Unmasking alpha diversity,cladogenesis and biogeographical patterning in an ancient panarthropod lineage (Onychophora: Peripatopsidae: Opisthopatus cinctipes) with the description of five novel species

Speciation and biogeographical patterning in the velvet worm Opisthopatus cinctipes was examined under a null hypothesis that numerous discrete lineages are nested within the species. A total of 184 O. cinctipes specimens, together with a single specimen of each of the two congeneric point endemic sister species (O. roseus and O. herbertorum), were collected throughout the forest archipelago in the Eastern Cape, KwaZulu‐Natal and Mpumalanga provinces of South Africa. All specimens were sequenced for two partial mitochondrial DNA loci (COI and 12S rRNA), while a single specimen from each locality was sequenced for the nuclear 18S rRNA locus. Evolutionary relationships were assessed using maximum‐likelihood and Bayesian inferences, while divergence time estimations were conducted using BEAST. A Bayesian species delimitation approach was undertaken to explore the number of possible novel lineages nested within Opisthopatus, while population genetic structure was examined for the COI locus using ARLEQUIN. Phylogenetic results revealed that O. cinctipes is a species complex comprising seven geographically discrete and statistically well‐supported clades. An independent statistical approach to species delimitations circumscribed ca. 67 species. Results from divergence time estimation and rate constancy tests revealed near constant net diversification occurring throughout the Eocene and Oligocene with subdivision of ranges during the Miocene. Gross morphological characters such as leg pair number within O. cinctipes were invariant, while dorsal and ventral integument colour was highly polymorphic. However, scanning electron microscopy revealed considerable differences both between and within clades. The caveats associated with both morphological and algorithmic delineation of species boundaries are discussed. The five novel Opisthopatus species are described.     

Unravelling evolutionary lineages among South African velvet worms (Onychophora: Peripatopsis) provides evidence for widespread cryptic speciation

The endemic South African velvet worm genus Peripatopsis currently contains eight recognized species described from variable morphological characters and the current taxonomy is unsatisfactory. In an attempt to investigate evolutionary relationships within Peripatopsis, we collected 137 individuals from 34 sample localities for six of the eight species. Sequence data derived from two partial mitochondrial (mt)DNA gene loci (COI and 12S rRNA), as well as partial sequence data from the ribosomal nuclear 18S rDNA locus in combination with gross morphological characters and scanning electron microscopy (SEM), was used to examine evolutionary relationships. Phylogenetic relationships were investigated using minimum evolution (ME) and Bayesian inferences (BI). Additionally, we also undertook a maximum likelihood (ML) analyses on the combined DNA sequence data set. The combined DNA evidence topologies derived from the ME, BI, and ML was highly congruent and was characterized by the presence of multiple lineages within recognized taxa. Peripatopsis clavigera, Peripatopsis moseleyi, and Peripatopsis sedgwicki each comprised two evolutionary lineages; Peripatopsis capensis comprised three; and Peripatopsis balfouri comprised six operational taxonomic units respectively. Genealogical exclusivity at both mtDNA and nuclear DNA among the geographically coherent groups coupled with pronounced sequence divergence suggested a two‐fold increase in the number of species within Peripatopsis. Previously used gross morphological characters (such as the number of leg pairs and colour) were either highly variable within operational taxonomic units, or were invariant, suggesting that alternative morphological characters are necessary for species discrimination. SEM results revealed potentially useful diagnostic characters that can discriminate between at least discriminate some of the newly‐identified lineages. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society 2009, 97 , 200–216.     

DNA barcoding reveals twelve lineages with properties of phylogenetic and biological species within Melitaea didyma sensu lato (Lepidoptera,Nymphalidae)

The complex of butterfly taxa close to Melitaea didyma includes the traditionally recognized species Melitaea didyma, Melitaea didymoides and Melitaea sutschana, the taxa that were recognized as species only relatively recently (Melitaea latonigena, Melitaea interrupta, Melitaea chitralensis and Melitaea mixta) as well as numerous described subspecies and forms with unclear taxonomic status. Here analysis of mitochondrial DNA barcodes is used to demonstrate that this complex is monophyletic group consisting of at least 12 major haplogroups strongly differentiated with respect to the gene COI. Six of these haplogroups are shown to correspond to six of the above-mentioned species (Melitaea didymoides, Melitaea sutschana, Melitaea latonigena, Melitaea interrupta, Melitaea chitralensis and Melitaea mixta). It is hypothesized that each of the remaining six haplogroups also represents a distinct species (Melitaea mauretanica, Melitaea occidentalis, Melitaea didyma, Melitaea neera, Melitaea liliputana and Melitaea turkestanica), since merging these haplogroups would result in a polyphyletic assemblage and the genetic distances between them are comparable with those found between the other six previously recognized species.     

Morphological, cytogenetic and allozymic variation within Cephalofovea (Onychophora: Peripatopsidae) with descriptions of three new species

Variation within and between populations of Cephalofovea (Peripatopsidae) has been examined by allozyme, karyological and morphological analyses. Four groups are recognized on the basis of allozyme electrophoresis. One group includes specimens from the type locality of the only described species of the genus, C. tomahmontis. While karyotypic and morphological character states show considerable inter-group variation, the distributions of these states among groups are not concordant when different characters are compared. However, each group of populations is uniquely defined by the full suite of character states it possesses. The four groups are recognized here as distinct species with three species described as new.     

Ultrastructure of the eggshell and its formation in Planipapillus mundus (Onychophora: Peripatopsidae)

Although the majority of onychophorans are viviparous or ovoviviparous, oviparity has been described in a number of species found exclusively in Australia and New Zealand. Light microscopy and scanning and transmission electron microscopy were used to examine developing eggs and the reproductive tract of the oviparous Planipapillus mundus. Deposited eggs and fully developed eggs dissected from the terminal end of the uteri have an outer thick, slightly opaque chorion, and an inner thin, transparent vitelline membrane. The chorion comprises an outermost extrachorion, sculptured with domes equally spaced over the surface; a middle exochorion, with pores occurring in a pattern of distribution equivalent to that of the domes of the extrachorion above; and an innermost, thick endochorion consisting of a spongelike reticulum of cavities comparable to the respiratory network found in insect eggs. The vitelline membrane lies beneath the chorion, from which it is separated by a fluid‐filled space. The vitelline membrane tightly invests the developing egg. Examination of oocytes in the ovary and developing eggs at various stages of passage through the uterus indicate that the majority of chorion deposition occurs in the midregion of the uterus, where vast networks of endoplasmic reticulum are present in the columnar epithelium. The vitelline membrane, however, is believed to begin its development as a primary egg membrane, surrounding the developing oocytes in the ovary. The vitelline membrane is transformed after fertilization, presumably by secretions from the anterior region of the uterus; hence, it should be more accurately referred to as a fertilization membrane. Aspects of the reproductive biology of P. mundus are also included. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.     

Pangenome inventory of Burkholderia sensu lato,Burkholderia sensu stricto,and the Burkholderia cepacia complex reveals the uniqueness of Burkholderia catarinensis

Here the pangenome analysis of Burkholderia sensu lato (s.l.) was performed for the first time, together with an updated analysis of the pangenome of Burkholderia sensu stricto, and Burkholderia cepacia complex (Bcc) focusing on the Bcc B. catarinensis specific features of its re-sequenced genome. The pangenome of Burkholderia s.l., Burkholderia s.s., and of the Bcc was open, composed of more than 96% of accessory genes, and more than 62% of unknown genes. Functional annotations showed that secondary metabolism genes belonged to the variable portion of genomes, which might explain their production of several compounds with varied bioactivities. Taken together, this work showed the great variability and uniqueness of these genomes and revealed an underexplored unknown potential in poorly characterized genes. Regarding B. catarinensis 89^T, its genome harbors genes related to hydrolases production and plant growth promotion. This draft genome will be valuable for further investigation of its biotechnological potentials.     

Anatomy and systematics of Dendroseris (sensu lato)

Anatomical study of the genusDendroseris (Compositae: Cichorieae), endemic to the Juan Fernandez Islands, was undertaken to determine if segregate genera were valid. Other questions include the significance of pith bundles and of receptacular bristles, and whether the ancestors of these peculiar rosette trees and shrubs were woody or herbaceous. Anatomical evidence, when added to that from gross morphology, suggests that the segregation as distinct genera ofRea, Phoenicoseris, andHesperoseris is probably not justified, and that they are better treated as subgenera ofDendroseris. Differences in pollen morphology, floral trichomes, achene and leaf anatomy provide good species characteristics. These all appear, respectively, as variations on a basic plan, andDendroseris can be envisaged as derived from a common stock in the Juan Fernandez Islands. The genus is not particularly primitive within the family or tribe. The presence of additional bundles in the flowers ofD. litoralis may be interpreted as related to gigantism. The separate corolla lobes inD. gigantea probably do not represent a vestige of an actinomorphic condition. Pith bundles inDendroseris may have been present in ancestors; in any case, they seem likely to have increased in prominence with increase in stem diameter. Available evidence seems to favor the interpretation of growth forms inDendroseris as derived from an herbaceous ancestry.     

A pheromonal function for the crural glands of the onychophoran Cephalofovea tomahmontis (Onychophora: Peripatopsidae)

A characteristic feature of onychophorans is the presence of crural glands in males. These exocrine glands open on the ventral surface at the base of the legs. Their restriction to males suggests a sexual function. Histochemical staining of the glands indicates that their secretion has both a lipid and a protein component. Behavioural bioassays show that the secretion acts as a pheromone attractive to conspecific females. The production of a sex pheromone in onychophorans is discussed in relation to their ecology and phylogeny.     

Cryptic goldfields: a molecular phylogenetic reinvestigation of Lasthenia californica sensu lato and close relatives (Compositae: Heliantheae sensu lato)

Maximum parsimony analysis of DNA sequence data from the internal and external transcribed spacer (ITS and ETS) regions of 18S-26S nuclear ribosomal DNA and the 3' trnK intron of chloroplast DNA from over 60 populations of Lasthenia sect. Amphiachaenia yielded a well-supported tree showing that the most common species of Lasthenia, L. californica sensu lato (s.l.), is not monophyletic. Members of Lasthenia californica s.l. belong to two well-supported but morphologically cryptic clades. One clade includes members of L. macrantha; the other represents a basally divergent lineage in L. sect. Amphiachaenia. Members of each clade can be diagnosed by pappus morphology and by geographic distribution, except for epappose plants that occur in a broad region of sympatry in central California. Overall diversification in the clade corresponding to L. sect. Amphiachaenia has been accompanied by minimal morphological divergence, which has resulted in previously underappreciated cryptic diversity.     

Saccharomyces barnetti andSaccharomyces spencerorum: two new species ofSaccharomyces sensu lato (van der Walt)

In the course of a study of DNA base sequence homology, 19 strains labelled asSaccharomyces exiguus, its imperfect state,Candida holmii, orC. milleri were examined. Results confirmed the separation ofC. milleri as a separate species. The remaining strains can be divided into three distinct groups of genomic relatedness. The type cultures ofS. exiguus andC. holmii form a cluster with 10 other strains showing variable reassociation values ranging from 100 to 40%. The remaining four strains comprise two separate species showing no nucleotide relatedness between themselves nor to either theS. exiguus complex or toC. milleri. Physiological analyses demonstrate that it is possible to separate these four taxa on the basis of a few simple tests. The two new species are described respectively asSaccharomyces barnetti honoring James Barnett in recognition of his invaluable work in the field of yeast taxonomy andSaccharomyces spencerorum in honor of J.F.T. and Dorothy M. Spencer who have made innumerable contributions to the genetics and biotechnological application of yeasts.     

Multilocus microsatellite typing (MLMT) of strains from Turkey and Cyprus reveals a novel monophyletic L. donovani sensu lato group

Background

New foci of human CL caused by strains of the Leishmania donovani (L. donovani) complex have been recently described in Cyprus and the Çukurova region in Turkey (L. infantum) situated 150 km north of Cyprus. Cypriot strains were typed by Multilocus Enzyme Electrophoresis (MLEE) using the Montpellier (MON) system as L. donovani zymodeme MON-37. However, multilocus microsatellite typing (MLMT) has shown that this zymodeme is paraphyletic; composed of distantly related genetic subgroups of different geographical origin. Consequently the origin of the Cypriot strains remained enigmatic.

Methodology/Principal Findings

The Cypriot strains were compared with a set of Turkish isolates obtained from a CL patient and sand fly vectors in south-east Turkey (Çukurova region; CUK strains) and from a VL patient in the south-west (Kuşadasi; EP59 strain). These Turkish strains were initially analyzed using the K26-PCR assay that discriminates MON-1 strains by their amplicon size. In line with previous DNA-based data, the strains were inferred to the L. donovani complex and characterized as non MON-1. For these strains MLEE typing revealed two novel zymodemes; L. donovani MON-309 (CUK strains) and MON-308 (EP59). A population genetic analysis of the Turkish isolates was performed using 14 hyper-variable microsatellite loci. The genotypic profiles of 68 previously analyzed L. donovani complex strains from major endemic regions were included for comparison. Population structures were inferred by combination of Bayesian model-based and distance-based approaches. MLMT placed the Turkish and Cypriot strains in a subclade of a newly discovered, genetically distinct L. infantum monophyletic group, suggesting that the Cypriot strains may originate from Turkey.

Conclusion

The discovery of a genetically distinct L. infantum monophyletic group in the south-eastern Mediterranean stresses the importance of species genetic characterization towards better understanding, monitoring and controlling the spread of leishmaniasis in this region.     

Disentangling the divergence and cladogenesis in the freshwater crab species (Potamonautidae: Potamonautes perlatus sensu lato) in the Cape Fold Mountains,South Africa,with the description of two novel cryptic lineages

River networks of major drainages can form barriers that shape the phylogeography of freshwater organisms, particularly those with low dispersal capabilities. Freshwater crab species' distributions can be used to examine hydrological patterns to expose historical drainage interconnectivity. We used molecular sequence data (mitochondrial and nuclear DNA) and divergence time estimations to determine the phylogeography of the freshwater crab, Potamonautes perlatus sensu lato, from six drainage systems along the Cape Fold Mountains, South Africa. Two major clades were detected: clade 1 comprised two geographically discrete haploclades occurring in southern flowing drainages, whereas clade 2 included specimens from western flowing drainages. Divergence time estimations suggested a Pleistocene (c. 2.61 Mya) divergence of P. perlatus s.l. The Pleistocene was associated with arid conditions and drainage contractions. However, it is likely that during the mesic conditions of the Pleistocene, P. perlatus s.l. migrated and diverged into contemporary patterns. We conclude that three lineages are nested within P. perlatus s.l., two representing novel species. Potamonautes perlatus sensu stricto is confined to western flowing drainages. The two novel species both occurring in southern flowing drainages are described here: P otamonautes barbarai sp. nov. occurs in the Gamtoos and Gourits Rivers and P otamonautes barnardi sp. nov. in the Breede River. © 2014 The Linnean Society of London     

The use of chromosomal data in the systematics of viviparous onychophorans from Australia (Onychophora: Peripatopsidae)

A chromosomal analysis of populations of viviparous Australian onychophorans has uncovered a large radiation in karyotypic form. Chromosome numbers of 18, 26, 30, 32, 33 and 34 were observed, and these classes could be further subdivided on the basis of internal size relationships. Given the practical difficulties with the systematics of this group, the use of chromosomal data promises to be particularly enlightening. This is the first time any karyotypic data have been published for onychophorans since a single species was analysed in 1900.     

Phylogeny and Classification of Prunus sensu lato （Rosaceae）

The classification of the economically important genus Prunus L. sensu lato （s.L） is controversial due to the high levels of convergent or the parallel evolution of morphological characters. In the present study, phylogenetic analyses of fifteen main segregates of Prunus s.I. represented by eighty-four species were conducted with maximum parsimony and Bayesian approaches using twelve chloroplast regions （atpB- rbcL, matK, ndhF, psbA-trnH, rbcL, rpL 16, rpoC1, rps16, trnS-G, trnL, trnL-F and ycfl） and three nuclear genes （ITS, s6pdh and Sbel） to explore their infrageneric used to develop a new, phylogeny-based classification relationships. The results of these analyses were of Prunus s.I. Our phylogenetic reconstructions resolved three main clades of Prunus s.I. with strong supports. We adopted a broad-sensed genus, Prunus, and recognised three subgenera corresponding to the three main clades： subgenus Padus, subgenus Cerasus and subgenus Prunus. Seven sections of subgenus Prunus were recognised. The dwarf cherries, which were previously assigned to subgenus Cerasus, were included in this subgenus Prunus. One new section name, Prunus L. subgenus Prunus section Persicae （T. T. yu ＆ L. T. Lu） S. L. Zhou and one new species name, Prunus tianshanica （Pojarkov） S. Shi, were proposed.