Evaluating,predicting and mapping belowground carbon stores in Kenyan mangroves

Despite covering only approximately 138 000 km², mangroves are globally important carbon sinks with carbon density values three to four times that of terrestrial forests. A key challenge in evaluating the carbon benefits from mangrove forest conservation is the lack of rigorous spatially resolved estimates of mangrove sediment carbon stocks; most mangrove carbon is stored belowground. Previous work has focused on detailed estimations of carbon stores over relatively small areas, which has obvious limitations in terms of generality and scope of application. Most studies have focused only on quantifying the top 1 m of belowground carbon (BGC). Carbon stored at depths beyond 1 m, and the effects of mangrove species, location and environmental context on these stores, are poorly studied. This study investigated these variables at two sites (Gazi and Vanga in the south of Kenya) and used the data to produce a country‐specific BGC predictive model for Kenya and map BGC store estimates throughout Kenya at spatial scales relevant for climate change research, forest management and REDD+ (reduced emissions from deforestation and degradation). The results revealed that mangrove species was the most reliable predictor of BGC; Rhizophora muronata had the highest mean BGC with 1485.5 t C ha^?1. Applying the species‐based predictive model to a base map of species distribution in Kenya for the year 2010 with a 2.5 m² resolution produced an estimate of 69.41 Mt C [±9.15 95% confidence interval (C.I.)] for BGC in Kenyan mangroves. When applied to a 1992 mangrove distribution map, the BGC estimate was 75.65 Mt C (±12.21 95% C.I.), an 8.3% loss in BGC stores between 1992 and 2010 in Kenya. The country‐level mangrove map provides a valuable tool for assessing carbon stocks and visualizing the distribution of BGC. Estimates at the 2.5 m² resolution provide sufficient details for highlighting and prioritizing areas for mangrove conservation and restoration.     

Software for genome mapping by fingerprinting techniques

A genome mapping package has been developed for reading andassembling data from clones analysed by restriction enzyme fragmentationand polyacrylamide gel electrophoresis. The package comprises:data entry; matching; assembly; statistical analysis; modelling.Data entry can be either manual or by a semiautomatic systembased on a scanning densitometer. The primary emphasis in theanalytical routines is on flexibility and interactive convenience,so that the operator has full knowledge of and control overthe growing map, but a variety of automatic options are included.The package continually grows to meet the needs of the Caenorhabditisproject. Received on July 17, 1987; accepted on November 20, 1987     

Small-scale mapping of indeterminate arborescent acroporid coral (Acropora cervicornis) patches

Coral Reefs - Western Atlantic populations of the staghorn coral Acropora cervicornis have drastically declined over the past few decades. Hence, interest in its ecology and spatial extent has...     

New techniques for physical mapping of the human genome.

We describe improvements in techniques and strategies used for making maps of the human genome. The methods currently used are changing and evolving rapidly. Today's techniques can produce ordered arrays of DNA fragments and overlapping sets of DNA clones covering extensive genomic regions, but they are relatively slow and tedious. Methods under development will speed the process considerably. New developments include a range of applications of the polymerase chain reaction, enhanced procedures for high resolution in situ hybridization, and improved methods for generating, manipulating, and cloning large DNA fragments. More detailed genetic and physical maps will be useful for finding genes, including those associated with human diseases, long before the complete DNA sequence of the human genome is available.     

Orthopterans in small steppe patches: an investigation for the best-fit model of the species-area curve and evidences for their non-random distribution in the patches

Distribution of orthopterans were studied in 27 steppe patches in the Buda Hills, Hungary. The smallest patches were about 300 m², the largest ‘continents’ were over 100 000 m². We collected 692 imagoes of 32 species and 1 201 imagoes of 28 species in July 1992 and July 1993, respectively. We found that the best-fit models for the species-area curves were both the power function and exponential models. The multivariate regression model incorporated area and distance from large patches as significant factors in determining the number of species. The correlation analysis revealed that the elevation and the height of grass vegetation also influenced the distribution of species. We applied three methods for testing whether the distribution of orthopterans was random or not. First, we compared the observed species-area curves with the expected curves. Second, we compared the small-to-large and large-to-small cumulative curves. Finally, we compared the observed species-area curves with the rarefaction curves. All three methods for both years showed that the occurrence of orthopterans in the steppe patches was not random. A collection of small islands harboured more orthopteran species than one or two large patches of the same area.     

Ecophysiology of mangroves

Conclusion Mangrove forests are of major ecological and commercial importance, yet the future of these resources is threatened by pollution, development and over-exploitation. There is an urgent need to develop sound management practices based on a functional understanding of the physical and biological processes underlying mangrove ecosystem dynamics. Such biological processes include dispersal (Rabinowitz 1978), herbivory (Smith 1987) and the physiological bases of species interactions and responses to environmental factors. Understanding these processes is essential for the development of more comprehensive and predictive modelling of mangrove ecosystem dynamics than has previously been possible.     

Application of bootstrap techniques to physical mapping

Ordering genetic markers or clones from a genomic library into a physical map is a central problem in genetics. In the presence of errors, there is no efficient algorithm known that solves this problem. Based on a standard heuristic algorithm for it, we present a method to construct a confidence neighborhood for a computed solution. We compute a confidence value for putative local solutions derived from bootstrap replicates of the original solution. In the reliable parts, the confidence neighborhood and the computed solution tend to coincide. In regions that are ill-defined by the data, the neighborhood contains additional reasonable alternatives. This offers the possibility of designing further experiments for the badly defined regions to improve the quality of the physical map. We analyze our approach by a simulation study and by application to a dataset of the genome of the bacterium Xylella fastidiosa.     

Tidal asymmetry in creeks surrounded by saltflats and mangroves with small swamp slopes

Most mangrove swamp/salt flat systems have tidal currents that are ebb dominated, however, some systems show only slight ebb dominance despite having a very large swamp volume relative to the creek volume. Cocoa Ck in northern Australia is such a system. Results are presented from a simple analytical model for flow in Cocoa creek together with detailed water level observations in the swamps. It was found that the primary factor reducing the ebb dominance of this system was the very low slope of the swamp surface. During rising tides, water floods as sheet flow; however, on ebb tides, the surface water slope in the swamp becomes greater than the swamp surface slope, with the result that areas of swamp closest to the main feeder creek (Cocoa Ck) dry before areas furthest from the creek. Thus, about an hour after ebb tide commences, there is a large quantity of water perched on the salt flats/mangroves, tens of centimetres higher than the water in the creek. This water cannot leave the swamp via sheet flow, but must leave through a very small and shallow creek which is also highly constricted by vegetation. This effectively increases the friction on ebb tides and results in a delay in water leaving the swamps and salt flats, reducing any tendency towards ebb dominance.     

Distance learning techniques for ontology similarity measuring and ontology mapping

Recent years, a large amount of ontology learning algorithms have been applied in different disciplines and engineering. The ontology model is presented as a graph and the key of ontology algorithms is similarity measuring between concepts. In the learning frameworks, the information of each ontology vertex is expressed as a vector, thus the similarity measuring can be determined via the distance of the corresponding vector. In this paper, we study how to get an optimal distance function in the ontology setting. The tricks we presented are divided into two parts: first, the ontology distance learning technology in the setting that the ontology data have no labels; then, the distance learning approaches in the setting that the given ontology data are carrying real numbers as their labels. The result data of the four simulation experiments reveal that our new ontology trick has high efficiency and accuracy in ontology similarity measure and ontology mapping in special engineering applications.     

Similarity in occupancy of different-sized forest patches by small mammals on clearcuts: conservation implications for red-backed voles and small mustelids

Many mammalian species decline on forest sites that are harvested by clearcutting because of a loss of food, cover, and other components of stand structure. Small mustelids are impacted negatively as is the southern red-backed vole (Myodes gapperi), a principal prey species, that disappears from clearcuts within a year of harvest. These effects may be potentially ameliorated by aggregated retention harvests that leave unlogged patches on clearcuts. We tested three hypotheses (H) that (H₁) abundance, reproduction, and survival of M. gapperi populations, (H₂) total abundance, species richness, and diversity of the forest-floor small mammal community, and (H₃) the presence of small mustelids would be greater in large than small patches of retention forest on new clearcuts. We measured demographic responses of M. gapperi, total small mammals, and the presence of small mustelids (American marten, Martes americana, and small weasels (Mustela spp.)) from 2014 to 2016 in replicated treatments of four sizes (ha) of retention patches (means of 0.53, 1.50, 4.13, and 18.73) near Elkhart in south-central British Columbia, Canada. Mean abundance, reproduction, and survival attributes of M. gapperi were similar among treatment sites over the 3-year study. Overall mean abundance ranged from 3.5 to 5.3 voles per line in patches while this microtine was extirpated on clearcut sites (i.e., no forest patches). The similarity in population dynamics among the various forest patches across a gradient of increasing patch size of 4.5 to 35.3 times did not support H₁. Mean abundance, species richness, and diversity of total forest-floor small mammals were similar among treatment sites, and hence did not support H₂. Although not formally significant, mean species diversity did show a consistent increase from the largest (0.82) to the smallest (1.11) patch size, owing primarily to the presence of several generalist species such as Neotamias amoenus, Microtus, and Sorex in nearby early successional habitat. Small mustelids were present at similar levels among patch sizes, presumably in response to abundance of small mammal prey, and hence did not support H₃. Although our results were relatively short-term, the detailed assessment of population dynamics of M. gapperi indicated that habitat quality was sufficient to maintain this species regardless of patch sizes, ranging from 0.3 to 20.0 ha. Similarly, the total forest-floor small mammal community and presence of small mustelids also followed this pattern. All sizes of forest patches have conservation value and will help to maintain abundance and diversity of forest mammals, both predator and prey species, on clearcuts. Longer-term studies (e.g., at 5- to 10-year intervals) are essential to determine if our results are sustainable in augmenting forest restoration.

     

New cloning vectors and techniques for easy and rapid restriction mapping

We have modified plasmid, phage lambda and cosmid cloning vectors to be of general use for easily and unambiguously determining restriction maps of recombinant DNA molecules. Each vector is constructed so that it contains the rarely found NotI restriction site joined to a short synthetic linker sequence that is followed by a multiple cloning site. DNA cloned into these vectors may be restriction-mapped by either of two methods. In one technique, the cloned DNA is completely digested with NotI, followed by partial digestion with any other restriction enzyme. After electrophoresis and transfer to a nylon membrane, the fragments are hybridized to a labeled probe complementary to the NotI linker. In the second technique, referred to as recession hybridization detection, cloned DNA is digested with NotI and then briefly treated with exonuclease III to recess the 3' ends. After hybridizing a labeled complementary oligodeoxynucleotide to the single-stranded 5' end containing the linker sequence, the DNA is partially digested with another restriction enzyme, electrophoresed and the gel is exposed to x-ray film. With either method the size of each labeled fragment corresponds directly to the distance that a restriction site is located from the NotI linker terminus. Methods for obtaining partial restriction enzyme digests have been devised so that as many as 20 different enzymes may be conveniently mapped on a single gel in little more than a day. The vectors and techniques described may also be adapted to automated or semi-automated devices that read fragment lengths and calculate the resulting restriction map.(ABSTRACT TRUNCATED AT 250 WORDS)     

Viability of ecological processes in small Afromontane forest patches in South Africa

Abstract The conservation of biodiversity is dependent on protecting ecosystem‐level processes. We investigated the effects of fragment size and habitat edge on the relative functioning of three ecological processes – decomposition, predation and regeneration of trees – in small Afromontane forests in KwaZulu‐Natal, South Africa. Ten sampling stations were placed in each of four forest categories: the interior of three large indigenous forest fragments (100 m from the edge), the edges of these large fragments, 10 small indigenous fragments (<1 ha) and 10 small exotic woodlands (<0.5 ha). Fragment size and edge effects did not affect the abundance of the amphipod Talitriator africana, a litter decomposer, and overall dung beetle abundance and species richness significantly. Bird egg predation was marginally greater at large patch edges compared with the other forest categories, while seed predation did not differ among forest categories. Tree seedling assemblage composition did not differ significantly among large patch interiors and edges, and small indigenous fragments. Sapling and canopy assemblage composition each differed significantly among these three indigenous forest categories. Thus, while tree recruitment was not negatively affected by patch size or distance from the edge, conditions in small fragments and at edges appear to affect the composition of advanced tree regeneration. These ecological processes in Afromontane forests appear to be resilient to fragmentation effects. We speculate that this is because the organisms in these forests have evolved under fragmented conditions. Repeated extreme changes in climate and vegetation over the Pleistocene have acted as significant distribution and ecological extinction filters on these southern hemisphere forest biota, resulting in fauna and flora that are potentially resilient to contemporary fragmentation effects. We argue that because small patches and habitat edges appear to be ecologically viable they should be included in future conservation decisions.     

Synchrony in small mammal populations of montane forest patches in southern India

1. Small mammal populations were studied in montane evergreen forests in the Nilgiris, southern India, using live-trapping from January 1994 to September 1996. Two sites were selected, one with a single large forest patch and adjoining plantations, and the other with several small forest patches separated by grassland.
2. Nine species were recorded, of which eight were trapped in the forest patches, two in the grasslands and five in plantations. Rattus rattus was the most abundant species (2–36 individuals ha⁻¹) followed by Suncus montanus (0–11 individuals ha⁻¹). Densities of seven other species recorded were very low.
3. Synchrony in various population variables – density, biomass, mean weight, density of adults and adult females, and proportion of adults, adult females and sub-adults – was examined for Rattus rattus populations in the forest patches and plantations. Density and biomass were studied in seven other species recorded at these sites. Spearman's rank order correlation was used as a measure of synchrony between the population variables.
4. Within-site synchrony was higher than between-site synchrony in population characters. Synchrony was also higher between plots within the unfragmented site than they were between plots in the fragmented site. Relatively high synchrony in proportions of adults, adult females and juveniles in the forest patches implied that breeding is probably influenced by climate and food availability, which are seasonal in this habitat.
5. Given the small patch sizes (≈1–10 ha) and low population sizes, asynchrony is likely to be an outcome of demographic and environmental stochasticity, and low dispersal rates may impede establishment of synchrony.     

DNA fiber mapping techniques for the assembly of high-resolution physical maps.

High-resolution physical maps are indispensable for directed sequencing projects or the finishing stages of shotgun sequencing projects. These maps are also critical for the positional cloning of disease genes and genetic elements that regulate gene expression. Typically, physical maps are based on ordered sets of large insert DNA clones from cosmid, P1/PAC/BAC, or yeast artificial chromosome (YAC) libraries. Recent technical developments provide detailed information about overlaps or gaps between clones and precisely locate the position of sequence tagged sites or expressed sequences, and thus support efforts to determine the complete sequence of the human genome and model organisms. Assembly of physical maps is greatly facilitated by hybridization of non-isotopically labeled DNA probes onto DNA molecules that were released from interphase cell nuclei or recombinant DNA clones, stretched to some extent and then immobilized on a solid support. The bound DNA, collectively called "DNA fibers," may consist of single DNA molecules in some experiments or bundles of chromatin fibers in others. Once released from the interphase nuclei, the DNA fibers become more accessible to probes and detection reagents. Hybridization efficiency is therefore increased, allowing the detection of DNA targets as small as a few hundred base pairs. This review summarizes different approaches to DNA fiber mapping and discusses the detection sensitivity and mapping accuracy as well as recent achievements in mapping expressed sequence tags and DNA replication sites.     

Abundance and distribution of small infauna in mangroves of Missionary Bay, north Queensland, Australia

To assess the occurrence, spatial distribution and species composition of small infauna on a mangrove shore, core samples were taken along a transect in Missionary Bay at Hinchinbrook Island, north-east Australia. Three sites were arranged within the mangrove forest and one site was located in an adjacent mudflat. The sites were surveyed four times between November 1988 and October 1989. Based on the records from all samples and sites, 39 taxa were identified. Diversity (H') ranged from 1.18 to 2.38. Overall, total abundances of small infauna (retained on a 0.25 mm sieve) reached a mean value of 5,477 ind.m-2, with little variation throughout the transect or over time. Species numbers and diversity were higher in the mudflat than at the mangrove sites. The taxonomic composition changed between the mangrove forest and the mudflat: Oligochaeta were more abundant in mangrove sediments, whereas Polychaeta dominated in the mudflat. Of the polychaetes, Capitellidae were almost restricted to the mangrove sites, Sabellidae were recorded frequently at all sites, and Sigambra parva and Myriochele sp. were confined to the mudflat and the mangrove fringe. These species accounted also for dissimilarities between sites. Multivariate analyses showed a distinct assemblage at the mudflat compared to the mangrove sites. This survey showed that small infauna is an abundant component of mangrove sediments, which has been previously underestimated.