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FIGURE 4 in A revised molecular phylogeny reveals polyphyly in Schistura (Teleostei: Cypriniformes: Nemacheilidae)

FIGURE 4. Species of Schistura included in the phylogenetic analysis; all are from Thailand. Clade 1: (A) S. desmotes, UF 188065, 38.9 mm SL, Ping River, Chiang Mai Province; (B) S. robertsi, UF 185741, 50.8 mm SL, Tapee River, Nakhon Si Thammarat Province. Clade 2: (C) S. mahnerti, UF 188061, 71.9 mm SL, stream, Mae Khlong basin, Kanchanaburi Province; (D) S. geisleri, UF 191830, 28.0 mm SL, Wae Creek, Yan River basin, Surat Thani Province. Clade 3: (E) S. aurantiaca, UF 188063, 39.9 mm SL, Pracham Mai River, Kanchanaburi Province; (F) S. balteata, UF 191473, 52.0 mm SL, Pilok River, Kanchanaburi Province. Photographs by Zachary Randall and Jarred Randall.

FIGURE 2 in A revised molecular phylogeny reveals polyphyly in Schistura (Teleostei: Cypriniformes: Nemacheilidae)

FIGURE 2. Phylogenetic estimate of relationships within the family Nemacheilidae generated with a 50% majority-rule consensus for the cytochrome b gene using MrBayes.

FIGURE 1 in A revised molecular phylogeny reveals polyphyly in Schistura (Teleostei: Cypriniformes: Nemacheilidae)

FIGURE 1. Bayesian consensus phylogeny depicting genus- and species-level relationships within the family Nemacheilidae. This tree was derived from a combined analysis of cytochrome b and D-loop gene fragments (1,116 bp and 776 bp, respectively).

FIGURE 3 in A revised molecular phylogeny reveals polyphyly in Schistura (Teleostei: Cypriniformes: Nemacheilidae)

FIGURE 3. Phylogenetic estimate of relationships within the family Nemacheilidae generated with a 50% majority-rule consensus for the D-loop gene using MrBayes.

opencc-zeroDec 2017View details →

Data from: The Tetramerium lineage (Acanthaceae, Justicieae) revisited: phylogenetic relationships reveal polyphyly of many new world genera accompanied by rampant evolution of floral morphology

Molecular data confirm monophyly of the Tetramerium lineage (Acanthaceae, Justicieae), a group of nearly 200 species, ca. 75% from the New World (NW) and the remainder from Asia or Africa. Compared to our earlier work, > 50% more in-group taxa were sampled (nearly 2/3 of known taxa now sampled) and added ~20% more sequence data. We time-calibrate the phylogeny using primary fossil evidence and the larger context of a calibrated phylogeny for Acanthaceae. Many aspects of relationship are strongly supported but uncertainty remains about a number of phylogenetically isolated taxa (e.g., African Angkalanthus, Chorisochora; NW Ancistranthus) and some aspects of relationships among clades remain weakly supported. The group originated in the OW and began diversifying about 11.5 Ma. A single dispersal event to the NW occurred about 8.3 Ma, likely from Africa to southwestern North America. A number of major clades, particularly in the NW, are less than 5 Ma old and species in many clades are substantially younger. Several NW clades – even those with <10 species – comprise species that are markedly heterogeneous in floral traits likely reflecting selection by pollinators. Many NW genera are not monophyletic, which is not surprising given that floral traits have been relied upon taxonomically. Diversification rate analysis revealed no significant shifts resulting in a gradual increase in number of lineages with time. The Tetramerium lineage is now phylogenetically well characterized but remains enigmatic from the perspective of morphological evidence for many aspects of relationships. The lineage is usefully thought of as a 'clade complex': as a species complex is of morphologically confusing species, a 'clade complex' is of clades that are not well characterized morphologically.

opencc-zeroJul 2019View details →

Data from: Polyphyly of Mesadenus (Orchidaceae, Spiranthinae) and a new genus from the Espinhaço Range, Southeastern Brazil

Mesadenus displays an odd disjunction, with most species found in the southeastern USA, the Caribbean, and Mexico south to El Salvador, and two outliers occurring in southeastern Brazil. A recent molecular phylogenetic study showed that, as currently delimited, Mesadenus is polyphyletic, and further study of this little-known genus is required. Here we assessed relationships in Mesadenus and to other genera conducting a cladistic parsimony analysis of nucleotide sequences of nuclear (ITS) and plastid DNA (matK-trnK, trnL-trnF) for an enlarged sample of taxa, including five out of six currently accepted species of Mesadenus and representatives of nearly all (36 out of 41) genera of Spiranthinae, plus suitable outgroups. Detailed comparison of vegetative and floral attributes of relevant taxa was also conducted. Our results confirm polyphyly of Mesadenus and support creation of a new genus, Espinhassoa, to include Brazilian 'Mesadenus' glaziovii and 'M.' rhombiglossus (as Espinhassoa glaziovii and E. rhombiglossa, respectively). An identification key, descriptions, and illustrations of the two species herein included in Espinhassoa are provided.

opencc-zeroDec 2016View details →

Data from: Polyphyly of Arundinoideae (Poaceae) and evolution of the twisted geniculate lemma awn

Background and Aims: Subfamily Arundinoideae represents one of the last unsolved taxonomic mysteries in the grass family (Poaceae) due to the narrow and remote distributions of many of its 19 morphologically and ecologically heterogeneous genera. Resolving the phylogenetic relationships of these genera could have substantial implications for understanding character evolution in the grasses, for example the twisted geniculate awn – a hygroscopic awn that has been shown to be important in seed germination for some grass species. In this study, the phylogenetic positions of most arundinoid genera were determined using DNA from herbarium specimens, and their placement affects interpretation of this ecologically important trait. Methods: A phylogenetic analysis was conducted on a matrix of full-plastome sequences from 123 species in 107 genera representing all grass subfamilies, with 15 of the 19 genera in subfamily Arundinoideae. Parsimony and maximum likelihood mapping approaches were used to estimate ancestral states for presence of a geniculate lemma awn with a twisted column across Poaceae. Lastly, anatomical characters were examined for former arundinoid taxa using light microscopy and scanning electron microscopy. Key Results: Four genera traditionally included in Arundinoideae fell outside the subfamily in the plastome phylogeny, with the remaining 11 genera forming Arundinoideae sensu stricto. The twisted geniculate awn has originated independently at least five times in the PACMAD grasses, in the subfamilies Panicoideae, Danthonioideae/Chloridoideae and Arundinoideae. Morphological and anatomical characters support the new positions of the misplaced arundinoid genera in the phylogeny, but also highlight convergent and parallel evolution in the grasses. Conclusions: In placing the majority of arundinoid genera in a phylogenetic framework, our study answers one of the last remaining big questions in grass taxonomy while highlighting examples of convergent evolution in an ecologically important trait, the hygroscopic, twisted geniculate awn.

opencc-zeroDec 2017View details →

Data from: The polyphyly of Plasmodium: comprehensive phylogenetic analyses of the malaria parasites (order Haemosporida) reveal widespread taxonomic conflict

The evolutionary relationships among the apicomplexan blood pathogens known as the malaria parasites (order Haemosporida), some of which infect nearly 200 million humans each year, has remained a vexing phylogenetic problem due to limitations in taxon sampling, character sampling, and the extreme nucleotide base composition biases that are characteristic of this clade. Previous phylogenetic work on the malaria parasites has often lacked sufficient representation of the broad taxonomic diversity within the Haemosporida or the multi-locus sequence data needed to resolve deep evolutionary relationships, rendering our understanding of haemosporidian life history evolution and the origin of the human malaria parasites incomplete. Here we present the most comprehensive phylogenetic analysis of the malaria parasites conducted to date, using samples from a broad diversity of vertebrate hosts that includes numerous enigmatic and poorly known haemosporidian lineages in addition to genome-wide multi-locus sequence data. We find that if base composition differences were corrected for during phylogenetic analysis, we recovered a well-supported topology indicating that the evolutionary history of the malaria parasites was characterized by a complex series of transitions in life history strategies and host usage. Notably we find that Plasmodium, the malaria parasite genus that includes the species of human medical concern, is polyphyletic with the life history traits characteristic of this genus having evolved in a dynamic manner across the phylogeny. We find support for multiple instances of gain and loss of asexual proliferation in host blood cells and production of hemozoin pigment, two traits that have been used for taxonomic classification as well as considered to be important factors for parasite virulence and used as drug targets. Lastly, our analysis illustrates the need for a widespread reassessment of malaria parasite taxonomy.

opennotspecifiedDec 2010View details →

FIGURE 3 in A phylogenetic reassessment of African fossorial skinks in the subfamily Acontinae (Squamata: Scincidae): evidence for parallelism and polyphyly

FIGURE 3. The revised acontine taxonomy. Dotted line shows placement of Acontias percivali based on analysis of the mitochondrial dataset.

opennotspecifiedDec 2010View details →

FIGURE 2 in A phylogenetic reassessment of African fossorial skinks in the subfamily Acontinae (Squamata: Scincidae): evidence for parallelism and polyphyly

FIGURE 2. Majority rule consensus tree for Bayesian analysis of the combined dataset. Mean tree likelihood = -16416. Thickened branches indicate posterior probabilities ≥0.98; bootstrap values (≥70%) for ML and MP (italicized) analyses are placed at nodes. Note the polyphyletic status of the genus Typhlosaurus, whose branches are depicted in gray.

opennotspecifiedDec 2010View details →

FIGURE 1 in A phylogenetic reassessment of African fossorial skinks in the subfamily Acontinae (Squamata: Scincidae): evidence for parallelism and polyphyly

FIGURE 1. Majority rule consensus trees for Bayesian analyses of the mitochondrial (Cytb, Co1, 16s) and nuclear (Rag1) datasets. Mean tree likelihoods are -10962 (mitochondrial) and -3634 (Rag1). Posterior probabilities ≥0.98 and ML bootstrap values ≥70% (italicized) are adjacent nodes. Topologies are rooted to the three outgroup taxa (not shown).

Figure 18 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)

Figure 18. Dorsal fin of Insperanos nattereri, MZUSP 5429, 138.7 mm SL. DFS: dorsal fin stay, DR: distal radial, MR: medial radial, Ns: neural spine, PR: proximal radial, Sn: supraneural.

Figure 16 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)

Figure 16. Pectoral fin of Anostomoides nattereri, MZUSP 5429, 138.7 mm SL, in lateral view (A) and in detail in medial view (B, C). Co: coracoid, Cl: cleithrum, Dr: distal radial, Exs: extrascapular, Msc: mesocoracoid, Pcl 1-3: postcleithra 1-3, Pr: proximal radials, Pt: posttemporal, Scl: supracleithrum.

Figure 20 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)

Figure 20. Caudal fin of Insperanos nattereri, MZUSP 5429, 138.7 mm SL. Ep1–3: epural s1–3; H1-6: hipurals 1–6; Hs: haemal spine; Mnp: modified neural process, Ns: neural spine, Opc: opisthural cartilage, Ph: parhypural, Un1–2: uroneurals 1–2, Us: urostyle.

Figure 5 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)

Figure 5. Cranium of Anostomoides nattereri in (A) dorsal and (B) ventral views, MZUSP 5429, 138.7 mm SL. Bl: Baudelot ligament, Boc: basioccipital, C1-4: centra 1–4, CLA: claustrum, Epo: epiotic, Exo: exoccipital, Fro: frontal, In: intercalar, Let: lateral ethmoid, LpC2: lateral process of centrum 2, Mes: mesethmoid, Os: os suspensorium, Osph: orbitosphenoid, Par: parietal, Pro: prootic, Pto: pterotic, Psph: parasphenoid, Ptsph: pterosphenoid, Rb4: rib of vertebra 4, SOc: supraoccipital, Sph: sphenotic, Tr: tripus, Vom: vomer.

Figure 12 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)

Figure 12. Summarized phylogenetic relationships of the Anostomidae and selected outgroup Characiformes, based on a node and tip calibrated Bayesian Inference analysis of combined data from morphology (158 characters) and six gene sequences (COI, Cytb, Myh6, Rag1, Rag2, 16S). See Supporting Information (Fig. S1) for the cladogram including the complete set of terminals.

Figure 4 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)

Figure 4. Cranium of Anostomoides nattereri in lateral view. A, MZUSP 5429, 138.7 mm SL. B, MZUSP 110595, 232 mm SL. Boc: basioccipital, Cla: claustrum, Epo: epiotic, Exo: exoccipital, Fro: frontal, In: intercalar, Let: lateral ethmoid, LpC2: lateral process of centrum 2, Mes: mesethmoid, NA4: neural arch of centrum 4, Nc: neural complex, NS4: neural spine of centrum 4, Os: os suspensorium, Osph: orbitosphenoid, Par: parietal, Pro: prootic, Pto: pterotic, Psph: parasphenoid, Ptsph, pterosphenoid, Sc: scaphium, SOc: supraoccipital, Sph: sphenotic, Tr: tripus, Vom: vomer.

Figure 15 in Total evidence phylogenetic analysis reveals polyphyly of Anostomoides and uncovers an unexpectedly ancient genus of Anostomidae fishes (Characiformes)

Figure 15. Maximum likelihood reconstructions of mesethmoid, maxilla and papilla evolution performed on a pruned version of the maximum clade credibility tree. Reconstructions for maxilla width (character 52) were conducted under an all-rates different transition model, while other reconstructions used an equal rates models of evolution. All models were selected using the Akaike information criterion.