A taxonomic revision of Encyclia (Orchidaceae: Laeliinae) in Costa Rica

A taxonomic revision of Encyclia (Orchidaceae) in Costa Rica is presented. The taxonomic history of the genus and its phylogenetic position are discussed. Characters of vegetative and floral morphology are described and their taxonomic significance is discussed. The genus is treated as comprising nine species in the country and a key to species is provided. Each taxon is described on the basis of Costa Rican material, illustrated in a composite plate, and its distribution within the country is assessed. Distribution maps for all the taxa are given. Overall distribution, derivation of name, synonymy, notes on species ecology and diagnostic features are presented for each taxon. The names Encyclia tonduziana and Epidendrum mooreanum are typified. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 395–448.     

Habitat selection and seasonal patterns of activity and foraging of mantled howling monkeys(Alouatta Palliata) in Northeastern Costa Rica

I conducted a 15- month ecological study of habitat preferences and activity and foraging patterns of two troops of mantled howling monkeys, Alouatta palliata,in a lowland rain forest at La Selva Biological Reserve in northeastern Costa Rica. The two troops specialized on different habitats in spite of the fact that both of them had all habitats available and were not constrained by neighboring troops since the population density of howlers is low (7- 15 howlers/km ² ).Troop 1 spent the majority of time in primary forest (80%) followed by secondary forest (10%), while troop 2 spent the majority of time in undisturbed riparian habitat (60%) followed by primary forest (30%). Habitat sampling indicates that neither the total number of stems, species, or families nor the diversity (Shannon index) or evenness is a good indicator for howler habitat selection. Instead the density of trees from the 12 species most commonly consumed by each troop is the most important factor. Activity and foraging patterns were not dependent upon the season as has been described for howling monkeys in forests with a more pronounced dry season at Barro Colorado Island, Panama, and La Pacifica in northwestern Costa Rica. This is likely a result of the more constant food supply at La Selva, combined with less intraspecific competition due to the low howler density. The intraspecific variability of foraging patterns and troop- specific habitat specialization observed in Alouatta palliatashould be considered in the conservation biology of primates. Primate relocation programs should include not only an ecological assessment of the release site but also a comparison of the release site with the habitat that the groups currently occupy.     

Gastropods and bivalves taken as by-catch in the deep-water shrimp trawl-fishery along the Pacific coast of Costa Rica,Central America

Deep-water habitats are among the least studied but most vulnerable environments. By-catch data from deep-water fisheries in Latin America are limited, and detailed reports on associated molluscs are scarce. This study provides information on deep-water shelled molluscs collected between 2010 and 2011 by commercial shrimp trawling fisheries along the Pacific coast of Costa Rica at depths from 112 to 271?m. Twenty-six species were identified, 23 gastropods and three bivalves. Our data extend the depth range of 14 species, and Homalopoma cf. grippii is reported for the first time for Costa Rica. The most common species were the gastropods Fusinus spectrum, Polystira nobilis and Solenosteira gatesi. Only one species (Sinum debile) was captured below 250?m. The catch of molluscs per unit effort was influenced by depth, but not by seasonality or geographic area. It is speculated that these long-lasting bottom-trawling activities have caused negative effects on species diversity and mollusc biomass. Nevertheless, a monitoring program is recommended to assess possible impacts of this type of fishery on mollusc diversity and biomass.     

Biogeographical analysis of two Polypodium species complexes (Polypodiaceae) in Mexico and Central America

We analyzed the geographical and elevational distributions of two Polypodium complexes from Mexico and Central America. Distribution data of nine species of the Polypodium colpodes complex and the Polypodium plesiosorum complex were obtained from almost 1500 herbarium specimens, field collections in Mexico and Costa Rica, and literature studies. The presence of each species was recorded for each Mesoamerican country, in 1° × 1° grid‐cells and biogeographical provinces. The rarity of species was also evaluated. Although the two complexes show extensive overlap, the P. colpodes complex is distributed mainly along the Pacific versant of Mexico and Central America, whereas the P. plesiosorum complex occurs mainly along the Atlantic versant. Those biogeographical provinces with maximum species diversity are Chiapas (seven species), Sierra Madre del Sur (six species), and the Trans‐Mexican Volcanic belt (six species). Grid‐cells with more species are located mainly in the mountains of central‐southern Mexico and northern Central America. Richness does not decrease or increase with latitude. Elevation distributions showed that most Polypodium species are concentrated in the montane interval and three species groups were recognized based on elevational preferences. Polypodium colpodes and P. plesiosorum are the most widely distributed species, whereas Polypodium castaneum and Polypodium flagellare are the only two species that possess the three attributes of rarity (narrow geographical distribution, high habitat specificity, and scarce local populations). Polypodium species of both complexes are present mainly in the montane regions of the study area and show some degree of geographical sympatry, especially in southern Mexico and northern Central America. This overlapping is explained by the elevation tolerance within montane systems and because most species inhabit three or more vegetation types. The distributional patterns of these complexes coincided with the three regional highlands of Mesoamerica, which are separated from each other by the Isthmus of Tehuantepec and by the lowlands of Nicaragua. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ?? , ??–??.     

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.     

Revision of the New World genus Quichuana Knab, 1913 (Diptera: Syrphidae), including descriptions of 24 new species

The species of the New World syrphid genus, Quichuana Knab, 1913 (Diptera: Syrphidae: Eristalini), are revised and the genus is re‐diagnosed. Twenty‐four new species are described, bringing the total number considered valid to 48. New species were mostly reared from Bolivia, Brazil, Costa Rica, El Salvador, Mexico, Peru, Trinidad, and Venezuela. The male of Quichuana picadoi is described for the first time. Quichuana championi is proposed as a synonym of Quichuana cincta, Quichuana aurata as a synonym of Quichuana angustiventris, and Quichuana sepiapennis as a synonym of Quichuana calathea. Quichuana inca var. brevicera is raised to specific status. Lectotypes are designated for Helophilus auratus, Quichuana bezzii, Quichuana fasciata, and Quichuana parisii. A species‐level identification key for both males and females is provided. Male genitalia of 18 species are illustrated. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 72–131.     

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     

The systematics and biology of the Costa Rican species of parasitic wasps in the Thyreodon genus-group (Hymenoptera: Ichneumonidae)

This paper presents an eco‐taxonomic study of the Neotropical representatives of the Thyreodon genus‐group (Hymenoptera: Ichneumonidae) present in Costa Rica, i.e. species of the genera Thyreodon and Rhynchophion. These ichneumonids are koinobiont endoparasitoids of the larvae of Sphingidae and Saturniidae. Intensive sampling in Costa Rica, conducted over 15 years, has revealed the presence of 23 species (12 of which are described here as new –Rhynchophion woodi, Thyreodon woodleyi, T. papei, T. whitfieldi, T. deansi, T. walkerae, T. sharkeyi, T. zitaniae, T. delvarei, T. schauffi, T. darlingi and T. carmeani), whereas earlier studies recognized only nine species in the same area. Several of the additional species we found are simply very scarce and thus unlikely to be encountered except by the type of intensive survey that, in the tropics, has only been conducted in Costa Rica. In some other cases, it has become apparent that more than one species has previously been confused under a single name. Thyreodon rufothorax Cameron is shown to be morphologically and biologically distinct from T. atriventris (Cresson), with which it has long been synonymized, and the relatively well‐known, chromatically distinctive species ‘T. laticinctus Cresson’ and ‘T. morosus Smith’ are both shown to be complexes of sibling species. Reared series have been essential in facilitating the separation of the species in these complexes. An illustrated key is provided to separate all taxa using simple morphological characters. Fourteen of the 23 species have been reared, and all have been found to be restricted to one or a few species of hosts, species of Thyreodon primarily on macroglossine Sphingidae (with one species on Saturniidae) and species of Rhynchophion on sphingine sphingids of the genus Manduca. No two species of these ichneumonids attack the same host caterpillar species, and not all species of macroglossines present in the study area are attacked by species in this genus‐group. Most species are apparently rather rare. Many have only been collected by rearing on a few occasions, other species have been collected at light (six in total) or in Malaise traps (ten in total), or by hand‐netting (20 in total), but no one method collected all of the species present in the principal study area, the Area Conservacion de Guanacaste. The two New World genera Rhynchophion and Thyreodon are found to be related to the Old World genera Dictyonotus and Euryophion, the former of which comprises species that are also sphingid parasitoids, whereas species of the latter attack the caterpillars of other large bombycoid moths, Saturniidae and Eupterotidae. A cladistic analysis shows that Thyreodon is the sister‐lineage to Dictyonotus, and Euryophion is the most basal lineage in the genus‐group. © 2004 The Linnean Society of London, Zoological Journal of the Linnean Society, 2004, 141 , 297–351.     

Ecological niche differences betweenAlouatta palliata andCebus capucinus comparing feeding modes,branch use,and diet

During the wet season, two sympatric species of primates,Alouatta palliata (mantled howlers) andCebus capucinus (white-faced capuchins), were assayed for feeding niche differences through behavioral and habitat use patterns at Refugio de Fauna Silvestre Curu in Costa Rica. Differences in the use of relative diameter and thickness of branches and five different modes of feeding were compared between the species. White-faced capuchins used more manipulative modes of obtaining food, a wider range of arboreal habitat, and had a more diverse diet than mantled howlers. Mantled howlers may be more restricted than white-faced capuchins in arboreal microhabitat use due to their possible need for large support branches during feeding bouts and resting periods. We report that differences in feeding behaviors, diet, and arboreal habitat use seem to play a large role in separating these species niches.     

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.     

A synopsis of Costa Rican Ruellia (Acanthaceae), with descriptions of four new species

We describe four new species of Ruellia from Costa Rica; three from the Osa Peninsula, Puntarenas province (R. exilis, R. mira, R. odorata), and one from the southwestern corner of San José province (R. norvegigratiosa). Ruellia matagalpae is reported as a new record for the country. New combinations are made in Ruellia for the two Costa Rican species of Blechum (R. blechum and R. costaricensis). Three species are reduced to synonymy, and another species is considered doubtfully worthy of recognition. Notable range extensions are reported for two species. Corollas and fruits of all 22 Costa Rican species of Ruellia are shown and compared as easily used identification aids. An informal guide to species groups and a dichotomous key to the 22 species are presented.     

Biogeographically dynamic genetic structure bridging two continents in the monotypic Central American rodent Ototylomys phyllotis

Central America is an ideal region in which to study patterns of historical divergence and population genetic differentiation, because of its extraordinarily dynamic biogeographical, tectonic, and climatic history. The rodent Ototylomys phyllotis is the only extant species of the genus Ototylomys and is distributed within this region from the Isthmus of Tehuantepec, Mexico, to central Costa Rica, offering an excellent opportunity to study spatial and temporal patterns of population structure of the species and to explain the ecological and evolutionary processes responsible for those patterns. We estimated the genetic diversity and structure within and between populations of O. phyllotis, times of divergence, and migration patterns using mitochondrial DNA and a comprehensive combination of phylogenetic and phylogeographical computational analyses. Our results support monophyly of the genus Ototylomys. We identified three major phylogeographical lineages within O. phyllotis that are linked to its diversification and coincide with the main geological features that shaped Middle America. The origin of the genus was before 3.35 Mya, prior to the Great American Biotic Interchange (GABI), and its initial occurrence was near the centre of its current distribution (Honduras/El Salvador), from which it later spread (3.20–2.84 Mya) following a series of GABI pulses. The species showed an initial northward dispersal to the Chiapas and Guatemala highlands (2.27 Mya) followed by diversification. A later dispersal (1.82 Mya) occurred toward both the south (Nicaragua, Costa Rica) and the north (Belize). The Yucatan peninsula was colonized (0.8 Mya) by individuals from Belize. Extremely high radiation and range expansion occurred throughout the entire range, the highest of which was in the Yucatan peninsula (0.125 Mya). © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 593–610.     

Taxonomic revision and molecular phylogeny of the fig wasp genus AnidarnesBouček, 1993 (Hymenoptera: Sycophaginae)

Besides the pollinators (Agaonidae), several chalcidoid lineages of nonpollinating fig wasps are strictly dependent on Ficus (Moraceae) for reproduction. Overall, nonpollinating fig wasps have not received much consideration. Reliable phylogenetic and taxonomic frameworks are lacking for most groups, which hampers progress in our understanding of the evolution and functioning of fig wasp communities. Here we focus on Anidarnes Bou?ek (Sycophaginae), a member of the Neotropical fig wasp community. We present a detailed morphological analysis as well as the first molecular phylogeny of the genus inferred from two nuclear and two mitochondrial genes (Cytb, COI, EF‐1α and 28S rRNA, 3937 bp). Twelve species are recognised, illustrated and a key to their identification is provided. Of those, only three were previously described and are redescribed here: A. bicolor (Ashmead); A. globiceps (Mayr) and A. brevicauda Bou?ek. In addition, nine new species are described: Anidarnes brevior sp.n . Farache & Rasplus (Costa Rica); A. dissidens sp.n. Farache & Rasplus (Brazil); A. gracilis sp.n. Farache & Rasplus (Costa Rica); A. isophlebiae sp.n. Farache & Rasplus (Costa Rica); A. jimeneziae sp.n. Farache & Rasplus (Costa Rica); A. longiscutellum sp.n. Farache & Rasplus (Brazil); A. martinae sp.n. Farache & Rasplus (U.S.A., Florida); A. nigrus sp.n. Farache & Rasplus (Colombia) and A. rugosus sp.n. Farache & Rasplus (Brazil). Finally, phylogenetic relationships inferred using parsimony, bayesian and maximum likelihood methods are discussed in the light of our morphological observations and the host fig tree taxonomy.     

Systematic revision of Neotropical Achalcus and a related new genus (Diptera: Dolichopodidae, Achalcinae) with comments on their phylogeny, ecology and zoogeography

A revision of the species of the subfamily Achalcinae of the Neotropical region is presented. A new genus, Australachalcus gen. nov. , is erected based on the presence of six dorsocentral bristles and synapomorphies in the hypopygium. Eight new Achalcus species ( bilineatus , brevicornis , costaricensis , cyanocephalus , maculipennis , micromorphoides , niger , tibialis ) and eight new Australachalcus species ( acornis , browni , cummingi , incisicornis , pseudorobustus , robustus , setosus , variabilis ) are described, and Achalcus albipalpus Parent, A. brevinervis Van Duzee, A. longicornis Van Duzee and Enlinia edwardsae (Van Duzee) are newly referred to Australachalcus and redescribed. A key to males of all species and females of eight species is provided. One Palaearctic species, Achalcus melanotrichus Mik, and nine New Zealand Achalcus species ( chaetifemoratus , luteipes , medius , minor , minusculus , minutus , nigroscutatus , relictus , separatus ) described by Parent are also transferred to Australachalcus . In Neotropical Achalcinae, three Achalcus and more than four different Australachalcus species groups can be distinguished, whereas all Holarctic Achalcus species belong to the single A. flavicollis species group. In the Neotropics, Australachalcus is nearly entirely confined to Chile, whereas Achalcus is recorded from Costa Rica, Venezuela, Ecuador, Colombia, Peru and Chile, with no or little overlap in distribution between the separate species groups. Beyond Chile, most achalcine species treated here were collected at higher altitudes. Most Chilean species are only active during the southern summer, whereas in Costa Rica achalcine representatives are encountered throughout the year.  © 2005 The Linnean Society of London, Zoological Journal of the Linnean Society , 2005, 143 , 27–73.     

Trophic ecology of juvenile bull sharks (Carcharhinus leucas) in the Coyote estuary,Costa Rica

Bull shark (Carcharhinus leucas) is a near-threatened elasmobranch species capable of moving between the fresh and salty waters of tropical and subtropical coastal areas, for which we still lack important ecological information. During their first years of life, bull sharks use estuarine systems as nursery areas, making them highly susceptible to environmental and anthropogenic pressures. We studied the trophic ecology of juveniles found in the Coyote estuary, a potential nursery area in Costa Rica, to understand the potential impact of further bull shark declines and gain knowledge that could aid in their conservation. We analysed the trophic ecology of juvenile bull sharks [81–103 cm total length (TL)] in the Coyote estuary, Costa Rica, using stable isotopes of δ¹⁵N and δ¹³C. Since one problem using this technique in juveniles is the confounding effect of the maternal signature, we sampled different tissues (muscle and plasma), verified the status of the shark's umbilical scar and identified the size at which the isotope signature is a result of the animal's current diet. The isotopic values of the muscle tissue reflected the maternal isotopic signature. In contrast, plasma values reflected the diet of juvenile bull sharks >95 cm TL and with a closed umbilical scar. Juvenile bull sharks fed primarily on teleost fishes of the order Anguilliformes and Siluriformes, and have a high trophic position (≥4.0) in the Coyote estuary. Our findings suggest that this estuary is an important feeding site for juvenile bull sharks of the Pacific of Costa Rica. Thus, the protection of essential habitats such as the Coyote estuary will benefit not only bull shark conservation, but also the conservation of an array of fish species that also use this habitat as a rookery, many of which are of commercial interest.     

A new species of Dicrotendipes (Diptera: Chironomidae) from Costa Rica

The adult male of Dicrotendipes baru is described from the Dominical area of southwestern Costa Rica. The species is characterized by its elongate club-like superior volsella. This species represents the third member of the genus known from Costa Rica.     

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.     

The tropical <Emphasis Type="Italic">Polyporus tricholoma</Emphasis> (Polyporaceae) — Taxonomy,phylogeny, and the development of methods to detect cryptic species

The stipitate pore-bearing fungus Polyporus tricholoma (Polyporus infrageneric group Polyporellus) is commonly reported from Mesoamerica and more rarely from the palaeotropics. Collections from Puerto Rico, Mexico, and Costa Rica did not differ morphologically, but their monokaryotic cultures revealed the existence of three interINcompatibility groups. These putative cryptic species exist sympatrically in Costa Rica. Sequencing, restriction enzyme digestion, and specific primers targeting the ITS region of nuclear ribosomal DNA (ITS 1-5.8S-ITS2) could only partly be used for detecting intercompatibility groups. Heterogeneity within the rDNA repeat was observed. Molecular evidence supports the existence of a close relative in Australia.     

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.