Molecular and morphological criteria for revision of the genus Microcoleus (Oscillatoriales,Cyanobacteria)

Ninety‐two strains of Microcoleus vaginatus (=nomenclatural‐type species of the genus Microcoleus Desmazières ex Gomont) and Phormidium autumnale Trevisan ex Gomont from a wide diversity of regions and biotopes were examined using a combination of morphological and molecular methods. Phylogenies based on the 16S rDNA and 16S‐23S ITS (partial) demonstrated that the 92 strains, together with a number of strains in GenBank, were members of a highly supported monophyletic clade of strains (Bayesian posterior probability = 1.0) distant from the species‐cluster containing the generitype of Phormidium. Similarity of the 16S rRNA gene exceeded 95.5% among all members of the Microcoleus clade, but was less than 95% between any Microcoleus strains and species outside of the clade (e.g., Phormidium sensu stricto). These findings, which are in agreement with earlier studies on these taxa, necessitate the revision of Microcoleus to include P. autumnale. Furthermore, the cluster of Phormidium species in the P. autumnale group (known as Group VII) must be moved into Microcoleus as well, and these nomenclatural transfers are included in this study. The main diacritical characters defining Microcoleus are related to the cytomorphology of trichomes, including: narrowed trichome ends, calyptra, cells shorter than wide up to more or less isodiametric, and facultative presence of sheaths. The majority of species are 4–10 μm in diameter. The possession of multiple trichomes in a common sheath is present facultatively in many but not all species.     

Seed dispersal of Diospyros virginiana in the past and the present: Evidence for a generalist evolutionary strategy

Several North American trees are hypothesized to have lost their co‐evolved seed disperser during the late‐Pleistocene extinction and are therefore considered anachronistic. We tested this hypothesis for the American persimmon (Diospyros virginiana) by studying the effects of gut passage of proposed seed dispersers on seedling survival and growth, natural fruiting characteristics, and modern animal consumption patterns. We tested gut passage effects on persimmon seeds using three native living species, the raccoon (Procyon lotor), Virginia opossum (Didelphis virginiana), and coyote (Canis latrans), and two Pleistocene analogs; the Asian elephant (Elephas maximus) and alpaca (Vicugna pacos). Persimmon seeds excreted by raccoons, coyotes, and elephants survived gut transit. Gut passage did not affect sprouting success, but did tend to decrease time to sprout and increase seedling quality. Under field conditions, persimmon fruits were palatable on the parent tree and on the ground for an equal duration, but most fruits were consumed on the ground. Seven vertebrate species fed upon persimmon fruits, with the white‐tailed deer (Odocoileus virginianus)—a species not capable of dispersing persimmon seeds—comprising over 90% of detections. Conversely, potential living seed dispersers were rarely detected. Our results suggest the American persimmon evolved to attract a variety of seed dispersers and thus is not anachronistic. However, human‐induced changes in mammal communities could be affecting successful seed dispersal. We argue that changes in the relative abundance of mammals during the Anthropocene may be modifying seed dispersal patterns, leading to potential changes in forest community composition.     

Leaf morphological analyses in four European oak species (Quercus) and their hybrids: A comparison of traditional and geometric morphometric methods

Abstract

In this study, leaf morphology was assessed in a mixed oak stand (western France) using two geometric morphometric (landmark and outline) datasets and one dataset of 19 leaf measures. Adult oaks (817 oaks), comprising four white oak species (Quercus petraea, Q. robur, Q. pubescens and Q. pyrenaica), were sampled for DNA extraction and genetic analysis (nuclear microsatellites). Leaf morphology was assessed on 336 oaks, comprising pure species and hybrids as determined by genetic assignment. This comparative study of oak leaf morphology, based on the use of two free size geometric morphometric methods and a set of leaf measurements, combined with the genetic assignment of individuals to pure species or hybrids, provided information about the differences among species and the intermediate leaf morphology of their hybrids.     

Molecular phylogeny of the diatom genera Amphora and Halamphora (Bacillariophyta) with a focus on morphological and ecological evolution

The taxonomic history of the diatom genus Amphora is one of a broad early morphological concept resulting in the inclusion of a diversity of taxa, followed by an extended period of revision and refinement. The introduction of molecular systematics has increased the pace of revision and has largely resolved the relationships between the major lineages, indicating homoplasy in the evolution of amphoroid symmetry. Within the two largest monophyletic lineages, the genus Halamphora and the now taxonomically refined genus Amphora, the intrageneric morphological and ecological relationships have yet to be explored within a phylogenetic framework. Critical among this is whether the range of morphological features exhibited within these diverse genera are reflective of evolutionary groupings or, as with many previously studied amphoroid features, are nonhomologous when examined phylogenetically. Presented here is a four‐marker molecular phylogeny that includes 31 taxa from the genus Amphora and 77 taxa from the genus Halamphora collected from fresh, brackish, and salt waters from coastal and inland habitats of the United States and Japan. These phylogenies illustrate complex patterns in the evolution of frustule morphology and ecology within the genera and the implications of this on the taxonomy, classification, and organization of the genera are discussed.     

A biogeographical profile of the sand cockroach Arenivaga floridensis and its bearing on origin hypotheses for Florida scrub biota

Florida scrub is a xeric ecosystem associated with the peninsula's sand ridges, whose intermittent Pliocene–Pleistocene isolation is considered key to scrub endemism. One scrub origin hypothesis posits endemics were sourced by the Pliocene dispersal of arid‐adapted taxa from southwestern North America; a second invokes Pleistocene migration within eastern North America. Only one study to date has explicitly tested these competing hypotheses, supporting an eastern origin for certain scrub angiosperms. For further perspective, we conducted a genetic analysis of an endemic arthropod, the Florida sand cockroach (Arenivaga floridensis), with two aims: (1) to reconstruct the peninsular colonization and residence history of A. floridensis and (2) determine whether its biogeographic profile favors either origin hypothesis. We sequenced the cox2 mitochondrial gene for 237 specimens (65 populations) as well as additional loci (cox1, nuclear H3) for a subset of Florida roaches and congeners. Using Network and Bayesian inference methods, we identified three major lineages whose genetic differentiation and phylogeographical structure correspond with late Pliocene peninsula insularization, indicating Arenivaga was present and broadly distributed in Florida at that time. Stem and crown divergence estimates (6.36 Ma; 2.78 Ma) between A. floridensis and western sister taxa span a period of extensive dispersal by western biota along an arid Gulf Coast corridor. These phylogeographical and phylogenetic results yield a biogeographic profile consistent with the western origin hypothesis. Moreover, age estimates for the roach's peninsular residence complement those of several other endemics, favoring a Pliocene (or earlier) inception of the scrub ecosystem. We argue that eastern versus western hypotheses are not mutually exclusive; rather, a composite history of colonization involving disparate biotas better explains the diverse endemism of Florida scrub.     

Population genetics structure of glyphosate‐resistant Johnsongrass (Sorghum halepense L. Pers) does not support a single origin of the resistance

Single sequence repeats (SSR) developed for Sorghum bicolor were used to characterize the genetic distance of 46 different Sorghum halepense (Johnsongrass) accessions from Argentina some of which have evolved toward glyphosate resistance. Since Johnsongrass is an allotetraploid and only one subgenome is homologous to cultivated sorghum, some SSR loci amplified up to two alleles while others (presumably more conserved loci) amplified up to four alleles. Twelve SSR providing information of 24 loci representative of Johnsongrass genome were selected for genetic distance characterization. All of them were highly polymorphic, which was evidenced by the number of different alleles found in the samples studied, in some of them up to 20. UPGMA and Mantel analysis showed that Johnsongrass glyphosate‐resistant accessions that belong to different geographic regions do not share similar genetic backgrounds. In contrast, they show closer similarity to their neighboring susceptible counterparts. Discriminant Analysis of Principal Components using the clusters identified by K‐means support the lack of a clear pattern of association among samples and resistance status or province of origin. Consequently, these results do not support a single genetic origin of glyphosate resistance. Nucleotide sequencing of the 5‐enolpyruvylshikimate‐3‐phosphate synthase (EPSPS) encoding gene from glyphosate‐resistant and susceptible accessions collected from different geographic origins showed that none presented expected mutations in aminoacid positions 101 and 106 which are diagnostic of target‐site resistance mechanism.     

Molecular and morphological delimitation and generic classification of the family Oocystaceae (Trebouxiophyceae,Chlorophyta)

The family Oocystaceae (Chlorophyta) is a group of morphologically and ultrastructurally distinct green algae that constitute a well‐supported clade in the class Trebouxiophyceae. Despite the family's clear delimitation, which is based on specific cell wall features, only a few members of the Oocystaceae have been examined using data other than morphological. In previous studies of Trebouxiophyceae, after the establishment of molecular phylogeny, the taxonomic status of the family was called into question. The genus Oocystis proved to be paraphyletic and some species were excluded from Oocystaceae, while a few other species were newly redefined as members of this family. We investigated 54 strains assigned to the Oocystaceae using morphological, ultrastructural and molecular data (SSU rRNA and rbcL genes) to clarify the monophyly of and diversity within Oocystaceae. Oonephris obesa and Nephrocytium agardhianum clustered within the Chlorophyceae and thus are no longer members of the Oocystaceae. On the other hand, we transferred the coenobial Willea vilhelmii to the Oocystaceae. Our findings combined with those of previous studies resulted in the most robust definition of the family to date. The division of the family into three subfamilies and five morphological clades was suggested. Taxonomical adjustments in the genera Neglectella, Oocystidium, Oocystis, and Ooplanctella were established based on congruent molecular and morphological data. We expect further taxonomical changes in the genera Crucigeniella, Eremosphaera, Franceia, Lagerheimia, Oocystis, and Willea in the future.     

Identification and Molecular Characterization of Nocardia sp. as a New Causal Agent of Tobacco False Broomrape

Tobacco false broomrape disease is a serious problem in tropical countries. To identify its cause, experiments were conducted in tobacco fields. Six actinomycete strains were isolated from white succulent outgrowths of tobacco roots and their pathogenicity was confirmed by biological testing. Based on phenotypic and 16S rRNA gene sequence BLAST analysis, the strains were identified as members of the genus Nocardia. This association was also confirmed by secA1 gene phylogenetic analysis. This is the first report of Nocardia sp. as the cause of tobacco false broomrape.     

Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring‐ and autumn‐spawners confined to early postglacial arrival

Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring‐ or winter‐spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring‐ and autumn‐spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C. sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring‐spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C. sardinella were confirmed. However, the inclusion of Siberian C. sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C. albula clades and were clearly distinct from those in North American C. sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized.     

Molecular markers provide evidence for a broad‐fronted recolonisation of the widespread calcareous grassland species Sanguisorba minor from southern and cryptic northern refugia

• Calcareous grasslands belong to the most species‐rich and endangered habitats in Europe. However, little is known about the origin of the species typically occurring in these grasslands. In this study we analysed the glacial and post‐glacial history of Sanguisorba minor, a typical plant species frequently occurring in calcareous grasslands.
• The study comprised 38 populations throughout the whole distribution range of the species across Europe. We used molecular markers (AFLP) and applied Bayesian cluster analysis as well as spatial principal components analysis (sPCA) to identify glacial refugia and post‐glacial migration routes to Central Europe.
• Our study revealed significant differences in the level of genetic variation and the occurrence of rare fragments within populations of S. minor and a distinct separation of eastern and western lineages. The analyses uncovered traditional southern but also cryptic northern refugia and point towards a broad fronted post‐glacial recolonisation.
• Based on these results we postulate that incomplete lineage sorting may have contributed to the detected pattern of genetic variation and that S. minor recolonised Central Europe post‐glacially from Iberia and northern glacial refugia in France, Belgium or Germany. Our results highlight the importance of refugial areas for the conservation of intraspecific variation in calcareous grassland species.

     

Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals,a free‐spawning marine invertebrate

Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self‐recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef‐building species remain scarce. Here, we document the first genetic estimates of self‐recruitment and dispersal distances in a free‐spawning marine invertebrate, the hydrocoral Millepora cf. platyphylla. Using twelve microsatellite markers, we gathered genotypic information from 3,160 georeferenced colonies collected over 27,000 m² of a single reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope, and back reef. Although the adult population was predominantly clonal (85% were clones), our parentage analysis revealed a moderate self‐recruitment rate with a minimum of 8% of sexual propagules produced locally. Assigned offspring often settled at <10 m from their parents and dispersal events decrease with increasing geographic distance. There were no discrepancies between the dispersal distances of offspring assigned to parents belonging to clonal versus nonclonal genotypes. Interhabitat dispersal events via cross‐reef transport were also detected for sexual and asexual propagules. Sibship analysis showed that full siblings recruit nearby on the reef (more than 40% settled at <30 m), resulting in sibling aggregations. Our findings highlight the importance of self‐recruitment together with clonality in stabilizing population dynamics, which may ultimately enhance local sustainability and resilience to disturbance.     

Dampening effects of long‐term experimental drought on growth and mortality rates of a Holm oak forest

Forests respond to increasing intensities and frequencies of drought by reducing growth and with higher tree mortality rates. Little is known, however, about the long‐term consequences of generally drier conditions and more frequent extreme droughts. A Holm oak forest was exposed to experimental rainfall manipulation for 13 years to study the effect of increasing drought on growth and mortality of the dominant species Quercus ilex, Phillyrea latifolia, and Arbutus unedo. The drought treatment reduced stem growth of A. unedo (?66.5%) and Q. ilex (?17.5%), whereas P. latifolia remained unaffected. Higher stem mortality rates were noticeable in Q. ilex (+42.3%), but not in the other two species. Stem growth was a function of the drought index of early spring in the three species. Stem mortality rates depended on the drought index of winter and spring for Q. ilex and in spring and summer for P. latifolia, but showed no relation to climate in A. unedo. Following a long and intense drought (2005–2006), stem growth of Q. ilex and P. latifolia increased, whereas it decreased in A. unedo. Q. ilex also enhanced its survival after this period. Furthermore, the effect of drought treatment on stem growth in Q. ilex and A. unedo was attenuated as the study progressed. These results highlight the different vulnerabilities of Mediterranean species to more frequent and intense droughts, which may lead to partial species substitution and changes in forest structure and thus in carbon uptake. The response to drought, however, changed over time. Decreased intra‐ and interspecific competition after extreme events with high mortality, together with probable morphological and physiological acclimation to drought during the study period, may, at least in the short term, buffer forests against drier conditions. The long‐term effects of drought consequently deserve more attention, because the ecosystemic responses are unlikely to be stable over time.Nontechnical summaryIn this study, we evaluate the effect of long‐term (13 years) experimental drought on growth and mortality rates of three forest Mediterranean species, and their response to the different intensities and durations of natural drought. We provide evidence for species‐specific responses to drought, what may eventually lead to a partial community shift favoring the more drought‐resistant species. However, we also report a dampening of the treatment effect on the two drought‐sensitive species, which may indicate a potential adaptation to drier conditions at the ecosystem or population level. These results are thus relevant to account for the stabilizing processes that would alter the initial response of ecosystem to drought through changes in plant physiology, morphology, and demography compensation.     

Evolution and disappearance of sympatric Coregonus albula in a changing environment—A case study of the only remaining population pair in Sweden

During the past 50 years, Fennoscandian populations of spring‐spawning Baltic cisco (Coregonus albula), sympatric to common autumn‐spawners, have declined or disappeared; for example, three out of four known spring‐spawning populations in Sweden are regarded as extinct. Over the same period, the climate has changed and populations have been subject to other anthropogenic stressors. We compared historic (1960s) and recent (1990–2000s) morphological data from the still‐existent sympatric cisco populations in Lake Fegen, Sweden. Phenotypic changes were found for spring‐spawners making them more similar to the sympatric autumn‐spawners that had remained virtually unchanged. Based on results for other salmoniform fishes, a phenotypically plastic response to increased temperature during early development appears unlikely. The recent material was also analyzed with microsatellite markers; long‐term effective population size in spring‐spawners was estimated to be about 20 times lower than autumn‐spawners, with signs of long‐term gene flow in both directions and a recent genetic bottleneck in spring‐spawners. We suggest the change toward a less distinct phenotype in spring‐spawners to reflect a recent increase in gene flow from autumn‐spawners. Time since divergence was estimated to only c. 1,900 years (95% CI: 400–5,900), but still the Fegen populations represent the most morphologically and genetically distinct sympatric populations studied. Consequently, we hypothesize that less distinct population pairs can be even younger and that spring‐spawning may have repeatedly evolved and disappeared in several lakes since the end of the last glaciation, concurrent with changed environmental conditions.     

Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc

Climate change, fisheries' pressure on penguin prey, and direct human disturbance of wildlife have all been implicated in causing large shifts in the abundance and distribution of penguins in the Southern Ocean. Without mark‐recapture studies, understanding how colonies form and, by extension, how ranges shift is challenging. Genetic studies, particularly focused on newly established colonies, provide a snapshot of colonization and can reveal the extent to which shifts in abundance and occupancy result from changes in demographic rates (e.g., reproduction and survival) or migration among suitable patches of habitat. Here, we describe the population structure of a colonial seabird breeding across a large latitudinal range in the Southern Ocean. Using multilocus microsatellite genotype data from 510 Gentoo penguin (Pygoscelis papua) individuals from 14 colonies along the Scotia Arc and Antarctic Peninsula, together with mitochondrial DNA data, we find strong genetic differentiation between colonies north and south of the Polar Front, that coincides geographically with the taxonomic boundary separating the subspecies P. p. papua and P. p. ellsworthii. Using a discrete Bayesian phylogeographic approach, we show that southern Gentoos expanded from a possible glacial refuge in the center of their current range, colonizing regions to the north and south through rare, long‐distance dispersal. Our findings show that this dispersal is important for new colony foundation and range expansion in a seabird species that ordinarily exhibits high levels of natal philopatry, though persistent oceanographic features serve as barriers to movement.     

A landscape genetics approach reveals ecological‐based differentiation in populations of holm oak (Quercus ilex L.) at the northern limit of its range

The holm oak plays a relevant role in the functioning of Mediterranean forests. In the area north of Garda Lake, Italian Prealps, holm oak populations are at the northernmost edge of their distribution. Being peripheral, these populations are of particular interest for ecological, evolutionary and conservation studies. Through an explicit individual‐based landscape genetics approach, we addressed the following questions: (1) are levels of genetic variation reduced in these marginal populations compared with central populations?; (2) despite the narrow geographical scale, do individual‐based analyses have some power to detect genetic differentiation?; (3) do environmental and/or climatic factors exert a role in shaping patterns of genetic variation and differentiation? Through a Bayesian method, we identified three clusters whose genetic variability can be considered to be of the same order as that recorded in central Quercus ilex populations. Although being geographically very close (< 20 km), the differentiation was statistically significant (P < 0.05) with global F _st and Φ _Pt values of 0.019 and 0.038, respectively. Geography and phylogeography could not be invoked to explain this differentiation. A redundancy discriminant analysis revealed that relevant eco‐pedological and climatic features, such as soil depth, aspect, elevation and humidity, were correlated with the observed pattern of differentiation. Toblino was ecologically separated from the other clusters, as it lies on deep soil with subhumid conditions. The differentiation of the Brione–Ranzo–Val Busa cluster appeared to be related to superficial soils and drier conditions, whereas the Nanzone–Padaro cluster was differentiated mainly according to its mid‐elevation. Coupling spatial and genetic information on a local scale proved to be effective to investigate the evolutionary and demographic history of peripheral populations. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

Phylogenetics of tribe Sabiceeae (Ixoroideae,Rubiaceae) revisited,with a new subgeneric classification for Sabicea

Tribe Sabiceeae (Ixoroideae, Rubiaceae) has undergone recent taxonomical changes with the incorporation of the related genera Ecpoma, Pseudosabicea and Stipularia into the type genus Sabicea. We use phylogenetic analysis and morphological data to verify the relationships among members of the tribe, including the most comprehensive taxon sampling of the tribe to date with 74 of 145 species. Sequence data from the nuclear internal transcribed spacer (ITS) and three plastid markers (petD, rps16, trnT–F) were used to infer relationships among the members of the tribe. Individual analyses using maximum likelihood, parsimony and Bayesian approaches reveal several supported clades: the former genus Stipularia is resolved as a monophyletic unit, but Ecpoma is monophyletic only if Sabicea urbaniana and Sabicea xanthotricha are included (corresponding to Sabicea subgenus Stipulariopsis sensu Wernham). Pseudosabicea is biphyletic, with one clade corresponding to section Anisophyllae of Hallé (1964) and the other one to the other sections (Floribundae and Sphaericae) of the genus. Eleven morphological characteristics were recorded for all species studied and seven have been mapped onto the phylogenetic tree to study their evolution in the group and assess their value for the classification of Sabicea s.l. Finally, our study shows that a combination of diagnostic characteristics should be used to differentiate each group and we propose to recognise four subgenera in Sabicea.     

Community structures of N2‐fixing bacteria associated with the phyllosphere of a Holm oak forest and their response to drought

Biological nitrogen (N) fixation is a key pathway in terrestrial ecosystems and is therefore critical for understanding the responses of ecosystems to global environmental changes. The free‐living diazotrophic community is distributed along the canopy‐to‐soil profile, but the ecological significance of epiphyllic N₂ fixers, despite their functional relevance, on plant foliar surfaces remains very poorly understood compared with the N₂‐fixing community in forest litter and soils. We assessed the community structure of N₂ fixers and overall bacteria by genetic fingerprinting (t‐RFLP) to explore the seasonal successional patterns of the microbial community in the natural phyllosphere of a Holm oak (Quercus ilex) forest submitted to 12‐year field experiment of rain exclusion mimicking the conditions of drought projected for the coming decades. Leaves of Holm oak were analysed in different seasons over a period of 1.5 years. The bacterial community of the phyllosphere did not correspond to the surrounding soil biome in the same area. These analyses provided field evidence for the presence of free‐living diazotrophs associated with the tissues of leaves of Holm oak, the dominant tree species of many Mediterranean forests. The results also revealed that the community composition is affected seasonally and inter‐annually by the environment, and that the composition shifts in response to climate change. Drought treatment increased the richness of the epiphyllic microbial community, especially during the summer. These changes were associated with higher C:N ratios of leaves observed in response to drought in semiarid areas. This epiphyllic microbiota that can potentially fix N₂ extends the capacity of plants to adapt to the environment.