Spatial variation in juvenile and adult Ecklonia radiata (Laminariales) sporophytes

Juvenile and adult sporophytes of Ecklonia radiata were counted on in-shore and off-shore reefs at Marmion (Perth, Western Australia), across spatial scales of kilometres, 10s of metres and metres. The position on in-shore reefs vs. off-shore reefs did not influence recruit and adult kelp density. There was considerable site-to-site (kilometres) variation in densities of recruits but not adults. The majority of variation in both recruit and adult densities was found between quadrats separated by a few metres. There was no relationship between abundance of recruits and abundance of adult sporophytes at any of the spatial levels of investigation, suggesting a decoupling of recruitment and canopy processes. The results emphasise the patchy nature of kelp canopy distribution and suggest that relatively small-scale processes, acting on scales of a few metres, are of primary importance in generating heterogeneity in the canopy of these kelps.     

Effects of kelp canopies on bleaching and photosynthetic activity of encrusting coralline algae

Canopy-forming algae often coexist with an understorey of encrusting coralline algae that bleach following the loss of canopies. We tested the hypothesis that canopy loss causes a reduction in photosynthetic activity of encrusting coralline algae concomitant with their bleaching. When canopies were experimentally removed, corallines bleached and their photosynthetic activity was rapidly reduced to half their activity observed under canopies. This result prompted us to test, and subsequently accept, the hypothesis that exposure of understorey corallines to enhanced light intensity per se (simulation of canopy loss) acts as a mechanism that causes bleaching and reduced photosynthetic activity. Despite bleaching, encrusting corallines maintained reduced levels of photosynthetic activity, and this may explain why, under certain conditions, bleached corallines can persist in the absence of canopy-forming algae. Nevertheless, our data provide evidence that the positive association between canopy-forming algae and encrusting coralline algae is maintained because of shade provided by the canopy.     

Root mass distribution patterns under standardised conditions in species of Chionochloa and Festuca from New Zealand

The vertical biomass allocation patterns of roots grown under standardised conditions were determined for species representing the major New Zealand indigenous grass genera Chionochloa and Festuca. Ten ramets, each of 2–3 tillers from garden collections of each species were grown in irrigated vertical sand columns in a glasshouse, and harvested after 168 days. Chionochloa teretifolia, Chionochloa macra, and Chionochloa crassiusucula, characteristic of alpine environments failed to produce new roots and died. However, most of the Chionochloa taxa (Chionochloa beddiei, Chionochloa pallens, Chionochloa rigida ssp. rigida, Chionochloa rubra ssp. cuprea, Chionochloa vireta), developed extensive new roots that reached the base of the one metre sand column. Roots of Chionochloa cheesemanii and Chionochloa conspicua reached 80–90 cm depth. Two Festuca taxa (Festuca actae, Festuca luciarum) had roots to 1 m depth, and roots of Festuca coxii, Festuca matthewsii ssp. latifundii, Festuca matthewsii ssp. matthewsii, Festuca multinodis, and Festuca novae-zelandiae grew to 70–90 cm depth. The edaphic specialists (Festuca deflexa, Chionochloa spiralis, Chionochloa defracta) were all shallow rooting.Species of Festuca maintained at least 40% of the root mass in the upper 10 cm of the column and most of the Chionochloa taxa had less than 40% of root mass in the upper zone. Genotype level variation in root mass less than 10 cm deep was greater in Chionochloa than in Festuca, and least in the edaphic specialist grasses.     

Development and application of tools for incursion response: Lessons learned from the management of the fouling pest Didemnum vexillum

In October 2001, an unidentified didemnid ascidian, was recorded for the first time in New Zealand, smothering wharf piles and moorings in a northern harbour. A heavily-fouled barge then translocated the ascidian to an international shipping port some 500 km south, near the heart of the New Zealand mussel industry. The species was subsequently identified as Didemnum vexillum, but its status as indigenous or non-indigenous was disputed. Nonetheless, its presence was regarded as a significant threat to the mussel industry because of its demonstrated invasiveness on artificial structures, and its ability to over-grow and smother mussels.From the barge's mooring area, D. vexillum subsequently spread to the seabed beneath, and to nearby vessels and artificial structures (i.e., barges, recreational vessels, moorings, salmon cages and wharf piles). Given the likelihood that infected vectors would spread the ascidian to mussel farms in the region, and in consideration of a benefit-cost analysis, an eradication program for D. vexillum was instigated. This paper provides a chronology of events surrounding the initial detection and spread of the ascidian, and describes the development of incursion response tools for the different substrata that were infected. The treatments included smothering soft-sediment habitats with uncontaminated dredge spoil, wrapping wharf piles with plastic, smothering rip-rap habitats using a geotextile fabric, and various other approaches based on water blasting, air drying or chlorine dosing. While many of the response methods were completely effective at eliminating D. vexillum from different substrata, the program overall failed to eradicate the organism from the region. The reasons for this failure are documented, and the important lessons learned are highlighted, as a contribution to the successful management of invasive species in the future.     

A closer look at the “Protopithecus” fossil assemblages: new genus and species from Bahia,Brazil

The recently extinct large-bodied New World monkey Protopithecus brasiliensis Lund 1836 was named based on a distal humerus and proximal femur found in the Lagoa Santa cave system in the southeastern Brazilian state of Minas Gerais. These bones are from an animal about twice the size of the largest extant platyrrhines. One hundred and seventy-five years later, a nearly complete skeleton was discovered in the Toca da Boa Vista caves in the neighboring state of Bahia and was allocated to the same taxon as it was the first platyrrhine fossil of comparable size found since the originals. Our detailed study of the equivalent elements, however, reveals important morphological differences that do not correspond to intraspecific variation as we know it in related platyrrhine taxa. The presence of both an expanded brachioradialis flange on the humerus and gluteal tuberosity on the femur of the Bahian skeleton distinguishes it from the Lagoa Santa fossil as well as from all other platyrrhines. Further cranial and postcranial evidence suggests a closer relationship of the former with the alouattine Alouatta, while the limited Lund material fits more comfortably with the ateline clade. Therefore, we propose to limit P. brasiliensis Lund to the distal humerus and proximal femur from Lagoa Santa and erect a new genus and species for the skeleton from Toca da Boa Vista. Cartelles coimbrafilhoi was a large-bodied frugivore with a relatively small brain and diverse locomotor repertoire including both suspension and climbing that expands the range of platyrrhine biodiversity beyond the dimensions of the living neotropical primates.     

Molecular phylogenetics and taxonomic reassessment of four Indian representatives of the genus Nymphaea

Because the classification of Nymphaea in India has been reported to be confusing, molecular taxonomic revision of four Indian representatives of the genus namely N. nouchali, N. pubescens, N. rubra and N. tetragona based on ITS, trnK intron and matK gene is presented and discussed. Molecular evidence provided here is in disagreement about the taxonomic identity of one specimen of N. nouchali and indicated a probable misidentification of N. tetragona. Interestingly, sequence analysis revealed lack of or low sequence divergence between N. pubescens and N. rubra. Phylogenetic relationship among members of Nymphaea subg. Lotos, represented by all known species viz. N. lotus, N. petersiana, N. pubescens and N. rubra was also conducted. Maximum parsimony analysis of the combined data matrix depicted two clades with N. petersiana and N. lotus forming one, N. pubescens and N. rubra representing the other. Bayesian inference showed N. petersiana as first branching, followed by N. lotus with N. pubescens and N. rubra emerging as a separate clade. The results indicated no close association between N. petersiana and N. nouchali, thereby, contradicting the morphology-based treatment of placing N. petersiana in synonymy under N. capensis and N. nouchali, respectively.     

Spatial and temporal regulation of the homeotic selector gene Antennapedia is required for the establishment of leg identity in Drosophila

Antennapedia is one of the homeotic selector genes required for specification of segment identity in Drosophila. Dominant mutations that ectopically express Antennapedia cause transformation of antenna to leg. Loss-of-function mutations cause partial transformation of leg to antenna. Here we examine the role of Antennapedia in the establishment of leg identity in light of recent advances in our understanding of antennal development. In Antennapedia mutant clones in the leg disc, Homothorax and Distal-less are coexpressed and act via spineless to transform proximal femur to antenna. Antennapedia is negatively regulated during leg development by Distal-less, spineless, and dachshund and this reduced Antennapedia expression is needed for the proper development of distal leg elements. These findings suggest that the temporal and spatial regulation of the homeotic selector gene Antennapedia in the leg disc is necessary for normal leg development in Drosophila.     

Human impacts in soft‐sediment assemblages at Casey Station,East Antarctica: Spatial variation,taxonomic resolution and data transformation

Abstract Differences between marine soft‐sediment assemblages at disturbed (two waste dumps, a sewage outfall and a wharf) and control locations were found at Casey Station, Antarctica. These differences were significant against considerable background spatial variability. Core samples were collected by divers using a hierarchical, spatially nested sampling design incorporating four scales: (i) locations (thousands of metres apart); (ii) sites (hundreds of metres apart); (iii) plots (tens of metres apart); and (iv) among replicates within plots (approximately 1 metre apart). Control locations had greater species richness and diversity than disturbed locations and there were many taxa found at control locations that were not recorded at disturbed locations. Assemblages at disturbed locations were less variable than those at control locations. In contrast, populations of some dominant species were more variable at disturbed locations than at control locations. Significant variation in populations of individual taxa was also found at all scales and although greatest at the level of location, variation was also large at the smallest scale, between replicate cores, indicating significant small‐scale patchiness in populations of taxa. Patterns of assemblage structure were similar at fine (77 taxa) and medium (aggregated to 33 taxa) levels of taxonomic resolution, but changed at coarse levels of resolution (nine phyla). Soft‐sediment assemblages at Casey Station are markedly different from those reported from other areas of Antarctica. Assemblages at Casey are almost completely dominated by crustaceans (up to 99% total abundance) and polychaetes are rare or in very low abundances in most areas investigated in the region. This is also the first demonstration that small Antarctic research stations (population 20–50 people) may cause impacts that are detectable in the adjacent marine environment.     

Exploring myriapod segmentation: the expression patterns of even-skipped,engrailed, and wingless in a centipede

Segment formation is critical to arthropod development, yet there is still relatively little known about this process in most arthropods. Here, we present the expression patterns of the genes even-skipped (eve), engrailed, and wingless in a centipede, Lithobius atkinsoni. Despite some differences when compared with the patterns in insects and crustaceans, the expression of these genes in the centipede suggests that their basic roles are conserved across the mandibulate arthropods. For example, unlike the seven pair-rule stripes of eve expression in the Drosophila embryonic germband, the centipede eve gene is expressed strongly in the posterior of the embryo, and in only a few stripes between newly formed segments. Nonetheless, this pattern likely reflects a conserved role for eve in the process of segment formation, within the different context of a short-germband mode of embryonic development. In the centipede, the genes wingless and engrailed are expressed in stripes along the middle and posterior of each segment, respectively, similar to their expression in Drosophila. The adjacent expression of the engrailed and wingless stripes suggests that the regulatory relationship between the two genes may be conserved in the centipede, and thus this pathway may be a fundamental mechanism of segmental development in most arthropods.     

The high-affinity cAMP phosphodiesterase of Saccharomyces cerevisiae is the major determinant of cAMP levels in stationary phase: involvement of different branches of the Ras-cyclic AMP pathway in stress responses

The Ras-cyclic AMP (cAMP) pathway is a major determinant of intrinsic stress resistance of the yeast Saccharomyces cerevisiae. Here, we isolated IRA2, encoding the Ras GTPase activator, as a global stress response gene. Subsequently, we studied the other negative regulators on the separate branch of the Ras-cAMP pathway, the low- or high-affinity cAMP phosphodiesterase encoded by PDE1 or PDE2, respectively. Deletion of PDE2, similar to ira2 deletion, rendered cells sensitive to freeze-thawing, peroxides, paraquat, cycloheximide, heavy metals, NaCl, heat, or cold shock. However, deletion of PDE1 did not affect stress tolerance, although it exacerbated stress sensitivity caused by the pde2 deletion, indicating that PDE1 can partly compensate for PDE2. Deletion of IRA2 uniquely led to high sensitivity to cumene hydroperoxide, suggesting that IRA2 may have a distinct role for the response to this stress. Stress sensitivity of yeast cells in general correlated with the basal level of cAMP. Interestingly, yeast cells lacking PDE2 maintained higher cAMP levels in stationary phase than exponential growth phase, suggesting that Pde2p is the major regulator of cAMP levels in stationary phase. Depletion of Ras activity could not effectively suppress stress sensitivity caused by lack of cAMP phosphodiesterases although it could suppress stress sensitivity caused by lack of IRA2, indicating that cAMP accumulation in stationary phase can be mediated by other signaling proteins in addition to Ras. Our study shows that control of cAMP basal levels is important for determining intrinsic stress tolerance of yeast, and that the cAMP level during stationary phase is a result of a dynamic balance between its rates of synthesis and degradation.     

Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection

Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species'' prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic. We identify four DRB codons, predicted to be involved in antigen binding, that are evolving under adaptive evolution. Our data suggest diversity at DRB may be maintained by balancing selection, consistent with the role of this locus as an antigen-binding region and the species'' recent history of mass mortality during a series of bacterial epizootics. Phylogenetic analyses of DQB and DRB sequences from pinnipeds and other carnivores revealed significant allelic diversity, but little phylogenetic depth or structure among pinniped alleles; thus, we could neither confirm nor refute the possibility of trans-species polymorphism in this group. The phylogenetic pattern observed however, suggests some significant evolutionary constraint on these loci in the recent past, with the pattern consistent with that expected following an epizootic event. These data may help further elucidate some of the genetic factors underlying the unusually high susceptibility to bacterial infection of the threatened NZSL, and help us to better understand the extent and pattern of MHC diversity in pinnipeds.     

Detecting growth under environmental extremes: Spatial and temporal patterns in nucleic acid ratios in two Antarctic bivalves

Growth of Antarctic benthic organisms is very slow due to temperature and food availability, and subtle differences in growth rate may be difficult to detect. Nucleic acid ratios (RNA/DNA, RNA/protein or total RNA concentration) are measures of protein synthesis potential and may be used to assess short-term growth rate in a range of marine organisms. We quantified nucleic acid ratios in the scallop Adamussium colbecki and the clam Laternula elliptica at five locations in the Ross Sea, Antarctica. We were able to detect species-specific, habitat-specific, and seasonal differences in nucleic acid ratios and related these to associated differences in primary productivity. By using nucleic acid ratios, future studies could relatively easily obtain a measure of growth rate from a multitude of locations with contrasting habitat characteristics, food availability and temperature regimes around the Antarctic continent. This would yield a unique understanding of spatial and temporal patterns in bivalve growth in this extreme environment.     

Diurnal variation in relative photosynthetic performance in giant kelp Macrocystis pyrifera (Phaeophyceae, Laminariales) at different depths as estimated using PAM fluorometry

Pulse-amplitude modulated (PAM) fluorometry allows instantaneous estimates of photosynthetic rates, but may well produce variable measurements of photosynthetic activity depending on time of day, recent light history, internal fluctuations, and environmental variability. To investigate this, we compare estimates of diurnal variability in relative photosynthetic performance for the giant kelp, Macrocystis pyrifera (L.) C. Agardh, obtained from PAM fluorometry at three depths during 3 days characterized by different light conditions, and for two different blade ages. Sampling in the mid morning, late morning, early afternoon and late afternoon, we examined diurnal changes in relative photosynthetic performance in meristematic tissue and older blades occurring near the bottom, in the mid water, and at the water surface. Measures of maximum relative electron transport rates (rETR_max), minimum saturating irradiance (E_k), photosynthetic efficiency (α) and maximum quantum yield (F_v/F_m) show that giant kelp blades in the mid water and near the bottom exhibit little to no photosynthetic changes during the day. Near the surface, however, blades exhibit photosynthetic characteristics similar to light-adapted species in that they begin the day acclimated to low light, acclimate to increasing irradiance during the day, and end the day acclimated to low light. Consequently, while estimates of rETR_max were highest during the midday for all sample depths and days, they were also always highest near the surface for both old blades (112.16 ± 8.7, 98.6 ± 14.7, 70.16 ± 5.7) and meristematic tissue (109.0 ± 9.0, 86.9 ± 1.9, 59.2 ± 11.6, surface, mid water and bottom, respectively). Similar patterns were observed for E_k for both old blades (169.2 ± 5.4, 88.0 ± 11.2, 83.8 ± 5.2) and meristematic tissue (138.4 ± 11.5, 96.6 ± 4.69, 68.4 ± 10.6). In contrast, estimates of F_v/F_m were lowest near the surface during the midday for both old blades (0.6 ± 0.02, 0.73 ± 0.69, 0.75 ± 0.01) and meristematic tissue (0.58 ± 0.02, 0.69 ± 0.05, 0.74 ± 0.01, surface, mid water and bottom, respectively). These patterns coincided with similar patterns in ambient light, which was most variable and reached its greatest values near the surface during the midday.     

Spatial and temporal effects of pre-seeding plates with invasive ascidians: Growth, recruitment and community composition

Many shallow water subtidal habitats in Massachusetts, USA have recently been invaded by five non-indigenous ascidian species: Ascidiella aspersa, Botrylloides violaceus, Didemnum sp., Diplosoma listerianum and Styela clava. This study examined the effects of seawater temperature, as a proxy for climate change, on B. violaceus and D. listerianum and the impact these ascidians have on native sessile fouling communities. Field experiments were conducted over a four month period at two locations (Lynn and Woods Hole, MA) to examine growth dynamics over regional thermal and geographic ranges. Invasive ascidians occupied as much as 80% of the primary substratum and accounted for the majority of species richness. B. violaceus and D. listerianum growth were similar at both study sites, but initial colony growth of D. listerianum was positively affected by temperature. B. violaceus and D. listerianum exhibited rapid two-week growth rates during the summer months with more rapid growth at the warmer Woods Hole site. Competition for space between B. violaceus and D. listerianum typically resulted in neutral borders between colonies. Overgrowth occurred if the colony of one species was disproportionably larger than the colony of the other species. Recruitment and growth of native species influenced the long-term composition of experimental communities more than the pre-seeding with B. violaceus or D. listerianum colonies. Elevated temperatures, however, increased initial growth of B. violaceus and D. listerianum and may have facilitated the species success to invade the communities during crucial periods of introduction. With projected global climate change, a rise in sea surface temperatures may exacerbate the cumulative impacts of invasions on benthic communities and facilitate the invasion of other non-native ascidian species.     

Perilla frutescens seed agar, a new medium for identification of the Cryptococcus species complex: evaluation for all major molecular types

Here we present a new and simple medium made by Perilla frutescens seed as a tool for identification of the Cryptococcus species complex, namely Cryptococcus neoformans and Cryptococcus gattii. Its usefulness was evaluated for all major molecular types within the Cryptococcus species complex. As a result, this medium is better for identification of the species complex compared with Guizotia abyssinica or Helianthus annuus seed medium.     

Dental and phylogeographic patterns of variation in gorillas

Gorilla patterns of variation have great relevance for studies of human evolution. In this study, molar morphometrics were used to evaluate patterns of geographic variation in gorillas. Dental specimens of 323 adult individuals, drawn from the current distribution of gorillas in equatorial Africa were divided into 14 populations. Discriminant analyses and Mahalanobis distances were used to study population structure.Results reveal that: 1) the West and East African gorillas form distinct clusters, 2) the Cross River gorillas are well separated from the rest of the western populations, 3) gorillas from the Virunga mountains and the Bwindi Forest can be differentiated from the lowland gorillas of Utu and Mwenga-Fizi, 4) the Tshiaberimu gorillas are distinct from other eastern gorillas, and the Kahuzi-Biega gorillas are affiliated with them. These findings provide support for a species distinction between Gorilla gorilla and Gorilla beringei, with subspecies G. g. diehli, G. g. gorilla, G. b. graueri, G. b. beringei, and possibly, G. b. rex-pygmaeorum. Clear correspondence between dental and other patterns of taxonomic diversity demonstrates that dental data reveal underlying genetic patterns of differentiation.Dental distances increased predictably with altitude but not with geographic distances, indicating that altitudinal segregation explains gorilla patterns of population divergence better than isolation-by-distance. The phylogeographic pattern of gorilla dental metric variation supports the idea that Plio-Pleistocene climatic fluctuations and local mountain building activity in Africa affected gorilla phylogeography. I propose that West Africa comprised the historic center of gorilla distribution and experienced drift-gene flow equilibrium, whereas Nigeria and East Africa were at the periphery, where climatic instability and altitudinal variation promoted drift and genetic differentiation. This understanding of gorilla population structure has implications for gorilla conservation, and for understanding the distribution of sympatric chimpanzees and Plio-Pleistocene hominins.     

Predicting understorey structure from the presence and composition of canopies: an assembly rule for marine algae

Assembly rules provide a useful framework for predicting patterns of community assembly under defined environmental conditions. Habitat created by canopy-forming algae (such as kelps) provides a promising system for identifying assembly rules because canopies typically have a large and predictable influence on understorey communities. Across >1,000 km of subtidal South Australian coastline, we identified natural associations between assemblages of understorey algae and (1) monospecific canopies of Ecklonia radiata, (2) canopies comprised of E. radiata mixed with Fucales (Cystophora spp. and Sargassum spp.), and (3) gaps among canopies of algae. We were able to recreate these associations with experimental tests that quantified the assembly of understorey algae among these three habitat types. We propose the assembly rule that understorey communities on subtidal rocky coast in South Australia will be (1) monopolised by encrusting coralline algae beneath monospecific canopies of E. radiata, (2) comprised of encrusting corallines, encrusting non-corallines, and sparse covers of articulated corallines, beneath mixed E. radiata-Fucales canopies, and (3) comprised of extensive covers of articulated corallines and filamentous turfs, as well as sparse covers of foliose algae and juvenile canopy-formers, within gaps. Consistencies between natural patterns and experimental effects demonstrate how algal canopies can act as a filter to limit the subsets of species from the locally available pool that are able to assemble beneath them. Moreover, the subsets of species that assemble to subtidal rocky substrata in South Australia appear to be predictable, given knowledge of the presence and composition of canopies incorporating E. radiata.