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Inter- and intraspecific mitochondrial DNA variation in North American bears (Ursus)

We assessed mitochondrial DNA variation in North American black bears (Ursus americanus), brown bears (Ursus arctos), and polar bears (Ursus maritimus). Divergent mitochondrial DNA haplotypes (0.05 base substitutions per nucleotide) were identified in populations of black bears from Montana and Oregon. In contrast, very similar haplotypes occur in black bears across North America. This discordance of haplotype phylogeny and geographic distribution indicates that there has been maintenance of polymorphism and considerable gene flow throughout the history of the species. Intraspecific mitochondrial DNA sequence divergence in brown bears and polar bears is lower than in black bears. The two morphological forms of U. arctos, grizzly and coastal brown bears, are not in distinct mtDNA lineages. Interspecific comparisons indicate that brown bears and polar bears share similar mitochondrial DNA (0.023 base substitutions per nucleotide) which is quite divergent (0.078 base substitutions per nucleotide) from that of black bears. High mitochondrial DNA divergence within black bears and paraphyletic relationships of brown and polar bear mitochondrial DNA indicate that intraspecific variation across species' ranges should be considered in phylogenetic analyses of mitochondrial DNA.

Canadian Journal of Zoology↗

Sex identification of polar bears from blood and tissue samples

Polar bears ( Ursus maritimus ) can be adversely affected by hunting and other human perturbations because of low population densities and low reproduction rates. The sustainable take of adult females may be as low as 1.5% of the population. Females and accompanying young are most vulnerable to hunting, and hunters have not consistently reported the sex composition of the harvest, therefore a method to confirm the sexes of polar bears harvested in Alaska is needed. Evidence of the sex of harvested animals is often not available, but blood or other tissue samples often are. We extracted DNA from tissue and blood samples, and amplified segments of zinc finger (ZFX and ZFY) genes from both X and Y chromosomes with the polymerase chain reaction. Digestion of amplified portions of the X chromosome with the restriction enzyme Hae III resulted in subdivision of the original amplified segment into four smaller fragments. Digestion with Hae III did not subdivide the original segment amplified from the Y chromosome. The differing fragment sizes produced patterns in gel electrophoresis that distinguished samples from male and female bears 100% of the time. This technique is applicable to the investigation of many wildlife management and research questions.

Alaska↗

Prodigious polyphyly in imperilled freshwater pearly-mussels (Bivalvia: Unionidae): a phylogenetic test of species and generic designations

Unionid bivalves or freshwater pearly-mussels (Unionoidea: Unionidae) serve as an exemplary system for examining many of the problems facing systematists and conservation biologists today. Most of the species and genera were described in the late 1800s and early 1900s, but few phylogenetic studies have been conducted to test conventional views of species and classification. Pearly-mussels of Gulf Coastal drainages of the southeastern United States from the Escambia (southern Alabama to Florida) to the Suwannee Rivers (Florida) are a unique fauna comprised of approximately 100 species, with about 30 endemic to the region. In this study, mitochondrial cytochrome c oxidase subunit I and 16S rRNA gene sequences were used to test the monophyly and to estimate evolutionary relationships of five unionid species representing three different genera. The molecular phylogenies depict all three genera as polyphyletic. The prodigious polyphyly exhibited within unionids is due to incorrect notions of homology and false assumptions about missing anatomical data. In contrast, the molecular phylogeny provides evidence to support the recognition of all five unionid species as distinct evolutionary entities. Furthermore, molecular genealogical evidence supports the elevation of Quincuncina infucata (Conrad) of the Suwannee River to species level, for which Q. kleiniana (Lea) is available.

Geological Society Special Publication↗

Archaeal diversity and CO2 fixers in carbonate-/siliciclastic-rock groundwater ecosystems

Groundwater environments provide habitats for diverse microbial communities, and although Archaea usually represent a minor fraction of communities, they are involved in key biogeochemical cycles. We analysed the archaeal diversity within a mixed carbonate-rock/siliciclastic-rock aquifer system, vertically from surface soils to subsurface groundwater including aquifer and aquitard rocks. Archaeal diversity was also characterized along a monitoring well transect that spanned surface land uses from forest/woodland to grassland and cropland. Sequencing of 16S rRNA genes showed that only a few surface soil-inhabiting Archaea were present in the groundwater suggesting a restricted input from the surface. Dominant groups in the groundwater belonged to the marine group I (MG-I) Thaumarchaeota and the Woesearchaeota. Most of the groups detected in the aquitard and aquifer rock samples belonged to either cultured or predicted lithoautotrophs (e.g., Thaumarchaeota or Hadesarchaea). Furthermore, to target autotrophs, a series of 13 CO 2 stable isotope-probing experiments were conducted using filter pieces obtained after filtration of 10,000 L of groundwater to concentrate cells. These incubations identified the SAGMCG Thaumarchaeota and Bathyarchaeota as groundwater autotrophs. Overall, the results suggest that the majority of Archaea on rocks are fixing CO 2 , while archaeal autotrophy seems to be limited in the groundwater.

Archaea↗

Molecular systematics of Serrasalmidae: Deciphering the identities of piranha species and unraveling their evolutionary histories

Piranhas and their relatives have proven to be a challenging group from a systematic perspective, with difficulties in identification of species, linking of juveniles to adults, diagnosis of genera, and recognition of higher-level clades. In this study we add new molecular data consisting of three mitochondrial regions for museum vouchered and photo-documented representatives of the Serrasalmidae. These are combined with existing serrasalmid sequences in GenBank to address species and higher-level questions within the piranhas using parsimony and Bayesian methods. We found robust support for the monophyly of Serrasalmus manueli , but not for Serrasalmus gouldingi when GenBank specimens identified as S. gouldingi were included in the analysis. " Serrasalmus gouldingi " sequences in GenBank may, however, be misidentified. Linking of juveniles to adults of the same species was greatly facilitated by the addition of sequence data. Based on our sampling and identifications, our data robustly reject the monophyly of the genera Serrasalmus and Pristobrycon . We found evidence for a well-supported clade comprised of Serrasalmus , Pygocentrus , and Pristobrycon (in part). This clade was robustly supported in separate and combined analyses of gene regions, and was also supported by a unique molecular character, the loss of a tandem repeat in the control region. Analysis of specimens and a literature review suggest this clade is also characterized by the presence of a pre-anal spine and ectopterygoid teeth. A persistent polytomy at the base of this clade was dated using an independent calibration as 1.8 million years old, corresponding to the beginning of the Pleistocene Epoch, and suggesting an origin for this clade more recent than dates cited in the recent literature. The sister group to this clade is also robustly supported, and consists of Catoprion , Pygopristis , and Pristobrycon striolatus . If the term piranha is to refer to a monophyletic clade, it should be restricted to Serrasalmus , Pygocentrus , and Pristobrycon (in part), or expanded to include these taxa plus Pygopristis , Catoprion , and Pristobrycon striolatus .

Zootaxa↗

Taxonomic revision of Phascogale tapoatafa (Meyer, 1793) (Dasyuridae; Marsupialia), including descriptions of two new subspecies and confirmation of P. pirata Thomas, 1904 as a ‘Top End’ endemic

The Australian Brush-tailed Phascogale ( Phascogale tapoatafa sensu lato ) has a broad but highly fragmented distribution around the periphery of the Australian continent and all populations are under significant ongoing threat to survival. A new appraisal of morphological and molecular diversity within the group reveals that the population in the ‘Top End’ of the Northern Territory is specifically distinct from all others, including those in the Kimberley region of Western Australia to the west and on Cape York of Queensland to the east. The name P. pirata Thomas, 1904 is available for the ‘Top End’ taxon. Three geographically disjunct populations are distinguished at subspecies level within P. tapoatafa on a suite of external and cranio-dental features; these are found in southeast Australia from South Australia to mid-coastal Queensland (nominotypical tapoatafa ), southwest Western Australia ( wambenger subsp. nov.), and the Kimberley region of Western Australia ( kimberleyensis subsp. nov.). A potential fourth subspecies occurs on Cape York but remains too poorly represented in collections for adequate characterization. Molecular divergence estimates based on partial sequences of the mitochondrial cytochrome b gene indicate that the range disjunction across southern Australia probably dates from the Late Pliocene, with the multiple disjunctions across northern Australia being more recent though almost certainly exceeding 400,000 years. An argument is made for the continued use of the subspecies rank in Australian mammalogy, despite a general lack of consistency in its current application.

Zootaxa↗

A new biogeographically disjunct giant gecko ( Gehyra : Gekkonidae: Reptilia) from the East Melanesian Islands

The East Melanesian Islands have been a focal area for research into island biogeography and community ecology. However, previously undescribed and biogeographically significant new species endemic to this region continue to be discovered. Here we describe a phylogenetically distinct (~20% divergence at the mitochondrial ND2 gene) and biogeographically disjunct new species of gecko in the genus Gehyra , from the Admiralty and St Matthias Islands. Gehyra rohan sp. nov. can be distinguished from all congeners by the combination of its very large size, ring of bright orange scales around the eye, moderate degree of lateral folding on the limbs and body, and aspects of head, body and tail scalation. Molecular data indicate mid to late Miocene divergence of the new species from nearest relatives occurring nearly 2000 kilometres away in Vanuatu and Fiji. Large Gehyra have not been recorded on the intervening large islands of the Bismark Archipelago (New Britain and New Ireland) and the Solomon Islands, suggesting this dispersal pre-dated the current configuration of these islands, extinction in intervening regions, or potentially elements of both. Conversely, low genetic divergence between disjunct samples on Manus and Mussau implies recent overseas dispersal via either natural or anthropogenic means.

Zootaxa↗

Tackling an intractable problem: Can greater taxon sampling help resolve relationships within the Stenopelmatoidea (Orthoptera: Ensifera)?

The relationships among and within the families that comprise the orthopteran superfamily Stenopelmatoidea (suborder Ensifera) remain poorly understood. We developed a phylogenetic hypothesis based on Bayesian analysis of two nuclear ribosomal and one mitochondrial gene for 118 individuals (84 de novo and 34 from GenBank). These included Gryllacrididae from North, Central, and South America, South Africa and Madagascar, Australia and Papua New Guinea; Stenopelmatidae from North and Central America and South Africa; Anostostomatidae from North and Central America, Papua New Guinea, New Zealand, Australia, and South Africa; members of the Australian endemic Cooloola (three species); and a representative of Lezina from the Middle East. We also included representatives of all other major ensiferan families: Prophalangopsidae, Rhaphidophoridae, Schizodactylidae, Tettigoniidae, Gryllidae, Gryllotalpidae and Myrmecophilidae and representatives of the suborder Caelifera as outgroups. Bayesian analyses of concatenated sequence data supported a clade of Stenopelmatoidea inclusive of all analyzed members of Gryllacrididae, Stenopelmatidae, Anostostomatidae, Lezina and Cooloola. We found Gryllacrididae worldwide to be monophyletic, while we did not recover a monophyletic Stenopelmatidae nor Anostostomatidae. Australian Cooloola clustered in a clade composed of Australian, New Zealand, and some (but not all) North American Anostostomatidae. Lezina was included in a clade of New World Anostostomatidae. Finally, we compiled and compared karyotypes and sound production characteristics for each supported group. Chromosome number, centromere position, drumming, and stridulation differed among some groups, but also show variation within groups. This preliminary trait information may contribute toward future studies of trait evolution. Despite greater taxon sampling within Stenopelmatoidea than previous efforts, some relationships among the families examined continue to remain elusive.

Zootaxa↗

Detection and quantification of Renibacterium salmoninarum DNA in salmonid tissues by real-time quantitative polymerase chain reaction analysis

Renibacterium salmoninarum is an important salmonid pathogen that is difficult to culture. We developed and assessed a real-time, quantitative, polymerase chain reaction (qPCR) assay for the detection and enumeration of R. salmoninarum. The qPCR is based on TaqMan technology and amplifies a 69-base pair (bp) region of the gene encoding the major soluble antigen (MSA) of R. salmoninarum. The qPCR assay consistently detected as few as 5 R. salmoninarum cells per reaction in kidney tissue. The specificity of the qPCR was confirmed by testing the DNA extracts from a panel of microorganisms that were either common fish pathogens or reported to cause false-positive reactions in the enzyme-linked immunosorbent assay (ELISA). Kidney samples from 38 juvenile Chinook salmon (Oncorhynchus tshawytscha) in a naturally infected population were examined by real-time qPCR, a nested PCR, and ELISA, and prevalences of R. salmoninarum detected were 71, 66, and 71%, respectively. The qPCR should be a valuable tool for evaluating the R. salmoninarum infection status of salmonids.

Journal of Veterinary Diagnostic Investigation↗

Analytical validation of a real-time reverse transcription polymerase chain reaction test for Pan-American lineage H7 subtype Avian influenza viruses

A real-time reverse transcription polymerase chain reaction test for the identification of the H7 subtype in North American Avian influenza viruses (AIVs) was first reported in 2002; however, recent AIV surveillance efforts in wild birds and H7 outbreaks in poultry demonstrated that the 2002 test did not detect all H7 AIVs present in North and South America. Therefore, a new test, the 2008 Pan-American H7 test, was developed by using recently available H7 nucleotide sequences. The analytical specificity of the new assay was characterized with an RNA panel composed of 19 H7 viruses from around the world and RNA from all hemagglutinin subtypes except H16. Specificity for North and South American lineage H7 viruses was observed. Assay limits of detection were determined to be between 103 and 104 gene copies per reaction with in vitro transcribed RNA, and 100.0 and 10 0.8 50% egg infectious doses per reaction. The 2008 Pan-American H7 test also was shown to perform similarly to the 2002 test with specimens from chickens experimentally exposed to A/Chicken/BritishColumbia/314514-2/04 H7N3 highly pathogenic AIV. Furthermore, the 2008 test was able to detect 100% (n = 27) of the H7 AIV isolates recovered from North American wild birds in a 2006-2007 sample set (none of which were detected by the 2002 H7 test).

Journal of Veterinary Diagnostic Investigation↗

Comparison of the membrane-filtration fluorescent antibody test, the enzyme-linked immunosorbent assay, and the polymerase chain reaction to detect Renibacterium salmoninarum in salmon ovarian fluid

Ovarian fluid samples from naturally infected chinook salmon ( Oncorhynchus tshawytscha ) were examined for the presence of Renibacterium salmoninarum by the membrane-filtration fluorescent antibody test (MF-FAT), an antigen capture enzyme-linked immunosorbent assay (ELISA), and a nested polymerase chain reaction (PCR). On the basis of the MF-FAT, 64% (66/103) samples contained detectable levels of R. salmoninarum cells. Among the positive fish, the R. salmoninarum concentrations ranged from 25 cells/ml to 4.3 × 10 9 cells/ml. A soluble antigenic fraction of R. salmoninarum was detected in 39% of the fish (40/103) by the ELISA. The ELISA is considered one of the most sensitive detection methods for bacterial kidney disease in tissues, yet it did not detect R. salmoninarum antigen consistently at bacterial cell concentrations below about 1.3 × 10 4 cells/ml according to the MF-FAT counts. When total DNA was extracted and tested in a nested PCR designed to amplify a 320-base-pair region of the gene encoding a soluble 57-kD protein of R. salmoninarum , 100% of the 100 samples tested were positive. The results provided strong evidence that R. salmoninarum may be present in ovarian fluids thought to be free of the bacterium on the basis of standard diagnostic methods.

Journal of Veterinary Diagnostic Investigation↗

Microbial sulfate reduction and metal attenuation in pH 4 acid mine water

Sediments recovered from the flooded mine workings of the Penn Mine, a Cu-Zn mine abandoned since the early 1960s, were cultured for anaerobic bacteria over a range of pH (4.0 to 7.5). The molecular biology of sediments and cultures was studied to determine whether sulfate-reducing bacteria (SRB) were active in moderately acidic conditions present in the underground mine workings. Here we document multiple, independent analyses and show evidence that sulfate reduction and associated metal attenuation are occurring in the pH-4 mine environment. Water-chemistry analyses of the mine water reveal: (1) preferential complexation and precipitation by H2S of Cu and Cd, relative to Zn; (2) stable isotope ratios of 34S/32S and 18O/16O in dissolved SO4 that are 2-3 ??? heavier in the mine water, relative to those in surface waters; (3) reduction/oxidation conditions and dissolved gas concentrations consistent with conditions to support anaerobic processes such as sulfate reduction. Scanning electron microscope (SEM) analyses of sediment show 1.5-micrometer, spherical ZnS precipitates. Phospholipid fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analyses of Penn Mine sediment show a high biomass level with a moderately diverse community structure composed primarily of iron- and sulfate-reducing bacteria. Cultures of sediment from the mine produced dissolved sulfide at pH values near 7 and near 4, forming precipitates of either iron sulfide or elemental sulfur. DGGE coupled with sequence and phylogenetic analysis of 16S rDNA gene segments showed populations of Desulfosporosinus and Desulfitobacterium in Penn Mine sediment and laboratory cultures. ?? 2007 Church et al; licensee BioMed Central Ltd.

Geochemical Transactions↗

Population structure and plumage polymorphism: the intraspecific evolutionary relationships of a polymorphic raptor, Buteo jamaicensis harlani

Background Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations. Results To address the evolutionary relationships within this group, we used data from 17 nuclear microsatellite loci, 430 base pairs of the mitochondrial control region, and 829 base pairs of the melanocortin 1 receptor ( Mc1r ) to investigate molecular genetic differentiation among three B. jamaicensis subspecies ( B. j. borealis , B. j. calurus , B. j. harlani ). Bayesian clustering analyses of nuclear microsatellite loci showed no significant differences between B. j. harlani and B. j. borealis . Differences observed between B. j. harlani and B. j. borealis in mitochondrial and microsatellite data were equivalent to those found between morphologically similar subspecies, B. j. borealis and B. j. calurus , and estimates of migration rates among all three subspecies were high. No consistent differences were observed in Mc1r data between B. j. harlani and other B. jamaicensis subspecies or between light and dark color morphs within B. j. calurus , suggesting that Mc1r does not play a significant role in B. jamaicensis melanism. Conclusions These data suggest recent interbreeding and gene flow between B. j. harlani and the other B. jamaicensis subspecies examined, providing no support for the historical designation of B. j. harlani as a distinct species.

BMC Evolutionary Biology↗

Chromosome rearrangements, recombination suppression, and limited segregation distortion in hybrids between Yellowstone cutthroat trout ( Oncorhynchus clarkii bouvieri ) and rainbow trout ( O. mykiss )

Background Introgressive hybridization is an important evolutionary process that can lead to the creation of novel genome structures and thus potentially new genetic variation for selection to act upon. On the other hand, hybridization with introduced species can threaten native species, such as cutthroat trout ( Oncorhynchus clarkii ) following the introduction of rainbow trout ( O. mykiss ). Neither the evolutionary consequences nor conservation implications of rainbow trout introgression in cutthroat trout is well understood. Therefore, we generated a genetic linkage map for rainbow-Yellowstone cutthroat trout ( O. clarkii bouvieri ) hybrids to evaluate genome processes that may help explain how introgression affects hybrid genome evolution. Results The hybrid map closely aligned with the rainbow trout map (a cutthroat trout map does not exist), sharing all but one linkage group. This linkage group (RYHyb20) represented a fusion between an acrocentric (Omy28) and a metacentric chromosome (Omy20) in rainbow trout. Additional mapping in Yellowstone cutthroat trout indicated the two rainbow trout homologues were fused in the Yellowstone genome. Variation in the number of hybrid linkage groups (28 or 29) likely depended on a Robertsonian rearrangement polymorphism within the rainbow trout stock. Comparison between the female-merged F 1 map and a female consensus rainbow trout map revealed that introgression suppressed recombination across large genomic regions in 5 hybrid linkage groups. Two of these linkage groups (RYHyb20 and RYHyb25_29) contained confirmed chromosome rearrangements between rainbow and Yellowstone cutthroat trout indicating that rearrangements may suppress recombination. The frequency of allelic and genotypic segregation distortion varied among parents and families, suggesting few incompatibilities exist between rainbow and Yellowstone cutthroat trout genomes. Conclusions Chromosome rearrangements suppressed recombination in the hybrids. This result supports several previous findings demonstrating that recombination suppression restricts gene flow between chromosomes that differ by arrangement. Conservation of synteny and map order between the hybrid and rainbow trout maps and minimal segregation distortion in the hybrids suggest rainbow and Yellowstone cutthroat trout genomes freely introgress across chromosomes with similar arrangement. Taken together, these results suggest that rearrangements impede introgression. Recombination suppression across rearrangements could enable large portions of non-recombined chromosomes to persist within admixed populations.

BMC Genomics↗

In vitro prion protein conversion suggests risk of bighorn sheep (Ovis canadensis) to transmissible spongiform encephalopathies

Background: Transmissible spongiform encephalopathies (TSEs) affect both domestic sheep (scrapie) and captive and free-ranging cervids (chronic wasting disease; CWD). The geographical range of bighorn sheep (Ovis canadensis; BHS) overlaps with states or provinces that have contained scrapie-positive sheep or goats and areas with present epizootics of CWD in cervids. No TSEs have been documented in BHS, but the susceptibility of this species to TSEs remains unknown. Results: We acquired a library of BHS tissues and found no evidence of preexisting TSEs in these animals. The prion protein gene (Prnp) in all BHS in our library was identical to scrapie-susceptible domestic sheep (A 136 R 154 Q 171 ). Using an in vitro prion protein conversion assay, which has been previously used to assess TSE species barriers and, in our study appears to recollect known species barriers in mice, we assessed the potential transmissibility of TSEs to BHS. As expected based upon Prnp genotype, we observed BHS prion protein conversion by classical scrapie agent and evidence for a species barrier between transmissible mink encephalopathy (TME) and BHS. Interestingly, our data suggest that the species barrier of BHS to white-tailed deer or wapiti CWD agents is likely low. We also used protein misfolding cyclic amplification to confirm that CWD, but not TME, can template prion protein misfolding in A 136 R 154 Q 171 genotype sheep. Conclusions: Our results indicate the in vitro conversion assay used in our study does mimic the species barrier of mice to the TSE agents that we tested. Based on Prnp genotype and results from conversion assays, BHS are likely to be susceptible to infection by classical scrapie. Despite mismatches in amino acids thought to modulate prion protein conversion, our data indicate that A136R154Q171 genotype sheep prion protein is misfolded by CWD agent, suggesting that these animals could be susceptible to CWD. Further investigation of TSE transmissibility to BHS, including animal studies, is warranted. The lack of reported TSEs in BHS may be attributable to other host factors or a lack of TSE surveillance in this species.

BMC Veterinary Research↗

Global phylodynamic analysis of avian paramyxovirus-1 provides evidence of inter-host transmission and intercontinental spatial diffusion

Background Avian avulavirus (commonly known as avian paramyxovirus-1 or APMV-1) can cause disease of varying severity in both domestic and wild birds. Understanding how viruses move among hosts and geography would be useful for informing prevention and control efforts. A Bayesian statistical framework was employed to estimate the evolutionary history of 1602 complete fusion gene APMV-1 sequences collected from 1970 to 2016 in order to infer viral transmission between avian host orders and diffusion among geographic regions. Ancestral states were estimated with a non-reversible continuous-time Markov chain model, allowing transition rates between discrete states to be calculated. The evolutionary analyses were stratified by APMV-1 classes I ( n = 198) and II ( n = 1404), and only those sequences collected between 2006 and 2016 were allowed to contribute host and location information to the viral migration networks. Results While the current data was unable to assess impact of host domestication status on APMV-1 diffusion, these analyses supported the sharing of APMV-1 among divergent host taxa. The highest supported transition rate for both classes existed from domestic chickens to Anseriformes (class I:6.18 transitions/year, 95% highest posterior density (HPD) 0.31–20.02, Bayes factor (BF) = 367.2; class II:2.88 transitions/year, 95%HPD 1.9–4.06, BF = 34,582.9). Further, among class II viruses, domestic chickens also acted as a source for Columbiformes (BF = 34,582.9), other Galliformes (BF = 34,582.9), and Psittaciformes (BF = 34,582.9). Columbiformes was also a highly supported source to Anseriformes (BF = 322.0) and domestic chickens (BF = 402.6). Additionally, our results provide support for the diffusion of viruses among continents and regions, but no interhemispheric viral exchange between 2006 and 2016. Among class II viruses, the highest transition rates were estimated from South Asia to the Middle East (1.21 transitions/year; 95%HPD 0.36–2.45; BF = 67,107.8), from Europe to East Asia (1.17 transitions/year; 95%HPD 0.12–2.61; BF = 436.2) and from Europe to Africa (1.06 transitions/year, 95%HPD 0.07–2.51; BF = 169.3). Conclusions While migration appears to occur infrequently, geographic movement may be important in determining viral diversification and population structure. In contrast, inter-order transmission of APMV-1 may occur readily, but most events are transient with few lineages persisting in novel hosts.

BMC Evolutionary Biology↗

Genetic diversity and connectivity of chemosynthetic cold seep mussels from the U.S. Atlantic margin

Background Deep-sea mussels in the subfamily Bathymodiolinae have unique adaptations to colonize hydrothermal-vent and cold-seep environments throughout the world ocean. These invertebrates function as important ecosystem engineers, creating heterogeneous habitat and promoting biodiversity in the deep sea. Despite their ecological significance, efforts to assess the diversity and connectivity of this group are extremely limited. Here, we present the first genomic-scale diversity assessments of the recently discovered bathymodioline cold-seep communities along the U.S. Atlantic margin, dominated by Gigantidas childressi and Bathymodiolus heckerae . Results A Restriction-site Associated DNA Sequencing (RADSeq) approach was used on 177 bathymodiolines to examine genetic diversity and population structure within and between seep sites. Assessments of genetic differentiation using single-nucleotide polymorphism (SNP) data revealed high gene flow among sites, with the shallower and more northern sites serving as source populations for deeper occurring G. childressi . No evidence was found for genetic diversification across depth in G. childressi , likely due to their high dispersal capabilities. Kinship analyses indicated a high degree of relatedness among individuals, and at least 10–20% of local recruits within a particular site. We also discovered candidate adaptive loci in G. childressi and B. heckerae that suggest differences in developmental processes and depth-related and metabolic adaptations to chemosynthetic environments. Conclusions These results highlight putative source communities for an important ecosystem engineer in the deep sea that may be considered in future conservation efforts. Our results also provide clues into species-specific adaptations that enable survival and potential speciation within chemosynthetic ecosystems.

Atlantic Ocean, Baltimore Canyon Seep, Blake Ridge↗

Effect of growth rate on transcriptomic responses to immune stimulation in wild-type, domesticated, and GH-transgenic coho salmon

Background Transcriptomic responses to immune stimulation were investigated in coho salmon (Oncorhynchus kisutch) with distinct growth phenotypes. Wild-type fish were contrasted to strains with accelerated growth arising either from selective breeding (i.e. domestication) or genetic modification. Such distinct routes to accelerated growth may have unique implications for relationships and/or trade-offs between growth and immune function. Results RNA-Seq was performed on liver and head kidney in four ‘growth response groups’ injected with polyinosinic-polycytidylic acid (Poly I:C; viral mimic), peptidoglycan (PGN; bacterial mimic) or PBS (control). These groups were: 1) ‘W’: wild-type, 2) ‘TF’: growth hormone (GH) transgenic salmon with ~ 3-fold higher growth-rate than W, 3) ‘TR’: GH transgenic fish ration restricted to possess a growth-rate equal to W, and 4) ‘D’: domesticated non-transgenic fish showing growth-rate intermediate to W and TF. D and TF showed a higher similarity in transcriptomic response compared to W and TR. Several immune genes showed constitutive expression differences among growth response groups, including perforin 1 and C-C motif chemokine 19-like. Among the affected immune pathways, most were up-regulated by Poly I:C and PGN. In response to PGN, the c-type lectin receptor signalling pathway responded uniquely in TF and TR. In response to stimulation with both immune mimics, TR responded more strongly than other groups. Further, group-specific pathway responses to PGN stimulation included NOD-like receptor signalling in W and platelet activation in TR. TF consistently showed the most attenuated immune response relative to W, and more DEGs were apparent in TR than TF and D relative to W, suggesting that a non-satiating ration coupled with elevated circulating GH levels may cause TR to possess enhanced immune capabilities. Alternatively, TF and D salmon are prevented from acquiring the same level of immune response as TR due to direction of energy to high overall somatic growth. Further study of the effects of ration restriction in growth-modified fishes is warranted. Conclusions These findings improve our understanding of the pleiotropic effects of growth modification on the immunological responses of fish, revealing unique immune pathway responses depending on the mechanism of growth acceleration and nutritional availability.

BMC Genomics↗