POLYTOMIES AND THE POWER OF PHYLOGENETIC INFERENCE

Although phylogenetic hypotheses can provide insights into mechanisms of evolution, their utility is limited by our inability to differentiate simultaneous speciation events (hard polytomies) from rapid cladogenesis (soft polytomies). In the present paper, we tested the potential for statistical power analysis to differentiate between hard and soft polytomies in molecular phytogenies. Classical power analysis typically is used a priori to determine the sample size required to detect a particular effect size at a particular level of significance (a) with a certain power (1 – β). A posteriori, power analysis is used to infer whether failure to reject a null hypothesis results from lack of an effect or from insufficient data (i.e., low power). We adapted this approach to molecular data to infer whether polytomies result from simultaneous branching events or from insufficient sequence information. We then used this approach to determine the amount of sequence data (sample size) required to detect a positive branch length (effect size). A worked example is provided based on the auklets (Charadriiformes: Alcidae), a group of seabirds among which relationships are represented by a polytomy, despite analyses of over 3000 bp of sequence data. We demonstrate the calculation of effect sizes and sample sizes from sequence data using a normal curve test for difference of a proportion from an expected value and a t-test for a difference of a mean from an expected value. Power analyses indicated that the data for the auklets should be sufficient to differentiate speciation events that occurred at least 100,000 yr apart (the duration of the shortest glacial and interglacial events of the Pleistocene), 2.6 million years ago.     

Parasite histories and novel phylogenetic tools: alternative approaches to inferring parasite evolution from molecular markers

Parasitological research is often contingent on the knowledge of the phylogeny/genealogy of the studied group. Although molecular phylogenetics has proved to be a powerful tool in such investigations, its application in the traditional fashion, based on a tree inference from the primary nucleotide sequences may, in many cases, be insufficient or even improper. These limitations are due to a number of factors, such as a scarcity/ambiguity of phylogenetic information in the sequences, an intricacy of gene relationships at low phylogenetic levels, or a lack of criteria when deciding among several competing coevolutionary scenarios. With respect to the importance of a precise and reliable phylogenetic background in many biological studies, attempts are being made to extend molecular phylogenetics with a variety of new data sources and methodologies. In this review, selected approaches potentially applicable to parasitological research are presented and their advantages as well as drawbacks are discussed. These issues include the usage of idiosyncratic markers (unique features with presumably low probability of homoplasy), such as insertion of mobile elements, gene rearrangements and secondary structure features; the problem of ancestral polymorphism and reticulate relationships at low phylogenetic levels; and the utility of a molecular clock to facilitate discrimination among alternative scenarios in host-parasite coevolution.     

Evolution on oceanic islands: molecular phylogenetic approaches to understanding pattern and process

By their very nature oceanic island ecosystems offer great opportunities for the study of evolution and have for a long time been recognized as natural laboratories for studying evolution owing to their discrete geographical nature and diversity of species and habitats. The development of molecular genetic methods for phylogenetic reconstruction has been a significant advance for evolutionary biologists, providing a tool for answering questions about the diversity among the flora and fauna on such islands. These questions relate to both the origin and causes of species diversity both within an archipelago and on individual islands. Within a phylogenetic framework one can answer fundamental questions such as whether ecologically and/or morphologically similar species on different islands are the result of island colonization or convergent evolution. Testing hypotheses about ages of the individual species groups or entire community assemblages is also possible within a phylogenetic framework. Evolutionary biologists and ecologists are increasingly turning to molecular phylogenetics for studying oceanic island plant and animal communities and it is important to review what has been attempted and achieved so far, with some cautionary notes about interpreting phylogeographical pattern on oceanic islands.     

Molecular phylogenetic perspective on the evolution of the deep-sea fish genusCyclothone (Stomiiformes: Gonostomatidae)

A portion of mitochondrially encoded 12S and 16S ribosomal RNA genes were sequenced from 13 currently recognized species of the midwater deep-sea fish genusCyclothone (Stomiiformes: Gonostomatidae) and three gonostomatid outgroup taxa. Phylogenetic analyses using maximum parsimony and maximum likelihood methods were performed on unambiguously aligned, combined sequences (803 bp) of the two genes. The resultant tree topologies from the two methods were congruent, being robust and supported by various tree statistics, enabling the evolutionary history ofCyclothone to be described in detail. The molecular phylogeny demonstrated striking inconsistencies with previously proposed “natural groups”, although the latter could be confidently refuted by the molecular data. The most significant characteristic of the evolutionary history ofCyclothone was the independent acquisition of an apomorphic depth habitat from the relatively ancestral, lower mesopelagic habitat, by each of three major distinct lineages that had diverged earlier in their evolution. Moreover, such macroevolutionary habitat shifts had been necessarily accompanied by morphological and ecological novelties, presumably originating from paedomorphosis. Repeated evolution of such changes strongly suggests ontogenetic plasticity inCyclothone which could enable these fishes to acquire larval-like, simple organization of body structure. Such a body plan could help them subsist in food-poor surroundings and regulate reproductive variables that take advantage of increasing larval survival toward shallower depths. Recent speciation events, on the contrary, have produced contemporary sister species of allopatric (or microallopatric) distributions, but few morphological and ecological differences. Even if remarkable miniaturization has occurred, such as in the Mediterranean endemicC. pygmaea, it had to have been a simple truncation of ancestral species' ontogeny without attendance of any discernible paedomorphic features. On the basis of the fossil record, geological history of the Mediterranean region, and ectotherm molecular divergence rate, it was estimated thatCyclothone radiation had already started in the early-middle Miocene (17–20 million years ago).     

Dynamics of the evolution of Batesian mimicry: molecular phylogenetic analysis of ant-mimicking Myrmarachne (Araneae: Salticidae) species and their ant models

Batesian mimicry is seen as an example of evolution by natural selection, with predation as the main driving force. The mimic is under selective pressure to resemble its model, whereas it is disadvantageous for the model to be associated with the palatable mimic. In consequence one might expect there to be an evolutionary arms race, similar to the one involving host-parasite coevolution. In this study, the evolutionary dynamics of a Batesian mimicry system of model ants and ant-mimicking salticids is investigated by comparing the phylogenies of the two groups. Although Batesian mimics are expected to coevolve with their models, we found the phylogenetic patterns of the models and the mimics to be indicative of adaptive radiation by the mimic rather than co-speciation between the mimic and the model. This shows that there is strong selection pressure on Myrmarachne, leading to a high degree of polymorphism. There is also evidence of sympatric speciation in Myrmarachne, the reproductive isolation possibly driven by female mate choice in polymorphic species.     

Cytotaxonomy of Gallinula melanops (Gruiformes,Rallidae): Karyotype evolution and phylogenetic inference

Although Rallidae is the most diverse family within Gruiformes, there is little information concerning the karyotype of the species in this group. In fact, Gallinula melanops, a species of Rallidae found in Brazil, is among the few species studied cytogenetically, but only with conventional staining and repetitive DNA mapping, showing 2n=80. Thus, in order to understand the karyotypic evolution and phylogeny of this group, the present study aimed to analyze the karyotype of G. melanops by classical and molecular cytogenetics, comparing the results with other species of Gruiformes. The results show that G. melanops has the same chromosome rearrangements as described in Gallinula chloropus (Clade Fulica), including fission of ancestral chromosomes 4 and 5 of Gallus gallus (GGA), beyond the fusion between two of segments resultants of the GGA4/GGA5, also fusions between the chromosomes GGA6/GGA7. Thus, despite the fact that some authors have suggested the inclusion of G. melanops in genus Porphyriops, our molecular cytogenetic results confirm its place in the Gallinula genus.     

Evaluation of reported sediment samples from 20 Ma using a molecular phylogenetic approach: comment on Liu et al. (2017)

Liu et al. reported the cultivation and DNA sequencing of 69 fungal isolates (Ascomycota and Basidiomycota) from ancient subseafloor sediments, suggesting that they represent living fungal populations that have persisted for over 20 million years. Because these findings could bring about a paradigm shift in our understanding of the spatial breadth of the deep subsurface biosphere as well as the longevity of ancient DNA, it is extremely important to verify that their samples represent pure ancient fungi from 20 million years ago without contamination by modern species. For this purpose, we estimated the divergence times of Dikarya (Ascomycota + Basidiomycota) and Mucoromycota fungi assuming that the fungal isolates were actually sampled from 20 Ma (mega-annum) sediments and evaluated the validity of the sample ages. Using this approach, we estimate that the age of the last common ancestor of Dikarya and Mucoromycota fungi greatly exceeds the age of the Earth. Our finding emphasizes the importance of using reliable approaches to confirm the dating of ancient samples.     

Patagial complex evolution in hummingbirds and swifts (Apodiformes): a molecular phylogenetic perspective

Studies of the role of flight in vertebrate evolution often have focused on the propatagial muscle complex because this structure forms the wing's leading edge. However, historical narratives about the evolution of flight anatomy are compromised because traditional higher-level taxonomies typically are based in part on the propatagium itself. To avoid this circularity, I used a consensus molecular phylogeny to examine propatagial evolution in the highly aerial sister groups, hummingbirds and swifts (Apodiformes). Mapping of anatomy on molecular-based phylogeny indicates that structural variation in M .  tensor propatagialis pars brevis (TPB) is congruent with the major subclades of both hummingbirds and swifts. However, the humeral tendon and broad attachment of the fleshy belly of TPB with M .  extensor metacarpi radialis (EMR) most likely underwent parallel change in hummingbirds and swifts, while the distal tendon present only in hummingbirds changed from a thin sheet to a strong tendon. The combination of divergent (within hummingbirds or swifts) and parallel (between hummingbirds and swifts) evolutionary patterns implies that the taxonomic value of the propatagial complex in apodiformes depends on anatomical component and level of divergence. The congruence of anatomy with molecular phylogeny provides independent criteria for designating relatively ancestral versus derived clades of apodiformes. Based on these polarities, living hummingbirds and swifts express additional parallel trends from arboreal to more aerial foraging styles, and from depauperate to species-rich clades. Within apodiformes, the link of flight anatomy with taxonomic and ecologic diversity suggests that elaboration of locomotor modes was important for apodiform diversification, echoing a similar pattern for birds relative to their reptilian ancestors.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 211–219.     

Large-scale phylogenetic analysis provides insights into the diversification and evolution of sessilid peritrich ciliates (Protista: Ciliophora)

The Peritrichia is a speciose and morphologically distinctive assemblage of ciliated protists that was first observed by Antonie van Leeuwenhoek over 340 years ago. In the last two decades, the phylogenetic relationships of this group have been increasingly debated as morphological and molecular analyses have generated contrasting conclusions, mainly owing to limited sampling. In the present study, we performed expanded phylogenetic analyses of 152 sessilid peritrichs collected from 14 different provinces of China and 141 SSU rDNA peritrich sequences from GenBank. The results of the analyses revealed new divergent relationships between and within major clades that challenge the morphological classification of this group including, (1) the recovery of four major phylogenetically divergent clades in the monophyletic order Sessilida, (2) aboral structures such as the stalk and spasmoneme were evolutionary labile, (3) the stalk or/and spasmoneme was lost in each divergent clade indicating that parallel evolution occurred in sessilid peritrichs and (4) the life cycle and habit drive the diversity of aboral structures as well as diversification and evolution in peritrichs.     

Tertiary plotopterids (Aves, Plotopteridae) and a novel hypothesis on the phylogenetic relationships of penguins (Spheniscidae)

Plotopterids (Aves: Plotopteridae) are extinct wing-propelled diving birds which exhibit a strikingly similar wing morphology to penguins (Spheniscidae), but also share derived characters with 'pelecaniform' birds that are absent in penguins. The similarities between Plotopteridae and Spheniscidae have hitherto been attributed to convergence, and plotopterids were considered to be most closely related to the 'pelecaniform' Phalacrocoracidae (cormorants) and Anhingidae (anhingas). However, here I show that assignment of plotopterids to 'pelecaniform' birds does not necessarily preclude them from being the sister taxon of penguins. Cladistic analysis of 68 morphological characters resulted in sister group relationship between Plotopteridae and Spheniscidae, and the clade (Plotopteridae + Spheniscidae) was shown to be the sister taxon of the Suloidea, i.e. a clade including Sulidae (boobies and gannets), Phalacrocoracidae, and Anhingidae. Derived characters are discussed which support this novel hypothesis. Paedomorphosis probably accounts for the absence of derived characters in penguins that are shared by Plotopteridae and members of the Steganopodes. Plotopterids exemplify the importance of fossil birds for analyzing the phylogenetic relationships of modern taxa that exhibit a highly apomorphic morphology.     

Episodic chromosomal evolution in Planipapillus (Onychophora: Peripatopsidae): a phylogenetic approach to evolutionary dynamics and speciation

Planipapillus, a clade of onychophorans from southeastern Australia, exhibits substantial chromosomal variation. In the context of a robust phylogeny based on nuclear and mitochondrial sequence data, we evaluate models of chromosomal evolution and speciation that differ in the roles assigned to selection, mutation, and drift. Permutation tests suggest that all chromosome rearrangements in the clade have been centric fusions and, on the basis of parsimony and maximum-likelihood methods with independent estimates of branch lengths, we conclude that at least 31 centric fusions have been fixed in Planipapillus. A likelihood-ratio test approach, which is independent of our point estimates of ancestral states, rejects an evolutionary model in which the mutation rate is constant and centric fusions are effectively neutral. In contrast to the nucleotide sequence data, which are consistent with neutrality and rate constancy, centric fusions in Planipapillus are underdominant, spontaneous fusion rates vary among lineages, or both. We predict an inverse relationship between rates of chromosomal evolution and historical population size. Chromosomal evolution may play a role in speciation in Planipapillus, both by interactions between centric fusions with monobrachial homology and by the accumulation of multiple weakly underdominant fusions.     

Genome size and karyotype evolution in the slipper orchids (Cypripedioideae: Orchidaceae)

Nuclear DNA contents (4C) were estimated by Feulgen microdensitometry in 27 species of slipper orchids. These data and recent information concerning the molecular systematics of Cypripedioideae allow an interesting re-evaluation of karyotype and genome size variation among slipper orchids in a phylogenetic context. DNA amounts differed 5.7-fold, from 24.4 pg in Phragmipedium longifolium to 138.1 pg in Paphiopedilum wardii. The most derived clades of the conduplicate-leaved slipper orchids have undergone a radical process of genome fragmentation that is most parsimoniously explained by Robertsonian changes involving centric fission. This process seems to have occurred independently of genome size variation. However, it may reflect environmental or selective pressures favoring higher numbers of linkage groups in the karyotype.     

Interrelationships and evolution of the east Asian grass lizards, Takydromus (Squamata: Lacertidae)

The east Asian lacertid lizard genus, Takydromus , is well-defined but its relationships to other primitive Palaearctic lacertids are still uncertain and, although it has similarities to the lower Miocene Miolacerta, Takydromus does not appear to be identical with this. The 16 or 17 recognizable species are reviewed and a key provided for their identification; the remaining area of uncertainty about species boundaries is the Takydromus sexlineatus group in Assam. A phylogeny for Takydromus is estimated using a data set of 35 morphological characters drawn from external features, skeleton and soft-parts. There are two main constituent clades which may be informally recognized as Takydromus s.s. and Platyplacopus. Platyplacopus is subtropical and perhaps relict, whereas Takydromus ranges from temperate to tropical areas. The two clades have different ranges of eggs per clutch. In both of them, elongate forms that climb extensively in flimsy vegetation have evolved and have independently acquired similar features that confer performance advantages in this situation. Interestingly, the order of assembly of tliese features is markedly different.     

Morphological and phylogenetic studies of Cytospora (Valsaceae,Diaporthales) isolates from Chinese scholar tree,with description of a new species

Cytospora species are the most serious and widespread pathogens associated with canker disease on multiple plants. In this study, three species, i.e., Cytospora sophoricola, C. chrysosperma, and C. sophorae, which were isolated from Sophora in China, are described and illustrated based on their morphological characteristics and phylogenetic analyses. Cytospora sophoricola was distinguished clearly by its larger disc, multiple ostioles, cystic and multiple locules, and specific cultural characteristics, i.e., protruding fruiting bodies. Maximum parsimony and maximum likelihood analysis showed that it did not cluster with any known species of Cytospora, so it is described as a new species. Cytospora sophorae is a previously reported species from Sophora, which is redescribed based on new isolates and additional observations. Another species was identified as C. chrysosperma, which is reported for the first time on Sophora, so Papilionaceae is shown to be a new host family for C. chrysosperma. The morphological affinities of these species with related taxa are discussed, while the phylogenetic relationships of these species with other fungus in the genus Cytospora were elucidated based on their internal transcribed spacer (ITS) rRNA region sequences.