Population genomics reveals structure at the individual,host‐tree scale and persistence of genotypic variants of the undomesticated yeast Saccharomyces paradoxus in a natural woodland

Genetic diversity in experimental, domesticated and wild populations of the related yeasts, Saccharomyces cerevisiae and Saccharomyces paradoxus, has been well described at the global scale. We investigated the population genomics of a local population on a small spatial scale to address two main questions. First, is there genomic variation in a S. paradoxus population at a spatial scale spanning centimetres (microsites) to tens of metres? Second, does the distribution of genomic variants persist over time? Our sample consisted of 42 S. paradoxus strains from 2014 and 43 strains from 2015 collected from the same 72 microsites around four host trees (Quercus rubra and Quercus alba) within 1 km² in a mixed hardwood forest in southern Ontario. Six additional S. paradoxus strains recovered from adjacent maple and beech trees in 2015 are also included in the sample. Whole‐genome sequencing and genomic SNP analysis revealed five differentiated groups (clades) within the sampled area. The signal of persistence of genotypes in their microsites from 2014 to 2015 was highly significant. Isolates from the same tree tended to be more related than strains from different trees, with limited evidence of dispersal between trees. In growth assays, one genotype had a significantly longer lag phase than the other strains. Our results indicate that different clades coexist at fine spatial scale and that population structure persists over at least a one‐year interval in these wild yeasts, suggesting the efficacy of yearly sampling to follow longer term genetic dynamics in future studies.     

The interaction of Saccharomyces paradoxus with its natural competitors on oak bark

The natural history of the model yeast Saccharomyces cerevisiae is poorly understood and confounded by domestication. In nature, S. cerevisiae and its undomesticated relative S. paradoxus are usually found on the bark of oak trees, a habitat very different from wine or other human fermentations. It is unclear whether the oak trees are really the primary habitat for wild yeast, or whether this apparent association is due to biased sampling. We use culturing and high‐throughput environmental sequencing to show that S. paradoxus is a very rare member of the oak bark microbial community. We find that S. paradoxus can grow well on sterile medium made from oak bark, but that its growth is strongly suppressed when the other members of the community are present. We purified a set of twelve common fungal and bacterial species from the oak bark community and tested how each affected the growth of S. paradoxus in direct competition on oak bark medium at summer and winter temperatures, identifying both positive and negative interactions. One Pseudomonas species produces a diffusible toxin that suppresses S. paradoxus as effectively as either the whole set of twelve species together or the complete community present in nonsterilized oak medium. Conversely, one of the twelve species, Mucilaginibacter sp., had the opposite effect and promoted S. paradoxus growth at low temperatures. We conclude that, in its natural oak tree habitat, S. paradoxus is a rare species whose success depends on the much more abundant microbial species surrounding it.     

Timing and body condition of dichromatic Black Redstarts during autumn migration

Individual variation in postjuvenile molt in male Black Redstart is pronounced with about 90% of young males retaining female‐like coloration (cairei plumage type) and about 10% acquiring adult male‐like feathers (paradoxus plumage type). We examined whether autumn migration timing and body condition differed between individuals of the two plumage types. We used the data of 10,977 Black Redstarts captured during autumn at a ringing site in northern Switzerland where a protocol to record plumage types of captures has been applied since 1980. As cairei individuals cannot be distinguished from young females while sexing is comparatively easy for paradoxus individuals, the proportion of missing data on sex was likely to be higher for cairei individuals than for paradoxus individuals. We formally accounted for captures with unidentified sex using a Bayesian approach and conducted a simulation study to show that our approach was able to provide unbiased results even if the proportion of unsexed captures was high. Applying the method to the Black Redstart data, we found that the proportion of individuals with paradoxus plumage type increased from 7.6% in 1980 to 18.1% in 2013. Individuals with the paradoxus plumage type were on average 0.25 g heavier and had 0.62 mm longer third primaries than individuals with the cairei plumage type. However, we found no support for our expectation of later migration of paradoxus males compared to cairei individuals based on the assumption that paradoxus individuals should occupy autumn territories like adult males. Our results shed new light on the understudied timing of autumn migration in birds and are in line with available studies on Black Redstarts, suggesting a molt‐constraint that allows only young males in good body condition to molt into adult‐like plumages.     

An unusual macrourid larva (Gadiformes) from San Juan Island, Washington, USA

An unusual macrourid larva was collected in Friday Harbor, San Juan Island, Washington, USA. This specimen is remarkable in appearance having very long anterior dorsal- and pelvic-fin rays, with flattened distal ends free of the fin membrane, and a long, whiplike, heavily pigmented caudal filament. It is similar to smaller Coryphaenoides pectoralis larvae reported from the California Current region, and different from larger specimens of C. pectoralis from the northern North Pacific. Counts and other morphological similarities suggest that this larva should be tentatively assigned to genus Coryphaenoides.     

Characterizing the molecular variation among American marten (Martes americana) subspecies from Oregon and California

We investigated the subspecific identity of a rediscovered population of American martens within the range of a presumed extinct subspecies (Martes americana humboldtensis) by comparing mitochondrial DNA sequence diversity from contemporary individuals within the described ranges of M. a. humboldtensis, nearby ranges of M. a. caurina and M. a. sierrae, and a museum specimen of M. a. humboldtensis. Martens from the rediscovered population shared a haplotype (#2) with the museum specimen. This haplotype was found only in the coastal regions of Oregon and California, suggesting that the rediscovered population represents descendants of a relictual population that previously existed in coastal California. The subspecific boundary between M. a. humboldtensis and M. a. caurina may not be valid, because haplotype #2 was shared between coastal Oregon and coastal California populations and no known contemporary or historical biogeographic barriers prevent north–south movement. Thus, marten populations currently located in coastal forests of California and Oregon should be managed collectively to preserve the connectivity that our data suggest occurred historically. M. a. sierrae differed substantially from both M. a. humboldtensis and M. a. caurina, suggesting marten populations were not a historically genetically homogeneous population and divergence may have occurred in separate glacial refugia.     

First Isolation of the Yeast <Emphasis Type="Italic">Saccharomyces paradoxus</Emphasis> in Western Siberia

Two ascomycetous yeast strains have been isolated near Novosibirsk from oak exudate. The strains have been identified as Saccharomyces paradoxus Bachinskaya based on the results of biochemical tests. The conspecificity of the isolates with S. paradoxus was confirmed by electrophoretic karyotyping and restriction analysis of the ITS region of its rDNA. This first isolation of S. paradoxus in Siberia provides evidence for the continuity of its natural habitats.__________Translated from Mikrobiologiya, Vol. 74, No. 4, 2005, pp. 533–536.Original Russian Text Copyright © 2005 by Yurkov.     

Measuring microbial fitness in a field reciprocal transplant experiment

Microbial fitness is easy to measure in the laboratory, but difficult to measure in the field. Laboratory fitness assays make use of controlled conditions and genetically modified organisms, neither of which are available in the field. Among other applications, fitness assays can help researchers detect adaptation to different habitats or locations. We designed a competitive fitness assay to detect adaptation of Saccharomyces paradoxus isolates to the habitat they were isolated from (oak or larch leaf litter). The assay accurately measures relative fitness by tracking genotype frequency changes in the field using digital droplet PCR (DDPCR). We expected locally adapted S. paradoxus strains to increase in frequency over time when growing on the leaf litter type from which they were isolated. The DDPCR assay successfully detected fitness differences among S. paradoxus strains, but did not find a tendency for strains to be adapted to the habitat they were isolated from. Instead, we found that the natural alleles of the hexose transport gene we used to distinguish S. paradoxus strains had significant effects on fitness. The origin of a strain also affected its fitness: strains isolated from oak litter were generally fitter than strains from larch litter. Our results suggest that dispersal limitation and genetic drift shape S. paradoxus populations in the forest more than local selection does, although further research is needed to confirm this. Tracking genotype frequency changes using DDPCR is a practical and accurate microbial fitness assay for natural environments.     

Descriptive morphology of yolk sac larval Solenostomus paradoxus collected from Libong Island, Trang, southern Thailand

Yolk-sac larvae of Solenostomus paradoxus are described from 19 specimens (2.8–5.1 mm in body length) discharged from the brood pouch of a single female collected by hand at Libong Island, Trang, southern Thailand, on 30 January 2002. Although the larvae of S. paradoxus were closely similar to those of S. cyanopterus in general appearance and pigmentation patterns, the former differed in lacking clusters of melanophores on the edge of the dorsal finfold and dark oblique streaks on the dorsal and ventral finfolds near the tail tip.     

Abiotic edaphic factors affecting the growth of a threatened North American Sunflower, Helianthus paradoxus (Asteraceae)

This study evaluated the relationships among soil moisture, soil salinity, and soil oxygen on the growth of Helianthus paradoxus (Asteraceae), a threatened inland salt marsh species of western North America. The study was conducted in large growth boxes (1×2×0.3 m) tilted at an angle to achieve a saturated to dry water gradient similar to that found in the marsh. This experimental design allowed the evaluation of major abiotic factors (soil moisture and soil salinity) which have been shown to be potentially important for this species, while removing major biotic factors, such as competition from other community dominants. Maximum aboveground biomass occurred in the middle rows of the boxes, where surface soil water was reduced and subsurface soil water was intermediate in the gradient. Regression analyses indicated that H. paradoxus would grow best where surface soil water is approximately 5%, subsurface soil water ranges from 20 to 30%, and where surface soil salinity is less than 0.5 g kg⁻¹. Edaphic variables, particularly soil moisture and soil salinity, affect the growth of H. paradoxus. Data presented here suggest that the survival of this species depends on maintenance of the hydrologic regime.     

The fin spine of a new holocephalan from the lower jurassic of Lyme Regis,Dorset, England

A fin spine previously described as ‘Myriacanthus paradoxus’ Agassiz from the Lower Lias (Lower Jurassic) of Lyme Regis, is allocated to the new genus and species Recurvacanthus uniserialis. The spine is unusual in possessing a single median row of four large, hook-like, downturned denticles on the distal part of the posterior wall. It is concluded that the unique specimen should be classified with the myriacanthoid chimaeriform holocephalans since it possesses a tubercular ornament on the lateral walls.     

Differences in morphological features of the sacculus of the inner ear of two hakes (Merluccius capensis and M. paradoxus,gadiformes) inhabits from different depth of sea

The morphology of the sensory epithelia of the sacculus in two species of hake, Merluccius capensis and M. paradoxus, was analyzed by scanning electron microscopy (SEM). The sensory epithelia have two morphological features that are very different from other gadiform species. These include the presence of two large areas which are only linked by a narrow neck, and the larger proportion of hair cells oriented in the rostrocaudal axis than in other species. The deeper-dwelling species, M. paradoxus, has a larger proportion of hair cell with short ciliary bundles than does the shallower-dwelling species, M. capensis. These morphological specializations could improve the acoustic diserimination and localization capabilities of these species, possibly related to an increase in sensitivity to higher frequency sounds in the deeper-dwelling species. © 1992 Wiley-Liss, Inc.     

Spatial,ontogenetic and interspecific variability in stable isotope ratios of nitrogen and carbon of Merluccius capensis and Merluccius paradoxus off South Africa

General linear models (GLMs) were used to determine the relative importance of interspecific, ontogenetic and spatial effects in explaining variability in stable isotope ratios of nitrogen (δ¹⁵N) and carbon (δ¹³C) of the co‐occurring Cape hakes Merluccius capensis and Merluccius paradoxus off South Africa. Significant GLMs were derived for both isotopes, explaining 74 and 56% of observed variance in Merluccius spp. δ¹⁵N and δ¹³C, respectively. Spatial effects (west or south coast) contributed most towards explaining variability in the δ¹⁵N model, with Merluccius spp. off the west coast having higher (by c. 1·4‰) δ¹⁵N levels than Merluccius spp. off the south coast. Fish size and species were also significant in explaining variability in δ¹⁵N, with both species showing significant linear increases in δ¹⁵N with size and M. capensis having higher (by c. 0·7‰) δ¹⁵N values than M. paradoxus. Species and coast explained most and similar amounts of variability in the δ¹³C model, with M. capensis having higher (by c. 0·8‰) δ¹³C values than M. paradoxus, and values being lower (by c. 0·7‰) for fishes off the west coast compared with the south coast. These results not only corroborate the knowledge of Merluccius spp. feeding ecology gained from dietary studies, in particular the ontogenetic change in trophic level corresponding to a changing diet, but also that M. capensis feeds at a slightly higher trophic level than M. paradoxus. The spatial difference in Merluccius spp. δ¹⁵N appears due to a difference in isotopic baseline, and not as a result of Merluccius spp. feeding higher in the food web off the west than the south coast, and provides new evidence that corroborates previous observations of biogeographic differences in isotopic baselines around the South African coast. This study also provides quantitative data on the relative trophic level and trophic width of Cape hakes over a large size range that can be used in ecosystem models of the southern Benguela.     

New Systematic Insights in the Ceramium Sinicolacomplex: Resurrection of C. Interruptum S. & G. (Ceramiaceae,Rhodophyta)

Setchell & Gardner (1924) provided a taxonomic treatment for the genus Ceramium from lower California and the Gulf of California, Mexico, in which they described several new species, including C. sinicola S. & G. described from Ensenada, BCN and C. interruptum S. & G. described from the vicinity of La Paz, BCS. The latter was later reduced to variety rank in C. sinicolaby Dawson (1950), a taxonomic decision that has subsequently been widely adopted. Phylogenetic analyses inferred from three molecular markers (chloroplast‐encoded rbcL, the RUBISCO spacer, and nuclear encoded SSU rDNA) from recent collections from the Pacific North‐west (California, Oregon) and the Gulf of California reveal a well supported assemblage of three corticated taxa: C. codicolaJ. Ag. 1894, C. sinicola and C. sinicola var. interruptum. Sequence divergence values among the three taxa are sufficient to warrant separate species ranking; hence, we reinstate C. interruptum as a widely distributed epiphyte for the region. C. sinicolais more closely related to C. codicolathan to C. interruptum, with the former two restricted to the host Codium. The molecule‐based relationships are congruent with evolutionary trends in cortication pattern and attachment mode.     

Seasonal Change in Bacterial Flora and Biomass in Mountain Snow from the Tateyama Mountains, Japan, Analyzed by 16S rRNA Gene Sequencing and Real-Time PCR

The bacterial flora and biomass in mountain snow from the Tateyama Mountains, Toyama Prefecture, Japan, one of the heaviest snowfall regions in the world, were analyzed by amplified ribosomal DNA restriction analysis followed by 16S rRNA gene sequencing and DNA quantification by real-time PCR. Samples of surface snow collected in various months during the melting season contained a psychrophilic bacterium, Cryobacterium psychrophilum, and two psychrotrophic bacteria, Variovorax paradoxus and Janthinobacterium lividum. Bacterial colonies that developed in an in situ meltwater medium at 4°C were revealed to be V. paradoxus. The biomasses of C. psychrophilum, J. lividum, and V. paradoxus, as estimated by real-time PCR, showed large increases during the melting season from March to October (2.0 × 10⁵-fold, 1.5 × 10⁵-fold, and 1.0 × 10⁴-fold increases, respectively), suggesting their rapid growth in the surface snow. The biomasses of C. psychrophilum and J. lividum increased significantly from March to April, reached a maximum in August, and dropped at the end of the melting season. In contrast, the biomass of V. paradoxus did not increase as rapidly during the early melting season but continued to increase from June until October. The differences in development observed among these bacterial species suggest that their growth was promoted by different nutrients and/or environmental conditions in the snow. Since these three types of bacteria have also been reported to be present in a glacier in Antarctica and a Greenland ice core, they seem to be specialized members of the snow biota that are distributed in snow and ice environments in various parts of the world.     

CULTURE STUDIES ON REPRODUCTION OF SPERMATOCHNUS PARADOXUS (PHAEOPHYCEAE,CHORDARIALES)1

The life history of Spermatochnus paradoxus (Roth) Kütz. isolated from the Mediterranean Sea was studied in culture. Meiospores develop to a microscopic stage (microthallus) which at 20°C perpetuates asexually by plurilocular sporangia and formation of new microthalli. At 9°C microthalli act as homothallic gametophytes. Fusion of isogametes results in a diploid microthallus which, after differentiation of an apical cell, leads back to Spermatochnus plants. In addition, gametes develop without fusion to form haploid macrothalli, the further fate of which has not been determined. Chromosome numbers alternate between n = 20 ± 2 in the microthalli and 2n = 41 ± 4 in macrothalli.     

Genetic structure of California's elk: a legacy of extirpations,reintroductions, population expansions,and admixture

California, USA, is home to 3 subspecies of North American elk (Cervus canadensis): Roosevelt (C. c. roosevelti), Rocky Mountain (C. c. nelsoni), and tule (C. c. nannodes). Effective management requires a baseline understanding of each subspecies' range, admixture zones, and geographic patterns of genetic diversity. To address these questions, we genotyped 1,271 individual elk from California (n = 1,204) and reference populations of Rocky Mountain and Roosevelt elk from Nevada (n = 32) and Oregon (n = 35), USA. Using 19 polymorphic microsatellite loci, we detected admixture between Roosevelt and Rocky Mountain elk at a contact zone in northern California, and between Roosevelt and tule elk in north-coastal California and central-coastal California. We identified a genetically distinct population of Roosevelt elk in northwestern California, likely reflecting the remnant population that survived a large demographic decline from overhunting during the 1800s. Tule elk exhibited lower levels of heterozygosity (0.44 ± 0.03 [SD]) and allelic richness (2.9 ± 0.2) than Rocky Mountain (0.58 ± 0.05, 4.9 ± 0.4, respectively) and Roosevelt (0.50 ± 0.06, 4.4 ± 0.6, respectively) elk. Among tule elk populations, heterozygosity varied, with the lowest heterozygosity (0.23 ± 0.05) corresponding to the oldest enclosed herd used over the past century as a source of translocations. Among tule elk populations, genetic structure revealed several cases of successful and unsuccessful reintroduction or augmentation attempts. Results provide an essential baseline for future monitoring and decisions about harvest management, translocations to preserve genetic diversity, and landscape-level conservation planning to maintain, enhance, or obstruct connectivity of elk populations. Genome-wide sequencing and analyses are needed to quantify inbreeding absolutely and assess genetic load and the age of admixture where subspecies currently exchange genes.     

Length–weight relationships of six fish species from the headstream region of the Dongjiang River,China

Dongjiang River, a main tributary of the Pearl River, is geographically situated in South China. The present study describes the length–weight relationships (LWRs) of six fish species (Acrossocheilus paradoxus, Barbodes semifasciolatus, Onychostoma elongatum, Microphysogobio fukiensis, Microphysogobio kiatingensis, Metzia lineata) from the headstream region of the river including five Chinese endemic species (A. paradoxus, B. semifasciolatu, O. elongatum, Mi. fukiensis, Mi. kiatingensis). Fish species of five genera of the same family were collected quarterly from April 2012 to October 2014 by using non‐selective fishing gears: drag nets (5 m, mesh‐size 3 cm), drift gillnets (30 × 15 m, mesh‐size 5 mm), fish cages (4 m, mouth opening 40 × 40 cm), scoop nets (mesh‐size 0.5‐1 cm), and electro‐fishing (12V, 200 Hz). The parameter a and b in the LWR equations (W = a L^b) ranged from 0.0014 to 0.0228, and 2.89 to 3.18, respectively. Compared with FishBase, this study provides the first LWR records for four cyprinids (A. paradoxus, B. semifasciolatu, O. elongatum, Me. lineata) and a new record of maximum body length for O. elongatum.     

Enhancing yeast cell viability after dehydration by modification of the lipid profile

In the present study, we analysed metabolite features during the dehydration-rehydration process for different yeast species genetically closely related to S. cerevisiae, in order to determine whether metabolites might play a role in cell viability. We ranked the species S. cerevisiae, S. paradoxus, S. kudriavzevii, L. kluyveri, N. castellii, S. mikatae, S. bayanus, and S. servazzii according to their viability rate after the dehydration-rehydration process, and showed that desiccation tolerance across the species did not correlate with the intracellular content of trehalose or glycogen. Cell lipid composition was also investigated during this process, to see whether the content of triacylglycerols and phosphatidylcholine showed significant variations across the species. The increase of phosphatidylcholine level increase in both S. paradoxus and S. bayanus cells grown in supplemented media enhanced both their cell viability after stress imposition and lipid storage.     

Evaluating the resolution power of new microsatellites for species identification and stock delimitation in the Cape hakes Merluccius paradoxus and Merluccius capensis (Teleostei: Merlucciidae)

The utility of 15 new and 17 previously published microsatellite markers was evaluated for species identification and stock delimitation in the deep‐water hake Merluccius paradoxus and the shallow‐water hake Merluccius capensis. A total of 14 microsatellites were polymorphic in M. paradoxus and 10 in M. capensis. Two markers could individually discriminate the species using Bayesian clustering methods and a statistical power analysis showed that the set of markers for each species is likely to detect subtle genetic differentiation (F_ST < 0·006) that will be valuable to delimit and characterize genetic stocks.