Brief communication: Ectocranial suture closure in Pongo: Pattern and phylogeny

Ectocranial suture fusion patterns have been shown to contain biological and phylogenetic information. Previously the patterns of Homo, Pan, and Gorilla have been described. These data reflect the phylogenetic relationships among these species. In this study, we applied similar methodology to Pongo to determine the suture synostosis progression of this genus, and to allow comparison to previously reported data on other large‐bodied hominoids. We hypothesized these data would strengthen the argument that suture synostosis patterns reflect the phylogeny of primate taxa. Results indicate that the synostosis of vault sutures in Pongo is similar to that reported for Gorilla (excluding Pan and Homo). However, the lateral‐anterior pattern of fusion, in which there is a strong superior to inferior pattern, for Pongo is unique among these species, reflecting its phylogenetic distinctness among great ape taxa. Am J Phys Anthropol, 2010. © 2010 Wiley‐Liss, Inc.     

Geometric morphometric analyses of hominid proximal femora: Taxonomic and phylogenetic considerations

The proximal femur has long been used to distinguish fossil hominin taxa. Specifically, the genus Homo is said to be characterized by larger femoral heads, shorter femoral necks, and more lateral flare of the greater trochanter than are members of the genera Australopithecus or Paranthropus. Here, a digitizing arm was used to collect landmark data on recent human (n=82), chimpanzee (n=16), and gorilla (n=20) femora and casts of six fossil hominin femora in order to test whether one can discriminate extant and fossil hominid (sensu lato) femora into different taxa using three-dimensional (3D) geometric morphometric analyses. Twenty proximal femoral landmarks were chosen to best quantify the shape differences between hominin genera. These data were first subjected to Procrustes analysis. The resultant fitted coordinate values were then subjected to PCA. PC scores were used to compute a dissimilarity matrix that was subjected to cluster analyses. Results indicate that one can easily distinguish Homo, Pan, and Gorilla from each other based on proximal femur shape, and one can distinguish Pliocene and Early Pleistocene hominin femora from those of recent Homo. It is more difficult to distinguish Early Pleistocene Homo proximal femora from those of Australopithecus or Paranthropus, but cluster analyses appear to separate the fossil hominins into four groups: an early australopith cluster that is an outlier from other fossil hominins; and two clusters that are sister taxa to each other: a late australopith/Paranthropus group and an early Homo group.     

Emergence of the genus Homo: From concept to taxonomy

The main goal of this paper is to present an overview of hypotheses concerning early Homo specimens and to discuss the definition of the genus Homo in the light of recent discoveries. For some authors, all the specimens attributed to early Homo belong to one unique species. For others, this group (Homo habilis sensu lato) is heterogeneous and could be splitted into two groups: H. habilis and Homo rudolfensis. Some researchers have also proposed to put the species habilis and rudolfensis into the genera Australopithecus or Kenyanthropus. Therefore, two scenarios concerning first humans seem to emerge. An emergence of the genus Homo, as early as 2.8 Ma, with Homo sp. specimens and the species H. habilis and H. rudolfensis, another at 1.9 Ma with Homo ergaster. According to the recent archaeological and paleoanthropological discoveries, these criteria often considered to be crucial for the definition of the genus Homo, as the cranial capacity, the humanlike manipulative abilities, the habitual erect posture and bipedal gait, the language ability and the capacity to make tools are now obsolete.     

Additional rDNA ITS sequences and its phylogenetic consequences for the genus Leveillula with emphasis on conidium morphology

Taxonomy of the genus Leveillula has long been considered as a challenge in powdery mildew systematics. The rDNA diversity has recently been used for phylogenetic analysis of several specimens of the genus Leveillula. In the present study, additional rDNA ITS sequences are provided and a new phylogenetic analysis is carried out aiming at a better understanding of the genetic diversity in the genus Leveillula. New analyses confirmed that L. taurica is unique in the genus, as it exhibits an intraspecific gene sequence diversity considerably higher than in other species. In several cases L. taurica s. lat. on a certain host plant species has a sequence different from L. taurica on other host plants. Moreover, DNA data indicated different lineages among L. taurica specimens which were hardly distinguishable by morphology. More than one genotype occurring on a single host is sometimes possible. According to these results, several races such as Leveillula on Artemisia, Acroptilon, Onobrychis, are molecularly well characterized. While there is enough molecular evidence to delimit such races as independent taxa, clear morphological delimitations between these new and already published taxa are very difficult or even impossible. However, ecological features, and above all, host specificity for biotrophic fungi such as powdery mildew, would be a good criterion to discriminate cryptic taxa along with rDNA sequences. In fact, many collections of Leveillula strains on different hosts show their own type of conidial morphology, which is usually consistent for a strain on a single host species. Hence, we have proposed to describe new species for Leveillula on some host plants such as Artemisia, Acroptilon, Echinops and Onobrychis.     

Disproportionate Cochlear Length in Genus Homo Shows a High Phylogenetic Signal during Apes’ Hearing Evolution

Changes in lifestyles and body weight affected mammal life-history evolution but little is known about how they shaped species’ sensory systems. Since auditory sensitivity impacts communication tasks and environmental acoustic awareness, it may have represented a deciding factor during mammal evolution, including apes. Here, we statistically measure the influence of phylogeny and allometry on the variation of five cochlear morphological features associated with hearing capacities across 22 living and 5 fossil catarrhine species. We find high phylogenetic signals for absolute and relative cochlear length only. Comparisons between fossil cochleae and reconstructed ape ancestral morphotypes show that Australopithecus absolute and relative cochlear lengths are explicable by phylogeny and concordant with the hypothetized ((Pan,Homo),Gorilla) and (Pan,Homo) most recent common ancestors. Conversely, deviations of the Paranthropus oval window area from these most recent common ancestors are not explicable by phylogeny and body weight alone, but suggest instead rapid evolutionary changes (directional selection) of its hearing organ. Premodern (Homo erectus) and modern human cochleae set apart from living non-human catarrhines and australopiths. They show cochlear relative lengths and oval window areas larger than expected for their body mass, two features corresponding to increased low-frequency sensitivity more recent than 2 million years ago. The uniqueness of the “hypertrophied” cochlea in the genus Homo (as opposed to the australopiths) and the significantly high phylogenetic signal of this organ among apes indicate its usefulness to identify homologies and monophyletic groups in the hominid fossil record.     

Phytochemical,phylogenetic, and anti-inflammatory evaluation of 43 Urtica accessions (stinging nettle) based on UPLC–Q-TOF-MS metabolomic profiles

Several species of the genus Urtica (especially Urtica dioica, Urticaceae), are used medicinally to treat a variety of ailments. To better understand the chemical diversity of the genus and to compare different accessions and different taxa of Urtica, 63 leaf samples representing a broad geographical, taxonomical and morphological diversity were evaluated under controlled conditions. A molecular phylogeny for all taxa investigated was prepared to compare phytochemical similarity with phylogenetic relatedness. Metabolites were analyzed via UPLC–PDA–MS and multivariate data analyses. In total, 43 metabolites were identified, with phenolic compounds and hydroxy fatty acids as the dominant substance groups. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) provides a first structured chemotaxonomy of the genus. The molecular data present a highly resolved phylogeny with well-supported clades and subclades. U. dioica is retrieved as both para- and polyphyletic. European members of the U. dioica group and the North American subspecies share a rather similar metabolite profile and were largely retrieved as one, nearly exclusive cluster by metabolite data. This latter cluster also includes – remotely related – Urtica urens, which is pharmaceutically used in the same way as U. dioica. However, most highly supported phylogenetic clades were not retrieved in the metabolite cluster analyses. Overall, metabolite profiles indicate considerable phytochemical diversity in the genus, which largely falls into a group characterized by high contents of hydroxy fatty acids (e.g., most Andean-American taxa) and another group characterized by high contents of phenolic acids (especially the U. dioica-clade). Anti-inflammatory in vitro COX1 enzyme inhibition assays suggest that bioactivity may be predicted by gross metabolic profiling in Urtica.     

Molecular phylogeny of Anaphalis (Asteraceae, Gnaphalieae) with biogeographic implications in the Northern Hemisphere

Anaphalis is the largest Asian genus in the tribe Gnaphalieae (Asteraceae) and has its greatest species diversity in the eastern Himalayas. The nuclear internal and external transcribed spacers were sequenced for Anaphalis species, with an emphasis on the eastern Himalayan taxa to examine the monophyly and construct the phylogenetic relationships of and within the genus. The results suggest that all species of Anaphalis are nested with Helichrysum, showing a close relationship with a Mediterranean–Asian group of Helichrysum. Although the monophyly of Anaphalis is only weakly supported, two clades within the genus are well recognized, each consisting of two subgroups. The inferred phylogenetic relationships within Anaphalis correspond to the shape of leaf base, rather than the morphology of the capitula and phyllaries that are usually used for species delimitation and classification in the genus. All four subgroups of Anaphalis are common and diversified in the eastern Himalayas with multiple dispersals out of this region. The sole North American species of Anaphalis is best hypothesized to be the result of long-distance dispersal or overland migration via Bering land bridge from Asia. Our analyses suggest that the extant distribution of Anaphalis has most likely resulted one radiation into the eastern Himalayas followed by repeated independent dispersals and/or radiations mostly into eastern Asia but also into the western Himalayas, North America, and southeast Asia.     

Integrative taxonomy approach for analysing evolutionary history of the tribe Euseiini Chant & McMurtry (Acari: Phytoseiidae)

Phylogenetic relationships within the mite Family Phytoseiidae are little known. The presently accepted classification is based on the opinion of specialists, but not on cladistics analysis. The present paper focuses on the tribe Euseiini, containing 271 species, three subtribes and 10 genera. It aims to determine phylogenetic relationships between these taxa and test their monophyly. Molecular analysis combining six markers has been carried out for taxa we succeeded in collecting. Morphological, biogeographic and ecological data have been analysed to determine how these factors can explain the evolutionary relationships emphasized on the phylogenetic tree. Those analyses have been carried out for the taxa available for the molecular study, but also for all species of the tribe. The tribe Euseiini and the two subtribes considered are monophyletic (at least considering the available taxa), supporting the present hypothesis on Phytoseiidae classification. However, the genus Iphiseius seems to not be valid and its unique species is included in the genus Euseius. Clades that were observed within the genus Euseius do not match with recent work on species groups within this genus. It seems that some morphological features such as an insemination apparatus shape and seta length on the dorsal shield constitute some elements explaining the clusters within the genus Euseius. Biogeographic and ecological data analysis led us to hypothesize a west Gondwanian origin of the tribe Euseiini (Africa and Neotropical areas) on Rosids plants (especially of the Orders Malpiphiales and Fabales: subclass Fabidae). Further analyses are still required to (i) take into account more taxa (especially rare ones and species from the Ethiopian part), (ii) to consider more accurate morphological features through more powerful microscopic apparatus, and (iii) to associate a phylogenetic and evolutionary scenario to life traits (pollen feeders).     

Phylogenetic position of Octosporea muscaedomesticae (Microsporidia) and its relationship to Octosporea bayeri based on small subunit rDNA analysis

Comparative phylogenetic analysis of the small subunit rDNA sequence of Octosporea muscaedomesticae (Flu, 1911) (type species) (Microsporidia) isolated from the blowfly Phormia regina (Diptera:Calliphoridae) is presented. Neighbor Joining bootstrap, Maximum Parsimony and Maximum Likelihood analyses with 38 microsporidian taxa representing five major clades of Microsporidia placed O. muscaedomesticae on a separate branch within a clade containing parasites of freshwater hosts. O. muscaedomesticae differed from Octosporea bayeri, a parasite of the microcrustacean, Daphnia magna (Cladocera:Daphniidae) by 29% demonstrating that the latter microsporidium is not closely related to the type species at the generic level, and should not be placed within the genus Octosporea, a conclusion that is further supported by morphological and developmental differences. Considering the number of disparately related hosts from which Octosporea species have been previously described based mostly on developmental and morphological characters it is likely that many will not fit the current definition of the genus, and it is possible that molecular analysis of these species will show that this genus as defined represents a polyphyletic grouping of unrelated taxa.     

Molecular systematics of small-eared shrews (Soricomorpha,Mammalia) within Cryptotis mexicanus species group from Mesoamérica

Cryptotis mexicanus species group is the most diverse group of Cryptotis shrews in the Mesoamerican highlands (ca.13 species). In México, eight endemic species occurs and several taxa are endangered. The species’ limits and phylogenetic relationships of these taxa have been recently examined using morphology; nevertheless, little is known about phylogenetic relationships among Cryptotis species at the molecular level. Therefore, our research included a mitochondrial DNA marker as a source of additional information to corroborate taxonomic identification and produce a phylogenetic hypothesis of the C. mexicanus species group. We were particularly interested in the status of Cryptotis magnus, a species considered as relict on the basis of primitive characters. Based on the analyses of genetic sequences of a high number of Cryptotis species, outgroups, and phylogenetic analyses of parsimony and Bayesian inference, we confirmed that Cryptotis genus consists of different lineages that represent species groups. A detailed analysis suggests that C. magnus is a species that shares an evolutionary history with the C. mexicanus species group because it is imbedded within this group. In particular, our data strongly support that C. magnus and Cryptotis phillipsii are sister groups, a pair of species that inhabit allopatrically Southern México.     

Phylogenetic relationship in Fritillaria spp. of Iran inferred from ribosomal ITS and chloroplast trnL-trnF sequence data

The genus Fritillaria embraces up to 165 taxa in the family Liliaceae, most of which are of high medicinal and ornamental value and importance. In this study, 44 specimens of the genus representing 9 species were collected from their natural habitats located in 10 provinces of Iran. Phylogenetic analysis was performed based on DNA sequences of the internal transcribed spacer (ITS) of the nuclear ribosomal cistron and the trnL-trnF regions. The phylogeny was constructed using the neighbor joining inference method. Results indicate that the examined samples were evidently diverged into 2 distinct clades. Members of the subgenera Fritillaria and Rhinopetalum formed one clade while the other clade contained the subgenera Theresia and Petilium. There can be seen a high degree of similarity between the only yellow-colored crown imperial specimen and the red-colored specimens. The endemic species of Fritillaria straussii, Fritillaria zagrica and Fritillaria kotschyana which their status within the subgenera known in the genus Fritillaria has been remained undefined, fell into the subgenus Fritillaria. The clades also had relatively reasonable distribution patterns based on the genetic structure, geographical conditions and climate specifications. This study revealed the feasibility of the ITS and trnL-trnF DNA sequence for phylogeny of the genus Fritillaria. This is the first phylogenetic analysis of Fritillaria spp. in Iran.     

Variation in enamel thickness within the genus Homo

Recent humans and their fossil relatives are classified as having thick molar enamel, one of very few dental traits that distinguish hominins from living African apes. However, little is known about enamel thickness in the earliest members of the genus Homo, and recent studies of later Homo report considerable intra- and inter-specific variation. In order to assess taxonomic, geographic, and temporal trends in enamel thickness, we applied micro-computed tomographic imaging to 150 fossil Homo teeth spanning two million years. Early Homo postcanine teeth from Africa and Asia show highly variable average and relative enamel thickness (AET and RET) values. Three molars from South Africa exceed Homo AET and RET ranges, resembling the hyper thick Paranthropus condition. Most later Homo groups (archaic European and north African Homo, and fossil and recent Homo sapiens) possess absolutely and relatively thick enamel across the entire dentition. In contrast, Neanderthals show relatively thin enamel in their incisors, canines, premolars, and molars, although incisor AET values are similar to H. sapiens. Comparisons of recent and fossil H. sapiens reveal that dental size reduction has led to a disproportionate decrease in coronal dentine compared with enamel (although both are reduced), leading to relatively thicker enamel in recent humans. General characterizations of hominins as having ‘thick enamel’ thus oversimplify a surprisingly variable craniodental trait with limited taxonomic utility within a genus. Moreover, estimates of dental attrition rates employed in paleodemographic reconstruction may be biased when this variation is not considered. Additional research is necessary to reconstruct hominin dietary ecology since thick enamel is not a prerequisite for hard-object feeding, and it is present in most later Homo species despite advances in technology and food processing.     

Phylogenetic relationships between Hystrix and its closely related genera (Triticeae; Poaceae) based on nuclear Acc1, DMC1 and chloroplast trnL-F sequences

To estimate the phylogenetic relationship of polyploid Hystrix in Triticeae, two single-copy nuclear genes (Acc1 and DMC1) and chloroplast trnL-F sequences of six Hystrix taxa were analyzed with those of nine Leymus species (NsXm), four Elymus species (StH) and 13 diploid taxa from seven monogenomic genera. Phylogenetic analyses reveal that Hystrix taxa contain two distinct types of genome constitution, despite the overall morphological and ecological similarity among Hystrix taxa. One type of genome constitution is StH (Hy. patula) as Elymus, the other is NsXm (Hy. californica, Hy. coreana, Hy. duthiei, Hy. duthiei ssp. longearistata and Hy. komarovii) as Leymus. The St, H and Ns genomes in Hystrix are donated by Pseudoroegneria, Hordeum and Psathyrostachys, respectively. The donor of the Xm genome is closely related to Agropyron (P). The trnL-F data especially indicate that there has been a maternal haplotype polymorphism in Hystrix species. Based on these results, we suggest that Hy. coreana, Hy. duthiei, Hy. duthiei ssp. longearistata, Hy. komarovii and Hy. californica should be included in the genus Leymus, and Hy. patula in the genus Elymus.     

Taxonomic delimitation of <Emphasis Type="Italic">Fulvifomes robiniae</Emphasis> (Hymenochaetales,Basidiomycota) and related species in America: <Emphasis Type="Italic">F. squamosus</Emphasis> sp. nov.

Morphological revision of Fulvifomes robiniae, as well as phylogenetic inferences based on nITS and nLSU markers, indicated that the species has a narrower concept in its morphology and distribution. Other morphologically related taxa arise from this taxonomic approach. Fulvifomes cedrelae is not accepted as a synonym of F. robiniae, and Fulvifomes squamosus sp. nov. is described as new based on Peruvian specimens. Based on morphology, phylogenetic relationships and host distributions, the taxonomic implication for the genus and other related taxa are discussed.     

Phylogenetic Classification at Generic Level in the Absence of Distinct Phylogenetic Patterns of Phenotypical Variation: A Case Study in Graphidaceae (Ascomycota)

Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking complex morphologies. Taxonomists then can either merge the groups or split taxa into smaller entities. Due to the nature of binomial nomenclature, this decision is of special importance at the generic level. Here we propose a new approach to choose among classification alternatives using a combination of morphology-based phylogenetic binning and a multiresponse permutation procedure to test for morphological differences among clades. We illustrate the use of this method in the tribe Thelotremateae focusing on the genus Chapsa, a group of lichenized fungi in which our phylogenetic estimate is in conflict with traditional classification and the morphological and chemical characters do not show a clear phylogenetic pattern. We generated 75 new DNA sequences of mitochondrial SSU rDNA, nuclear LSU rDNA and the protein-coding RPB2. This data set was used to infer phylogenetic estimates using maximum likelihood and Bayesian approaches. The genus Chapsa was found to be polyphyletic, forming four well-supported clades, three of which clustering into one unsupported clade, and the other, supported clade forming two supported subclades. While these clades cannot be readily separated morphologically, the combined binning/multiresponse permutation procedure showed that accepting the four clades as different genera each reflects the phenotypical pattern significantly better than accepting two genera (or five genera if splitting the first clade). Another species within the Thelotremateae, Thelotrema petractoides, a unique taxon with carbonized excipulum resembling Schizotrema, was shown to fall outside Thelotrema. Consequently, the new genera Astrochapsa, Crutarndina, Pseudochapsa, and Pseudotopeliopsis are described here and 39 new combinations are proposed.     

Systematics and phylogenetic species delimitation within Polinices s.l. (Caenogastropoda: Naticidae) based on molecular data and shell morphology

Here, we present the first phylogenetic analysis of a group of species taxonomically assigned to Polinices sensu latu (Naticidae, Gastropoda) based on molecular data sets. Polinices s.l. represents a speciose group of the infaunal gastropod family Naticidae, including species that have often been assigned to subgenera of Polinices [e.g. P. (Neverita), P. (Euspira), P. (Conuber) and P. (Mammilla)] based on conchological data. The results of our molecular phylogenetic analysis confirm the validity of five genera, Conuber, Polinices, Mammilla, Euspira and Neverita, including four that have been used previously mainly as subgenera of Polinices s.l. Our results furthermore indicate a close relationship of members of the Polinicinae to Sinum??a genus traditionally placed in the naticid subfamily Sininae. We furthermore present conchological analyses to determine the validity of shell characters used traditionally in species designation in the genus Polinices. Our data reveal several characters (e.g. protoconch, operculum colour, parietal callus) to be informative, while many characters show a high degree of homoplasy (e.g. umbilicus, shell form). Among the species arranged in the genus Polinices s.s., four conchologically very similar taxa often subsumed under the common Indo-Pacific species P. mammilla are separated distinctly in phylogenetic analyses. Despite their striking conchological similarities, none of these four taxa are related directly to each other. Additional conchological analyses of available name-bearing type specimens and type figures reveal the four ??mammilla??-like white Polinices species to include true P. mammilla and three additional species, which could be assigned to P. constanti (replacement name for P. dubius), P. jukesii and possibly P. tawhitirahia, based on protoconch and operculum characteristics.     

The changing face of genus Homo

Since its introduction in the 18th century, the genus Homo has undergone a number of reinterpretations, all of which have served to make it a more inclusive taxon. In this paper, we trace this trend towards greater inclusiveness, and explain how it has affected the way Homo is defined. We then demonstrate that the current criteria for identifying species of Homo are difficult, if not impossible, to operate using paleoanthropological evidence. We discuss alternative, verifiable, criteria, and show that when these new criteria are applied to Homo, two species, Homo habilis and Homo rudolfensis, fail to meet them. We contend that the lowest boundary of Homo should be redrawn so that the earliest species in the genus is Homo ergaster, or early African Homo erectus. The appearance of this species at around 1.9 Myr appears to mark a distinct shift in hominin adaptive strategy involving morphological and behavioral innovations.     

Molecular phylogeny of baculiform desmid taxa (Zygnematophyceae)

The baculiform, rod-like morphotypes belong to several phylogenetic lineages within Desmidiaceae (Zygnematophyceae, Viridiplantae). Some, for example the genus Pleurotaenium, form independent lineages, but reductive evolution of complicated desmid cells toward baculiform morphology also occurred in individual lineages, for example Micrasterias. In this genus, the rod like Triploceras forms evolved from more complex ancestors. In this study, we tested for an independent position of the subtropical and tropical genus Triplastrum, previously separated from Triploceras on the basis of morphological data. In addition, monophyly of Pleurotaenium was also investigated with multiple isolates corresponding to seven species of this genus, including the morphologically dissimilar P. nodosum and P. ovatum. Finally, two isolates of Docidium baculum were also investigated. Molecular phylogenetic analysis of concatenated rbcL?+?coxIII sequence data implied that the baculiform taxa investigated were in three distantly related positions within Desmidiaceae. The genus Triplastrum proved to be unrelated to Triploceras, because it clustered in the “omniradiate” lineage of Desmidiaceae among morphologically dissimilar taxa. The genus Pleurotaenium was monophyletic, but P. ovatum was recovered in a weakly supported sister position to all the other members of the genus. The trnG^ucc phylogeny of Pleurotaenium taxa concurred with the rbcL?+?coxIII phylogram, and generally revealed the poor morphological concepts of some species in this genus. The most common taxa P. ehrenbergii and P. trabecula were resolved as polyphyletic because their strains were distributed among several strongly supported clades. However, strains of P. nodosum and P. archeri formed separate, well supported lineages within the genus.