Taxonomic classification of the reef coral family Mussidae (Cnidaria: Anthozoa: Scleractinia)

Molecular analyses are transforming our understanding of the evolution of scleractinian corals and conflict with traditional classification, which is based on skeletal morphology. A new classification system, which integrates molecular and morphological data, is essential for documenting patterns of biodiversity and establishing priorities for marine conservation, as well as providing the morphological characters needed for linking present‐day corals with fossil species. The present monograph is the first in a series whose goal is to develop such an integrated system. It addresses the taxonomic relationships of 55 Recent zooxanthellate genera (one new) in seven families (one new), which were previously assigned to the suborder Faviina (eight genera are transferred to incertae sedis). The present monograph has two objectives. First, we introduce the higher‐level classification system for the 46 genera whose relationships are clear. Second, we formally revise the taxonomy of those corals belonging to the newly discovered family‐level clade (restricted today to the western Atlantic and Caribbean regions); this revised family Mussidae consists of ten genera (one of which is new) and 26 species that were previously assigned to the ‘traditional’ families Faviidae and Mussidae. To guide in discovering morphologic characters diagnostic of higher‐level taxa, we mapped a total of 38 morphologic characters [19 macromorphology, eight micromorphology, 11 microstructure] onto a molecular tree consisting of 67 species [22 Indo‐Pacific and seven Atlantic species in the traditional family Faviidae; 13 Indo‐Pacific and ten Atlantic species in the traditional family Mussidae; 13 species in the traditional families Merulinidae (5), Pectiniidae (7), and Trachyphylliidae (1); two Atlantic species of traditional Montastraea], and trace character histories using parsimony. To evaluate the overall effectiveness of morphological data in phylogeny reconstruction, we performed morphology‐based phylogenetic analyses using 27 (80 states) of the 38 characters, and compared morphological trees with molecular trees. The results of the ancestral state reconstructions revealed extensive homoplasy in almost all morphological characters. Family‐ and subfamily‐level molecular clades [previously identified as XVII?XXI] are best distinguished on the basis of the shapes of septal teeth and corresponding microstructure. The newly revised family Mussidae (XXI) has septal teeth with regular pointed tips (a symplesiomorphy) and a stout blocky appearance. It has two subfamilies, Mussinae and Faviinae. The subfamily Mussinae is distinguished by spine‐shaped teeth and widely spaced costoseptal clusters of calcification centres. The subfamily Faviinae is distinguished by blocky, pointed tricorne or paddle‐shaped teeth with elliptical bases, transverse structures such as carinae that cross the septal plane, and well‐developed aligned granules. Defining diagnostic characters for the broader data set is more challenging. In analyses of taxonomic subsets of the data set that were defined by clade, morphological phylogenetic analyses clearly distinguished the families Mussidae (XXI) and Lobophylliidae (XIX), as well as the two subfamilies of Mussidae (Mussinae, Faviinae), with one exception (Homophyllia australis). However, analyses of the entire 67‐species data set distinguished the family Lobophylliidae (XIX), but not the Merulinidae (XVII) and not the newly defined Mussidae (XXI), although the subfamily Mussinae was recovered as monophyletic. Some lower‐level relationships within the Merulinidae (XVII) agree with molecular results, but this particular family is especially problematic and requires additional molecular and morphological study. Future work including fossils will not only allow estimation of divergence times but also facilitate examination of the relationship between these divergences and changes in the environment and biogeography. Published 2012. This article is a U.S. Government work and is in the public domain in the USA. Zoological Journal of the Linnean Society, 2012, 166 , 465–529.     

Recent Bryological Literature

Abstract

Members of the moss family Hylocomiaceae have been hypothesized to belong to more than one major clade. While molecular studies performed so far are inconclusive regarding Hylocomiaceae relationships, morphological data are used here to test this hypothesis, based on species representing all genera of the Hylocomiaceae as well as some genera that possibly belong to this family. The results of the analysis suggest that Hylocomiaceae members belong to two major clades, one including mainly northern temperate species and one mainly tropical to subtropical taxa, with most of the latter species found in S.E. Asia. With the morphological context provided here, the next step in the investigation of this family should include both studies of more taxa outside the family, to correctly infer the phylogenetic relationships in a larger framework, and the addition of data from several molecular markers belonging to more than one genome.     

Phylogenetic relationships within Aglaopheniidae (Cnidaria,Hydrozoa) reveal unexpected generic diversity

Morphology can be misleading in the representation of phylogenetic relationships, especially in simple organisms like cnidarians and particularly in hydrozoans. These suspension feeders are widely distributed in many marine ecosystems, and the family Aglaopheniidae Marktanner‐Turneretscher, 1890 is among the most diverse and visible, especially on tropical coral reefs. The taxonomy of this family is based on morphological characters with emphasis on reproductive structures for the identification of genera. This study is the most comprehensive molecular phylogeny of the Aglaopheniidae to date, including six genera and 38 species, of which 13 were investigated for the first time and sampled on tropical coral reefs throughout the Indo‐Pacific region. For newly sampled individuals, we sequenced the 16S rRNA, the nuclear locus comprising the complete ITS1‐5.8S rRNA gene‐ITS2 and the first intron of the calmodulin nuclear gene. Phylogenetic analyses of the data revealed and confirmed a general polyphyly, or doubtful monophyly, of all sampled genera in tropical regions based on both the mitochondrial and nuclear markers. Our results revealed that several morphological characters used today are unsuited to resolve phylogenetic relationships between species and genera, as well as the high phyletic diversity within this family. Future revision of the classification of this family will require extensive geographic sampling and the use of an integrative approach.     

A phylogeny reconstruction of the Dendrophylliidae (Cnidaria,Scleractinia) based on molecular and micromorphological criteria,and its ecological implications

Recent molecular phylogenetic studies have shown that most traditional families of zooxanthellate shallow‐water scleractinians are polyphyletic, whereas most families mainly composed of deep‐sea and azooxanthellate species are monophyletic. In this context, the family Dendrophylliidae (Cnidaria, Scleractinia) has unique features. It shows a remarkable variation of morphological and ecological traits by including species that are either colonial or solitary, zooxanthellate or azooxanthellate, and inhabiting shallow or deep water. Despite this morphological heterogeneity, recent molecular works have confirmed that this family is monophyletic. Nevertheless, what so far is known about the evolutionary relationships within this family, is predominantly based on skeleton macromorphology, while most of its species have remained unstudied from a molecular point of view. Therefore, we analysed 11 dendrophylliid genera, four of which were investigated for the first time, and 30 species at molecular, micromorphological and microstructural levels. We present a robust molecular phylogeny reconstruction based on two mitochondrial markers (COI and the intergenic spacer between COI and 16S) and one nuclear (rDNA), which is used as basis to compare micromorphogical and microstructural character states within the family. The monophyly of the Dendrophylliidae is well supported by molecular data and also by the presence of rapid accretion deposits, which are ca. 5 μm in diameter and arranged in irregular clusters, and fibres that thicken the skeleton organized in small patches of a few micrometres in diameter. However, all genera represented by at least two species are not monophyletic, Tubastraea excluded. They were defined by traditional macromorphological characters that appear affected by convergence, homoplasy and intraspecific variation. Micromorphogical and microstructural analyses do not support the distinction of clades, with the exception of the organization of thickening deposits for the Tubastraea clade.     

Reconciling taxonomy and phylogeny in the bristleworm family Eunicidae (polychaete,Annelida)

Eunicid annelids inhabit diverse marine habitats worldwide, have ecological and economic importance and have been pictured in the news as giant predator worms. They compose a traditional stable taxon recently supported as monophyletic but characterized by plesiomorphies. Most genera within the family have been recovered as paraphyletic in previous studies. We present a phylogenetic hypothesis for eunicid based on molecular (COI, 16S rDNA, 18S rDNA) and morphological data (213 characters), including an explicit attempt to account for serial homology. Eunicidae as well as monophyletic genera Marphysa sensu stricto and Lysidice is redefined based on synapomorphies. Nematonereis is synonymized to Lysidice. Leodice and Nicidion are resurrected to name monophyletic groups including species previously included in Eunice and Marphysa sensu lato. Traditional diagnostic characters such as the absence/presence of peristomial cirri, lateral antennae and branchiae are homoplasies and not informative at the generic level. Different coding of traditional characters (i.e. articulation of prostomial appendages) and novel characters of prostomial features and regionalization of the body support the monophyly of the family and genera level clades. Thus, the phylogenetic hypothesis presented here and the evolution of characters provided background information for taxonomic changes yielding evolutionary meaningful classification and diagnoses for the family and genera.     

Advances in molecular systematics of the vetigastropod superfamily Trochoidea

Williams, S.T. (2012). Advances in molecular systematics of the vetigastropod superfamily Trochoidea. —Zoologica Scripta, 41, 571–595. The gastropod superfamily Trochoidea Rafinesque, 1815 is comprised of a diverse range of species, including large and charismatic species of commercial value as well as many small or enigmatic taxa that are only recently being represented in molecular studies. This study includes the first sequences for rarely collected species from the genera Gaza Watson, 1879, Callogaza Dall, 1881, Antimargarita Powell, 1951 and Kaiparathina Laws, 1941. There is also greater taxon sampling of genera that have proved difficult to place in previous phylogenetic analyses, like Tectus Montfort, 1810, Tegula Lesson, 1832, Margarites Gray, 1847, Margarella Thiele, 1893 and trochoid skeneimorphs. There is also greater sampling of poorly represented families Solariellidae and Liotiidae. Bayesian analysis of combined gene data sets based on four (28S, 12S, 16S and COI) or five genes (plus 18S) suggests that there are eight, possibly nine families in Trochoidea including the families Margaritidae and Tegulidae, which are recognized for the first time at familial rank. Other trochoidean families confirmed are Calliostomatidae, Liotiidae, Skeneidae, Solariellidae, Trochidae and Turbinidae. A clade including Cittarium and the commercially important genera Rochia and Tectus may represent a possible ninth family, but this is not formally recognized or described here and awaits confirmation from further studies. Relationships among families were not generally well supported except in the 5‐gene tree. In the 5‐gene tree, Turbinidae, Liotiidae, Tegulidae, Cittarium, Rochia and Tectus form a well‐supported clade consistent with the previous molecular and morphological studies linking these groups. This clade forms another well‐supported clade with Margaritidae and Solariellidae. Trochidae is sister to Calliostomatidae with strong support. Subfamilial relationships within Trochidae are consistent with recent molecular studies, with the addition of one new subfamily, Kaiparathininae Marshall 1993 (previously a tribe). Only two subfamilies are recognized within Turbinidae, both with calcareous opercula: Prisogasterinae and Turbininae. Calliostomatidae includes a new subfamily Margarellinae. Its assignment to Calliostomatidae, although well supported by molecular evidence, is surprising considering morphological evidence.     

Molecular phylogeny of the armored catfish family Callichthyidae (Ostariophysi, Siluriformes)

The family Callichthyidae comprises eight genera of fishes widely distributed across the Neotropical region. In the present study, sequences of the mitochondrial genes 12S rRNA, 16S rRNA, ND4, tRNAHis, and tRNASer were obtained from 28 callichthyid specimens. The sample included 12 species of Corydoras, three species of Aspidoras, two species of Brochis, Dianema, Lepthoplosternum, and Megalechis, and two local populations of Callichthys and Hoplosternum. Sequences of Nematogenys inermis (Nematogenyidae), Trichomycterus areolatus, and Henonemus punctatus (Trichomycteridae), Astroblepus sp. (Astroblepidae), and Neoplecostomus paranensis, Delturus parahybae, and Hemipsilichthys nimius (Loricariidae) were included as the outgroup. Phylogenetic analyses were performed by using the methods of maximum parsimony and maximum likelihood. The results of almost all analyses were very similar. The family Callichthyidae is monophyletic and comprises two natural groups: the subfamilies Corydoradinae (Aspidoras, Brochis, and Corydoras) and Callichthyinae (Callichthys, Dianema, Hoplosternum, Lepthoplosternum, and Megalechis), as previously demonstrated by morphological studies. The relationships observed within these subfamilies are in several ways different from those previously proposed on the basis of morphological data. Molecular results were compared with the morphologic and cytogenetic data available on the family.     

A single origin for the limnetic–euryhaline taxa in the Corbulidae (Bivalvia)

The bivalve family Corbulidae, known colloquially as ‘basket clams’, includes species tolerating a wide variety of habitats ranging from open marine to freshwater. Previous studies of corbulid phylogenetics have been based mainly on shell morphology and to some extent soft tissue anatomy. However, these studies have been inadequate for corbulid classification because of difficulties in determining the inter‐relationships of primarily marine species with non‐marine species, the latter commonly exhibiting highly divergent morphological, ecological and environmental characteristics from their marine counterparts. The first molecular phylogenetic study of the Corbulidae is presented herein, analysing DNA sequences from the 18S rRNA and 28S rRNA genes, separately and in combination. Fifteen corbulid species and 14 outgroup taxa were included in the analyses. Corbulidae is resolved as monophyletic, comprising three groups with varying support. The non‐marine species form one group that we name as the subclade ‘limnetic–euryhaline Corbulidae’ (LEC) and comprising the genera Lentidium, Erodona and Potamocorbula. This LEC, which is consistently recovered as monophyletic, is globally distributed. The marine Corbulidae are divided into two well‐supported lineages in combined analyses although there are inconsistencies in their membership between single‐gene analyses. One of the two lineages consists of primarily Western Pacific taxa and the other of North American and Caribbean taxa. Finally, the authors advocate further study on the LEC to mitigate potential biological invasions beyond their native distribution.     

More evidence for pervasive paraphyly in scleractinian corals: Systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data

Coral taxonomy and systematics continue to be plagued by a host of problems. Due to high phenotypic variability within species, morphological approaches have often failed to recognize natural taxa, and molecular techniques have yet to be applied to many groups. Here, we summarize the levels of paraphyly found for scleractinian corals and test, based on new data, whether paraphyly is also a significant problem in Faviidae, the second-most speciose hermatypic scleractinian family. Using both DNA sequence and morphological data we find that, regardless of analysis technique (maximum parsimony, maximum likelihood and Bayesian likelihood), many conventional taxonomic groups are not monophyletic. Based on two mitochondrial markers (COI and a noncoding region) that we amplified for 81 samples representing 41 faviid species and 13 genera, five genera that are represented by more than one species are paraphyletic, as is the family Faviidae. The morphological characters currently used to identify these corals similarly fail to recover many genera. Furthermore, trees based on both data types are incongruent, and total evidence analysis does little to salvage conventional taxonomic groupings. Morphological convergence, phenotypic variability in response to the environment, and recent speciation are likely causes for these conflicts, which suggest that the present classification of corals is in need of a major overhaul. We propose more detailed studies of problematic faviid taxa using standardized morphological, mitochondrial, and nuclear genetic markers to facilitate combining of data.     

Phylogeny of the family Trogidae (Coleoptera: Scarabaeoidea) inferred from mitochondrial and nuclear ribosomal DNA sequence data

Trogidae constitute a monophyletic and biologically unique family within Scarabaeoidea, being the only keratinophagous group in the superfamily. Traditionally, the family has been divided into three distinctive genera, Polynoncus Burmeister, Omorgus Erichson and Trox Fabricius. Although the taxonomy of the group is relatively well studied, changes to the existing classification have recently been proposed and the family as currently constituted has not been subjected to phylogenetic analyses. Here we present a molecular phylogeny for this cosmopolitan family based on three partially sequenced gene regions: 16S rRNA, 18S rRNA and 28S rRNA (domain 2). Included in the analyses are representatives belonging to four of the five extant genera (and three of the four subgenera) from all major zoogeographic regions, representing about 20% of the known trogid species diversity in the family. Phylogenetic analyses performed included parsimony and Bayesian inference. We deduce their historical biogeography by using trogid fossils as calibration points for divergence estimates. Our analyses resolved relationships between and within genera and subgenera that are largely congruent with existing phylogeny hypotheses based on morphological data. We recovered four well‐supported radiations: Polynoncus, Omorgus, Holarctic Trox and African Phoberus MacLeay. On the basis of this study, it is proposed that taxonomic changes to the generic classification of the family be made. The subgenera Trox and Phoberus should be elevated to genera to include the Holarctic and all the Afrotropical species, respectively, and Afromorgus returned to subgeneric rank. Estimates of divergence time are consistent with a Pangaean origin of the family in the Early Jurassic. The subsequent diversification of the major lineages is largely attributed to the break‐up of Pangaea and Gondwana in the Middle Jurassic and early Late Cretaceous, respectively.     

Mitochondrial and nuclear markers support the monophyly of Dolichopodidae and suggest a rapid origin of the subfamilies (Diptera: Empidoidea)

Abstract. The Dolichopodidae is a species‐rich dipteran group with almost 7000 described species. The monophyly of the subfamilies and their relationships remain largely unknown because the polarities of key morphological characters are unclear and molecular data are available only for 9 of the 19 proposed subfamilies. Here we test whether molecular data from two nuclear (18S, 28S) and four mitochondrial (12S, 16S, Cytb, COI) genes can resolve the higher‐level relationships within the family. Our study is based on 76 Oriental species from 12 dolichopodid subfamilies and uses eight species of Empididae and Hybotidae as outgroups. Parsimony and likelihood analyses confirm the monophyly of the Dolichopodidae, as well as the monophyly of five of the ten subfamilies represented by more than two species [Sympycninae, Sciapodinae, Dolichopodinae, Hydrophorinae (excluding tribe Aphrosylini), Neurigoninae]. There is strong support for restoring the tribe Aphrosylini as a separate subfamily Aphrosylinae. The monophyly of Medeterinae, Peloropeodinae and Diaphorinae is dependent on which tree reconstruction technique is used, how indels are coded, and whether the fast‐evolving sites are excluded. Overall, we find that our sample of Oriental species is largely compatible with the subfamily concepts that were developed for the northern temperate fauna. However, our data provide little support for relationships between the subfamilies. Branch lengths, saturation, and distance plots suggest that this is probably the result of the rapid origin of dolichopodid subfamilies over a relatively short time. We find that genera that are difficult to place into subfamilies based on morphological characters are generally also difficult to place using molecular data. We predict that a dense, balanced taxon sample and protein‐encoding nuclear genes will be needed to resolve the higher‐level relationships in the Dolichopodidae.     

Molecular phylogenetic evidence for the evolution of specialization in anemonefishes.

Anemonefishes (genera: Amphiprion and Premnas; family Pomacentridae) are a group of 28 species of coral reef fishes that are found in obligate symbiosis with large tropical sea anemones. A phylogenetic hypothesis based on morphological analyses of this group suggests that the ancestral anemonefish was a generalist with similar morphology to other pomacentrids, and that it gave rise to other anemonefish species that were more specialized for living with particular species of host anemones. To test this hypothesis we constructed a molecular phylogeny for the anemonefishes by sequencing 1140 base pairs of the cytochrome b gene and 522 base pairs of the 16S rRNA gene for six species of anemonefishes (representatives of all subgenera and species complexes) and two other pomacentrid species. Three methods of phylogenetic analysis all strongly supported the conclusion that anemonefishes are a monophyletic group. The molecular phylogeny differs from the tree based on morphological data in that the two species of specialized anemonefishes (Premnas biaculeatus and Amphiprion ocellaris) were assigned to a basal position within the clade, and the extreme host generalist (Amphiprion clarkii) to a more derived position. Thus, the initial anemonefish ancestors were probably host specialists and subsequent speciation events led to a combination of generalist and specialist groups. Further phylogenetic studies of additional anemonefish species are required to substantiate this hypothesis.     

Treehopper trees: phylogeny of Membracidae (Hemiptera: Cicadomorpha: Membracoidea) based on molecules and morphology

Abstract. Recent independent phylogenetic analyses of membracid relationships based on molecular and morphological data have identified monophyletic lineages within the family. However, the results of these studies have not fully resolved treehopper phylogeny, and relationships among some higher membracid lineages remain in doubt. Portions of three datasets (958 aligned nucleotides from elongation factor‐1α, 2363 aligned nucleotides from 28S ribosomal DNA, and eighty‐three morphological features of adults and nymphs) introduced in recent studies were reanalysed separately and in combination with two new molecular datasets (321 aligned nucleotides from wingless and 1829 aligned nucleotides from 18S ribosomal DNA). The results of the combined data analyses, contrary to previous analyses of morphological data alone, grouped membracids into two well‐supported lineages, one comprising Stegaspidinae and Centrotinae, the other comprising Membracinae, Darninae and Smiliinae. The analyses recovered Centrotinae, Membracinae and Darninae as monophyletic groups, but Stegaspidinae was paraphyletic with respect to Centrotinae, and Smiliinae was polyphyletic with Micrutalini placed as a sister group to the clade comprising Membracinae, Darninae and Smiliinae. These results are consistent with the following hypotheses, proposed previously based on an analysis of morphological data: (1) the posterior pronotal process was derived and lost multiple times during the evolution of Membracidae; (2) Membracidae originated in the New World and reached the Old World subsequently via dispersal; (3) maternal care evolved independently multiple times and may or may not have been preceded by the acquisition of ant mutualism.     

Phylogenetic relationships in the Lejeuneaceae (Hepaticae) inferred using ITS sequences of nuclear ribosomal DNA

Sequences of the ITS1–5.8S–ITS2 region of nuclear ribosomal DNA were generated for 12 species from 9 genera of Lejeuneaceae and a single species of Jubulaceae (outgroup). The taxon sampling of Lejeuneaceae included representatives of the two widely recognized subfamilies, Lejeuneoideae and Ptychanthoideae. The molecular dataset was analysed independently and in combination with a morphological dataset. The nrITS dataset and the combined dataset resulted in identical topologies. The genus Bryopteris, sometimes treated as a separate family Bryopteridaceae, is nested within the Lejeuneaceae subfamily Ptychanthoideae. Lejeuneaceae subfamily Lejeuneoideae proved to be paraphyletic with the tribe Lejeuneeae sister to Ptychanthoideae, albeit without significant bootstrap support. The tribes Brachiolejeuneeae and Cheilolejeuneeae of Lejeuneoideae, established recently based on morphological evidence, are well supported in bootstrap analyses both of the ITS and the combined molecular–morphological datasets. The results support classifications of Lejeuneaceae based on morphological data and demonstrate the usefulness of the ITS region for phylogenetic studies within or among closely related genera of Lejeuneaceae.     

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.     

Molecular phylogeny of the fungus gnat tribe Exechiini (Mycetophilidae, Diptera)

The phylogenetic relationships within the fungus gnat tribe Exechiini have been left unattended for many years. Recent studies have not shed much light on the intergeneric relationship within the tribe. Here the first attempt to resolve the phylogeny of the tribe Exechiini using molecular markers is presented. The nuclear 18S and the mitochondrial 16S, and cytochrome oxidase subunit I (COI) genes were successfully sequenced for 20 species representing 15 Exechiini genera and five outgroup genera. Bayesian, maximum parsimony and maximum likelihood analyses revealed basically congruent tree topologies and the monophyly of Exechiini, including the genus Cordyla , is confirmed. The molecular data corroborate previous morphological studies in several aspects. Cordyla is found in a basal clade together with Brachypeza , Pseudorymosia and Stigmatomeria . The splitting of the genera Allodiopsis s.l. and Brevicornu s.l. as well as the sistergroup relationship of Exechia and Exechiopsis is also supported. The limited phylogenetic information provided by morphological characters is mirrored in the limited resolution of the molecular markers used in this study. Short internal and long-terminal branches obtained may indicate a rapid radiation of the Exechiini genera during a short evolutionary period.     

Molecular phylogeny and biogeography of the Neotropical cichlid fish tribe Cichlasomatini (Teleostei: Cichlidae: Cichlasomatinae)

We have conducted the first comprehensive molecular phylogeny of the tribe Cichlasomatini including all valid genera as well as important species of questionable generic status. To recover the relationships among cichlasomatine genera and to test their monophyly we analyzed sequences from two mitochondrial (16S rRNA, cytochrome b) and one nuclear marker (first intron of S7 ribosomal gene) totalling 2236 bp. Our data suggest that all genera except Aequidens are monophyletic, but we found important disagreements between the traditional morphological relationships and the phylogeny based on our molecular data. Our analyses support the following conclusions: (a) Aequidens sensu stricto is paraphyletic, including also Cichlasoma (CA clade); (b) Krobia is not closely related to Bujurquina and includes also the Guyanan Aequidens species A. potaroensis and probably A. paloemeuensis (KA clade). (c) Bujurquina and Tahuantinsuyoa are sister groups, closely related to an undescribed genus formed by the 'Aequidens'pulcher-'Aequidens'rivulatus groups (BTA clade). (d) Nannacara (plus Ivanacara) and Cleithracara are found as sister groups (NIC clade). Acaronia is most probably the sister group of the BTA clade, and Laetacara may be the sister group of this clade. Estimation of divergence times suggests that the divergence of Cichlasomatini started around 44Mya with the vicariance between coastal rivers of the Guyanas (KA and NIC clades) and remaining cis-andean South America, followed by evolution of the Acaronia-Laetacara-BTA clade in Western Amazon, and the CA clade in the Eastern Amazon. Vicariant divergence has played importantly in evolution of cichlasomatine genera, with dispersal limited to later range extension of species within genera.     

An integrative approach to the evolution of shrimps of the genus Palaemon (Decapoda,Palaemonidae)

Shrimps of the genus Palaemon Weber, 1795 comprise of 86 species with a wide morphological and ecological variability along the tropical and temperate regions. Studies based on molecular data have indicated that despite a recent taxonomic rearrangement, it may remain not monophyletic. On the other hand, cladistic, morphological analyses have suggested the presence of synapomorphies, implying a natural status for the genus. In this work, a broad taxonomic and molecular sampling is applied to verify whether Palaemon is a monophyletic taxon and, based on the recovered phylogeny, identify geographical and morphological patterns related to the lineages. Partial sequences of 16S rRNA, histone H3 and 18S rRNA from 60 species of Palaemon and 15 species from other genera of Palaemonidae were analysed. In addition, previously used characters as well as novel diagnostic characters were scrutinized. The present phylogeny indicates that the species of Palaemon fall into three distinct lineages and that the colonization of America and Europe likely occurred multiple times. Morphological characters allow for the identification of at least four monophyletic groups in Palaemon; two of which are monospecific at the moment. Based on the present results, it may become necessary to establish two new genera (to accommodate Palaemon concinnus and Palaemon mercedae, respectively), as well as re‐erect the genus Alaocaris Holthuis, 1949 for Palaemon antrorum, potentially including a further six American species.     

Combined phylogenetic analysis of the subclass Marchantiidae (Marchantiophyta): towards a robustly diagnosed classification

The most extensive combined phylogenetic analyses of the subclass Marchantiidae yet undertaken was conducted on the basis of morphological and molecular data. The morphological data comprised 126 characters and 56 species. Taxonomic sampling included 35 ingroup species with all genera and orders of Marchantiidae sampled, and 21 outgroup species with two genera of Blasiidae (Marchantiopsida), 15 species of Jungermanniopsida (the three subclasses represented) and the three genera of Haplomitriopsida. Takakia ceratophylla (Bryophyta) was employed to root the trees. Character sampling involved 92 gametophytic and 34 sporophytic traits, supplemented with ten continuous characters. Molecular data included 11 molecular markers: one nuclear ribosomal (26S), three mitochondrial genes (nad1, nad5, rps3) and seven chloroplast regions (atpB, psbT‐psbH, rbcL, ITS, rpoC1, rps4, psbA). Searches were performed under extended implied weighting, weighting the character blocks against the average homoplasy. Clade stability was assessed across three additional weighting schemes (implied weighting corrected for missing entries, standard implied weighting and equal weighting) in three datasets (molecular, morphological and combined). The contribution from different biological phases regarding node recovery and diagnosis was evaluated. Our results agree with many of the previous studies but cast doubt on some relationships, mainly at the family and interfamily level. The combined analyses underlined the fact that, by combining data, taxonomic enhancements could be achieved regarding taxon delimitation and quality of diagnosis. Support values for many clades of previous molecular studies were improved by the addition of morphological data. The long‐held assumption that morphology may render spurious or low‐quality results in this taxonomic group is challenged. The morphological trends previously proposed are re‐evaluated in light of the new phylogenetic scheme.