Distribution and diversity of begomoviruses in tomato and sweet pepper plants in Costa Rica

Begomoviruses (genus Begomovirus, family Geminiviridae) have emerged as important plant pathogens in tropical and subtropical regions worldwide. Although these viruses were reported during the 1970s in Costa Rica, they are still poorly known. Therefore, the objective of this study was to analyse the diversity and distribution of begomoviruses in commercial tomato and sweet pepper fields from different agricultural production systems of the major growing regions of Costa Rica. A total of 651 plants were randomly sampled from greenhouses and open field crops during 2011 and 2012 in three different geographical locations. The bipartite begomoviruses Tomato yellow mottle virus, Tomato leaf curl Sinaloa virus and Pepper golden mosaic virus, and the monopartite begomovirus Tomato yellow leaf curl virus were detected in the collected samples. The complete genome of isolates from each species was cloned and sequenced. The frequency of detection of these four begomoviruses in the analysed samples ranged from 0 to 9%, the presence, and the prevalent virus varied largely according to the geographical location, the host (tomato and pepper), and the production system (greenhouses or open fields). An association between geographical region and begomovirus species was observed suggesting that in Costa Rica the heterogeneity on climate, topography and agricultural system might influence the distribution of begomovirus species in the country. A broader survey needs to be conducted to confirm it, although these preliminary results may contribute to the management of begomoviruses in Costa Rica.     

Phytogeography of the bryophyte floras of oak forests and páramo of the Cordillera de Talamanca, Costa Rica

Aim Central America is a biogeographically interesting area because of its location between the rich and very different biota of North and South America. We aim to assess phytogeographical patterns in the bryophyte floras of oak forests and páramo of the Cordillera de Talamanca, Costa Rica. Location Tropical America, in particular the montane area of Cordillera de Talamanca, Costa Rica. Methods The analysis is based on a new critical inventory of the montane bryophyte flora of Cordillera de Talamanca. All species were assigned to phytogeographical elements on the basis of their currently known distribution. Absolute and percentage similarities were employed to evaluate floristic affinities. Results A total of 401 species [191 hepatics (liverworts), one hornwort, 209 mosses] are recorded; of these, 251 species (128 hepatics, one hornwort, 122 mosses) occur in oak forests. Ninety‐three per cent of all oak forest species are tropical in distribution, the remaining 7% are temperate (4%) and cosmopolitan (3%) species. The neotropical element includes almost 74% of the species, the wide tropical element (pantropical, amphi‐atlantic, amphi‐pacific) only 19%. A significant part of the neotropical species from oak forests are species with tropical Andean‐centred ranges (27%). As compared with bryophyte species, vascular plant genera in the study region are represented by fewer neotropical, more temperate and more amphi‐pacific taxa. Bryophyte floras of different microhabitats within the oak forest and epiphytic bryophyte floras on Quercus copeyensis in primary, early secondary and late secondary oak forest show a similar phytogeographical make‐up to the total oak forest bryophyte flora. Comparison of oak forest and páramo reveals a greater affinity of the páramo bryophyte flora to temperate regions and the great importance of the páramo element in páramo. Surprisingly, oak forests have more Central American endemics than páramo. Main conclusions (1) Providing first insights into the phytogeographical patterns of the bryophyte flora of oak forests and páramo, we are able to confirm general phytogeographical trends recorded from vascular plant genera of the study area although the latter were more rich in temperate taxa. (2) Andean‐centred species are a conspicuous element in the bryophyte flora of Cordillera de Talamanca, reflecting the close historical connection between the montane bryophyte floras of Costa Rica and South America. (3) High percentages of Central American endemics in the bryophyte flora of the oak forests suggest the importance of climatic changes associated with Pleistocene glaciations for allopatric speciation.     

Species distribution models predict the geographic expansion of an enzootic amphibian pathogen

Globally, numerous amphibian species have declined due to the introduction of the chytrid fungus Batrachochytrium dendrobatidis (Bd). However, the understanding of the spatiotemporal dynamics remains incomplete. Therefore, estimating the current geographic distribution of Bd is urgently needed, especially in countries like Costa Rica, where susceptible species are still recovering from Bd‐driven declines. We conducted model tuning and spatial analysis to compare the habitat suitability for epizootic and enzootic Bd in Costa Rica and to identify data‐deficient regions, opportunistic sampling, and Bd hotspots. Our dataset combined two methods of detection (histology and PCR methods) for a total of 451 Bd‐positive records from 34 localities. We found that the distribution of enzootic Bd in Costa Rica increased 60% since previous estimates in the early 2000s and extended to highlands and dry lowlands that were considered unsuitable for Bd. We also found that Bd is common across protected lands (80%) and within the herpetological provinces containing the highest amphibian richness and endemism in Costa Rica. Opportunistic sampling of Bd has focused on sites where epizootics occurred with the strongest intensity, leading to deficient or absent sampling across the Talamanca Range, the Nicoya Peninsula, and the northern lowlands. Our results showed that PCR increased the power of Bd detection in lowlands and favored the identification of Bd hotspots across the Caribbean side of Costa Rica. Our results add to the understanding of disease spread during enzootics and can be used to identify new hotspots for disease to mitigate future outbreaks of this pathogen. Abstract in Spanish is available with online material     

A preliminary survey of the Chironomidae (Diptera) of Costa Rica,with emphasis on the lotic fauna

Extensive collections of Chironomidae were made in Costa Rica, Central America, during 1986 and 1987. Fifty-five genera and at least 148 species belonging to the subfamilies Podonominae, Tanypodinae, Orthocladiinae and Chironomidae were found. Chironominae and Orthocladiinae predominated. Only one species of Podonominae was collected. Tanypodinae was represented by many genera, but species richness was low.Cricotopus was the most widespread and diverse genus of Orthocladiinae. Among the Chironominae the generaPolypedilum, Pseudochironomus, Tanytarsus andRheotanytarsus showed high species richness. Several species were collected that could not be assigned to genus. A number of range extensions were recorded for taxa found in the Neotropical region for the first time and for Neotropical taxa recorded outside of South America for the first time. The Costa Rican chironomid fauna consists of cosmopolitan, holarctic and neotropical components. There is probably an endemic Central American chironomid fauna at the species level.     

Addendum to the checklist of the helminth parasites of vertebrates in Costa Rica

In this work, we present an addendum to the "Checklist of the helminth parasites of vertebrates in Costa Rica" with a parasite-host list as well as a host-parasite list. This addendum updates the available information on this group of parasites in Costa Rica, since very recently a new input has been made to describe the helminth fauna of vertebrates, particularly at the Area de Conservación de Guanacaste. In this paper, we add 33 records, representing 23 species. This raises the number of helminth species described in vertebrates from Costa Rica to 325, represented by 89 species of digeneans, 23 of monogeneans. 63 of cestodes, 13 of acanthocephalans, and 137 of nematodes. In total, 133 species of vertebrates have been studied for helminths in Costa Rica (31 species of fishes. 7 amphibians, 18 reptiles, 40 birds, and 37 mammals). Currently, 67 species (20.6 %) have been recorded as new species from Costa Rica and most of them are endemic to particular regions. The Colecci6n de Helmintos de Costa Rica, housed at the Universidad de Costa Rica (UCR), San José, is the depositary of only 23% of the species recorded so far; however this situation is changing and people recognizes.     

Multiplex specific PCR for identification of the genera Actinopolyspora and Streptomonospora, two groups of strictly halophilic filamentous actinomycetes

The genera Actinopolyspora and Streptomonospora are two groups of extremely halophilic filamentous actinomycetes. Members of these two genera are isolated frequently, probably due to the high occurrence of these actinomycetes in the hypersaline soil environment. Although members of these genera can be identified by micromorphological criteria, the extensive chemotaxonomic characterization of each new isolates is a time-consuming task which cannot always be undertaken when handling large numbers of isolates as is the case in natural products screening programmes. In this work, the design of one set of genus-specific PCR primers which allows rapid detection of members of the genus Actinopolyspora by means of PCR amplification is presented. And we developed a multiplex PCR protocol for identification of the species of the genera Actinopolyspora and Streptomonospora, simultaneously. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Three new species in the neotropical genus <Emphasis Type="Italic">Clidemia</Emphasis> (Melastomataceae: Miconieae)

We here propose and describe three new species of Clidemia: C. aguilarii from Costa Rica and Panama; C. aurantiaca from Costa Rica, Panama, and Ecuador; and C. subpeltata, a Costa Rican endemic. Phenological notes, distribution maps, line drawings, color images of the live plants in the wild, and discussions comparing the new species to their presumed closest relatives are provided.     

Checklist of the helminth parasites of vertebrates in Costa Rica

Helminth parasites of vertebrates have been studied in Costa Rica for more than 50 years. Survey work on this group of parasites is far from complete. We assembled a database with all the records of helminth parasites of wild and domestic vertebrates in Costa Rica. Information was obtained from different sources such as literature search (all published accounts) and parasite collections. Here we present a checklist with a parasite-host list as well as a host-parasite list. Up to now, 303 species have been recorded, including 81 species of digeneans, 23 monogeneans, 63 cestodes, 12 acanthocephalans, and 124 nematodes. In total, 108 species of vertebrates have been studied for helminths in Costa Rica (31 species of fishes, 7 amphibians, 14 reptiles, 20 birds, and 36 mammals). This represents only 3.8% of the vertebrate fauna of Costa Rica since about 2,855 species of vertebrates occur in the country. Interestingly, 58 species (19.1 %) were recorded as new species from Costa Rica and most of them are endemic to particular regions. Considering the valuable information that parasites provide because it is synergistic with all the information about the natural history of the hosts, helminth parasites of vertebrates in Costa Rica should be considered within any initiatives to accomplish the national inventory of biological resources. Starting with this compilation work, the Colección de Helmintos de Costa Rica (CHCR), hosted at the Facultad de Microbiología, Universidad de Costa Rica, has re-emerged and it is our hope that it will have the standards of quality to assure that it will become the national depository of helminths in the country.     

中国裸瘦足蝇属两新种（双翅目：瘦足蝇科）

记述中国瘦足蝇科裸瘦足蝇属Cliobata Enderlein 2新种:浅褐裸瘦足蝇Cliobata ecruis sp. nov.和周氏裸瘦足蝇Cliobata choui sp. nov.。浅褐裸瘦足蝇的鉴别特征为体浅褐色,胸部褐色具黄色斑;翅近端部具宽的透明带;生殖叉褐色,其臂部几乎与基部等长,臂基部中央具新月形凹陷。周氏裸瘦足蝇的鉴别特征为体黑色;翅近端部透明带窄;生殖叉黑褐色,其臂部长于基部,臂基部中央具半圆形凹陷。新种模式标本保存在中国农业大学昆虫博物馆。     

Marine biodiversity of Costa Rica: the phyla Sipuncula and Echiura

Fourteen species of Sipuncula belonging to 9 genera have been reported from Costa Rican waters, mostly from the Pacific coast. Three of these species are new records for Costa Rica (Phascolion strombus (Montagu 1804), Aspidosiphon (Aspidosiphon) muelleri Diesing 1851, and Aspidosiphon (Aspidosiphon) gracilis schnehageni (W. Fisher 1946)). One species of Echiura, Thalassema steinbecki Fisher 1946, in the order Echiuroinea, has been reported from the Pacific coast of Costa Rica.     

Some Entolomataceae (Agaricales) from Costa Rica

A preliminary account of Entolomataceae from Costa Rica is presented. Three new taxa are described, two inClitopilus, one inRhodocybe, and three new combinations are proposed inInocephalus. Five taxa ofClitopilus are reported for the first time from Costa Rica and a key to species is provided. Four species ofRhodocybe are discussed and a key to the six species known from Costa Rica is also provided.Alboleptonia earlei, Inocephalus murraii, Inocephalus quadratum, Rhodocybe incarnata andRhodocybe pseudonitellina are now known to occur in Costa Rica.     

Marine biodiversity of Costa Rica: Crustacea: Infraorder Anomura

The anomuran crabs are among the best known crustacean groups from the Pacific coast. However, this group is poorly known from the Caribbean coast of Costa Rica. In this compilation based on the literature and the collection at the Zoology Museum, Biology School, University of Costa Rica, we report the presence of 114 species of the Infraorder Anomura for Costa Rica, 20 species from the Caribbean, 96 species from the Pacific (two are present on both coasts). Twenty-nine species are new reports for Costa Rica, 15 from the Caribbean coast (74% of the total of species from that coast) and 14 from the Pacific (15% of the total from the Pacific). The range often species is extended to Costa Rica, siete from the Caribbean and three from the Pacific. Six species are reported for the first time from Cocos Island, where there are also four endemic species.     

The grasshoppers of Costa Rica: a survey of the parameters influencing their conservation and survival

Seventy-five per cent of the acridomorph fauna of Costa Rica is confined to the wet forest environment. This habitat also has a disproportionately large proportion of species which are of restricted distribution within the country or are endemic to Costa Rica or are flightless. The grasshoppers of dry forest, grassland and swamp habitats have in general the reverse properties: they include relatively few species and most of these are capable of flight and are widely distributed both within and outside of Costa Rica. The major factor influencing the long-term survival (or, conversely, the extinction) of the major part of the grasshopper fauna of Costa Rica is likely to be the preservation (or destruction) of the wet forest habitat.     

Widespread co‐occurrence of divergent mitochondrial haplotype lineages in a Central American species of poison frog (Oophaga pumilio)

Aim To analyse the phylogeographic structure of the strawberry poison frog, Oophaga pumilio (Dendrobatidae), across a large part of its range using a combination of mitochondrial and nuclear markers. Location Costa Rica and Panama. Methods Sequence analyses of a mitochondrial (cytochrome b) and a nuclear (RAG‐1) gene fragment as well as analyses of seven microsatellite loci were carried out on 269 individuals of O. pumilio sampled from 24 localities and on two individuals of O. vicentei. Results Two main mitochondrial haplotype lineages, corresponding to a northern (north Costa Rica) and a southern (south Costa Rica and eastern Panama) lineage, were identified. They differed by up to 7% uncorrected distance. We observed co‐occurrence of both lineages in seven populations in Costa Rica and Panama, indicating a pattern of extensive admixture. The two main mitochondrial lineages of O. pumilio roughly corresponded to a previously described phylogeographic pattern. Microsatellites indicate admixture spanning over a wide geographic area, but significant variation between the northern and southern groups was also found with microsatellite data. While microsatellite data reconstructed a separation south of an assumed Caribbean valley barrier, mitochondrial haplotypes of the ‘southern lineage’ shifted this barrier towards the north. Main conclusions Despite admixture, all three markers showed significant variation between the northern and southern groups. Phylogeographical breaks known from other anuran species in the study region could not be verified for O. pumilio. The unexpected clustering of the population from Escudo de Veraguas and the individuals of O. vincentei with the northern O. pumilio lineage indicates the need for a fundamental and careful taxonomic revision, including an interspecific phylogeography of the entire genus.     

Reproductive plasticity in <Emphasis Type="Italic">Petrolisthes armatus</Emphasis> (Anomura,Porcellanidae): a comparison between a Pacific and an Atlantic population

The porcellanid crab Petrolisthes armatus, with a known geographic distribution covering a wide range of latitudes, was selected to conduct a comparative study on egg production and reproductive output between two populations from Pacific and Atlantic coasts. Ovigerous females were collected between September and November 2005 in Punta Morales, Pacific coast of Costa Rica (n = 137) and from March 2005 to July 2006 in Araçá region, São Paulo, Brazil (n = 46). The mean size of females was statistically different between both populations with larger females from Brazil than Costa Rica (7.9 ± 1.31 and 6.6 ± 0.95 mm CW, respectively). Likewise, egg production was significantly different in both populations and started in Pacific Costa Rica at a smaller female size than in Brazil. Specimens from Pacific Costa Rica produced roughly three times more eggs than equally sized females from Brazil, while newly extruded embryos were larger in Brazil than in Costa Rica (0.045 and 0.039 mm³, respectively). Egg volume increased during embryogenesis by 112.8 and 164.5% in Costa Rican and Brazilian populations, respectively. The egg water content increased steadily in both populations; however, eggs produced in Brazil contained always more water than those from the same developmental stage in Costa Rica. Average reproductive output (based on dry weight) was substantially lower in Brazil (0.031) than in Costa Rica (0.065). Our results confirm an impressive intraspecific plasticity of reproductive features in an intertidal decapod. The observed phenotypical variability might be related to local environmental conditions as well as to the location of the studied population concerning its geographic range of distribution.     

New records of benthic marine algae and Cyanobacteria for Costa Rica,and a comparison with other Central American countries

We present the results of an intensive sampling program carried out from 2000 to 2007 along both coasts of Costa Rica, Central America. The presence of 44 species of benthic marine algae is reported for the first time for Costa Rica. Most of the new records are Rhodophyta (27 spp.), followed by Chlorophyta (15 spp.), and Heterokontophyta, Phaeophycea (2 spp.). Overall, the currently known marine flora of Costa Rica is comprised of 446 benthic marine algae and 24 Cyanobacteria. This species number is an under estimation, and will increase when species of benthic marine algae from taxonomic groups where only limited information is available (e.g., microfilamentous benthic marine algae, Cyanobacteria) are included. The Caribbean coast harbors considerably more benthic marine algae (318 spp.) than the Pacific coast (190 spp.); such a trend has been observed in all neighboring countries. Compared to other Central American countries, Costa Rica has the highest number of reported benthic marine algae; however, Panama may have a similarly high diversity after unpublished results from a Rhodophyta survey (Wysor, unpublished) are included. Sixty-two species have been found along both the Pacific and Caribbean coasts of Costa Rica; we discuss this result in relation to the emergence of the Central American Isthmus.     

A new species of Columnea and range extension in the Gesneriaceae from Costa Rica

Columnea lariensis is described and illustrated as a new species from the Talamanca Mountains, Costa Rica. It is similar to C. canarina from Panama. Alloplectus weirii is here reported for the first time from Mesoamerica and an illustration is provided.

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Resumen   Columnea lariensis de la Cordillera de Talamanca, Costa Rica, es descrita e ilustrada. Es similar a C. canarina de Panamá. Alloplectus weirii se reporta para Mesoamérica por primera vez y se incluye una ilustración de la misma.

     

Geographic Variation in Male Sexual Signals in Strawberry Poison Frogs (Dendrobates pumilio)

In this paper, we compare the advertisement calls of 207 neotropical strawberry poison frogs (Dendrobates pumilio) collected in 21 localities along a transect from northern Costa Rica to western Panama. Populations varied most in call duration and call rate, while pulse rate and duty cycle were less variable. Multivariate analyses showed that call variation followed a cline with higher call rates, shorter calls, lower duty cycles and higher pulse rates in the southeast. Body size decreased towards the southeast and explained most variation in dominant frequency, as well as some residual variation in call rate. We conclude that a combination of geography and morphology is largely responsible for call variation within this species. Two inferred bio‐acoustic groups were roughly in accordance with two genetic groups, geographically separated in central Costa Rica. However, genetic distances among populations did not co‐vary with call dissimilarity after correction for geographic distances. Thus, differences in calls between genetic groups are probably mainly a result of clinal variation. These findings agree with the general observation that bio‐acoustic variation is often not (highly) associated with genetic divergence. Moreover, colour polymorphism observed among Panamanian populations was not reflected in a higher variability in call parameters relative to the monomorphic Costa Rican populations.     

Diversity of the free-living marine and freshwater Copepoda (Crustacea) in Costa Rica: a review

The studies on marine copepods of Costa Rica started in the 1990’s and focused on the largest coastal-estuarine systems in the country, particularly along the Pacific coast. Diversity is widely variable among these systems: 40 species have been recorded in the Culebra Bay influenced by upwelling, northern Pacific coast, only 12 in the Gulf of Nicoya estuarine system, and 38 in Golfo Dulce, an anoxic basin in the southern Pacific coast of the country. Freshwater environments of Costa Rica are known to harbor a moderate diversity of continental copepods (25 species), which includes 6 calanoids, 17 cyclopoids and only two harpacticoids. Of the +100 freshwater species recorded in Central America, six are known only from Costa Rica, and one appears to be endemic to this country. The freshwater copepod fauna of Costa Rica is clearly the best known in Central America. Overall, six of the 10 orders of Copepoda are reported from Costa Rica. A previous summary by 2001 of the free-living copepod diversity in the country included 80 marine species (67 pelagic, 13 benthic). By 2009, the number of marine species increased to 209: 164 from the Pacific (49% of the copepod fauna from the Eastern Tropical Pacific) and 45 from the Caribbean coast (8% of species known from the Caribbean Basin). Both the Caribbean and Pacific species lists are growing. Additional collections of copepods at Cocos Island, an oceanic island 530 km away of the Pacific coast, have revealed many new records, including five new marine species from Costa Rica. Currently, the known diversity of marine copepods of Costa Rica is still in development and represents up to 52.6% of the total marine microcrustaceans recorded in the country. Future sampling and taxonomic efforts in the marine habitats should emphasize oceanic environments including deep waters but also littoral communities. Several Costa Rican records of freshwater copepods are likely to represent undescribed species. Also, the biogeographic relevance of the inland copepod fauna of Costa Rica requires more detailed surveys.