Intraspecific genetic differentiation of Leporinus friderici (Anostomidae, Pisces) in French Guiana and Brazil: a genetic approach to the refuge theory

A genetic study was carried out on a neotropical fish species to illustrate the refuge theory, whose main principles are summarized. The geographical structure of the anostomid species Leporinus friderici was analysed in French Guiana and Brazil by horizontal starch gel electrophoresis. Fifteen enzymatic systems corresponding to 21 loci were studied, revealing the following particularities: (1) specimens of fish from six independent coastal rivers of French Guiana form two groups geographically situated on either side of the Kourou River; (2) two alleles can serve as geographic markers, Ldh2 ( l30 ) showing an affinity between the populations in eastern French Guiana and Brazil, and Me 1 ( 300 ) being specific to the west.
These observations are probably related to the refuges that were formed in the Quaternary in South America, especially on the Guiana Shield. We consider that the populations of French Guiana are separated into two groups at the boundary between the two migratory flows, one arising in the west from the refuge of the Guiana Shield and the other in the east from a nearby undetermined Amazonian refuge.     

Genetic variation and geographical structure of five mouse-sized opossums (Marsupialia, Didelphidae) throughout the Guiana Region

Aim and location To study the patterns of genetic variation and geographical structure of five forest‐dwelling didelphid species distributed throughout the Guiana Region (Marmosops parvidens, M. pinheiroi, Monodelphis brevicaudata, Marmosa murina, Micoureus demerarae) and place the results for wide‐ranging species (M. murina, M. demerarae) in the broader geographical context of the rest of the taxon ranges based on published data. Methods Variation in the mitochondrial cytochrome b gene were analysed in order to assess intra‐specific sequence divergence as well as haplotypic and nucleotide diversity among populations. Relationships between haplotypes were inferred by cladistic (maximum parsimony) and probabilistic (maximum likelihood) approaches, allowing comparisons between tree topologies and patterns of populations geographical distribution. Results Phylogenetic analysis of the Guiana Region populations suggest the lack of common patterns of geographical structure among mouse‐sized opossums except for both Marmosops species. Marmosops parvidens and M. pinheiroi showed individuals from Surinam strongly related with those from Guyana, and haplotypes from French Guiana having a basal position. Concerning Micoureus demerarae, haplotypes from Venezuela were positioned as ancestral, in contrast with Monodelphis brevicaudata, whose French Guiana haplotypes were clustered in a basal position. No evidence of geographical structure was observed for Marmosa murina. Genetic variation within Guiana Region populations fluctuated between 1% for M. murina and 7% in the case of M. brevicaudata. Regarding the widely distributed species, phylogeographical structure at the scale of the Amazon Basin suggests that Guiana Region populations are the sister group of south‐eastern Amazonian and Atlantic Forest populations, thus resulting in an eastern clade well separated from the western Amazonian regions. Main conclusions Monophyly of mouse‐sized opossums haplotypes over the Guiana Region confirms the presence of a well‐differentiated zoogeographical area relative to other Amazonia bioregions. Low genetic diversity among Guiana Region samples suggests a relatively recent origin of populations dating from later Miocene and Pleistocene periods. Moreover, nucleotide and haplotypic diversity values suggest an evolutionary scenario of rapid population growth and dispersal over the Guiana territory, from an ancestral population with small effective size. Dispersal events – rather than vicariance – seem to be responsible for the present genetic and phylogeographical patterns observed in the Guiana Region.     

Captive‐born intergeneric hybrid of a Guiana and bottlenose dolphin: Sotalia guianensis×Tursiops truncatus

Bottlenose dolphins (Tursiops truncatus) and Guiana dolphin (Sotalia guianensis) live in sympatry along the Caribbean Coast of Central and South America and social interactions between these species have been described in the Caribbean Coast of Costa Rica, including sexual encounters. Here we examine and document the only known hybridization event between a male Guiana dolphin and a female bottlenose dolphin, in captivity at Oceanario Islas del Rosario (Colombian Caribbean), using photographic and genetic evidence from mitochondrial DNA markers and nuclear autosomal introns. Zoo Biol 29:647–657, 2010. © 2009 Wiley‐Liss, Inc.     

Characterization of polymorphic microsatellite markers for Microcyclus ulei,causal agent of South American leaf blight of rubber trees

South American leaf blight caused by the ascomycete Microcyclus ulei is the most harmful disease of the rubber tree in Latin America and a potential threat to Asiatic and African natural rubber production. Until now, the variability of this fungus was assessed through observation of pathogenicity of isolates on a range of rubber tree clones with known resistance reactions. The present study describes the process used to design 11 microsatellite markers and evaluates their usefulness in detecting genetic polymorphism. Nine of these markers were polymorphic among six isolates from Brazil (with two to three alleles per locus) and five markers were polymorphic among four isolates from French Guiana (with two to four alleles per locus).     

Polymorphic microsatellites for the study of fragmented populations of Pitcairnia geyskesii L. B. Smith (Bromeliaceae), a specific saxicolous species of inselbergs in French Guiana

Pitcairnia geyskesii is a saxicolous bromeliad endemic to the granitic inselbergs of French Guiana and Surinam. Seven polymorphic microsatellite markers were characterized to investigate the polymorphism among individuals sampled on five inselbergs in French Guiana. The total number of alleles per locus varied from four to 14. Mean observed heterozygosities at each microsatellite locus ranged from 0.114 to 0.629. This set of microsatellites offers an efficient tool for more detailed investigations on the genetic structure of fragmented populations living on such a singular and insular habitat within tropical rainforest.     

Development and characterization of microsatellite markers for a monoecious Ficus species,Ficus insipida,and cross‐species amplification among different sections of Ficus

The animal‐mediated pollination and seed‐dispersal mutualisms of Ficus species give them key roles in tropical ecosystems, but may make them vulnerable to habitat fragmentation. The development of highly polymorphic markers is needed to analyse their genetic diversity and investigate the effects of fragmentation on gene flow. Of thirteen microsatellite loci isolated from Ficus insipida, a monoecious species in French Guiana, eleven were polymorphic (two to six alleles each). High levels of variation were found among loci; expected heterozygosities ranged from 0.151 to 0.715. All markers revealed a broad cross‐species affinity when tested in 23 other Ficus species.     

Current genetic differentiation of Coffea canephora Pierre ex A. Froehn in the Guineo-Congolian African zone: cumulative impact of ancient climatic changes and recent human activities

Background  

Among Coffea species, C. canephora has the widest natural distribution area in tropical African forests. It represents a good model for analyzing the geographical distribution of diversity in relation to locations proposed as part of the "refuge theory". In this study, we used both microsatellite (simple sequence repeat, SSR) and restriction fragment length polymorphism (RFLP) markers to investigate the genetic variation pattern of C. canephora in the Guineo-Congolean distribution zone.     

A survey of adult anophelines in French Guiana: enhanced descriptions of species distribution and biting responses

In French Guiana, Anopheles darlingi is considered the main malaria vector. However, several reports have hypothesized the implication of other anopheline species in malaria transmission for the territory. Data on the ecology of these other potential vectors is rare or even unexplored in French Guiana. The aim of this study was to describe the biting habits of several anopheline species in multiple localities in French Guiana. Six sampling sites yielded 1,083 anopheline adults. Results indicated the presence of An. darlingi in all study locations and it was the only species to be collected inside villages. Other anophelines collected included An. aquasalis, An. braziliensis, An. intermedius, An. mediopunctatus, An. nuneztovari, An. oswaldoi, and An. triannulatus, all of which were associated with open areas and forests. The environment and time, at which biting behavior was recorded, varied for each species. It was noted that An. oswaldoi showed a daytime rhythm in open areas. This study is the first to report on the biting habits of a range of anophelines in French Guiana that may play a role in malaria transmission. This information is vital to fully describe the risk of malaria transmission and thereby design appropriate vector control measures and malaria prevention programs.     

Enzyme markers in inbred rat strains: Genetics of new markers and strain profiles

Twenty-six inbred strains of the laboratory rat (Rattus norvegicus) were examined for electrophoretic variation at an estimated 97 genetic loci. In addition to previously documented markers, variation was observed for the enzymes aconitase, aldehyde dehydrogenase, and alkaline phosphatase. The genetic basis of these markers (Acon-1, Ahd-2, and Akp-1) was confirmed. Linkage analysis between 35 pairwise comparisons revealed that the markers Fh-1 and Pep-3 are linked. The strain profiles of the 25 inbred strains at 11 electrophoretic markers are given.     

The Effect of Refuge on Dermestes ater (Coleoptera: Dermestidae) Predation on Musca domestica (Diptera: Muscidae): Refuge for Prey or the Predator?

It is believed that habitat heterogeneity can change the extent of predator-prey interactions. Therefore, in this study we examined the effect of habitat heterogeneity (characterized here as an addition of refuge) on D. ater predation on M. domestica. Predation of D. ater on M. domestica larvae was carried out in experimental habitats with and without refuge, and examined at different prey densities. The number of prey eaten by beetles over 24 h of predator-prey interaction was recorded, and we investigated the strength of interaction between prey and predator in both experimental habitats by determining predator functional response. The mean number of prey eaten by beetles in the presence of refuge was significantly higher than in the absence of refuge. Females had greater weight gains than males. Logistic regression analyses revealed the type II functional response for both experimental habitats, even though data did not fit well into the random predator model. Results suggest that the addition of refuge in fact enhanced predation, as prey consumption increased in the presence of refuge. Predators kept in the presence of refuge also consumed more prey at high prey densities. Thus, we concluded that the addition of refuge was an important component mediating D. ater-M. domestica population interactions. Refuge actually acted as a refuge for predators from prey, since prey behaviors detrimental to predators were reduced in this case.     

The impact of Bt maize as a natal host on adult head capsule width in field populations of western corn rootworm

The success of the current resistance management plan for transgenic maize, Zea mays L. (Poaceae), targeting the rootworm complex hinges upon high rates of mating between resistant and susceptible beetles. However, differences in the fitness of adult beetles could result in assortative mating, which could, in turn, change the rate of resistance evolution. Adult head capsule widths of naturally occurring populations of western corn rootworm, Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), were examined in a variety of refuge configurations. Beetles were classified into treatments based on the hybrid – non‐Bt refuge or Bt maize targeting larval rootworms (hereafter Bt‐RW maize) – and location – proximity to other Bt‐RW or refuge plants – of the natal host plant. Treatments included the following: a refuge plant surrounded by other refuge plants, a refuge plant located near a Bt‐RW plant, a Bt‐RW plant surrounded by Bt‐RW plants, and a Bt‐RW plant located near a refuge plant. The mean head capsule width of males emerging from Bt‐RW plants was significantly smaller than the mean head capsule width of males emerging from refuge plants. These results indicate that males emerging from Bt‐RW maize plants may be exposed to sublethal doses of the Bt toxin as larvae. No differences were detected between females emerging from refuge plants compared with Bt‐RW plants. Overall mean head capsule width decreased as the season progressed, regardless of treatment. The diminished head capsule width of western corn rootworm males emerging from Bt‐RW maize may act to enhance resistance management, particularly in a seed mix refuge system.     

Niche overlap and diet composition of three sympatric coastal dolphin species in the southwest Atlantic Ocean

Sympatric species are expected to differ in ecological requirements to minimize niche overlap and avoid competition. Here we assess the trophic interactions among three coexisting dolphin species from southern Brazil: the franciscana dolphin (Pontoporia blainvillei), the Guiana dolphin (Sotalia guianensis), and the Lahille's bottlenose dolphin (Tursiops truncatus gephyreus). We evaluated temporal variation in carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope values of bone collagen to examine potential dietary shifts resulting from increased fishing activity over the past three decades. We estimated the degree of niche overlap among these species and the contribution of potential prey sources to their diet. δ¹⁵N values were consistent among species and across years, while δ¹³C values increased for Guiana dolphins and decreased for bottlenose dolphins, suggesting changes in diet and/or foraging habitats through time. The similar δ¹³C and δ¹⁵N values and the high niche overlap between Guiana and bottlenose dolphins indicate that these species are primarily feeding on demersal prey. The franciscana diet is primarily composed of pelagic prey, resulting in a lower niche overlap in comparison with the other dolphin species. Our study provides further information about the foraging ecology of this unique dolphin community in southern Brazil with implications for its management and conservation.     

Systematic review of Atractus schach (Serpentes: Dipsadidae) species complex from the Guiana Shield with description of three new species

The Guiana Shield harbours one of the best preserved and largest extents of tropical forest on Earth and an immense biodiversity. The herpetofauna of this region remains poorly known. The species-rich snake genus Atractus contains ～140 species, many with complicated taxonomic histories, including A. schach. Examination of specimens in museums and newly collected material from French Guiana has allowed the illustration of hemipenial morphology for the first time and an expanded diagnosis. Concatenated molecular phylogenetic (mitochondrial and nuclear genes) and phenotypic (morphometrics, external and hemipenial morphology) analyses confirm non-monophyly of the A. flammigerus group and indicate that A. schach is a species complex with three new species described here. The geographic distribution of A. schach sensu stricto is restricted to Guiana, Surinam, and French Guiana north of Tumucumaque massif. Populations tentatively assigned to A. schach from the east from French Guiana in the Roura lowlands to Almeirim, and from central Amazonia between the Negro and Trombetas rivers in Brazil are also recognized as new species. Our results suggest that populations from south of the Amazon River are not conspecific with those from the Guiana Shield.

http://www.zoobank.org/urn:lsid:zoobank.org:pub:A7AE40BC-4716-4302-B3BE-1F43600B0A72     

Effects of large Saduria entomon (Isopoda) on spatial distribution of their small S. entomon and Monoporeia affinis (Amphipoda) prey

We performed laboratory experiments to investigate the effects of predator avoidance and numerical effects of predation on spatial distribution of small Saduria entomon (Isopoda) and Monoporeia affinis (Amphipoda), with large S. entomon as predators. The horizontal distribution and mortality of the prey species, separately and together, were studied in aquaria with a spatial horizontal refuge. We also estimated effects of refuge on mortality of small S. entomon and M. affinis by experiments without the refuge net. In addition, we investigated whether predation risk from large S. entomon influenced the swimming activity of M. affinis, to clarify the mechanisms behind the spatial distribution. Both small S. entomon and M. affinis avoided large S. entomon. The avoidance behaviour of M. fffinis contributed about 10 times more to the high proportion in the refuge than numerical effects of predation. Due to the low mortality of small S. entomon the avoidance behaviour of this species was even more important for the spatial distribution. The combined effect of avoidance behaviour and predation in both species was aggregation, producting a positive correlation between the species in density. M. affinis showed two types of avoidance behaviour. In the activity experiments they reduced activity by 36% and buried themselves in the sediment. In the refuge experiments we also observed avoidance behaviour with the emigration rate from the predator compartment being twice the immigration rate. The refuge did not lower predation mortality in M. affinis, probably due to the small scale of the experimental units in relation to the mobility of the species. Predation mortality in small S. entomon was higher in absence of a refuge and especially high in absence of M. affinis.     

Response of Endangered Desert Fish Populations to a Constructed Refuge

The U.S. Bureau of Reclamation created a shallow, 110-m channel to provide habitat for two endangered fishes, Cyprinodon elegans (Comanche Springs pupfish) and Gambusia nobilis (Pecos gambusia), at the site of the fishes' former natural habitat. The ciénega (marsh) associated with Phantom Lake Spring in Jeff Davis County, Texas, was destroyed by the creation of an irrigation canal system. In 1993, the endangered fishes were stocked into the refuge with individuals from the irrigation canals, and in the case of C. elegans, hatchery stocks. The condition of habitat, status of fish populations, and fish ecology within the refuge were then monitored for two years. The abundance and density of both species increased in accordance with aquatic plant development. Cyprinodon elegans abundance peaked after one year and stabilized at an average density of 14.7/m² by the end of our study. Juvenile C. elegans were always rare, which may indicate that the population reached the refuge's carrying capacity and that recruitment is low. Gambusia nobilis was the most abundant fish in the refuge (average density 96/m²), used the entire refuge, and outcom-peted nonindigenous G. geiseri. The two Gambusia species used similar habitats but showed almost no dietary overlap. High densities of aquatic plants reduced the amount of open water areas necessary for C. elegans. The refuge will sustain the two endangered fishes at this historic site of endemism while maintaining flow to the irrigation system; however, the refuge is not equivalent to a restored ciénega.     

Ticks (Ixodidae) on humans in South America

Twenty eight species of Ixodidae have been found on man in South America (21 Amblyomma, 1 Boophilus, 2 Dermacentor, 2 Haemaphysalis, 1 Ixodes and 1 Rhipicephalus species). Most of them are rarely found on man. However, three species frequently parasitize humans in restricted areas of Argentina (A. neumanni reported from 46 localities), Uruguay (A. triste from 21 sites) and Argentina–Brazil (A. parvum from 27 localities). The most widespread ticks are A. cajennense (134 localities in Argentina, Bolivia, Brazil, Colombia, Ecuador, French Guiana, Guyana, Paraguay, Suriname and Venezuela), A. ovale (37 localities in Argentina, Brazil, Ecuador, French Guiana, Guyana, Paraguay, Suriname and Venezuela) and A. oblongoguttatum (28 sites in Brazil, Colombia, French Guiana, Guyana, Suriname and Venezuela). Amblyomma aureolatum (18 localities in Argentina, Brazil, French Guiana and Paraguay), A. cajennense, and A. triste are vectors of rickettsioses to man in South America. A better understanding of the respective roles of these and other tick species in transmitting pathogens to humans will require further local investigations. Amblyomma ticks should be the main subjects of these studies followed by species of Boophilus, Dermacentor, Haemaphysalis and Rhipicephalus species. In contrast with North America, Europe and Asia, ticks of the genus Ixodes do not appear to be major players in transmitting diseases to human. Indeed, there is only one record of an Ixodes collected while feeding on man for all South America.     

Can protective attributes of artificial refuges offset predation risk in lizards?

Artificial refuges are often used to supplement habitat in areas where natural shelters have been degraded or removed. Although artificial refuges are intended to support particular species, they may be equally attractive and accessible to others, including predators. We explored the influence of snake predation risk and shelter attributes on the overnight use of different artificial refuges (timber, tiles, and iron) using the predator‐prey relationship between Boulenger's skink, Morethia boulengeri and the curl snake, Suta suta. We collected adult M. boulengeri from two bioregions in south‐eastern Australia: the Riverina, where the two species co‐occur, and the South Western Slopes, where S. suta does not occur. Two adult S. suta were collected for use as chemical donors. We conducted four experiments on overnight refuge choice to determine: (i) predator‐scent avoidance, (ii) artificial refuge preferences, (iii) a trade‐off between a preferred refuge and predator‐avoidance, and (iv) the effect of gap height on refuge preference. We found that skinks avoided predator‐scented refuges in favour of identical, but unscented refuges. Skinks preferred timber refuges, and most skinks maintained this preference when predator‐scent was added. However, when gap height was manipulated, skinks shifted to the refuge with the smallest gap. Skinks displayed complex regional variation in behaviour; skinks from both bioregions avoided predator‐scent, but in the trade‐off experiment, skinks from the South Western Slopes were less likely to avoid predator‐scented timber refuges than those from the Riverina. Our findings suggest that protective refuge attributes, such as small gap height, can offset the risk implied by predator‐scent within a refuge. This study highlights the need to consider predator‐prey interactions when designing and using artificial refuges for habitat restoration or biological monitoring.     

Characterization of low-molecular-weight glutenin subunit Glu-B3 genes and development of STS markers in common wheat (Triticum aestivum L.)

Low-molecular-weight glutenin subunit (LMW-GS) Glu-B3 has a significant influence on the processing quality of the end-use products of common wheat. To characterize the LMW-GS genes at the Glu-B3 locus, gene-specific PCR primers were designed to amplify eight near-isogenic lines and Cheyenne with different Glu-B3 alleles (a, b, c, d, e, f, g, h and i) defined by protein electrophoretic mobility. The complete coding regions of four Glu-B3 genes with complete coding sequence were obtained and designated as GluB3-1, GluB3-2, GluB3-3 and GluB3-4. Ten allele-specific PCR markers designed from the SNPs present in the sequenced variants discriminated the Glu-B3 proteins of electrophoretic mobility alleles a, b, c, d, e, f, g, h and i. These markers were validated on 161 wheat varieties and advanced lines with different Glu-B3 alleles, thus confirming that the markers can be used in marker-assisted breeding for wheat grain processing quality. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. L. H. Wang and X. L. Zhao contributed equally to this study.     

Training fish for restocking: refuge and predator training in the hatchery has limited benefits for a marine fish

Large numbers of hatchery-reared fish are released in stocking programmes; however, success is limited by high mortality. Predation is seen as the main cause of deaths but might be reduced by training fish before release to avoid predators and/or use refuge. In this study on a potential restocking species, yellowfin bream Acanthopagrus australis, the effects of predator training and refuge on the behaviour of fish in the hatchery were tested. In the first experiment, juvenile bream were exposed to predatory mangrove jack (Lutjanus argentimaculatus) fed exclusively on bream flesh while housed in tanks with and without refuge. Predator training altered fish behaviour when fish were re-exposed to predators, but the effects were subtle and varied between groups of fish. In contrast, refuge created strong and consistent changes in behaviour, significantly slowing down the amount of time that fish took to consume food. A second experiment focused on the effects of refuge. Bream were trained to use artificial seagrass or house bricks as refuge and then exposed to mangrove jacks in a laboratory predation experiment. When refuge was available, fish significantly slowed down their feeding rate. There was a small, transient increase in survival for fish given seagrass refuges, but this was irrespective of whether the bream were trained to use refuge. The results of this study indicate that the use of refuge may be innate and the benefits of refuge may be available to naive hatchery-reared fish or fish trained to use refuge shortly before release. This suggests that there is potential to improve post-release survival of fingerlings without time-consuming and expensive hatchery training.