Cryptic speciation in Brazilian Epiperipatus (Onychophora: Peripatidae) reveals an underestimated diversity among the peripatid velvet worms

Background

Taxonomical studies of the neotropical Peripatidae (Onychophora, velvet worms) have proven difficult, due to intraspecific variation and uniformity of morphological characters across this onychophoran subgroup. We therefore used molecular approaches, in addition to morphological methods, to explore the diversity of Epiperipatus from the Minas Gerais State of Brazil.

Methodology/Principal Findings

Our analyses revealed three new species. While Epiperipatus diadenoproctus sp. nov. can be distinguished from E. adenocryptus sp. nov. and E. paurognostus sp. nov. based on morphology and specific nucleotide positions in the mitochondrial cytochrome c oxidase subunit I (COI) and small ribosomal subunit RNA gene sequences (12S rRNA), anatomical differences between the two latter species are not evident. However, our phylogenetic analyses of molecular data suggest that they are cryptic species, with high Bayesian posterior probabilities and bootstrap and Bremer support values for each species clade. The sister group relationship of E. adenocryptus sp. nov. and E. paurognostus sp. nov. in our analyses correlates with the remarkable morphological similarity of these two species. To assess the species status of the new species, we performed a statistical parsimony network analysis based on 582 base pairs of the COI gene in our specimens, with the connection probability set to 95%. Our findings revealed no connections between groups of haplotypes, which have been recognized as allopatric lineages in our phylogenetic analyses, thus supporting our suggestion that they are separate species.

Conclusions/Significance

Our findings suggest high cryptic species diversity and endemism among the neotropical Peripatidae and demonstrate that the combination of morphological and molecular approaches is helpful for clarifying the taxonomy and species diversity of this apparently large and diverse onychophoran group.     

Taxonomic review of Cratocerus Dejean, 1829 (Coleoptera,Carabidae) with the description of six new species

A diagnosis of the South and Central American genus Cratocerus Dejean (Coleoptera: Carabidae) and a key to all species is provided. Eight species are recognized including six species that are newly described: Cratocerus sinesetosus sp. n. from French Guiana and Peru; Cratocerus multisetosus sp. n. from Costa Rica and Panama; Cratocerus tanyae sp. n. from Costa Rica, Guatemala, and Mexico; Cratocerus indupalmensis sp. n. a species widely distributed throughout Central and South America; Cratocerus kavanaughi sp. n. from French Guiana and Peru; and Cratocerus culpepperi sp. n. from Peru. A lectotype for Cratocerus sulcatus Chaudoir is designated. Habitus images are provided along with illustrations and images of male genitalia, female genitalia, and diagnostic morphological characters.     

SPECIES BOUNDARIES IN THE TOXIC DINOFLAGELLATE PROROCENTRUM LIMA (DINOPHYCEAE,PROROCENTRALES), BASED ON MORPHOLOGICAL AND PHYLOGENETIC CHARACTERS1

Wild and cultured specimens of Prorocentrum lima (Ehrenb.) F. Stein from 26 widely different areas in 13 countries were examined in order to determine consistent characters for delimiting species boundaries in this taxon. The morphological characters valve shape, valve size, valve ornamentation, number and shape of valve pores, number and shape of marginal pores, and periflagellar platelets were observed using LM and SEM, and two molecular genetic regions were sequenced. We identified stable morphological characters that were consistent among wild specimens and all cultures, which were valve shape, valve ornamentation, and number and arrangement of periflagellar platelets. All cultures of P. lima identified by these characters formed a monophyletic group in phylogenetic analyses based on the two genes, which, however, included the species Prorocentrum arenarium. P. arenarium was determined to be within the range of morphological variation of P. lima, and therefore we synonymize the two taxa. Within this monophyletic group, P. lima was divided into several subclades in the all phylogenetic analyses. There were no morphological characters specifically related to any one subclade. The subclades appeared to correlate broadly to sample collection regions, suggesting that geographically separated populations may have become genetically distinct within this epi‐benthic species. We have emended species boundaries in P. lima.     

The Phyllodonta latrata (Guenée) species group in Costa Rica (Geometridae,Ennominae)

Historically, the name Phyllodonta latrata (Guenée) has been applied to what is a complex of three undescribed species in Costa Rica. They are very similar in maculation, but can be differentiated by genitalic characters and barcodes. P. alajuela Sullivan, sp. n. occurs at lower altitudes in the northwestern part of Costa Rica whereas P. intermediata Sullivan, sp. n. and P. esperanza Sullivan, sp. n. are found at partially overlapping altitudes in the central mountain ranges.     

A new genus and species of Coenosiini from Costa Rica (Diptera,Muscidae, Coenosiinae)

Palpilongus gen. n. is herein described for one species – Palpilongus bifurcus sp. n., from Costa Rica, based on male and females. The striking morphological characters of the species – palpus very long, about as long as prementum; upper calypter truncate and very short and setae of male sternite 5 bifurcated, confirm that this new species is also a new genus in the tribe Coenosiini. Male and female terminalia were dissected and illustrated.     

Comparative sperm ultrastructure in Nemertea

Although the monophyly of Nemertea is strongly supported by unique morphological characters and results of molecular phylogenetic studies, their ingroup relationships are largely unresolved. To contribute solving this problem we studied sperm ultrastructure of 12 nemertean species that belong to different subtaxa representing the commonly recognized major monophyletic groups. The study yielded a set of 26 characters with an unexpected variation among species of the same genus (Tubulanus and Procephalothrix species), whereas other species varied in metric values or only one character state (Ramphogordius). In some species, the sperm nucleus has grooves (Zygonemertes virescens, Amphiporus imparispinosus) that may be twisted and give a spiral shape to the sperm head (Paranemertes peregrina, Emplectonema gracile). To make the characters from sperm ultrastructure accessible for further phylogenetic analyses, they were coded in a character matrix. Published data for eight species turned out to be sufficiently detailed to be included. Comparative evaluation of available information on the sperm ultrastructure suggests that subtaxa of Heteronemertea and Hoplonemertea are supported as monophyletic by sperm morphology. However, the data do not provide information on the existing contradictions regarding the internal relationships of “Palaeonemertea.” Nevertheless, our study provides evidence that sperm ultrastructure yields numerous potentially informative characters that will be included in upcoming phylogenetic analyses. J. Morphol. 2010. © 2010 Wiley‐Liss, Inc.     

A new species ofLentinula (Agaricales) from Central America

Lentinula aciculospora sp. nov. is described from a single Province in Costa Rica. Stature and habit of basidiomata of this species are similar to some otherLentinula taxa (i.e.L. edodes), but the elongate-cylindrical shape of basidiospores is a distinctive character ofL. aciculospora. The mating system ofL. aciculospora is tetrapolar as also found in other species of the genus, but this species is genetically isolated fromL. boryana, and all morphological variants ofL. edodes.     

Compilation of morphological and molecular data,a necessity for taxonomy: The case of Hormogaster abbatissae sp. n. (Annelida,Clitellata, Hormogastridae)

Conflict among data sources can be frequent in evolutionary biology, especially in cases where one character set poses limitations to resolution. Earthworm taxonomy, for example, remains a challenge because of the limited number of morphological characters taxonomically valuable. An explanation to this may be morphological convergence due to adaptation to a homogeneous habitat, resulting in high degrees of homoplasy. This sometimes impedes clear morphological diagnosis of species. Combination of morphology with molecular techniques has recently aided taxonomy in many groups difficult to delimit morphologically. Here we apply an integrative approach by combining morphological and molecular data, including also some ecological features, to describe a new earthworm species in the family Hormogastridae, Hormogaster abbatissae sp. n., collected in Sant Joan de les Abadesses (Girona, Spain). Its anatomical and morphological characters are discussed in relation to the most similar Hormogastridae species, which are not the closest species in a phylogenetic analysis of molecular data. Species delimitation using the GMYC method and genetic divergences with the closest species are also considered. The information supplied by the morphological and molecular sources is contradictory, and thus we discuss issues with species delimitation in other similar situations. Decisions should be based on a profound knowledge of the morphology of the studied group but results from molecular analyses should also be considered.     

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.     

Polystichum lilianae sp. nov. (Dryopteridaceae) and its relationships to P. fournieri and P. turrialbae

Morphological, isozyme, and cytological analyses of the small, pale-scaled polystichums from oakdominated montane rain forests in Costa Rica and Mexico reveal the presence of a separable undescribed species endemic to the Cordillera de Talamanca of Costa Rica. The new taxon,Polystichum lilianae, is an allotetraploid hypothesized to have the sympatricP. turrialbae as one diploid progenitor based on isozyme characters. The isozyme and morphometric data also support the inclusion ofP. smithii, described from southern Mexico, inP. turrialbae, described from Costa Rica. The namePolystichum fournieri, formerly used for all of these plants, applies to species endemic to Oaxaca and Chiapas, Mexico. It is not a progenitor ofP. lilianae.     

Using 18S rDNA to resolve diaptomid copepod (Copepoda: Calanoida: Diaptomidae) phylogeny: an example with the North American genera

The phylogenetic relationships among the numerous genera of diaptomid copepods remain elusive due to difficulties in obtaining sufficient numbers of phylogenetically informative morphological characters for cladistic analysis. Molecular phylogenetic techniques offer high potential to resolve phylogenetic relationships in the absence of sufficient morphological characters because of the ease in which many characters can be unambiguously coded. I present the first molecular phylogeny for diaptomid copepod genera using 18S rDNA. Specifically, I test Light’s (1939) hypothesis regarding the interrelationships among the North American diaptomid genera. The 18S phylogeny is remarkably consistent with Light’s hypothesis. The endemic North American genera represent a monophyletic group exclusive of the non-endemic genera. Moreover, his hypothesized basal genus for the North America genera, Hesperodiaptomus, is the basal genus in this analysis. However, his Leptodiaptomus group is not reciprocally monophyletic with his Hesperodiaptomus group, but is rather a derived member of the latter group. Finally, the genus Mastigodiaptomus is found to be more closely allied with the non-endemic genera, as Light suggested. This phylogeny contributes heavily to the understanding of phylogenetic relationships among North American diaptomids and has large implications for the systematics of diaptomids in general. The use of 18S rDNA sequences in phylogenetic analyses of diaptomid copepods can be used to confirm the monophyly of recognized genera, the interrelationships among genera, and subsequent biogeographic interpretation of the family’s diversification. The use of molecular data, such as 18S rDNA sequences, to test phylogenetic hypotheses based on a very limited number of morphological characters will be a particularly useful approach to phylogenetic analysis in this system.     

Morphology and molecular phylogeny of the benthic dinoflagellates (Dinophyceae,Peridiniales) Amphidiniopsis crumena n. sp. and Amphidiniopsis nileribanjensis n. sp.

Amphidiniopsis is a benthic, heterotrophic and thecate dinoflagellate genus that has a smaller epitheca and larger hypotheca. The genus contains 24 described species, but is considered to be polyphyletic based on morphological characters and molecular phylogenetics. In this study, two new species were discovered from two distant sampling localities, Amphidiniopsis crumena sp. nov. from Japan, and Amphidiniopsis nileribanjensis sp. nov., from Australia. These species have a uniquely shaped, additional second postcingular plate. Both species are dorsoventrally flattened, an apical hook is present, and have six postcingular plates. The plate formula is: APC 4′ 3a 7″ ?C 4?S 6″′ 2″″. The cells of these species were examined with LM and SEM, and molecular phylogenic analyses were performed using 18S and 28S rDNA. These species are distinguished by the presence of spines on the hypotheca and touching of the sixth postcingular plate and the anterior sulcal plate. Their shape and disposition of several thecal plates also differ. Molecular phylogenetic analyses showed that the two new species formed a monophyletic clade and did not belong to any morphogroup proposed by previous studies. Considering the morphological features and the molecular phylogenetic results, a new morphogroup is proposed, Amphidiniopsis morphogroup VI (‘crumena group’).     

How many marmoset (Primates: Cebidae: Callitrichinae) genera are there? A phylogenetic analysis based on multiple morphological systems

The marmosets, tribe Callitrichini, are the most speciose clade in the subfamily Callitrichinae, containing 21 species. However, there is no consensus among molecular and morphological systematists as to how many genera should be recognized for the group. To test the morphological support for the alternative generic classifications, this study presents a comprehensive phylogenetic analysis. It is the first such analysis to include all 21 species and employ continuous and discrete osteological, pelage and tegument, karyological and vocal characters. This dataset was combined with nucleotide sequences from two mitochondrial and four nuclear regions. Separate analyses showed that, among morphological datasets, osteological characters were best at solving relationships at more inclusive levels, whilst pelage characters were most informative at the interspecific level. This suggests the presence of different transformation rates for the two character sets. When a single most parsimonious tree was obtained using the 83‐character matrix, three main clades were identified, supporting the division of the marmosets into three genera: Callithrix, Cebuella and Mico. The total evidence analysis that included an additional 3481 molecular characters corroborated most of the morphology‐based clades and also supported a three‐genus classification of the marmosets. This is the first morphological study to support an Amazonian marmoset clade (Cebuella + Mico), which is also strongly supported in exclusively molecular phylogenies, and to synonimize Callibella under Mico.     

The fish pathogen Flavobacterium columnare represents four distinct species: Flavobacterium columnare,Flavobacterium covae sp. nov., Flavobacterium davisii sp. nov. and Flavobacterium oreochromis sp. nov., and emended description of Flavobacterium columnare

Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish and four discrete genetic groups exist within the species, suggesting that the species designation requires revision. The present study determined the taxonomic status of the four genetic groups of F. columnare using polyphasic and phylogenomic approaches and included five representative isolates from each genetic group (including type strain ATCC 23463^T; genetic group 1). 16S rRNA gene sequence analysis revealed genetic group 2 isolate AL-02-36^T, genetic group 3 isolate 90-106^T, and genetic group 4 isolate Costa Rica 04-02-TN^T shared less than <98.8 % sequence identity to F. columnare ATCC 23463^T. Phylogenetic analyses of 16S rRNA and gyrB genes using different methodologies demonstrated the four genetic groups formed well-supported and distinct clades within the genus Flavobacterium. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (GGDC) values between F. columnare ATCC 23463^T, genetic group 2 isolate AL-02-36^T, genetic group 3 isolate 90-106^T, and genetic group 4 isolate Costa Rica 04-02-TN^T were less than 90.84% and 42.7%, respectively. Biochemical and physiological characteristics were similar among the four genetic groups; however, quantitative differences in fatty acid profiles were detected and MALDI-TOF analyses demonstrated numerous distinguishing peaks unique to each genetic group. Chemotaxonomic, MALDI-TOF characterization and ANI/GGDC calculations afforded differentiation between the genetic groups, indicating each group is a discrete species. Herein, the names F. covae sp. nov. (AL-02-36^T), F. davisii sp. nov. (90-106^T), and F. oreochromis sp. nov. (Costa Rica 04-02-TN^T) are proposed to represent genetic groups 2, 3, and 4, respectively.     

Leaf structure of Bromelia and its significance for the evolution of Bromelioideae (Bromeliaceae)

This study investigated the leaf structure of Bromelia and its importance for understanding the evolution of Bromelioideae (Bromeliaceae). Because of the scarcity of informative molecular characters in Bromeliaceae, this study evaluates the relevance of anatomical characters for the taxonomy and phylogeny of Bromelia and the subfamily Bromelioideae. Anatomical studies in monocots have shown that the combined application of anatomical and external morphological characters from leaf structure can improve the taxonomic delimitation of species, genera and subgenera, and is very informative for inferring phylogenies. The current study analyzed the leaves of 27 species of Bromelia and found that the most important characters for the systematics of this group are the occurrence of a water storage hypodermis, the number of stalk cells of peltate scales, the presence of a ribbed abaxial surface, the occurrence of palisade parenchyma on the adaxial side, the shape of the cells that surround the air lacunae, the presence of raphides and secretory channels, and the occurrence of fibrous extensions on the bundle sheath on minor veins. Combining our results with those described for the family, we made a list of the anatomical characters that can be used in phylogenetic studies of Bromelioideae.