Cryptic lineages and potential introgression in a mixed-ploidy species (Phragmites australis) across temperate China

Polyploidization and hybridization are very common in natural plant species, and mixed-ploidy species provide a unique opportunity to study the effects of evolutionary history, local abundance, and ploidy level on the direction and extent of introgression between intraspecific lineages. First, we delimited two morphologically cryptic lineages of Phragmites australis Trin. ex Steud. in temperate China using 11 nuclear microsatellites and two chloroplast DNA fragments with 225 samples from China as well as 11 samples from Oceania and Europe. Our evidence supported that haplotype O and haplotype P were two relatively independent lineages with low and high ploidy levels, respectively; haplotype M might be ancient and could have undergone a complex evolutionary history. Then we examined the lineage divergence and compared the introgression patterns between two major lineages along geographical and abundance gradients with a large number of samples (n = 1067) collected from China. The sympatric coexistence of two lineages in north and northeast China implies an ongoing or potential introgression between them. Cline analysis showed that the level of genetic admixture were significantly correlated with longitude rather than latitude. Our results also suggested that ploidy level could deeply influence the introgression asymmetry, and the effect of the current local abundance on introgression might be covered by the past coexistence time driven by phylogeographic history. Our study draws a baseline for future research on the ecological and evolutionary consequences of migration and introgression of Chinese P. australis under global change.     

Effects of summer drawdown on cyprinid fish larvae in Lake Biwa, Japan

The effects of artificial water-level manipulations in Lake Biwa, initiated in 1992 to prevent flooding, on cyprinid fish larvae were assessed by measuring and estimating the topographic change in the reed zones. The shallow, litter-accumulated water in those zones was inhabited by larvae of two species, Carassius spp. and Cyprinus carpio. More than 70% (by volume) of these shallow areas in Lake Biwa was estimated to be lost when the water level was artificially lowered by 30cm from June to October 1997. During the low water level period, significantly fewer eggs of these cyprinid fishes were collected in a reed zone than in April and May of the same year, a comparison with a previous study suggesting that spawning of the fishes was inhibited during the period of low water level. The artificial reductions in water level probably resulted in a significant decrease in the volume of shallow water in the lake and may be linked to the drastic decline in these cyprinid fishes.     

Tracing the origin of Gulf Coast Phragmites (Poaceae): A story of long-distance dispersal and hybridization

? Premise of the study: Long-distance dispersal can affect speciation processes in two opposing ways. Dispersal can promote geographic isolation or it can bring together geographically distant and distantly related genotypes, thus counteracting local differentiation. We used the Gulf Coast of North America (GC), a "hot spot" of reed diversity and evolutionary dynamics, as a model system to study the diversification processes within the invasive, cosmopolitan, polyploid grass Phragmites. ? Methods: Genetic diversity was studied using collections representing all species of the genus and from all continents (except Antarctica). A range of molecular markers, including chloroplast and nuclear sequences, microsatellites, and AFLPs, was analyzed to detect DNA variation from the population to the species level and to infer phylogenetic relationships across continents. ? Key results: An interspecific hybrid, Phragmites mauritianus × P. australis, and four P. australis cp-DNA haplotypes from Africa, Europe, and North America have been dispersed to the GC and interbreed with each other. ? Conclusions: Long-distance dispersal and weak breeding barriers appear to be recurring phenomena, not only in the GC, but worldwide. We present data strongly suggesting that interspecific hybridization and introgression among different Phragmites species take place and appear to have contributed significantly to the diversification processes within the genus. Hence, the application of traditional species concepts within Phragmites might be inappropriate.     

四种生态型芦苇叶中离子分布对生境的生理适应

采用X射线微区分析技术 ,测定了 4种生态型芦苇 (Phragmitesaustralis (CaV .)Trin .exSteud .)叶的表皮泡状细胞、叶肉细胞和叶脉维管束鞘细胞离子的含量。结果表明 :沼泽芦苇的鞘细胞内 ,K 、Na 、Ca2 、Mg2 和Cl-分布均较叶肉细胞和泡状细胞高。沙丘芦苇的泡状细胞中Ca2 分布较叶肉细胞和鞘细胞高 ,而Mg2 在其叶肉细胞 ,以及K 、Na 和Cl- 在其鞘细胞内分布均较高。在轻度盐化草甸芦苇的叶肉细胞内分布较多的Na 和Mg2 ,而在鞘细胞内K 、Ca2 和Cl- 的分布均较叶肉细胞和泡状细胞为高。重度盐化草甸芦苇的泡状细胞内Na 和Mg2 的分布较多 ;同样 ,在叶肉细胞中K 、Ca2 和Cl- 的分布也较多。最后 ,讨论了上述各种离子在不同生态型芦苇叶内分布的状况 ,以及与其环境适应的生理意义。     

Cytogeography of the Phleum pratense group (Poaceae) in the Carpathians and Pannonia

Cytogeographical variability within the Phleum pratense group in the Carpathians and adjacent part of Pannonian lowland, based on 132 populations analysed by flow cytometry, is described. Only diploid and hexaploid plants were detected among 635 samples from the studied area. Diploids were found to be less frequent (127 plants, 20%) than hexaploids (508, 80%). With the exception of the single pure diploid population, diploids always co-occured with hexaploids (30 localities, 22.7%). The majority of populations (101, 76.5%) consisted of hexaploid plants. Most mixed populations occur in the Western Carpathians (26). In the Eastern Carpathians, mixed populations are much rarer, with three populations in Ukraine and one in Romania. In the Southern Carpathians, only hexaploids occur. The conventional taxonomic concept of the two species, diploid P. bertolonii and hexaploid P. pratense , was followed in spite of their sympatric occurence. Distribution maps based on chromosome number data from previous studies and on ploidy level estimates are given for both species in the studied area. The pattern of different distribution of the two taxa within the Carpathians is discussed.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 157 , 475–485.     

Echosounding observations of coverage,height, PVI,and biomass of submerged macrophytes in the southern basin of Lake Biwa,Japan

We have developed a procedure to process echosounding data to map the distribution of submerged aquatic macrophytes in the southern basin of Lake Biwa, a water body that has a surface area of 52 km² and a mean depth of 4 m. Echosounding observations were made along 27 transect lines spaced at 500-m intervals on August 4 and September 2 and 30, 2003. Quantitative vegetation data including percent coverage, mean vegetation height, and percent vegetation infestation were directly determined using image data from the echosounder recorded digitally on videotape. Based on the image data from an echosounder, a regression model was developed for estimating biomass of submerged macrophytes. The regression model using the total echo strength as the explanatory variable could reliably estimate macrophyte biomass up to 300 g m⁻². Distribution maps of macrophyte height and biomass suggest that the recent summer decline of submerged macrophytes started earlier in shallow areas (<3 m of depth) than deep areas (>4 m) in the southern basin of Lake Biwa.     

DNA ploidy-level variation in native and invasive populations of Lythrum salicaria at a large geographical scale

Aim  This study aimed to document precisely the patterns of DNA ploidy variation in the native and secondary ranges of Lythrum salicaria distribution. The hypothesis that species invasiveness had been induced by a switch in ploidy level was addressed.
Location  Europe, Middle East, North America.
Methods  DNA ploidy levels of 1884 progenies of 578+ plants collected at 124 localities were determined by DAPI flow cytometry.
Results  Large cytotype variation (2 x , 3 x , 4 x and 6 x ) was found across the native area of distribution (64 populations covering 12 European and two Middle Eastern countries). DNA hexaploids were detected for the first time, and rare DNA triploids were reliably confirmed. DNA tetraploids largely prevailed across the native range studied, while DNA diploids and DNA hexaploids were recorded only in Israel and Turkey, respectively. DNA triploid progenies occurred in one population from Hungary (together with DNA tetraploids). Sympatric growth of DNA tetraploids and DNA hexaploids was repeatedly encountered in Turkey. In contrast, cytotype uniformity was a typical feature of the invasive North American plants. Sixty populations, covering 13 states of the USA and provinces of Canada, were characterized by the presence of only DNA tetraploids.
Main conclusions  Several L. salicaria cytotypes (2 x , 3 x , 4 x , 6 x ) occur in the native range of distribution, with much variation concentrated in the Middle Eastern countries, whereas only DNA tetraploids appeared to occur in North America. Our data show that the invasive spread of North American populations was not triggered by differences in ploidy level. Alternative explanations should be sought.     

Phylogeny and historical demography of endemic fishes in Lake Biwa: the ancient lake as a promoter of evolution and diversification of freshwater fishes in western Japan

To elucidate the origins of the endemic fish of Lake Biwa, an ancient lake in Japan, and the role of the lake in the diversification of freshwater fish in western Japan, we established a molecular phylogenetic framework with an absolute time scale and inferred the historical demography of a large set of fish species in and around the lake. We used mtDNA sequences obtained from a total of 190 specimens, including 11 endemic species of Lake Biwa and their related species, for phylogenetic analyses with divergence time estimations and from a total of 2319 specimens of 42 species (including 14 endemics) occurring in the lake for population genetic analyses. Phylogenetic analysis suggested that some of the endemic species diverged from their closest relatives earlier (1.3–13.0 Ma) than the period in which the present environmental characteristics of the lake started to develop (ca. 0.4 Ma), whereas others diverged more recently (after 0.4 Ma). In contrast, historical demographic parameters suggested that almost all species, including endemic and nonendemic ones, expanded their populations after the development of the present lake environment. In phylogeographic analyses, common or very close haplotypes of some species were obtained from Lake Biwa and other regions of western Japan. The phylogenetic and historical demographic evidence suggests that there was a time lag between phylogenetic divergence and population establishment and that phenotypic adaptation of some endemic species to the limnetic environment occurred much later than the divergences of those endemic lineages. Population structure and phylogeographic patterns suggest that Lake Biwa has functioned not only as the center of adaptive evolution but also as a reservoir for fish diversity in western Japan.     

Seasonal Vertical Migration and Aestivation of <Emphasis Type="Italic">Rhyacodrilus hiemalis</Emphasis> (Tubificidae,Clitellata) in the Sediment of Lake Biwa,Japan

The vertical distribution of the tubificid worm Rhyacodrilus hiemalis Ohtaka, the numerically dominant species of oligochaete in the littoral of Lake Biwa, was studied with special reference to seasonal vertical migration in the lake sediment. Monthly collections of lake sediment cores were made using PVC tubes. Core sections of sample sediments ranged from 76 to 117 cm. The vertical distribution of the worms showed no diurnal variation; therefore diel vertical migration was not evident. Seasonal downward migration started in April, and upward migration started in October. From December to March, almost all worms remained in the near-surface sediment layer (surface to 30 cm deep), while from July to September almost all worms remained deeper than 30 cm. However, few individuals migrated deeper than 90 cm. No discontinuous layers were found in grain size composition, water content, loss on ignition, particulate carbon, nitrogen or phosphorus. In deep sediment there was no free oxygen, as evidenced by negative ORP values. For 4 months in summer, R. hiemalis aestivated, probably utilizing anaerobic respiration. It appeared that R. hiemalis moved deeper in the sediment in response to sediment temperature, because sediment temperatures in the deep layers seemed to converge at around 20–21 °C in the summer months. The life history traits of seasonal vertical migration and summer aestivation perhaps arose as an adaptation to the climatic conditions accompanying the geographical origin of R. hiemalis, and they also serve to minimize predation risk during summer when most invertebrate predatory fishes are active.     

Occurrence of the endangered species Nitellopsis obtusa (Charales,Charophyceae) in western Japan and the genetic differences within and among Japanese populations

Nitellopsis obtusa (Charales, Charophyceae) are widely distributed from Europe to Asia; however, this species has been recorded in only the five lakes in central Honshu in Japan. This species was thought to be extinct in Japan, but was rediscovered in limited areas of Lake Kawaguchi in central Honshu. More recently, we discovered more Japanese populations of N. obtusa in Lake Biwa in western Honshu, and it became clear that the species had a broader distribution in Japan than originally believed. In addition, although only male or female thalli have been collected at each lake, both male and female thalli were found from Lake Biwa. This is the first report of a potentially sexual population of N. obtusa in Japan. The DNA sequences of three chloroplast DNA markers, including both coding and non‐coding regions, were identical in all specimens from Lake Kawaguchi and Lake Nojiri (Central Honshu), and differed from those of Lake Biwa and German specimens. Although Japanese and German specimens were genetically similar, Japanese specimens displayed considerable genetic diversity according to locality.     

Effects of temperature, and availability of nitrogen and phosphorus on the abundance of Anabaena and Microcystis in Lake Biwa, Japan: an experimental approach

Under optimal nutrient conditions, both Microcystis sp. and Anabaena sp. isolated from Lake Biwa grew optimally at 28–32°C but differed in maximal growth rates, phosphate uptake kinetics, maximal phosphorus quotas, and growth responses to nitrogen and phosphorus limitation. The maximal growth rates of Microcystis and Anabaena were 1.6 and 1.25 divisions day⁻¹, respectively. With phosphate and nitrate in the growth-limiting range, the growth of Microcystis was optimal at an N : P ratio of 100 : 1 (by weight) and declined at lower (nitrogen limitation) and higher (phosphorus limitation) ratios. In contrast, Anabaena growth rates did not change at N : P ratios from 1000 : 1 to 10 : 1. Starting with cells containing the maximal phosphorus quota, Microcystis growth in minus-phosphorus medium ceased in 7–9 days, compared with 12–13 days for Anabaena. The phosphate turnover time in cultures starved to their minimum cell quotas was 7.9 min for Microcystis and 0.6 min for Anabaena. Microcystis had a higher K _s (0.12 μg P l⁻¹ 10⁻⁶ cells) and lower V _max (9.63 μg P l⁻¹ h⁻¹ 10⁻⁶ cells), than Anabaena (K _s 0.02 μg P l⁻¹ h⁻¹ 10⁻⁶ cells; V _max 46.25 63 μg P l⁻¹ h⁻¹ 10⁻⁶ cells), suggesting that Microcystis would not be able to grow well in phosphorus-limited waters. We conclude that in spite of the higher growth rate under ideal conditions, Microcystis does not usually bloom in the North Basin because of low availability of phosphorus and nitrogen. Although Anabaena has an efficient phosphorus-uptake system, its main strategy for growth in low-phosphorus environments may depend on storage of phosphorus during periods of abundant phosphorus supply, which are rare in the North Basin. Received: July 31, 2000 / Accepted: October 18, 2000     

Isolation and characterisation of microsatellite loci in Calystegia soldanella (Convolvulaceae), an endangered coastal plant isolated in Lake Biwa,Japan

Eight microsatellite loci of Calystegia soldanella useful for comparisons of the genetic structure of isolated populations in the ancient Lake Biwa and coastal populations in Japan were isolated and characterised. The number of alleles ranged from 2 to 5. The expected (H _E) and observed (H _O) heterozygosities were 0.097–0.583 and 0.000–0.380, respectively, from 100 individuals from Lake Biwa and coastal populations. Seven of the eight loci exhibited significantly fewer heterozygotes than expected based on the Hardy–Weinberg equilibrium (P < 0.05). These primers amplifying microsatellites in C. soldanella may provide a population genetics tool useful in the establishment of a conservation strategy.     

Seasonal variation in biomass and photosynthetic activity of epilithic algae on a rock at the upper littoral area in the north basin of Lake Biwa, Japan

Vertical distributions of biomass and the photosynthetic activity of epilithic algae were observed seasonally with regard to their physical and chemical parameters along a rocky shoreline of the upper littoral area in the north basin of Lake Biwa. Chlorophyll a amounts in epilithic algae showed a marked change with depth from spring to early summer. The algal biomass showed higher values on the lower part of a large rock in early spring, and gradually increased on the upper part as a result of the growth of Spirogyra sp., a filamentous Chlorophyceae. This growth seems to be associated with a rise in water temperature, with the biomass at the upper depths seeming to be affected by a hydraulic disturbance. The standing crop of epilithic algae showed a maximum value in June and declined to a minimum in August because of the corresponding proliferation or disappearance of Spirogyra as well as changes in the water level. The maximum value of the assimilation number calculated from the potential photosynthetic rate of epilithic algae was obtained at the lower depths in June when Spirogyra grew vigorously. Appreciably high assimilation numbers were also observed in summer and fall, although chlorophyll a amounts were low. The present study is the first in a series to clarify the contribution of epilithic algae on rocky areas to productivity throughout the entire littoral ecosystem.     

Flow cytometric,chromosomal and morphometric analyses challenge current taxonomic concepts in the Portulaca oleracea complex (Portulacaeae,Caryophyllales)

Portulaca oleracea is a noxious annual weed of worldwide distribution in temperate to tropical climates. Its taxonomy has been treated in contradictory ways in the past. Various microspecies have been described, lumped into a single species by other authors. We re‐examined the importance of seed size and ploidy variation, previously applied as the most important taxonomic characters, for systematic classification based on accessions from Europe, Asia, Africa and South America using flow cytometry, chromosome counting and morphometry. Sixteen microspecies and six transitional forms, covering the ploidy and seed character variation, proposed for the complex, were studied from 178 populations. Portulaca grandiflora was included as a reference species from outside the complex. DNA hyper‐pentaploidy or hexaploidy were inferred for the majority of accessions which exhibited the full range of seed size. It is recommended that the only species of lower ploidy (either diploid based on x = 12 or tetraploid based on x = 12) encountered, P. nicaraguensis, should be separated from the P. oleracea complex as it deviates in base chromosome number and monoploid genome size. The frequency distribution of seed size was continuous and unimodal within the wild taxa of the complex and in pairs of taxa defined by testa sculpture. Seed size of DNA hexaploids was slightly negatively correlated with sample/standard fluorescence intensities. Our results conflict with the current microspecies concept. Possible reasons underlying the discrepancy are discussed and strategies for future systematic research are suggested. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 144–156.     

Recent colonization by a coastal plant of inland habitats at an ancient freshwater lake,Lake Biwa: multilocus sequencing and a demographic history of Lathyrus japonicus (Fabaceae)

Ancient lakes have been recognized as “long‐term isolated islands” in terrestrial ecosystems. Lake Biwa, one of the few ancient lakes that formed around 4 million years ago, harbors many coastal species that commonly inhabit seashores. The beach pea, Lathyrus japonicus, is a typical coastal species of this freshwater lake, where morphological, physiological, and genetic differentiations have been reported between Biwa and coastal populations. Whether Biwa populations were isolated for long periods throughout Pleistocene climatic oscillations and subsequent range shifts is unclear. We assessed population genetic structure and demography of beach pea in this ancient freshwater lake using the sequences of eight nuclear loci. The results of STRUCTURE analyses showed evidence of admixture between Biwa and coastal populations, reflecting recent gene flow. The estimated demographic parameters implemented by the isolation with migration model (IM model) revealed a recent divergence (postglacial period) of Biwa populations, with some gene flow from Biwa to coastal populations. In addition, Biwa populations were significantly smaller in size than the ancestral or coastal populations. Our study suggests that a Holocene thermal maximum, when transgression could allow seeds from coastal plants to access Lake Biwa, was involved in the origin of the Biwa populations and their genetic divergence. Thus, coastal populations might have migrated to Lake Biwa relatively recently. Our study concluded that ancestral migrants in Lake Biwa were derived from small founding populations and accelerated genetic isolation of Biwa populations during short‐term isolation.     

Diversification along a benthic to pelagic gradient contributes to fish diversity in the world's largest lake (Lake Baikal,Russia)

Insights into the generation of diversity in both plants and animals have relied heavily on studying speciation in adaptive radiations. Russia's Lake Baikal has facilitated a putative adaptive radiation of cottid fishes (sculpins), some of which are highly specialized to inhabit novel niches created by the lake's unique geology and ecology. Here, we test evolutionary relationships and novel morphological adaptation in a piece of this radiation: the Baikal cottid genus, Cottocomephorus, a morphologically derived benthopelagic genus of three described species. We used a combination of mitochondrial DNA and restriction site associated DNA sequencing from all Cottocomephorus species. Analysis of mitochondrial cytochrome b haplotypes was only able to two resolve two lineages: C. grewingkii and C. comephoroides/inermis. Phylogenetic inference, principal component analysis, and faststructure of genome-wide SNPs uncovered three lineages within Cottocomephorus: C. comephoroides, C. inermis and C. grewingkii. We found recent divergence and admixture between C. comephoroides and C. inermis and deep divergence between these two species and C. grewingkii. Contrasting other fish radiations, we found no evidence of ancient hybridization among Cottocomephorus species. Digital morphology revealed highly derived pelagic phenotypes that reflect divergence by specialization to the benthopelagic niche in Cottocomephorus. Among Cottocomephorus species, we found evidence of ongoing adaptation to the pelagic zone. This pattern highlights the importance of speciation along a benthic-pelagic gradient seen in Cottocomephorus and across other adaptive fish radiations.     

Distribution and population dynamics of ostracodes (Crustacea,Ostracoda) in a karstic lake: Lake Banyoles (Catalonia,Spain)

Qualitative and quantitative benthic samples were collected monthly between December 1986 and December 1987 from several stations at various depths and basins in the karstic Lake Banyoles (Catalonia, Spain), to study the spatial distribution and seasonality of ostracodes. A total of eight ostracode species were found in the lake. Of these, Candona neglecta Sars, Isocypris beauchampi Paris and Cypria ophtalmica Jurine were the most common ostracodes at all depth stations. Darwinula stevensoni Brady & Robertson, Ilyocypris species (I. bradyi Sars and I. gibba (Ramdohr)), Cyprideis torosa (Jones) and Cyclocypris ovum Jurine, on the other hand, were confined to sublittoral and littoral areas of the lake.Substrate and organic matter content appeared to be relevant factors determining the distribution of ostracode species at the different stations. The highest abundance of ostracodes were in the sublittoral (Basin IV–7 m and Basin I-5 m) where the substrate was coarse and sediment had a high organic matter content (>35% LOI). Low oxygen levels in the hypolimnetic waters (i.e. < 1 mg l^–1) may explain the absence of ostracodes at deeper zones in stations where the anoxic period lasts more than four months. On the other hand, low temperatures seem to favour the development of C. neglecta and D. stevensoni, while with higher temperatures I. beauchampi, C. torosa and C. ovum increased their abundances. However, no clear pattern can be observed, so ostracode species in Lake Banyoles, apparently, have non-seasonal life histories.