BACKGROUND
pseudoscorpions comprise an ancient order of arachnids, with fossils dating to the devonian  <cit> .
other orders of arachnids, such as spiders and scorpions, have unusual mitochondrial genomic features, including reduced trna genes and reversed patterns of nucleotide composition, when compared both with other chelicerates and with arthropods as a whole.
no mitochondrial genome from a pseudoscorpion has previously been published, so patterns of molecular evolution in pseudoscorpion mitochondrial genomes are completely unknown.
given the unusual patterns of molecular evolution found in other chelicerate mitochondrial genomes, we sought to determine whether pseudoscorpion mitochondrial genomes shared any of these unusual properties.
mitochondrial rna structures and evolution
transfer rnas function to add peptides to an amino acid chain as they pass through the ribosome, and hence are essential for protein synthesis.
their cloverleaf-shaped secondary structure is highly conserved across all domains of life, which suggests that little structural deviation is tolerated for this essential molecule.
in general, while metazoan mitochondria encode smaller trnas than their nuclear counterparts, they maintain sequence to encode a cloverleaf secondary structure.
however, some metazoans show inferred structural variation in trnas encoded by the mitochondrial genome.
metazoan mitochondrial genomes typically encode  <dig> trna genes, which are specific for the  <dig> essential amino acids, with alternative versions of trna-ser and trna-leu that possess alternate anticodons.
most metazoan mitochondrial genes for trna-ser lack the sequence to encode the dhu arm .
because metazoans share this feature, it has been inferred that the loss of the d-arm from the trna-ser gene occurred before the divergence of metazoans  <cit> .
some diverse metazoan lineages possess a few mitochondrial trna genes that lack the canonical cloverleaf structure, and instead are missing either the tΨc arm  or the d-arm.
these few lineages are widely diverged, such that the gene reduction must be independently evolved.
the first discovery of aberrant mitochondrial trna genes was from secernentean nematodes, in which all  <dig> mitochondrial trna genes lack sequence to encode cloverleaf trnas  <cit> .
some lineages of chelicerates have been found to possess transfer rna genes that code for trnas whose secondary structures are inferred to lack one arm of the canonical cloverleaf trna.
however, unlike in secernentean nematodes, chelicerates show variation among lineages as to whether a specific trna lacks an arm, and as to whether the missing arm is a t-arm or a d-arm  <cit> .
such aberrant trna genes have been found in spiders, acariform mites, vinegaroons, and scorpions .
opisthothelae spiders possess the most severely truncated trna genes yet found, and lack sequence to encode both a t-arm and the 3' aminoacyl acceptor stem  <cit> .
in contrast, the mitochondrial genomes that have been sequenced so far from parasitiform ticks and mites, mesothele spiders, amblypygids, sea spiders, horseshoe crabs, ricinuleids, solifuges, and harvestmen all contain typical trna genes.
mitochondrial genomes encode two ribosomal rna subunits that form the core of the mitochondrial ribosome complex.
within arthropods, there is great variation in the reported length of these sequences, with most variation occurring in the length of the large rrna subunit gene, often termed lsu rrna, l-rrna, or 16s.
in chelicerates, the reported lengths of the lsu rrna genes range from about  <dig> to  <dig> nucleotides .
the small ribosomal rna gene, often termed ssu rrna, s-rrna, or 12s, also varies in size , but proportionally less so than the lsu rrna gene.
although reported lengths of the mitochondrial ribosomal genes vary greatly, it is not possible to accurately infer the lengths of these genes without knowing the secondary structures that they encode.
this is because it is difficult to distinguish between intergenic sequence and the actual ends of the ribosomal genes.
hence, most reported lengths of the ribosomal genes actually report the length of the sequence between the genes that bound the ribosomal genes.
it is difficult to infer secondary structure without having a good structural model for comparison.
this task has been greatly aided by the publication of the crystal structure of a bacterial ribosome  <cit> .
this study also mapped onto the rrna secondary structure the points where the ribosomal rna makes contact with the trna as it passes through the ribosome  <cit> .
these contact sites are near the center of the ribosome, and due to their essential nature, should be conserved in all organisms.
gene rearrangements
the arrangement of the  <dig> protein-coding genes found in mitochondrial genomes is broadly conserved among the major animal phyla .
within chelicerata, the same mitochondrial gene arrangement is shared by taxa from at least five orders, including xiphosura, amblypygi, and some taxa from araneae, parasitiformes, and scorpiones  <cit> .
this gene arrangement has been inferred to be the ancestral arrangement, because it is shared among these diverse lineages.
this arrangement consists of  <dig> protein-coding genes and  <dig> trna genes encoded on the same strand.
because the majority of genes are encoded on this strand, it is referred to as the major strand, whereas the opposite strand is referred to as the minor strand.
in metazoans, trna genes are generally much more evolutionarily mobile than protein-coding genes  <cit> , and among chelicerate orders, they show varying degrees of rearrangement.
taxa from the chelicerate orders solifugae, thelyphonida, and ricinulei -- as well as buthidae scorpions, phalangiidae harvestmen, and opisthothele spiders -- differ in the location of some of their trna genes, while sharing identical protein-coding gene order.
in chelicerates, rearrangements of mitochondrial protein-coding genes have been reported only for some parasitiform ticks  <cit>  and a mite  <cit> , some sea spiders  <cit> , and all acariform mites  <cit> .
nucleotide bias
most metazoan mitochondrial genomes possess an overall cytosine and adenine  nucleotide bias on their major coding strand  <cit> .
this ca bias is thought to result from the asymmetrical way in which mitochondrial genomes replicate.
during mitochondrial dna replication in vertebrates, for example, the leading strand and lagging strand remain single-stranded for differing periods of time, leaving one strand more prone to mutations.
this creates a mutational bias in the occurrence of deaminations of cytosine and adenine  <cit> .
despite strand specific mutational biases, metazoan lineages have been found to vary in their nucleotide bias, such that some taxa possess mt genomes with a guanine and thymine  bias on their major strand.
in arthropods, this reversed bias has been suggested to result from an inversion of the origin of replication  <cit> , such that the opposite strand is now prone to deamination-induced mutational bias.
if this is the case, then we would expect that changes in nucleotide skew would be correlated with genome rearrangements that affect the orientation of the origin of replication.
pseudoscorpion relationships
in order to interpret the evolution of genomic features, it is necessary to know the phylogenetic relationships of the organisms whose genomes have been sequenced.
among chelicerate lineages, some groupings have been recovered rather consistently in phylogenetic analyses, but many relationships have not been firmly established.
the relationship of pseudoscorpions to the other chelicerates has not been well-established.
the chelicerate order pseudoscorpiones contains  <dig> families and almost  <dig> described species  <cit> .
some morphological analyses place pseudoscorpiones as sister group to the order solifugae  <cit> , as do some analyses of morphology combined with molecular sequence data  <cit> , although with low bootstrap support.
other combined analyses of morphology and molecular data place pseudoscorpions as sister to scorpions  <cit> .
in both phylogenomic analyses of many nuclear loci  <cit>  and analyses of ribosomal dna sequences  <cit> , the position of pseudoscorpions is essentially unresolved, with very low support.
in sum, there is conflict among different types of data and in some cases very low support for the phylogenetic affinities of pseudoscorpions.
this lack of consensus warrants the exploration of new data sources for phylogenetic analyses.
in this study, we sequenced the mitochondrial genomes of two widely divergent taxa of pseudoscorpions.
we explore patterns of molecular evolution of the genome, as well as chelicerate relationships inferred by mitogenomic data.
we find that all of the mitochondrial rna encoding genes are greatly reduced in size in pseudoscorpions, and that this reduction in size is accompanied by loss of helices from the trna and lsu rrna secondary structures.
we examine patterns of mitochondrial genome nucleotide skew for all chelicerates in a phylogenetic framework.
RESULTS
genome size and arrangement
both pseudoscorpion mitochondrial genomes are circular and encode the typical set of  <dig> mitochondrial genes.
the mt genome arrangements of both pseudoscorpions differ from the ancestral chelicerate genome arrangement .
the mt genome of pseudogarypus banksi   differs in the location of three of its  <dig> protein-coding genes  and the ssu rrna gene, relative to the ancestral arrangement.
additionally,  <dig> of the trna genes are in different locations , gln, his, pro, ser, and phe).
of these trna genes, those coding for trna-arg, trna-glu, and trna-gln are on the opposite strand as that in the ancestral condition.
we also found a large region  of repeated sequence located between the trna-leu and nd <dig> genes.
much of this region appears to consist of repeat units similar to the trna-lys gene, although this gene is not located in the adjacent region.
this duplicated region is responsible for a substantial increase in genome size compared with other chelicerates, which typically have genomes close to  <dig> kb.
the largest chelicerate mt genomes have been found in acariform mites in the family trombiculidae   <cit> , and the genome of pseudogarypus approaches this size at  <dig>  nts.
in contrast, the size of the mt genome of paratemnoides   is  <dig>  nts in length -- similar to the sizes of spider and mite mt genomes, but about  <dig> nt shorter than that of pseudogarypus.
the mt genome of paratemnoides is rearranged only with respect to six trna genes , gln or met, and tyr).
of these, the genes coding for trna-pro and trna-tyr are located on the strand opposite of that of the ancestral condition.
none of the gene boundaries or inversions of genes onto the opposite strand that differ from the ancestral arrangement are shared between these two species .
this indicates that translocation of the genes must have occurred independently in these lineages, after their divergence from an ancestral pseudoscorpion.
the typical model to explain how mitochondrial gene rearrangements occur in animals is via tandem duplication of a part of the genome followed by random deletion of genes  <cit> .
however, tandem duplication followed by random deletion cannot explain how genes come to be encoded on the opposite strand of a mitochondrial genome.
shao et al.
hypothesized that inter-mitochondrial dna recombination may explain how genes of chigger mites came to be encoded on the opposite mitochondrial strand  <cit> .
likewise, excision of a piece of the mitochondrial genome, followed by circularization, breakage of the circle, then recombination back into the original mitochondrial genome has been suggested to explain the current gene arrangement for the harvestman phalangium opilio  <cit> .
recombination could also explain the current gene arrangements found in both of the pseudoscorpion mt genomes in the present study.
although recombination has not been thought to be important in the evolution of vertebrate mitochondrial genomes, it appears that it must occur among at least some chelicerate lineages.
most chelicerate mitochondrial genomes maintain the same arrangement of protein-coding genes  <cit> .
however, all mitochondrial genomes of acariform mites possess rearranged genes, many with rearranged protein-coding genes  <cit> .
the pseudoscorpion pseudogarypus also possesses rearranged protein-coding genes.
it shares this feature with acariform mites, but not with all pseudoscorpions, as paratemnoides has the same protein-coding gene order as the ancestral chelicerate.
trna genes
all mt trna genes of paratemnoides lack sequence to encode a cloverleaf trna secondary structure.
instead,  <dig> of these genes are inferred to encode trnas that lack a t-arm , while the gene coding for trna-ser lacks the sequence to encode a d-arm.
in pseudogarypus, only  <dig> or  <dig> of the mt trna genes have the potential to form a cloverleaf trna.
it is possible that the trna-leu gene encodes a trna with a cloverleaf secondary structure, but if so, there are two mismatches in the acceptor stem, and a weak 2-bp t-arm stem.
alternatively, the trna-leu gene encodes a trna that lacks a t-arm, but has a perfectly paired acceptor stem.
both alternatives are illustrated in figure 2b.
if trna-leu lacks a t-arm, then a total of  <dig> trna genes are inferred to encode trnas that lack t-arms.
the other  <dig> mt trna genes are inferred to encode trnas that lack d-arms, including the gene coding for trna-ser .
although some arachnid lineages contain species whose mitochondria possess many trna genes without sequence to encode a cloverleaf-shaped trna, the pseudoscorpions in this study show some of the most widespread losses of trna arms yet documented among metazoans.
the only other chelicerate lineages to show this extent of loss from their trna genes are acariform mites.
some acariform mites have been found to possess mitochondrial genomes in which all  <dig> of their trna genes are inferred to encode trnas that lack either a d-arm or a t-arm  <cit> .
paratemnoides joins the short list of taxa with mt genome-wide losses of canonical trna genes.
in addition to some chelicerates and secernentean nematodes, gall midge insects have also been found to have severely truncated trna genes  <cit> , similar to those of opisthothele spiders.
so far, genome-wide losses of t- or d-arm-encoding mitochondrial trna sequences have been restricted to the ecdysozoa.
within spiders, there is variation among taxa in the identity and number of trna genes that lack t-arms.
when this variation was traced onto a phylogenetic tree, it was found that once a trna gene loses sequence to encode a d- or t-arm, sequence to encode these arms is not regained  <cit> .
we find variation among these two pseudoscorpion lineages in whether the d- or t-arm sequence has been lost from a given trna gene.
these two pseudoscorpions show shared losses of t-arms from  <dig> or  <dig> trna genes that are specific for asp, glu, gln, gly, his, leu, pro, ser, thr, trp, tyr, val, and likely leu.
however, in pseudogarypus the trna genes specific for ala, asn, cys, ile, and phe all lack d-arms.
the loss of d-arm sequence from these  <dig> trna genes must have occurred after the divergence of the major pseudoscorpion lineages, because the trna homologues in paratemnoides possess d-arm sequence, but lack t-arm sequence.
the trna-arg, trna-lys, trna-met, and perhaps the trna-leu genes, code for cloverleaf-shaped trnas in pseudogarypus, therefore we can infer that the ancestral pseudoscorpion also possessed full-length trna genes for these trnas.
in sum, based upon these two genomes from the deeply diverged pseudoscorpion lineages feaelloidea and cheliferoidea, we can infer that the common ancestor of extant pseudoscorpions had likely lost sequences to encode canonical secondary structures for multiple different mt trnas.
it is not clear why some lineages of chelicerates have lost sequence to encode either the d-arm or t-arm from their mt trna genes.
in general, chelicerates that lack canonical mt trna genes also tend to have rearranged mt genomes.
for example, all opisthothele spiders and acariform mites have mt trna genes that are rearranged with respect to the ancestral chelicerate, and all possess many mt trna genes that lack the ability to encode cloverleaf trnas.
however, while this trend is also true within pseudoscorpions, it does not explain the variation in trna gene reduction.
the more rearranged mt genome of pseudogarypus has fewer non-canonical trna genes , whereas paratemnoides exhibits less rearrangement, yet all its trna genes lack sequence to encode cloverleaf trnas.
rrna genes
the ribosomal rna genes of both pseudoscorpions are extremely short for chelicerates and other arthropods.
pseudogarypus has a smaller mt lsu rrna than paratemnoides .
this is one of the shortest mt lsu rrna lengths reported for any chelicerate; only some acariform mites and some spiders possess equally short lsu rrna genes.
typically, chelicerates have lsu rrna genes of  <dig> to  <dig> nts.
the three orders of chelicerates that have historically been inferred as most closely related to pseudoscorpions  are harvestmen, solifuges, and scorpions.
the mitochondrial genomes of representative taxa from these lineages have lsu rrna genes ranging from about  <dig> nts  to  <dig> nts .
decreases in size of the lsu rrna genes could be due to reductions spread throughout the gene, or reductions concentrated in specific areas, such as the ends of the gene.
reductions that occurred throughout the gene would result in decreases of the sizes of many to most of the helices in the secondary and tertiary structures of the rrna.
reductions concentrated in specific areas could cause losses of entire helices, similar to the inferred losses of helices that have occurred in pseudoscorpion mt trnas.
we inferred the secondary structures of both pseudoscorpion lsu rrnas, to determine where within the molecule the reductions had occurred.
these structures are depicted in figures 3a and 3b.
to assess the location and extent of reductions, we compared the secondary structures we inferred for the lsu rrna genes from both pseudoscorpions to that of the opilionid phalangium opilio  <cit> .
we found that both of the pseudoscorpions have lost helices d14-d <dig> , which should be located between helices d <dig> and d <dig> .
this two-part d14-d <dig> helix is typically present in the arthropod lsu rrnas secondary structures that have been inferred  <cit> .
within chelicerates, helices d14-d <dig> are present in the amblypygid damon diadema  <cit>  and in the harvestman phalangium opilio  <cit> .
these helices are missing in some of the acariform mites that have been analyzed , but appear to be present in other acariformes .
the crystal structure of the bacterial ribosome of thermus thermophilus has been used to infer the contact sites between the rna core of the ribosome and trnas during translation  <cit> .
based on our comparison of inferred lsu rrna secondary structures of pseudoscorpions to the structure of the lsu rrna of t. thermophilus, the nucleotides at the end of helix d <dig> should make contact with the d and t loops of the a-site trna within the ribosome during translation.
the d14-d <dig> helices are lacking in both pseudoscorpion lsu rrnas, suggesting either that this contact point has been lost and is not essential for protein synthesis, or that this trna-ribosome contact site has moved to another location.
the g <dig> helix of the lsu rrna is also not present in either pseudoscorpion .
this helix should be encoded immediately downstream of the g <dig> helix, but instead, only a short g <dig> helix is present.
the g <dig> helix  is located at the core of the bacterial ribosome, and makes contact with the d and t loops of the e-site trna as the trna exits the ribosome during translation  <cit> .
both pseudoscorpions lack a large region of the 5'end of the lsu rrna gene, which typically codes for a series of helices, referred to as domain i in the bacterial lsu rrna, or following the notation in  <cit> , the b region.
the secondary structure for this region was difficult to infer accurately, so we have less confidence in the accuracy of our reconstruction.
however, it appears that helices b <dig>  b <dig>  and b <dig> have all been lost relative to those of phalangium.
nucleotides in the b <dig> helix  base pair with the e-site trna as the trna exits the ribosome  <cit> .
two other regions of helices have been lost in one or both pseudoscorpions lsu rrnas, but all of the other trna-rrna contact sites appear to be present in both pseudoscorpions.
both pseudoscorpions lack the d <dig> helix, which should be located immediately adjacent to the d <dig> helix, or it may instead be very reduced compared to that of phalangium.
the lsu rrna of pseudogarypus lacks helices e1-e <dig> that are present in paratemnoides.
this helix is present in harvestmen  <cit> , and in amblypygids  <cit> .
in summary, we find that the reduction in length of the lsu rrna gene was accompanied by the loss of some helices from the secondary structure of the lsu rrna.
both pseudoscorpions share the losses of the same  <dig> helices, at least two of which appear to be rna-rna contact points within the ribosome.
we infer that the loss of these helices must have occurred after the divergence of the pseudoscorpion ancestor from harvestmen, as phalangium opilio possesses these helices.
the lengths of the small ribosomal rna genes are also reduced in pseudoscorpions, although proportionally less than the lsu rrna genes.
the absolute length of these genes in chelicerates can be more difficult to determine than that of the lsu rrna gene, because the 5' end of the ssu rrna gene typically abuts the non-coding region , which is poorly conserved in chelicerates.
additionally, while the 5' end of the ssu rrna is structurally fairly conserved, its sequence is not conserved.
therefore, only approximations of gene length are possible when we have only dna sequence data as a guide.
pseudogarypus has a smaller mt ssu rrna than paratemnoides .
these are somewhat shorter lengths than the mt ssu rrna genes of harvestmen, solifuges, and scorpions.
the mt ssu rrna genes in those taxa range from  <dig> nts in solifuges  to  <dig> nts in harvestmen  to about  <dig> nts in scorpions .
during protein synthesis, the ssu rrna region of the ribosome makes contact primarily with the anticodon region of the trna, while the lsu rrna has contact sites with the t-arm and with the d-arm of the trna .
therefore, if the trnas of pseudoscorpions are structurally coevolving with the ribosome that they interact with, we may predict that we would see length differences primarily in the lsu of the ribosome, but not necessarily in the ssu of the ribosome.
additionally, we would predict that the length differences would primarily be concentrated in the rrna-trna contact sites of the lsu of the ribosome.
it has previously been shown that the substitution rate for the nucleotide sites in the lsu rrna gene scale with their distance from the center of the ribosome, across all domains of life  <cit> .
this finding corroborates how important the core of the ribosome is for all organisms.
the loss of trna-ribosome contact sites in pseudoscorpion lsu rrna suggests that pseudoscorpion mt ribosomes may have evolved some remarkable changes in their structure and interactions with their trnas.
we have previously suggested that shortened ribosomes are correlated with shortened trna genes in chelicerates  <cit> .
the finding of shortened trna and rrna genes in pseudoscorpions provides an additional example of such a co-occurrence.
the co-occurrence of short rna-encoding genes may be due to pressures to decrease genome size overall, or due to compensatory evolution of the trnas with the ribosome with which they interact.
if trna-ribosome contact sites were lost or mutated in the ribosome, it would have allowed the trna genes to accrue mutations at these contact sites.
non-functional sites could be deleted from the trna genes via random genetic drift.
alternatively, if there is a replicative advantage to having a small genome, then selection could act to eliminate non-essential regions of the genome.
however, the compact trna and lsu rrna genes of pseudogarypus are not mirrored by a compact genome.
its mt genome possesses an apparently non-coding region that increases the size of the genome substantially over that of paratemnoides.
it is plausible that this non-coding region is due to a relatively recent insertion, and that selection for small genome size has not occurred long enough for us to see the evolutionary reduction in, or loss of, this insert.
alternatively, it is possible that the insert is more ancient, and that selection has acted to a greater degree to eliminate rna helices in the ribosome and trnas in a concerted manner.
our findings of losses of trna-rrna contact sites in both the trnas and the lsu rrna suggest that natural selection has acted such that these structures have coevolved to maintain function during protein synthesis.
phylogenetic analyses
the data set used for phylogenetic analyses consisted of  <dig> amino acids, with about 73% of the initial alignment of  <dig> amino acids retained after gblocks trimming of the  <dig> protein-coding alignments.
the level of sequence conservation varied among genes.
the most conserved genes retained over 90% of their amino acids , many genes retained 60-76% of their amino acids , and the atp <dig>  nd <dig>  nd4l, and nd <dig> genes possessed the lowest levels of sequence conservation .
phylogenetic analyses of all  <dig> mitochondrial protein-coding gene sequences from a diverse group of chelicerates  yield phylogenetic trees that consistently recover the pseudoscorpions as a monophyletic group .
surprisingly, pseudoscorpions are found as sister group to acariform mites, with 100% bootstrap support.
the arachnid order acari is found to be paraphyletic, with one well-supported clade of acariformes and one clade of parasitiformes.
this result is in agreement with other recent analyses that have recovered acari as diphyletic  <cit> .
we evaluated the alternative hypothesis, that acari is a monophyletic group, but this hypothesis was rejected by the approximately unbiased  test , with a ln likelihood score of - <dig>  for the unconstrained tree, and a ln likelihood score of - <dig>  for the monophyletic acari topology.
the other orders for which we have data from multiple mitochondrial genomes also are recovered as monophyletic: the spiders , scorpions , sea spiders , and ticks and parasitic mites .
hence, except for acari, our analyses always recover all named orders of arachnids as monophyletic.
our analyses also always recover the subphylum chelicerata with high support.
in contrast, we do not find arachnida to be monophyletic, due to the placement of the xiphosurans  and pycnogonida  amongst the arachnids.
we examined the alternative hypothesis of arachnid monophyly, but this hypothesis was rejected by the au test .
we also did not find support for pseudoscorpiones as the sister lineage to solifugae, as the au test strongly rejected this hypothesis .
we found that the protein-coding genes of both pseudoscorpions and acariform mites are characterized by high numbers of substitutions, resulting in long branches in phylogenetic analyses.
additionally, we know that variation in amino acid skew is found among chelicerates  <cit> .
therefore, we undertook a series of analyses to determine whether the placement of these two lineages as sister groups could be caused by an artificial grouping due to saturation of the sequences or due to similarities in amino acid skew.
to determine whether long-branch-attraction due to sequence saturation could be causing acariformes to group with pseudoscorpiones, we first eliminated acariform taxa with particularly long branches from our analyses.
we found that this had no effect on the placement of pseudoscorpions as sister to acariform mites .
in addition to likelihood analyses, we also undertook a series of bayesian analyses, using the same models of evolution as for likelihood.
all bayesian analyses recovered acariformes as the sister clade to pseudoscorpiones with high posterior probabilities.
we also recovered the sister-group relationship of acariformes with pseudoscorpiones in all  <dig> chains we ran with phylobayes using a cat site-heterogeneous mixture model.
in  <dig> of these chains, pycnogonids were recovered as the sister group to other chelicerates, whereas in  <dig> analyses they placed as derived within the arachnids.
in no analysis did we recover a monophyletic arachnida, as horseshoe crabs always were recovered as the sister lineage to solifuges .
coding mitochondrial nucleotides as either purines or pyrimidines  has been shown to recover deep-level relationships and to increase phylogenetic signal  <cit> .
we implemented ry recoding at 3rd codon positions only and at 1st and 3rd codon positions, and in both cases we recovered acariformes as the sister clade to pseudoscorpiones with 92% and 70% bootstrap support, respectively .
we found 62% bootstrap support for this grouping when we implemented a variation of ry recoding termed the neutral transitions excluded  method  <cit> .
it was striking that both acariformes and pseudoscorpiones show long branches on the amino acid phylogenetic trees.
this indicates that a large number of amino acid substitutions have occurred within these lineages.
to reduce the possibility that amino acids are saturated and causing long-branch-attraction artifacts, we recoded amino acids into  <dig> physiochemical functional groups.
we have previously found this method successful at recovering some nodes among chelicerate lineages  <cit> .
the resultant phylogenetic tree  still recovered acariformes and pseudoscorpiones as sister lineages with 100% bootstrap support.
the mitochondrial genome comprises only a portion of an organism's overall genetic makeup, and some researchers advocate using a combination of both organelle and nuclear loci when making phylogenetic inferences .
when using only a region of an organism's genetic makeup to infer its evolutionary history, several potential problems could exist.
the genetic marker may show a pattern of retention of an ancestral polymorphism if it is used to infer recent divergences, and therefore may not accurately reflect species divergence.
however, incomplete sorting of ancestral polymorphisms should not be a problem when making phylogenetic inferences among ancient lineages, such as among chelicerates.
genetic markers for inferring ancient divergences may be problematic if the sequences are so diverged that they are saturated, or alternatively, if mutational bias or natural selection has influenced sequence composition.
if any of these occur, it may lead to incongruence among different data sets, and to incorrect phylogenetic hypotheses.
although mtdna has generally been viewed as evolving neutrally, and therefore not likely to cause incorrect phylogenetic inferences due to selection, pronounced convergent selection has been found to influence the evolution of some mitochondrial genomes  <cit> .
base composition and nucleotide bias
the nucleotide composition of both pseudoscorpion mt genomes shows an overall at bias.
the mt genome composition of the major coding strand of pseudogarypus possesses an at frequency of  <dig> %, while that of paratemnoides is  <dig> %.
both mt genomes also show cg nucleotide skews on their major coding strands.
the overall cg skews for each of the major coding strands of the mitochondrial genomes are  <dig>  for paratemnoides and  <dig>  for pseudogarypus.
this is almost identical to the cg skews for all  <dig> of the protein-coding genes, which showed a cg skew of  <dig>  in paratemnoides, and  <dig>  for pseudogarypus.
the cg and at skews of each of the protein-coding genes, linearly arranged along the lengths of their genomes, is graphically depicted in figure  <dig>  third-codon positions tend to show a greater skew than either first or second positions , with an average cg skew of  <dig>  for paratemnoides and  <dig>  for pseudogarypus.
however, there is gene-by-gene variation in cg skew for each codon position .
distribution and evolution of nucleotide bias among chelicerates
a ca bias on the major strand of the mt genome is typical of many chelicerates, and of arthropods in general.
the amount of variation in nucleotide skew that has been found within chelicerata is among the greatest in any arthropod lineages.
some distantly related orders of arachnids -- such as spiders, scorpions, and some acariform mites -- possess mt genomes with a pronounced gt bias e.g.
<cit> .
however, many chelicerate lineages -- including xiphosurans, amblypygids, vinegaroons, and camel spiders -- possess a ca nucleotide bias on their major coding strand  <cit> .
within the chelicerate group pycnogonida , there exists wide variation in mt genome nucleotide skew, ranging from a pronounced gt bias to a ca bias  <cit> .
to better understand the distribution of nucleotide skew, we plotted its distribution onto a phylogenetic tree.
to more fully comprehend the nuances in nucleotide skew among different protein-coding genes, we examined skew separately for each of the  <dig> genes, and at each of the three codon positions.
because this is an immense amount of information, we present a visual overview of the skew distribution for each codon position and for each gene in figure  <dig>  because gene order varies among the different chelicerate taxa, the genes are arranged in alphabetical order, to allow gene-by-gene comparisons between taxa.
additional file  <dig> provides the data that was used to create these graphics, and the protein-coding gene arrangement found in these taxa.
we find that skew varies dramatically among chelicerate taxa.
some taxa show a clear ca bias  for all of their protein-coding genes located on the major strand.
these include the taxa walchia and pseudocellus from the divergent acariformes and ricinulei lineages.
other taxa have a strong gt bias  on their major coding strand, including all scorpions and all true  spiders.
most taxa, including both pseudoscorpions, exhibit a ca bias at their 1st and 3rd codon positions, but a ct bias at 2nd positions.
some taxa show little bias in their nucleotide composition at 3rd codon positions .
among many chelicerate lineages, there appears to be a seemingly random phylogenetic distribution of nucleotide skew.
the pycnogonida display everything ranging from a strong ca bias to a marked gt bias to an almost non-biased nucleotide distribution.
this degree of variation exists even within a single genus, with one species of nymphon possessing a strong ca bias and another a strong gt bias.
acariformes also show a range of skew values, from ca-biased to gt-biased to very little nucleotide bias.
in contrast, skew seems to be conserved in some chelicerate lineages.
a gt bias apparently arose after the divergence of true spiders from their common ancestor with mesothele spiders, and the opisthothele lineage has remained gt-biased since then.
likewise, all scorpions sequenced so far exhibit a gt bias, suggesting that this trait was inherited from the common ancestor of scorpions, and retained throughout scorpion's evolutionary history.
these patterns of skew distribution do not seem to coincide with gene rearrangements .
it has been suggested that inversions of the origin of replication could have caused changes in mutational biases on the major strand from ca to gt in multiple arthropods  <cit> .
if this is the case, then it may be expected that genomes prone to rearrangements are also the ones that tend to have major coding strands that are no longer ca-biased.
additionally, if changes in nucleotide skew on the major strand are due to inversion of the control region or origin of replication onto the minor strand, then recombination must have occurred.
given the high degree of variation in nucleotide skew in chelicerates, this would suggest that recombination has occurred fairly frequently within chelicerate mitochondrial genomes.
it is not known with certainty where the origin of replication is located within chelicerate mitochondrial genomes, or even whether there are multiple origins.
the origin of replication was determined for multiple species of insects, and found to differ in location between holometabolous and hemimetabolous insects  <cit> .
additional studies such as these are needed in chelicerates in order to understand how the origin of replication influences the nucleotide biases of the mt genome.
it has previously been found that bacteria show a mutational bias toward at  <cit> .
it is argued that variation in at nucleotide content found among bacterial genomes is best explained either by selection acting on the probability of fixation of mutations, or by selection favoring biased gene conversion  <cit> .
mitochondria are derived from bacteria, so it may not be surprising that most mitochondrial genomes show a similar at bias.
likewise, the variation in nucleotide content found among chelicerate mitochondrial genomes on the major coding strand either must be due to natural selection affecting which mutations becomes substituted, or must reflect neutral substitutions governed by mutational bias.
previous reports have assumed that the variation in nucleotide skew found among chelicerates is due to changes in the mutational bias within the mitochondrial genome  <cit> .
however, it is also plausible that selection has helped to shape nucleotide use in genomes that do not have a ca skew.
a phylogenetic pattern of seemingly random distribution of a trait is consistent with a pattern selection may leave if it has acted upon that trait.
the evolutionary reversal of a ca bias to a gt bias found in some lineages of chelicerates may be due to selection, rather than to neutral processes, although it is not clear what the selective force may be.
phylogenetic implications
it is somewhat surprising that all our phylogenetic analyses of mt protein-coding genes are in agreement that pseudoscorpions and acariform mites are sister lineages.
previous analyses using nuclear-encoded genes have found either conflicting placements of pseudoscorpions depending upon the method of analysis, or less than 50% bootstrap support for the placement of pseudoscorpions  <cit> .
while a plethora of different phylogenetic hypotheses for the relationships of pseudoscorpions have been proposed by previous workers, morphological hypotheses have tended to place pseudoscorpions as most closely allied to solifuges, scorpions, and harvestmen.
no phylogenetic hypothesis proposed thus far has had a high level of assessable, statistical support.
however, a quandary exists in how to interpret our phylogenetic data, as our results would require independent origins of some morphological traits that may be expected not exhibit homoplasy.
the structure of sperm and male genitalia suggests that pseudoscorpiones are not closely related to solifugae  <cit> , but instead, the similarities of sperm structures in solifugae suggest that they are the sister group to acariformes  <cit> .
recent analyses of nuclear rrna sequences also support a sister-group relationship of solifugae with acariformes  <cit> ).
these authors also discuss several morphological synapomorphies that solifugae shares with acariformes.
we do not recover such a grouping with our mitochondrial data, and instead repeatedly find strong support for an acariformes + pseudoscorpiones clade, as well as a distantly related xiphosura + solifugae clade.
in light of the well-supported relationship between pseudoscorpions and acariformes, we are led to ask whether any morphological characters might also support this surprising relationship.
both pseudoscorpions and mites possess trachea, but it is known that other chelicerate lineages, such as opiliones, also possess trachea.
in fact, there is some historical precedent for grouping the tracheate arachnids, but this grouping has been largely dismissed by arachnologists because trachea are known to have arisen independently within some arthropod lineages.
dunlop and alberti  <cit>  summarized the similarities of the parasitiform and acariform lineages with other arachnids.
they describe two features that are shared among these lineages and pseudoscorpions.
these are the presence of a ventrally moving finger on the chelicera, and the presence of an anterior projection termed the epistomal plate, which possesses flap-like lips.
however, these features are also shared with solifugae, a group that we recover as most closely related to horseshoe crabs.
there are features at the molecular level that are shared by acariformes and pseudoscorpiones.
intriguingly, the mt genomes of acariform mites also exhibit widespread loss of arms from their trna genes.
in fact, no acariform mites or pseudoscorpions so far sequenced possess a complete set of "typical" trna genes, but instead some to all of their trna genes do not encode either d-arm or t-arm sequences.
as discussed previously, these taxa vary as to which trnas are missing an arm, and whether it is a t-arm or d-arm.
therefore, it is not likely that acariform mites and pseudoscorpions share the loss of a specific trna helix as a synapomorphy.
instead, it is more likely that they share the propensity to lose helices from their trna genes.
both pseudoscorpions and acariforms have extremely short ribosomal rna genes.
we have shown that losses of helices of specific regions of the lsu rrna are shared by both pseudoscorpions, and therefore these losses likely pre-date the loss of sequence to encode cloverleaf shaped trnas.
further analyses of additional pseudoscorpion and acariform mite rrna secondary structures will allow insight into whether these lineages share the loss of helices that may be involved in trna d- or t-loop contact with the ribosome.
acariform mites and pseudoscorpions also exhibit extensive gene rearrangements.
however, these taxa do not share the same gene arrangement, and even the two pseudoscorpions differ in their genome organization.
to date, the only other chelicerates that have been found to have genome rearrangements of protein-coding genes are some parasitiformes, and pycnogonids in the family nymphonidae.
intriguingly, these orders were recovered as a monophyletic group in our phylogenetic analyses .
rate of molecular evolution
the pseudoscorpion amino acid sequences are on long branches on our phylogenetic trees.
because branch length is proportional to the number of substitutions, it indicates that many substitutions separate pseudogarypus from paratemnoides, and from their most recent common ancestor with other chelicerates.
these branches are longer than those found among any other chelicerate lineage, except for acariformes .
this indicates either that pseudoscorpions and acariformes are more ancient lineages than other chelicerate lineages, or that they have elevated rates of sequence evolution.
these two alternate scenarios are difficult to tease apart.
fossil pseudoscorpions dated to about  <dig> million years old have been found in devonian deposits  <cit> .
even older acariform mite, opilionid, and scorpion fossils have been found, and are dated to 410- <dig> mya .
therefore, fossil data alone does not allow us to infer that pseudoscorpions have accumulated more mutations than scorpions and spiders simply because they are older.
the lack of an older pseudoscorpion fossil does not necessarily indicate that the lineage is not older, as it is possible that older fossils remain to be discovered.
pseudoscorpion mt genomes show some gene rearrangements, including rearranged protein-coding genes in pseudogarypus.
some studies have linked the degree of gene rearrangements with the rate of molecular evolution  <cit> .
the degree of mitochondrial protein-coding gene rearrangements and the rate of evolution may indeed be somewhat interrelated in chelicerates.
the acariform mites, pycnogonids in the family nymphonidae, and pseudoscorpions all have protein-coding genes that are rearranged from the ancestral condition, and all show many amino acid substitutions, i.e.
long branches, on the phylogenetic trees we reconstructed, consistent with elevated rates of substitution.
CONCLUSIONS
we find that all of the rna-encoding genes in pseudoscorpion mitochondrial genomes are greatly reduced in size, and that this size reduction coincides with the loss of helices from trna and lsu rrna secondary structures.
we infer that some of the helices that have been lost in the lsu rrna are in regions that would normally contact the missing trna helices during protein-synthesis, suggesting coevolution of trna and rrna secondary structures.
we find wide variation in nucleotide skew in all mitochondrial protein-coding genes among taxa within chelicerates and conclude that the skew cannot be predicted at the deepest phylogenetic levels.
we also find that there have been rearrangements of genes within the mt genomes of pseudoscorpions.
however, these rearrangements appear not to have affected the distribution of nucleotide skew in the genome, as would be predicted if rearrangements influenced the orientation of the origin of replication.
our phylogenetic analyses unfailingly place pseudoscorpions as the sister lineage to acariformes, and not to lineages with which they apparently share more anatomical features.
similarities due to shared nucleotide or amino acid skew are likely not responsible for incorrectly placing pseudoscorpiones with acariformes, as these lineages do not share the same patterns of nucleotide skew.
indeed, nucleotide skew appears to have little effect on phylogeny reconstruction using amino acids, as lineages with reversed skew are scattered across our phylogenetic trees.
we find several morphological features at the molecular level that pseudoscorpiones do share with acariformes.
these include  the propensity for the evolutionary loss of sequence to encode d- or t-arms from trna genes,  a propensity for genome rearrangements, and  reduction in size of rrna genes.
further sequencing of pseudoscorpion and acariform mitochondrial genomes and analyses of their trna and rrna secondary structures will allow a more complete understanding of the degree to which the shared genomic changes they have undergone may be due to shared ancestry or to convergent evolution.

 pseudoscorpions comprise an ancient order of arachnids, with fossils dating to the devonian. other orders of arachnids, such as spiders and scorpions, have unusual mitochondrial genomic features, including reduced trna genes and reversed patterns of nucleotide composition, when compared both with other chelicerates and with arthropods as a whole. no mitochondrial genome from a pseudoscorpion has previously been published, so patterns of molecular evolution in pseudoscorpion mitochondrial genomes are completely unknown. given the unusual patterns of molecular evolution found in other chelicerate mitochondrial genomes, we sought to determine whether pseudoscorpion mitochondrial genomes shared any of these unusual properties. mitochondrial rna structures and evolution transfer rnas function to add peptides to an amino acid chain as they pass through the ribosome, and hence are essential for protein synthesis. their cloverleaf-shaped secondary structure is highly conserved across all domains of life, which suggests that little structural deviation is tolerated for this essential molecule. in general, while metazoan mitochondria encode smaller trnas than their nuclear counterparts, they maintain sequence to encode a cloverleaf secondary structure. however, some metazoans show inferred structural variation in trnas encoded by the mitochondrial genome. metazoan mitochondrial genomes typically encode trna genes, which are specific for the essential amino acids, with alternative versions of trna-ser and trna-leu that possess alternate anticodons. most metazoan mitochondrial genes for trna-ser lack the sequence to encode the dhu arm. because metazoans share this feature, it has been inferred that the loss of the d-arm from the trna-ser gene occurred before the divergence of metazoans. some diverse metazoan lineages possess a few mitochondrial trna genes that lack the canonical cloverleaf structure, and instead are missing either the tΨc arm or the d-arm. these few lineages are widely diverged, such that the gene reduction must be independently evolved. the first discovery of aberrant mitochondrial trna genes was from secernentean nematodes, in which all mitochondrial trna genes lack sequence to encode cloverleaf trnas. some lineages of chelicerates have been found to possess transfer rna genes that code for trnas whose secondary structures are inferred to lack one arm of the canonical cloverleaf trna. however, unlike in secernentean nematodes, chelicerates show variation among lineages as to whether a specific trna lacks an arm, and as to whether the missing arm is a t-arm or a d-arm. such aberrant trna genes have been found in spiders, acariform mites, vinegaroons, and scorpions. opisthothelae spiders possess the most severely truncated trna genes yet found, and lack sequence to encode both a t-arm and the 3' aminoacyl acceptor stem. in contrast, the mitochondrial genomes that have been sequenced so far from parasitiform ticks and mites, mesothele spiders, amblypygids, sea spiders, horseshoe crabs, ricinuleids, solifuges, and harvestmen all contain typical trna genes. mitochondrial genomes encode two ribosomal rna subunits that form the core of the mitochondrial ribosome complex. within arthropods, there is great variation in the reported length of these sequences, with most variation occurring in the length of the large rrna subunit gene, often termed lsu rrna, l-rrna, or 16s. in chelicerates, the reported lengths of the lsu rrna genes range from about to nucleotides. the small ribosomal rna gene, often termed ssu rrna, s-rrna, or 12s, also varies in size, but proportionally less so than the lsu rrna gene. although reported lengths of the mitochondrial ribosomal genes vary greatly, it is not possible to accurately infer the lengths of these genes without knowing the secondary structures that they encode. this is because it is difficult to distinguish between intergenic sequence and the actual ends of the ribosomal genes. hence, most reported lengths of the ribosomal genes actually report the length of the sequence between the genes that bound the ribosomal genes. it is difficult to infer secondary structure without having a good structural model for comparison. this task has been greatly aided by the publication of the crystal structure of a bacterial ribosome. this study also mapped onto the rrna secondary structure the points where the ribosomal rna makes contact with the trna as it passes through the ribosome. these contact sites are near the center of the ribosome, and due to their essential nature, should be conserved in all organisms. gene rearrangements the arrangement of the protein-coding genes found in mitochondrial genomes is broadly conserved among the major animal phyla. within chelicerata, the same mitochondrial gene arrangement is shared by taxa from at least five orders, including xiphosura, amblypygi, and some taxa from araneae, parasitiformes, and scorpiones. this gene arrangement has been inferred to be the ancestral arrangement, because it is shared among these diverse lineages. this arrangement consists of protein-coding genes and trna genes encoded on the same strand. because the majority of genes are encoded on this strand, it is referred to as the major strand, whereas the opposite strand is referred to as the minor strand. in metazoans, trna genes are generally much more evolutionarily mobile than protein-coding genes, and among chelicerate orders, they show varying degrees of rearrangement. taxa from the chelicerate orders solifugae, thelyphonida, and ricinulei -- as well as buthidae scorpions, phalangiidae harvestmen, and opisthothele spiders -- differ in the location of some of their trna genes, while sharing identical protein-coding gene order. in chelicerates, rearrangements of mitochondrial protein-coding genes have been reported only for some parasitiform ticks and a mite, some sea spiders, and all acariform mites. nucleotide bias most metazoan mitochondrial genomes possess an overall cytosine and adenine nucleotide bias on their major coding strand. this ca bias is thought to result from the asymmetrical way in which mitochondrial genomes replicate. during mitochondrial dna replication in vertebrates, for example, the leading strand and lagging strand remain single-stranded for differing periods of time, leaving one strand more prone to mutations. this creates a mutational bias in the occurrence of deaminations of cytosine and adenine. despite strand specific mutational biases, metazoan lineages have been found to vary in their nucleotide bias, such that some taxa possess mt genomes with a guanine and thymine bias on their major strand. in arthropods, this reversed bias has been suggested to result from an inversion of the origin of replication, such that the opposite strand is now prone to deamination-induced mutational bias. if this is the case, then we would expect that changes in nucleotide skew would be correlated with genome rearrangements that affect the orientation of the origin of replication. pseudoscorpion relationships in order to interpret the evolution of genomic features, it is necessary to know the phylogenetic relationships of the organisms whose genomes have been sequenced. among chelicerate lineages, some groupings have been recovered rather consistently in phylogenetic analyses, but many relationships have not been firmly established. the relationship of pseudoscorpions to the other chelicerates has not been well-established. the chelicerate order pseudoscorpiones contains families and almost described species. some morphological analyses place pseudoscorpiones as sister group to the order solifugae, as do some analyses of morphology combined with molecular sequence data, although with low bootstrap support. other combined analyses of morphology and molecular data place pseudoscorpions as sister to scorpions. in both phylogenomic analyses of many nuclear loci and analyses of ribosomal dna sequences, the position of pseudoscorpions is essentially unresolved, with very low support. in sum, there is conflict among different types of data and in some cases very low support for the phylogenetic affinities of pseudoscorpions. this lack of consensus warrants the exploration of new data sources for phylogenetic analyses. in this study, we sequenced the mitochondrial genomes of two widely divergent taxa of pseudoscorpions. we explore patterns of molecular evolution of the genome, as well as chelicerate relationships inferred by mitogenomic data. we find that all of the mitochondrial rna encoding genes are greatly reduced in size in pseudoscorpions, and that this reduction in size is accompanied by loss of helices from the trna and lsu rrna secondary structures. we examine patterns of mitochondrial genome nucleotide skew for all chelicerates in a phylogenetic framework.  genome size and arrangement both pseudoscorpion mitochondrial genomes are circular and encode the typical set of mitochondrial genes. the mt genome arrangements of both pseudoscorpions differ from the ancestral chelicerate genome arrangement. the mt genome of pseudogarypus banksi differs in the location of three of its protein-coding genes and the ssu rrna gene, relative to the ancestral arrangement. additionally, of the trna genes are in different locations, gln, his, pro, ser, and phe). of these trna genes, those coding for trna-arg, trna-glu, and trna-gln are on the opposite strand as that in the ancestral condition. we also found a large region of repeated sequence located between the trna-leu and nd genes. much of this region appears to consist of repeat units similar to the trna-lys gene, although this gene is not located in the adjacent region. this duplicated region is responsible for a substantial increase in genome size compared with other chelicerates, which typically have genomes close to kb. the largest chelicerate mt genomes have been found in acariform mites in the family trombiculidae, and the genome of pseudogarypus approaches this size at nts. in contrast, the size of the mt genome of paratemnoides is nts in length -- similar to the sizes of spider and mite mt genomes, but about nt shorter than that of pseudogarypus. the mt genome of paratemnoides is rearranged only with respect to six trna genes, gln or met, and tyr). of these, the genes coding for trna-pro and trna-tyr are located on the strand opposite of that of the ancestral condition. none of the gene boundaries or inversions of genes onto the opposite strand that differ from the ancestral arrangement are shared between these two species. this indicates that translocation of the genes must have occurred independently in these lineages, after their divergence from an ancestral pseudoscorpion. the typical model to explain how mitochondrial gene rearrangements occur in animals is via tandem duplication of a part of the genome followed by random deletion of genes. however, tandem duplication followed by random deletion cannot explain how genes come to be encoded on the opposite strand of a mitochondrial genome. shao et al. hypothesized that inter-mitochondrial dna recombination may explain how genes of chigger mites came to be encoded on the opposite mitochondrial strand. likewise, excision of a piece of the mitochondrial genome, followed by circularization, breakage of the circle, then recombination back into the original mitochondrial genome has been suggested to explain the current gene arrangement for the harvestman phalangium opilio. recombination could also explain the current gene arrangements found in both of the pseudoscorpion mt genomes in the present study. although recombination has not been thought to be important in the evolution of vertebrate mitochondrial genomes, it appears that it must occur among at least some chelicerate lineages. most chelicerate mitochondrial genomes maintain the same arrangement of protein-coding genes. however, all mitochondrial genomes of acariform mites possess rearranged genes, many with rearranged protein-coding genes. the pseudoscorpion pseudogarypus also possesses rearranged protein-coding genes. it shares this feature with acariform mites, but not with all pseudoscorpions, as paratemnoides has the same protein-coding gene order as the ancestral chelicerate. trna genes all mt trna genes of paratemnoides lack sequence to encode a cloverleaf trna secondary structure. instead, of these genes are inferred to encode trnas that lack a t-arm, while the gene coding for trna-ser lacks the sequence to encode a d-arm. in pseudogarypus, only or of the mt trna genes have the potential to form a cloverleaf trna. it is possible that the trna-leu gene encodes a trna with a cloverleaf secondary structure, but if so, there are two mismatches in the acceptor stem, and a weak 2-bp t-arm stem. alternatively, the trna-leu gene encodes a trna that lacks a t-arm, but has a perfectly paired acceptor stem. both alternatives are illustrated in figure 2b. if trna-leu lacks a t-arm, then a total of trna genes are inferred to encode trnas that lack t-arms. the other mt trna genes are inferred to encode trnas that lack d-arms, including the gene coding for trna-ser. although some arachnid lineages contain species whose mitochondria possess many trna genes without sequence to encode a cloverleaf-shaped trna, the pseudoscorpions in this study show some of the most widespread losses of trna arms yet documented among metazoans. the only other chelicerate lineages to show this extent of loss from their trna genes are acariform mites. some acariform mites have been found to possess mitochondrial genomes in which all of their trna genes are inferred to encode trnas that lack either a d-arm or a t-arm. paratemnoides joins the short list of taxa with mt genome-wide losses of canonical trna genes. in addition to some chelicerates and secernentean nematodes, gall midge insects have also been found to have severely truncated trna genes, similar to those of opisthothele spiders. so far, genome-wide losses of t- or d-arm-encoding mitochondrial trna sequences have been restricted to the ecdysozoa. within spiders, there is variation among taxa in the identity and number of trna genes that lack t-arms. when this variation was traced onto a phylogenetic tree, it was found that once a trna gene loses sequence to encode a d- or t-arm, sequence to encode these arms is not regained. we find variation among these two pseudoscorpion lineages in whether the d- or t-arm sequence has been lost from a given trna gene. these two pseudoscorpions show shared losses of t-arms from or trna genes that are specific for asp, glu, gln, gly, his, leu, pro, ser, thr, trp, tyr, val, and likely leu. however, in pseudogarypus the trna genes specific for ala, asn, cys, ile, and phe all lack d-arms. the loss of d-arm sequence from these trna genes must have occurred after the divergence of the major pseudoscorpion lineages, because the trna homologues in paratemnoides possess d-arm sequence, but lack t-arm sequence. the trna-arg, trna-lys, trna-met, and perhaps the trna-leu genes, code for cloverleaf-shaped trnas in pseudogarypus, therefore we can infer that the ancestral pseudoscorpion also possessed full-length trna genes for these trnas. in sum, based upon these two genomes from the deeply diverged pseudoscorpion lineages feaelloidea and cheliferoidea, we can infer that the common ancestor of extant pseudoscorpions had likely lost sequences to encode canonical secondary structures for multiple different mt trnas. it is not clear why some lineages of chelicerates have lost sequence to encode either the d-arm or t-arm from their mt trna genes. in general, chelicerates that lack canonical mt trna genes also tend to have rearranged mt genomes. for example, all opisthothele spiders and acariform mites have mt trna genes that are rearranged with respect to the ancestral chelicerate, and all possess many mt trna genes that lack the ability to encode cloverleaf trnas. however, while this trend is also true within pseudoscorpions, it does not explain the variation in trna gene reduction. the more rearranged mt genome of pseudogarypus has fewer non-canonical trna genes, whereas paratemnoides exhibits less rearrangement, yet all its trna genes lack sequence to encode cloverleaf trnas. rrna genes the ribosomal rna genes of both pseudoscorpions are extremely short for chelicerates and other arthropods. pseudogarypus has a smaller mt lsu rrna than paratemnoides. this is one of the shortest mt lsu rrna lengths reported for any chelicerate; only some acariform mites and some spiders possess equally short lsu rrna genes. typically, chelicerates have lsu rrna genes of to nts. the three orders of chelicerates that have historically been inferred as most closely related to pseudoscorpions are harvestmen, solifuges, and scorpions. the mitochondrial genomes of representative taxa from these lineages have lsu rrna genes ranging from about nts to nts. decreases in size of the lsu rrna genes could be due to reductions spread throughout the gene, or reductions concentrated in specific areas, such as the ends of the gene. reductions that occurred throughout the gene would result in decreases of the sizes of many to most of the helices in the secondary and tertiary structures of the rrna. reductions concentrated in specific areas could cause losses of entire helices, similar to the inferred losses of helices that have occurred in pseudoscorpion mt trnas. we inferred the secondary structures of both pseudoscorpion lsu rrnas, to determine where within the molecule the reductions had occurred. these structures are depicted in figures 3a and 3b. to assess the location and extent of reductions, we compared the secondary structures we inferred for the lsu rrna genes from both pseudoscorpions to that of the opilionid phalangium opilio. we found that both of the pseudoscorpions have lost helices d14-d, which should be located between helices d and d. this two-part d14-d helix is typically present in the arthropod lsu rrnas secondary structures that have been inferred. within chelicerates, helices d14-d are present in the amblypygid damon diadema and in the harvestman phalangium opilio. these helices are missing in some of the acariform mites that have been analyzed, but appear to be present in other acariformes. the crystal structure of the bacterial ribosome of thermus thermophilus has been used to infer the contact sites between the rna core of the ribosome and trnas during translation. based on our comparison of inferred lsu rrna secondary structures of pseudoscorpions to the structure of the lsu rrna of t. thermophilus, the nucleotides at the end of helix d should make contact with the d and t loops of the a-site trna within the ribosome during translation. the d14-d helices are lacking in both pseudoscorpion lsu rrnas, suggesting either that this contact point has been lost and is not essential for protein synthesis, or that this trna-ribosome contact site has moved to another location. the g helix of the lsu rrna is also not present in either pseudoscorpion. this helix should be encoded immediately downstream of the g helix, but instead, only a short g helix is present. the g helix is located at the core of the bacterial ribosome, and makes contact with the d and t loops of the e-site trna as the trna exits the ribosome during translation. both pseudoscorpions lack a large region of the 5'end of the lsu rrna gene, which typically codes for a series of helices, referred to as domain i in the bacterial lsu rrna, or following the notation in, the b region. the secondary structure for this region was difficult to infer accurately, so we have less confidence in the accuracy of our reconstruction. however, it appears that helices b b and b have all been lost relative to those of phalangium. nucleotides in the b helix base pair with the e-site trna as the trna exits the ribosome. two other regions of helices have been lost in one or both pseudoscorpions lsu rrnas, but all of the other trna-rrna contact sites appear to be present in both pseudoscorpions. both pseudoscorpions lack the d helix, which should be located immediately adjacent to the d helix, or it may instead be very reduced compared to that of phalangium. the lsu rrna of pseudogarypus lacks helices e1-e that are present in paratemnoides. this helix is present in harvestmen, and in amblypygids. in summary, we find that the reduction in length of the lsu rrna gene was accompanied by the loss of some helices from the secondary structure of the lsu rrna. both pseudoscorpions share the losses of the same helices, at least two of which appear to be rna-rna contact points within the ribosome. we infer that the loss of these helices must have occurred after the divergence of the pseudoscorpion ancestor from harvestmen, as phalangium opilio possesses these helices. the lengths of the small ribosomal rna genes are also reduced in pseudoscorpions, although proportionally less than the lsu rrna genes. the absolute length of these genes in chelicerates can be more difficult to determine than that of the lsu rrna gene, because the 5' end of the ssu rrna gene typically abuts the non-coding region, which is poorly conserved in chelicerates. additionally, while the 5' end of the ssu rrna is structurally fairly conserved, its sequence is not conserved. therefore, only approximations of gene length are possible when we have only dna sequence data as a guide. pseudogarypus has a smaller mt ssu rrna than paratemnoides. these are somewhat shorter lengths than the mt ssu rrna genes of harvestmen, solifuges, and scorpions. the mt ssu rrna genes in those taxa range from nts in solifuges to nts in harvestmen to about nts in scorpions. during protein synthesis, the ssu rrna region of the ribosome makes contact primarily with the anticodon region of the trna, while the lsu rrna has contact sites with the t-arm and with the d-arm of the trna. therefore, if the trnas of pseudoscorpions are structurally coevolving with the ribosome that they interact with, we may predict that we would see length differences primarily in the lsu of the ribosome, but not necessarily in the ssu of the ribosome. additionally, we would predict that the length differences would primarily be concentrated in the rrna-trna contact sites of the lsu of the ribosome. it has previously been shown that the substitution rate for the nucleotide sites in the lsu rrna gene scale with their distance from the center of the ribosome, across all domains of life. this finding corroborates how important the core of the ribosome is for all organisms. the loss of trna-ribosome contact sites in pseudoscorpion lsu rrna suggests that pseudoscorpion mt ribosomes may have evolved some remarkable changes in their structure and interactions with their trnas. we have previously suggested that shortened ribosomes are correlated with shortened trna genes in chelicerates. the finding of shortened trna and rrna genes in pseudoscorpions provides an additional example of such a co-occurrence. the co-occurrence of short rna-encoding genes may be due to pressures to decrease genome size overall, or due to compensatory evolution of the trnas with the ribosome with which they interact. if trna-ribosome contact sites were lost or mutated in the ribosome, it would have allowed the trna genes to accrue mutations at these contact sites. non-functional sites could be deleted from the trna genes via random genetic drift. alternatively, if there is a replicative advantage to having a small genome, then selection could act to eliminate non-essential regions of the genome. however, the compact trna and lsu rrna genes of pseudogarypus are not mirrored by a compact genome. its mt genome possesses an apparently non-coding region that increases the size of the genome substantially over that of paratemnoides. it is plausible that this non-coding region is due to a relatively recent insertion, and that selection for small genome size has not occurred long enough for us to see the evolutionary reduction in, or loss of, this insert. alternatively, it is possible that the insert is more ancient, and that selection has acted to a greater degree to eliminate rna helices in the ribosome and trnas in a concerted manner. our findings of losses of trna-rrna contact sites in both the trnas and the lsu rrna suggest that natural selection has acted such that these structures have coevolved to maintain function during protein synthesis. phylogenetic analyses the data set used for phylogenetic analyses consisted of amino acids, with about 73% of the initial alignment of amino acids retained after gblocks trimming of the protein-coding alignments. the level of sequence conservation varied among genes. the most conserved genes retained over 90% of their amino acids, many genes retained 60-76% of their amino acids, and the atp nd nd4l, and nd genes possessed the lowest levels of sequence conservation. phylogenetic analyses of all mitochondrial protein-coding gene sequences from a diverse group of chelicerates yield phylogenetic trees that consistently recover the pseudoscorpions as a monophyletic group. surprisingly, pseudoscorpions are found as sister group to acariform mites, with 100% bootstrap support. the arachnid order acari is found to be paraphyletic, with one well-supported clade of acariformes and one clade of parasitiformes. this result is in agreement with other recent analyses that have recovered acari as diphyletic. we evaluated the alternative hypothesis, that acari is a monophyletic group, but this hypothesis was rejected by the approximately unbiased test, with a ln likelihood score of - for the unconstrained tree, and a ln likelihood score of - for the monophyletic acari topology. the other orders for which we have data from multiple mitochondrial genomes also are recovered as monophyletic: the spiders, scorpions, sea spiders, and ticks and parasitic mites. hence, except for acari, our analyses always recover all named orders of arachnids as monophyletic. our analyses also always recover the subphylum chelicerata with high support. in contrast, we do not find arachnida to be monophyletic, due to the placement of the xiphosurans and pycnogonida amongst the arachnids. we examined the alternative hypothesis of arachnid monophyly, but this hypothesis was rejected by the au test. we also did not find support for pseudoscorpiones as the sister lineage to solifugae, as the au test strongly rejected this hypothesis. we found that the protein-coding genes of both pseudoscorpions and acariform mites are characterized by high numbers of substitutions, resulting in long branches in phylogenetic analyses. additionally, we know that variation in amino acid skew is found among chelicerates. therefore, we undertook a series of analyses to determine whether the placement of these two lineages as sister groups could be caused by an artificial grouping due to saturation of the sequences or due to similarities in amino acid skew. to determine whether long-branch-attraction due to sequence saturation could be causing acariformes to group with pseudoscorpiones, we first eliminated acariform taxa with particularly long branches from our analyses. we found that this had no effect on the placement of pseudoscorpions as sister to acariform mites. in addition to likelihood analyses, we also undertook a series of bayesian analyses, using the same models of evolution as for likelihood. all bayesian analyses recovered acariformes as the sister clade to pseudoscorpiones with high posterior probabilities. we also recovered the sister-group relationship of acariformes with pseudoscorpiones in all chains we ran with phylobayes using a cat site-heterogeneous mixture model. in of these chains, pycnogonids were recovered as the sister group to other chelicerates, whereas in analyses they placed as derived within the arachnids. in no analysis did we recover a monophyletic arachnida, as horseshoe crabs always were recovered as the sister lineage to solifuges. coding mitochondrial nucleotides as either purines or pyrimidines has been shown to recover deep-level relationships and to increase phylogenetic signal. we implemented ry recoding at 3rd codon positions only and at 1st and 3rd codon positions, and in both cases we recovered acariformes as the sister clade to pseudoscorpiones with 92% and 70% bootstrap support, respectively. we found 62% bootstrap support for this grouping when we implemented a variation of ry recoding termed the neutral transitions excluded method. it was striking that both acariformes and pseudoscorpiones show long branches on the amino acid phylogenetic trees. this indicates that a large number of amino acid substitutions have occurred within these lineages. to reduce the possibility that amino acids are saturated and causing long-branch-attraction artifacts, we recoded amino acids into physiochemical functional groups. we have previously found this method successful at recovering some nodes among chelicerate lineages. the resultant phylogenetic tree still recovered acariformes and pseudoscorpiones as sister lineages with 100% bootstrap support. the mitochondrial genome comprises only a portion of an organism's overall genetic makeup, and some researchers advocate using a combination of both organelle and nuclear loci when making phylogenetic inferences. when using only a region of an organism's genetic makeup to infer its evolutionary history, several potential problems could exist. the genetic marker may show a pattern of retention of an ancestral polymorphism if it is used to infer recent divergences, and therefore may not accurately reflect species divergence. however, incomplete sorting of ancestral polymorphisms should not be a problem when making phylogenetic inferences among ancient lineages, such as among chelicerates. genetic markers for inferring ancient divergences may be problematic if the sequences are so diverged that they are saturated, or alternatively, if mutational bias or natural selection has influenced sequence composition. if any of these occur, it may lead to incongruence among different data sets, and to incorrect phylogenetic hypotheses. although mtdna has generally been viewed as evolving neutrally, and therefore not likely to cause incorrect phylogenetic inferences due to selection, pronounced convergent selection has been found to influence the evolution of some mitochondrial genomes. base composition and nucleotide bias the nucleotide composition of both pseudoscorpion mt genomes shows an overall at bias. the mt genome composition of the major coding strand of pseudogarypus possesses an at frequency of %, while that of paratemnoides is %. both mt genomes also show cg nucleotide skews on their major coding strands. the overall cg skews for each of the major coding strands of the mitochondrial genomes are for paratemnoides and for pseudogarypus. this is almost identical to the cg skews for all of the protein-coding genes, which showed a cg skew of in paratemnoides, and for pseudogarypus. the cg and at skews of each of the protein-coding genes, linearly arranged along the lengths of their genomes, is graphically depicted in figure third-codon positions tend to show a greater skew than either first or second positions, with an average cg skew of for paratemnoides and for pseudogarypus. however, there is gene-by-gene variation in cg skew for each codon position. distribution and evolution of nucleotide bias among chelicerates a ca bias on the major strand of the mt genome is typical of many chelicerates, and of arthropods in general. the amount of variation in nucleotide skew that has been found within chelicerata is among the greatest in any arthropod lineages. some distantly related orders of arachnids -- such as spiders, scorpions, and some acariform mites -- possess mt genomes with a pronounced gt bias e.g.. however, many chelicerate lineages -- including xiphosurans, amblypygids, vinegaroons, and camel spiders -- possess a ca nucleotide bias on their major coding strand. within the chelicerate group pycnogonida, there exists wide variation in mt genome nucleotide skew, ranging from a pronounced gt bias to a ca bias. to better understand the distribution of nucleotide skew, we plotted its distribution onto a phylogenetic tree. to more fully comprehend the nuances in nucleotide skew among different protein-coding genes, we examined skew separately for each of the genes, and at each of the three codon positions. because this is an immense amount of information, we present a visual overview of the skew distribution for each codon position and for each gene in figure because gene order varies among the different chelicerate taxa, the genes are arranged in alphabetical order, to allow gene-by-gene comparisons between taxa. additional file provides the data that was used to create these graphics, and the protein-coding gene arrangement found in these taxa. we find that skew varies dramatically among chelicerate taxa. some taxa show a clear ca bias for all of their protein-coding genes located on the major strand. these include the taxa walchia and pseudocellus from the divergent acariformes and ricinulei lineages. other taxa have a strong gt bias on their major coding strand, including all scorpions and all true spiders. most taxa, including both pseudoscorpions, exhibit a ca bias at their 1st and 3rd codon positions, but a ct bias at 2nd positions. some taxa show little bias in their nucleotide composition at 3rd codon positions. among many chelicerate lineages, there appears to be a seemingly random phylogenetic distribution of nucleotide skew. the pycnogonida display everything ranging from a strong ca bias to a marked gt bias to an almost non-biased nucleotide distribution. this degree of variation exists even within a single genus, with one species of nymphon possessing a strong ca bias and another a strong gt bias. acariformes also show a range of skew values, from ca-biased to gt-biased to very little nucleotide bias. in contrast, skew seems to be conserved in some chelicerate lineages. a gt bias apparently arose after the divergence of true spiders from their common ancestor with mesothele spiders, and the opisthothele lineage has remained gt-biased since then. likewise, all scorpions sequenced so far exhibit a gt bias, suggesting that this trait was inherited from the common ancestor of scorpions, and retained throughout scorpion's evolutionary history. these patterns of skew distribution do not seem to coincide with gene rearrangements. it has been suggested that inversions of the origin of replication could have caused changes in mutational biases on the major strand from ca to gt in multiple arthropods. if this is the case, then it may be expected that genomes prone to rearrangements are also the ones that tend to have major coding strands that are no longer ca-biased. additionally, if changes in nucleotide skew on the major strand are due to inversion of the control region or origin of replication onto the minor strand, then recombination must have occurred. given the high degree of variation in nucleotide skew in chelicerates, this would suggest that recombination has occurred fairly frequently within chelicerate mitochondrial genomes. it is not known with certainty where the origin of replication is located within chelicerate mitochondrial genomes, or even whether there are multiple origins. the origin of replication was determined for multiple species of insects, and found to differ in location between holometabolous and hemimetabolous insects. additional studies such as these are needed in chelicerates in order to understand how the origin of replication influences the nucleotide biases of the mt genome. it has previously been found that bacteria show a mutational bias toward at. it is argued that variation in at nucleotide content found among bacterial genomes is best explained either by selection acting on the probability of fixation of mutations, or by selection favoring biased gene conversion. mitochondria are derived from bacteria, so it may not be surprising that most mitochondrial genomes show a similar at bias. likewise, the variation in nucleotide content found among chelicerate mitochondrial genomes on the major coding strand either must be due to natural selection affecting which mutations becomes substituted, or must reflect neutral substitutions governed by mutational bias. previous reports have assumed that the variation in nucleotide skew found among chelicerates is due to changes in the mutational bias within the mitochondrial genome. however, it is also plausible that selection has helped to shape nucleotide use in genomes that do not have a ca skew. a phylogenetic pattern of seemingly random distribution of a trait is consistent with a pattern selection may leave if it has acted upon that trait. the evolutionary reversal of a ca bias to a gt bias found in some lineages of chelicerates may be due to selection, rather than to neutral processes, although it is not clear what the selective force may be. phylogenetic implications it is somewhat surprising that all our phylogenetic analyses of mt protein-coding genes are in agreement that pseudoscorpions and acariform mites are sister lineages. previous analyses using nuclear-encoded genes have found either conflicting placements of pseudoscorpions depending upon the method of analysis, or less than 50% bootstrap support for the placement of pseudoscorpions. while a plethora of different phylogenetic hypotheses for the relationships of pseudoscorpions have been proposed by previous workers, morphological hypotheses have tended to place pseudoscorpions as most closely allied to solifuges, scorpions, and harvestmen. no phylogenetic hypothesis proposed thus far has had a high level of assessable, statistical support. however, a quandary exists in how to interpret our phylogenetic data, as our results would require independent origins of some morphological traits that may be expected not exhibit homoplasy. the structure of sperm and male genitalia suggests that pseudoscorpiones are not closely related to solifugae, but instead, the similarities of sperm structures in solifugae suggest that they are the sister group to acariformes. recent analyses of nuclear rrna sequences also support a sister-group relationship of solifugae with acariformes ). these authors also discuss several morphological synapomorphies that solifugae shares with acariformes. we do not recover such a grouping with our mitochondrial data, and instead repeatedly find strong support for an acariformes + pseudoscorpiones clade, as well as a distantly related xiphosura + solifugae clade. in light of the well-supported relationship between pseudoscorpions and acariformes, we are led to ask whether any morphological characters might also support this surprising relationship. both pseudoscorpions and mites possess trachea, but it is known that other chelicerate lineages, such as opiliones, also possess trachea. in fact, there is some historical precedent for grouping the tracheate arachnids, but this grouping has been largely dismissed by arachnologists because trachea are known to have arisen independently within some arthropod lineages. dunlop and alberti summarized the similarities of the parasitiform and acariform lineages with other arachnids. they describe two features that are shared among these lineages and pseudoscorpions. these are the presence of a ventrally moving finger on the chelicera, and the presence of an anterior projection termed the epistomal plate, which possesses flap-like lips. however, these features are also shared with solifugae, a group that we recover as most closely related to horseshoe crabs. there are features at the molecular level that are shared by acariformes and pseudoscorpiones. intriguingly, the mt genomes of acariform mites also exhibit widespread loss of arms from their trna genes. in fact, no acariform mites or pseudoscorpions so far sequenced possess a complete set of "typical" trna genes, but instead some to all of their trna genes do not encode either d-arm or t-arm sequences. as discussed previously, these taxa vary as to which trnas are missing an arm, and whether it is a t-arm or d-arm. therefore, it is not likely that acariform mites and pseudoscorpions share the loss of a specific trna helix as a synapomorphy. instead, it is more likely that they share the propensity to lose helices from their trna genes. both pseudoscorpions and acariforms have extremely short ribosomal rna genes. we have shown that losses of helices of specific regions of the lsu rrna are shared by both pseudoscorpions, and therefore these losses likely pre-date the loss of sequence to encode cloverleaf shaped trnas. further analyses of additional pseudoscorpion and acariform mite rrna secondary structures will allow insight into whether these lineages share the loss of helices that may be involved in trna d- or t-loop contact with the ribosome. acariform mites and pseudoscorpions also exhibit extensive gene rearrangements. however, these taxa do not share the same gene arrangement, and even the two pseudoscorpions differ in their genome organization. to date, the only other chelicerates that have been found to have genome rearrangements of protein-coding genes are some parasitiformes, and pycnogonids in the family nymphonidae. intriguingly, these orders were recovered as a monophyletic group in our phylogenetic analyses. rate of molecular evolution the pseudoscorpion amino acid sequences are on long branches on our phylogenetic trees. because branch length is proportional to the number of substitutions, it indicates that many substitutions separate pseudogarypus from paratemnoides, and from their most recent common ancestor with other chelicerates. these branches are longer than those found among any other chelicerate lineage, except for acariformes. this indicates either that pseudoscorpions and acariformes are more ancient lineages than other chelicerate lineages, or that they have elevated rates of sequence evolution. these two alternate scenarios are difficult to tease apart. fossil pseudoscorpions dated to about million years old have been found in devonian deposits. even older acariform mite, opilionid, and scorpion fossils have been found, and are dated to 410- mya. therefore, fossil data alone does not allow us to infer that pseudoscorpions have accumulated more mutations than scorpions and spiders simply because they are older. the lack of an older pseudoscorpion fossil does not necessarily indicate that the lineage is not older, as it is possible that older fossils remain to be discovered. pseudoscorpion mt genomes show some gene rearrangements, including rearranged protein-coding genes in pseudogarypus. some studies have linked the degree of gene rearrangements with the rate of molecular evolution. the degree of mitochondrial protein-coding gene rearrangements and the rate of evolution may indeed be somewhat interrelated in chelicerates. the acariform mites, pycnogonids in the family nymphonidae, and pseudoscorpions all have protein-coding genes that are rearranged from the ancestral condition, and all show many amino acid substitutions, i.e. long branches, on the phylogenetic trees we reconstructed, consistent with elevated rates of substitution.  we find that all of the rna-encoding genes in pseudoscorpion mitochondrial genomes are greatly reduced in size, and that this size reduction coincides with the loss of helices from trna and lsu rrna secondary structures. we infer that some of the helices that have been lost in the lsu rrna are in regions that would normally contact the missing trna helices during protein-synthesis, suggesting coevolution of trna and rrna secondary structures. we find wide variation in nucleotide skew in all mitochondrial protein-coding genes among taxa within chelicerates and conclude that the skew cannot be predicted at the deepest phylogenetic levels. we also find that there have been rearrangements of genes within the mt genomes of pseudoscorpions. however, these rearrangements appear not to have affected the distribution of nucleotide skew in the genome, as would be predicted if rearrangements influenced the orientation of the origin of replication. our phylogenetic analyses unfailingly place pseudoscorpions as the sister lineage to acariformes, and not to lineages with which they apparently share more anatomical features. similarities due to shared nucleotide or amino acid skew are likely not responsible for incorrectly placing pseudoscorpiones with acariformes, as these lineages do not share the same patterns of nucleotide skew. indeed, nucleotide skew appears to have little effect on phylogeny reconstruction using amino acids, as lineages with reversed skew are scattered across our phylogenetic trees. we find several morphological features at the molecular level that pseudoscorpiones do share with acariformes. these include the propensity for the evolutionary loss of sequence to encode d- or t-arms from trna genes, a propensity for genome rearrangements, and reduction in size of rrna genes. further sequencing of pseudoscorpion and acariform mitochondrial genomes and analyses of their trna and rrna secondary structures will allow a more complete understanding of the degree to which the shared genomic changes they have undergone may be due to shared ancestry or to convergent evolution. 
most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the ca nucleotide bias typical for arthropods on their major coding strand, and instead possess a gt bias. based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with trna t-arms or d-arms as they pass through the ribosome during protein synthesis. phylogenetic analyses of all mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites. no mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of chelicerata possess unusual features, including short rrna genes and trna genes that lack sequence to encode arms of the canonical cloverleaf-shaped trna. additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes. we sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order pseudoscorpiones. yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a ca bias on the major coding strand. we find that these genomes possess unusually short trna genes that do not encode cloverleaf-shaped trna structures. indeed, in one genome, all trna genes lack sequence to encode canonical cloverleaf structures. one genome is rearranged with respect to the location of protein-coding genes, the small rrna gene, and at least trna genes. the other genome contains trna genes in novel locations. the well-supported phylogenetic placement of pseudoscorpions as sister to acariformes differs from some previous analyses based on morphology. the mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. we inferred secondary structures of the lsu rrnas from both pseudoscorpions, and find that they have lost multiple helices.
 pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. no mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of chelicerata possess unusual features, including short rrna genes and trna genes that lack sequence to encode arms of the canonical cloverleaf-shaped trna. additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes.  we sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order pseudoscorpiones. we find that these genomes possess unusually short trna genes that do not encode cloverleaf-shaped trna structures. indeed, in one genome, all trna genes lack sequence to encode canonical cloverleaf structures. we also find that the large ribosomal rna genes are substantially shorter than those of most arthropods. we inferred secondary structures of the lsu rrnas from both pseudoscorpions, and find that they have lost multiple helices. based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with trna t-arms or d-arms as they pass through the ribosome during protein synthesis. the mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. one genome is rearranged with respect to the location of protein-coding genes, the small rrna gene, and at least trna genes. the other genome contains trna genes in novel locations. most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the ca nucleotide bias typical for arthropods on their major coding strand, and instead possess a gt bias. yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a ca bias on the major coding strand. phylogenetic analyses of all mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites.  the well-supported phylogenetic placement of pseudoscorpions as sister to acariformes differs from some previous analyses based on morphology. however, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred trna and rrna structures. chelicerataarachnidanucleotide skewtrna secondary structurelsu rrna secondary structuregenome rearrangements 