Diversity and evolution of leaflet anatomical characters in the Pterocarpus clade (Fabaceae: Papilionoideae)

The Pterocarpus clade includes 23 genera previously attributed to different Fabaceae tribes. The recent rearrangements of many genera in the clade do not recognize morphological synapomorphies. This study aimed to identify new synapomorphies for the Pterocarpus clade, to identify characters supporting inter-generic relationships currently resolved only by molecular data and to identify diagnostic characters at the genus and species levels. Subterminal leaflets of the studied genera were selected and analyzed using light and scanning electron microscopy. Ancestral reconstruction was performed using morphological and anatomical characters of 16 genera of the Pterocarpus clade. The convex epidermal relief in the region of the main vein indicated the relationship among all genera of the group. Anchor-like multicellular trichomes are features shared by Brya and Cranocarpus, which are the sister group to the other genera of the clade. Subepidermal layers are features shared by the Centrolobium, Etaballia, Paramachaerium, Pterocarpus and Tipuana genera, and the sclerenchyma sheath in the leaflet margin is reported in the Discolobium, Riedeliella and Platymiscium genera. Bulbous based glandular trichomes and vesicular glandular trichomes are diagnostic at the species level in Centrolobium and Pterocarpus, respectively. The leaflet characters investigated can be useful for the taxonomic delimitation at both the genus and species levels of the Pterocarpus clade. Our dataset provides new synapomorphies, elucidates the inter-generic relationships and reinforces the phylogenetic classification of the Pterocarpus clade resolved by molecular data.

Synapomorphies Behind Shared Derived Characters: Examples from the Great Apes' Genomic Data

Phylogenetic systematics (e.g., cladistics) is one of the most important analytical frameworks of modern Biology. It seems to be common knowledge that within phylogenetics, 'groups' must be defined based solely on the synapomorphies or on the "derived" characters that unite two or more taxa in a clade or monophyletic group. Thus, the idea of synapomorphy seems to be of fundamental influence and importance. Here I will show that the most common and straightforward understanding of synapomorphy as a shared derived character is not sufficient and eventually must be rejected in favor of Nelson's relational interpretation of such term. Arguing for this point and using three examples from previously published Apes' genomic matrices, I explicitly demonstrate that the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon, may be successfully recovered by three-taxon statement analysis (3TA) and three-taxon statement average consensus analysis (3TS-ACA) even if all of the evident standard shared derived molecular characters of the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon, have been excluded from the molecular alignments. Neither conventional Maximum Parsimony nor Maximum Likelihood or Bayesian Inference can do this in such situation. Thus, our results show that the relationship (Pongo (Gorilla (Homo, Pan))) with Hylobatidae as a sister taxon has appeared, in some way, behind standard shared derived characters: the last ones could be excluded, but the relationship remains the same.

A phylogenomic approach to reconstruct interrelationships of main clupeocephalan lineages with a critical discussion of morphological apomorphies

BACKGROUND

Previous molecular studies on the phylogeny and classification of clupeocephalan fishes revealed numerous new taxonomic entities. For re-analysing these taxa, we perform target gene capturing and subsequent next generation sequencing of putative ortholog exons of major clupeocephalan lineages. Sequence information for the RNA bait design was derived from publicly available genomes of bony fishes. Newly acquired sequence data comprising > 800 exon sequences was subsequently used for phylogenetic reconstructions.

RESULTS

Our results support monophyletic Otomorpha comprising Alepocephaliformes. Within Ostariophysi, Gonorynchiformes are sister to a clade comprising Cypriniformes, Characiformes, Siluriformes and Gymnotiformes, where the interrelationships of Characiformes, Siluriformes and Gymnotiformes remain enigmatic. Euteleosts comprise four major clades: Lepidogalaxiiformes, Protacanthopterygii, Stomiatii, and Galaxiiformes plus Neoteleostei. The monotypic Lepidogalaxiiformes form the sister-group to all remaining euteleosts. Protacanthopterygii, comprising Argentini-, Esoci- and Salmoniformes, is sister to Stomiatii (Osmeriformes and Stomiatiformes) and Galaxiiformes plus Neoteleostei.

CONCLUSIONS

Several proposed monophyla defined by morphological apomorphies within the Clupeocephalan phylogeny are confirmed by the phylogenetic estimates presented herein. However, other morphologically described groups cannot be reconciled with molecular phylogenies. Thus, numerous morphological apomoprhies of supposed monophyla are called into question. The interpretation of suggested morphological synapomorphies of otomorph fishes is strongly affected by the inclusion of deep-sea inhabiting, and to that effect morphologically adapted Alepocephaliformes. Our revision of these potential synapomorphies, in the context that Alepocephaliformes are otomorph fishes, reveals that only a single character of the total nine characters proposed as synapomorphic for the group is clearly valid for all otomorphs. Three further characters remain possible apomorphies since their status remains unclear in the deep-sea adapted Alepocephaliformes showing developmental lag and lacking a swim bladder. Further, our analysis places Galaxiiformes as sister group to neoteleosts, which contradicts some previous molecular phylogenetic studies. This needs further investigation from a morphological perspective, as suggested synapomophies for several euteleostean lineages are challenged or still lacking. For the verification of results presented herein, a denser phylogenomic-level taxon sampling should be applied.

Revised classification of the righteye flounders (Teleostei: Pleuronectidae) based on multilocus phylogeny with complete taxon sampling

Members of the family Pleuronectidae are common representatives of the marine benthic fauna inhabiting northern regions of the Atlantic and Pacific oceans. The most recent comprehensive classification of the family, based entirely on morphological synapomorphies, recognized five subfamilies, 23 genera, and 61 extant species. However, several subsequent molecular studies have shown that many synapomorphic characters discovered in the morphological study might represent homoplasies, thereby questioning the reliance on these characters with the warning that they may provide misleading information for testing other morphology-based evolutionary hypotheses. In the present study, we propose a comprehensive taxonomic reassessment of the family Pleuronectidae based on the molecular phylogeny reconstructed from four nuclear and three mitochondrial loci and represented by complete taxon sampling of all but one valid species currently assigned to this family. To check for robustness of the phylogenetic hypothesis, we analyzed the effect of base compositional heterogeneity on phylogenetic signal for each locus and compared six different gene partitioning schemes. The final dataset, comprising 14 partitions and 154 individuals, was used to reconstruct phylogenetic trees in RAxML, MrBayes and BEAST2. Alternative topologies for several questionable nodes were compared using Bayes factors. The topology with the highest marginal likelihood was selected as the final phylogenetic tree for inferring pleuronectid relationships and character evolution. Based on our results, we recognize the Pleuronectidae comprising five subfamilies, 24 genera and 59 species. Our new phylogeny comprises five major monophyletic groups within the family, which we define as the subfamilies within the family: Atheresthinae, Pleuronichthyinae, Microstominae, Hippoglossinae and Pleuronectinae. Taxonomic composition of most of these subfamilies is different from that proposed in previous classifications. We also re-assess hypotheses proposed in earlier studies regarding intra-relationships of species of each lineage. Results of the current study contribute to better understanding of the evolutionary relationships of pleuronectid flatfishes based on molecular evidence, and they also provide the framework towards future comprehensive morphological revision of constituent lineages within the family Pleuronectidae.