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     

Phylogenetic relationships and biogeography of the genus Algansea Girard (Cypriniformes: Cyprinidae) of central Mexico inferred from molecular data

Background  

The genus Algansea is one of the most representative freshwater fish groups in central Mexico due to its wide geographic distribution and unusual level of endemicity. Despite the small number of species, this genus has had an unsettled taxonomic history due to high levels of intraspecific morphological variation. Moreover, several phylogenetic hypotheses among congeners have been proposed but have had the following shortcomings: the use of homoplasious morphological characters, the use of character codification and polarisation methods that lacked objectivity, and incomplete taxonomic sampling. In this study, a phylogenetic analysis among species of Algansea is presented. This analysis is based upon two molecular markers, the mitochondrial gene cytochrome b and the first intron of the ribosomal protein S7 gene.     

The primates of the Neotropics: genomes and chromosomes

The classification of neotropical primates has been controversial. Different arrangements have been proposed, depending on taxonomic criteria and on the traits selected for phylogenetic reconstructions. These include gross morphologic characters, karyotypic attributes and DNA sequence data of nuclear and mitochondrial genes and of repetitive genomic components. These approaches have substantially clarified the main intergeneric relationships although several intrageneric arrangements still remain to be elucidated. In this review, we compare karyologic and molecular data of this speciose group.     

OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics

Background  

Molecular sequence data have become the standard in modern day phylogenetics. In particular, several long-standing questions of mammalian evolutionary history have been recently resolved thanks to the use of molecular characters. Yet, most studies have focused on only a handful of standard markers. The availability of an ever increasing number of whole genome sequences is a golden mine for modern systematics. Genomic data now provide the opportunity to select new markers that are potentially relevant for further resolving branches of the mammalian phylogenetic tree at various taxonomic levels.     

Phylogenetic analysis of the true water bugs (Insecta: Hemiptera: Heteroptera: Nepomorpha): evidence from mitochondrial genomes

Background  

The true water bugs are grouped in infraorder Nepomorpha (Insecta: Hemiptera: Heteroptera) and are of great economic importance. The phylogenetic relationships within Nepomorpha and the taxonomic hierarchies of Pleoidea and Aphelocheiroidea are uncertain. Most of the previous studies were based on morphological characters without algorithmic assessment. In the latest study, the molecular markers employed in phylogenetic analyses were partial sequences of 16S rDNA and 18S rDNA with a total length about 1 kb. Up to now, no mitochondrial genome of the true water bugs has been sequenced, which is one of the largest data sets that could be compared across animal taxa. In this study we analyzed the unresolved problems in Nepomorpha using evidence from mitochondrial genomes.     

Data congruence, paedomorphosis and salamanders

Background

The retention of ancestral juvenile characters by adult stages of descendants is called paedomorphosis. However, this process can mislead phylogenetic analyses based on morphological data, even in combination with molecular data, because the assessment if a character is primary absent or secondary lost is difficult. Thus, the detection of incongruence between morphological and molecular data is necessary to investigate the reliability of simultaneous analyses. Different methods have been proposed to detect data congruence or incongruence. Five of them (PABA, PBS, NDI, LILD, DRI) are used herein to assess incongruence between morphological and molecular data in a case study addressing salamander phylogeny, which comprises several supposedly paedomorphic taxa. Therefore, previously published data sets were compiled herein. Furthermore, two strategies ameliorating effects of paedomorphosis on phylogenetic studies were tested herein using a statistical rigor. Additionally, efficiency of the different methods to assess incongruence was analyzed using this empirical data set. Finally, a test statistic is presented for all these methods except DRI.

Results

The addition of morphological data to molecular data results in both different positions of three of the four paedomorphic taxa and strong incongruence, but treating the morphological data using different strategies ameliorating the negative impact of paedomorphosis revokes these changes and minimizes the conflict. Of these strategies the strategy to just exclude paedomorphic character traits seem to be most beneficial. Of the three molecular partitions analyzed herein the RAG1 partition seems to be the most suitable to resolve deep salamander phylogeny. The rRNA and mtDNA partition are either too conserved or too variable, respectively. Of the different methods to detect incongruence, the NDI and PABA approaches are more conservative in the indication of incongruence than LILD and PBS.

Conclusion

Paedomorphosis induces strong conflicts and can mislead the phylogenetic analyses even in combined analyses. However, different strategies are efficiently minimizing these problems. Though the exploration of different methods to detect incongruence is preferable NDI and PABA are more conservative than the others and NDI is computational less extensive than PABA.     

Integrated taxonomy of the <Emphasis Type="Italic">Asplenium normale</Emphasis> complex (Aspleniaceae) in China and adjacent areas

The Asplenium normale D. Don complex comprises several taxa that are either diploid or tetraploid. The tetraploids are assumed to have originated from diploid ancestors by relatively recent autopolyploidization or allopolyploidization. Some of the diploids are readily recognized morphologically but most of the taxa have until now been placed into a single species. However, phylogenetic studies have challenged this treatment and emphasized the notion that the taxonomic treatment of this complex needs to be revised. An integrative taxonomic approach was employed to delimit species in the complex using cytological, morphological, and DNA sequence data. Initially, we employed a diploid first approach to establish a robust taxonomic framework. Special efforts were made to collect and identify the diploid progenitors of each polyploid lineage identified in the plastid DNA based phylogenetic hypothesis. A total of six distinct diploid species were identified. The distinctive nature of the six diploids is strongly supported by sequence differences in plastid DNA and nuclear loci, as well as by the results of morphometric analysis. Diagnostic morphological characters were identified to distinguish the six diploid species, resulting in their revised taxonomy, which includes two novel species, namely, Asplenium normaloides and A. guangdongense. Further studies to strengthen the taxonomic classification of all of the tetraploid taxa are warranted.     

Phylogeny in Echinocereus (Cactaceae) based on combined morphological and molecular evidence: taxonomic implications

Echinocereus is a morphologically diverse genus that includes 64 species grouped into eight taxonomic sections based on morphological traits. In previous molecular phylogenetic analyses, the relationships amongst Echinocereus species were not entirely revealed and useful characters to recognize clades were not provided. The inclusion of several sources of evidence in a phylogenetic analysis is likely to produce more supported hypotheses. Therefore, we performed a combined phylogenetic analysis with a set of 44 morphological characters and six chloroplast DNA sequences. Topologies from parsimony and Bayesian analyses were mostly congruent. However, the relationships of E. poselgeri were not consistent between analyses. A second Bayesian analysis using a long-branch extraction test resulted in a topology with the morphological position of E. poselgeri congruent with that in parsimony analysis. Parsimony and Bayesian analyses corroborated the monophyly of Echinocereus, which included eight monophyletic groups. The combined phylogeny integrated into different clades those taxa that were not determined in previous analyses and changed the relationships of some recognized clades. The clades did not recover the recent infrageneric classification. In the present study, a new sectional classification for Echinocereus is proposed based on the eight recovered clades, which is supported by a combination of morphological and molecular characters. An identification key for sections in the genus is included.     

Molecular phylogenies challenge the classification of Polymastiidae (Porifera,Demospongiae) based on morphology

Polymastiidae Gray, 1867 is a worldwide distributed sponge family, which has a great significance for understanding of the demosponge deep phylogeny since the former order Hadromerida Topsent, 1894 has been recently split based on the molecular evidence and a new separate order has been established for the polymastiids. However, molecular data obtained from Polymastiidae so far are scarce, while the phylogenetic reconstruction based on morphology has faced a deficit of characters along with the vagueness of their states. The present study is a phylogenetic reconstruction of Polymastiidae based on novel data on two molecular markers, cytochrome oxidase subunit I and large subunit ribosomal DNA, obtained from a broad set of species. Monophyly of the family and nonmonophyly of four polymastiid genera are revealed, suggesting a high level of homoplasy of morphological characters, which are therefore not an appropriate base for the natural classification of Polymastiidae. Although the presented phylogenies cannot yet provide an alternative classification scheme, several strongly supported clades, which may be used as reference points in future classification, are recovered and three taxonomic actions are proposed: transfer of one species from Radiella to Polymastia Bowerbank, 1862; transfer of three species from Radiella Schmidt, 1870 to Spinularia Gray, 1867; and the consequent abandonment of Radiella.     

An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models

Background  

Tunicates have been recently revealed to be the closest living relatives of vertebrates. Yet, with more than 2500 described species, details of their evolutionary history are still obscure. From a molecular point of view, tunicate phylogenetic relationships have been mostly studied based on analyses of 18S rRNA sequences, which indicate several major clades at odds with the traditional class-level arrangements. Nonetheless, substantial uncertainty remains about the phylogenetic relationships and taxonomic status of key groups such as the Aplousobranchia, Appendicularia, and Thaliacea.     

Phylogeny and morphological evolution of the amblystegiaceae (Bryopsida)

To circumscribe the moss family Amblystegiaceae, we performed a broad-scale analysis of trnL-trnF spacer sequence data for 168 species of the Hypnales and 11 species of the Hookeriales and additional analyses of trnL-trnF and atpB-rbcL (chloroplast DNA), one nuclear region, the internal transcribed spacers of 18S-26S rDNA, and 68 morphological characters for a reduced data set of 54 species of Hypnales. The traditionally circumscribed Amblystegiaceae are polyphyletic and include the Amblystegiaceae s. str. and the Calliergonaceae fam. nov., plus several taxa closely related to other Hypnalean families. Generic relationships within the redefined Amblystegiaceae were investigated by analyzing data from the three DNA regions and morphology as used in the broader analysis. Reconstruction of morphological evolution was evaluated using maximum-parsimony and maximum-likelihood. Numerous independent character-state transitions implied by the phylogeny suggest that morphological characters that have traditionally been used to delineate the Amblystegiaceae are homoplastic. Sporophytic traits, which are generally given primacy over gametophytic traits in moss classification, are more labile than previously thought, and many characters that are related to sporophyte specializations are strongly correlated with habitat conditions. The evolution of several gametophyte features previously thought to be reliable for delineating the family are also strongly correlated with habitat. These observations help to explain the instability of the Amblystegiaceae in previous taxonomic and phylogenetic analyses based on morphology.     

Do orthologous gene phylogenies really support tree-thinking?

Background  

Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes.     

Cryptic diversity in Brevipalpus mites (Tenuipalpidae)

Defining the taxonomic identity of organisms is a prerequisite for their study, and in the case of economically important species, misidentification may lead to the application of inappropriate prevention and control strategies. Flat mites of the Brevipalpus genus include several crop pests and the systematics of these mites represents a challenge for acarologists. Many of the most economically important Brevipalpus species have repeatedly been inaccurately identified. Such problematic classification has been attributed to the likely occurrence of cryptic species in the genus. In this study, we used an integrative approach that combined molecular analyses, including sequence‐based species delimitation, with detailed morphological identification using traits that have recently showed to be taxonomically informative. Sequences of mitochondrial cytochrome c oxidase subunit I (COI) were obtained from individuals collected from host plants belonging to 14 genera and 13 families across 29 locations in the Americas (Brazil, Chile, USA). The phylogenetic analyses included previously published Brevipalpus sequences from GenBank, and the final data set was classified into 44 haplotypes. Six putative species were recognised by COI‐based species delimitation analysis, and morphological evidence supported each of these species. The integrative approach revealed the occurrence of cryptic species in the Brevipalpus genus and contributed to the clarification of previously noted incongruences. The results presented here allow for the evaluation of taxonomic characteristics in a phylogenetic context and indicate new characters for the differentiation of Brevipalpus species. In addition, Brevipalpus incognitus n. sp. Ferragut & Navia, a cryptic species detected in this study, is described based on morphological and molecular traits. Implications of the advances in Brevipalpus systematics presented herein with respect to pest management are briefly discussed.     

Population structure and plumage polymorphism: The intraspecific evolutionary relationships of a polymorphic raptor, <Emphasis Type="Italic">Buteo jamaicensis harlani</Emphasis>

Background  

Phenotypic and molecular genetic data often provide conflicting patterns of intraspecific relationships confounding phylogenetic inference, particularly among birds where a variety of environmental factors may influence plumage characters. Among diurnal raptors, the taxonomic relationship of Buteo jamaicensis harlani to other B. jamaicensis subspecies has been long debated because of the polytypic nature of the plumage characteristics used in subspecies or species designations.     

Speciation and phylogeography in the cosmopolitan marine moon jelly, Aurelia sp

Background  

The cosmopolitan moon jelly Aurelia is characterized by high degrees of morphological and ecological plasticity, and subsequently by an unclear taxonomic status. The latter has been revised repeatedly over the last century, dividing the genus Aurelia in as many as 12 or as little as two species. We used molecular data and phenotypic traits to unravel speciation processes and phylogeographic patterns in Aurelia.