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The higher-level phylogeny of Neuroptera is explored here based on the newly determined mitochondrial genomic data, with a special focus on the interfamilial relationships of this group. Despite considerable progress in our understanding of neuropteran relationships, several mutually exclusive hypotheses have come out according to morphology-based analyses and molecular sequence data. The evaluation of these hypotheses is hampered by the limited taxonomic coverage of previous studies. In this paper, we sequenced four mitochondrial genomes to improve the taxonomic sampling for families: Myrmeleontidae, Ascalaphidae and outgroup Corydalidae. Phylogenetic analyses were run using various inference methods to (1) confirm that Coniopterygidae is sister to all other Neuroptera; (2) place Hemerobiidae as sister to Chrysopidae; (3) support the monophyly of Myrmeleontiformia and define its interfamilial relationships; and (4) recover Myrmeleontidae as paraphyletic due to the nested Ascalaphidae.
Pubmed ID: 30717195
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Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.
View all literature mentionsA Bayesian Monte Carlo Markov Chain (MCMC) sampler software for phylogenetic reconstruction. Its main distinguishing feature is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments.
View all literature mentionsSoftware package as multiple alignment program for amino acid or nucleotide sequences. Can align up to 500 sequences or maximum file size of 1 MB. First version of MAFFT used algorithm based on progressive alignment, in which sequences were clustered with help of Fast Fourier Transform. Subsequent versions have added other algorithms and modes of operation, including options for faster alignment of large numbers of sequences, higher accuracy alignments, alignment of non-coding RNA sequences, and addition of new sequences to existing alignments.
View all literature mentionsNucleotide sequence alignment and alignment cleaning based on amino acid information. Users can paste nt-sequences into the application and select the desired protein alignment method and the genetic code, and the option for alignment cleaning.
View all literature mentionsPackage of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree.
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