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As the relationship between hexapods and crustaceans (Pancrustacea) is well accepted, the affinity of myriapods depends on the position of the outgroup. (A) Unrooted tree with two possible outgroup positions. (B) If the outgroup branches between Pancrustacea and myriapods + chelicerates the tree supports the Myriochelata hypothesis. (C) If the outgroup branches closer to Chelicerata the tree supports a monophyletic Mandibulata. Giribet and colleagues (Giribet et al., 2005) proposed a similar figure in which they also consider different position for the Pycnogonids (either basal to chelicerates or to arthropod).
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The choice of an appropriate outgroup is a fundamental prerequisite when the difference between two conflicting phylogenetic hypotheses depends on the position of the root. This is the case for the myriapods that may group either with Pancrustacea forming a clade called Mandibulata, in accordance with morphological characters, or with chelicerates...
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Context 1
... in particular the position of the myriapods rel- ative to other arthropod classes. As the sister group relationship be- tween crustaceans and hexapods is well accepted (with myriapods and chelicerates lying outside this 'pancrustacean' group) the ques- tion of the affinities of myriapods depends entirely on the position of the outgroup ( Fig. 1) and makes this problematic node an appropri- ate case for studying the effects of outgroup ...
Context 2
... the difference between the Mandibulata and Myriochelata trees lies simply in the position of the root of the tree ( Fig. 1) and furthermore, the signal is anticipated to be subtle, it is clear that the choice of outgroup may have a significant impact on phy- logeny estimation around this ...
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Background
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Citations
... As such, nodes can easily "flip-flop" with the addition of ingroup samples. Furthermore, ingroup phylogenetic signal can also become obscured if the phylogenetic distance between the outgroup and the ingroup is too large (wheeler 1990;huelsenbeck et al. 2002;rota-Stabelli & telford, 2008;rosenfeld et al. 2012;kirchberger et al. 2014;. In all previous analyses, the pulchellus group was used as the outgroup following wood et al. (2012) whereas herein, the ingroup was rooted with the sister group of the brevipalmatus group-the shwetaungorum group (Grismer et al. 2021b). ...
Model based integrative analyses supports the recognition of a new species of the Cyrtodactylus brevipalmatus group from Phuket Island, Thailand. Cyrtodactylus thalang sp. nov. is most closely related to the sister species C. brevipalmatus from the Thai-Malay Peninsula and C. cf. brevipalmatus from Langkawi Island, Kedah State, Peninsular Malaysia. Based on the mitochondrial gene ND2, C. thalang sp. nov. bears an uncorrected pairwise sequence divergence of 14.7% and 15.1% from C. cf. brevipalmatus and C. brevipalmatus, respectively, significantly different (p<0.05) mean values of meristic and morphometric characters, and discrete categorical morphological differences. A multiple factor analysis morphospatially statistically placed C. thalang sp. nov. well outside all other species of the brevipalmatus group. The BAYAREALIKE model of a BioGeoBEARS analysis indicated the origin of the brevipalmatus group was in western Indochina with subsequent south to north speciation along the Tenasserim Mountains followed by a west to east invasion of northern Thailand, Laos, and northwestern Vietnam northeast of the Chao Phraya Basin and north of the Khorat Plateau.
... In both cases, one thousand bootstrap pseudo-replicates were used to test the reliability of the inferred trees. Phylogenetic trees were constructed using a midpoint root and without the use of other outgroups, as previously proposed for families with highly divergent outgroups, which is the case for the PLEKHA family (Wheeler, 1990;Foster and Hickey, 1999;Huelsenbeck et al., 2002;Shavit et al., 2007;Rota-Stabelli and Telford, 2008;Rosenfeld et al., 2012). ...
Plekha7 is a key adherens junction component involved in numerous functions in mammalian cells. Plekha7 is the most studied member of the PLEKHA protein family, which includes eight members with diverse functions. However, the evolutionary history of Plekha7 remains unexplored. Here, we outline the phylogeny and identify the origins of this gene and its paralogs. We show that Plekha7, together with Plekha4, Plekha5, and Plekha6, belong to a subfamily that we name PLEKHA4/5/6/7. This subfamily is distinct from the other Plekha proteins, which form two additional separate subfamilies, namely PLEKHA1/2 and PLEKHA3/8. Sequence, phylogenetic, exon-intron organization, and syntenic analyses reveal that the PLEKHA4/5/6/7 subfamily is represented by a single gene in invertebrates, which remained single in the last common ancestor of all chordates and underwent gene duplications distinctly in jawless and jawed vertebrates. In the latter species, a first round of gene duplications gave rise to the Plekha4/7 and Plekha5/6 pairs and a second round to the four extant members of the subfamily. These observations are consistent with the 1R/2R hypothesis of vertebrate genome evolution. Plekha7 and Plekha5 also exist in two copies in ray-finned fishes, due to the Teleostei-specific whole genome duplication. Similarities between the vertebrate Plekha4/5/6/7 members and non-chordate sequences are restricted to their N-terminal PH domains, whereas similarities across the remaining protein molecule are only sporadically found among few invertebrate species and are limited to the coiled-coil and extreme C-terminal ends. The vertebrate Plekha4/5/6/7 proteins contain extensive intrinsically disordered domains, which are topologically and structurally conserved in all chordates, but not in non-chordate invertebrates. In summary, our study sheds light on the origins and evolution of Plekha7 and the PLEKHA4/5/6/7 subfamily and unveils new critical information suitable for future functional studies of this still understudied group of proteins.
... Most of these studies also examined relationships using different outgroup taxa even when using similar inference methods (Table S1). Rota-Stabelli & Telford (2008) have suggested that the choice of an appropriate outgroup is a fundamental prerequisite when the differences between two conflicting phylogenetic hypotheses depends on the position of the root. Hence, the question arises: if we increase taxon sampling and choose appropriate outgroups, can this give us enough information to obtain an accurate phylogeny? ...
Background
The phylogenetic relationships of Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) remain unresolved. Different researchers have supported one of three hypotheses (Palaeoptera, Chiastomyaria or Metapterygota) based on data from different morphological characters and molecular markers, sometimes even re-assessing the same transcriptomes or mitochondrial genomes. The appropriate choice of outgroups and more taxon sampling is thought to eliminate artificial phylogenetic relationships and obtain an accurate phylogeny. Hence, in the current study, we sequenced 28 mt genomes from Ephemeroptera, Odonata and Plecoptera to further investigate phylogenetic relationships, the probability of each of the three hypotheses, and to examine mt gene arrangements in these species. We selected three different combinations of outgroups to analyze how outgroup choice affected the phylogenetic relationships of Odonata and Ephemeroptera.
Methods
Mitochondrial genomes from 28 species of mayflies, dragonflies, damselflies and stoneflies were sequenced. We used Bayesian inference (BI) and Maximum likelihood (ML) analyses for each dataset to reconstruct an accurate phylogeny of these winged insect orders. The effect of outgroup choice was assessed by separate analyses using three outgroups combinations: (a) four bristletails and three silverfish as outgroups, (b) five bristletails and three silverfish as outgroups, or (c) five diplurans as outgroups.
Results
Among these sequenced mitogenomes we found the gene arrangement IMQM in Heptageniidae (Ephemeroptera), and an inverted and translocated tRNA-Ile between the 12S RNA gene and the control region in Ephemerellidae (Ephemeroptera). The IMQM gene arrangement in Heptageniidae (Ephemeroptera) can be explained via the tandem-duplication and random loss model, and the transposition and inversion of tRNA-Ile genes in Ephemerellidae can be explained through the recombination and tandem duplication-random loss (TDRL) model. Our phylogenetic analysis strongly supported the Chiastomyaria hypothesis in three different outgroup combinations in BI analyses. The results also show that suitable outgroups are very important to determining phylogenetic relationships in the rapid evolution of insects especially among Ephemeroptera and Odonata. The mt genome is a suitable marker to investigate the phylogeny of inter-order and inter-family relationships of insects but outgroup choice is very important for deriving these relationships among winged insects. Hence, we must carefully choose the correct outgroup in order to discuss the relationships of Ephemeroptera and Odonata.
... Because of its higher mutation rate, MtDNA is, in general, more prone to saturation than the nuclear genome [49]. Accordingly, we would expect to underestimate the number of observed mutations in mtDNA dataset compared to the nDNA one with the consequences that nodes using mtDNA dataset should appear younger than they are. ...
... The final explanation is the stochasticity embedded in small (four genes) datasets, such as the ones we have used. The stochasticity in the mtDNA tree may have been exacerbated by systematic errors related to the fast-evolving nature of the mtDNA [49,50] and to evident high level of apomorphies, as revealed by the longer terminal branches in the mtDNA tree compared with the nDNA one. The different phylogenetic signal, however, does not seem to relate to the amount of missing data as the mitochondrial alignment is more complete than the nuclear one (38% of missing data in mtDNA vs. 45% in nDNA). ...
One-third of all mosquitoes belong to the Aedini, a tribe comprising common vectors of viral zoonoses such as Aedes aegypti and Aedes albopictus. To improve our understanding of their evolution, we present an updated multigene estimate of Aedini phylogeny and divergence, focusing on the disentanglement between nuclear and mitochondrial phylogenetic signals. We first show that there are some phylogenetic discrepancies between nuclear and mitochondrial markers which may be caused by wrong taxa assignment in samples collections or by some stochastic effect due to small gene samples. We indeed show that the concatenated dataset is model and framework dependent, indicating a general paucity of signal. Our Bayesian calibrated divergence estimates point toward a mosquito radiation in the mid-Jurassic and an Aedes radiation from the mid-Cretaceous on. We observe, however a strong chronological incongruence between mitochondrial and nuclear data, the latter providing divergence times within the Aedini significantly younger than the former. We show that this incongruence is consistent over different datasets and taxon sampling and that may be explained by either peculiar evolutionary event such as different levels of saturation in certain lineages or a past history of hybridization throughout the genus. Overall, our updated picture of Aedini phylogeny, reveal a strong nuclear-mitochondrial incongruence which may be of help in setting the research agenda for future phylogenomic studies of Aedini mosquitoes.
... This resulted in a reduction of the dataset by approximately 62% from 387 987 to 148 945 sites. We tested the effects of outgroup selection on the recovered topology, since the inclusion of distant outgroups with highly divergent sequences relative to the ingroup can lead to the recovery of misleading topologies [47,48]. Moreover, distant outgroups reduce the precision of molecular clock estimates [49]. ...
Stick and leaf insects (Phasmatodea) are a distinctive insect order whose members are characterized by mimicking various plant tissues such as twigs, foliage and bark. Unfortunately, the phylogenetic relationships among phasmatodean subfamilies and the timescale of their evolution remain uncertain. Recent molecular clock analyses have suggested a Cretaceous–Palaeogene origin of crown Phasmatodea and a subsequent Cenozoic radiation, contrasting with fossil evidence. Here, we analysed transcriptomic data from a broad diversity of phasmatodeans and, combined with the assembly of a new suite of fossil calibrations, we elucidate the evolutionary history of stick and leaf insects. Our results differ from recent studies in the position of the leaf insects (Phylliinae), which are recovered as sister to a clade comprising Clitumninae, Lancerocercata, Lonchodinae, Necrosciinae and Xenophasmina. We recover a Permian to Triassic origin of crown Phasmatodea coinciding with the radiation of early insectivorous parareptiles, amphibians and synapsids. Aschiphasmatinae and Neophasmatodea diverged in the Jurassic–Early Cretaceous. A second spur in origination occurred in the Late Cretaceous, coinciding with the Cretaceous Terrestrial Revolution, and was probably driven by visual predators such as stem birds (Enantiornithes) and the radiation of angiosperms.
... Phylogenetic analysis denotes various important information including the degree of relationship among genera, species and strains, diversity of geographical isolates, and the origin and evolution of plant viruses [42,43]. An appropriate selection of ingroups and outgroups are crucial steps in phylogenetic analysis as they significantly impact on tree topology and root position [44,45]. Ingroups should be a group of closely related species, whereas, outgroups should be distantly related to the ingroups but should have enough homologous sites to confirm that the tree is constructed upon comparison of homologous sites [46]. ...
... Globally, a number of researchers used identical potato virus identification techniques to our study [9,10,38,40,44,[47][48][49]. However, as NGS are efficient methods for characterization of novel viruses [27][28][29], a number of novel viruses can be identified by using NGS from the collected tuber samples in the future. ...
Potato (Solanum tuberosum) is a major food source in the whole world including Bangladesh. Viral diseases are the key constraint for sustainable potato production by reducing both quality and quantity. To determine the present status of eight important potato viruses in Bangladesh, tuber samples were collected from three major potato growing regions (Munshiganj, Jessore and Bogra districts) in January–February 2017 and February 2018. Reverse transcription polymerase chain reaction (RT-PCR) with coat protein (CP)-specific primers were used to amplify CP sequences of the respective viruses, and confirmed by sequencing, which were deposited in the GenBank. Results indicated that the tuber samples were subjected to Potato leafroll virus (PLRV), Potato virus X (PVX), Potato virus Y (PVY), Potato virus S (PVS), Potato virus H (PVH), Potato aucuba mosaic virus (PAMV) and Potato virus M (PVM) infection, whereas mixed infections were very common. Phylogenetic analysis revealed that the PLRV from this study was closely related to a Canadian and a Chinese isolate, respectively; PVX was closely related to a Canadian and a Chinese isolate, respectively; PVY was closely related to a Chinese isolate; PVS was closely related to a Chinese and an Iranian isolate, respectively; PAMV was closely related to a Canadian isolate; PVH was closely related to a Huhhot isolate of China; and PVM was closely related to an Indian and an Iranian isolate, respectively. As far as we know, PAMV in this study is the first report in Bangladesh. These findings will provide a great scope for appropriate virus control strategies to virus free potato production in Bangladesh.
... Their wide use stems from the ease of getting new sequence data for a set of clearly orthologous genes, which can be readily compared to an increasing amount of available mitogenomic sequences. Mitogenomes have been used many times to solve controversial systematic relationships at inter-ordinal (Rota-Stabelli and Telford, 2008;Song et al., 2015;Rutschmann et al., 2017) or intra-ordinal (Bourguignon et al., 2018;Li et al., 2017;Timmermans et al., 2014) taxonomic levels. ...
Phasmatodea species diversity lies almost entirely within its suborder Euphasmatodea, which exhibits a pantropical distribution and is considered to derive from a recent and rapid evolutionary radiation. To shed light on Euphasmatodea origins and diversification, we assembled the mitogenomes of 17 species from transcriptomic sequencing data and analysed them along with 22 already available Phasmatodea mitogenomes and 33 mitogenomes representing most of the Polyneoptera lineages. Maximum Likelihood and Bayesian Inference approaches retrieved consistent topologies, both showing the widespread conflict between phylogenetic approaches and traditional systematics. We performed a divergence time analysis leveraging ten fossil specimens representative of most polyneopteran lineages: the time tree obtained supports an older radiation of the clade with respect to previous hypotheses. Euphasmatodea diversification is inferred to have started ~ 187 million years ago, suggesting that the Triassic-Jurassic mass extinction and the breakup of Pangea could have contributed to the process. We also investigated Euphasmatodea mitogenomes patterns of dN, dS and dN/dS ratio throughout our time-tree, trying to characterize the selective regime which may have shaped the clade evolution.
... In contrast, by employing different outgroup taxa (real or random, close or distant), the study yielded spurious roots in every case (Table 1). Even closely related outgroup taxa, such as Rosales, yielded topology alterations and weakly supported ingroup relationships, probably caused by a weak phylogenetic signal in the internal branches of Fabales, which are sensitive to the smallest changes (Graham et al. 1998;Graham et al. 2002;Rota-Stabelli and Telford 2008), or otherwise by the possibility of our level of gene and (or) taxon sampling not providing enough phylogenetic signal. ...
... In such cases neither sampling sister outgroups nor sampling more outgroup taxa will necessarily help in obtaining a robust tree. However, in the current study, exclusion of outgroup taxa with both ML and BEAST analyses presented a highly supported network (Table 1), and the same pattern was also shown by many previous studies (e.g., Graham et al. 1998;Rota-Stabelli and Telford 2008;Kodandaramaiah et al. 2010;Kirchberger et al. 2014). Here, the low support values were probably not caused by uncertain relationships (i.e., topology problem) within the order, because outgroup free analyses yielded very strong support and stable rooting (Graham et al. 1998). ...
Fabales is a cosmopolitan angiosperm order which consists of four families, Leguminosae (Fabaceae), Polygalaceae, Surianaceae and Quillajaceae. Despite the great interest in this group, a convincing phylogeny of the order is still not available. Therefore, the aim of the current study is to explicitly test for possible LBA problems within Fabales for the first time and determine whether low tree stemminess and unequal branch lengths could worsen this problem. Supermatrix analysis of Fabales was carried out using previously published plastid matK, trnL, rbcL and newly sequenced nuclear sqd1 regions for 678 taxa in total, including 43 outgroup taxa from families of Fabidae. We employed additional analyses, such as simulations, network analyses, sampling different outgroup taxa (random or real), removing fast evolving sites and fast evolving taxa and molecular clock rooting, to identify both long branch attraction (LBA) and/or rooting problems. These analyses clearly show that the Fabales phylogeny has been influenced by the sampling of outgroup taxa, but not LBA. However, network analyses show that even though it is weak, there is a consistent phylogenetic signal among the rapidly radiated Fabales families, which can be traced by further analyses. While, molecular clock rooting analysis yielded a (Leguminosae(Polygalaceae(Surianaceae+Quillajaceae))) topology with strong support for the first time here, supermatrix analyses yielded a ((Leguminosae+Polygalaceae)(Surianaceae+Quillajaceae)) with low-moderate support.
... Currently, a close relationship of Crustacea and Hexapoda (building the Tetraconata or Pancrustacea) and the Myriapoda being the sister group to the Tetraconata (a clade termed Mandibulata) is widely accepted (e.g., [5][6][7][8]). However, alternative views on their relationship have been postulated, including concepts such as Tracheata/Atelocerata (Myriapoda + Hexapoda) and Myriochelata/Paradoxopoda (Chelicerata + Myriapoda) (e.g., [9,10])). In particular, the internal phylogeny of the major taxa is far from clear. ...
Despite numerous approaches to the resolution of euarthropod phylogeny, mainly based on modern sequenceinformation and traditional external morphology, the resulting hypotheses are often contradictory and leave manyquestions about euarthropod evolution unanswered. The comparison of developmental and structural aspects ofthe nervous system has shown to be a valuable contribution to the assessment of current phylogenetichypotheses. One promising approach for the generation of new character sets is the morphology of transmittersystems and the discovery of individually identifiable neurons, which allow phylogenetic comparisons on the singlecell level. In this context, the serotonin transmitter system has been investigated to a considerable degree. Studiesto date have yielded important stimuli to our understanding of euarthropod relationships and the evolution of theirnervous systems. However, data on other transmitter systems remain fragmented, and their value with respect tophylogenetic questions remains speculative. The biogenic amine histamine is a promising transmitter; a substantialamount of data has been reported in the literature and the homology of some histaminergic neurons has beensuggested. Here, we present a comprehensive review of histaminergic neurons in the ventral nerve cord ofEuarthropoda. Using immunocytochemical labeling of histamine combined with confocal laser-scanningmicroscopy, we investigated the transmitter system in phylogenetically relevant taxa, such as Zygentoma,Remipedia, Diplopoda, and Arachnida. By reconstructing ground patterns, we evaluated the significance of thisspecific character set for euarthropod phylogeny. With this approach, we identified a set of neurons, which can beconsidered homologous within the respective major taxon. In conclusion, the histaminergic system contains usefulinformation for our understanding of euarthropod phylogeny, supporting the proposed clades Tetraconata andMandibulata. Furthermore, this character set has considerable potential to help resolve relationships within themajor clades at a deeper level of taxonomy, due to the considerable variability in neurite morphology.
... Homoplasy (i.e., convergence due to hidden substitutions) is the best studied cause of LBA, and has previously been acknowledged as a concern when inferring immune gene phylogenies (41). Fortunately, it can often be counteracted by breaking long branches with additional taxa (43)(44)(45), applying site-heterogeneous models of evolution (42,46), removing fast-evolving sites (47), and/or identifying the best outgroup (48)(49)(50)(51), in addition to using outgroupfree methods (41,(52)(53)(54)(55) to root the tree. Compositional heterogeneity, resulting from differing codon usage preferences among sequences under comparison can also lead to LBA through non-phylogenetic similarity between lineages (56,57), and can be remedied by applying time-heterogeneous models of evolution (58,59), or removing compositionally biased sites or sequences (56,57,60,61). ...
Interferons orchestrate host antiviral responses in jawed vertebrates. They are categorized into three classes; IFN1 and IFN3 are the primary antiviral cytokine lineages, while IFN2 responds to a broader variety of pathogens. The evolutionary relationships within and between these three classes have proven difficult to resolve. Here, we reassess interferon evolution, considering key phylogenetic pitfalls including taxon sampling, alignment quality, model adequacy, and outgroup choice. We reveal that cartilaginous fishes, and hence the jawed vertebrate ancestor, possess(ed) orthologs of all three interferon classes. We show that IFN3 groups sister to IFN1, resolve the origins of the human IFN3 lineages, and find that intronless IFN3s emerged at least three times. IFN2 genes are highly conserved, except for IFN-γ-rel, which we confirm resulted from a teleost-specific duplication. Our analyses show that IFN1 phylogeny is highly sensitive to phylogenetic error. By accounting for this, we describe a new backbone IFN1 phylogeny that implies several IFN1 genes existed in the jawed vertebrate ancestor. One of these is represented by the intronless IFN1s of tetrapods, including mammalian-like repertoires of reptile IFN1s and a subset of amphibian IFN1s, in addition to newly-identified intron-containing shark IFN1 genes. IFN-f, previously only found in teleosts, likely represents another ancestral jawed vertebrate IFN1 family member, suggesting the current classification of fish IFN1s into two groups based on the number of cysteines may need revision. The providence of the remaining fish IFN1s and the coelacanth IFN1s proved difficult to resolve, but they may also be ancestral jawed vertebrate IFN1 lineages. Finally, a large group of amphibian-specific IFN1s falls sister to all other IFN1s and was likely also present in the jawed vertebrate ancestor. Our results verify that intronless IFN1s have evolved multiple times in amphibians and indicate that no one-to-one orthology exists between mammal and reptile IFN1s. Our data also imply that diversification of the multiple IFN1s present in the jawed vertebrate ancestor has occurred through a rapid birth-death process, consistent with functional maintenance over a 450-million-year host-pathogen arms race. In summary, this study reveals a new model of interferon evolution important to our understanding of jawed vertebrate antiviral immunity.
