Limited Phylogenetic Information Research Articles

Molecular detection of Rickettsia raoultii, Rickettsia tamurae, and associated pathogens from ticks parasitizing water deer (Hydropotes inermis argyropus) in South Korea

Most defined Rickettsiales, which can be transmitted by ticks, are known to be important zoonotic pathogens. Some of these pathogens can cause severe diseases in humans, including anaplasmosis, rickettsioses, and ehrlichiosis. Previous studies in South Korea have investigated tick-borne pathogens (TBPs) residing in ticks found on grassy vegetation and animals. However, there is limited phylogenetic information on TBPs in ticks parasitizing Korean water deer (KWD; Hydropotes inermis argyropus). This study evaluated the prevalence, risk factors (regions, tick stages, and tick species), and coinfections of TBPs in ticks parasitizing KWD. Were collected a total of 283 hard ticks, including Haemaphysalis longicornis, Haemaphysalis flava, and Ixodes nipponensis from KWD in South Korea from 2013 to 2017. In 173 tested tick pools, genes for seven TBPs, namely Rickettsia raoultii (20 %), Rickettsia tamurae (1 %), Candidatus Rickettsia longicornii (31 %), Ehrlichia canis (3 %), Anaplasma capra (3 %), Anaplasma bovis (2 %), and Anaplasma sp. (1 %), were detected. The unidentified Anaplasma sp. isolates revealed a 98.4 %–99.3 % sequence identity with Anaplasma sp. in GenBank sequences obtained from ticks. To the best of our knowledge, this is the first study to report the presence of the emerging human pathogen R. tamurae in South Korea. These results should increase awareness about the need for continued development of epidemiological control measures, and medical and veterinary communities must be informed of their high infection potential and clinical complexity in humans.

A Phylogenetic, Biogeographic, and Taxonomic study of all Extant Species of Anolis (Squamata; Iguanidae).

Anolis lizards (anoles) are textbook study organisms in evolution and ecology. Although several topics in evolutionary biology have been elucidated by the study of anoles, progress in some areas has been hampered by limited phylogenetic information on this group. Here, we present a phylogenetic analysis of all 379 extant species of Anolis, with new phylogenetic data for 139 species including new DNA data for 101 species. We use the resulting estimates as a basis for defining anole clade names under the principles of phylogenetic nomenclature and to examine the biogeographic history of anoles. Our new taxonomic treatment achieves the supposed advantages of recent subdivisions of anoles that employed ranked Linnaean-based nomenclature while avoiding the pitfalls of those approaches regarding artificial constraints imposed by ranks. Our biogeographic analyses demonstrate complexity in the dispersal history of anoles, including multiple crossings of the Isthmus of Panama, two invasions of the Caribbean, single invasions to Jamaica and Cuba, and a single evolutionary dispersal from the Caribbean to the mainland that resulted in substantial anole diversity. Our comprehensive phylogenetic estimate of anoles should prove useful for rigorous testing of many comparative evolutionary hypotheses. [Anoles; biogeography; lizards; Neotropics; phylogeny; taxonomy].

Mitochondrial genomes of praying mantises (Dictyoptera, Mantodea): rearrangement, duplication, and reassignment of tRNA genes.

Insect mitochondrial genomes (mitogenomes) contain a conserved set of 37 genes for an extensive diversity of lineages. Previously reported dictyopteran mitogenomes share this conserved mitochondrial gene arrangement, although surprisingly little is known about the mitogenome of Mantodea. We sequenced eight mantodean mitogenomes including the first representatives of two families: Hymenopodidae and Liturgusidae. Only two of these genomes retain the typical insect gene arrangement. In three Liturgusidae species, the trnM genes have translocated. Four species of mantis (Creobroter gemmata, Mantis religiosa, Statilia sp., and Theopompa sp.-HN) have multiple identical tandem duplication of trnR, and Statilia sp. additionally includes five extra duplicate trnW. These extra trnR and trnW in Statilia sp. are erratically arranged and form another novel gene order. Interestingly, the extra trnW is converted from trnR by the process of point mutation at anticodon, which is the first case of tRNA reassignment for an insect. Furthermore, no significant differences were observed amongst mantodean mitogenomes with variable copies of tRNA according to comparative analysis of codon usage. Combined with phylogenetic analysis, the characteristics of tRNA only possess limited phylogenetic information in this research. Nevertheless, these features of gene rearrangement, duplication, and reassignment provide valuable information toward understanding mitogenome evolution in insects.

Analysis of a Rapid Evolutionary Radiation Using Ultraconserved Elements: Evidence for a Bias in Some Multispecies Coalescent Methods

Rapid evolutionary radiations are expected to require large amounts of sequence data to resolve. To resolve these types of relationships many systematists believe that it will be necessary to collect data by next-generation sequencing (NGS) and use multispecies coalescent ("species tree") methods. Ultraconserved element (UCE) sequence capture is becoming a popular method to leverage the high throughput of NGS to address problems in vertebrate phylogenetics. Here we examine the performance of UCE data for gallopheasants (true pheasants and allies), a clade that underwent a rapid radiation 10-15 Ma. Relationships among gallopheasant genera have been difficult to establish. We used this rapid radiation to assess the performance of species tree methods, using ∼600 kilobases of DNA sequence data from ∼1500 UCEs. We also integrated information from traditional markers (nuclear intron data from 15 loci and three mitochondrial gene regions). Species tree methods exhibited troubling behavior. Two methods [Maximum Pseudolikelihood for Estimating Species Trees (MP-EST) and Accurate Species TRee ALgorithm (ASTRAL)] appeared to perform optimally when the set of input gene trees was limited to the most variable UCEs, though ASTRAL appeared to be more robust than MP-EST to input trees generated using less variable UCEs. In contrast, the rooted triplet consensus method implemented in Triplec performed better when the largest set of input gene trees was used. We also found that all three species tree methods exhibited a surprising degree of dependence on the program used to estimate input gene trees, suggesting that the details of likelihood calculations (e.g., numerical optimization) are important for loci with limited phylogenetic information. As an alternative to summary species tree methods we explored the performance of SuperMatrix Rooted Triple - Maximum Likelihood (SMRT-ML), a concatenation method that is consistent even when gene trees exhibit topological differences due to the multispecies coalescent. We found that SMRT-ML performed well for UCE data. Our results suggest that UCE data have excellent prospects for the resolution of difficult evolutionary radiations, though specific attention may need to be given to the details of the methods used to estimate species trees.

Helena, the hidden beauty: Resolving the most common West Eurasian mtDNA control region haplotype by massively parallel sequencing an Italian population sample.

The analysis of mitochondrial (mt)DNA is a powerful tool in forensic genetics when nuclear markers fail to give results or maternal relatedness is investigated. The mtDNA control region (CR) contains highly condensed variation and is therefore routinely typed. Some samples exhibit an identical haplotype in this restricted range. Thus, they convey only weak evidence in forensic queries and limited phylogenetic information. However, a CR match does not imply that also the mtDNA coding regions are identical or samples belong to the same phylogenetic lineage. This is especially the case for the most frequent West Eurasian CR haplotype 263G 315.1C 16519C, which is observed in various clades within haplogroup H and occurs at a frequency of 3-4% in many European populations. In this study, we investigated the power of massively parallel complete mtGenome sequencing in 29 Italian samples displaying the most common West Eurasian CR haplotype - and found an unexpected high diversity. Twenty-eight different haplotypes falling into 19 described sub-clades of haplogroup H were revealed in the samples with identical CR sequences. This study demonstrates the benefit of complete mtGenome sequencing for forensic applications to enforce maximum discrimination, more comprehensive heteroplasmy detection, as well as highest phylogenetic resolution.

Molecular phylogenetic analyses redefine seven major clades and reveal 22 new generic clades in the fungal family Boletaceae

Mushrooms in the basidiomycete family Boletaceae are ecologically and economically very important. However, due to the morphological complexity and the limited phylogenetic information on the various species and genera of this fungal family, our understanding of its systematics and evolution remains rudimentary. In this study, DNA sequences of four genes (nrLSU, tef1-α, rpb1, and rpb2) were newly obtained from ca. 200 representative specimens of Boletaceae. Our phylogenetic analyses revealed seven major clades at the subfamily level, namely Austroboletoideae, Boletoideae, Chalciporoideae, Leccinoideae, Xerocomoideae, Zangioideae, and the Pulveroboletus Group. In addition, 59 genus-level clades were identified, of which 22 were uncovered for the first time. These 22 clades were mainly placed in Boletoideae and the Pulveroboletus Group. The results further indicated that the characters frequently used in the morphology-based taxonomy of Boletaceae, such as basidiospore ornamentation, the form of the basidioma, and the stuffed pores each had multiple origins within the family, suggesting that the use of such features for high-level classification of Boletaceae should be de-emphasized and combined with other characters.

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.

Phylogenetic analysis of the Malvadendrina clade (Malvaceae s.l.) based on plastid DNA sequences

Phylogenetic relationships within Malvaceae s.l., a clade that includes the traditional families Bombacaceae, Malvaceae s.str., Sterculiaceae, and Tiliaceae, have become greatly clarified thanks to recent molecular systematic research. In this paper, we use DNA sequences of four plastid regions ( atpB, matK, ndhF, and rbcL) to study relationships within Malvadendrina, one of the two major clades of Malvaceae s.l. The four data sets were generally in agreement, but five terminal taxa manifested highly unexpected affinities in the rbcL partition, and the non-coding sequences of the trnK intron were found to provide limited phylogenetic information for resolving relationships at the base of Malvadendrina. The remaining data strongly support the existence of six major clades within Malvadendrina: Brownlowioideae, Dombeyoideae, Helicteroideae, Malvatheca (comprising Bombacoideae and Malvoideae), Sterculioideae, and Tilioideae. These data also resolve the placement of two problematic taxa: Nesogordonia (in Dombeyoideae) and Mortoniodendron (in Tilioideae). The relationships among the six clades are not definitively resolved, but the best-supported topology has Dombeyoideae as sister to the remainder of Malvadendrina (posterior probability PP = 80 % ) and Sterculioideae as sister to Malvatheca ( PP = 86 % ). This early branching position of Dombeyoideae is supported by similarities in floral characters between members of that clade and outgroup taxa in Byttnerioideae. Similarly, the sister-group relationship of Sterculioideae and Malvatheca receives support from androecial characteristics, like subsessile or sessile anthers and an absence of staminodes, shared by these two clades.

Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known.

Statistical randomization tests in evolutionary biology often require a set of random, computer-generated trees. For example, earlier studies have shown how large numbers of computer-generated trees can be used to conduct phylogenetic comparative analyses even when the phylogeny is uncertain or unknown. These methods were limited, however, in that (in the absence of molecular sequence or other data) they allowed users to assume that no phylogenetic information was available or that all possible trees were known. Intermediate situations where only a taxonomy or other limited phylogenetic information (e.g., polytomies) are available are technically more difficult. The current study describes a procedure for generating random samples of phylogenies while incorporating limited phylogenetic information (e.g., four taxa belong together in a subclade). The procedure can be used to conduct comparative analyses when the phylogeny is only partially resolved or can be used in other randomization tests in which large numbers of possible phylogenies are needed.

High levels of mitochondrial cytochrome b divergence in annual killifishes of the genus Cynolebias (Cyprinodontiformes, Rivulidae)

Phylogenetic relationships based on 324 base pairs of the mitochondrial cytochrome b gene were examined in 14 species of the genus Cynolebias. The monophyly of the genus relative to three outgroup taxa belonging to the family Rivulidae was supported by the sequence data. Bootstrap values corroborated the existence of intrageneric monophyletic units in both parsimony and Neighbour-joining analyses. These include a Cynolebias bellottii–C. wolterstorffi clade, a C. adloffi-2, C. duraznensis, C. viarius and C. adloffi-1 group, and a C. gymnoventris,C. luteoflammulatus pair and the strongly supported assemblage that includes C. prognathus and C. cheradophilus clade. Phylogenetic relationships remain poorly supported for C. nigripinnis, C. affinis and C. alexandri, and unresolved among the previous ingroup clades. Cytochrome b sequences reveal an unexpectedly high level of divergence among species of the genus Cynolebias. Consequently, cytochrome b shows good resolution of recent cladogenetic events but limited phylogenetic information at deeper nodes. High levels of sequence divergence span a broad range withinCynolebias . The highest sequence divergence (c. 28%) occurred among C. antenori and the remaining species of the genus. The minimum divergence value (4.5%) is exhibited by sympatric species C. cheradophilus andC. prognathus .

High levels of mitochondrial cytochrome b divergence in annual killifishes of the genus Cynolebias (Cyprinodontiformes, Rivulidae)

Phylogenetic relationships based on 324 base pairs of the mitochondrial cytochrome b gene were examined in 14 species of the genus Cynolebias. The monophyly of the genus relative to three outgroup taxa belonging to the family Rivulidae was supported by the sequence data. Bootstrap values corroborated the existence of intrageneric monophyletic units in both parsimony and Neighbour-joining analyses. These include a Cynolebias bellottii-C. wolterstorffl clade, a C. adloJfi-2, C. duraznensis, C. viarius and C adloffi-1 group, and a C. gymnoventris, C. luteoflammulatus pair and the strongly supported assemblage that includes C. prognalhus and C. cheradophilus clade. Phylogenetic relationships remain poorly supported for C. nigripinnis, C. affinis and C. alexandri, and unresolved among the previous ingroup clades. Cytochrome b sequences reveal an unexpectedly high level of divergence among species of the genus Cynolebias. Consequently, cytochrome b shows good resolution of recent cladogenetic events but limited phylogenetic information at deeper nodes. High levels of sequence divergence span a broad range within Cynolebias. The highest sequence divergence (c. 28%) occurred among C. antenori and the remaining species of the genus. The minimum divergence value (4.5%) is exhibited by sympatric species C. cheradophilus and C. prognathus.

Bacterial phylogeny based on comparative sequence analysis.

Comparative sequence analysis of small subunit rRNA is currently one of the most important methods for the elucidation of bacterial phylogeny as well as bacterial identification. Phylogenetic investigations targeting alternative phylogenetic markers such as large subunit rRNA, elongation factors, and ATPases have shown that 16S rRNA-based trees reflect the history of the corresponding organisms globally. However, in comparison with three to four billion years of evolution the phylogenetic information content of these markers is limited. Consequently, the limited resolution power of the marker molecules allows only a spot check of the evolutionary history of microorganisms. This is often indicated by locally different topologies of trees based on different markers, data sets or the application of different treeing approaches. Sequence peculiarities as well as methods and parameters for data analysis were studied with respect to their effects on the results of phylogenetic investigations. It is shown that only careful data analysis starting with a proper alignment, followed by the analysis of positional variability, rates and character of change, testing various data selections, applying alternative treeing methods and, finally, performing confidence tests, allows reasonable utilization of the limited phylogenetic information.