Ecological niche separation in the Polynucleobacter subclusters linked to quality of dissolved organic matter: a demonstration using a high sensitivity cultivation-based approach

The free-living, cosmopolitan, freshwater betaproteobacterial bacterioplankton genus Polynucleobacter was detected in different years in 11 lakes of varying types and a river using the size-exclusion assay method (SEAM). Of the 350 strains isolated, 228 (65.1%) were affiliated with the Polynucleobacter subclusters PnecC (30.0%) and PnecD (35.1%). Significant positive correlations between fluorescence in situ hybridization and SEAM data were observed in the relative abundance of PnecC and PnecD bacteria to Polynucleobacter communities (PnecC?+?PnecD). Isolates were mainly PnecC bacteria in the samples with a high specific UV absorbance at 254?nm (SUVA(254) ), and a low total hydrolysable neutral carbohydrate and amino acid (THneutralCH?+?THAA) content of the dissolved organic matter (DOM) fraction, which is known to be correlated with a high humic content. In contrast, the PnecD bacteria were abundant in samples with high chlorophyll a and/or THneutralCH?+?THAA concentrations, indicative of primary productivity. With few exceptions, differences in the relative abundance of PnecC and PnecD in each sample, determined using a high-sensitivity cultivation-based approach, were due to DOM quality. These results suggest that the major DOM component in the field, which is allochthonously or autochthonously derived, is a key factor for ecological niche separation between PnecC and PnecD subclusters.     

Ecophysiological differences of betaproteobacterial populations in two hydrochemically distinct compartments of a subtropical lagoon

We studied the population sizes and substrate incorporation patterns of three phylogenetic groups of Betaproteobacteria in a coastal subtropical lagoon that is characterized by a sharp transition from humic freshwater to turbid brackish water. Various cellular processes were addressed by short-term incubations with four radiolabelled compounds and microautoradiographic assessment of substrate incorporation. Group-specific differences in the abundances and the respective physiological state of the three populations were observed upon transfer from the humic-rich compartment to the main body of the lagoon (estimated at 1–2 days). Members of the clade B of Polynucleobacter (PnecB) experienced only an insignificant change in cell numbers, but displayed a general metabolic downshift, carbon metabolism (glucose incorporation) being most affected. By contrast, bacteria from the closely related Polynucleobacter C clade (PnecC) clearly differed in total abundances and in the numbers of DNA-synthesizing or glucose incorporating cells. At the same time, PnecC bacteria maintained comparable levels of protein synthesis (leucine uptake) in both lagoon compartments, and the proportion of cells incorporating N -acetylglucosamine was even higher in the main body of the lagoon. Members of the R-BT lineage showed little changes in cell numbers, DNA synthesis and carbon metabolism. Altogether, the observed patterns of substrate metabolism suggest that different bacterial populations in the lagoon undergo specific physiological adjustments in response to changing environmental conditions.     

Low Intraspecific Diversity in a Polynucleobacter Subcluster Population Numerically Dominating Bacterioplankton of a Freshwater Pond

Cultivation-dependent and -independent methods were combined to investigate the microdiversity of a Polynucleobacter subcluster population (Betaproteobacteria) numerically dominating the bacterioplankton of a small, humic freshwater pond. Complete coverage of the population by cultivation allowed the analysis of microdiversity beyond the phylogenetic resolution of ribosomal markers. Fluorescent in situ hybridization with two probes specific for the narrow subcluster C (PnecC bacteria) of the Polynucleobacter cluster revealed that this population contributed up to 60% to the total number of bacterioplankton cells. Microdiversity was investigated for a date at which the highest relative numbers of PnecC were observed. A clone library of fragments of the ribosomal operon (16S rRNA genes, complete 16S-23S internal transcribed spacer 1 [ITS1], partial 23S rRNA genes) amplified with universal bacterial primers was constructed. The library was stepwise screened for fragments from PnecC bacteria and for different ITS genotypes of PnecC bacteria. The isolated PnecC strains were characterized by sequencing of the 16S rRNA genes and the ITS1. Both the clone library and the established culture collection contained only the same three ITS genotypes, and one of them contributed 46% to the entire number of clones. Genomic fingerprinting of the isolates with several methods always resulted in the detection of only one fingerprint per ITS genotype. We conclude that a Polynucleobacter population with an extremely low intraspecific diversity and an uneven structure numerically dominated the bacterioplankton community in the investigated habitat. This low intraspecific diversity is in strong contrast to the high intraspecific diversities found in marine bacterial populations.     

Temperature modulated effects of nutrients on phytoplankton changes in a mountain lake

Piburger See, a dimictic mountain lake in Austria, experienced moderate cultural eutrophication in the 1950s. Lake restoration led to a re-oligotrophication in the 1990s with a decrease in seasonal phytoplankton biovolume until the late 1990s, but a reversed trend from the early 2000s onwards. We hypothesize that recent changes in phytoplankton biomass and functional structure are triggered by changes in lake nitrogen and silica concentrations, and we expect climate-related factors to modulate the trophic status of Piburger See. Phytoplankton data were analyzed by non-metric multidimensional scaling (NMDS) applied on biovolume of morpho-functional groups, combined with correlation analyses of environmental variables. Since the 2000s, short-term changes in phytoplankton of Piburger See were explained by varying concentrations and ratios of nitrogen and silica, while the inter-annual variability in phytoplankton species composition was rather attributed to superimposed rising water temperature and lake thermal stability. Our results underline the co-dominant role of phosphorus and nitrogen as phytoplankton drivers in lakes that experience periods of nitrogen limitation. The combined impact of nutrients and climate on phytoplankton development can thus mimic short-term increases in the trophic level of less productive lakes.     

Low intraspecific diversity in a polynucleobacter subcluster population numerically dominating bacterioplankton of a freshwater pond

Cultivation-dependent and -independent methods were combined to investigate the microdiversity of a Polynucleobacter subcluster population (Betaproteobacteria) numerically dominating the bacterioplankton of a small, humic freshwater pond. Complete coverage of the population by cultivation allowed the analysis of microdiversity beyond the phylogenetic resolution of ribosomal markers. Fluorescent in situ hybridization with two probes specific for the narrow subcluster C (PnecC bacteria) of the Polynucleobacter cluster revealed that this population contributed up to 60% to the total number of bacterioplankton cells. Microdiversity was investigated for a date at which the highest relative numbers of PnecC were observed. A clone library of fragments of the ribosomal operon (16S rRNA genes, complete 16S-23S internal transcribed spacer 1 [ITS1], partial 23S rRNA genes) amplified with universal bacterial primers was constructed. The library was stepwise screened for fragments from PnecC bacteria and for different ITS genotypes of PnecC bacteria. The isolated PnecC strains were characterized by sequencing of the 16S rRNA genes and the ITS1. Both the clone library and the established culture collection contained only the same three ITS genotypes, and one of them contributed 46% to the entire number of clones. Genomic fingerprinting of the isolates with several methods always resulted in the detection of only one fingerprint per ITS genotype. We conclude that a Polynucleobacter population with an extremely low intraspecific diversity and an uneven structure numerically dominated the bacterioplankton community in the investigated habitat. This low intraspecific diversity is in strong contrast to the high intraspecific diversities found in marine bacterial populations.     

Modulation of microbial predator-prey dynamics by phosphorus availability: growth patterns and survival strategies of bacterial phylogenetic clades

We simultaneously studied the impact of top-down (protistan grazing) and bottom-up (phosphorus availability) factors on the numbers and biomasses of bacteria from various phylogenetic lineages, and on their growth and activity parameters in the oligo-mesotrophic Piburger See, Austria. Enhanced grazing resulted in decreased proportions of bacteria with high nucleic acid content (high-NA bacteria) and lower detection rates by FISH. There was a change in the composition of the bacterial assemblage, whereby Betaproteobacteria were heavily grazed while Alphaproteobacteria and Cytophaga-Flavobacterium-Bacteroides were less affected by predators. Changes in bacterial assemblage composition were also apparent in the treatments enriched with phosphorus, and even more pronounced in the incubations in dialysis tubes (allowing relatively free nutrient exchange). Here, Betaproteobacteria became dominant and appeared to act as successful opportunistic competitors for nutrients. In contrast, Actinobacteria did not respond to surplus phosphorus by population growth, and, moreover, maintained their small size, which resulted in a very low biomass contribution. In addition, significant relationships between high-NA bacteria and several bacterial phylogenetic clades were found, indicating an enhanced activity status. By combining several single-cell methods, new insight is gained into the competitive abilities of freshwater bacteria from a variety of phylogenetic lineages under contrasting sets of bottom-up and top-down constraints.     

Interactions of temperature and nutrient changes: effects on phytoplankton in the Piburger See (Tyrol,Austria)

1. Contemporary limnological and palaeolimnological data from Piburger See (Eastern Alps, Austria) allowed the reconstruction of its trophic state since the late 19th century and the assessment of changes in phytoplankton biomass and species composition in relation to selected environmental parameters. 2. A radiometrically dated sediment core from Piburger See was analysed for geochemical parameters, spheroidal carbonaceous particles (SCPs), bacterial and algal pigments, and diatoms. The low SCP sediment inventory assigns Piburger See to the ‘cleaner’ sites in Europe with respect to fossil‐fuel related air pollution. The sedimentary pigment and diatom record reveals moderate eutrophication during the 20th century, followed by a slow re‐oligotrophication since the mid‐1980s because of lake restoration starting in 1970. 3. Epilimnetic temperature for Piburger See was reconstructed using air temperature records. A pronounced temperature increase has been recorded during the mid‐1940s and since the late‐20th century, both promoting algal growth and changes in species composition (e.g. increase in centric diatoms and recent bloom of Asterionella formosa). 4. Climate scenarios project additional substantial warming for this mountain lake by the end of the 21st century which will be most pronounced during the growing season. The predicted change in lake water temperature and thermal dynamics represents a key driver for the trophic and ecological status of Piburger See in the future.     

Phylogeography of isolated freshwater three-spined stickleback Gasterosteus aculeatus populations in the Adriatic Sea basin

Analyses of mitochondrial (mt) DNA and microsatellite variation were carried out to examine the relationships between 10 freshwater populations of three-spined sticklebacks Gasterosteus aculeatus along the eastern coast of the Adriatic Sea. Partial sequences of the mtDNA control region and cytochrome b gene, in addition to 15 microsatellite loci, were used to analyse populations from four isolated river catchments. Results uncovered an Adriatic lineage that was clearly divergent from the European lineage, and confirmed that the most divergent and ancient populations are located within the Adriatic lineage as compared with other European populations. Two northern Adriatic populations formed independent clades within the European mitochondrial lineage, suggesting different colonization histories of the different Adriatic populations. Nuclear marker analyses also indicated deep divergence between Adriatic and European populations, albeit with some discordance between the mtDNA phylogeny of the northern Adriatic populations, further highlighting the strong differentiation among the Adriatic populations. The southern populations within the Adriatic lineage were further organized into distinct clades corresponding to respective river catchments and sub-clades corresponding to river tributaries, reflecting a high degree of population structuring within a small geographic region, concurrent with suggestions of existence of several microrefugia within the Balkan Peninsula. The highly divergent clades and haplotypes unique to the southern Adriatic populations further suggest, in accordance with an earlier, more limited survey, that southern Adriatic populations represent an important reservoir for ancient genetic diversity of G. aculeatus.     

Substrate incorporation patterns of bacterioplankton populations in stratified and mixed waters of a humic lake

Bacterial incorporation of glucose, leucine, acetate and 4-hydroxybenzoic acid (HBA) was investigated in an artificially divided humic lake (Grosse Fuchskuhle, Germany). Two basins with contrasting influx of allochthonous organic carbon were sampled during late summer stratification (oxic and anoxic layers) and after autumn mixing. High total and cell-specific incorporation rates were observed for glucose and HBA in stratified and mixed waters respectively, but only a small fraction of bacteria visibly incorporated HBA. The oxic layer of the more humic-rich basin featured a significantly lower fraction of glucose incorporating cells and substantially higher proportions of acetate assimilating bacteria. Niche differentiation was observed in two betaproteobacterial populations: cells affiliated with the Polynucleobacter C subcluster efficiently incorporated acetate but little glucose, whereas the opposite was found for members of the R-BT065 clade. By contrast, leucine incorporation was variable in both taxa. Considering the high concentrations and rapid photochemical generation of organic acids in humic waters our results may help to explain the success of the Polynucleobacter C lineage in such habitats. Specific substrate or habitat preferences were also present in three subgroups of the actinobacterial acI lineage: The numerically dominant clade in oxic waters (acI-840-1) was absent in the anoxic zone and did not incorporate acetate. A second group (acI-840-2) was found both in the epi- and hypolimnion, whereas the third one (acI-840-3) only occurred in anoxic waters. Altogether our results suggest a constitutive preference for some substrates versus an adaptive utilization of others in the studied microbial groups.     

Phylogeny and biogeography of the alpine newt Mesotriton alpestris (Salamandridae, Caudata), inferred from mtDNA sequences

In this paper, we performed phylogenetic analyses of Mesotriton alpestris populations from the entire range of species distribution, using fragments of two mtDNA genes, cytochrome b (309bp) and 16S rRNA ( approximately 500bp). Sequence diversity patterns and phylogenetic analyses reveal the existence of a relict lineage (Clade A) of late Miocene origin, comprising populations from south-eastern Serbia. This lineage is proposed to be ancestor to a western and an eastern lineage, which diverged during the middle Pliocene. The western lineage is further divided in two clades (Clades B, C) of middle Pliocene origin that represent populations from Italy (B) and populations from central Europe and Iberia (C). Further subdivision, dated back to the middle-late Pliocene, was found within the eastern lineage, representing southern (Clade D) and central-northern (Clade E) Balkan populations, respectively. Extensive sequence divergence, implying greater isolation in multiple refugia, is found within eastern clades, while the western clades seem to have been involved in the colonization of central, western and north-eastern Europe from a hypothetical refugium in central Europe. The extent of divergence does not support the current taxonomy indicating cryptic speciation in the Balkans, while paedomorphic lineages were found to have been evolved during early-middle Pleistocene probably as a response to the ongoing dramatic climatic oscillations.     

Ubiquity of Polynucleobacter necessarius ssp. asymbioticus in lentic freshwater habitats of a heterogenous 2000 km2 area

We present a survey on the distribution and habitat range of Polynucleobacter necessarius ssp. asymbioticus (PnecC), a numerically and functionally important taxon in the plankton of freshwater systems. We systematically sampled stagnant freshwater habitats in a heterogeneous 2000 km² area, together with ecologically different habitats outside this area. In total, 137 lakes, ponds and puddles were investigated, which represent an enormous diversity of habitats differing, e.g. in depth (< 10 cm – 171 m) and pH (3.9–8.5). PnecC bacteria were detected by cultivation‐independent methods in all investigated habitats, and their presence was confirmed by cultivation of strains from selected habitats representing the whole studied ecological range. The determined relative abundance of the subspecies ranged from values close to the detection limit of FISH (0.2%) to 67% (average 14.5%), and the highest observed absolute abundance was 5.3 × 10⁶ cells ml^?1. Statistical analyses revealed that the abundance of PnecC bacteria was partially controlled by factors linked to concentrations of humic substances, which support the hypothesis that these bacteria utilize photodegradation products of humic substances. Based on the revealed statistical relationships, an average relative abundance of this subspecies of 20% in global freshwater habitats was extrapolated. Our study provides important implications for the current debate on ubiquity and biogeography in microorganisms.     

镜湖萼花臂尾轮虫（Brachionus calyciflorus）种群遗传多样性的季节变化

运用随机扩增多态DNA（RAPD）技术研究了于2005年春季和夏季采自芜湖市镜湖的萼花臂尾轮虫（Brachionus calyciflorus）种群基因组DNA多态性。从44个随机引物中筛选出10个谱带清晰、重复性好的引物。10个引物共检测到76个位点,其中65个位点显多态性,多态位点比例（P）为85.5%。对RAPD扩增结果进行聚类分析,基于遗传距离指数构建了萼花臂尾轮虫的UPGMA和ME系统树。经计算,各克隆平均遗传距离指数为0.5219,春季种群内遗传距离指数（0.4416）大于夏季种群内遗传距离指数（0.4304）;两季节种群间遗传距离指数为0.6010,明显大于季节种群内遗传距离指数。16个克隆分别聚在2个主要簇群中,在UPGMA系统树中,春季种群和夏季种群明显分聚在两个主要支系中;而在ME树中,除了夏季Su2克隆和春季种群聚到一个支系外,其它夏季种群则聚在一个独立支系中。上述结果表明,春季种群和夏季种群在遗传上具有较大的差异;镜湖萼花臂尾轮虫种群存在着明显的季节更替,而Su2克隆可能是春季和夏季种群间的过渡。     

Primary structure of three minor isoforms of amphioxus sarcoplasmic calcium-binding proteins.

Previously we reported the amino acid sequences of 4 well-defined sacroplasmic, high-affinity Ca(2+)-binding proteins in the protochordate amphioxus, Branchiostoma lanceolatum [1]. Here we report on the complete amino acid sequence determination of 3 additional minor isoforms. The seven isoforms differ from each other in 9 positions of a contiguous 17-residue-long segment (positions 20-36) and can be classified in a alpha (ASCP I, III and IV) and a beta lineage (ASCP II, V, VI and VII).     

Roseobacter and SAR11 dominate microbial glucose uptake in coastal North Sea waters

Bacterial assemblages in coastal pelagic environments are exposed to pronounced temporal and spatial fluctuations in the availability of monomeric substrates. Little is known about the response of particular bacterial groups to such variability. We studied glucose incorporation at various concentrations (0.1-100 nM) by bacteria related to Roseobacter, SAR11, Gammaproteobacteria and Cytophaga-Flavobacteria in coastal North Sea waters in late winter and during a spring phytoplankton bloom dominated by Phaeocystis sp. (March and May 2004 respectively). Both the fraction of glucose-assimilating bacterial cells and the rate of substrate incorporation per active cell were higher in May. The respective contributions of the studied groups to all glucose-assimilating Bacteria were related to substrate concentration. The majority of glucose-incorporating bacterial cells at the lower concentrations were members of the Roseobacter and SAR11 clades. At both time-points the two groups formed approximately equal fractions of all glucose-incorporating bacteria. This was due to a small population of highly active Roseobacter cells and high abundances of SAR11 bacteria with low proportions of glucose-incorporating cells. By contrast, the proportion of active cells from the Cytophaga-Flavobacteria lineage substantially increased at higher levels of available substrate. The determination of concentration-dependent substrate incorporation patterns may help to better understand the different ecophysiological niches of bacterioplankton populations.     

The hidden diversity of Coleodactylus amazonicus (Sphaerodactylinae,Gekkota) revealed by molecular data

Coleodactylus amazonicus, a small leaf-litter diurnal gecko widely distributed in Amazon Basin, has been considered a single species with no significant morphological differences between populations along its range. A recent molecular study, however, detected large genetic differences between populations of central Amazonia and those in the easternmost part of the Amazon Basin, suggesting the presence of taxonomically unrecognised diversity. In this study, DNA sequences of three mitochondrial (16S, cytb, and ND4) and two nuclear genes (RAG-1, c-mos) were used to investigate whether the species currently identified as C.amazonicus contains morphologically cryptic species lineages. The present phylogenetic analysis reveals further genetic subdivision including at least five potential species lineages, restricted to northeastern (lineage A), southeastern (lineage B), central-northern (lineage E) and central-southern (lineages C and D) parts of Amazon Basin. All clades are characterized by exclusive groups of alleles for both nuclear genes and highly divergent mitochondrial haplotype clades, with corrected pairwise net sequence divergence between sister lineages ranging from 9.1% to 20.7% for the entire mtDNA dataset. Results of this study suggest that the real diversity of “C. amazonicus” has been underestimated due to its apparent cryptic diversification.     

Mitochondrial DNA D‐loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens

This study sought to assess mitochondrial DNA (mtDNA) diversity and phylogeographic structure of chickens from five agro‐ecological zones of Zimbabwe. Furthermore, chickens from Zimbabwe were compared with populations from other geographical regions (Malawi, Sudan and Germany) and other management systems (broiler and layer purebred lines). Finally, haplotypes of these animals were aligned to chicken sequences, taken from GenBank, that reflected populations of presumed centres of domestication. A 455‐bp fragment of the mtDNA D‐loop region was sequenced in 283 chickens of 14 populations. Thirty‐two variable sites that defined 34 haplotypes were observed. In Zimbabwean chickens, diversity within ecotypes accounted for 96.8% of the variation, indicating little differentiation between ecotypes. The 34 haplotypes clustered into three clades that corresponded to (i) Zimbabwean and Malawian chickens, (ii) broiler and layer purebred lines and Northwest European chickens, and (iii) a mixture of chickens from Zimbabwe, Sudan, Northwest Europe and the purebred lines. Diversity among clades explained more than 80% of the total variation. Results indicated the existence of two distinct maternal lineages evenly distributed among the five Zimbabwean chicken ecotypes. For one of these lineages, chickens from Zimbabwe and Malawi shared major haplotypes with chicken populations that have a Southeast Asian background. The second maternal lineage, probably from the Indian subcontinent, was common to the five Zimbabwean chicken ecotypes, Sudanese and Northwest European chickens as well as purebred broiler and layer chicken lines. A third maternal lineage excluded Zimbabwean and other African chickens and clustered with haplotypes presumably originating from South China.     

Differential sorting of beta tubulin isotypes into colchicine-stable microtubules during neuronal and muscle differentiation of embryonal carcinoma cells.

Pluripotent P19 embryonal carcinoma (EC) cells were differentiated along the neuronal and muscle pathways. Comparisons of class I, II, III, and IV beta tubulin isotypes in total and colchicine-stable microtubule (MT) arrays from uncommitted EC, neuronal, and muscle cells were made by immunoblotting and by indirect immunofluorescence microscopy. In undifferentiated EC cells the relative amounts of these four isotypes are the same in both the total and stable MT populations. Subcellular sorting of beta tubulin isotypes was demonstrated in both neuronal and muscle differentiated cells. During neuronal differentiation, class II beta tubulin is preferentially incorporated into the colchicine-stable MTs while class III beta tubulin is preferentially found in the colchicine-labile MTs. The subcellular sorting of class II into stable MTs correlates with the increased staining of MAP 1B, and with the expression of MAP 2C and tau. Although muscle differentiated cells express class II beta tubulin, stable MTs in these cells do not preferentially incorporate this isotype but instead show increased incorporation of class IV beta tubulin. Muscle cells do not show high levels of MAP 1B and do not express MAP 2C or tau. These results are consistent with the hypothesis that a subcellular sorting of tubulin isotypes is the result of a complex interaction between tubulin isotypes and MT-associated proteins.     

Spatial Distribution of the Nematode Fauna and Production of Three Nematodes (Tobrilus gracilis,Monhystera stagnalis,Ethmolaimus pratensis) in the Profundal of Piburger See (Austria, 913 m a.s.l)

The species composition and the spatial distribution of the nematode fauna of Piburger See is discussed briefly. The study then concentrates on the three species (Tobrilus gracilis, Monhystera stagnalis, Ethmolaimus pratensis) which form the lake's profundal nematode fauna between depths of roughly 8 and 13 meters. This profundal fauna is separated by a distinct metalimnetic abundance minimum from the very diverse littoral community. In addition to taxonomic and ecological considerations, the zonation of the three species within their main habitat is described, and life cycles cohort production as well as annual production are evaluated from the field data. Total annual nematode production within the profundal habitat (8–13 m) in Piburger See amounts to 11.6 kg per hectare. 65 % of which are contributed by T. gracilis, 22 % by M. stagnalis and 13 % by E. pratensis. For the whole area under observation (6 to 13.5 m, including the scarcely populated border zones) mean annual nematode production is 7 kg per hectare.     

Gene structure dynamics and divergence of the polygalacturonase gene family of plants and fungus.

Whole copies of the polygalacturonase (PG) genes from rice (Oryza sativa subsp. japonica) and a filamentous fungus (Aspergillus oryzae) were isolated. The orthologs of the rice PGs were also retrieved from other plant species. The 106 plant PGs analyzed were divided into 5 clades, A, B, C, D, and E. The fungus PGs were classified into 3 clades, of which one formed a loose cluster with clade E of the plant PGs. Four domain motifs (I, II, III, IV) were identified in all PGs. Motifs II and III were split by introns such as G/DDC and CGPGHGIS/IGSLG, respectively. In plant PGs there were 446 introns in total and 3.98 introns per gene. Intron phase distribution was 65.5% for phase 0, 19.7% for phase 1, and 14.8% for phase 2 in plant PGs. In the PGs of A. oryzae there were 37 introns of phase 0 (59.5%), phase 1 (24.3%), and phase 2 (16.2%), with 2.47 introns per gene. The 5 clades of plant PGs were divided into 3 basic gene structure lineages. Intron positions and phases were conserved among the PGs in the first 2 lineages. The third lineage consisted of PGs of clade E, which also carried highly conserved introns at different positions from other PGs. Intron positions were not as highly conserved in fungus PGs as in plant PGs. The introns in the current PGs have been present since before the divergence of monocots from dicots. The results obtained show that differential losses of introns created gene diversity, which was followed by segmental and tandem duplication in plant PGs.     

Genomewide patterns of variation in genetic diversity are shared among populations,species and higher‐order taxa

Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes (N_e) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage‐specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N_e. Utilizing population‐level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N_e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population‐scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations (F_ST, PBS, d_xy) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.