Single-copy nuclear genes resolve the phylogeny of the holometabolous insects

Background  

Evolutionary relationships among the 11 extant orders of insects that undergo complete metamorphosis, called Holometabola, remain either unresolved or contentious, but are extremely important as a context for accurate comparative biology of insect model organisms. The most phylogenetically enigmatic holometabolan insects are Strepsiptera or twisted wing parasites, whose evolutionary relationship to any other insect order is unconfirmed. They have been controversially proposed as the closest relatives of the flies, based on rDNA, and a possible homeotic transformation in the common ancestor of both groups that would make the reduced forewings of Strepsiptera homologous to the reduced hindwings of Diptera. Here we present evidence from nucleotide sequences of six single-copy nuclear protein coding genes used to reconstruct phylogenetic relationships and estimate evolutionary divergence times for all holometabolan orders.     

Mitochondrial genomes in the Hymenoptera and their utility as phylogenetic markers

Abstract.  In this study, we assessed the ability of mitochondrial genome sequences to recover a test phylogeny of five hymenopteran taxa from which phylogenetic relationships are well accepted. Our analyses indicated that the test phylogeny was well recovered in all nucleotide Bayesian analyses when all the available holometabolan (i.e. outgroup) taxa were included, but only in Bayesian analyses excluding third codon positions when only the hymenopteran representatives and a single outgroup were included. This result suggests that taxon sampling of the outgroup might be as important as taxon sampling of the ingroup when recovering hymenopteran phylogenetic relationships using whole mitochondrial genomes. Parsimony analyses were more sensitive to both taxon sampling and the analytical model than Bayesian analyses, and analyses using the protein dataset did not recover the test phylogeny. In general, mitochondrial genomes did not resolve the position of the Hymenoptera within the Holometabola with confidence, suggesting that an increased taxon sampling, both within the Holometabola and among outgroups, is necessary.     

Morphological and molecular evidence converge upon a robust phylogeny of the megadiverse Holometabola

We present the largest morphological character set ever compiled for Holometabola. This was made possible through an optimized acquisition of data. Based on our analyses and recently published hypotheses based on molecular data, we discuss higher‐level phylogeny and evolutionary changes. We comment on the information content of different character systems and discuss the role of morphology in the age of phylogenomics. Microcomputer tomography in combination with other techniques proved highly efficient for acquiring and documenting morphological data. Detailed anatomical information (356 characters) is now available for 30 representatives of all holometabolan orders. A combination of traditional and novel techniques complemented each other and rapidly provided reliable data. In addition, our approach facilitates documenting the anatomy of model organisms. Our results show little congruence with studies based on rRNA, but confirm most clades retrieved in a recent study based on nuclear genes: Holometabola excluding Hymenoptera, Coleopterida (= Strepsiptera + Coleoptera), Neuropterida excl. Neuroptera, and Mecoptera. Mecopterida (= Antliophora + Amphiesmenoptera) was retrieved only in Bayesian analyses. All orders except Megaloptera are monophyletic. Problems in the analyses are caused by taxa with numerous autapomorphies and/or inapplicable character states due to the loss of major structures (such as wings). Different factors have contributed to the evolutionary success of various holometabolan lineages. It is likely that good flying performance, the ability to occupy different habitats as larvae and adults, parasitism, liquid feeding, and co‐evolution with flowering plants have played important roles. We argue that even in the “age of phylogenomics”, comparative morphology will still play a vital role. In addition, morphology is essential for reconstructing major evolutionary transformations at the phenotypic level, for testing evolutionary scenarios, and for placing fossil taxa.
© The Willi Hennig Society 2010.     

A Unique Box in 28S rRNA Is Shared by the Enigmatic Insect Order Zoraptera and Dictyoptera

The position of the Zoraptera remains one of the most challenging and uncertain concerns in ordinal-level phylogenies of the insects. Zoraptera have been viewed as having a close relationship with five different groups of Polyneoptera, or as being allied to the Paraneoptera or even Holometabola. Although rDNAs have been widely used in phylogenetic studies of insects, the application of the complete 28S rDNA are still scattered in only a few orders. In this study, a secondary structure model of the complete 28S rRNAs of insects was reconstructed based on all orders of Insecta. It was found that one length-variable region, D3-4, is particularly distinctive. The length and/or sequence of D3-4 is conservative within each order of Polyneoptera, but it can be divided into two types between the different orders of the supercohort, of which the enigmatic order Zoraptera and Dictyoptera share one type, while the remaining orders of Polyneoptera share the other. Additionally, independent evidence from phylogenetic results support the clade (Zoraptera+Dictyoptera) as well. Thus, the similarity of D3-4 between Zoraptera and Dictyoptera can serve as potentially valuable autapomorphy or synapomorphy in phylogeny reconstruction. The clades of (Plecoptera+Dermaptera) and ((Grylloblattodea+Mantophasmatodea)+(Embiodea+Phasmatodea)) were also recovered in the phylogenetic study. In addition, considering the other studies based on rDNAs, this study reached the highest congruence with previous phylogenetic studies of Holometabola based on nuclear protein coding genes or morphology characters. Future comparative studies of secondary structures across deep divergences and additional taxa are likely to reveal conserved patterns, structures and motifs that can provide support for major phylogenetic lineages.     

The compact mitochondrial genome of Zorotypus medoensis provides insights into phylogenetic position of Zoraptera

Background

Zoraptera, generally regarded as a member of Polyneoptera, represents one of the most enigmatic insect orders. Although phylogenetic analyses based on a wide array of morphological and/or nuclear data have been performed, the position of Zoraptera is still under debate. Mitochondrial genome (mitogenome) information is commonly considered to be preferable to reconstruct phylogenetic relationships, but no efforts have been made to incorporate it in Zorapteran phylogeny. To characterize Zoraptera mitogenome features and provide insights into its phylogenetic placement, here we sequenced, for the first time, one complete mitogenome of Zoraptera and reconstructed the phylogeny of Polyneoptera.

Results

The mitogenome of Zorotypus medoensis with an A + T content of 72.50% is composed of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a noncoding A + T-rich region. The gene content and arrangement are identical to those considered ancestral for insects. This mitogenome shows a number of very unusual features. First, it is very compact, comprising 14,572 bp, and is the smallest among all known polyneopteran mitogenomes. Second, both noncoding sequences and coding genes exhibit a significant decrease in size compared with those of other polyneopterans. Third, Z. medoensis mitogenome has experienced an accelerated substitution rate. Fourth, truncated secondary structures of tRNA genes occur with loss of dihydrouridine (DHU) arm in trnC, trnR, and trnS(AGN) and loss of TΨC arm in trnH and trnT. The phylogenetic analyses based on the mitogenome sequence information indicate that Zoraptera, represented by Z. medoensis, is recovered as sister to Embioptera. However, both Zoraptera and Embioptera exhibit very long branches in phylogenetic trees.

Conclusions

Characterization of Z. medoensis mitogenome contributes to our understanding of the enigmatic Zoraptera. Mitogenome data demonstrate an overall strong resolution of deep-level phylogenies of Polyneoptera but not Insecta. It is preferable to expand taxon sampling of Zoraptera and other poorly represented orders in future to break up long branches.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1156) contains supplementary material, which is available to authorized users.     

脉翅总目系统发育研究进展

脉翅总目是全变态类昆虫中起源较早的古老类群之一,有关该类群的分类及系统发育研究对阐明全变态类昆虫的起源演化具有重要意义。文章就脉翅总目的系统地位、目级阶元、科级阶元和属种级阶元的系统发育几个方面的研究进行综述,着重介绍近年来国内外取得的研究成果,其中包括基于形态和分子数据所得的最新系统发育假设。最后,对脉翅总目系统发育研究中尚未解决的主要问题进行归纳。     

白纹方蟹线粒体基因组全序列测定及方蟹总科比较分析

为探讨该总科内部亲缘关系及其与线粒体基因排序之间的相关性,研究以方蟹科(Grapsidae)白纹方蟹(Grapsus albolineatus)为代表种,测定其线粒体基因组全序列。其全长为15577 bp,包含13个蛋白编码基因,22个tRNA基因, 2个rRNA基因和1个控制区。基因组碱基组成为33.4%A、12.0%G、20.6%C和34.0%T,具有明显的AT偏向性(67.4%)。除ATP8和ND1以GTG作为起始密码子外,其余蛋白编码基因均以ATN作为起始密码子;除COⅡ和Cyt b以T作为不完全终止密码子外,其余基因均以TAN作为终止密码子。亮氨酸(Leu)和半胱氨酸(Cys)分别是使用频率最高(15.28%)和最低(0.81%)的两种密码子。除tRNA-Ser1缺少DHU臂外,其余tRNA均能形成典型的三叶草结构。基于13个蛋白编码基因的核苷酸序列同时构建了方蟹总科的贝叶斯树(BI)和最大似然树(ML),两种方法构建的系统发育树扑拓结构一致,均显示所有方蟹科(Grapsidae)种类聚在一起,其中白纹方蟹与同属的细纹方蟹(G. tenuicrustatus)的亲缘关系最近;...     

Empirical evaluation of partitioning schemes for phylogenetic analyses of mitogenomic data: An avian case study

Whole mitochondrial genome sequences have been used in studies of animal phylogeny for two decades, and current technologies make them ever more available, but methods for their analysis are lagging and best practices have not been established. Most studies ignore variation in base composition and evolutionary rate within the mitogenome that can bias phylogenetic inference, or attempt to avoid it by excluding parts of the mitogenome from analysis. In contrast, partitioned analyses accommodate heterogeneity, without discarding data, by applying separate evolutionary models to differing portions of the mitogenome. To facilitate use of complete mitogenomic sequences in phylogenetics, we (1) suggest a set of categories for dividing mitogenomic datasets into subsets, (2) explore differences in evolutionary dynamics among those subsets, and (3) apply a method for combining data subsets with similar properties to produce effective and efficient partitioning schemes. We demonstrate these procedures with a case study, using the mitogenomes of species in the grackles and allies clade of New World blackbirds (Icteridae). We found that the most useful categories for partitioning were codon position, RNA secondary structure pairing, and the coding/noncoding distinction, and that a scheme with nine data groups outperformed all of the more complex alternatives (up to 44 data groups) that we tested. As hoped, we found that analyses using whole mitogenomic sequences yielded much better-resolved and more strongly-supported hypotheses of the phylogenetic history of that locus than did a conventional 2-kilobase sample (i.e. sequences of the cytochrome b and ND2 genes). Mitogenomes have much untapped potential for phylogenetics, especially of birds, a taxon for which they have been little exploited except in investigations of ordinal-level relationships.     

The Entire Mitochondrial Genome of Macrophthalmus abbreviatus Reveals Insights into the Phylogeny and Gene Rearrangements of Brachyura

Brachyuran crabs comprise the most species-rich clades among extant Decapoda and are divided into several major superfamilies. However, the phylogeny of Brachyuran remains controversial, comprehensive analysis of the overall phylogeny is still lacking. Complete mitochondrial genome (mitogenome) can indicate phylogenetic relationships, as well as useful information for gene rearrangement mechanisms and molecular evolution. In this study, we firstly sequenced and annotated the complete mitogenome of Macrophthalmus abbreviatus (Brachyura; Macrophthalmidae). The mitogenome length of M. abbreviatus is 16,322 bp, containing the entire set of 37 genes and a control region typically observed in Brachyuran mitogenomes. The genome composition of M. abbreviatus was highly A+T biased 76.3% showing positive AT-skew (0.033) and negative GC-skew (??0.351). In M. abbreviatus mitogenome, most tRNA genes were folded into the clover-leaf secondary structure except trnH, trnS1 and trnC, which was similar to the other species in Macrophthalmidae. Phylogenetic analysis showed that all families form a monophyletic, and Varunidae and Macrophthalmidae clustered into a monophyletic clade as sister groups. Comparative analyses of rearrangement among Brachyura revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) had the same gene order, which reinforced the result of phylogeny. The combined results of two aspects revealed that the polyphyly of Ocypodoidea and Grapsoidea were well supported. In general, the results obtained in this research will contribute to further studies on molecular based for the classification and gene rearrangements of Macrophthalmidae or even Brachyura.

     

Comparative mitochondrial genomic analysis of Macrophthalmus pacificus and insights into the phylogeny of the Ocypodoidea & Grapsoidea

Grapsoidea and Ocypodoidea, two of the most abundant and economically important groups in Brachyura, are of great commercial value to fisheries and aquaculture. However, the taxonomy of Ocypodoidea and Grapsoidea has long been highly disputed. Previous studies have investigated this problem through phylogenetic analysis based on limited taxonomic sampling, with different reports proposing either monophyly or paraphyly, but no definitive conclusion has been reached. In this study, the complete mitogenome of Macrophthalmus pacificus (Ocypodoidea, Macrophthalmidae) is reported on and the relationship between Ocypodoidea and Grapsoidea is further investigated. Sequencing the M. pacificus mitogenome, which is a closed circular molecule containing a typical 37 genes, preliminarily determined the ancestral gene order of Macrophthalmidae, which is consistent with previous studies. Comparative analyses of gene order among Ocypodoidea and Grapsoidea revealed that Varunidae (Grapsoidea) and Macrophthalmidae (Ocypodoidea) have the same rearrangement, which confirms previous research. Larger data analysis revealed that these two families (Varunidae and Macrophthalmidae) cluster into a monophyletic clade as sister groups. Rearrangement and phylogeny lines of evidence is concluded that Varunidae and Macrophthalmidae may be of common origin. Furthermore, the remaining Ocypodoidea and Grapsoidea families mix paraphyletically in the phylogenetic tree. Therefore, both gene rearrangement and phylogenetic analysis support the paraphyly of Ocypodoidea and Grapsoidea, which reinforces this view. These findings provide important information regarding Brachyura's phylogenetic relationships, which demonstrates the advantage of mitogenome sequence data in phylogenetic studies.     

The complete mitochondrial genome of Pardosa pusiola (Araneae,Lycosidae) and its phylogenetic implications

The mitochondrial genome (mitogenome) is useful for identification and phylogenetic analyses among arthropods, but there are no sufficient mitogenome data for wolf spiders. To enrich the mitogenome database of wolf spiders, the complete mitogenome of Pardosa pusiola was sequenced by high-throughput sequencing. It is 14,284 bp, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). It represents a high bias toward A and T nucleotides with an A + T content of 76.49%. The mitogenome exhibited a negative AT skew (−0.13) and a positive GC skew (0.32). Most PCGs started with ATN codons and ended with TAA, TAG, or an incomplete T. In addition, most tRNAs had aberrant secondary structures with the absence of DHU arm or TΨC arm. Analysis performed with CREx software demonstrated that large-scale rearrangements of tRNAs were observed in the mitogenome of P. pusiola as compared with the putative ancestral mitogenome. The Bayesian inference (BI) and maximum likelihood (ML) phylogenetic trees based on the 13 PCGs of 25 spiders had the same topology, which could be presented as (Araneidae + (Agelenidae + (Dictynidae + Desidae)) + (Salticidae + (Thomisidae + (Oxyopidae + (Pisauridae + Lycosidae))))). This study offers a useful genetic resource for the taxonomy and phylogeny of spiders.     

Deciphering Metazoan Phylogeny: The Need for Additional Molecular Data

SYNOPSIS. Our interpretation of the evolution of development,morphology, and diversity of multicellular animals hinges ona clear understanding of the phylogenetic relationships of metazoans.Currently, the field of metazoan phylogeny is in a state offlux, with new hypotheses of metazoan relationships emergingfrom analyses of 18S rDNA sequence data. Some of these analyseshave been limited in the numbers of taxa analyzed, others, withnumerous taxa analyzed, have not resolved deep level branchingpatterns, and all are hampered by properties of the 18S geneitself. Corroboration of the results from 18S rDNA analysescan come from additional molecular data sets, such as highlyconserved nuclear coding genes, mitochondria gene order, orgene duplication events. The enormous task of data accumulationfor additional molecular data from many representative taxacan most efficiently be undertaken in a coordinated, collaborativeeffort among different lab groups. Ultimately, a combined analysisof several independent data sets will be possible and may providea more stable, robust phylogeny for the Metazoa.     

The complete mitochondrial genome sequence of the black-capped capuchin (Cebus apella)

The phylogenetic relationships of primates have been extensively investigated, but key issues remain unresolved. Complete mitochondrial genome (mitogenome) data have many advantages in phylogenetic analyses, but such data are available for only 46 primate species. In this work, we determined the complete mitogenome sequence of the black-capped capuchin (Cebus apella). The genome was 16,538 bp in size and consisted of 13 protein-coding genes, 22 tRNAs, two rRNAs and a control region. The genome organization, nucleotide composition and codon usage did not differ significantly from those of other primates. The control region contained several distinct repeat motifs, including a putative termination-associated sequence (TAS) and several conserved sequence blocks (CSB-F, E, D, C, B and 1). Among the protein-coding genes, the COII gene had lower nonsynonymous and synonymous substitutions rates while the ATP8 and ND4 genes had higher rates. A phylogenetic analysis using Maximum likelihood and Bayesian methods and the complete mitogenome data for platyrrhine species confirmed the basal position of the Callicebinae and the sister relationship between Atelinae and Cebidae, as well as the sister relationship between Aotinae (Aotus) and Cebinae (Cebus/Saimiri) in Cebidae. These conclusions agreed with the most recent molecular phylogenetic investigations on primates. This work provides a framework for the use of complete mitogenome information in phylogenetic analyses of the Platyrrhini and primates in general.     

Three New Ranidae Mitogenomes and the Evolution of Mitochondrial Gene Rearrangements among Ranidae Species

Various types of gene rearrangements have been discovered in the mitogenoes of the frog family Ranidae.In this study,we determined the complete mitogenome sequence of three Rana frogs.By combining the available mitogenomic data sets from Gen Bank,we evaluated the phylogenetic relationships of Ranidae at the mitogenome level and analyzed mitogenome rearrangement cases within Ranidae.The three frogs shared an identical mitogenome organization that was extremely similar to the typical Neobatrachian-type arrangement.Except for the genus Babina,the monophyly of each genus was well supported.The genus Amnirana occupied the most basal position among the Ranidae.The[Lithobates+Rana]was the closest sister group of Odorrana.The diversity of mitochondrial gene arrangements in ranid species was unexpectedly high,with 47 mitogenomes from 40 ranids being classified into 10 different gene rearrangement types.Some taxa owned their unique gene rearrangement characteristics,which had significant implication for their phylogeny analysis.All rearrangement events discovered in the Ranidae mitogenomes can be explained by the duplication and random loss model.     

被子植物系统发育深层关系研究: 进展与挑战

被子植物系统发育学是研究被子植物及其各类群间亲缘关系与进化历史的学科。从20世纪90年代起, 核苷酸和氨基酸序列等分子数据开始被广泛运用于被子植物系统发育研究, 经过20多年的发展, 从使用单个或联合少数几个细胞器基因, 到近期应用整个叶绿体基因组来重建被子植物的系统发育关系, 目、科水平上的被子植物系统发育框架已被广泛接受。在这个框架中, 基部类群、主要的5个分支(即真双子叶植物、单子叶植物、木兰类、金粟兰目和金鱼藻目)、每个分支所包含的目以及几个大分支包括的核心类群等都具有高度支持。与此同时, 细胞器基因还存在一些固有的问题, 例如单亲遗传、系统发育信息量有限等, 因此近年来双亲遗传的核基因在被子植物系统发育研究中的重要性逐渐得到关注, 并在不同分类阶元的研究中都取得了一定进展。但是, 被子植物系统发育中仍然存在一些难以确定的关系, 例如被子植物5个分支之间的关系、真双子叶植物内部某些类群的位置等。本文简述了20多年来被子植物系统发育深层关系的主要研究进展, 讨论了被子植物系统发育学常用的细胞器基因和核基因的选用, 已经确定和尚未确定系统发育位置的主要类群, 以及研究中尚存在的问题和可能的解决方法。     

Phylogeny of the Oriental Drosophila melanogaster species group: a multilocus reconstruction

The melanogaster species group of Drosophila (subgenus Sophophora) has long been a favored model for evolutionary studies because of its morphological and ecological diversity and wide geographic distribution. However, phylogenetic relationships among species and subgroups within this lineage are not well understood. We reconstructed the phylogeny of 17 species representing 7 "oriental" species subgroups, which are especially closely related to D. melanogaster. We used DNA sequences of four nuclear and two mitochondrial loci in an attempt to obtain the best possible estimate of species phylogeny and to assess the extent and sources of remaining uncertainties. Comparison of trees derived from single-gene data sets allowed us to identify several strongly supported clades, which were also consistently seen in combined analyses. The relationships among these clades are less certain. The combined data set contains data partitions that are incongruent with each other. Trees reconstructed from the combined data set and from internally homogenous data sets consisting of three or four genes each differ at several deep nodes. The total data set tree is fully resolved and strongly supported at most nodes. Statistical tests indicated that this tree is compatible with all individual and combined data sets. Therefore, we accepted this tree as the most likely model of historical relationships. We compared the new molecular phylogeny to earlier estimates based on morphology and chromosome structure and discuss its taxonomic and evolutionary implications.     

The complete mitochondrial genome of Eterusia aedea (Lepidoptera,Zygaenidae) and comparison with other zygaenid moths

Zygaenidae comprises >1036 species, including many folivorous pests in agriculture. In the present study, the complete mitochondrial genome (mitogenome) of a major pest of tea trees, Eterusia aedea was determined. The 15,196-bp circular genome contained the common set of 37 mitochondrial genes (including 13 protein-coding genes, two rRNA genes, and 22 tRNA genes) and exhibited the similar genomic features to reported Zygaenidae mitogenome. Comparative analyses of Zygaenidae mitogenomes showed a typical evolutionary trend of lepidopteran mitogenomes. In addition, we also investigated the gene order of lepidopteran mitogenomes and proposed that the novel gene order trnA-trnR-trnN-trnE-trnS-trnF from Zygaenidae and Gelechiidae and most other gene rearrangements of this tRNA cluster evolved independently. Finally, the mitogenomic phylogeny of Lepidoptera was reconstructed based on multiple mitochondrial datasets. And all the phylogenetic results revealed the sister relationships of Cossoidea and Zygaenoidea with both BI and ML methods, which is the first stable mitogenomic evidence for this clade.     

三种蚜虫的线粒体基因组数据

完整的线粒体基因组已被广泛应用于分子进化、基因组学、系统发育等方面的研究。蚜虫是一类重要的农林业害虫, 但目前公开报道的蚜虫完整线粒体基因组非常有限, 因此获得更多的基因组数据对相关研究具有重要价值。本文报道了榕毛管蚜(Greenidea ficicola)、橘二叉蚜(Aphis aurantia)和油杉纩蚜(Mindarus keteleerifoliae) 3种蚜虫的完整线粒体基因组的序列、详细注释信息、基因结构图、密码子使用情况等。该数据集可为昆虫系统发育关系、种群分化格局、害虫防治等方面的工作提供帮助。     

When is enough,enough in phylogenetics? A case in point from Hordeum (Poaceae)

Direct optimization was used to reconstruct the phylogeny of the 26 diploid taxa included in the genus Hordeum. The total data set was composed of 16 nucleotide sequence regions from the nuclear as well as the plastid genome. The nine nuclear regions were from single‐copy, protein coding genes located on six of the seven chromosome pairs in the diploid H. vulgare genome. The seven plastid regions comprise protein coding genes as well as intergenic regions. Studies of character congruence between data partitions showed no correlation between chromosomal location and congruence among the nuclear sequences and a level of congruence among the plastid sequences comparable with the level among the nuclear sequences. Combined analysis of all data resolved the phylogeny completely with most clades being robust and well supported. However, due to incongruence among data partitions some relationships are still and likely to remain ambiguously inferred. Rather than adding still more genes to the phylogenetic analyses, patterns of incongruence may be better explored by adding data from multiple specimens per taxon. For some species relationships the plastid data appear positively misleading, emphasizing the need for caution if plastid data are the only or dominant type of data used for phylogenetic reconstruction and subsequent re‐classification.
© The Willi Hennig Society 2011.     

Mitogenome phylogenetics: the impact of using single regions and partitioning schemes on topology, substitution rate and divergence time estimation

The availability of mitochondrial genome sequences is growing as a result of recent technological advances in molecular biology. In phylogenetic analyses, the complete mitogenome is increasingly becoming the marker of choice, usually providing better phylogenetic resolution and precision relative to traditional markers such as cytochrome b (CYTB) and the control region (CR). In some cases, the differences in phylogenetic estimates between mitogenomic and single-gene markers have yielded incongruent conclusions. By comparing phylogenetic estimates made from different genes, we identified the most informative mitochondrial regions and evaluated the minimum amount of data necessary to reproduce the same results as the mitogenome. We compared results among individual genes and the mitogenome for recently published complete mitogenome datasets of selected delphinids (Delphinidae) and killer whales (genus Orcinus). Using Bayesian phylogenetic methods, we investigated differences in estimation of topologies, divergence dates, and clock-like behavior among genes for both datasets. Although the most informative regions were not the same for each taxonomic group (COX1, CYTB, ND3 and ATP6 for Orcinus, and ND1, COX1 and ND4 for Delphinidae), in both cases they were equivalent to less than a quarter of the complete mitogenome. This suggests that gene information content can vary among groups, but can be adequately represented by a portion of the complete sequence. Although our results indicate that complete mitogenomes provide the highest phylogenetic resolution and most precise date estimates, a minimum amount of data can be selected using our approach when the complete sequence is unavailable. Studies based on single genes can benefit from the addition of a few more mitochondrial markers, producing topologies and date estimates similar to those obtained using the entire mitogenome.