Phylogenetic relationships of the genus Dugesia (Platyhelminthes, Tricladida, Paludicola)

A phylogenetic analysis was performed on the genera and subgenera within the freshwater triclad family Dugesiidae, based on 19 terminal taxa and 17 morphological characters. The phylogenetic tree proposed has length of 27 steps and consistency index of 0.66. This phylogenetic hypothesis implies that the current genus Dugesia is paraphyletic and that its subgenera Girardia, Schmidiea and Dugesia S.S. should be elevated to the rank of genus. The genera Cura, Spathula and Neppia are presumed monophyletic by default because the database was unable to provide autapomorphies for any of these genera. The genera Dugesia S.S. and Neppia share sistergroup relationship. Several characters are discussed which were previously considered to be of phylogenetic importance but were not included in the present analysis. It is emphasized that sensory organs form potentially useful set of phylogenetic characters for the Dugesiidae.     

Phylogenetic signal in the song of crests and kinglets (Aves: Regulus)

Territorial song structures are often the most prominent characters for distinguishing closely related taxa among songbirds. Learning processes may cause convergent evolution of passerine songs, but phylogenetic information of acoustic traits can be investigated with the help of molecular phylogenies, which are not affected by cultural evolutionary processes. We used a phylogeny based on cytochrome b sequences to trace the evolution of territorial song within the genus Regulus. Five discrete song units are defined as basic components of regulid song via sonagraphic measurements. Traits of each unit are traced on a molecular tree and a mean acoustic character difference between taxon pairs is calculated. Acoustic divergence between regulid taxa correlates strongly with genetic distances. Syntax features of complete songs and of single units are most consistent with the molecular data, whereas the abundance of certain element types is not. Whether song characters are innate or learned was interpreted using hand-reared birds in aviary experiments. We found that convergent character evolution seems to be most probable for learned acoustic traits. We conclude that syntax traits of whole verses or subunits of territorial song, especially innate song structures, are the most reliable acoustic traits for phylogenetic reconstructions in Regulus.     

Molecular phylogeny reveals the repeated evolution of complex male genital traits in the New Zealand moth genus Izatha (Lepidoptera: Xyloryctidae)

Male genitalia are among the most rapidly evolving and divergent morphological structures and sexual selection is known to drive this phenomenon in many taxa. Because of their diversity, even within a single genus, genital characters are frequently used to infer relationships among closely‐related species. Moths within the genus Izatha (Xyloryctidae) are ideal candidates for investigating the phylogenetic patterns of genital evolution as they display great variation in male genital structure and complexity. We determined the evolutionary relationships among 31 species of Izatha by constructing a molecular phylogeny of the genus based on the mitochondrial cytochrome oxidase subunit I gene and the isocitrate dehydrogenase and carbamoylphosphate synthase domain protein nuclear genes. This allowed estimations of ancestral male genital character states and patterns of male genital diversification using maximum‐likelihood models. The genus is divided into two well‐supported clades and two poorly supported clades at the root of the phylogeny with incomplete phylogenetic resolution within two species groups, likely due to rapid speciation. Izatha display a number of apomorphic phallic traits including cornuti (sclerotized spines) which are either discharged into the female during copulation (deciduous cornuti) or fixed to the male phallus (compound and fish‐hook cornuti). Within the genus, there is a reduction of secondary genital characters – the uncus and gnathos – but an elaboration of another grasping structure, the juxta; the potential origin and functionality of these male genital traits are discussed. Overall, some male genital characters provided a good indication of species relationships; however, several parts of the complex male genitalia of Izatha show evidence of homoplasy and convergence highlighting the problems of using these traits in determining species relationships. Additionally, this convergence has highlighted that complex genital structures may evolve repeatedly and independently within a lineage.     

Phylogenetic interrelationships,taxonomy, and reductive evolution in the Neotropical electric fish genus Hypopygus (Teleostei,Ostariophysi, Gymnotiformes)

A phylogenetic reconstruction of the Neotropical electric fish genus Hypopygus based on 47 parsimony‐informative morphological characters is presented. A series of synapomorphies support the hypothesis of monophyly of Hypopygus, and partially resolve species‐level relationships within the genus. Hypopygus species are recognized here as miniaturized fishes based on two criteria; first, a derived condition of diminutive body size, and; second, the presence of a suite of reductive morphological characters, including partial or total losses, simplifications, and reductions of the anal‐fin rays, scales, cranial bones, and laterosensory canal system. Reductive characters associated with miniaturization comprise 45% of the total number of characters in the phylogenetic reconstruction of the genus. Miniaturization and reductive morphological evolution in Hypopygus are discussed here in the phylogenetic context. A taxonomic revision of Hypopygus is presented, in which five new species are described, two species previously assigned to the genus are redescribed, and a single known species of Stegostenopos is redescribed and included in Hypopygus as a junior synonym. Distribution maps and a key for all eight valid species of Hypopygus are provided, based on the examination of 5014 catalogued museum specimens. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1096–1156.     

Phylogenetic analysis of the Pinnotheridae (Crustacea, Brachyura) based on larval morphology, with emphasis on the Dissodactylus species complex

Comparative larval morphology was used to elucidate phylogenetic relationships within the Pinnotheridae and the Dissodactylus species complex. Within the family, seven zoeal and six megalopal characters suggested two equally parsimonious phylogenetic hypotheses for pinnotherid larvae, both with Ostracotheres tridacnae representing the sister group for the Dissodactylus complex. Results indicated that the genus Pinnotheres is a polyphyletic taxon, and that the traditional subfamilial arrangement comprises paraphyletic taxa within the subfamilies Pinnotherinae and Pinnothereliinae. Certain evidence has suggested that Fabia and Juxtafubia should be excluded from the Pinnotherinae and placed into the Pinnothereliinae. Larval and adult morphology suggested that Pinnotheres politus should be included within Tumidotheres. The phylogenetic analysis within the Dissodactylus complex involved one zoeal and 16 megalopal characters. Results suggested a single phylogenetic hypothesis based on larval morphology. Combining adult morphology with larval evidence resulted in two equally parsimonious phylogenetic hypotheses, one of which agreed with a previously suggested hypothesis based only on adult characters.     

Phylogeny and reclassification of the Caucasigenini radiation from the Caucasus region (Gastropoda,Hygromiidae)

The Caucasigenini is an endemic radiation of hygromiid land snails from the Caucasus region. A phylogenetic analysis of morphological characters of the genitalia and the shell showed that the morphological characters are insufficient for resolving the relationships within the Caucasigenini. Convergences of the few parsimony informative characters in other groups of the Hygromiidae demonstrate that these characters are not reliable indicators of phylogenetic relationships. Phylogenetic analyses of sequences of cox1, 16S rDNA, 5.8S rDNA, ITS2 and 28S rDNA revealed several well‐supported groups. The relationships among these groups could not be resolved. It is likely that these groups originated in a rapid radiation during the uplift of the Caucasus. Based on the molecular phylogeny, we propose a new classification of the species of the Caucasigenini and establish a new genus, Lazicana gen. n.     

Character- and tree-based delimitation of species in the 'Cichlasoma' facetum group (Teleostei, Cichlidae) with the description of a new genus

The 'Cichlasoma' facetum group is part of the taxonomically complex group of Neotropical cichlid fishes of the tribe Heroini. Many species groups and unplaced species of heroines are still left without a generic name following the revision of the genus Cichlasoma . We describe here the 'Cichlasoma' facetum group as a new genus, Australoheros , and provide evidence for its monophyly based on phylogenetic analyses of morphological and mtDNA characters. Australoheros is morphologically characterized by the lowest values in meristic characters among heroines and by three apomorphic characters in coloration pattern. In addition to the three described species of Australoheros , our results of species delimitation based on a combination of tree- and character-based approaches identify seven putatively new species of Australoheros . Several coding schemes of morphological characters are used to recover the intrageneric relationships within the genus, resulting in very similar topologies. Discovery of additional species within the genus is expected once material from the whole distribution area is studied.     

The Influence of Phylogeny on the Social Behaviour of Macaques (Primates: Cercopithecidae, genus Macaca)

The macaques are the most geographically widespread and behaviourally diverse primate genus. Many of the diversified features of social behaviour and organization in this genus have been attributed to socio-ecological differences. However, some core aspects of social behaviour and organization appear to be highly conservative, suggesting a high degree of phylogenetic inertia. A recently derived classification of macaque social organization, as well as a large range of social and physical traits, were analysed for 16 species to ascertain the role of phylogeny in explaining the distribution of these traits within the genus Macaca . These traits were mapped onto two alternative phylogenies. The pattern of social organization, based on the degree of asymmetry in social relations, exhibited a high and significant level of phylogenetic inertia, as did seven of the 22 individual traits compared. A profile constructed of the most likely ancestral state for this character matrix showed that it most closely resembles the pattern present in the Barbary macaque ( M. sylvanus ), which, based on both molecular and morphological data, most closely resembles the ancestral macaque.     

Hidden biodiversity: total evidence phylogenetics and evolution of morphological traits in a highly diverse lineage of endogean ground beetles,Typhlocharis Dieck, 1869 (Carabidae,Trechinae, Anillini)

Typhlocharis is the most diverse eyeless endogean ground beetle genus known to date, with 62 species all endemic to the West Mediterranean region. The lineage is characterized by a conservative and singular body plan within Carabidae that contrasts with a high morphological diversity in many traits. We provide an exhaustive phylogeny of the lineage through the study of 92 morphological characters from all 62 described species and 45 potential new species from 70 additional populations, and the combination of morphological and available molecular data, in the first total evidence phylogenetic approach for a highly diverse endogean lineage. We tracked the evolution of morphological traits over the obtained phylogenies. Results suggest eight morphologically distinct clades, which do not correspond to the species groups proposed formerly. Ancestral state reconstructions and phylogenetic signal analyses of morphological traits revealed that some of the previously key characters to the classification of Typhlocharis, such as the umbilicate series or the apical denticles of elytra, are highly homoplasic, whereas other characters show stronger phylogenetic signal, including structures in the antennae, gula, pronotum and last abdominal ventrite. This evidence supports the split of Typhlocharis into three genera: Lusotyphlus gen. nov. ; Typhlocharis Dieck, 1869 and Microcharidius Coiffait, 1969 (revalidated), forming the subtribe Typhlocharina Jeanne, 1973.     

Molecular systematics, zoogeography, and evolutionary ecology of the atlantic parrotfish genus Sparisoma

Parrotfishes of the genus Sparisoma (Scaridae) are ecologically important tropical reef fishes restricted to the Atlantic Ocean. We investigated phylogenetic relationships among the eight extant species within this genus using mitochondrially encoded 12S and 16S ribosomal genes. Our molecular data support the view that (i) Sparisoma originated approximately 14-35 million years ago (mya), probably in the tropical western Atlantic, off Brazil; (ii) there have been at least four discrete bouts of cladogenesis within the genus, with the most recent one ( approximately 2.8-5.6 mya) involving four events in both the east and the west Atlantic and across the Atlantic; and (iii) the genus invaded the eastern Atlantic on two different occasions, probably by at least two different routes. The data also offer support for Bellwood's ideas concerning the evolutionary changes in adult feeding patterns and habitat use within Scarids. Specifically, they support the evolutionary position of the ecological traits of Sparisoma as intermediate within the family.     

The lower cretaceous ferns in the genus Anemia (Schizaeceae), Potomac group of Virginia, and relationships within the genus

Based on characters of the fertile fronds, two species of fossil ferns from the Lower Cretaceous Potomac Group of the U.S.A., originally described as species of Osmunda by Fontaine in 1889, are transferred to the genus Anemia. The two species display primitive characters for that genus. Analysis of these and other characters of Anemia and related species, using parsimony and compatibility programs, suggests possible phylogenetic arrangements and facilitates delimination of three taxonomic units within Anemia that were already distinct during Cretaceous time. The subgenera Coptophyllum and Anemia are shown to be paraphyletic in the suggested phylogenies and the schemes agree with the known stratigraphy of the fossil ferns.     

Phylogenetic relationships, biogeography and speciation in the avian genus Saxicola

The avian genus Saxicola is distributed throughout Africa, Asia, Europe and various islands across Oceania. Despite the fact that the group has great potential as a model to test evolutionary hypotheses due to the extensive variability in life history patterns recorded between and within species, the phylogenetic relationships among species and subspecies of this genus are poorly understood. We undertook a systematic investigation of the relationships within this genus with three main objectives in mind, (1) to test the monophyly of the genus; (2) to ascertain geographical origin and dispersal sequence; and (3) to test for monophyly within the most morphologically diverse species, S. torquata and S. caprata. We studied sequence data from the mitochondrial cytochrome b gene from 11 of the 12 recognized species and 15 of the 45 described subspecies. Four clades, two exclusively Asian, one Eurasian, and the fourth encompassing Eurasia and Africa, were identified. Based on our analyses, monophyly of the genus Saxicola is not supported and an Asian origin for the genus can be inferred. Results from DIVA analyses, tree topology and nodal age estimates suggest independent colonisation events from Asia to Africa and from Asia to the Western Palearctic, with the Sahara desert acting as a natural barrier for S. torquata. Subspecies and populations of S. torquata are not monophyletic due to S. tectes, S. dacotiae and S. leucura grouping within this complex. Subspecies and populations of S. caprata are monophyletic. Importantly, within S. torquata and S. caprata, slight morphological traits and plumage colour pattern differences used to recognize subspecies are indicative of the greater cryptic diversification that has occurred within this genus.     

Estimating phylogenetic inertia in Tithonia (Asteraceae): a comparative approach

Abstract.— Phylogenetic inertia is a difficult issue in evolutionary biology because we have yet to reach a consensus about how to measure it. In this study a comparative approach is used to evaluate phylogenetic inertia in 14 demographic and morphological characters in 10 species and one subspecies of the genus Tithonia (Asteraceae). Three different methods, autocorrelational analysis, phylogenetic correlograms, and ancestor-state reconstruction, were used to evaluate phylogenetic inertia in these traits. Results were highly dependent on the method applied. Autoregression and phylogenetic eigenvector regression (PVR) methods found more inertia in morphological traits. In contrast, phylogenetic correlograms and ancestor-state reconstruction suggest that morphological characters exhibit less phylogenetic inertia than demographic ones. The differences between results are discussed and methods are compared in an effort to understand phylogenetic inertia more thoroughly.     

石山苣苔属(苦苣苔科)花形态演化及分类学意义

石山苣苔属(苦苣苔科)约30种,主要分布于我国南部的石灰岩地区.目前该属已知物种数虽少但花形态极其多样,是该科中分类最为困难的类群之一.基于分子证据,其它8个属中花形态迥异的一些物种被并入石山苣苔属.然而,该属花形态的演化趋势缺乏系统性的研究,传统分类对属的界定与分子系统学研究结果相矛盾的原因,以及是否有形态特征支持新界定的石山苣苔属还不清楚.该研究中,总共编码了19种石山苣苔属植物和9种报春苣苔属植物的35个形态特征,其中包括26个花部形态特征,在分子系统树上追踪了它们的演化路径.结果表明:无论属内还是属间,多数花部形态特征,尤其以往属的分类界定特征,在演化过程中变化频繁且发生了高度同塑性演化,这是导致传统形态分类不自然的关键因素.此外,在观察研究的所有特征中,花丝和柱头的差异可能在石山苣苔属植物共同祖先中经历了演变,或可用于区分石山苣苔属与其姐妹报春苣苔属的大多数种类.因此,在苦苣苔科植物的分类学研究中应当慎用这些花部性状作为分类依据,而且应对形态特征进行广泛地观察研究,在密集的取样和分辨率更高、更可靠的系统树上追踪它们的演化规律.更为重要的是,需要进一步研究导致复杂形态性状演化的内在分子调控机理和外在的自然选择动力,最终更加深入地理解石山苣苔属等典型喀斯特植物的演化过程和机理.     

The ITS region of groundwater amphipods: length,secondary structure and phylogenetic information content in Crangonyctoids and Niphargids

The phylogenetic analysis of groundwater amphipods is challenging due to the lack of suitable morphological characters. However, molecular phylogenies based on the 18S and 28S nuclear genes of two Crangonyctoidea species endemic to Iceland, Crymostygius thingvallensis and Crangonyx islandicus, support the taxonomy of these species on the basis of morphological characters. Molecular analyses suggest that the genus Crangonyx is paraphyletic, with the species that is found in Eurasia being highly divergent genetically from the species present in North America and Iceland. Studies of the phylogenetic relationships within the genus Niphargus also warrant further work. The nuclear ITS2 region has recently been proposed as a barcoding marker for plants and animals. In addition, ITS2 has been used to build phylogenies at high taxonomic levels by including its secondary structure. In this study, we want to evaluate the applicability of the ITS region for this group of species and describe its characteristics. The taxonomy of C. thingvallensis, as well as the paraphyly of the genus Crangonyx, is supported herein by phylogenies based on the ITS2 variation. The secondary structure and the length of the ITS2 sequences of the Crangonyctoidea and the Niphargidae species studied are highly variable and are characterized by duplications. The ITS2 sequence of Niphargus plateaui is the longest metazoan sequence deposited in the ITS2 database so far. Although saturation was observed in the nucleotide variation of this marker, the addition of the secondary structure information for the reconstruction of the phylogeny did not add support to the phylogenetic trees. The ITS1 region, which is known to be more variable than ITS2 and bears a large duplication within C. islandicus, was found to be less useful for phylogenetic reconstruction.     

57 Systematics of hydropuntia montagne (gracilariaceae,gracilariales, rhodophyta) based on comparative morphology and rbcL sequence analysis

The taxonomic validity of the genus Hydropuntia Montagne (1843) (including Polycavernosa) within the Gracilariaceae (Gracilariales, Rhodophyta) is controversial. Morphological characters that define species of Hydropuntia are said to be variable and to overlap with those of Gracilaria. Here we present a global phylogenetic study of the family based on a Bayesian analysis of a large rbcL DNA sequence dataset indicating that the genus Hydropuntia forms a well supported monophyletic clade within the family, and recognize Hydropuntia as a genus distinct from Gracilaria. We also conducted smaller phylogenetic analyses in which thirty four Hydropuntia rbcL sequences resulted in two major clades within the genus, comprising a Caribbean clade and an Indo‐Pacific clade. Diagnostic reproductive stages that separate these two clades will be illustrated.     

Phylogenetic study of the species within the family Streptomycetaceae

Species of the genus Streptomyces, which constitute the vast majority of taxa within the family Streptomycetaceae, are a predominant component of the microbial population in soils throughout the world and have been the subject of extensive isolation and screening efforts over the years because they are a major source of commercially and medically important secondary metabolites. Taxonomic characterization of Streptomyces strains has been a challenge due to the large number of described species, greater than any other microbial genus, resulting from academic and industrial activities. The methods used for characterization have evolved through several phases over the years from those based largely on morphological observations, to subsequent classifications based on numerical taxonomic analyses of standardized sets of phenotypic characters and, most recently, to the use of molecular phylogenetic analyses of gene sequences. The present phylogenetic study examines almost all described species (615 taxa) within the family Streptomycetaceae based on 16S rRNA gene sequences and illustrates the species diversity within this family, which is observed to contain 130 statistically supported clades, as well as many unsupported and single member clusters. Many of the observed clades are consistent with earlier morphological and numerical taxonomic studies, but it is apparent that insufficient variation is present in the 16S rRNA gene sequence within the species of this family to permit bootstrap-supported resolution of relationships between many of the individual clusters.     

Conservation of cytoplasmic organization in the cystidia of Suillus species

Cystidia of Suillus americanus and S. granulatus (Boletales) were examined cytochemically and ultrastructurally with cells prepared by freeze substitution. We present the first study showing ultrastructural details and cytological functions of the cystidium to be conserved in two closely related species. The results are presented for inclusion in the AFTOL Structural and Biochemical Database to aid in the application of morphological characters to phylogenetic studies. The cystidia of these Suillus species appear to be united by a series of conserved characters, including specialized secretion mechanisms, smooth tubular endoplasmic reticulum and abundant free ribosomes. The conservation of these subcellular traits among members of this genus suggests that ultrastructural details of cystidia may provide a suite of phylogenetically informative characters. Inclusion of such characters in phylogenetic analyses might resolve or provide support for monophyletic groups at the level of family or genus.     

Molecular phylogeny,diagnostics, and diversity of plant‐parasitic nematodes of the genus Hemicycliophora (Nematoda: Hemicycliophoridae)

The genus Hemicycliophora (Nematoda: Hemicycliophoridae) contains 132 valid species of plant‐parasitic nematodes, collectively known as ‘sheath nematodes’. Hemicycliophora spp. are characterized morphologically by a long stylet with rounded basal knobs and a cuticular sheath, present in juvenile and adult stages. Populations of 20 valid and 14 putative species of Hemicycliophora and Loofia from several countries were characterized morphologically using light (LM) and scanning electron microscopy (SEM) and molecularly using the D2‐D3 segments of 28S rRNA and internal transcribed spacer (ITS) rRNA gene sequences. LM and SEM observations provided new details on the morphology of these species. PCR‐restriction fragment length polymorphisms (PCR‐RFLPs) of the D2‐D3 of 28S rDNA were proposed for identification of the species. Phylogenetic relationships within populations of 36 species of the genus Hemicycliophora using 102 D2‐D3 of 28S rDNA and 97 ITS rRNA gene sequences as inferred from Bayesian analysis are reconstructed and discussed. Ancestral state reconstructions of diagnostic characters (body and stylet length, number of body annuli, shape of vulval lip and tail), using maximum parsimony and Bayesian inference, revealed that none of the traits are individually reliable characters for classifying the studied sheath nematode. The Shimodaira–Hasegawa test rejected the validity of the genus Loofia. This is the most complete phylogenetic analysis of Hemicycliophora species conducted so far. © 2014 The Linnean Society of London