Chimpanzee (Pan troglodytes verus) Density and Environmental Gradients at Their Biogeographical Range Edge

International Journal of Primatology - Identifying ecological gradients at the range edge of a species is an essential step in revealing the underlying mechanisms and constraints that limit the...     

Assessing Modes of Speciation: Range Asymmetry and Biogeographical Congruence

Lynch [1989, in "Speciation and Its Consequences" (D. Otte and J. A. Endler, Eds.), pp. 527–553, Sinauer, Sunderland, MA, proposed a methodology for assessing the frequency of occurrence of various modes of initiating species formation, using a combination of phylogenetic relationships and relative size of geographic ranges for sister species and sister groups. Historical biogeography provides an alternative criterion for assessing modes of species formation. Species whose distributions conform to a general (replicated in multiple clades) pattern of area relationships are deemed to be the result of vicariance (including microvicariance) regardless of the details of current geographic range. Species exhibiting unique biogeographic distributions are the result of peripheral isolates speciation and postspeciation dispersal. Lineage duplications indicate sympatric speciation. An empirical assessment of this alternative approach was performed using the most recent phylogenetic trees and geographical distribution data on the Mesoamerican poeciliid fish comprising the genera Xiphophorus and Heterandria . The single area cladogram produced by secondary Brooks Parsimony Analysis indicates 3 vicariant events (accounting for seven extant species and the common ancestor of the northern swordtails, which are not further analyzed) and at least 13 episodes of peripheral isolates speciation. Two of the 10 areas considered in previous analyses are vicariant areas of endemism, 1 is historically unique due to a single episode of peripheral isolates speciation, and the remaining 7 have reticulated histories of speciation. The results corroborate inferences of speciation modes made by Lynch for the same data.     

Quantification of Loss and Change in Floridian Reef Coral Populations

Six coral reef locations between Miami and Key West were markedwith stainless steel stakes and rephotographed periodicallybetween 1984 and 1991. The monitored areas included two photostationsin the Looe Key National Marine Sanctuary, two photostationsin the Key Largo National Marine Sanctuary, and two photostationsin the Biscayne National Park. Stations were monitored for speciesnumber, percent cover, and species diversity of the scleractinianand hydrozoan stony corals. Monitoring began in 1984 for photostationsin the National Marine Sanctuaries and in 1989 for stationsin the National Park. All six areas lost coral species between the initial surveyyear and 1991. Survey areas lost between one and four species;these losses constituted between 13% and 29% of their speciesrichness. Five of the six areas lost live coral cover. Basedupon photographs taken repeatedly at these locations, net lossesranged between 7.3% and 43.9%. In the one station showing anincrease in coral cover, the increase was only for the canopybranches of Acropora palmata; understory branches of this samespecies lost surface area at the same rate as canopy branchesgained area. For most of the common species, there was a reductionin the total number of living colonies in the community, anda diminution in the number of large, mature colonies. Throughoutthe study period, there was no recruitment to any of the photostationsby any of the massive frame building coral species. Mortality of this magnitude is often associated with hurricanedamage, but in this survey the losses occurred during a periodwithout catastrophic storms. Sources of mortality identifiablein the photographs include (1) black band disease and (2) "bleaching"other potential sources of mortality are also considered. Weconclude, for our survey areas, that loss rates of this magnitudecannot be sustained for protracted periods if the coral communityis to persist in a configuration resembling historical coralreef community structure in the Florida Keys.     

Long Range Linkage Disequilibrium across the Human Genome

Long-range linkage disequilibria (LRLD) between sites that are widely separated on chromosomes may suggest that population admixture, epistatic selection, or other evolutionary forces are at work. We quantified patterns of LRLD on a chromosome-wide level in the YRI population of the HapMap dataset of single nucleotide polymorphisms (SNPs). We calculated the disequilibrium between all pairs of SNPs on each chromosome (a total of >2×10¹¹ values) and evaluated significance of overall disequilibrium using randomization. The results show an excess of associations between pairs of distant sites (separated by >0.25 cM) on all of the 22 autosomes. We discuss possible explanations for this observation.     

Length-Based Assessment of Coral Reef Fish Populations in the Main and Northwestern Hawaiian Islands

The coral reef fish community of Hawaii is composed of hundreds of species, supports a multimillion dollar fishing and tourism industry, and is of great cultural importance to the local population. However, a major stock assessment of Hawaiian coral reef fish populations has not yet been conducted. Here we used the robust indicator variable “average length in the exploited phase of the population (L¯)”, estimated from size composition data from commercial fisheries trip reports and fishery-independent diver surveys, to evaluate exploitation rates for 19 Hawaiian reef fishes. By and large, the average lengths obtained from diver surveys agreed well with those from commercial data. We used the estimated exploitation rates coupled with life history parameters synthesized from the literature to parameterize a numerical population model and generate stock sustainability metrics such as spawning potential ratios (SPR). We found good agreement between predicted average lengths in an unfished population (from our population model) and those observed from diver surveys in the largely unexploited Northwestern Hawaiian Islands. Of 19 exploited reef fish species assessed in the main Hawaiian Islands, 9 had SPRs close to or below the 30% overfishing threshold. In general, longer-lived species such as surgeonfishes, the redlip parrotfish (Scarus rubroviolaceus), and the gray snapper (Aprion virescens) had the lowest SPRs, while short-lived species such as goatfishes and jacks, as well as two invasive species (Lutjanus kasmira and Cephalopholis argus), had SPRs above the 30% threshold.     

Biogeographical patterns of abundant and rare bacterial biospheres in paddy soils across East Asia

Soil bacterial communities play fundamental roles in ecosystem functioning and often display a skewed distribution of abundant and rare taxa. So far, relatively little is known about the biogeographical patterns and mechanisms structuring the assembly of abundant and rare biospheres of soil bacterial communities. Here, we studied the geographical distribution of different bacterial sub-communities by examining the relative influence of environmental selection and dispersal limitation on taxa distributions in paddy soils across East Asia. Our results indicated that the geographical patterns of four different bacterial sub-communities consistently displayed significant distance–decay relationships (DDRs). In addition, we found niche breadth and dispersal rates to significantly explain differences in community assembly of abundant and rare taxa, directly affecting the strength of DDRs. While conditionally rare and abundant taxa displayed the strongest DDR due to higher environmental filtering and dispersal limitation, moderate taxa sub-communities had the weakest DDR due to greater environmental tolerance and dispersal rate. Random forest models indicated that soil pH (9.13%–49.78%) and average annual air temperature (16.59%–46.49%) were the most important predictors of the variation in the bacterial community. This study advances our understanding of the intrinsic links between fundamental ecological processes and microbial biogeographical patterns in paddy soils.     

Variation in Siderophore Biosynthetic Gene Distribution and Production across Environmental and Faecal Populations of Escherichia coli

Iron is essential for Escherichia coli growth and survival in the host and the external environment, but its availability is generally low due to the poor solubility of its ferric form in aqueous environments and the presence of iron-withholding proteins in the host. Most E. coli can increase access to iron by excreting siderophores such as enterobactin, which have a very strong affinity for Fe³⁺. A smaller proportion of isolates can generate up to 3 additional siderophores linked with pathogenesis; aerobactin, salmochelin, and yersiniabactin. However, non-pathogenic E. coli are also able to synthesise these virulence-associated siderophores. This raises questions about their role in the ecology of E. coli, beyond virulence, and whether specific siderophores might be linked with persistence in the external environment. Under the assumption that selection favours phenotypes that confer a fitness advantage, we compared siderophore production and gene distribution in E. coli isolated either from agricultural plants or the faeces of healthy mammals. This population-level comparison has revealed that under iron limiting growth conditions plant-associated isolates produced lower amounts of siderophores than faecal isolates. Additionally, multiplex PCR showed that environmental isolates were less likely to contain loci associated with aerobactin and yersiniabactin synthesis. Although aerobactin was linked with strong siderophore excretion, a significant difference in production was still observed between plant and faecal isolates when the analysis was restricted to strains only able to synthesise enterobactin. This finding suggests that the regulatory response to iron limitation may be an important trait associated with adaptation to the non-host environment. Our findings are consistent with the hypothesis that the ability to produce multiple siderophores facilitates E. coli gut colonisation and plays an important role in E. coli commensalism.     

Biogeography and Change among Regional Coral Communities across the Western Indian Ocean

Coral reefs are biodiverse ecosystems structured by abiotic and biotic factors operating across many spatial scales. Regional-scale interactions between climate change, biogeography and fisheries management remain poorly understood. Here, we evaluated large-scale patterns of coral communities in the western Indian Ocean after a major coral bleaching event in 1998. We surveyed 291 coral reef sites in 11 countries and over 30° of latitude between 2004 and 2011 to evaluate variations in coral communities post 1998 across gradients in latitude, mainland-island geography and fisheries management. We used linear mixed-effect hierarchical models to assess total coral cover, the abundance of four major coral families (acroporids, faviids, pocilloporids and poritiids), coral genus richness and diversity, and the bleaching susceptibility of the coral communities. We found strong latitudinal and geographic gradients in coral community structure and composition that supports the presence of a high coral cover and diversity area that harbours temperature-sensitive taxa in the northern Mozambique Channel between Tanzania, northern Mozambique and northern Madagascar. Coral communities in the more northern latitudes of Kenya, Seychelles and the Maldives were generally composed of fewer bleaching-tolerant coral taxa and with reduced richness and diversity. There was also evidence for continued declines in the abundance of temperature-sensitive taxa and community change after 2004. While there are limitations of our regional dataset in terms of spatial and temporal replication, these patterns suggest that large-scale interactions between biogeographic factors and strong temperature anomalies influence coral communities while smaller-scale factors, such as the effect of fisheries closures, were weak. The northern Mozambique Channel, while not immune to temperature disturbances, shows continued signs of resistance to climate disturbances and remains a priority for future regional conservation and management actions.     

Utilization of Mucus from the Coral Acropora palmata by the Pathogen Serratia marcescens and by Environmental and Coral Commensal Bacteria

In recent years, diseases of corals caused by opportunistic pathogens have become widespread. How opportunistic pathogens establish on coral surfaces, interact with native microbiota, and cause disease is not yet clear. This study compared the utilization of coral mucus by coral-associated commensal bacteria (“Photobacterium mandapamensis” and Halomonas meridiana) and by opportunistic Serratia marcescens pathogens. S. marcescens PDL100 (a pathogen associated with white pox disease of Acroporid corals) grew to higher population densities on components of mucus from the host coral. In an in vitro coculture on mucus from Acropora palmata, S. marcescens PDL100 isolates outgrew coral isolates. The white pox pathogen did not differ from other bacteria in growth on mucus from a nonhost coral, Montastraea faveolata. The ability of S. marcescens to cause disease in acroporid corals may be due, at least in part, to the ability of strain PDL100 to build to higher population numbers within the mucus surface layer of its acroporid host. During growth on mucus from A. palmata, similar glycosidase activities were present in coral commensal bacteria, in S. marcescens PDL100, and in environmental and human isolates of S. marcescens. The temporal regulation of these activities during growth on mucus, however, was distinct in the isolates. During early stages of growth on mucus, enzymatic activities in S. marcescens PDL100 were most similar to those in coral commensals. After overnight incubation on mucus, enzymatic activities in a white pox pathogen were most similar to those in pathogenic Serratia strains isolated from human mucosal surfaces.Serratia is a gammaproteobacterium frequently isolated from waters, plants, and animals (7). Some isolates of Serratia are well-characterized symbionts of invertebrates. Serratia marcescens and Serratia liquefaciens have been identified as vertically transmitted symbionts of the sugar beet maggot (9). Serratia colonizes male and female reproductive tracts of the maggots, eggs, and pharyngeal filter. There, the bacteria are hypothesized to aid in metamorphosis by digesting chitinous puparial walls (9). In the gut of another insect, the diamondback moth, strains of S. marcescens appear to live as commensals capable of modestly (5 to 8%) increasing growth rates of the host (8). Serratia strains have also been isolated from feces and cloacal swabs from clinically normal captive birds, but not from organs or carcasses of sick or diseased animals housed within the same facility (3, 20). Serratia spp. have also been linked to diseases of invertebrate animals and their larvae (for reviews, see references 7, 15, and 21). To cause diseases in nematodes and flies, S. marcescens first colonizes the intestines, degrades cells of the alimentary tract and then spreads to other organs (14, 21). There are, however, exceptions to this mode of infection. Serratia entomophila, the causal agent of amber disease in grubs, grows within the alimentary tract of the animal to >10⁶ CFU. However, bacteria neither attach to nor colonize surfaces of the gut; rather, they adhere to gut contents (10) and cause the appearance of signs by producing the Sep toxin that inhibits accumulation of the insect''s digestive serine proteases and disrupts the cytoskeletal network (6). It appears, therefore, that various isolates of Serratia are capable of entering into a full range of interactions (from mutualistic to commensal to pathogenic) with their animal hosts (for reviews, see references 7, 15, and 21).A strain of S. marcescens, PDL100, was shown to be associated with white pox disease of the threatened Caribbean coral Acropora palmata (22, 27). White pox disease results in coral tissue necrosis, exposing carbonate skeleton at a rate of 2.5 cm² day⁻¹ (22). It is not yet clear how S. marcescens PDL100 colonizes and infects corals. It is likely that to cause disease, the pathogen first needs to colonize and establish within the coral surface mucus layer.The coral surface mucus layer contains polymers of mixed origin. Coral mucus is made in the mucocytes of the polyp, where the photosynthate produced by the coral symbiotic dinoflagellate Symbiodinium spp. is converted into polymers that are excreted onto the coral surface (for a review, see reference 2). A glycoprotein is the major component of coral mucus from both hard and soft corals (16, 17, 19). The composition of the glycoprotein differs among coral species (4, 17). The mucus polymer of Acropora formosa, for example, contains 36 to 38% of neutral sugars, 18 to 22% of amino sugars, and 19 to 30% of amino acids; lipids make up 4.2% of the polymer (17). In the mucus of A. formosa, the oligosaccharide decorations (two to four sugar residues long) are attached to the polypeptide backbone by an O-glycosidic link to serine or threonine through the carbon 1 of mannose (16). The glycoproteins from A. formosa and Pseudopterogorgia americana corals contain terminal arabinose residues linked by a β1→2 or β1→3 bond. In the mucus of acroporid corals, arabinose, N-acetyl-glucosamine, mannose, glucose, galactose, N-acetyl-galactosamine, and fucose were the major sugars; serine and threonine were the major amino acids (4, 17). The elucidation of the chemical structure of coral mucus is complicated by the fact that the mucus contains excretions of coral mucocytes, extracellular substances produced by the associated microbiota as well as oligomers that may result from the degradation of these polymers (for reviews, see references 2 and 24).In this study, we tested the hypothesis that S. marcescens PDL100 is capable of a more extensive utilization of A. palmata mucus than other environmental or pathogenic isolates of S. marcescens. This hypothesis is based on the recent discoveries that pathogenic and commensal host-associated bacteria differ in their patterns of carbon source utilization during growth on components of the mucus that lines host surfaces (5, 26). These different strategies of mucus utilization may allow pathogenic bacteria to outcompete native residents and establish within the host''s mucosa (5, 13, 26). To test this hypothesis, growth of the strain PDL100 on coral mucus and enzymatic activities induced during growth on mucus were assayed and compared to those of pathogenic and environmental isolates of S. marcescens and three native coral-associated bacteria.     

Quantifying Spatial Genetic Structuring in Mesophotic Populations of the Precious Coral Corallium rubrum

While shallow water red coral populations have been overharvested in the past, nowadays, commercial harvesting shifted its pressure on mesophotic organisms. An understanding of red coral population structure, particularly larval dispersal patterns and connectivity among harvested populations is paramount to the viability of the species. In order to determine patterns of genetic spatial structuring of deep water Corallium rubrum populations, for the first time, colonies found between 58–118 m depth within the Tyrrhenian Sea were collected and analyzed. Ten microsatellite loci and two regions of mitochondrial DNA (mtMSH and mtC) were used to quantify patterns of genetic diversity within populations and to define population structuring at spatial scales from tens of metres to hundreds of kilometres. Microsatellites showed heterozygote deficiencies in all populations. Significant levels of genetic differentiation were observed at all investigated spatial scales, suggesting that populations are likely to be isolated. This differentiation may by the results of biological interactions, occurring within a small spatial scale and/or abiotic factors acting at a larger scale. Mitochondrial markers revealed significant genetic structuring at spatial scales greater then 100 km showing the occurrence of a barrier to gene flow between northern and southern Tyrrhenian populations. These findings provide support for the establishment of marine protected areas in the deep sea and off-shore reefs, in order to effectively maintain genetic diversity of mesophotic red coral populations.     

Gene Flow and Genetic Diversity of a Broadcast-Spawning Coral in Northern Peripheral Populations

Recently, reef-building coral populations have been decreasing worldwide due to various disturbances. Population genetic studies are helpful for estimating the genetic connectivity among populations of marine sessile organisms with metapopulation structures such as corals. Moreover, the relationship between latitude and genetic diversity is informative when evaluating the fragility of populations. In this study, using highly variable markers, we examined the population genetics of the broadcast-spawning coral Acropora digitifera at 19 sites in seven regions along the 1,000 km long island chain of Nansei Islands, Japan. This area includes both subtropical and temperate habitats. Thus, the coral populations around the Nansei Islands in Japan are northern peripheral populations that would be subjected to environmental stresses different from those in tropical areas. The existence of high genetic connectivity across this large geographic area was suggested for all sites (F _ST≤0.033) although small but significant genetic differentiation was detected among populations in geographically close sites and regions. In addition, A. digitifera appears to be distributed throughout the Nansei Islands without losing genetic diversity. Therefore, A. digitifera populations in the Nansei Islands may be able to recover relatively rapidly even when high disturbances of coral communities occur locally if populations on other reefs are properly maintained.     

Leveraging Genetic Variability across Populations for the Identification of Causal Variants

Genome-wide association studies have been performed extensively in the last few years, resulting in many new discoveries of genomic regions that are associated with complex traits. It is often the case that a SNP found to be associated with the condition is not the causal SNP, but a proxy to it as a result of linkage disequilibrium. For the identification of the actual causal SNP, fine-mapping follow-up is performed, either with the use of dense genotyping or by sequencing of the region. In either case, if the causal SNP is in high linkage disequilibrium with other SNPs, the fine-mapping procedure will require a very large sample size for the identification of the causal SNP. Here, we show that by leveraging genetic variability across populations, we significantly increase the localization success rate (LSR) for a causal SNP in a follow-up study that involves multiple populations as compared to a study that involves only one population. Thus, the average power for detection of the causal variant will be higher in a joint analysis than that in studies in which only one population is analyzed at a time. On the basis of this observation, we developed a framework to efficiently search for a follow-up study design: our framework searches for the best combination of populations from a pool of available populations to maximize the LSR for detection of a causal variant. This framework and its accompanying software can be used to considerably enhance the power of fine-mapping studies.     

Generalized Maximum Range Tests for Pairwise Comparisons of Several Populations

A multiple comparison procedure (MCP) is proposed for the comparison of all pairs of several independent samples. This MCP is essentially the closed procedure with union-intersection tests based on given single tests Q_ij for the minimal hypotheses H_ij. In such cases where the α-levels of the nominal tests associated with the MCP can be exhausted, this MCP has a uniformly higher all pair power than any refined Bonferroni test using the same Q_ij. Two different general algorithms are described in section 3. A probability inequality for ranges of i.i.d. random variables which is useful for some algorithms is proved in section 4. Section 5 contains the application to independent normally distributed estimates and section 6 the comparisons of polynomial distributions by multivariate ranges. Further applications are possible. Tables of the 0.05-bounds for the tests of section 5 and 6 are enclosed.     

Chimerism in Wild Adult Populations of the Broadcast Spawning Coral Acropora millepora on the Great Barrier Reef

Background

Chimeras are organisms containing tissues or cells of two or more genetically distinct individuals, and are known to exist in at least nine phyla of protists, plants, and animals. Although widespread and common in marine invertebrates, the extent of chimerism in wild populations of reef corals is unknown.

Methodology/Principal Findings

The extent of chimerism was explored within two populations of a common coral, Acropora millepora, on the Great Barrier Reef, Australia, by using up to 12 polymorphic DNA microsatellite loci. At least 2% and 5% of Magnetic Island and Pelorus Island populations of A. millepora, respectively, were found to be chimeras (3% overall), based on conservative estimates. A slightly less conservative estimate indicated that 5% of colonies in each population were chimeras. These values are likely to be vast underestimates of the true extent of chimerism, as our sampling protocol was restricted to a maximum of eight branches per colony, while most colonies consist of hundreds of branches. Genotypes within chimeric corals showed high relatedness, indicating that genetic similarity is a prerequisite for long-term acceptance of non-self genotypes within coral colonies.

Conclusions/Significance

While some brooding corals have been shown to form genetic chimeras in their early life history stages under experimental conditions, this study provides the first genetic evidence of the occurrence of coral chimeras in the wild and of chimerism in a broadcast spawning species. We hypothesize that chimerism is more widespread in corals than previously thought, and suggest that this has important implications for their resilience, potentially enhancing their capacity to compete for space and respond to stressors such as pathogen infection.     

Additive Partitioning of Coral Reef Fish Diversity across Hierarchical Spatial Scales throughout the Caribbean

There is an increasing need to examine regional patterns of diversity in coral-reef systems since their biodiversity is declining globally. In this sense, additive partitioning might be useful since it quantifies the contribution of alpha and beta to total diversity across different scales. We applied this approach using an unbalanced design across four hierarchical scales (80 sites, 22 subregions, six ecoregions, and the Caribbean basin). Reef-fish species were compiled from the Reef Environmental Education Foundation (REEF) database and distributions were confirmed with published data. Permutation tests were used to compare observed values to those expected by chance. The primary objective was to identify patterns of reef-fish diversity across multiple spatial scales under different scenarios, examining factors such as fisheries and demographic connectivity. Total diversity at the Caribbean scale was attributed to β-diversity (nearly 62% of the species), with the highest β-diversity at the site scale. α¯-diversity was higher than expected by chance in all scenarios and at all studied scales. This suggests that fish assemblages are more homogenous than expected, particularly at the ecoregion scale. Within each ecoregion, diversity was mainly attributed to alpha, except for the Southern ecoregion where there was a greater difference in species among sites. β-components were lower than expected in all ecoregions, indicating that fishes within each ecoregion are a subsample of the same species pool. The scenario involving the effects of fisheries showed a shift in dominance for β-diversity from regions to subregions, with no major changes to the diversity patterns. In contrast, demographic connectivity partially explained the diversity pattern. β-components were low within connectivity regions and higher than expected by chance when comparing between them. Our results highlight the importance of ecoregions as a spatial scale to conserve local and regional coral reef-fish diversity.     

Reef-Fidelity and Migration of Tiger Sharks,Galeocerdo cuvier,across the Coral Sea

Knowledge of the habitat use and migration patterns of large sharks is important for assessing the effectiveness of large predator Marine Protected Areas (MPAs), vulnerability to fisheries and environmental influences, and management of shark–human interactions. Here we compare movement, reef-fidelity, and ocean migration for tiger sharks, Galeocerdo cuvier, across the Coral Sea, with an emphasis on New Caledonia. Thirty-three tiger sharks (1.54 to 3.9 m total length) were tagged with passive acoustic transmitters and their localised movements monitored on receiver arrays in New Caledonia, the Chesterfield and Lord Howe Islands in the Coral Sea, and the east coast of Queensland, Australia. Satellite tags were also used to determine habitat use and movements among habitats across the Coral Sea. Sub-adults and one male adult tiger shark displayed year-round residency in the Chesterfields with two females tagged in the Chesterfields and detected on the Great Barrier Reef, Australia, after 591 and 842 days respectively. In coastal barrier reefs, tiger sharks were transient at acoustic arrays and each individual demonstrated a unique pattern of occurrence. From 2009 to 2013, fourteen sharks with satellite and acoustic tags undertook wide-ranging movements up to 1114 km across the Coral Sea with eight detected back on acoustic arrays up to 405 days after being tagged. Tiger sharks dove 1136 m and utilised three-dimensional activity spaces averaged at 2360 km³. The Chesterfield Islands appear to be important habitat for sub-adults and adult male tiger sharks. Management strategies need to consider the wide-ranging movements of large (sub-adult and adult) male and female tiger sharks at the individual level, whereas fidelity to specific coastal reefs may be consistent across groups of individuals. Coastal barrier reef MPAs, however, only afford brief protection for large tiger sharks, therefore determining the importance of other oceanic Coral Sea reefs should be a priority for future research.