Multiple surveys employing a new sample‐processing protocol reveal the genetic diversity of placozoans in Japan

Placozoans, flat free‐living marine invertebrates, possess an extremely simple bauplan lacking neurons and muscle cells and represent one of the earliest‐branching metazoan phyla. They are widely distributed from temperate to tropical oceans. Based on mitochondrial 16S rRNA sequences, 19 haplotypes forming seven distinct clades have been reported in placozoans to date. In Japan, placozoans have been found at nine locations, but 16S genotyping has been performed at only two of these locations. Here, we propose a new processing protocol, “ethanol‐treated substrate sampling,” for collecting placozoans from natural environments. We also report the collection of placozoans from three new locations, the islands of Shikine‐jima, Chichi‐jima, and Haha‐jima, and we present the distribution of the 16S haplotypes of placozoans in Japan. Multiple surveys conducted at multiple locations yielded five haplotypes that were not reported previously, revealing high genetic diversity in Japan, especially at Shimoda and Shikine‐jima Island. The observed geographic distribution patterns were different among haplotypes; some were widely distributed, while others were sampled only from a single location. However, samplings conducted on different dates at the same sites yielded different haplotypes, suggesting that placozoans of a given haplotype do not inhabit the same site constantly throughout the year. Continued sampling efforts conducted during all seasons at multiple locations worldwide and the development of molecular markers within the haplotypes are needed to reveal the geographic distribution pattern and dispersal history of placozoans in greater detail.     

Field biology of placozoans (Trichoplax): distribution, diversity, biotic interactions

The goal of this review is to highlight what little is known,and point to the bulk of what is yet to be learned, about thenatural history of placozoans in the field—in order tostimulate a broader search for placozoans and a fuller explorationof their distribution, diversity, and all other aspects of theirenigmatic lives. The documented geographic distribution of placozoanslies mostly in the nearshore, warm, marine waters of the tropicsand subtropics. Although placozoans have long been viewed asbenthic organisms, they can be more readily collected from thewater column, well above the sea bottom. The full life-historyof placozoans is unknown, including the nature of this abundantpelagic phase and all details of sexual reproduction and development.We note observations on the biota associated with placozoansin field collections, in particular the other regular membersof the microcommunity in which placozoans occur on our collectingplates and on some factors influencing this assemblage. Amongthe animals found are some potential predators against whichplacozoans appear to be defended, although the mechanisms arestill to be examined. Also yet to be uncovered is the full breadthof diversity in this phylum, certainly underrepresented by itssingle named species. We report here greatly expanded distributionsfor known haplotypes and fresh specimens that include a newhaplotype, and we review the evidence that many more almostcertainly await discovery. We also describe some methods forcollecting and handling these small, fragile animals.     

Mapping and explaining wolf recolonization in France using dynamic occupancy models and opportunistic data

While large carnivores are recovering in Europe, assessing their distributions can help to predict and mitigate conflicts with human activities. Because they are highly mobile, elusive and live at very low density, modeling their distributions presents several challenges due to 1) their imperfect detectability, 2) their dynamic ranges over time and 3) their monitoring at large scales consisting mainly of opportunistic data without a formal measure of the sampling effort. Here, we focused on wolves Canis lupus that have been recolonizing France since the early 1990s. We evaluated the sampling effort a posteriori as the number of observers present per year in a cell based on their location and professional activities. We then assessed wolf range dynamics from 1994 to 2016, while accounting for species imperfect detection and time‐ and space‐varying sampling effort using dynamic site‐occupancy models. Ignoring the effect of sampling effort on species detectability led to underestimating the number of occupied sites by more than 50% on average. Colonization appeared to be negatively influenced by the proportion of a site with an altitude higher than 2500 m and positively influenced by the number of observed occupied sites at short and long‐distances, forest cover, farmland cover and mean altitude. The expansion rate, defined as the number of occupied sites in a given year divided by the number of occupied sites in the previous year, decreased over the first years of the study, then remained stable from 2000 to 2016. Our work shows that opportunistic data can be analyzed with species distribution models that control for imperfect detection, pending a quantification of sampling effort. Our approach has the potential for being used by decision‐makers to target sites where large carnivores are likely to occur and mitigate conflicts.     

Caribbean placozoan phylogeography

We here address placozoan distribution and phylogeography in five locations in the Caribbean Sea. We performed a coarse-resolution presence/absence survey of placozoans in Belize, Bermuda, Grenada, Jamaica, and Panama and a fine-resolution study of the distribution of placozoans in Twin Cays, Belize. Placozoans were recovered in every country sampled. Animals were sequenced at the mitochondrial 16S rDNA locus, and our analysis identified four of the five previously identified clades present in the Caribbean. In addition, we discovered two new haplotypes within one of these clades, and we found sympatric clades in Belize, Bermuda, Jamaica, and Panama. These studies provide further molecular evidence for species diversity within the Phylum Placozoa.     

Substrate binds in the S1 site of the F253A mutant of LeuT, a neurotransmitter sodium symporter homologue

LeuT serves as the model protein for understanding the relationships between structure, mechanism and pharmacology in neurotransmitter sodium symporters (NSSs). At the present time, however, there is a vigorous debate over whether there is a single high-affinity substrate site (S1) located at the original, crystallographically determined substrate site or whether there are two high-affinity substrates sites, one at the primary or S1 site and the other at a second site (S2) located at the base of the extracellular vestibule. In an effort to address the controversy over the number of high-affinity substrate sites in LeuT, one group studied the F253A mutant of LeuT and asserted that in this mutant substrate binds exclusively to the S2 site and that 1 mM clomipramine entirely ablates substrate binding to the S2 site. Here we study the binding of substrate to the F253A mutant of LeuT using ligand binding and X-ray crystallographic methods. Both experimental methods unambiguously show that substrate binds to the S1 site of the F253A mutant and that binding is retained in the presence of 1 mM clomipramine. These studies, in combination with previous work, are consistent with a mechanism for LeuT that involves a single high-affinity substrate binding site.     

Nitrogen Fixation in Bryophytes, Lichens, and Decaying Wood along a Soil-age Gradient in Hawaiian Montane Rain Forest

We determined rates of acetylene reduction and estimated total nitrogen fixation associated with bryophytes, lichens, and decaying wood in Hawaiian montane rain forest sites with underlying substrate ranging in age from 300 to 4.1 million years. Potential N fixation ranged from ca 0.2 kg/ha annually in the 300‐year‐old site to ca 1 kg/ha annually in the 150,000‐year‐old site. Rates of acetylene reduction were surprisingly uniform along the soil‐age gradient, except for high rates in symbiotic/associative fixers at the 150,000‐year‐old site and in heterotrophic fixers at the 2100‐year‐old site. Low fixation at the youngest site, where plant production is known to be N‐limited, suggests that demand for N alone does not govern N fixation. Total N fixation was highest in sites with low N:P ratios in leaves and stem wood, perhaps because epiphytic bryophytes and lichens depend on canopy leachate for mineral nutrients and because heterotrophic fixation is partly controlled by nutrient supply in the decomposing substrate; however, differences in substrate cover, rather than in fixation rates, had the largest effect on the total N input from fixation at these sites.     

Temporal, spatial and substrate-dependent variations of Danish hard-bottom macrofauna

Detailed knowledge of the Danish hard-bottom fauna is at present limited because of sampling problems. In this study, two different sampling units were used to yield quantitative results of the fauna on two stone reefs in Kattegat: natural holdfasts of Laminaria digitata and plastic pan-scourers imitating the holdfasts. On the two reefs a total of 135 taxa (102 species) were identified, representing 12 phyla. One species, the bryozoan Cribrilina cryptooecium, has not previously been recorded in Denmark. The fauna was characterized by a mixture of a large number of rare species, yielding high values on the Shannon-Wiener diversity index, and it showed a high degree of spatial and temporal variation. ANOSIM analyses showed a significant difference in species compositions between both sampling location, time and substrate type. The plastic pan-scourers proved to be a valuable substrate for quantitative investigations of the fauna. In contrast, the Laminaria holdfasts were too small and variable to be suitable for such studies. Electronic Publication     

烟台养马岛潮间带大型海藻分布特征及环境影响因素

2010年4月—2011年3月对烟台养马岛潮间带大型海藻进行了逐月调查.在养马岛潮间带共设置了A、B两个点,对大型海藻物种组成、生物量以及与环境变化的关系进行了研究.结果表明: 调查区域共有大型海藻35种,其中红藻24种,占总数的68.6%;绿藻6种,占总数的17.1%;褐藻5种,占总数的14.3%.夏季优势种以褐藻和绿藻为主,秋、冬、春季优势种以红藻和褐藻为主,鼠尾藻在各季节中均为优势种.大型海藻生物量呈现夏季高、冬季低的特点,生物量最高值出现在6月,A、B采样点大型海藻生物量最小值分别出现在1月和11月,具有温带海域藻类变化特点.温度、营养盐和pH对大型海藻生物量有显著影响.
     

Sample design effects in landscape genetics

An important research gap in landscape genetics is the impact of different field sampling designs on the ability to detect the effects of landscape pattern on gene flow. We evaluated how five different sampling regimes (random, linear, systematic, cluster, and single study site) affected the probability of correctly identifying the generating landscape process of population structure. Sampling regimes were chosen to represent a suite of designs common in field studies. We used genetic data generated from a spatially-explicit, individual-based program and simulated gene flow in a continuous population across a landscape with gradual spatial changes in resistance to movement. Additionally, we evaluated the sampling regimes using realistic and obtainable number of loci (10 and 20), number of alleles per locus (5 and 10), number of individuals sampled (10–300), and generational time after the landscape was introduced (20 and 400). For a simulated continuously distributed species, we found that random, linear, and systematic sampling regimes performed well with high sample sizes (>200), levels of polymorphism (10 alleles per locus), and number of molecular markers (20). The cluster and single study site sampling regimes were not able to correctly identify the generating process under any conditions and thus, are not advisable strategies for scenarios similar to our simulations. Our research emphasizes the importance of sampling data at ecologically appropriate spatial and temporal scales and suggests careful consideration for sampling near landscape components that are likely to most influence the genetic structure of the species. In addition, simulating sampling designs a priori could help guide filed data collection efforts     

Distribution and ecology of myxomycetes in the high-elevation oak forests of Cerro Bellavista, Costa Rica

Myxomycetes associated with a high-elevation (>3000 m) oak forest in the Talamanca Range of Costa Rica were studied for 7 mo. Field collections were supplemented with collections obtained from moist chamber cultures prepared with samples of bark and ground litter of Quercus costaricensis. Various microenvironmental parameters including pH, substrate moisture and diameter, height above the ground and canopy openness were recorded for each field collection, whereas macroenvironmental data for temperature and precipitation were obtained from a meteorological station near the study area. Niche breadth and niche overlap indices were calculated to assess possible resource partitioning by myxomycetes. Thirty-seven species were recorded, including 11 new records for Costa Rica, eight for Central America and one for the neotropics. Both PCA and NMS multivariate analyses indicated that pH and height above the ground explained most of the observed variation, although substrate diameter also seemed to be an important factor. Precipitation showed an inverse correlation with the number of fruitings, confirming its importance as a macroenvironmental factor. Niche overlap values were not higher for closely related species and values for niche breadths were similar for most of the more common species, suggesting that most members of the assemblage of myxomycetes present in the study site are ecological generalists.     

Diversity and microdistribution of black fly (Diptera: Simuliidae) assemblages in the tropical savanna streams of the Brazilian cerrado

We describe the abiotic factors affecting the distribution of black flies at a microhabitat scale, rather than at the regional scale usually present in the literature on the Neotropics. Black fly larvae were sampled from the Tocantins River and three tributaries, located in the Brazilian savanna (state of Tocantins, Brazil) during six bi-monthly sampling periods from October 2004-August 2005. At each sampling site, 15 random quadrats (30 x 30 cm) were sampled each period and for each quadrat were determined mean water velocity, predominant substrate type (rocks, riffle litter or riparian vegetation) and depth detrended correspondence analysis (DCA) was used to determine associations with current velocity, whereas correspondence analysis (CA) was used to estimate site specific current velocity associations. Canonical correspondence analysis (CCA) was used to identify general microhabitat associations. The CCA showed that most species had a trend towards riffle litter, except for Simulium nigrimanum associated with rocky substrate and Simulium cuasiexiguum associated with riparian vegetation. The DCA showed a well defined pattern of water velocity associations. The CA revealed that the species showed different speed associations from one site to another, suggesting different competitive pressures resulting in the occurrence of different realized niches.     

Annual changes in foliar nitrogen,phosphorus, and potassium levels of loblolly pine (pinus taeda L.) with site,and weather factors

The study investigated the fluctuation in foliar nutrient levels (over a period of approximately three years) on two sites of widely differing productivity for loblolly pine. Preliminary analysis at the end of the first year indicated large variations in foliar levels with time which were attributed to weather factors, and further sampling was initiated to evaluate the influence of weather. A lack of a stable period during any portion of the year was attributed to the indeterminate growth habit of loblolly pine, and this aspect, together with a strong statistical correlation of weather factors with foliar levels, suggests that if foliar nutrient levels are obtained by the method used in this study, results could not be recommended for use in site differentiation of this species. The weather factors most commonly correlated with foliar levels were average maximum and average minimum temperatures for certain periods preceeding the sampling date.     

Hydrocarbon Mineralization in Sediments and Plasmid Incidence in Sediment Bacteria from the Campeche Bank

Rates of degradation of radiolabeled hydrocarbons and incidence of bacterial plasmid DNA were investigated in sediment samples collected from the Campeche Bank, Gulf of Mexico, site of an offshore oil field containing several petroleum platforms. Overall rates of mineralization of [¹⁴C]hexadecane and [¹⁴C]phenanthrene measured for sediments were negligible; <1% of the substrate was converted to CO₂ in all cases. Low mineralization rates are ascribed to nutrient limitations and to lack of adaptation by microbial communities to hydrocarbon contaminants. Plasmid frequency data for sediment bacteria similarly showed no correlation with proximity to the oil field, but, instead, showed correlation with water column depth at each sampling site. Significant differences between sites were observed for proportion of isolates carrying single or multiple plasmids and mean number of plasmids per isolate, each of which increased as a function of depth.     

Biology and population dynamics of Porcellionides sexfasciatus (Crustacea,Isopoda, Oniscidea)

The biology and the population dynamics of Porcellionides sexfasciatus Budde-Lund (1879) were studied on a field and carried out at Garat Naam (Kasserine, Tunisia) from July 1996 to June 1998. The reproduction exhibited a seasonal pattern extending from February/March to October/November. The juveniles appeared in the population from April to November. Size frequency distributions were analysed and 14 cohorts were recognised during the sampling period. Six cohorts were identified at the first sampling and eight new ones on the other samplings. Among these latter cohorts, three were tracked till they disappeared. Minimum average length of new cohorts ranged from 3.07 +/- 0.35 mm to 3.47 +/- 0.2 mm. Maximum average length of cohorts was 10.42 mm. P. sexfasciatus is a semi-annual species (females producing two or three broods per year), with iteroparous and amphogenes females (females reproducing twice or more in their life and producing both males and females), and bivoltine life cycle (two generations per year). The females are able to produce two broods, in the laboratory, without new mating. Fecundity and fertility, corresponding to the number of eggs or embryos per brood, appeared positively correlated with females' size. Although oscillating throughout the year, the sex ratio was often in equilibrium.     

The most primitive metazoan animals,the placozoans,show high sensitivity to increasing ocean temperatures and acidities

The increase in atmospheric carbon dioxide (CO₂) leads to rising temperatures and acidification in the oceans, which directly or indirectly affects all marine organisms, from bacteria to animals. We here ask whether the simplest—and possibly also the oldest—metazoan animals, the placozoans, are particularly sensitive to ocean warming and acidification. Placozoans are found in all warm and temperate oceans and are soft‐bodied, microscopic invertebrates lacking any calcified structures, organs, or symmetry. We here show that placozoans respond highly sensitive to temperature and acidity stress. The data reveal differential responses in different placozoan lineages and encourage efforts to develop placozoans as a potential biomarker system.     

Assessment of Stream Restoration: Sources of Variation in Macroinvertebrate Recovery throughout an 11‐Year Study of Coal Mine Drainage Treatment

Stream restoration researchers have a complex array of alternative assessment methodologies using macroinvertebrates. We examined sources of variation among three field sampling methods and five metrics in three networked streams impacted by a circumneutral coal mine discharge treated midway through an 11‐year study. Constructed wetlands captured the primary stressor, 700 kg iron/day. Before pollution abatement, copious iron hydroxide smothered downstream sites for decades. Two second‐order streams and one fourth‐order receiving stream, each with matching locations upstream and downstream, were monitored midsummer from 1994 to 2004. We compared taxa density (TD) (number/sample), abundance, expected taxa richness (ETR), U.S. regional pollution tolerance values (RTV), and community similarity (CS) indices from 3 to 11 replicate samples/site using grab samples (i.e. D‐nets, rock washes) and incubated leaf packs. Variation due to sampling method, metric, location, and year significantly influenced outcomes when analyzed using regression and analysis of variance. TD, RTV, and CS indicated biological recovery lagged 6 years behind chemical improvement; ETR and abundance showed more severe, persistent impairment in the two, highly impacted second‐order streams compared to the fourth‐order stream. Incubated leaf packs offered a preview of stream recovery in downstream sites, providing clean food (leaves) and substrate (mesh) and attracted more taxa and abundance than grab samples. In light of the worldwide distribution of coal mining often accompanied by metal hydroxide deposits into streams, we suggest restoration project managers use a variety of sampling methods, metrics, and models to evaluate remediation of physical as well as chemical impairment from mining.     

Life cycle and population dynamic of Armadillidium pelagicum Arcangeli, 1955 (Isopoda, Oniscidea) at Aouina

Armadillidium pelagicum Arcangeli, 1955 is a terrestrial isopod endemic to the circum-Sicilian islands and the North of Tunisia. The life cycle and the population structure of this species were studied on a natural population at Aouina, in the surroundings of Tunis, over 16 months from, January 2000 to April 2001, by monthly or semi-monthly samplings. The ovigerous females were present from March/April to the end of August and absent from September to February/March. These observations indicate that A. pelagicum at Aouina has a seasonal reproduction, followed by a sexual rest. The recruitment period is spread from April/May to mid-September. The fecundity, estimated by the number of eggs in the marsupium of ovigerous females, exhibited a great variability, which is related to the weight of these females. The sex ratio underwent fluctuations throughout the sampling period. It was female-biased in most samplings. Mass frequency distribution was analysed and nine cohorts were identified during the sampling period. The field growth rates are high in the first life phase, decrease during winter and increase during spring. The characteristics of the life cycle of A. pelagicum at Aouina may be summarized as follows: (i) Semi-annual species, since females appear to produce up to five broods per year, (ii) iteroparous females, since females seem to reproduce twice or more in life; (iii) bivoltine life cycle, since the population produces two generations per year; (iv) variability of cohorts' life span.     

A comparative study of four dredges used for sampling benthic macroinvertebrates in rivers

SUMMARY. After considering the large number of dredges described in the literature, four light-weight dredges were chosen for manual operation from a small boat or the bank: Irish triangular dredge, small Fast dredge, medium-sized and large Naturalist's dredges. The dredges were tested in a series of trials at three sites in two rivers. A stratified random sample (number of sampling units, n = 5) was taken at each site and the modal particle sizes at sites 1–3 were 1–2 mm (fine gravel), 64–128 mm (larger stones) and 128–256 mm, respectively. The dredges usually took a similar range of stone sizes at each site but the design of the Fast dredge excluded larger stones (>16 mm). The Irish dredge sometimes failed to operate correctly. Variations in the volume of substrata taken with each dredge were large, both between sampling units in the same sample and between samples. The latter differences were partially due to the increase in the modal size of the stones, especially between sites 1 and 2, the different sampling areas of the dredges and the depth of penetration into the substratum. Penetration depth was probably greatest for the two Naturalist's dredges, smaller for the Fast dredge and smallest for the Irish dredge. In field trials, the relative abundances of major taxa were similar for most dredges at each site; major exceptions were the Fast dredge at site 2 and the Irish dredge at site 3. There was a high variability between sampling units in the same sample and therefore a lack of precision in the estimates of the mean number of invertebrates per sample. Therefore, the dredges cannot be used as quantitative samplers for the estimation of population density. Their adequacy as qualitative samplers for the estimation of total number of taxa per sample varied considerably and maximum estimates of their efficiencies for a small sample (n= 5) were <40% for the Irish and Fast dredges, >57% for the medium-sized Naturalist's dredge and >76% for the large Naturalist's dredge. There was a clear relationship between the number of taxa and the number of invertebrates taken at each site and this relationship was well described by a power law with an exponent within the range 0.18–0.53. The number of sampling units in the sample had no significant effect on the power-law equations for each site. The power-law equation was very similar for most of the dredges at each site, the only major exception being the Fast dredge at site 1. The implications of this relationship are discussed.     

Sampling Effort in Neotropical Primate Diet Studies: Collective Gains and Underlying Geographic and Taxonomic Biases

Primates are among the most observable and best studied mammalian orders, yet the distribution of sampling effort by primatologists has inevitably concentrated on a few genera and a limited number of study sites. We present the first systematic review of sampling effort and associated biases in wild primate field research, focusing on dietary studies across the Neotropics. Our literature review of all 24 neotropical primate ecospecies spans 42 years (1969–2011) and covers 290 dietary studies at 164 study sites across 17 countries. We use a standardized measure of sampling effort to assimilate data sets derived from multiple methodologies and attempt to understand the distribution of effort (total equivalent to 193,804 h) using geographic variables and primate species traits. Results indicate that there are both geographic and taxonomic biases, with sampling effort generally skewed towards large-bodied species occupying large geographic ranges, and concentrated at a select few primatology research hubs. We also note that full primate assemblages at any given study site are rarely investigated. Our assessment thus reveals severely undersampled primate taxa and geographic regions that must be considered in future research. Current biases could be ameliorated by deliberately targeting poorly studied genera anywhere in their geographic distribution, well-studied genera in poorly studied regions, and striving to study multiple sympatric taxa within a single site. Although continued inequalities in sampling effort are probably inevitable, this study shows that this need not inhibit successful compilations and meta-analyses, provided that adequate data on feeding records and sampling effort can be made available.     

Global Habitat Suitability and Ecological Niche Separation in the Phylum Placozoa

The enigmatic placozoans, which hold a key position in the metazoan Tree of Life, have attracted substantial attention in many areas of biological and biomedical research. While placozoans have become an emerging model system, their ecology and particularly biogeography remain widely unknown. In this study, we use modelling approaches to explore habitat preferences, and distribution pattern of the placozoans phylum. We provide hypotheses for discrete ecological niche separation between genetic placozoan lineages, which may also help to understand biogeography patterns in other small marine invertebrates. We, here, used maximum entropy modelling to predict placozoan distribution using 20 environmental grids of 9.2 km² resolution. In addition, we used recently developed metrics of niche overlap to compare habitat suitability models of three genetic clades. The predicted distributions range from 55°N to 44°S and are restricted to regions of intermediate to warm sea surface temperatures. High concentrations of salinity and low nutrient concentrations appear as secondary factors. Tests of niche equivalency reveal the largest differences between placozoan clades I and III. Interestingly, the genetically well-separated clades I and V appear to be ecologically very similar. Our habitat suitability models predict a wider latitudinal distribution for placozoans, than currently described, especially in the northern hemisphere. With respect to biogeography modelling, placozoans show patterns somewhere between higher metazoan taxa and marine microorganisms, with the first group usually showing complex biogeographies and the second usually showing “no biogeography.”