyses of admixture and introgression among hybridizing Heliconius butterflies

Introgressive hybridization is an important evolutionary process and new analytical methods provide substantial power to detect and quantify it. In this study we use variation in the frequency of 657 AFLP fragments and DNA sequence variation from 15 genes to measure the extent of admixture and the direction of interspecific gene flow among three Heliconius butterfly species that diverged recently as a result of natural selection for Miillerian mimicry, and which continue to hybridize. Bayesian clustering based on AFLP genotypes correctly delineated the three species and identified four H. cydno, three H. pachinus, and three H. melpomene individuals that were of mixed ancestry. Gene genealogies revealed substantial shared DNA sequence variation among all three species and coalescent simulations based on the Isolation with Migration (IM) model pointed to interspecific gene flow as its cause. The IM simulations further indicated that interspecific gene flow was significantly asymmetrical, with greater gene flow from H. pachinus into H. cydno (2Nm = 4.326) than the reverse (2Nm = 0.502), and unidirectional gene flow from H. cydno and H. pachinus into H. melpomene (2Nm = 0.294 and 0.252, respectively). These asymmetries are in the directions expected based on the genetics of wing patterning and the probability that hybrids of various phenotypes will survive and reproduce in different mimetic environments. This empirical demonstration of extensive interspecific gene flow is in contrast to a previous study which found little evidence of gene flow between another pair of hybridizing Heliconius species, H. himera and H. erato, and it highlights the critical role of natural selection in maintaining species diversity. Furthermore, these results lend support to the hypotheses that phenotypic diversification in the genus Heliconius has been fueled by introgressive hybridization and that reinforcement has driven the evolution of assortative mate preferences.     

On the occurrence of false positives in tests of migration under an isolation‐with‐migration model

The population genetic study of divergence is often carried out using a Bayesian genealogy sampler, like those implemented in ima2 and related programs, and these analyses frequently include a likelihood ratio test of the null hypothesis of no migration between populations. Cruickshank and Hahn (2014, Molecular Ecology, 23, 3133–3157) recently reported a high rate of false‐positive test results with ima2 for data simulated with small numbers of loci under models with no migration and recent splitting times. We confirm these findings and discover that they are caused by a failure of the assumptions underlying likelihood ratio tests that arises when using marginal likelihoods for a subset of model parameters. We also show that for small data sets, with little divergence between samples from two populations, an excellent fit can often be found by a model with a low migration rate and recent splitting time and a model with a high migration rate and a deep splitting time.     

Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data

Cases of geographically restricted co‐occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and Murina recondita are both endemic to Taiwan and are putative sister species. To test for nonallopatric divergence and gene flow in these taxa, we generated sequences using Sanger and next‐generation sequencing, and combined these with microsatellite data for coalescent‐based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita; however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species Murina eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *beast and isolation‐with‐migration and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.     

A population genomic analysis of species boundaries: neutral processes, adaptive divergence and introgression between two hybridizing plant species

Little is known about the nature of species boundaries between closely related plant species and about the extent of introgression as a consequence of hybridization upon secondary contact. To address these topics we analyzed genome-wide differentiation between two closely related Silene species, Silene latifolia and S. dioica , and assessed the strength of introgression in sympatry. More than 300 AFLP markers were genotyped in three allopatric and three sympatric populations of each species. Outlier analyses were performed separately for sympatric and allopatric populations. Both positive and negative outlier loci were found, indicating that divergent and balancing selection, respectively, have shaped patterns of divergence between the two species. Sympatric populations of the two species were found to be less differentiated genetically than allopatric populations, indicating that hybridization has led to gene introgression. We conclude that differentiation between S. latifolia and S. dioica has been shaped by a combination of introgression and selection. These results challenge the view that species differentiation is a genome-wide phenomenon, and instead support the idea that genomes can be porous and that species differentiation has a genic basis.     

World phylogeography and male‐mediated gene flow in the sandbar shark,Carcharhinus plumbeus

The sandbar shark, Carcharhinus plumbeus, is a large, cosmopolitan, coastal species. Females are thought to show philopatry to nursery grounds while males potentially migrate long distances, creating an opportunity for male‐mediated gene flow that may lead to discordance in patterns revealed by mitochondrial DNA (mtDNA) and nuclear markers. While this dynamic has been investigated in elasmobranchs over small spatial scales, it has not been examined at a global level. We examined patterns of historical phylogeography and contemporary gene flow by genotyping 329 individuals from nine locations throughout the species’ range at eight nuclear microsatellite markers and sequencing the complete mtDNA control region. Pairwise comparisons often resulted in fixation indices and divergence estimates of greater magnitude using mtDNA sequence data than microsatellite data. In addition, multiple methods of estimation suggested fewer populations based on microsatellite loci than on mtDNA sequence data. Coalescent analyses suggest divergence and restricted migration among Hawaii, Taiwan, eastern and western Australia using mtDNA sequence data and no divergence and high migration rates, between Taiwan and both Australian sites using microsatellite data. Evidence of secondary contact was detected between several localities and appears to be discreet in time rather than continuous. Collectively, these data suggest complex spatial/temporal relationships between shark populations that may feature pulses of female dispersal and more continuous male‐mediated gene flow.     

Reticulate evolution: ancient introgression of the Adriatic brown trout mtDNA in softmouth trout Salmo obtusirostris (Teleostei: Salmonidae)

Two populations of softmouth trout ( Salmo obtusirostris ) from the rivers Neretva (Bosnia and Herzegovina) and Jadro (Croatia), along with two neighbouring populations of brown trout ( Salmo trutta ) were analysed with a suite of genetic markers (two mtDNA genes, two nuclear genes, and nine microsatellites) as well as morphological characters. The Jadro softmouth trout were fixed for a brown trout mtDNA haplotype of the Adriatic lineage, which is 1.7% divergent from a previously described haplotype characteristic for the Neretva softmouth trout. All other genetic markers, as well as morphological analysis, supported the clear distinction of softmouth trout from the rivers Neretva and Jadro from brown trout in neighbouring populations, and thus a mtDNA capture event is assumed. Population specific microsatellite allele profiles, as well as a high number of private alleles for both populations of softmouth trout, support the hybridization between brown trout and the Jadro softmouth trout most likely being of ancient origin, thus leading to a reticulate evolutionary pattern of mtDNA in this taxon.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 139–152.     

Multiple ice‐binding proteins of probable prokaryotic origin in an Antarctic lake alga,Chlamydomonas sp. ICE‐MDV (Chlorophyceae)

Ice‐associated algae produce ice‐binding proteins (IBPs) to prevent freezing damage. The IBPs of the three chlorophytes that have been examined so far share little similarity across species, making it likely that they were acquired by horizontal gene transfer (HGT). To clarify the importance and source of IBPs in chlorophytes, we sequenced the IBP genes of another Antarctic chlorophyte, Chlamydomonas sp. ICE‐MDV (Chlamy‐ICE). Genomic DNA and total RNA were sequenced and screened for known ice‐associated genes. Chlamy‐ICE has as many as 50 IBP isoforms, indicating that they have an important role in survival. The IBPs are of the DUF3494 type and have similar exon structures. The DUF3494 sequences are much more closely related to prokaryotic sequences than they are to sequences in other chlorophytes, and the chlorophyte IBP and ribosomal 18S phylogenies are dissimilar. The multiple IBP isoforms found in Chlamy‐ICE and other algae may allow the algae to adapt to a greater variety of ice conditions than prokaryotes, which typically have a single IBP gene. The predicted structure of the DUF3494 domain has an ice‐binding face with an orderly array of hydrophilic side chains. The results indicate that Chlamy‐ICE acquired its IBP genes by HGT in a single event. The acquisitions of IBP genes by this and other species of Antarctic algae by HGT appear to be key evolutionary events that allowed algae to extend their ranges into polar environments.     

Notes on the long‐term transport of the scalloped hammerhead shark (Sphyrna lewini)

The capture and transport of scalloped hammerhead sharks (Sphyrna lewini Griffith and Smith, 1834) historically has represented a difficult, expensive, and uncertain undertaking for the public aquarium community. In this study, techniques were developed to improve the successful long‐term transport of S. lewini by mitigating some of the deleterious effects associated with hyperactivity and impaired swimming patterns. The relationship between the transport vessel size and shark sizes, numbers, and swimming behavior was considered when formulating the transport regime. By balancing these factors and adopting a comprehensive water treatment method, it was possible to extend the duration of a successful transport by up to 60 hr. Implications for the future transport of S. lewini and other free‐swimming sharks are discussed. Zoo Biol 21:243–251, 2002. © 2002 Wiley‐Liss, Inc.     

The genetic legacy of the 19th‐century decline of the British polecat: evidence for extensive introgression from feral ferrets

In the 19th century, the British polecat suffered a demographic contraction, as a consequence of direct persecution, reaching its lowest population in the years that preceded the First World War. The polecat is now recovering and expanding throughout Britain, but introgressive hybridization with feral ferrets has been reported, which could be masking the true range of the polecat and introducing domestic genes into the species. We used a fragment of the mitochondrial DNA control region and 11 microsatellite loci to characterize the frequency and extent of hybridization and introgression between the two species and assess whether the 19th‐century decline corresponded to a genetic bottleneck in the polecat. The proportion of admixture detected in the wild was high (31%) and hybrids were more frequently found outside Wales, suggesting that hybridization is more likely to occur along the eastern edge of the polecat's range expansion. The patterns observed in the mitochondrial and nuclear DNA data show that introgression was mediated by crosses between male polecats and female ferrets, whose offspring backcrossed with polecats. No first‐generation (F₁) hybrids were identified, and the broad range of observed admixture proportions agrees with a scenario of past extensive hybridization between the two species. Using several different methods to investigate demographic history, we did not find consistent evidence for a genetic bottleneck in the British polecat, a result that could be interpreted as a consequence of hybridization with ferrets. Our results highlight the importance of the Welsh polecat population for the conservation and restoration of the genetic identity of the British polecat.     

Testing hypotheses of mitochondrial gene‐tree paraphyly: unravelling mitochondrial capture of the Streak‐breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (Pomatorhinus musicus)

Species‐level paraphyly inferred from mitochondrial gene trees is a prevalent phenomenon in taxonomy and systematics, but there are several potential causes that are not easily explained by currently used methods. This study aimed to test the underlying causes behind the observed paraphyly of Streak‐breasted Scimitar Babbler (Pomatorhinus ruficollis) via statistical analyses of four mitochondrial (mtDNA) and nine nuclear (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis with respect to the Taiwan Scimitar Babbler (Pomatorhinus musicus), but nuclear genealogies support a sister‐group relationship. Predictive coalescent simulations imply several hypothetical explanations, the most likely being mitochondrial capture of P. ruficollis by P. musicus for the observed cyto‐nuclear incongruence. Further approximate Bayesian computation suggests a unidirectional introgression model with substantial level of gene flow from P. ruficollis to P. musicus during their initial divergence during the Late Pleistocene. This specific observation frames several potential causes for incongruent outcomes of mitochondrial and nuclear introgression in general, and on the whole, our results underscore the strength of multiple independent loci for species delimitation and importance of testing hypotheses that explain disparate causes of mitochondrial gene‐tree paraphyly.     

Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here, we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X‐linked loci. Clustering and geneflow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo‐Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction of MPB into three separate Pleistocene glacial refugia followed by postglacial range expansion and secondary contact. Distinct sets of SNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.     

Gene flow,divergent selection and resistance to introgression in two species of morning glories (Ipomoea)

Gene flow is thought to impede genetic divergence and speciation by homogenizing genomes. Recent theory and research suggest that sufficiently strong divergent selection can overpower gene flow, leading to loci that are highly differentiated compared to others. However, there are also alternative explanations for this pattern. Independent evidence that loci in highly differentiated regions are under divergent selection would allow these explanations to be distinguished, but such evidence is scarce. Here, we present multiple lines of evidence that many of the highly divergent SNPs in a pair of sister morning glory species, Ipomoea cordatotriloba and I. lacunosa, are the result of divergent selection in the face of gene flow. We analysed a SNP data set across the genome to assess the amount of gene flow, resistance to introgression and patterns of selection on loci resistant to introgression. We show that differentiation between the two species is much lower in sympatry than in allopatry, consistent with interspecific gene flow in sympatry. Gene flow appears to be substantially greater from I. lacunosa to I. cordatotriloba than in the reverse direction, resulting in sympatric and allopatric I. cordatotriloba being substantially more different than sympatric and allopatric I. lacunosa. Many SNPs highly differentiated in allopatry have experienced divergent selection, and, despite gene flow in sympatry, resist homogenization in sympatry. Finally, five out of eight floral and inflorescence characteristics measured exhibit asymmetric convergence in sympatry. Consistent with the pattern of gene flow, I. cordatotriloba traits become much more like those of I. lacunosa than the reverse. Our investigation reveals the complex interplay between selection and gene flow that can occur during the early stages of speciation.     

Microsatellite‐based analysis of genetic structure and gene flow of Mythimna separata (Walker) (Lepidoptera: Noctuidae) in China

The oriental armyworm, Mythimna separata, is a serious agricultural pest in China. Seasonal and roundtrip migration has recently led to sudden, localized outbreaks and crop losses. To evaluate genetic differentiation between populations in eastern and western China and elucidate gene flow, the genetic structure of 20 natural populations from nine provinces was examined using seven microsatellite markers. The results indicated high genetic diversity. However, little to moderate (0 < F_ST < 0.15) genetic differentiation was detected, and there was no correlation between genetic distance and geographical distance. Bayesian clustering analysis identified three groups whereas discriminant analysis of principal components identified ten clusters that were considered as two clear‐cut clusters and one admixed group. Gene flow occurred frequently in most population pairs, and an asymmetrical migration rate was detected in several pairwise population comparisons. The bottleneck test showed that few populations had experienced recent bottlenecks. Correspondingly, large‐scale and long‐distance migration of M. separata has caused low genetic differentiation and frequent gene exchange. Our findings are important for studying genetic evolution and help to improve predictions of M. separata outbreaks in China.     

Vertebrae in compression: Mechanical behavior of arches and centra in the gray smooth‐hound shark (Mustelus californicus)

In swimming sharks, vertebrae are subjected, in part, to compressive loads as axial muscles contract. We currently have no information about which vertebral elements, centra, arch cartilages, or both, actually bear compressive loads in cartilaginous vertebrae. To address this issue, the goal of this experiment was to determine the load‐bearing ability of arch and centrum cartilages in compression, to determine the material properties of shark vertebrae, and to document fracture patterns in the centra with and without the arches. Intact vertebrae and vertebrae with the arch cartilages experimentally removed (centra alone) were subjected to compressive loading to failure at a single strain rate. The maximum compressive forces sustained by the vertebrae and the centra are statistically indistinguishable. Thus we conclude that under these testing conditions the arch does not bear appreciable loads. Independent evidence for this conclusion comes from the fact that vertebrae fail in compression at the centra, and not at the arches. Overall, the results of these mechanical tests suggest that the neural arches are not the primary load‐bearing structure during axial compression. J. Morphol. 2010. © 2009 Wiley‐Liss, Inc.     

Differential introgression causes genealogical discordance in host races of Acrocercops transecta (Insecta: Lepidoptera)

Recently diverged populations often exhibit incomplete reproductive isolation, with a low level of gene flow continuing between populations. Previous studies have shown that, even under a low level of gene flow, genetic divergence between populations can proceed at the loci governing local adaptation and reproductive isolation but not at other neutral loci. A leaf‐mining moth, Acrocercops transecta, consists of Juglans‐ and Lyonia‐associated host races. The two host races differ in host preferences of ovipositing females and in larval adaptation to host plants but mate readily in the laboratory, producing fertile hybrids. The Juglans and Lyonia races are often sympatric in the wild, implying that gene introgression could occur in nature between the two host races. We tested this hypothesis by combining phylogenetic analyses with coalescent simulations, focusing on mitochondrial genes (COI and ND5) and the nuclear Tpi, Per and Ldh genes located on the Z‐chromosome. The mitochondrial genes clearly distinguished the Lyonia race from the Juglnas race, whereas the Tpi, Per and Ldh genealogies did not reflect the two host races. Coalescent simulations indicated gene flow at the three Z‐linked genes in both directions, whereas there was no introgression in the mitochondrial genes. The lack of introgression in mitochondrial genes suggests that female host preference is the primary force leading to the bifurcation of maternally inherited loci. Thus, the results show that a low level of gene flow coupled with the inflexible female host preference differentiates histories of divergence between maternally and biparentally inherited genes in this host race system.