Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree

Phylogenetic trees from multiple genes can be obtained in two fundamentally different ways. In one, gene sequences are concatenated into a super-gene alignment, which is then analyzed to generate the species tree. In the other, phylogenies are inferred separately from each gene, and a consensus of these gene phylogenies is used to represent the species tree. Here, we have compared these two approaches by means of computer simulation, using 448 parameter sets, including evolutionary rate, sequence length, base composition, and transition/transversion rate bias. In these simulations, we emphasized a worst-case scenario analysis in which 100 replicate datasets for each evolutionary parameter set (gene) were generated, and the replicate dataset that produced a tree topology showing the largest number of phylogenetic errors was selected to represent that parameter set. Both randomly selected and worst-case replicates were utilized to compare the consensus and concatenation approaches primarily using the neighbor-joining (NJ) method. We find that the concatenation approach yields more accurate trees, even when the sequences concatenated have evolved with very different substitution patterns and no attempts are made to accommodate these differences while inferring phylogenies. These results appear to hold true for parsimony and likelihood methods as well. The concatenation approach shows >95% accuracy with only 10 genes. However, this gain in accuracy is sometimes accompanied by reinforcement of certain systematic biases, resulting in spuriously high bootstrap support for incorrect partitions, whether we employ site, gene, or a combined bootstrap resampling approach. Therefore, it will be prudent to report the number of individual genes supporting an inferred clade in the concatenated sequence tree, in addition to the bootstrap support.     

Alternative methods for concatenation of core genes indicate a lack of resolution in deep nodes of the prokaryotic phylogeny

It has recently been proposed that a well-resolved Tree of Life can be achieved through concatenation of shared genes. There are, however, several difficulties with such an approach, especially in the prokaryotic part of this tree. We tackled some of them using a new combination of maximum likelihood-based methods, developed in order to practice as safe and careful concatenations as possible. First, we used the application concaterpillar on carefully aligned core genes. This application uses a hierarchical likelihood-ratio test framework to assess both the topological congruence between gene phylogenies (i.e., whether different genes share the same evolutionary history) and branch-length congruence (i.e., whether genes that share the same history share the same pattern of relative evolutionary rates). We thus tested if these core genes can be concatenated or should be instead categorized into different incongruent sets. Second, we developed a heat map approach studying the evolution of the phylogenetic support for different bipartitions, when the number of sites of different phylogenetic quality in the concatenation increases. These heatmaps allow us to follow which phylogenetic signals increase or decrease as the concatenation progresses and to detect emerging artifactual groupings, that is, groups that are more and more supported when more and more homoplasic sites are thrown in the analysis. We showed that, as far as 7 major prokaryotic lineages are concerned, only 22 core genes can be said to be congruent and can be safely concatenated. This number is even smaller than the number of genes retained to reconstruct a "Tree of One Per Cent." Furthermore, the concatenation of these 22 markers leads to an unresolved tree as the only groupings in the concatenation tree seem to reflect emerging artifacts. Using concatenated core genes as a valid framework to classify uncharacterized environmental sequences can thus be misleading.     

Multilocus sequence analysis reveals that Vibrio harveyi and V. campbellii are distinct species

Identification and classification of Vibrio species have relied upon band pattern methods (e.g., amplified fragment length polymorphism) and DNA-DNA hybridization. However, data generated by these methods cannot be used to build an online electronic taxonomy. In order to overcome these limitations, we developed the first standard multilocus sequence scheme focused on the ubiquitous and pathogenic Vibrio harveyi species group (i.e., V. harveyi, V. campbellii, V. rotiferianus, and a new as yet unnamed species). We examined a collection of 104 isolates from different geographical regions and hosts using segments of seven housekeeping genes. These two species formed separated clusters on the basis of topA, pyrH, ftsZ, and mreB gene sequences. The phylogenetic picture obtained by the other three loci, i.e., gyrB, recA, and gapA, was more complex though. V. campbellii appeared nested within V. harveyi in the recA trees, whereas V. harveyi formed a tight nested cluster within V. campbellii by gapA. The gyrB gene had no taxonomic resolution and grouped the two species together. The fuzziness observed in these three genes seems not be related to recombination but to low divergence due to the accumulation of only a few substitutions. In spite of this, the concatenated sequences provided evidence that the two species form two separated clusters. These clusters did not arise by recombination but by accumulation of point mutations. V. harveyi and V. campbellii isolates can be readily identified through the open database resource developed in this study (http://www.taxvibrio.lncc.br/). We argue that the species should be defined by evolutionary criteria. Strains of the same species will share at least 95% concatenated sequence similarity using the seven loci, and, most importantly, cospecific strains will form cohesive readily recognizable phylogenetic clades.     

Defining relationships between the known members of the cytochrome P450 3A subfamily, including five putative chimpanzee members

An analysis of the cytochrome P450 3A subfamily (CYP3A) was undertaken in order to define relationships across species among subfamily members. Some members were excluded due to incomplete sequences, while others were held in abeyance because of their almost complete homology. This is the first publication of five chimpanzee CYP3A genes-CYP3A4, CYP3A5, CYP3A7, CYP3A43, and CYP3A67. This project utilized two approaches for characterizing possible relationships-phylogenetic analysis and genomic structure. For the phylogenetic analysis, both nucleotide and amino acid sequences were aligned in silico using the CLUSTAL algorithm, and then visually inspected for accuracy. Three different computer software packages were utilized: MEGA 2.1, TREECON 1.3b, and PHYLIP 3.5. Multiple methods were used: neighbor-joining (NJ), minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML). The resulting topologies were compared against each other to define the consensus topology. In addition, the chimpanzee, human, mouse, and rat genome databases were searched for intron/exon information pertaining to the included genes. Both methods suggest the same conclusion, defining orthologs is plausible between similar species (i.e., mouse and rat), but is less useful between species of different orders (i.e., primate and rodent) or classes (i.e., mammal and avian).     

马铃薯Y病毒多基因系统发育分析及其在株系鉴定中的应用

为实现马铃薯Y病毒(Potato virus Y, PVY)常见株系的快速鉴定,本文以PVY的P1、HC-pro、VPg和CP 4个基因为研究对象建立了快速准确的多基因联合体系。根据基因的不同组合建立5个不同数据集,分别进行系统发育分析,并通过贝叶斯标签关联显著性(Bayesian tip-association significance, BaTS)分析各数据集中代表分离物与株系的关联性,以确定实现PVY快速鉴定的最佳组合。不同数据集的系统发育及BaTS分析结果显示,除了联合P1、VPg和CP 3个基因数据集外,其他4个数据集均无法实现PVY常见株系的准确鉴定。采用不同建树方法对联合P1、VPg和CP 3个基因数据集比较分析显示,基于ML法和NJ法的系统发育树在拓扑结构上基本一致,均优于基于贝叶斯算法的最大分支置信(maximum clade credibility, MCC)树。同时,以HLJ26分离物为研究对象,对建立的多基因联合体系进行实际应用,结果显示该分离物与PVY^NTN-NW株系的3个分离物SYR-Ⅱ-2-8、SYR-Ⅱ-Be1和SYR-Ⅱ-DrH以高置信值聚为一亚簇,表明该分离物可能属于PVY^NTN-NW株系(SYR-Ⅱ型)。重组分析显示,HLJ26基因组存在4个潜在的重组信号,分别位于P1、HC-pro/P3、VPg和CP的5°-末端,与PVY^NTN-NW株系(SYR-Ⅱ型)的重组位点相一致,表明其属于PVY^NTN-NW株系(SYR-Ⅱ型)。同时,应用多重RT-PCR成功扩增出约为1000 bp和400 bp的2个特异性片段,与PVY^NTN-NW株系(SYR-Ⅱ型)的特异条带大小相一致。这些结果进一步支持了多基因联合体系的鉴定结果。联合P1、VPg和CP 3个基因数据集系统发育分析,可以实现PVY常见株系的准确鉴定。     

Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of Crotalaria spp., Indigofera spp., Erythrina brucei and Glycine max growing in Ethiopia

Ethiopian Bradyrhizobium strains isolated from root nodules of Crotalaria spp., Indigofera spp., Erythina brucei and soybean (Glycine max) represented genetically diverse phylogenetic groups of the genus Bradyrhizobium. Strains were characterized using the amplified fragment length polymorphism fingerprinting technique (AFLP) and multilocus sequence analysis (MLSA) of core and symbiotic genes. Based on phylogenetic analyses of concatenated recA-glnII-rpoB-16S rRNA genes sequences, Bradyrhizobium strains were distributed into fifteen phylogenetic groups under B. japonicum and B. elkanii super clades. Some of the isolates belonged to the species B. yuanmingense, B. elkanii and B. japonicum type I. However, the majority of the isolates represented unnamed Bradyrhizobium genospecies and of these, two unique lineages that most likely represent novel Bradyrhizobium species were identified among Ethiopian strains. The nodulation nodA gene sequence analysis revealed that all Ethiopian Bradyrhizobium isolates belonged to nodA sub-clade III.3. Strains were further classified into 14 groups together with strains from Africa, as well as some originating from the other tropical and subtropics regions. Strains were also clustered into 14 groups in nodY/K phylogeny similarly to the nodA tree. The nifH phylogenies of the Ethiopian Bradyrhizobium were generally also congruent with the nodA gene phylogeny, supporting the monophyletic origin of the symbiotic genes in Bradyrhizobium. The phylogenies of nodA and nifH genes were also partially congruent with that inferred from the concatenated core genes sequences, reflecting that the strains obtained their symbiotic genes vertically from their ancestor as well as horizontally from more distantly related Bradyrhizobium species.     

Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous

Heterotachy occurs when the relative evolutionary rates among sites are not the same across lineages. Sequence alignments are likely to exhibit heterotachy with varying severity because the intensity of purifying selection and adaptive forces at a given amino acid or DNA sequence position is unlikely to be the same in different species. In a recent study, the influence of heterotachy on the performance of different phylogenetic methods was examined using computer simulation for a four-species phylogeny. Maximum parsimony (MP) was reported to generally outperform maximum likelihood (ML). However, our comparisons of MP and ML methods using the methods and evaluation criteria employed in that study, but considering the possible range of proportions of sites involved in heterotachy, contradict their findings and indicate that, in fact, ML is significantly superior to MP even under heterotachy.     

Model dependence of the phylogenetic inference: relationship among carnivores, Perissodactyls and cetartiodactyls as inferred from mitochondrial genome sequences

Some previous analysis of mitochondrial proteins strongly support the Carnivora/Perissodactyla grouping excluding Cetartiodactyla (Artiodactyla + Cetacea) as an outgroup, but the support of the hypothesis remains equivocal from the analysis of several nuclear-encoded proteins. In order to evaluate the strength of the support by mitochondrial proteins, phylogenetic relationship among Carnivora, Perissodactyla, and Cetartiodactyla was estimated with the ML method by using the updated data set of the 12 mitochondrial proteins with several alternative models. The analyses demonstrate that the phylogenetic inference depends on the model used in the ML analysis; i.e., whether the site-heterogeneity is taken into account and whether the rate parameters are estimated for each individual proteins or for the concatenated sequences. Although the analysis of concatenated sequences strongly supports the Carnivora/Perissodactyla grouping, the total evaluation of the separate analyses of individual proteins, which approximates the data better than the concatenated analysis, gives only ambiguous results, and therefore it is concluded that more data are needed to resolve this trichotomy.     

Multilocus phylogenetic analysis of the genus Aeromonas

A broad multilocus phylogenetic analysis (MLPA) of the representative diversity of a genus offers the opportunity to incorporate concatenated inter-species phylogenies into bacterial systematics. Recent analyses based on single housekeeping genes have provided coherent phylogenies of Aeromonas. However, to date, a multi-gene phylogenetic analysis has never been tackled. In the present study, the intra- and inter-species phylogenetic relationships of 115 strains representing all Aeromonas species described to date were investigated by MLPA. The study included the independent analysis of seven single gene fragments (gyrB, rpoD, recA, dnaJ, gyrA, dnaX, and atpD), and the tree resulting from the concatenated 4705 bp sequence. The phylogenies obtained were consistent with each other, and clustering agreed with the Aeromonas taxonomy recognized to date. The highest clustering robustness was found for the concatenated tree (i.e. all Aeromonas species split into 100% bootstrap clusters). Both possible chronometric distortions and poor resolution encountered when using single-gene analysis were buffered in the concatenated MLPA tree. However, reliable phylogenetic species delineation required an MLPA including several “bona fide” strains representing all described species.     

A whole-genome phylogeny of the family Pasteurellaceae

A phylogenomic approach was used to generate an amino acid phylogeny for 12 whole genomes representing 10 species in the family Pasteurellaceae. Orthology of genes was determined using an approach similar to OrthologID (http://nypg.bio.nyu.edu/orthologid/about.html) and resulted in the generation of a matrix with 3130 genes with 1,194,615 aligned amino acid characters of which 239,504 characters are phylogenetically informative. Phylogenetic analysis of the concatenated matrix using all standard approaches (maximum parsimony, maximum likelihood, and Bayesian analysis) results in a single extremely robust phylogenetic hypothesis for the species examined in this study. Remarkably, no single gene partition gives the same tree as the concatenated analysis. By analyzing partitioned support in the data matrix, we show that there is very little negative support emanating from individual gene partitions to suggest that the concatenated hypothesis is not tenable. The large number of characters in the matrix allows us to test hypotheses concerning missing data and character number in phylogenomic studies, and we conclude that matrices constructed using genome level information are very robust to missing data. We show that a very large number of concatenated gene sequences (>160) are needed to reliably obtain the same topology as the overall analysis.     

Complete sequence of the yak (Bos grunniens) mitochondrial genome and its evolutionary relationship with other ruminants

The yak (Bos grunniens) is the most important domesticated species in the Qinhai-Tibetan Plateau. In present study, the complete sequence of the yak mitochondrial genome was determined. Sequence analysis revealed that there are no differences with cattle in the yak mitochondrial genome organization. Interestingly, within the D-loop, the conserved sequence blocks are less conserved than surrounding regions. Neighbor-Joining (NJ) trees based on single genes, gene sets and concatenated genes of mitochondrial genome were constructed. The analysis identified the yak as a sister group of a cattle/zebu clade. Based on substitutions in 22 tRNA genes, 12S rRNA gene and 16S rRNA gene, the dating of divergence between yak and cattle/zebu, and yak and water buffalo, was proposed to have occurred 4.38-5.32 and 10.54-13.85 million years before present, respectively. This is consistent with the paleontologyical data. Yak and sheep/goat divergent dating predicts that their divergence occurred at 13.14-27.99 million years before the present day.     

The complete mitochondrial genome of the Asiatic cavity-nesting honeybee Apis cerana (Hymenoptera: Apidae)

In the present study, we determined the complete mitochondrial DNA (mtDNA) sequence of Apis cerana, the Asiatic cavity-nesting honeybee. We present here an analysis of features of its gene content and genome organization in comparison with Apis mellifera to assess the variation within the genus Apis and among main groups of Hymenoptera. The size of the entire mt genome of A. cerana is 15,895 bp, containing 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes and one control region. These genes are transcribed from both strands and have a nucleotide composition high in A and T. The contents of A+T of the complete genomes are 83.96% for A. cerana. The AT bias had a significant effect on both the codon usage pattern and amino acid composition of proteins. There are a total of 3672 codons in all 13 protein-coding genes, excluding termination codons. The most frequently used amino acid is Leu (15.52%), followed by Ile (12.85%), Phe (10.10%), Ser (9.15%) and Met (8.96%). Intergenic regions in the mt genome of A. cerana are 705 bp in total. The order and orientation of the gene arrangement pattern is identical to that of A. mellifera, except for the position of the tRNA-Ser(AGN) gene. Phylogenetic analyses using concatenated amino acid sequences of 13 protein-coding genes, with three different computational algorithms (NJ, MP and ML), all revealed two distinct groups with high statistical support, indicating that A. cerana and A. mellifera are two separate species, consistent with results of previous morphological and molecular studies. The complete mtDNA sequence of A. cerana provides additional genetic markers for studying population genetics, systematics and phylogeographics of honeybees.     

旋唇纲纤毛虫系统发育分子树构建的影响因素

以36种旋唇类高等类群纤毛虫的核糖体小亚基核苷酸(Small subunit ribosomal RNA,SS rRNA)基因序列为素材,比较研究了不同条件(包括外类群、内类群的选择,同一基因不同序列长度的组合,不同建树方法和不同分析软件的使用)对纤毛虫分子系统树构建结果的影响。结果表明,上述因素均可不同程度地影响拓扑结构。结果同时提示,在利用有限数据进行相关研究,特别是在对未明类群的系统关系分析中,必须充分考虑因建树条件的不同所带来的影响。作者同时也建议,在当前可用的分子信息欠充分的前提下,对于纤毛虫任何类群的分子系统学探讨而言,慎重形成结论并尽可能地结合和参照形态学、发生学等资讯,仍是需优先考虑的工作路线。     

Alveolate phylogeny inferred using concatenated ribosomal proteins

Dinoflagellates and apicomplexans are a strongly supported monophyletic group in rDNA phylogenies, although this phylogeny is not without controversy, particularly between the two groups. Here we use concatenated protein-coding genes from expressed sequence tags or genomic data to construct phylogenies including "typical" dinophycean dinoflagellates, a parasitic syndinian dinoflagellate, Amoebophrya sp., and two related species, Oxyrrhis marina, and Perkinsus marinus. Seventeen genes encoding proteins associated with the ribosome were selected for phylogenetic analysis. The dataset was limited for the most part by data availability from the dinoflagellates. Forty-five taxa from four major lineages were used: the heterokont outgroup, ciliates, dinoflagellates, and apicomplexans. Amoebophrya sp. was included in this phylogeny as a sole representative of the enigmatic marine alveolate or syndinian lineage. The atypical dinoflagellate O. marina, usually excluded from rDNA analyses due to long branches, was also included. The resulting phylogenies were well supported in concatenated analyses with only a few unstable or weakly supported branches; most features were consistent when different lineages were pruned from the tree or different genes were concatenated. The least stable branches involved the placement of Cryptosporidium spp. within the Apicomplexa and the relationships between P. marinus, Amoebophrya sp., and O. marina. Both bootstrap and approximately unbiased test results confirmed that P. marinus, Amoebophrya sp., O. marina, and the remaining dinoflagellates form a monophyletic lineage to the exclusion of Apicomplexa.     

The Complete Mitochondrial Genomes of Three Bristletails (Insecta: Archaeognatha): The Paraphyly of Machilidae and Insights into Archaeognathan Phylogeny

The order Archaeognatha was an ancient group of Hexapoda and was considered as the most primitive of living insects. Two extant families (Meinertellidae and Machilidae) consisted of approximately 500 species. This study determined 3 complete mitochondrial genomes and 2 nearly complete mitochondrial genome sequences of the bristletail. The size of the 5 mitochondrial genome sequences of bristletail were relatively modest, containing 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and one control region. The gene orders were identical to that of Drosophila yakuba and most bristletail species suggesting a conserved genome evolution within the Archaeognatha. In order to estimate archaeognathan evolutionary relationships, phylogenetic analyses were conducted using concatenated nucleotide sequences of 13 protein-coding genes, with four different computational algorithms (NJ, MP, ML and BI). Based on the results, the monophyly of the family Machilidae was challenged by both datasets (W12 and G12 datasets). The relationships among archaeognathan subfamilies seemed to be tangled and the subfamily Machilinae was also believed to be a paraphyletic group in our study.     

Flip‐flop organization in the chloroplast genome of Capsosiphon fulvescens (Ulvophyceae,Chlorophyta)

To better understand organelle genome evolution of the ulvophycean green alga Capsosiphon fulvescens, we sequenced and characterized its complete chloroplast genome. The circular chloroplast genome was 111,561 bp in length with 31.3% GC content that contained 108 genes including 77 protein‐coding genes, two copies of rRNA operons, and 27 tRNAs. In this analysis, we found the two types of isoform, called heteroplasmy, were likely caused by a flip‐flop organization. The flip‐flop mechanism may have caused structural variation and gene conversion in the chloroplast genome of C. fulvescens. In a phylogenetic analysis based on all available ulvophycean chloroplast genome data, including a new C. fulvescens genome, we found three major conflicting signals for C. fulvescens and its sister taxon Pseudoneochloris marina within 70 individual genes: (i) monophyly with Ulotrichales, (ii) monophyly with Ulvales, and (iii) monophyly with the clade of Ulotrichales and Ulvales. Although the 70‐gene concatenated phylogeny supported monophyly with Ulvales for both species, these complex phylogenetic signals of individual genes need further investigations using a data‐rich approach (i.e., organelle genome data) from broader taxon sampling.     

基于Cytb和COⅠ基因部分序列的15种麻蝇之间的系统发育关系(双翅目：麻蝇科)

本研究通过测序Cytb基因和COⅠ基因的部分序列来推定15种麻蝇之间的系统发育关系。在世界麻蝇名录中,本研究的15种麻蝇能够代表麻蝇属Sarcophaga的6个亚属。连接序列（972 bp）被用于系统发育分析;分析方法包括了了最大简约法、最大似然法以及贝叶斯法。我们的结果提示了亚麻蝇亚属Parasarcophaga、别麻蝇亚属Boettcherisca以及红麻蝇亚属Liopygia的单系性,同时也表明蛇麻蝇亚属Liosarcophaga和德麻蝇亚属Pandelleisca并不是单源的。不过,目前的研究并不能分辨野德麻蝇S. (Pandelleisca) similis和峨眉叉麻蝇S. (Robineauella) coei的系统发育位置。此外,最大简约分析和似然功能分析在scopariiformis-iwuensis进化枝和polystylata-hui进化枝的关系上产生了不一致的系统发育推断。因此,后续研究不仅需要其他的分子标记,也需要更多的分类取样。     

Concordance analysis in mitogenomic phylogenetics

Here I advocate the utility of Bayesian concordance analysis as a mechanism for exploring the magnitude and source of phylogenetic signal in concatenated mitogenomic phylogenetic studies. While typically applied to the study of independently evolving gene trees, Bayesian concordance analysis can also be applied to linked, but individually analyzed, gene regions using a prior probability that reflects the expectation of similar phylogenetic reconstructions. For true branches in the mitogenomic tree, concordance factors should represent the number of gene regions that contain phylogenetic signal for a particular clade. As a demonstration of the application of Bayesian concordance analysis to empirical data, I analyzed two different salamander (Hynobiidae and Plethodontidae) mitogenomic data sets using a gene-based partitioning strategy. The results revealed many strongly supported clades in the concatenated trees that have high concordance factors, permitting the inference that these are robustly resolved through phylogenetic signal distributed across the mitogenome. In contrast, a number of strongly supported clades in the concatenated tree received low concordance factors, indicating that their reconstruction is either driven primarily by phylogenetic signal in a small number of gene regions, or that they are inconsistent reconstructions influenced by properties of the data that can produce inaccurate trees (e.g., compositional bias, selection, etc.). Exploration of the Bayesian joint posterior distribution of trees highlighted partitions that contribute phylogenetic information to similar clade reconstructions. This approach was particularly insightful in the hynobiid data, where different combinations of genes were identified that support alternative tree reconstructions. Concatenated analysis of these different subsets of genes highlighted through Bayesian concordance analysis produced strongly supported and contrasting trees, demonstrating the potential for inconsistency in concatenated mitogenomic phylogenetics. The overall results presented here suggest that Bayesian concordance analysis can serve as an effective exploration of the influence of different gene regions in mitogenomic (and other organellar genomic) phylogenetic studies.     

Molecular characterization and phylogenetic analysis of ascarid nematodes from twenty-one species of captive wild mammals based on mitochondrial and nuclear sequences

SUMMARY Although ascarid nematodes are important parasites of wild animals of public health concern, few species of ascarids from wild animals have been studied at the molecular level so far. Here, the classification and phylogenetic relationships of roundworms from 21 species of captive wild animals have been studied by sequencing and analysis of parts of the ribosomal 18S and 28S genes and the mitochondrial (mt) 12S gene. Phylogenetic relationships were inferred by 3 methods (NJ/MP/ML) based on the data of single gene sequences and concatenated sequences. Homology analysis indicated that the 18S sequences were conserved among roundworms from all 21 species and that 28S showed interspecies variability. Divergence levels displayed in 12S suggested that 12S appears to be either intra- or interspecifically variable. Evolutionary trees indicated that the ascarids split into 2 families, 4 genera and 7 species, with high bootstrap support for each clade. Combined trees suggested that Baylisascaris ailuri is more closely related to B. transfuga than to B. schroederi. This study provides useful molecular markers for the classification, phylogenetic analysis and epidemiological investigation of roundworms from wild animals.     

Evaluating character partitioning and molecular models in plastid phylogenomics at low taxonomic levels: A case study using Amphilophium (Bignonieae,Bignoniaceae)

The accurate analyses of massive amounts of data obtained through next‐generation sequencing depend on the selection of appropriate evolutionary models. Many plastid phylogenomic studies typically analyze plastome data as a single partition, or divided by a region, using a concatenate “supergene” approach. The effects of molecular evolutionary models and character partition strategies on plastome‐based phylogenies have generally been evaluated at higher taxonomic levels in green plants. Using plastome data from 32 species of Amphilophium, a genus of Neotropical lianas, we explored potential sources of topological incongruence with different plastid genome datasets and approaches. Specifically, we evaluated the effects of compositional heterogeneity, codon usage bias, positive selection, and incomplete lineage sorting as sources of systematic error (i.e., the recovery of well‐supported conflicting topologies). We compared different datasets (e.g., non‐coding regions, exons, and codon‐aligned and translated amino acids) using concatenated approaches under site‐heterogeneous and site‐homogeneous models, as well as multispecies coalescent (MSC) methods. We found incongruences in recovered phylogenetic relationships, which were mainly located in short internodes. The MSC and concatenated approaches recovered similar topologies. The analysis of GC content and codon usage bias indicated higher substitution rates and AT excess at the third codon positions, and we found evidence of positive selection in 3% of amino acid sites. There were no significant differences among species in site biochemical profiles. We argue that the selection of appropriate partition strategies and evolutionary models is important to increase accuracy in phylogenetic relationships, even when using plastome datasets, which is still the primarily used genome in plant phylogenetics.