Molecular systematics in the genus Mucor with special regards to species encountered in cheese

The genus Mucor, a member of the order Mucorales, comprises different species encountered in cheeses. Although fungi play a fundamental role in cheese manufacturing and ripening, the taxonomy of many fungal species found in cheese is poorly defined; indeed, this is the case for Mucor spp. In the present study, we assessed the phylogenetic relationships among 70 Mucor strains, including 36 cheese isolates, by using a five gene phylogenetic approach combined with morphological analyses. Overall, at least six species of Mucor were identified among the cheese isolates including a possible new taxon. The present study also suggests that the genus Mucor comprises undescribed taxa and needs to be properly defined.     

Phylogenomic analysis suggests Coreidae and Alydidae (Hemiptera: Heteroptera) are not monophyletic

Next‐generation sequencing technologies (NGS) allow systematists to amass a wealth of genomic data from non‐model species for phylogenetic resolution at various temporal scales. However, phylogenetic inference for many lineages dominated by non‐model species has not yet benefited from NGS, which can complement Sanger sequencing studies. One such lineage, whose phylogenetic relationships remain uncertain, is the diverse, agriculturally important and charismatic Coreoidea (Hemiptera: Heteroptera). Given the lack of consensus on higher‐level relationships and the importance of a robust phylogeny for evolutionary hypothesis testing, we use a large data set comprised of hundreds of ultraconserved element (UCE) loci to infer the phylogeny of Coreoidea (excluding Stenocephalidae and Hyocephalidae), with emphasis on the families Coreidae and Alydidae. We generated three data sets by including alignments that contained loci sampled for at least 50%, 60%, or 70% of the total taxa, and inferred phylogeny using maximum likelihood and summary coalescent methods. Twenty‐six external morphological features used in relatively comprehensive phylogenetic analyses of coreoids were also re‐evaluated within our molecular phylogenetic framework. We recovered 439–970 loci per species (16%–36% of loci targeted) and combined this with previously generated UCE data for 12 taxa. All data sets, regardless of analytical approach, yielded topologically similar and strongly supported trees, with the exception of outgroup relationships and the position of Hydarinae. We recovered a monophyletic Coreoidea, with Rhopalidae highly supported as the sister group to Alydidae + Coreidae. Neither Alydidae nor Coreidae were monophyletic; the coreid subfamilies Hydarinae and Pseudophloeinae were recovered as more closely related to Alydidae than to other coreid subfamilies. Coreinae were paraphyletic with respect to Meropachyinae. Most morphological traits were homoplastic with several clades defined by few, if any, synapomorphies. Our results demonstrate the utility of phylogenomic approaches in generating robust hypotheses for taxa with long‐standing phylogenetic problems and highlight that novel insights may come from such approaches.     

Phylogenetic support for the monophyly of proetide trilobites

The monophyly of the order Proetida, the only trilobite group to survive the end‐Devonian mass extinction, has been regularly questioned since its erection almost three decades ago. Through analysis of a novel phylogenetic data set comprising 114 characters coded for 55 taxa, including both traditional members of the Proetida along with a number of other trilobite groups, the monophyly of proetide trilobites is rigorously tested for the first time. Proetida is shown to be monophyletic, united by the initial compound eye formation in early protaspids occurring at the lateral margin rather than the anterior margin, and the form of the protaspid glabella being tapering with a pre‐glabellar field. A number of adult characters, including the possession of a quadrate or shield‐shaped hypostome with angular posterior margins, the hypostome median body being divided by a deep groove that entirely traverses the median body, the presence of an enlarged thoracic spine on the sixth tergite and a tergite count of between 7 and 10, also define the basal node. Hystricurid and dimeropygoid trilobites are shown to resolve at the base of the group, while the remaining proetide taxa are divided between large proetoid and aulacopleuroid clades. Some taxa previously allied with Aulacopleuroidea, such as rorringtoniids and scharyiids, are retrieved as basal members of the Proetoidea.     

Molecular phylogeny of major lineages of Trichadenotecnum and a review of diagnostic morphological characters (Psocoptera: Psocidae)

Abstract. Phylogenetic relationships among species groups of Trichadenotecnum were inferred based on morphology and the partial sequences of five gene regions (mitochondrial 12S rDNA, 16S rDNA, cytochrome oxidase I, NADH dehydrogenase subunit 5 and nuclear 18S rDNA). All analyses supported the monophyly of Trichadenotecnum and all previously proposed species groups, except that T. circularoides was excluded from the spiniserrulum group. To examine the phylogenetic usefulness of morphological data, the morphological characters used in the construction of an earlier taxonomic system for Trichadenotecnum were mapped parsimoniously on the molecular tree. As a result: (1) commonly used forewing marking features (sparsely or extensively spotted) are considered to be very homoplastic and less informative of higher‐level phylogenetic relationships; (2) a broadly expanded epiproct lobe is considered to be independently evolved at least two or three times, and a detailed morphological re‐examination allows recognition of these convergent structures; (3) the short ventral valve of gonapophyses independently evolved at least three or four times, although this character was used initially to diagnose the spiniserrulum group.     

Phylogenetic relationships among sea anemones (Cnidaria: Anthozoa: Actiniaria)

Sea anemones (order Actiniaria) are among the most diverse and successful members of the anthozoan subclass Hexacorallia, being found at all depths and latitudes and in all marine habitats. Members of this group exhibit the greatest variation in anatomy, biology, and life history in Hexacorallia, and lack any morphological synapomorphy. Nonetheless, previous molecular phylogenetic studies have found that Actiniaria is monophyletic with respect to other extant hexacorallians. However, relationships within Actiniaria have remained unresolved, as none of these earlier works have included sufficient taxon sampling to estimate relationships within Actiniaria. We have analyzed sequences from two mitochondrial and two nuclear markers for representatives of approximately half of the family-level diversity within the order, and present the first phylogenetic tree for Actiniaria. We concur with previous studies that have suggested that molecular evolution is unusually slow in this group. We determine that taxonomic groups based on the absence of features tend not to be recovered as monophyletic, but that at least some classical anatomical features define monophyletic groups.     

A molecular approach to the tangled intrageneric relationships underlying phylogeny in Euplotes (Ciliophora, Spirotrichea).

The cosmopolitan genus Euplotes is remarkable among ciliates for its species richness. To understand the still tangled taxonomy and phylogenetic relationships within the genus, small subunit rRNA sequences of 11 morphologically defined species colonizing different habitats were determined. Euplotes 18S rRNA is unique among ciliates for its anomalous length and high evolutionary rate. Phylogenetic reconstruction pointed to a high divergence between this genus and the other Spirotrichea, together with a high variability within the genus. Some of the relationships within the Euplotes group were also resolved. Data from the literature, based on morphological features, habitat, and symbiotic relationships, have been compared with our results and are critically discussed. In many cases, the molecular phylogenetic analysis disagreed with species relatedness established on morphological and ecological grounds. The occurrence of a radiation phenomenon in the evolution of the genus is postulated.     

The role of character loss in phylogenetic reconstruction as exemplified for the Annelida

Annelid relationships are controversial, and molecular and morphological analyses provide incongruent estimates. Character loss is identified as a major confounding factor for phylogenetic analyses based on morphological data. A direct approach and an indirect approach for the identification of character loss are discussed. Character loss can frequently be found within annelids and examples of the loss of typical annelid characters, like chaetae, nuchal organs, coelomic cavities and other features, are given. A loss of segmentation is suggested for Sipuncula and Echiura; both are supported as annelid ingroups in molecular phylogenetic analyses. Moreover, character loss can be caused by some modes of heterochronic evolution (paedomorphosis) and, as shown for orbiniid and arenicolid polychaetes, paedomorphic taxa might be misplaced in phylogenies derived from morphology. Different approaches for dealing with character loss in cladistic analyses are discussed. Application of asymmetrical character state transformation costs or usage of a dynamic homology framework represents promising approaches. Identifying character loss prior to a phylogenetic analysis will help to refine morphological data matrices and improve phylogenetic analyses of annelid relationships.     

Morphological evolution in the variable resin-producing Detarieae (Fabaceae): do morphological characters retain a phylogenetic signal?

Background and Aims

Previous molecular phylogenetic studies disagree with the informal generic-level taxonomic groups based on morphology. In this study morphological characters in the caesalpinioid clade Detarieae are evaluated within a phylogenetic framework as a means of better understanding phylogenetic relationships and morphological evolution.

Methods

Morphological characters were observed and scored for representative species of Detarieae focusing on the resin-producing genera. Phylogenetic analyses were carried out with morphological characters alone and then combined with DNA sequences.

Key Results

Despite a high level of homoplasy, morphological data support several clades corresponding to those recovered in molecular phylogenetic analyses. The more strongly supported clades are each defined by at least one morphological synapomorphy. Several characters (e.g. apetaly) previously used to define informal generic groups evolved several times independently, leading to the differences observed with the molecular phylogenetic analyses. Although floral evolution is complex in Detarieae some patterns are recovered.

Conclusions

New informal taxonomic groupings are proposed based on the present findings. Floral evolution in the diverse Detarieae clade is characterized by a repeated tendency toward zygomorphy through the reduction of lateral petals and toward complete loss of petals.Key words: Caesalpinioideae, Detarieae, floral evolution, Leguminosae, morphology, phylogeny, resins, taxonomy     

Osteology and myology of the cephalic region and pectoral girdle of the Chinese catfish Cranoglanis bouderius,with a discussion on the autapomorphies and phylogenetic relationships of the Cranoglanididae (Teleostei: Siluriformes)

The cephalic and pectoral girdle structures of the Chinese catfish Cranoglanis bouderius are described and compared with those of other catfishes as the foundation for an analysis on the Cranoglanididae autapomorphies and also for a discussion on the phylogenetic relationships between the cranoglanidids and the other catfishes. Our observations and comparisons indicate that cranoglanidids are defined, at least, by four autapomorphies, namely: 1) the cartilages associated with the mandibular barbels are broad, somewhat circular; 2) epioccipital with a well-developed posterodorsal process, which presents a large, deep, circular posterior concavity; 3) a well-defined, deep, anteroposteriorly elongated concavity formed by both the frontal and the lateral ethmoid to receive the anteromedial surface of the metapterygoid; 4) the adductor mandibulae A3" is dorsally divided into two bundles and partially inserted on the posterior portion of the primordial ligament. With respect to the phylogenetic relationships of the Cranoglanididae, this study strongly suggests that these fishes are probably closely related to the Ariidae and the Claroteidae.     

Phylogenetic position of the Tardigrada based on the 18S ribosomal RNA gene sequences

The phylogenetic position of the Tardigrada remains uncertain. This is due to the limited information available, and the uncertainty of whether some characters are homologous or analogous with other taxa. Based on some morphological characters, current discussion centres on whether the taxon branches from the annelid-arthropod lineage, or lies within the arthropod complex. The molecular data presented here from an analysis of the 18S rRNA gene sequences are used to test the validity of these two hypotheses. Phylogenetic inference by the maximum parsimony and distance (neighbour-joining) methods suggests that the Tardigrada is a sister group of the major protostome eucoelomate assemblage that emerged before the arthropods, annelids, molluscs, and sipunculids evolved. The tardigrade clade also appears as an independent lineage separate from the nematode clade, thus supporting the current idea that tardigrades do not have a close aschelminth relationship. The molecular data also imply that several morphological features, considered significant in determining the phylogenetic relationships of tardigrades, are not synapomorphic characters.     

A new dimension in combining data? The use of morphology and phylogenomic data in metazoan systematics

Giribet, G. 2010. A new dimension in combining data? The use of morphology and phylogenomic data in metazoan systematics. —Acta Zoologica (Stockholm) 91 : 11–19 Animal phylogenies have been traditionally inferred by using the character state information derived from the observation of a diverse array of morphological and anatomical features, but the incorporation of molecular data into the toolkit of phylogenetic characters has shifted drastically the way researchers infer phylogenies. A main reason for this is the ease at which molecular data can be obtained, compared to, e.g., traditional histological and microscopical techniques. Researchers now routinely use genomic data for reconstructing relationships among animal phyla (using whole genomes or Expressed Sequence Tags) but the amount of morphological data available to study the same phylogenetic patterns has not grown accordingly. Given the disparity between the amounts of molecular and morphological data, some authors have questioned entire morphological programs. In this review I discuss issues related to the combinability of genomic and morphological data, the informativeness of each set of characters, and conclude with a discussion of how morphology could be made scalable by utilizing new techniques that allow for non‐intrusive examination of large amounts of preserved museum specimens. Morphology should therefore remains a strong field in evolutionary and comparative biology, as it continues to provide information for inferring phylogenetic patterns, is an important complement for the patterns derived from the molecular data, and it is the common nexus that allows studying fossil taxa with large data sets of molecular data.     

Levels of biological organization and the origin of novelty

The concept of novelty in evolutionary biology pertains to multiple tiers of biological organization from behavioral and morphological changes to changes at the molecular level. Identifying novel features requires assessments of similarity (homology and homoplasy) of relationships (phylogenetic history) and of shared developmental and genetic pathways or networks. After a brief discussion of how novelty is used in recent literature, we discuss whether the evolutionary approach to homology and homoplasy initially formulated by Lankester in the 19th century informs our understanding of novelty today. We then discuss six examples of morphological features described in the recent literature as novelties, and assess the basis upon which they are regarded as novel. The six are: origin of the turtle shell, transition from fish fins to tetrapod limbs, origination of the neural crest and neural crest cells, cement glands in frogs and casquettes in fish, whale bone-eating tubeworms, and the digestion of plant proteins by nematodes. The article concludes with a discussion of means of acquiring novel genetic information that can account for novelty recognized at higher levels. These are co-options of existing genetic circuitry, gene duplication followed by neofunctionalization, gene rearrangements through mobile genetic elements, and lateral gene transfer. We conclude that on the molecular level only the latter category provides novel genetic information, in that there is no homologous precursor. However, novel phenotypes can be generated through both neofunctionalization and gene rearrangements. Therefore, assigning phenotypic or genotypic "novelty" is contingent on the level of biological organization addressed.     

Identification of chaetognaths as protostomes is supported by the analysis of their mitochondrial genome

Determining the phylogenetic position of enigmatic phyla such as Chaetognatha is a longstanding challenge for biologists. Chaetognaths (or arrow worms) are small, bilaterally symmetrical metazoans. In the past decades, their relationships within the metazoans have been strongly debated because of embryological and morphological features shared with the two main branches of Bilateria: the deuterostomes and protostomes. Despite recent attempts based on molecular data, the Chaetognatha affinities have not yet been convincingly defined. To answer this fundamental question, we determined the complete mitochondrial DNA genome of Spadella cephaloptera. We report three unique features: it is the smallest metazoan mitochondrial genome known and lacks both atp8 and atp6 and all tRNA genes. Furthermore phylogenetic reconstructions show that Chaetognatha belongs to protostomes. This implies that some embryological characters observed in chaetognaths, such as a gut with a mouth not arising from blastopore (deuterostomy) and a mesoderm derived from archenteron (enterocoely), could be ancestral features (plesiomorphies) of bilaterians.     

The phylogenetic placement of Hollandichthys Eigenmann 1909 (Teleostei: Characidae) and related genera

The phylogenetic relationships among characids are complex with many genera remaining of uncertain systematic position inside the family. The genus Hollandichthys is one of these problematic genera. It has been considered as incertae sedis inside this family until two recently published phylogenies, one morphological and one molecular, arrived at alternative hypothesizes as to the relationships of Hollandichthys with Pseudochalceus or Rachoviscus, respectively. In this paper, we infer the phylogenetic relations of these taxa based on five genes (three mitochondrial - COI, ND2 and 16S; and two nuclear - Sia and Trop), totaling up to 2719 bp. The 41 analyzed species in the Characidae include four incertae sedis characid taxa once hypothesized as related to Hollandichthys, but never analyzed in a single phylogeny (Rachoviscus, Pseudochalceus, Nematocharax and Hyphessobrycon uruguayensis). Here we propose Rachoviscus as the sister-group of Hollandichthys, grouped in the large clade C previously defined, along with the remaining incertae sedis taxa studied here. In addition, we support the evidence that insemination evolved independently at least three times in the Characidae.     

Enrollment in the classification of trilobites

Enrollment is not as fundamental a character complex for the classification of Trilobita as Bergstrom (1973, Fossils and Strata 2; 1977. Lethaia 10 ) has claimed. Different enrollment styles occur within accepted monophyletic taxa, which cut across Bergstrom's (1973) classification and which support the concept of the Order Proetida Fortey & Owens, 1975. False phylogenetic relationships are deduced from unjustified a prior; assumptions about the nature of primitive and derived character states.
Einrollung ist kein so grundlegendes Merkmal für die Klassifizierung der Trilobiten, wie dies Bergström (1973, Fossils and Strata 2; 1977, Lethaia 10 ) gefordert hat. Das Auftreten verschiedener Einrollungs-weisen innerhalb anerkannter monophyletischer Taxa durchkreuzt nämlich seine Klassifizierung (1973), stützt aber die der Aufstellung der Ordnung Proetida Fortey & Owens 1975 zugrundeliegende Auf-fassung. Unrichtige apriori-Antworten auf die Frage, was primitive und was sekundäre Merkmale sind, führen zu irrigen Folgerungen über phylogenetische Zusammenhänge.
L'enroulement n'est pas, pour la classification des Trilobites, un ensemble de caracteres aussi fonda-mental que Bergström(1973, Fossils and Strata 2; 1977. Lethaia 10)a bien voulu le dire. Différents styles d'enroulement sont présents chez des taxa reconnus comme monophylétiques ce qui ne correspond pas á la classification de Bergström (1973) mais vient à I'appui de I'Ordre Proetida Fortey & Owens 1975. Des distinctions a prior; et insuffisamment fondées entre caractères primitifs et caractères évolués conduisent á l'establissement de relations phylogénétiques erronées.     

rRNA二级结构序列用于真菌系统学研究的方法初探

本文首次利用核酸二级结构特征代替核酸碱基作为探讨类群之间亲缘关系的信号,构建了基于结构特征的子囊菌部分类群的系统进化树。该方法以S(规范的碱基对),Q(不规范的碱基对),I(单链),B(侧环),M(多分枝环)和H(发卡结构)为代码将二级结构特征区分为6种不同的亚结构类型,然后将二级结构特征转换为结构序列,并进行结构序列分析。该方法使rRNA不只局限于碱基比较,拓展了其应用范围,为揭示分子的功能与进化的关系提供了线索。结果表明,结构序列分析可用于子囊菌的系统学研究;相对于核酸序列分析,结构分析的结果似乎更加清晰地体现子囊果的演化过程。     

Morphology and angiosperm systematics in the molecular era

Several ways in which morphology is used in systematic and evolutionary research in angiosperms are shown and illustrated with examples: 1) searches for special structural similarities, which can be used to find hints for hitherto unrecognized relationships in groups with unresolved phylogenetic position; 2) cladistic studies based on morphology and combined morphological and molecular analyses; 3) comparative morphological studies in new, morphologically puzzling clades derived from molecular studies; 4) studies of morphological character evolution, unusual evolutionary directions, and evolutionary lability based on molecular studies; and 5) studies of organ evolution. Conclusions: Goals of comparative morphology have shifted in the present molecular era. Morphology no longer plays the primary role in phylogenetic studies. However, new opportunities for morphology are opening up that were not present in the premolecular era: 1) phylogenetic studies with combined molecular and morphological analyses; 2) reconstruction of the evolution of morphological features based on molecularly derived cladograms; 3) refined analysis of morphological features induced by inconsistencies of previous molecular and molecular phylogenetic analyses; 4) better understanding of morphological features by judgment in a wider biological context; 5) increased potential for including fossils in morphological analyses; and 6) exploration of the evolution of morphological traits by integration of comparative structural and molecular developmental genetic aspects (Evo-Devo); this field is still in its infancy in botany; its advancement is one of the major goals of evolutionary botany.     

Neurophylogeny: Architecture of the nervous system and a fresh view on arthropod phyologeny

The phylogenetic relationships within the Arthropoda have beencontroversial for more than a century. Today, comparative studieson the structure and development of the nervous system contributeimportant arguments to this discussion, so that the term "neurophylogeny"was coined for this discipline. The large number of recent studieson the nervous system in various nonmodel arthropods indicatesthat we are far advanced in the process of analyzing the cellulararchitecture of the arthropod nervous system in a depth thatwill ultimately provide characters at a level of resolutionequal or even superior to that of characters traditionally usedin morphological phylogenetic studies. This article sets outto summarize the current state of the discussion on arthropodphylogeny and briefly evaluates the morphological charactersthat have been used as arguments in favor of the traditionalTracheata hypothesis. Then, a thorough overview is given ofcharacters derived from structure and development of the arthropodbrain and the ventral nerve cord from the cellular level tothe level of larger neuropil systems. These characters supportthe new Tetraconata hypothesis suggested by Dohle and provideevidence for a clade that unites malacostracan and remipedecrustaceans with the Hexapoda.