Genetic diversity across a vertebrate species' range: a test of the central-peripheral hypothesis

Although it has been long presumed that population genetic variability should decrease as a species' range margin is approached, results of empirical investigations remain ambiguous. Sampling strategies employed by many of these studies have not adequately sampled the entire range. Here we present the results of an investigation of population genetic diversity in a vertebrate species, the Italian agile frog, Rana latastei, sampled comprehensively across its entire range. Our results show that genetic variability is not correlated with population location with respect to the range periphery. Instead, the model that best explains the genetic variation detectable across the range is based on an east-to-west gradient of declining diversity. Although we cannot state definitively what has led to this distribution, the most likely explanation is that the range of Rana latastei expanded postglacially from a Balkan refugium.     

太白红杉群落物种多样性与环境因子的关系

定量研究了太白红杉群落物种多样性与环境因子的关系,结果表明:(1)海拔与物种丰富度和种间相遇机率呈极显著的负相关;与Shannon指数、Simpson指数和Pielou指数表现为"中间高度膨胀"的规律,即中等海拔高度上多样性高而低海拔和高海拔多样性较低。(2)岩石裸露度与物种丰富度呈显著的负相关。(3)土壤含水量与物种丰富度呈极显著的正相关;与种间相遇机率呈先降后升的趋势。(4)环境因子与物种多样性逐步回归结果是:海拔和岩石裸露度与物种丰富度关系密切,其回归方程为:S=90.62-0.02E-14.14B(r=0.769,P<0.05)。     

Molecular architecture of Pipistrellus pipistrellus/Pipistrellus pygmaeus complex (Chiroptera: Vespertilionidae): further cryptic species and Mediterranean origin of the divergence

Previous genetic analyses have demonstrated that two phonic types of one of the most common European bats, the Common pipistrelle, belong to distinct species, although they are almost identical morphologically (45 kHz Pipistrellus pipistrellus and 55 kHz Pipistrellus pygmaeus). To reconstruct the history of the species complex and explain the codistribution of both forms in Europe and the Mediterranean, we performed phylogenetic analysis based on a 402-bp portion of the cytochrome b gene. Particular attention was paid to the eastern and southern parts of the range where no data were available. We found further distinctive allopatric haplotypes from Libya and Morocco. The difference of about 6-7% described in the Libyan population suggests the occurrence of a new species in the southern Mediterranean. The species status of Moroccan population is also discussed. The phylogeographic patterns obtained and analysis of fossil records support the hypothesis of expansion of both species into Europe from the Mediterranean region during the Holocene. The allopatric speciation model fits our data best. The paleobiographic scenario envisaged is corroborated also by molecular clock estimations and correlations with Late Neogene environmental changes in the Mediterranean region which ended with the Messinian salinity crisis.     

Analysis of singleton ORFans in fully sequenced microbial genomes

Singleton sequence ORFans are orphan ORFs (open reading frames) that have no detectable sequence similarity to any other sequence in the databases. ORFans are of particular interest not only as evolutionary puzzles but also because we can learn little about them using bioinformatics tools. Here, we present a first systematic analysis of singleton ORFans in the first 60 fully sequenced microbial genomes. We show that although ORFans have been underemphasized, the number of ORFans is steadily growing, currently accounting for 23,634 sequences. At the same time, the percentage of ORFans as a fraction of all sequences is slowly diminishing, and is currently about 14%. Short ORFans comprise about 61% of all ORFans. The abundance of short ORFans may be due to a yet unexplained artifact. The data also suggest that the number of longer ORFans may soon diminish as more genomes of closely related organisms become available. To better address the questions about the functions and origins of ORFans, we propose to focus further studies on the longer ORFans, with emphasis on three new types of ORFans: ORFan modules, paralogous ORFans, and orthologous ORFans. We conclude that the large number of ORFans reflects an intrinsic property of the genetic material not yet fully understood. Further computational and experimental studies aimed at understanding Nature's protein diversity should also include ORFans.     

Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris

Forest tree species provide many examples of well-studied adaptive differentiation, where the search for the underlying genes might be possible. In earlier studies and in our common conditions in a greenhouse, northern populations set bud earlier than southern ones. A difference in latitude of origin of one degree corresponded to a change of 1.4 days in number of days to terminal bud set of seedlings. Earlier physiological and ecological genetics work in conifers and other plants have suggested that such variation could be governed by phytochromes. Nucleotide variation was examined at two phytochrome loci (PHYP and PHYO, homologues of the Arabidopsis thaliana PHYB and PHYA, respectively) in three populations: northern Finland, southern Finland and northern Spain. In our samples of 12-15 sequences (2980 and 1156 base pairs at the two loci) we found very low nonsynonymous variation; pi was 0.0003 and 0.0002 at PHYP and PHYO loci, respectively. There was no functional differentiation between populations at the photosensory domains of either locus. The overall silent variation was also low, only 0.0024 for the PHYP locus. The low estimates of silent variation are consistent with the estimated low synonymous substitution rates between Pinus sylvestris and Picea abies at the PHYO locus. Despite the low level of nucleotide variation, haplotypic diversity was relatively high (0.42 and 0.41 for fragments of 1156 nucleotides) at the two loci.     

The influence of the Miocene Mediterranean desiccation on the geographical expansion and genetic variation of Androcymbium gramineum (Cav.) McBride (Colchicaceae)

Chloroplast DNA (cpDNA) restriction site and isozyme data were combined to explore the spatial-temporal influence of the Messinian desiccation in the Mediterranean on the disjunct distribution of Androcymbium gramineum in Almería and Morocco (north and south of the straits of Gibraltar, respectively). Lack of evidence for different selective pressures, divergence time estimates based on the calibration of the isozyme molecular clock with the cpDNA data, the basal position of Almerian populations in the A. gramineum clade, and the much higher isozyme polymorphism in Almería suggest that (i) only a southern European range of A. gramineum existed before the Messinian [ approximately 11.2 million years ago (Ma), in the middle Miocene] and (ii) the desiccation of the Mediterranean basin about 5.5-4.5 Ma induced the migration of A. gramineum from Almería to Morocco (between 4.9 and 4.6 Ma, according to our time estimates). After the split into two allopatric units following the refilling of the Mediterranean, the major influence of drift associated with Plio-Pleistocene recurrent glaciation cycles and range expansions/contractions probably fostered the substantial interpopulation genetic differentiation observed within Almería (CGST = 0.41, average DNei = 0.185) and, to a lesser extent, within Morocco (CGST = 0.24, average DNei = 0.089), but did not hinder the maintenance of considerable levels of genetic variation in either geographical area (A = 2.14, HE = 0.230 and A = 1.90, HE = 0.213, respectively).     

Genetic structure and reproduction dynamics of Salix reinii during primary succession on Mount Fuji,as revealed by nuclear and chloroplast microsatellite analysis

The early stage of volcanic desert succession is underway on the southeastern slope of Mount Fuji. We used markers of nuclear microsatellites (simple sequence repeats; SSR) and chloroplast microsatellites (cpSSR) to investigate the population genetic structure and reproduction dynamics of Salix reinii, one of the dominant pioneer shrubs in this area. The number of S. reinii genets in a patch and the area of the largest genet within the patch increased with patch area, suggesting that both clonal growth and seedling recruitment are involved in the reproduction dynamics of S. reinii. Five polymorphic cpSSR markers were developed for S. reinii by sequencing the noncoding regions between universal sequences in the chloroplast genome. Nineteen different cpSSR haplotypes were identified, indicating that S. reinii pioneer genets were created by the long-distance dispersal of seeds originating from different mother genets around the study site, where all vegetation was destroyed during the last eruption. Furthermore, the clustered distributions of different haplotypes within each patch or plot suggested that newly colonized genets tended to be generated from seeds dispersed near the initially established mother genets. These results revealed that the establishment of the S. reinii population on the southeastern slope of Mount Fuji involved two sequential modes of seed dispersal: long-distance dispersal followed by short-distance dispersal.     

Population genetic structure of rock ptarmigan Lagopus mutus in Northern and Western Europe

Alpine species may be losing habitat because of global warming. Setting management priorities for such species is thus urgent and cannot be achieved without data on population structure. We studied the structure of rock ptarmigan (Lagopus mutus) populations in the Pyrenees, Alps and Norway, using six microsatellites. We found that rock ptarmigan in the Pyrenees were genetically impoverished compared with those in the Alps and Norway, and displayed a greater divergence (Pyrenees vs. Alps or Norway: theta(ST) = 0.16, Alps vs. Norway, theta(ST) = 0.04). In the Alps, despite a weak genetic differentiation between localities up to 200 km apart (theta(ST) = 0.011), a significant isolation-by-distance (IBD) effect was detected. When computed for each sex separately this IBD effect was significant for males but not for females, suggesting that males are highly philopatric.     

Genetic variation in organisms with sexual and asexual reproduction

The genetic variation in a partially asexual organism is investigated by two models suited for different time scales. Only selectively neutral variation is considered. Model 1 shows, by the use of a coalescence argument, that three sexually derived individuals per generation are sufficient to give a population the same pattern of allelic variation as found in fully sexually reproducing organisms. With less than one sexual event every third generation, the characteristic pattern expected for asexual organisms appear, with strong allelic divergence between the gene copies in individuals. At intermediary levels of sexuality, a complex situation reigns. The pair-wise allelic divergence under partial sexuality exceeds, however, always the corresponding value under full sexuality. These results apply to large populations with stable reproductive systems. In a more general framework, Model 2 shows that a small number of sexual individuals per generation is sufficient to make an apparently asexual population highly genotypically variable. The time scale in terms of generations needed to produce this effect is given by the population size and the inverse of the rate of sexuality.     

The relationship between species richness and productivity in metazoan parasite communities

Biodiversity is not distributed homogeneously in space, and it often covaries with productivity. The shape of the relationship between diversity and productivity, however, varies from a monotonic linear increase to a hump-shaped curve with maximum diversity values corresponding to intermediate productivity. The system studied and the spatial scale of study may affect this relationship. Parasite communities are useful models to test the productivity-diversity relationship because they consist of species belonging to a restricted set of higher taxa common to all host species. Using total parasite biovolume per host individual as a surrogate for community productivity, we tested the relationship between productivity and species richness among assemblages of metazoan parasites in 131 vertebrate host species. Across all host species, we found a linear relationship between total parasite biovolume and parasite species richness, with no trace of a hump-shaped curve. This result remained after corrections for the potential confounding effect of the number of host individuals examined per host species, host body mass, and phylogenetic relationships among host species. Although weaker, the linear relationship remained when the analyses were performed within the five vertebrate groups (fish, amphibians, reptiles, mammals and birds) instead of across all host species. These findings agree with the classic isolationist-interactive continuum of parasite communities that has become widely accepted in parasite ecology. They also suggest that parasite communities are not saturated with species, and that the addition of new species will result in increased total parasite biovolume per host. If the number of parasite species exploiting a host population is not regulated by processes arising from within the parasite community, external factors such as host characteristics may be the main determinants of parasite diversity.