Amphibian‐killing chytrid in Brazil comprises both locally endemic and globally expanding populations

Chytridiomycosis, caused by the fungus Batrachochytrium dendrobatidis (Bd), is the emerging infectious disease implicated in recent population declines and extinctions of amphibian species worldwide. Bd strains from regions of disease‐associated amphibian decline to date have all belonged to a single, hypervirulent clonal genotype (Bd‐GPL). However, earlier studies in the Atlantic Forest of southeastern Brazil detected a novel, putatively enzootic lineage (Bd‐Brazil), and indicated hybridization between Bd‐GPL and Bd‐Brazil. Here, we characterize the spatial distribution and population history of these sympatric lineages in the Brazilian Atlantic Forest. To investigate the genetic structure of Bd in this region, we collected and genotyped Bd strains along a 2400‐km transect of the Atlantic Forest. Bd‐Brazil genotypes were restricted to a narrow geographic range in the southern Atlantic Forest, while Bd‐GPL strains were widespread and largely geographically unstructured. Bd population genetics in this region support the hypothesis that the recently discovered Brazilian lineage is enzootic in the Atlantic Forest of Brazil and that Bd‐GPL is a more recently expanded invasive. We collected additional hybrid isolates that demonstrate the recurrence of hybridization between panzootic and enzootic lineages, thereby confirming the existence of a hybrid zone in the Serra da Graciosa mountain range of Paraná State. Our field observations suggest that Bd‐GPL may be more infective towards native Brazilian amphibians, and potentially more effective at dispersing across a fragmented landscape. We also provide further evidence of pathogen translocations mediated by the Brazilian ranaculture industry with implications for regulations and policies on global amphibian trade.     

Evidence for longitudinal migration by a “sedentary” Brazilian flycatcher,the Ash‐throated Casiornis

The digitalization of museum collections and concurrent increase in citizen‐science initiatives is ushering in an era of unprecedented availability of primary biodiversity data. These changes permit a reappraisal of phenological patterns of tropical species. I examined spatio‐temporal variation in the distribution patterns of an ostensibly sedentary endemic Brazilian flycatcher, the Ash‐throated Casiornis (Casiornis fuscus), using both specimen data from museums and sighting records and rich media data from citizen‐science initiatives. I found compelling evidence for partial intratropical longitudinal migration to Amazonia and the Cerrado biomes from the species’ core range in the semi‐desert Caatinga biome and adjacent ecotones. These records from outside of the Caatinga were distributed during the height of the dry season from April to October, although the Caatinga is not entirely vacated at this time. This pattern of partial migration leads to a doubling of the distributional range of Ash‐throated Casiornises and strongly suggests that the species is a breeding near‐endemic of the Caatinga biome. This pattern was potentially previously not apparent because of significant biases in specimen collection between biomes, giving a false sense of abundance in the Brazilian Amazon.     

Theobromine, theophylline, and caffeine in 42 samples and products of Guaraná (Paullinia cupana, Sapindaceae)

Guaranás, the carbonated beverages (sodas) of choice throughout much of Brazil, are mandated by Brazilian law to contain at least 300 mg guara’a (Paullinia cupana, Sapindaceae) seed per 100 ml soda. Were all the soda manufacturers adhering to the law, they would be consuming almost three times the annual production of seed. Guaraná seeds contain unusually high levels of caffeine, along with smaller amounts of the related purine alkaloids theobromine and theophylline. We investigated the purine alkaloid content of three ethnobotanical guaraná collections and 39 commercial products using HPLC/UV. Many of the products did contain caffeine as the major alkaloid, with traces of theobromine and theophylline. Numerous sodas and syrups contained up to ten times more theobromine than caffeine, and we suspect that these products were adulterated with cacao (Theobroma cacao, Sterculiaceae), the major source of theobromine.     

Tapping the archives: the sterol composition of marine sponge species,as determined non‐invasively from museum‐preserved specimens,reveals biogeographical features

Over 8600 species are currently recorded in the phylum Porifera (sponges). They produce a large diversity of biochemical compounds including sterols, with more than 250 different sterols identified. Some of these sterols are of great interest, due to their use for fingerprinting in ecological and biomarker (molecular fossil) studies. As a large number of identified extant species from biodiversity surveys are housed in museum collections, preserved in ethanol, these present a potentially rich source of identified specimens for comparative lipid analyses. Here, we show that, in at least one species, sterol distributions obtained from the ethanol used to preserve specimens of sponges were representative, and comparable to the sterol distribution obtained from wet‐frozen and from freeze‐dried tissue from the same species. We employed both GC‐MS and two‐dimensional gas chromatography—time‐of‐flight mass spectrometry (GC×GC‐TOFMS), with an improved signal‐to‐noise ratio for even minor constituents. Analysis of two additional specimens of the same species, but of different provenance, resulted in detection of marked differences in sterol composition, which could be attributed to variations in geography, environmental conditions, microbial communities, diet or cryptic speciation. The possibility of using ethanol from identified, preserved museum sponges could drastically increase the number of available samples. This could enable the study of their sterol complements, and the detailed investigation of differences due to geographical and oceanographic, phylogenetic, and other factors in unprecedented detail.     

Metazoan parasites as biological tags for stock discrimination of whitemouth croaker Micropogonias furnieri

Examination of 248 adult specimens of whitemouth croaker Micropogonias furnieri from five localities along the Brazilian coast revealed 8735 parasites belonging to 41 metazoan species. Samples from Ceará to Bahia and Rio de Janeiro to Santa Catarina showed a high level of correct assignation (92 and 87%, respectively) and cross assignation (i.e. almost all specimens misidentified in Ceará were assigned to Bahia and almost all specimens misidentified in Bahia were classified as Ceará), so samples were pooled in the northern and south‐eastern samples, and Rio Grande do Sul was considered a southern area. Eight parasite species were characteristic of the northern localities, five species were found just in the area associated with south‐eastern localities and two species were characteristic of the southern area providing first evidence of stock discreteness. The multivariate discriminant analysis successfully discriminated three groups of localities associated with three stocks of M. furnieri in Brazil: a northern stock associated with Ceará and Bahia, a south‐eastern stock related to Rio de Janeiro and Santa Catarina and a southern stock in the area of Rio Grande do Sul, which could be considered as the northern limit of the stock associated with the Common Fishing Zone of Uruguay and Argentina.     

Cranial morphological diversity of early,middle, and late Holocene Brazilian groups: Implications for human dispersion in Brazil

The history of human occupation in Brazil dates to at least 14 kyr BP, and the country has the largest record of early human remains from the continent. Despite the importance and richness of Brazilian human skeletal collections, the biological relationships between groups and their implications for knowledge about human dispersion in the country have not been properly explored. Here, we present a comprehensive assessment of the morphological affinities of human groups from East‐Central, Coastal, Northeast, and South Brazil from distinct periods and test for the best dispersion scenarios to explain the observed diversity across time. Our results, based on multivariate assessments of shape and goodness of fit tests of dispersion and adaptation models, favor the idea that Brazil experienced at least two large dispersion waves. The first dispersive event brought the morphological pattern that characterize Late Pleistocene groups continent‐wide and that persisted among East‐Central Brazil groups until recently. Within the area covered by our samples, the second wave was probably restricted to the coast and is associated with a distinct morphological pattern. Inland and coastal populations apparently did not interact significantly during the Holocene, as there is no clear signal of admixture between groups sharing the two morphological patterns. However, these results cannot be extended to the interior part of the country (Amazonia and Central Brazil), given the lack of skeletal samples in these regions. Am J Phys Anthropol 155:546–558, 2014. © 2014 Wiley Periodicals, Inc.     

Genetic diversity among Brazilian isolates of Beauveria bassiana: comparisons with non-Brazilian isolates and other Beauveria species

Aims:  The genetic diversity of Beauveria bassiana was investigated by comparing isolates of this species to each other (49 from different geographical regions of Brazil and 4 from USA) and to other Beauveria spp.
Methods and Results:  The isolates were examined by multilocus enzyme electrophoresis (MLEE), amplified fragment length polymorphism (AFLP), and rDNA sequencing. MLEE and AFLP revealed considerable genetic variability among B. bassiana isolates. Several isolates from South and Southeast Brazil had high similarity coefficients, providing evidence of at least one population with clonal structure. There were clear genomic differences between most Brazilian and USA B. bassiana isolates. A Mantel test using data generated by AFLP provided evidence that greater geographical distances were associated with higher genetic distances. AFLP and rDNA sequencing demonstrated notable genotypic variation between B. bassiana and other Beauveria spp.
Conclusion:  Geographical distance between populations apparently is an important factor influencing genotypic variability among B. bassiana populations in Brazil.
Significance and Impact of the Study:  This study characterized many B. bassiana isolates. The results indicate that certain Brazilian isolates are considerably different from others and possibly should be regarded as separate species from B. bassiana sensu latu . The information on genetic variation among the Brazilian isolates, therefore, will be important to comprehending the population structure of B. bassiana in Brazil.     

Breakdown of distyly and pin‐monomorphism in Psychotria carthagenensis Jacq. (Rubiaceae)

Rubiaceae contains the largest number of distylous species in the Angiosperms, but the evolution and control of distyly is poorly understood in this group. Atypical distylous populations and species have been described in this family and associated with disturbance, pollination failure and impaired reproductive success. Some of these atypical taxa belong to Psychotria, the largest genus in the family. In the present study, we investigate the pollination and breeding biology of Psychotria carthagenensis Jacq., a widely distributed species that has been described as typically distylous. Fieldwork was carried out mainly at the Panga Ecological Station, in Uberlândia, MG, Brazil. We carried out phenological observations, floral biology studies and hand pollination experiments within the Panga Ecological Station population. We complemented these data with herbarium and field surveys from elsewhere in Brazil. The studied population bloomed at the beginning of the rains (September–December). The main pollinators were Bombus and small Halictidae bees. The Panga Ecological Station population presented pin‐monomorphism with only two thrum individuals in more than 100 flowering individuals surveyed. Hand pollinations at the Panga Ecological Station showed self‐compatibility and intramorph compatibility. Typical distyly and isoplethy were found in other areas and both morphs appeared in herbarium material. However, pin‐monomorphism was also observed elsewhere in Brazil. Typical distyly, pin‐monomorphism and homostyly observed concurrently in Brazilian populations of P. carthagenensis indicate that alternative reproductive strategies, probably favoring selfing, appear to have developed independently in this species.     

Diversity biases in terrestrial mammalian assemblages and quantifying the differences between museum collections and published accounts: A case study from the Miocene of Nevada

Understanding diversity through time in the fossil record has primarily relied on the raw count of species within a given time interval, or species richness. These estimates are often derived from published fossil data, and standardized for sample size or geographic area. However, most methods that standardize richness by sample size are sensitive to changes in evenness, which introduces a potential problem with relying on published records: published accounts could be more even than the museum collections from which they are drawn. We address this bias in the context of mammalian paleodiversity, comparing published and museum collections of the Hemphillian Thousand Creek fauna to those of the Barstovian Virgin Valley fauna. We rarified specimen data, both number of identified specimens (NISP) and minimum number of individuals (MNI), and presence/absence data to compare published and museum data within and between faunas. Within faunas, published numbers of specimens are more even than museum samples, but the difference for localities in Virgin Valley is not significant. Neither published nor museum numbers of specimens indicate a significant difference between faunas, but the diversity pattern is reversed between the two data sets. Presence/absence rarefactions show no differences between sources; here, published data adequately sample the underlying museum records. Specimen-based evenness is not accurate in the published sample, and therefore we suggest that future studies of diversity in terrestrial mammalian assemblages must assess unpublished collections. Additionally, NISP data for Thousand Creek are more even than MNI data, suggesting that relying solely on NISP for assessing species diversity can also be misleading. Because publication bias alters richness and evenness, diversity estimates using published data must be circumspect about data sources.     

Marine fishes (Elasmobranchii and Teleostei) from the Santana Archipelago,a Marine Protected Area in the southwestern Atlantic

The Santana Archipelago (22°23′S, 41°42′W) is located at the northern limit of the South Brazil Bight in Southeastern Brazil, a major topographic feature of the South American continental shelf relevant in terms of fisheries, biogeography and conservation. Herein, the first inventory of the ichthyofauna of the Santana Archipelago is presented, with information on the distribution and conservation status of 147 species of the Teleostei and Elasmobranchii. Sampling was performed during 15 field expeditions between March 2013 and November 2015. A total of 6931 specimens were collected using bottom trawl, beach seine, hand net and scuba diving. Records of 28 species were based on photographs, and five species were recorded through underwater sighting. The Elasmobranchii was represented by nine species in eight families and six orders, and the Teleostei by 138 species in 54 families and 26 orders. Previous records of fishes from the Archipelago consist of 18 species deposited in fish collections; therefore, 129 species are reported herein for the first time. Most (114, 77.5%) species have large geographic distributions (western Atlantic: 81 species, 55.1%; eastern and western Atlantic: 33 species, 22.4%), but seven recorded species (4.8%) are endemic to the Brazilian Province. At the Global (IUCN) level, 12 species (8.1%) are threatened with extinction. Thirteen (8.8%) species are also considered as threatened at the Regional (Brazilian) level. These results highlight the relevance of the Santana Archipelago in the Brazilian conservationist context. Possible threats to the ichtyofauna of the Archipelago are discussed, and effective measures of conservation are presented.     

Sequence capture phylogenomics of historical ethanol‐preserved museum specimens: Unlocking the rest of the vault

Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics‐based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin‐fixed squamates and pinned insects. However, no study has thoroughly demonstrated this approach for historical ethanol‐preserved museum specimens. Alongside sequencing of “fresh” specimens preserved in >95% ethanol and stored at ?80°C, we used extraction techniques specifically designed for degraded DNA coupled with sequence capture protocols to sequence UCEs from historical museum specimens preserved in 70%–80% ethanol and stored at room temperature, the standard for such ethanol‐preserved museum collections. Across 35 fresh and 15 historical museum samples of the arachnid order Opiliones, an average of 345 UCE loci were included in phylogenomic matrices, with museum samples ranging from six to 495 loci. We successfully demonstrate the inclusion of historical ethanol‐preserved museum specimens in modern sequence capture phylogenomic studies, show a high frequency of variant bases at the species and population levels, and from off‐target reads successfully recover multiple loci traditionally sequenced in multilocus studies including mitochondrial loci and nuclear rRNA loci. The methods detailed in this study will allow researchers to potentially acquire genetic data from millions of ethanol‐preserved museum specimens held in collections worldwide.     

Brazilian melon landraces resistant to Podosphaera xanthii are unique germplasm resources

Podosphaera xanthii is the most important causal agent of powdery mildew in melon, a crop ranked within the most economically important species worldwide. The best strategy to face this fungus disease, which causes important production losses, is the development of genetically resistant cultivars. Genetic breeding programmes require sources of resistance, and a few ones have been reported in melon, mostly in Momordica and Acidulus horticultural groups. However, the existence of many races that reduces the durability of the resistance makes necessary to find new resistant genotypes with different genetic backgrounds. In this work, Brazilian germplasm, together with a set of Indian landraces, and the COMAV's (Institute for the Conservation and Breeding of Agricultural Biodiversity) melon core collection, representing the whole variability of the species, were assessed for resistance against some common races in Spain and Brazil and genotyped with a 123‐SNP (single nucleotide polymorphisms) genotyping platform to study the molecular relationships of the resistant accessions. In the first experiment, carried out in Valencia (Spain) in 2013, seventy‐nine melon accessions were evaluated using artificial inoculation. Five accessions selected as resistant were also evaluated against races 1, 3, and 5 in Mossoró (Brazil, 2015) and against race 3.5 in Valencia (2016) under greenhouse conditions, and under four field conditions in Brazil. The accessions, AL‐1, BA‐3, CE‐3, and RN‐2, within the Brazilian collection, presented resistance against all the races of P. xanthii assayed in all conditions tested. AL‐1, CE‐3 and RN‐2 were molecularly more similar to wild agrestis and Acidulus melons from Asia and Africa, while BA‐3 grouped with Momordica types. Molecular analysis also confirmed that these new Brazilian sources of resistance differ from those previously reported, constituting interesting materials to encourage genetic breeding programmes, especially in Brazil and Spain.     

Extension of the geographic range of Ateles chamek (Primates,Atelidae): evidence of river-barrier crossing by an amazonian primate

The black-faced black spider monkey (Ateles chamek) is endangered because of hunting and habitat loss. There are many gaps in our understanding of its geographic distribution. The Ucayali–Solimões–Amazon fluvial complex is currently recognized as the northern boundary of the species’ range, although published reports have indicated that it occurs north of the Rio Solimões. In this study we investigate published records, generate new field records, and assess the current information concerning the northern boundary of this species’ range. We conducted the study at the Mamirauá Sustainable Development Reserve in the central Brazilian Amazon, an area of 1,124,000 ha that consists entirely of Amazonian flooded forest (várzea). We collected data on the occurrence of the species from museum specimens and through field surveys, including interviews with local residents, direct observations, and the collection of new museum specimens. We confirmed the presence of A. chamek at 17 locations in the reserve, one of which was an island formed by a river bend cut-off that would have effectively taken any resident spider to the (new) north bank of the Solimões. We therefore conclude that fluvial dynamics were involved in creating the conditions for the dispersal and colonization of the species on the northern bank of the Rio Solimões. The data we present extends the known distribution of the species and increases its representation in protected areas.     

Hogfish Lachnolaimus maximus (Labridae) confirmed in the south‐western Atlantic Ocean

Based on material deposited in collections, photographic records and other reports from fishermen and divers, the occurrence of the hogfish Lachnolaimus maximus (Labridae) is confirmed in the south‐western Atlantic Ocean, near the Brazilian coast as far south as southern Brazil. The recognized range of this species should therefore be extended c. 3000 km further south.     

Isoenzymatic analysis of four Anopheles (Kerteszia) bellator Dyar & Knab (Diptera: Culicidae) populations

Anopheles bellator is a small silvatic bromelia-breeding mosquito and is a primary human malaria vector species in Southern Brazil. The bromelia-breeding habitat of the species should accompany the Atlantic forest coastal distribution, where bromeliads are abundant. Nonetheless, records on An. bellator collections show a gap in the species geographical distribution. An. bellator has been recorded in Southern Brazil and in the Brazilian states of Bahia and Paraíba. It appears again in the island of Trinidad, in Trinidad and Tobago. The aim of this work was to measure gene flow between different populations of An. bellator collected in the northern and southern extremes of the geographic distribution of this species. Mosquitoes were captured in forest borders in Santa Catarina, S?o Paulo, and Bahia states in Brazil and in the island of Trinidad in Republic of Trinidad and Tobago. Genetic distances varied between 0.076 and 0.680, based on enzymatic profiles from 11 distinct isoenzymes. Results indicate the existence of low-level gene flow between Brazilian populations of An. bellator, and a gene flow was even lower between the Brazilian and the Trinidad populations. This finding lead us to hypothesize that An. bellator did not spread along the coast, but reached northeastern areas through inland routes.     

Avian egg collections: museum collection bias driven by shape and size

Avian eggs exhibit substantial intra- and interspecific variation in shape, size and colour. Considerable efforts have been made to better understand the evolutionary drivers behind such variation, often using museum egg collections. Usually it is assumed that museum collections accurately represent the variation seen in natural populations, but this may not be the case if there is collection bias. Collection bias may lead to the over-representation of certain egg traits in collections, due to the aesthetic (or other) preferences of collectors. The aim of this study is to begin to look for the occurrence of potential collection bias in museum egg collections by comparing three shape indices (pointedness/asymmetry, elongation and polar asymmetry) and egg volume between subsets of eggs in museum collections with those of recently sampled eggs in the field for three different bird species: common guillemot Uria aalge, razorbill Alca torda and northern fulmar Fulmarus glacialis. We found no evidence of collection bias in our sampled razorbill and northern fulmar museum collection eggs, but some evidence for a bias in sampled museum collection eggs of common guillemots. Since the guillemot's egg differs from most bird eggs in being pyriform, we suggest that collection bias by historic egg collectors may be more prevalent in species with extreme egg traits. Researchers using museum egg collections to examine questions relating to egg shape should be aware of collection bias risks and consider how to minimise the effect of these possible biases on accumulated datasets.     

Triatoma rubrovaria (Blanchard, 1843) (Hemiptera: Reduviidae) I: isoenzymatic and chromatic patterns of five populations from the State of Rio Grande do Sul,Brazil

Triatoma rubrovaria has become the most frequently captured triatomine species since the control of T. infestans in the State of Rio Grande do Sul (RS), Brazil. In order to evaluate the genetic variability of this species, field collections were performed in four municipalities where it has been reported and distant from 75 to 322 km. Specimens were analyzed by color pattern and isoenzymes. Nine enzymatic loci were interpreted from nine enzymatic systems. The Santiago population was isolated from the others with chromatic monomorphism and diagnostic alleles at Idh and Pgm loci. The study shows the existence of, at least, two distinct populations of T. rubrovaria in RS with different phenotypic and genetic pattern.     

The true identity of Obama (Platyhelminthes: Geoplanidae) flatworm spreading across Europe

Since 2008 there have been many records in Europe (British Isles, Spain, France, Italy) of a large terrestrial planarian morphologically very similar to the Brazilian species Obama marmorata. Sequences of mitochondrial (Cox1) and nuclear (18S, 28S, ITS‐1 and EF) genes from European specimens and some from Brazil indicate that they belong to a species different from that of other specimens also collected in Brazil. Moreover, the phylogenetic results show that they are not sister‐species. Histological sections of both Brazilian and European specimens reveal subtle morphological differences between the two species. Obama marmorata is confined to Brazil, and the second, herein described new species, O bama nungara sp. nov. , is found in Brazil and Europe. These cryptic species may be syntopic in areas in Brazil. The new species occurs in human‐modified environments both in Brazil and in Europe. We also conclude that the specimens from Spain and Argentina identified previously as Obama marmorata belong to the new species.