Studies in the genus Maieta (Melastomataceae)

The intraspecific variation found withinMaieta guianensis Aublet is discussed, and a new variety,M. guianensis Aublet var.leticana Whiffin, is described. The variation found withinM. poeppigii Mart, ex Triana is compared to that withinM. guianensis, and a possible vegetative difference between the two species is discussed. A key to the taxa is provided.     

Heteroplasmy and Ancient Translocation of Mitochondrial DNA to the Nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) Complex

The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies.     

Individual relationship between aneuploidy of gill cells and growth rate in the cupped oysters Crassostrea angulata, C. gigas and their reciprocal hybrids

The Portuguese oyster, Crassostrea angulata, is taxonomically close to the Pacific oyster, C. gigas, but there are clear genetic and phenotypic differences between these taxa. Among those differences, the faster growth of C. gigas compared with C. angulata has often been observed in the field. Crosses between C. angulata and C. gigas were performed to investigate the relationship between growth variation and somatic aneuploidy at the individual level in the two taxa and their reciprocal hybrids. The different progenies were reared in Ria Formosa (Portugal) under standard farming conditions. Growth rate and survival were significantly higher in C. gigas than in C. angulata, and the hybrids showed intermediate performances. Significant differences were also observed in the proportion of aneuploid cells (PAC) and of missing chromosomes (PMC) between the two taxa, C. angulata showing the highest values. Intermediate values of PAC and PMC were observed in the hybrids, supporting additive genetic bases of these parameters. Our results also confirm the negative correlation between somatic aneuploidy and growth rate at the individual level, as previously reported in C. gigas.     

Epizoochory in a hedgerow habitat: seasonal variation and selective diaspore adhesion

Epizoochory has been less studied than other seed dispersal mechanisms, such as endozoochory, and generally only a small percentage of plant species show adaptations to this strategy. Nevertheless, epizoochorous seed dispersal can affect an appreciable number of herb species in forests and man-made habitats. Also, few studies have dealt with temporal variation in epizoochory. In this paper, medium-long distance epizoochory is analyzed in a hedgerow habitat for the first time, using a domestic dog in an area in northwest Spain. Special attention is paid to seasonal variation and differential traits of plant taxa involved. Approximately 30 % of available herb taxa were found attached to hair. The intermonthly difference in the frequency of the taxa involved in epizoochory was significant, and the overall peak was reached in June–October linked with diaspore ripening phenology. Ninety-three percent of the plant taxa adhered to hair had diaspores with traits facilitating epizoochory (hooks, spines, awns, rigid hairs), in comparison with 17 % for available plant taxa not adhered to hair. The taxa involved in epizoochory had larger diaspores than the rest of the available taxa, but ranged considerably in size. Numerous hooks covered the largest, heaviest diaspores, and allowed them to attach to hair. There was no significant difference in mean plant height between taxa involved in epizoochory and the rest of the available taxa. The difference in life span between taxa involved in epizoochory and the rest of available taxa was not significant, most of them being perennials in both cases. Seventy-three percent of all the available plant taxa were potential forest plants typically found in edges and gaps, and 64 % of the plant taxa involved in epizoochory were these kinds of potential forest plants. High or medium involuntary positive selection by the dog of diaspores of Taraxacum gr. officinale, Galium aparine, Geum urbanum, and Agrimonia eupatoria was observed. In conclusion, epizoochorous dispersal can be quantitatively and functionally important in hedgerow habitats during summer-autumn, affecting mainly herb taxa with specialized diaspores.     

Molecular markers reveal no genetic differentiation between Myrica rivas-martinezii and M. faya (Myricaceae)

Background and Aims

Myrica rivas-martinezii is a critically endangered endemic of the laurel forest of the Canary Islands and co-occurs very close to M. faya. Some authors suggest that M. rivas-martinezii and M. faya are two morphs of the same species, so molecular markers were used to estimate the levels and structuring of genetic variation within and among natural populations in order to evaluate genetic relationships between these two congeners.

Methods

Six polymorphic microsatellite (simple sequence repeat, SSR) markers were used to determine the genetic diversity and the genetic relationship between both Myrica species.

Key Results

Most of the natural populations analysed were in Hardy–Weinberg equilibrium for both taxa. Analysis of molecular variance (AMOVA) for both species revealed that most of the genetic variability detected was contained within populations (92·48 and 85·91 % for M. faya and M. rivas-martinezii, respectively), which it is consistent with outcrossing and dioecious plants. Estimates of interpopulation genetic variation, calculated from F_ST and G′_ST, were quite low in the two taxa, and these values did not increase substantially when M. rivas-martinezii and M. faya populations were compared. The UPGMA dendrogram based on Nei''s genetic distance clustered the populations by their island origin, independently of taxon. In fact, the mixture of individuals of both taxa did not appreciably disrupt the intrapopulational genetic cohesion, and only 3·76 % variation existed between species.

Conclusions

All the results obtained using molecular markers indicate clearly that both taxa share the same genetic pool, and they are probably the same taxa. Considering that M. rivas-martinezii is classified as at risk of extinction, there should be a change of focus of the current management actions for the conservation of this putatively endangered Canarian endemic.Key words: Canary Islands, conservation genetics, microsatellites, Myrica rivas-martinezii, Myrica faya, plant conservation     

Parallel Patterns of Morphological and Behavioral Variation among Host-Associated Populations of Two Gall Wasp Species

A powerful approach to address the general factors contributing to ecological speciation is to compare distantly related taxa that inhabit the same selective environments. In this design, similarities among taxa can elucidate general mechanisms of the process whereas differences may uncover specific factors important to the process for individual taxa. Herein, we present evidence of parallel patterns of morphological and behavioral variation among host-associated populations of two species of cynipid gall wasps, Belonocnema treatae and Disholcaspis quercusvirens, that each exhibit a life cycle intimately tied to the same two host plant environments, Quercus geminata and Q. virginiana. Across both gall-former species we find consistent differences in body size and gall morphology associated with host plant use, as well as strong differences in host plant preference, a measure of habitat isolation among populations. These consistent differences among taxa highlight the important role of host plant use in promoting reproductive isolation and morphological variation among herbivorous insect populations–a prerequisite for ecological speciation.     

A single nuclear locus phylogeny of soybean based on DNA sequence

Soybean [Glycine max (L.) Merr.] evolution was examined by sequencing portions of the restriction fragment length polymorphism (RFLP) locus A-199a of 21 taxa from the Glycininae and 1 from the Phaseoleae. Four hundred nucleotides were determined in each, aligned, and then compared for these taxa. Within the annual soybean subgenus (Soja), the four accessions differed at as many as 2.2% of the nucleotides. Among 13 perennial soybean species (subgenus Glycine), nucleotide variation ranged from 1.7% to 8.4%. The nucleotide difference between the two soybean subgenera was 3.0–7.0%. Nucleotide variation between the genus Glycine and the related genera of Neonotonia, Amphicarpa, Teramnus, and Phaseolus ranged from 8.2% to 16.4%. In addition to nucleotide substitutions, insertions/deletions (indels) differences were also observed and were consistent with nucleotide-based analysis. Cladistic analysis of the A-199a sequences was performed using Wagner parsimony to construct a soybean phylogeny. Sixteen equally parsimonious trees were produced from these data. The trees were 246 steps in length with a consistency index of 0.78. Indels distribution upon the consensus topology revealed a pattern congruent with the nucleotide-based phylogeny. The current taxonomic status of the soybean subgenera and the related genera of Neonotonia, Amphicarpa, and Teramnus were well-supported and appear monophyletic in this analysis. Homoplasy within the subgenus Glycine led to a lack of resolved topology for many of these 13 taxa. However, the Glycine clade topology was consistent with phylogenies proposed using crossing experiments and cpDNA RFLPs. These genera were arranged from ancestral to derived as: Teramnus, Amphicarpa, Neonotonia, and Glycine when Phaseolus vulgaris was used as an outgroup.     

Patterns of ecomorphological variation in the bats of western Madagascar: Comparisons among and between communities along a latitudinal gradient

The ecomorphology of 10 insectivorous bat species at three study zones in western Madagascar was examined using 567 specimens and based on 6 external, 11 cranial, 12 dental, and 11 wing measurements. The three study sites are located along a cline representing 11.6° of latitude. The southern most site has notable differences in vegetational and climatic regimes than the two more northern sites. Principal component analyses were conducted for each of the four datasets to examine the morphological space occupied by each species at the three sites. Most taxa showed clear intra-site separation and little inter-site variation. The exceptions included extensive morphological overlap in two taxa of Triaenops (cranial, dental, and wing), that have allopatric distributions, and between the sympatric Miniopterus manavi and Myotis goudoti (external, cranial, and dental). In the latter case, there was distinct separation in wing shape between these two taxa, which would allow them to exploit local habitats and prey in different manners. The only species that showed considerable inter-site variation was Hipposideros commersoni, which is sexually dimorphic, with individuals from the south being smaller than those in the north.     

Genetic diversity, structure, and patterns of differentiation in the genus Vitis

Vitis (Vitaceae) is a taxonomically complicated genus with ca. 60 taxa divided into two subgenera, Vitis and Muscadinia. We used population genetic approaches to gain insights into the genetic diversity, patterns of evolutionary differentiation and to decipher the taxonomic status of some of the controversial taxa within the genus Vitis. The distance- and model-based analyses were used to examine the phylogenetic structure within the genus Vitis using simple sequence repeat (SSR) and amplified fragment length polymorphism (AFLP) markers. The results closely matched the current classification, but some discrepancies in the identity of taxa at the specific and subspecific levels were still evident. The East Asia and the North American Vitis exhibited strong divergence and each group showed further differentiation into several subgroups with North American subgroups roughly matching the described series. The model based cluster analysis indicated 14 clusters as optimum to explain the genetic structure within the genus Vitis with most clusters containing a moderate frequency of admixed genotypes suggesting interspecific gene flow within the subgenus Vitis. Hierarchical partitioning of molecular variation indicated that a significant amount of the total variation (~74 % and ~69 % for SSRs and AFLPs, respectively) is accounted for by intraspecific variation as compared to the levels due to genetic differentiation among species within series (~17 % and ~20 % for SSRs and AFLPs, respectively) and among series within the genus Vitis (~9 % and ~10 % for SSRs and AFLPs, respectively). Overall, Vitis possesses mild genetic structure characterized by reticulation and incomplete lineage sorting of ancestral polymorphisms.     

Predictive functional profiling using marker gene sequences and community diversity analyses of microbes in full-scale anaerobic sludge digesters

Anaerobic digestion (AD) is widely used in treating the sewage sludge, as it can reduce the amount of sludge, eliminate pathogens and produce biofuel. To enhance the operational performance and stability of anaerobic bioreactors, operational and conventional chemical data from full-scale sludge anaerobic digesters were collected over a 2-year period and summarized, and the microbial community diversity of the sludge sample was investigated at various stages of the AD process. For the purpose of distinguishing between the functional and community diversity of the microbes, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) software was used to impute the prevalence of 16S rDNA marker gene sequences in the difference in various sludge samples. Meanwhile, a taxa analysis was also carried out to investigate the different sludge samples. The microbial community diversity analysis of one AD sludge sample showed that the most dominant bacterial genera were Saccharicrinis, Syntrophus, Anaerotruncus and Thermanaerothrix. Among archaea, acetoclastic Methanosaeta represented 56.0 %, and hydrogenotrophic Methanospirillum, Methanoculleus, Methanothermus and Methanolinea accounted for 41.3 % of all methanogens. The taxa, genetic and functional prediction analyses of the feedstock and AD sludge samples suggested great community diversity differences between them. The taxa of bacteria in two AD sludge samples were considerably different, but the abundances of the functional KEGG pathways took on similar levels. The numbers of identified pathogens were significantly lower in the digested sludge than in the feedstock, but the PICRUSt results showed the difference in “human diseases” abundances in the level-1 pathway between the two sludge samples was small.     

Effects of capacity on resource input and the aquatic metazoan community structure in phytotelmata

Aquatic metazoan communities in treeholes and bamboo stumps were studied on Tsushima Island, Japan, in March and June in relation to the habitat size and the resouce amount. The amount of leaf detritus increased with an increase in the capacity (volume) of the phytotelma. The input rate of leaves depended upon the opening area of the phytotelma. Twenty-one metazoan inhabitant taxa consisted of 17 dipteran saprophages, a helodid beetle larva, a nematoda, a naidid, and a predator,Toxorhynchites towadensis mosquito larva. Treeholes harbored 17 taxa and bamboo stumps 20; 16 taxa were common in both phytotelmata. The number of taxa and the biomass of metazoa per phytotelma was positively correlated with the capacity. The densities of dominant saprophages such as helodid, chironomid, andCulicoides larvae were positively correlated with the capacity of phytotelmata, and the variation in their abundance contributed much to the variation in the species composition in individual phytotelmata. With an increase in capacity, treeholes harbored more helodids andCulicoides, whereas bamboo stumps harbored more chironomids andDasyhelea. Thus, the amount of resource, species richness and biomass per phytotelma largely depended upon the capacity, and the difference in community structure between treeholes and bamboo stumps was attributable to the differential colonization patterns of different taxa.     

Relationships among Cedrus libani, C. brevifolia and C. atlantica as revealed by the morphological and anatomical needle characters

The main aim of the present study was testing the value of the morphological and anatomical characteristics of the needles in distinguishing Cedrus atlantica, C. libani and C. brevifolia. Nine populations were sampled in their natural habit and 25 characters were used to describe the variation of the brachyblast needles and to analyze the differences between species. The results indicated that morphological and anatomical needle characters provide valuable tools in discrimination of the taxa. The scored differences were statistically significant, as revealed in the Tukey’s t test, discrimination analysis and hierarchical analysis of variation. The results support treating C. libani, C. atlantica and C. brevifolia as independent species.     

Spore abortion index (SAI) as a promising tool of evaluation of spore fitness in ferns: an insight into sexual and apomictic species

Ferns reproduce through small and usually haploid spores. The general paradigm states that whereas species produce good shaped spores, hybrids are sterile and form aborted spores. Apomictic fern species represent an unusual case, and it is believed that they produce an unbalanced spore spectrum. Until now, no comprehensive comparison of sexual and apomictic taxa using extensive spore fitness data has been published. Based on a representative data set of 109 plants from 23 fern taxa, we accomplished the first robust analysis of spore fitness using spore abortion index (SAI), the ratio of aborted to all examined spores. One thousand spores were analyzed for each plant. Focusing mainly on two major European fern taxa (Asplenium, Dryopteris), we compared this trait for different fern reproductive types (sexual/apomicts/hybrids) and ploidy levels (diploid versus polyploid). Our results confirmed the general assumption that shows higher SAI for apomictic taxa (18%) when compared to sexual taxa (3%). Furthermore, hybrids are characterized by having almost all spores aborted (99.8%) with the notable exception of pentaploid Dryopteris × critica (93.1%), the hybrid between sexual and apomictic taxa. We found no significant difference in SAI between sexual taxa of various ploidy levels or between sexual taxa of genera Dryopteris and Asplenium. Additionally, we carried out an optimization of the SAI method, outlying important guidelines for the use of this method in the future.     

Different Level of Intraspecific Variation of the Bony Labyrinth Morphology in Slow- Versus Fast-Moving Primates

The vestibular system of the inner ear detects the motions of the head and is involved in maintaining balance. For this reason, this organ has been deeply studied and several scientists have tried to link its morphology with the locomotor behavior of an animal. Via high-resolution computed microtomography and geometric morphometric methods, we analyzed the intraspecific variation of the 3D morphology of the bony labyrinth (inner ear) in four species of primates differing in their locomotor adaptations: two being slow-moving taxa (Nycticebus and Perodicticus), and two being fast-moving taxa (Callithrix and Microcebus). Basically, there are very few analyses of the inter-individual variation of this organ in mammals in general, and this approach has never been attempted in primates thus far. Our results show that variation of the bony labyrinth morphology is expressed by the same ways in the different species (e.g., differences in the size, shape, and orientation of the semicircular canals, and in the width and height of the cochlea), but that slow-moving taxa exhibit a higher amount of intraspecific variation than do fast-moving taxa. Our results strengthen support for a previously published hypothesis, according to which a relaxation of the selective pressure applied to the morphology of the bony labyrinth is the likely reason for this higher amount of intraspecific variation in slow-moving taxa, and that it may be related to a reduced functional demand for rapid postural adjustments.     

Intraspecific spatial genetic differentiation of a Daphnia species within a long narrow reservoir

Environmental gradients influence the distribution and taxonomic composition of planktonic taxa, including Daphnia. In canyon-shaped reservoirs with pronounced horizontal gradients of food supply, predation pressure and other factors, not only species and interspecific hybrids but also clones within these taxa are non-randomly distributed. Using a long-term data set from a reservoir mostly dominated by a single Daphnia species, we evaluated whether intraspecific genetic differentiation can be frequently detected between upstream and downstream reservoir regions with different environmental conditions. We analysed variation at four allozyme loci (two species-specific and two polymorphic) to assess the taxonomic composition and intraspecific variation of Daphnia collected in different years (between 1995 and 2005) and periods of the growing season. D. galeata dominated in all samples, although other species and hybrids with D. galeata were also occasionally detected. Despite limited variation at the analysed loci, D. galeata from upstream and downstream regions were significantly genetically differentiated on seven out of twelve sampling dates. Although genetic drift in geographically distant subpopulations may contribute to differentiation, we presume that the observed patterns are primarily due to different selection regimes. We predict that a significant genetic differentiation within planktonic populations also occurs more frequently in natural water bodies.     

Towards a Transferable and Cost-Effective Plant AFLP Protocol

Amplified fragment length polymorphism (AFLP) is a powerful fingerprinting technique that is widely applied in ecological and population genetic studies. However, its routine use has been limited by high costs associated with the optimization of fluorescently labelled markers, especially for individual study systems. Here we develop a low-cost AFLP protocol that can be easily transferred between distantly related plant taxa. Three fluorescently labelled EcoRI-primers with anchors that target interspecifically conserved genomic regions were used in combination with a single non-labelled primer in our AFLP protocol. The protocol was used to genotype one gymnosperm, two monocot and three eudicot plant genera representing four invasive and four native angiosperm species (Pinus pinaster (Pinaceae), Pennisetum setaceum and Poa annua (Poaceae), Lantana camara (Verbenaceae), Bassia diffusa (Chenopodiaceae), Salvia lanceolata, Salvia africana-lutea, and Salvia africana-caerulea (Lamiaceae)). Highly polymorphic and reproducible genotypic fingerprints (between 37–144 polymorphic loci per species tested) were obtained for all taxa tested. Our single protocol was easily transferred between distantly related taxa. Measures of expected heterozygosity ranged from 0.139 to 0.196 for P. annua and from 0.168 to 0.272 for L. camara which compared well with previously published reports. In addition to ease of transferability of a single AFLP protocol, our protocol reduces costs associated with commercial kits by almost half. The use of highly conserved but abundant anchor sequences reduces the need for laborious screening for usable primers that result in polymorphic fingerprints, and appears to be the main reason for ease of transferability of our protocol between distantly related taxa.     

Molecular signatures of divergence and selection in closely related pine taxa

Efforts to detect loci under selection in plants have mostly focussed on single species. However, assuming that intraspecific divergence may lead to speciation, comparisons of genetic variation within and among recently diverged taxa can help to locate such genes. In this study, coalescent and outlier detection methods were used to assess nucleotide polymorphism and divergence at 79 nuclear gene fragments (1212 SNPs) in 16 populations (153 individuals) of the closely related, but phenotypically and ecologically distinct, pine taxa Pinus mugo, P. uliginosa and P. uncinata across their European distributions. Simultaneously, mitochondrial DNA markers, which are maternally inherited in pines and distributed by seeds at short geographic distance, were used to assess genetic relationships of the focal populations and taxa. The majority of nuclear loci showed homogenous patterns of variation between the taxa due to a high number of shared SNPs and haplotypes, similar levels of polymorphism, and low net divergence. However, against this common genetic background and an overall low population structure within taxa at mitochondrial markers, we identified several genes showing signatures of selection, accompanied by significant intra- and interspecific divergence. Our results indicate that loci involved in species divergence may be involved in intraspecific local adaptation.     

Genetic Variation at Nuclear Loci Fails to Distinguish Two Morphologically Distinct Species of Aquilegia

Aquilegia formosa and pubescens are two closely related species belonging to the columbine genus. Despite their morphological and ecological differences, previous studies have revealed a large degree of intercompatibility, as well as little sequence divergence between these two taxa [1], [2]. We compared the inter- and intraspecific patterns of variation for 9 nuclear loci, and found that the two species were practically indistinguishable at the level of DNA sequence polymorphism, indicating either very recent speciation or continued gene flow. As a comparison, we also analyzed variation at two loci across 30 other Aquilegia taxa; this revealed slightly more differentiation among taxa, which seemed best explained by geographic distance. By contrast, we found no evidence for isolation by distance on a more local geographic scale. We conclude that the extremely low levels of genetic differentiation between A. formosa and A.pubescens at neutral loci will facilitate future genome-wide scans for speciation genes.     

Atlas of foliar surface features in woody plants,VI. Carya (Juglandaceae) of north America

Scanning electron microscopy was used to examine foliar surface features such as trichome types and the micro-relief formed by cell contours, cuticular patterns, and epicuticular wax in the genusCarya. The fourteen taxa native to Mexico and eastern United States were sampled throughout their geographical ranges, and are represented here by specimens that include segregate taxa, interspecific hybrids, and mature and immature leaves of each. Six trichome types are recognized in this survey: acicular, fasciculate, multiradiate, solitary, capitate-glandular, and peltate scale. There are no consistent differences between representatives of either the two Sections of the genus or the two ploidy levels. Although there is significant inter- and intra-specific variation, the use of scanning electron microscopy provides few taxonomically useful characters or character-states beyond those already available through light microscopy. Foliar surfaces of the fourteen taxa and three hybrids are illustrated.     

A Comparative Analysis of Genetic Differentiation across Six Shared Willow Host Species in Leaf- and Bud-Galling Sawflies

Genetic divergence and speciation in plant-feeding insects could be driven by contrasting selection pressures imposed by different plant species and taxa. While numerous examples of host-associated differentiation (HAD) have been found, the overall importance of HAD in insect diversification remains unclear, as few studies have investigated its frequency in relation to all speciation events. One promising way to infer the prevalence and repeatability of HAD is to estimate genetic differentiation in multiple insect taxa that use the same set of hosts. To this end, we measured and compared variation in mitochondrial COI and nuclear ITS2 sequences in population samples of leaf-galling Pontania and bud-galling Euura sawflies (Hymenoptera: Tenthredinidae) collected from six Salix species in two replicate locations in northern Fennoscandia. We found evidence of frequent HAD in both species complexes, as individuals from the same willow species tended to cluster together on both mitochondrial and nuclear phylogenetic trees. Although few fixed differences among the putative species were found, hierarchical AMOVAs showed that most of the genetic variation in the samples was explained by host species rather than by sampling location. Nevertheless, the levels of HAD measured across specific pairs of host species were not correlated in the two focal galler groups. Hence, our results support the hypothesis of HAD as a central force in herbivore speciation, but also indicate that evolutionary trajectories are only weakly repeatable even in temporally overlapping radiations of related insect taxa.