Costus maasiorum: a new species of Neotropical Costaceae from western Ecuador

Western Ecuador harbours high plant diversity and endemism. The region of Manabí has known intense deforestation over the last decades, but lowland rain forests persist in a network of small forest fragment patches. Here, we describe two new magnoliid tree species from a small privately owned forest fragment known as La Esperanza reserve, in the El Carmen canton (Manabí): Aniba ecuadorica (Lauraceae) and Guatteria esperanzae (Annonaceae). For both species a detailed morphological description, a preliminary conservation status following IUCN criteria, distribution maps and high quality photographs are provided. This represents the second species of Aniba known to occur in western Ecuador, while there are 14 species of Guatteria documented for Ecuador west of the Andes. Aniba ecuadorica is only known from two localities and has a preliminary IUCN conservation status of Critically Endangered, while Guatteria esperanzae is known from six localities and is suggested to be Endangered. Finally, we provide a quick overview of Guatteria species in western Ecuador with a key to the species in the region. The description of these two new tree species underlines the important need of prospection and conservation of the remnant forests in the Manabí region of western Ecuador. We also stress the importance of privately owned forest fragments for biodiversity conservation.

Environmental gradients have the potential to influence genetic differentiation among populations ultimately leading to allopatric speciation. However, environmental gradients can also facilitate hybridization between closely related taxa. We investigated a putative hybrid zone in western Ecuador, involving two polytypic wren species (Aves: Troglodytidae), Campylorhynchus zonatus and C. fasciatus. Our study addressed two primary questions: (1) Is there evidence of population structure and genetic admixture between these taxa in western Ecuador? and (2) What are the relative contributions of isolation by distance and isolation by the environment to the observed genetic differentiation along the environmental gradient in this region? We analyzed 4409 single‐nucleotide polymorphisms (SNPs) from 112 blood samples sequenced using ddRadSeq and a de novo assembly. The optimum number of genetic clusters ranged from 2 to 4, aligning with geographic origins, known phylogenetics, and physical or ecological constraints. We observed notable transitions in admixture proportions along the environmental gradient in western Ecuador between C. z. brevirostris and the northern and southern genetic clusters of C. f. pallescens. Genetic differentiation between the two C. f. pallescens populations could be attributed to an unreported potential physical barrier in central western Ecuador, where the proximity of the Andes to the coastline restricts lowland habitats, limiting dispersal and gene flow, especially among dry‐habitat specialists. The observed admixture in C. f. pallescens suggests that this subspecies may be a hybrid between C. z. brevirostris and C. fasciatus, with varying degrees of admixture in western Ecuador and northwestern Peru. We found evidence of isolation by distance, while isolation by the environment was less pronounced but still significant for annual mean precipitation and precipitation seasonality. This study enhances our understanding of avian population genomics in tropical regions.

The promise of pharmacogenetics is to elucidate the inherited basis of differences between individual responses to drugs, in order to identify the right drug and dose for each patient. Genetic polymorphisms are implicated in the interindividual variability of the pharmacokinetic or pharmacodynamic characteristics of immunosuppressive drugs. The first pharmacogenetic trait identified was monogenic, and concerned the prototypic example of thiopurine methyltransferase (TPMT) implicated in azathioprine metabolism. Individuals with low TPMT activity, inherited in an autosomal codominant fashion, are at risk of drug-induced myelosuppression. TPMT activity determination and DNA-based tests are now used in clinical practice. It has been also demonstrated that there is a link between the polymorphisms of the cytochrome P450 3A5, 3A4 and the multidrug resistance-1 (MDR1) genes, and the daily dose necessary to achieve adequate blood tacrolimus levels. Analysis of MDR1 haplotypes or using the association of the different genes might further improve predictions. Since genotyping methods improve rapidly, it will soon be easy to test for thousands of single nucleotide polymorphisms in one assay. Present challenges are to determine the genes of interest and to validate such determination prospectively in clinical practice.

Much research has focused on identifying traits that can act as useful indicators of how habitat loss affects the extinction risk of species, and the results are mixed. We developed 2 simple, rapid-assessment models of the susceptibility of species to habitat loss. We based both on an index of range size, but one also incorporated an index of body mass and the other an index combining habitat and dietary specialization. We applied the models to samples of birds (Accipitridae and Bucerotidae) and to the lemurs of Madagascar and compared the models' classifications of risk with the IUCN's global threat status of each species. The model derived from ecological attributes was much more robust than the one derived from body mass. Ecological attributes identified threatened birds and lemurs with an average of 80% accuracy and endangered and critically endangered species with 100% accuracy and identified some species not currently listed as threatened that almost certainly warrant conservation consideration. Appropriate analysis of even fairly crude biological information can help raise early-warning flags to the relative susceptibilities of species to habitat loss and thus provide a useful and rapid technique for highlighting potential species-level conservation issues. Advantages of this approach to classifying risk include flexibility in the specialization parameters used as well as its applicability at a range of spatial scales.

Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease

Sharks, skates, rays and chimaeras (chondrichthyans) are of high conservation concern; especially obligate freshwater chondrichthyans, given their restricted ranges, proximity to humans, and threatened habitat. The biological traits that increase chondrichthyan susceptibility to extinction are well known. Less attention has been put on the human determinants of chondrichthyan conservation status. Socio-economic development, scientific research, and exploitation affect natural resource management and conservation. We assessed the relationship between these factors and chondrichthyan conservation. We ran generalized linear models with number of Threatened (THR), Least Concern (LC), and Data Deficient chondrichthyans as dependent variables, and indicators of socio-economic development (governance, human security, human development, and corruption indices), scientific research (number of papers on chondrichthyans), and exploitation (total, industrial, and foreign catch of chondrichthyans), as independent variables. Human density instead of exploitation was a predictor for obligate freshwater chondrichthyans. Socio-economic development (regardless of the index used) and scientific research were associated to desirable conservation status, such as low THR and high LC, for both marine and obligate freshwater species. Exploitation and human density (for obligate freshwater chondrichthyans) were associated to negative conservation status, i.e. high THR and low LC. Current human density projections translated into a 69% decrease in obligate freshwater chondrichthyans LC by 2050. Development produces desirable conservation status for chondrichthyans, but resource overconsumption must be reduced. Scientific research appears to assist sustainable use of chondrichthyan resources, and should be promoted in developing countries. Assessment and conservation of obligate freshwater chondrichthyans, and freshwater biota in general, must be pursued with urgency.

Begonia jocotocoi is a new species described from the Buenaventura Reserve in El Oro Province, south-west Ecuador. The new species morphologically resembles Begonia serotina, but differs by its minutely bullate leaf lamina (vs. smooth), the dense red long trichomes that cover the petioles and the lower surface of the leaf lamina, the latter of which distinctly become purple at maturity (vs. usually glabrous or occasionally with an indument of minute glandular white hairs and pale green below), presence of a pair of bracteoles directly beneath the pistillate flowers (vs. bracteoles absent), and the pedicels and also sometimes the abaxial surfaces of most floral whorls having a sparse cover of glandular hairs (vs. glabrous to puberulous). Photos of the new species and a distribution map are provided. Relationships with other species are discussed and the species’ preliminary conservation status is assigned as critically endangered (CR).

Background and aims – The genus Eulophia (Orchidaceae) is revised for Nigeria, Cameroon, Equatorial Guinea, Gabon, and the Republic of the Congo. The aims are: to present a morphological characterization of the main vegetative and reproductive features of Eulophia to clarify the delimitation of the taxa within the genus in the studied countries; to provide an updated identification key and an updated checklist of the genus with nomenclatural data, distribution maps, ecological information, and preliminary conservation status. This revision may serve as a basis for future studies of the genus in other regions of Africa.Material and methods – Relevant material kept in BM, BR, FHI, HBG, K, MA, P, and WAG was examined, using standard practices of herbarium taxonomy. Vegetative and reproductive structures were analysed. MapMaker was used to produce the distribution maps.Key results – A total of 24 species are recognised in the study area. The variability of perennating organs, leaves, sepals and petals, lip (including ornamentation), spur, and anther cap are described and depicted, and were found to be informative for species recognition. A taxonomic treatment is given with an identification key, synonymy, distribution maps, preliminary conservation status, and specimen citations. Eulophia galeoloides is neotypified, E. brevipetala, E. leonensis, E. penduliflora, and Lissochilus elatus are lectotypified. According to our study, we consider E. parvula a synonym of E. pyrophila. E. sordida is considered as a doubtful species in the study area.

We describe here the new species Pleroma goyazense, including illustrations, geographic distribution, habitat data, and preliminary conservation status according to the International Union for Conservation of Nature (IUCN) Red list criteria. We also propose to synonymize Pleroma nodosum under Pleroma robustum, a decision corroborated by the study of Pleroma species with similarities to P. goyazense. Pleroma goyazense is endemic to the state of Goiás, Brazil, occurring in cerrado rupestre (rupestrine savanna) on rocky outcrops or crevices, environments that are also shared by similar species P. crassirame and P. robustum. Pleroma goyazense differs from P. crassirame in having sparsely leaves arranged on the upper branches and pedoconnective stamens with a dorsal appendage. It also differs from P. robustum in having lanceolate, non-involucral bracteoles, and sepals acuminate at the apex.

Pyruszhaoxuanii is described as a new species from Guangdong Province, China, within the genus Pyrus, specifically under P.subg.Pashia. Although it shares morphological similarities with P.calleryana, P.zhaoxuanii can be distinguished by its uniquely small, obovate, leathery leaves, which have an obtuse apex and short petioles. A phylogenetic analysis based on single nucleotide polymorphisms (SNPs) indicated that P.zhaoxuanii forms an independent branch within Pyrus and is categorized in the Oriental clade, P.subg.Pashia. Currently, this species has only been recorded in the Danxiashan National Nature Reserve. Considering its potential distribution and population size, we recommend classifying this species as Least Concern (LC) according to the IUCN Red List classifications and criteria.

Single nucleotide polymorphisms (SNPs) are becoming increasingly popular markers for studying a variety of biological phenomena. This paper describes the development and analysis of a set of SNP markers for the basidiomycete fungus Tricholoma matsutake. T. matsutake is a gourmet mycorrhizal mushroom primarily associated with pine forests. However, little is known about its genetics and genomic variation, including SNP variation. To identify and analyse SNPs in T. matsutake, a genomic library was constructed and >72,000 nt were analysed from >200 random clones. Primers from 20 sequenced fragments were then designed to amplify and sequence >10,000 bp sequences from the original strain, from which the genomic library was constructed, as well as another strain from >350 km away; both strains were from south-western China. These two strains had similar intra-strain SNP frequencies (1.104 and 1.278 % per nucleotide, respectively). The combined analysis revealed that 14 of the 20 examined fragments contained SNPs, ranging from two to 47 per fragment, and yielding a total of 178 SNPs out of the 10 428 sequenced nucleotides (an SNP frequency of 1.707 %). Among the 178 SNPs, one site had three alternative nucleotides, while the remaining 177 had two each, with 148 transitions and 29 transversions, resulting in a combined transition to transversion ratio of 5.1. In addition, the haplotype phases of all SNPs within individual fragments for both strains were determined. Phylogenetic analyses of these haplotypes revealed three kinds of haplotype relationship, including haplotype sharing both within and between strains. Furthermore, a subset of the SNPs detectable by restriction enzyme digests was screened for its distribution among 31 additional wild strains from five distinct locations in south-western China. The implications of these SNPs and haplotypes for our understanding of the genetics, population history, ecology and evolution of this important mushroom species are discussed.

Using the fluorescence labeled capillary electrophoresis of multi-PCR technique, the single nucleotide polymorphism (SNP) typing system of fragment length discrepant allele specific fluorescence labeled multi-PCR technique is established based on the principle of allele-specific PCR. The typing of the 13 SNP loci can be completed simultaneously according to the length of PCR products and the number of product peaks. It appears a single product peak when the SNP is homozygous, and two product peaks with 4 bp differences will appear when it is heterozygous. By using this system, we conducted population census about allele frequencies for 13 autosomal SNP loci in Southern Liaoning Han samples, Mongolian samples in Inner Mongolia and Zhuang samples in Guangxi area, and got the allele frequencies of the 13 SNP loci in the three populations, then preliminarily discussed their genetic relationship by comparing their differences in allelic polymorphism. The results indicate that the allelic distributions of the 13 SNP loci in the three populations are polymorphic, and the difference is significant in some SNP loci (P< or =0.01). The sampling survey shows that the result is consistent with Hardy-Weinberg equilibrium, and Han population in southern Liaoning has relatively closer relationship with Mongolian in Inner Mongolia than with Zhuang population in Guangxi by origin.

A taxonomy of the genus Phyllodium Desv. in Cambodia, Laos, and Vietnam is presented. The plant specimens collected from the fields and herbarium specimens kept at Asian and European herbaria are examined. The IUCN conservation status of each species at regional and national levels is assessed. Five species are enumerated, viz., Phyllodium elegans (Lour.) Desv., P. kurzianum (Kuntze) H.Ohashi, P. longipes (Craib) Schindl., P. pulchellum (L.) Desv., and P. vestitum Benth. Lectotypification of two names, Desmodium longipes Craib and D. tonkinense Schindl., is performed. A key to the species, description, distribution, ecology, phenology, vernacular names, full list of specimens examined, and photographs are provided. The conservation status of five Phyllodium species varies across Cambodia, Laos, Vietnam, and Indochina. Phyllodium elegans and P. pulchellum are consistently Least Concern (LC) in all regions. Phyllodium kurzianum is Data Deficient (DD) in Laos, Near Threatened (NT) in Vietnam, and LC in Indochina. Phyllodium longipes is EN in Cambodia but LC elsewhere. Phyllodium vestitum is NT in Cambodia, Vulnerable (VU) in Laos and Vietnam, and LC in Indochina. The taxonomic information provided in this work will contribute to the advancement of the Flora of Cambodia, Laos, and Vietnam and the conservation status of each species proposed in this paper can be used for future conservation planning.

Baltic and Arctic ecotypes of the marine midge Clunio emerged from a recent adaptive radiation, which is based on standing genetic variation at many loci involved in time-keeping and nervous system development.

Baltic and Arctic ecotypes of the marine midge Clunio emerged from a recent adaptive radiation, which is based on standing genetic variation at many loci involved in time-keeping and nervous system development.