Data incongruence and the problem of avian louse phylogeny

Detailed morphological structure and phylogenetic relationships of Degeeriella punctifer (Phthiraptera: Philopteridae), a parasite of the bearded vulture Gypaetus barbatus (Accipitriformes: Accipitridae)

Habitat loss is one of the main threats to species survival and, in the case of parasites, it is their hosts that provide their habitat. Therefore, extinction even at local scale of host taxa also implies the extinction of their parasites in a process known as co-extinction. This is the case of the bearded vulture (Gypaetus barbatus), which almost became extinct at the beginning of the twentieth century. After several attempts, this species was successfully reintroduced into the Alps at the end of the twentieth century. We collected 25 lice specimens from an electrocuted bearded vulture from Susa (Italian Alps) that were morphologically identified as Degeeriella punctifer. Six individuals were studied by scanning electron microscopy, with particular emphasis on their cephalic sensorial structures, while four further specimens were characterized at molecular level by amplifying partial regions of the 12SrRNA, COX1 and elongation factor 1 alpha (EF-1) genes. From a morphological perspective, the number, type and arrangement of the sensillae on the two distal antennal segments is quite similar to that of other species of the family Philopteridae (Phthiraptera: Ischnocera). The mandibles and tarsal claws allow lice to cling firmly to their host's feathers. Phylogenetic analyses help unravel the paraphyletic nature of the genus Degeeriella and demonstrate the clear differentiation between lice parasitizing Accipitriformes and Falconiformes, as well as the close relationship between D. punctifer, D. fulva, D. nisus and Capraiella sp. that, along with other genera, parasitize rollers (Aves: Coraciiformes).

Structure, gene order, and nucleotide composition of mitochondrial genomes in parasitic lice from Amblycera

Parasitic lice have unique mitochondrial (mt) genomes characterized by rearranged gene orders, variable genome structures, and less AT content compared to most other insects. However, relatively little is known about the mt genomes of Amblycera, the suborder sister to all other parasitic lice. Comparing among nine different genera (including representative of all seven families), we show that Amblycera have variable and highly rearranged mt genomes. Some genera have fragmented genomes that vary considerably in length, whereas others have a single mt chromosome. Notably, these genomes are more AT-biased than most other lice. We also recover genus-level phylogenetic relationships among Amblycera that are consistent with those reported from large nuclear datasets, indicating that mt sequences are reliable for reconstructing evolutionary relationships in Amblycera. However, gene order data cannot reliably recover these same relationships. Overall, our results suggest that the mt genomes of lice, already know to be distinctive, are even more variable than previously thought.

Two lineages of kingfisher feather lice exhibit differing degrees of cospeciation with their hosts

Unlike most bird species, individual kingfisher species (Aves: Alcedinidae) are typically parasitized by only a single genus of louse (Alcedoffula, Alcedoecus, or Emersoniella). These louse genera are typically specific to a particular kingfisher subfamily. Specifically, Alcedoecus and Emersoniella parasitize Halcyoninae, whereas Alcedoffula parasitizes Alcedininae and Cerylinae. Although Emersoniella is geographically restricted to the Indo-Pacific region, Alcedoecus and Alcedoffula are geographically widespread. We used DNA sequences from two genes, the mitochondrial COI and nuclear EF-1α genes, to infer phylogenies for the two geographically widespread genera of kingfisher lice, Alcedoffula and Alcedoecus. These phylogenies included 47 kingfisher lice sampled from 11 of the 19 currently recognized genera of kingfishers. We compared louse phylogenies to host phylogenies to reconstruct their cophylogenetic history. Two distinct clades occur within Alcedoffula, one that infests Alcedininae and a second that infests Cerylinae. All species of Alcedoecus were found only on host species of the subfamily Halcyoninae. Cophylogenetic analysis indicated that Alcedoecus, as well as the clade of Alcedoffula occurring on Alcedininae, do not show evidence of cospeciation. In contrast, the clade of Alcedoffula occurring on Cerylinae showed strong evidence of cospeciation.

Data supporting a molecular phylogeny of the hyper-diverse genus Brueelia

Data is presented in support of a phylogenetic reconstruction of one of the largest, and most poorly understood, groups of lice: the Brueelia-complex (Bush et al., 2015[1]). Presented data include the voucher information and molecular data (GenBank accession numbers) of 333 ingroup taxa within the Brueelia-complex and 30 outgroup taxa selected from across the order Phthiraptera. Also included are phylogenetic reconstructions based on Bayesian inference analyses of combined COI and EF-1α sequences for Brueelia-complex species and outgroup taxa.

Unlocking the black box of feather louse diversity: A molecular phylogeny of the hyper-diverse genus Brueelia

Songbirds host one of the largest, and most poorly understood, groups of lice: the Brueelia-complex. The Brueelia-complex contains nearly one-tenth of all known louse species (Phthiraptera), and the genus Brueelia has over 300 species. To date, revisions have been confounded by extreme morphological variation, convergent evolution, and periodic movement of lice between unrelated hosts. Here we use Bayesian inference based on mitochondrial (COI) and nuclear (EF-1α) gene fragments to analyze the phylogenetic relationships among 333 individuals within the Brueelia-complex. We show that the genus Brueelia, as it is currently recognized, is paraphyletic. Many well-supported and morphologically unified clades within our phylogenetic reconstruction of Brueelia were previously described as genera. These genera should be recognized, and the erection of several new genera should be explored. We show that four distinct ecomorphs have evolved repeatedly within the Brueelia-complex, mirroring the evolutionary history of feather-lice across the entire order. We show that lice in the Brueelia-complex, with some notable exceptions, are extremely host specific and that the host family associations and geographic distributions of these lice are significantly correlated with our understanding of their phylogenetic history. Several ecological phenomena, including phoresis, may be responsible for the macroevolutionary patterns in this diverse group.

New approaches for unravelling reassortment pathways

BACKGROUND

Every year the human population encounters epidemic outbreaks of influenza, and history reveals recurring pandemics that have had devastating consequences. The current work focuses on the development of a robust algorithm for detecting influenza strains that have a composite genomic architecture. These influenza subtypes can be generated through a reassortment process, whereby a virus can inherit gene segments from two different types of influenza particles during replication. Reassortant strains are often not immediately recognised by the adaptive immune system of the hosts and hence may be the source of pandemic outbreaks. Owing to their importance in public health and their infectious ability, it is essential to identify reassortant influenza strains in order to understand the evolution of this virus and describe reassortment pathways that may be biased towards particular viral segments. Phylogenetic methods have been used traditionally to identify reassortant viruses. In many studies up to now, the assumption has been that if two phylogenetic trees differ, it is because reassortment has caused them to be different. While phylogenetic incongruence may be caused by real differences in evolutionary history, it can also be the result of phylogenetic error. Therefore, we wish to develop a method for distinguishing between topological inconsistency that is due to confounding effects and topological inconsistency that is due to reassortment.

RESULTS

The current work describes the implementation of two approaches for robustly identifying reassortment events. The algorithms rest on the idea of significance of difference between phylogenetic trees or phylogenetic tree sets, and subtree pruning and regrafting operations, which mimic the effect of reassortment on tree topologies. The first method is based on a maximum likelihood (ML) framework (MLreassort) and the second implements a Bayesian approach (Breassort) for reassortment detection. We focus on reassortment events that are found by both methods. We test both methods on a simulated dataset and on a small collection of real viral data isolated in Hong Kong in 1999.

CONCLUSIONS

The nature of segmented viral genomes present many challenges with respect to disease. The algorithms developed here can effectively identify reassortment events in small viral datasets and can be applied not only to influenza but also to other segmented viruses. Owing to computational demands of comparing tree topologies, further development in this area is necessary to allow their application to larger datasets.

Repeated adaptive divergence of microhabitat specialization in avian feather lice

Background

Repeated adaptive radiations are evident when phenotypic divergence occurs within lineages, but this divergence into different forms is convergent when compared across lineages. Classic examples of such repeated adaptive divergence occur in island (for example, Caribbean Anolis lizards) and lake systems (for example, African cichlids). Host-parasite systems in many respects are analogous to island systems, where host species represent isolated islands for parasites whose life cycle is highly tied to that of their hosts. Thus, host-parasite systems might exhibit interesting cases of repeated adaptive divergence as seen in island and lake systems.

The feather lice of birds spend their entire life cycle on the body of the host and occupy distinct microhabitats on the host: head, wing, body and generalist. These microhabitat specialists show pronounced morphological differences corresponding to how they escape from host preening. We tested whether these different microhabitat specialists were a case of repeated adaptive divergence by constructing both morphological and molecular phylogenies for a diversity of avian feather lice, including many examples of head, wing, body and generalist forms.

Results

Morphological and molecular based phylogenies were highly incongruent, which could be explained by rampant convergence in morphology related to microhabitat specialization on the host. In many cases lice from different microhabitat specializations, but from the same group of birds, were sister taxa.

Conclusions

This pattern indicates a process of repeated adaptive divergence of these parasites within host group, but convergence when comparing parasites across host groups. These results suggest that host-parasite systems might be another case in which repeated adaptive radiations could be relatively common, but potentially overlooked, because morphological convergence can obscure evolutionary relationships.

A new genus and species of Philopteridae (Phthiraptera: Ischnocera) from the trumpeters (Aves: Gruiformes: Psophiidae)

A new chewing louse genus and species belonging to the Philopteridae, namely, Palmaellus inexpectatus n. gen., n. sp., is described. The new genus is distinguished from the other ischnoceran genera hitherto described by its peculiar characters of the dorsal anterior head plate with 2 postero-lateral projections, pterothorax and abdomen with scarce chaetotaxy, male genitalia with simple mesomere and paramere lacking inner digitiform projection, and the genital region of female with postero-vulvar plates bearing setae. It is a parasite of the trumpeters, an avian family endemic to South America's Amazon Basin.

Molecular evolution of the vertebrate TLR1 gene family--a complex history of gene duplication, gene conversion, positive selection and co-evolution

Background

The Toll-like receptors represent a large superfamily of type I transmembrane glycoproteins, some common to a wide range of species and others are more restricted in their distribution. Most members of the Toll-like receptor superfamily have few paralogues; the exception is the TLR1 gene family with four closely related genes in mammals TLR1, TLR2, TLR6 and TLR10, and four in birds TLR1A, TLR1B, TLR2A and TLR2B. These genes were previously thought to have arisen by a series of independent gene duplications. To understand the evolutionary pattern of the TLR1 gene family in vertebrates further, we cloned the sequences of TLR1A, TLR1B, TLR2A and TLR2B in duck and turkey, constructed phylogenetic trees, predicted codons under positive selection and identified co-evolutionary amino acid pairs within the TLR1 gene family using sequences from 4 birds, 28 mammals, an amphibian and a fish.

Results

This detailed phylogenetic analysis not only clarifies the gene gains and losses within the TLR1 gene family of birds and mammals, but also defines orthologues between these vertebrates. In mammals, we predict amino acid sites under positive selection in TLR1, TLR2 and TLR6 but not TLR10. We detect co-evolution between amino acid residues in TLR2 and the other members of this gene family predicted to maintain their ability to form functional heterodimers. In birds, we predict positive selection in the TLR2A and TLR2B genes at functionally significant amino acid residues. We demonstrate that the TLR1 gene family has mostly been subject to purifying selection but has also responded to directional selection at a few sites, possibly in response to pathogen challenge.

Conclusions

Our phylogenetic and structural analyses of the vertebrate TLR1 family have clarified their evolutionary origins and predict amino acid residues likely to be important in the host's defense against invading pathogens.

Multiple lineages of lice pass through the K-Pg boundary

For modern lineages of birds and mammals, few fossils have been found that predate the Cretaceous-Palaeogene (K-Pg) boundary. However, molecular studies using fossil calibrations have shown that many of these lineages existed at that time. Both birds and mammals are parasitized by obligate ectoparasitic lice (Insecta: Phthiraptera), which have shared a long coevolutionary history with their hosts. Evaluating whether many lineages of lice passed through the K-Pg boundary would provide insight into the radiation of their hosts. Using molecular dating techniques, we demonstrate that the major louse suborders began to radiate before the K-Pg boundary. These data lend support to a Cretaceous diversification of many modern bird and mammal lineages.

Comparative phylogenetic histories of two louse genera found on Catharus thrushes and other birds

The louse genera Brueelia (Ischnocera) and Myrsidea (Amblycera) are broadly codistributed on songbirds (Passeriformes), but differ in a variety of life history characteristics. We used mitochondrial and nuclear DNA sequences to assess levels of genetic divergence and reconstruct phylogenies of these 2 genera, focusing especially on Catharus thrushes in North America. We then qualitatively compared the phylogenies and levels of divergence within these 2 genera of codistributed parasites. Neither Brueelia nor Myrsidea appears to cospeciate with Catharus thrushes or passerine birds in general. The Myrsidea phylogeny exhibits significant levels of biogeographic structure, whereas the Brueelia phylogeny does not. Myrsidea and Brueelia also differ in their levels of intra-generic genetic divergence, with Myrsidea showing higher levels of genetic divergence and host specificity than Brueelia. Our genetic data support traditional morphology-based taxonomy in several instances in which the same species of Brueelia has been reported on multiple host taxa, e.g., all migrant Catharus spp. carry B. antiqua, with little haplotype divergence. Myrsidea found on each Catharus sp. are in general genetically distinct, except for M. incerta, which parasitizes both Catharus ustulatus and Catharus minimus. The strong biogeographic signal in the Myrsidea phylogeny and higher relative levels of host specificity of Myrsidea spp. suggest that infrequent host-switching, followed by speciation, is shaping the evolutionary history of this group. In contrast, the relatively lower host specificity of Brueelia spp. suggests that host-switching, combined with more frequent ongoing dispersal, has been more important in the evolutionary history of Brueelia.

Multigene analysis of phylogenetic relationships and divergence times of primate sucking lice (Phthiraptera: Anoplura)

Cospeciation between hosts and parasites offers a unique opportunity to use information from parasites to infer events in host evolutionary history. Although lice (Insecta: Phthiraptera) are known to cospeciate with their hosts and have frequently served as important markers to infer host evolutionary history, most molecular studies are based on only one or two markers. Resulting phylogenies may, therefore, represent gene histories (rather than species histories), and analyses of multiple molecular markers are needed to increase confidence in the results of phylogenetic analyses. Herein, we phylogenetically examine nine molecular markers in primate sucking lice (Phthiraptera: Anoplura) and we use these markers to estimate divergence times among louse lineages. Individual and combined analyses of these nine markers are, for the most part, congruent, supporting relationships hypothesized in previous studies. Only one marker, the nuclear protein-coding gene Histone 3, has a significantly different tree topology compared to the other markers. The disparate evolutionary history of this marker, however, has no significant effect on topology or nodal support in the combined phylogenetic analyses. Therefore, phylogenetic results from the combined data set likely represent a solid hypothesis of species relationships. Additionally, we find that simultaneous use of multiple markers and calibration points provides the most reliable estimates of louse divergence times, in agreement with previous studies estimating divergences among species. Estimates of phylogenies and divergence times also allow us to verify the results of [Reed, D.L., Light, J.E., Allen, J.M., Kirchman, J.J., 2007. Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate lice. BMC Biol. 5, 7.]; there was probable contact between gorilla and archaic hominids roughly 3 Ma resulting in a host switch of Pthirus lice from gorillas to archaic hominids. Thus, these results provide further evidence that data from cospeciating organisms can yield important information about the evolutionary history of their hosts.

Evolution of the chicken Toll-like receptor gene family: a story of gene gain and gene loss

Background

Toll-like receptors (TLRs) perform a vital role in disease resistance through their recognition of pathogen associated molecular patterns (PAMPs). Recent advances in genomics allow comparison of TLR genes within and between many species. This study takes advantage of the recently sequenced chicken genome to determine the complete chicken TLR repertoire and place it in context of vertebrate genomic evolution.

Results

The chicken TLR repertoire consists of ten genes. Phylogenetic analyses show that six of these genes have orthologs in mammals and fish, while one is only shared by fish and three appear to be unique to birds. Furthermore the phylogeny shows that TLR1-like genes arose independently in fish, birds and mammals from an ancestral gene also shared by TLR6 and TLR10. All other TLRs were already present prior to the divergence of major vertebrate lineages 550 Mya (million years ago) and have since been lost in certain lineages. Phylogenetic analysis shows the absence of TLRs 8 and 9 in chicken to be the result of gene loss. The notable exception to the tendency of gene loss in TLR evolution is found in chicken TLRs 1 and 2, each of which underwent gene duplication about 147 and 65 Mya, respectively.

Conclusion

Comparative phylogenetic analysis of vertebrate TLR genes provides insight into their patterns and processes of gene evolution, with examples of both gene gain and gene loss. In addition, these comparisons clarify the nomenclature of TLR genes in vertebrates.

Phylogenetic concordance analysis shows an emerging pathogen is novel and endemic

Distinguishing whether pathogens are novel or endemic is critical for controlling emerging infectious diseases, an increasing threat to wildlife and human health. To test the endemic vs. novel pathogen hypothesis, we present a unique analysis of intraspecific host-pathogen phylogenetic concordance of tiger salamanders and an emerging Ranavirus throughout Western North America. There is significant non-concordance of host and virus gene trees, suggesting pathogen novelty. However, non-concordance has likely resulted from virus introductions by human movement of infected salamanders. When human-associated viral introductions are excluded, host and virus gene trees are identical, strongly supporting coevolution and endemism. A laboratory experiment showed an introduced virus strain is significantly more virulent than endemic strains, likely due to artificial selection for high virulence. Thus, our analysis of intraspecific phylogenetic concordance revealed that human introduction of viruses is the mechanism underlying tree non-concordance and possibly disease emergence via artificial selection.

MUSEUM SPECIMENS AND PHYLOGENIES ELUCIDATE ECOLOGY'S ROLE IN COEVOLUTIONARY ASSOCIATIONS BETWEEN MITES AND THEIR BEE HOSTS

Coevolutionary associations between hosts and symbionts (or parasites) are often reflected in correlated patterns of divergence as a consequence of limitations on dispersal and establishment on new hosts. Here we show that a phylogenetic correlation is observed between chaetodactylid mites and their hosts, the long-tongued bees; however, this association manifests itself in an atypical fashion. Recently derived mites tend to be associated with basal bee lineages, and vice versa, ruling out a process of cospeciation, and the existence of mites on multiple hosts also suggests ample opportunity for host shifts. An extensive survey of museum collections reveals a pattern of infrequent host shifts at a higher taxonomic level, and yet, frequent shifts at a lower level, which suggests that ecological constraints structure the coevolutionary history of the mites and bees. Certain bee traits, particularly aspects of their nesting behavior, provide a highly predictive framework for the observed pattern of host use, with 82.1% of taxa correctly classified. Thus, the museum survey and phylogenetic analyses provide a unique window into the central role ecology plays in this coevolutionary association. This role is apparent from two different perspectives--as (a) a constraining force evident in the historical processes underlying the significant correlation between the mite and bee phylogenies, as well as (b) by the highly nonrandom composition of bee taxa that serve as hosts to chaetodactylid mites.

Reinterpreting the origins of flamingo lice: cospeciation or host-switching?

The similarity of the louse faunas of flamingos and ducks has been used as evidence that these two groups of birds are closely related. However, the realization that ducks actually are more closely related to Galliformes caused many workers to reinterpret this similarity in parasite faunas as host switching from ducks to flamingos. Recent unexpected phylogenetic results on the relationships of waterbirds and their lice call for a reinterpretation of the origins of the lice of the enigmatic flamingos. Here, we bring together new evidence on the phylogenetic relationships of flamingos and their lice and show that the lice of flamingos and grebes are closely related because their hosts share a common ancestor (cospeciation). We also demonstrate that the similarity of the louse faunas of flamingos and ducks is a result of host switching from flamingos to ducks, rather than from ducks to flamingos.

Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion

In recent years, avian systematics has been characterized by a diminished reliance on morphological cladistics of modern taxa, intensive palaeornithogical research stimulated by new discoveries and an inundation by analyses based on DNA sequences. Unfortunately, in contrast to significant insights into basal origins, the broad picture of neornithine phylogeny remains largely unresolved. Morphological studies have emphasized characters of use in palaeontological contexts. Molecular studies, following disillusionment with the pioneering, but non-cladistic, work of Sibley and Ahlquist, have differed markedly from each other and from morphological works in both methods and findings. Consequently, at the turn of the millennium, points of robust agreement among schools concerning higher-order neornithine phylogeny have been limited to the two basalmost and several mid-level, primary groups. This paper describes a phylogenetic (cladistic) analysis of 150 taxa of Neornithes, including exemplars from all non-passeriform families, and subordinal representatives of Passeriformes. Thirty-five outgroup taxa encompassing Crocodylia, predominately theropod Dinosauria, and selected Mesozoic birds were used to root the trees. Based on study of specimens and the literature, 2954 morphological characters were defined; these characters have been described in a companion work, approximately one-third of which were multistate (i.e. comprised at least three states), and states within more than one-half of these multistate characters were ordered for analysis. Complete heuristic searches using 10 000 random-addition replicates recovered a total solution set of 97 well-resolved, most-parsimonious trees (MPTs). The set of MPTs was confirmed by an expanded heuristic search based on 10 000 random-addition replicates and a full ratchet-augmented exploration to ascertain global optima. A strict consensus tree of MPTs included only six trichotomies, i.e. nodes differing topologically among MPTs. Bootstrapping (based on 10 000 replicates) percentages and ratchet-minimized support (Bremer) indices indicated most nodes to be robust. Several fossil Neornithes (e.g. Dinornithiformes, Aepyornithiformes) were placed within the ingroup a posteriori either through unconstrained, heursitic searches based on the complete matrix augmented by these taxa separately or using backbone-constraints. Analysis confirmed the topology among outgroup Theropoda and achieved robust resolution at virtually all levels of the Neornithes. Findings included monophyly of the palaeognathous birds, comprising the sister taxa Tinamiformes and ratites, respectively, and the Anseriformes and Galliformes as monophyletic sister-groups, together forming the sister-group to other Neornithes exclusive of the Palaeognathae (Neoaves). Noteworthy inferences include: (i) the sister-group to remaining Neoaves comprises a diversity of marine and wading birds; (ii) Podicipedidae are the sister-group of Gaviidae, and not closely related to the Phoenicopteridae, as recently suggested; (iii) the traditional Pelecaniformes, including the shoebill (Balaeniceps rex) as sister-taxon to other members, are monophyletic; (iv) traditional Ciconiiformes are monophyletic; (v) Strigiformes and Falconiformes are sister-groups; (vi) Cathartidae is the sister-group of the remaining Falconiformes; (vii) Ralliformes (Rallidae and Heliornithidae) are the sister-group to the monophyletic Charadriiformes, with the traditionally composed Gruiformes and Turniciformes (Turnicidae and Mesitornithidae) sequentially paraphyletic to the entire foregoing clade; (viii) Opisthocomus hoazin is the sister-taxon to the Cuculiformes (including the Musophagidae); (ix) traditional Caprimulgiformes are monophyletic and the sister-group of the Apodiformes; (x) Trogoniformes are the sister-group of Coliiformes; (xi) Coraciiformes, Piciformes and Passeriformes are mutually monophyletic and closely related; and (xii) the Galbulae are retained within the Piciformes. Unresolved portions of the Neornithes (nodes having more than one most-parsimonious solution) comprised three parts of the tree: (a) several interfamilial nodes within the Charadriiformes; (b) a trichotomy comprising the (i) Psittaciformes, (ii) Columbiformes and (iii) Trogonomorphae (Trogoniformes, Coliiformes) + Passerimorphae (Coraciiformes, Piciformes, Passeriformes); and (c) a trichotomy comprising the Coraciiformes, Piciformes and Passeriformes. The remaining polytomies were among outgroups, although several of the highest-order nodes were only marginally supported; however, the majority of nodes were resolved and met or surpassed conventional standards of support. Quantitative comparisons with alternative hypotheses, examination of highly supportive and diagnostic characters for higher taxa, correspondences with prior studies, complementarity and philosophical differences with palaeontological phylogenetics, promises and challenges of palaeogeography and calibration of evolutionary rates of birds, and classes of promising evidence and future directions of study are reviewed. Homology, as applied to avian examples of apparent homologues, is considered in terms of recent theory, and a revised annotated classification of higher-order taxa of Neornithes and other closely related Theropoda is proposed. (c) 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 149, 1-95.

Characterization and phylogenetic analysis of a cnidarian LMP X-like cDNA

Proteasomes are multisubunit protease complexes which are partly responsible for metabolism of intracellular, ubiquitinylated proteins. Vertebrates have adapted a second and specialized structure responsible for the generation of peptides presented to the adaptive immune system and is thus, commonly referred to as the immunoproteasome. This complex is assembled from paralogous copies of subunits belonging to the constitutive, housekeeping proteasome. The immunoproteasome is more efficient in the generation of peptides for display on major histocompatibility complex (MHC) molecules. Important components of this complex are the paralogous members, LMP X and 7; where the latter replaces the former in the assembly of the immunoproteasome of vertebrates. In this report, we describe an LMP X-like cDNA from an endosymbiont-free gorgonian coral, Swiftia exserta. Cnidarians predate the phylogenetic divergence of protostomes and deuterostomes (P-D split), and are becoming an essential model for our comprehension of immune system evolution. Phylogenetic analyses of available sequences indicates that invertebrate LMP X-like sequences are outgroups to vertebrate LMP X and LMP 7, and is in agreement with previous observations that the duplication event giving rise to the two rapidly diverging lineages of proteasomal subunits occurred before jawed fished divergence.

Molecular systematics of the butterfly genus Ithomia (Lepidoptera: Ithomiinae): a composite phylogenetic hypothesis based on seven genes

Butterflies in the nymphalid subfamily Ithomiinae are brightly colored and involved in mimicry. Here we present a phylogenetic hypothesis for 23 of the 24 species in the genus Ithomia, based on seven different gene regions, representing 5 linkage groups and 4469 bp. We sequenced varying length regions of the following genes: (1) elongation factor 1alpha (Ef1alpha; 1028 bp); (2) tektin (tektin; 715 bp); (3) wingless (wg; 405 bp); (4) ribosomal protein L5 (RpL5; 722 bp, exons 1, 2, 3, and introns 1 and 2); and (5) mitochondrial cytochrome oxidase I, II (Co1 and Co2 and intervening leucine tRNA; 1599 bp). The results show incongruence between some genetic loci, although when alternate topologies are compared statistically it was generally true that one topology was supported by a majority of loci sampled. This highlights the need to sample widely across the genome in order to obtain a well-supported phylogenetic hypothesis. A combined evidence topology is presented based on a Bayesian analysis of all the gene regions, except the fast-evolving RpL5. The resulting hypothesis is concordant with the most probable relationships determined from our topological comparisons, although in some parts of the tree relationships remain weakly supported. The tree suggests diversification has largely occurred within biogeographic regions such as Central America, the Amazon, the southern and northern Andes, with only occasional dispersal (or vicariance) between such regions. This phylogenetic hypothesis can now be used to investigate patterns of diversification across the genus, such as the potential role of color pattern changes in speciation.