M.G. Fain’s research while affiliated with University of New Mexico and other places

Rhamnose-binding lectins (RBLs) in vertebrates function in immunity as pattern recognition receptors, opsonization agents, and activators of pro-inflammatory cytokines. Although they have been identified in some invertebrate taxa, their distribution, function, and evolutionary patterns in basal metazoans, remain largely unknown. A unique RBL-containing protein composed of 8 thrombospondin type 1 repeats (TSRs) and a single RBL domain has been identified in the colonial hydroid Hydractinia symbiolongicarpus. This Rhamnospondin (Rsp) gene was specifically and constitutively expressed in the mouth of feeding polyps. Here we report the full characterization of a second Rsp gene from a H. symbiolongicarpus BAC library. Rsp1 and Rsp2 were 1.1kb apart, shared the same domain architecture and were 93% identical. Introns differed substantially in size and sequence, excepting two introns that were nearly identical, suggesting the action of inter-locus recombination. Sequencing full-length cDNAs from a wild-type individual corroborated the exon boundaries predicted from genomic DNA and showed gene polymorphism at both loci. Database searches and phylogenetic analyses showed that Rsp was found only in hydrozoans, indicating that it is an innovation of the cnidarian class Hydrozoa. Phylogenetic analysis of Rsp sequences in hydroids show a tendency of clustering paralogous genes, suggesting that they have evolved by concerted evolution.

Opinions on the systematic relationships of birds in the avian order Gruiformes have been as diverse as the families included within it. Despite ongoing debate over monophyly of the order and relationships among its various members, recent opinion has converged on the monophyly of a "core" group of five families classified as the suborder Grues: the rails (Rallidae), the cranes (Gruidae), the Limpkin (Aramidae), the trumpeters (Psophiidae), and the finfoots (Heliornithidae). We present DNA sequence data from four mitochondrial (cytochrome b, 12S rRNA, Valine tRNA, and 16S rRNA) and three nuclear loci (intron 7 of beta-fibrinogen, intron 5 of alcohol dehydrogenase-I, and introns 3 through 5 of glyceraldehyde-3-phosphate dehydrogenase) to test previous hypotheses of interfamilial relationships within Grues, with particular attention to the enigmatic family Heliornithidae. Separate and combined analyses of these gene sequences confirm the monophyly of Grues as a whole, and of the five families individually, including all three species of Heliornithidae. The preferred topology unambiguously supports relationships among four of the five families, with only the position of Psophiidae remaining equivocal. Bayesian "relaxed-clock" dating methods suggest that the divergences of the three heliornithid species occurred in the mid-Tertiary, suggesting that their present disjunct pantropical distribution is a result of early- to mid-Tertiary dispersal.

Animal taxa display a wide array of immune-type receptors that differ in their specificities, diversity, and mode of evolution. These molecules ensure effective recognition of potential pathogens for subsequent neutralization and clearance. We have characterized a family of putative immune recognition molecules in the colonial hydroid Hydractinia symbiolongicarpus. A complementary DNA fragment with high similarity to the sea urchin L: -rhamnose-binding lectin was isolated and used to screen 9.5 genome equivalents of a H. symbiolongicarpus bacterial artificial chromosome library. One of the resulting 19 positive clones was sequenced and revealed the presence of a 5,111-bp gene organized in 13 exons and 12 introns. The gene was predicted to encode a 726-amino acid secreted modular protein composed of a signal peptide, an anonymous serine-rich domain, eight thrombospondin type 1 repeats, and a L: -rhamnose-binding lectin domain. The molecule was thus termed Rhamnospondin (Rsp). Southern hybridization and sequence analyses indicated the presence of a second Rsp gene. The cDNA from both Rsp genes was sequenced in 18 individuals, revealing high levels of genetic polymorphism. Nucleotide substitutions were distributed throughout the molecule and showed a significantly higher number of synonymous substitutions per synonymous sites than its nonsynonymous counterparts. Whole-mount in situ hybridization and semi-quantitative reverse transcription polymerase chain reaction of microorganism-challenged colonies indicated that Rsp molecules were specifically and constitutively expressed in the hypostome of gastrozooids' mouth. Thus, the combination of (1) comparative analysis on domain composition and function, (2) polymorphism, and (3) expression patterns, suggest that Rsp genes encode a family of putative immune recognition receptors, which may act by binding microorganisms invading the colony through the polyp's mouth.

The phylogeny of shorebirds (Aves: Charadriiformes) and their putative sister groups was reconstructed using approximately 5 kilobases of data from three nuclear loci and two mitochondrial genes, and compared to that based on two other nuclear loci. Charadriiformes represent a monophyletic group that consists of three monophyletic suborders Lari (i.e., Laridae [including Sternidae and Rynchopidae], Stercorariidae, Alcidae, Glareolidae, Dromadidae, and Turnicidae), Scolopaci (i.e., Scolopacidae [including Phalaropidae], Jacanidae, Rostratulidae, Thinocoridae, Pedionomidae), and Charadrii (i.e., Burhinidae, Chionididae, Charadriidae, Haematopodidae, Recurvirostridae, and presumably Ibidorhynchidae). The position of purported "gruiform" buttonquails within Charadriiformes is confirmed. Skimmers are most likely sister to terns alone, and plovers may be paraphyletic with respect to oystercatchers and stilts. The Egyptian Plover is not a member of the Glareolidae, but is instead relatively basal among Charadrii. None of the putative sisters of Charadriiformes were recovered as such. Hypotheses of non-monophyly and sister relationships of shorebirds are tested by multilocus analysis. The monophyly of and interfamilial relationships among shorebirds are confirmed and refined. Lineage-specific differences in evolutionary rates are more consistent across loci in shorebirds than other birds and may contribute to the congruence of locus-specific phylogenetic estimates in shorebirds.

Knowledge of avian phylogeny is prerequisite to understanding the circumstances and timing of the diversification of birds and the evolution of morphological, behavioral, and life-history traits. Recent molecular datasets have helped to elucidate the three most basal clades in the tree of living birds, but relationships among neoavian orders (the vast majority of birds) remain frustratingly vexing. Here, we examine intron 7 of the beta-fibrinogen gene in the most taxonomically inclusive survey of DNA sequences of nonpasserine bird families and orders to date. These data suggest that Neoaves consist of two sister clades with ecological parallelisms comparable to those found between marsupial and placental mammals. Some members of the putative respective clades have long been recognized as examples of convergent evolution, but it was not appreciated that they might be parts of diverse parallel radiations. In contrast, some traditional orders of birds are suggested by these data to be polyphyletic, with representative families in both radiations.

Previous analyses of DNA sequences for mitochondrial cytochrome-b and 12S rRNA, along with the nuclear protamine P1 genes, suggested that the New Guinean dasyurid genera Phascolosorex and Neophascogale (phascolosoricines) form the sister groups of quolls (Dasyurus) and Tasmanian devils (Sarcophilus). This runs counter to a common perception that phascolosoricines are anatomically primitive and only distantly related to other dasyurids. We report the DNA sequences of two additional mitochondrial loci (tRNAVal and 16S rRNA) and nuclear loci (interphotoreceptor binding protein exon 1, beta-fibrinogen intron 7) from Phascolosorex dorsalis, Neophascogale lorentzii, and all but three other dasyurid species. These sequences, along with those previously published, comprise a dataset of 7053 nucleotides. Phylogenetic analyses indicate that phascolosoricines form a clade that is highly resolved as sister to Dasyurus + Sarcophilus. This result is obtained independently by mitochondrial and nuclear genes, and cannot be attributed to taxon- or gene-sampling bias, compositional heterogeneity, or the use of overly simplistic phylogenetic estimation procedures. A re-evaluation of published morphological data bearing on the relationships of phascolosoricines demonstrates that, although the conflict with molecular results is significant, it is limited to a small number of correlated dental features that show considerable homoplasy in their evolution.

The relevant phenotypic traits and phylogenetic relationships between Burkholderia (Pseudomonas) sp. strain LB400 and B. cepacia ATCC 25416(T) were compared to determine the degree to which these two strains might be related. Strain LB400 degrades chlorinated biphenyls and has been a model system for potential use in the bioremediation of polychlorinated biphenyls, while some strains of B. cepacia are plant and human pathogens. The fatty acid methyl ester profile, sole carbon source utilization, and biochemical tests confirmed that strain LB400 was a member of the genus Burkholderia. The 16S rRNA gene sequence showed that this strain was not as closely related to B. cepacia as previously suspected or to other known pathogens of this genus, but is closely related to B. phenazinium, B. caribensis, B. graminis, and three unnamed Burkholderia spp. not known to be pathogenic.

The relevant phenotypic traits and phylogenetic relationships between Burkholderia (Pseudomonas) sp, strain LB400 and B. cepacia ATCC 25416(T) were compared to determine the degree to which these two strains might be related. Strain LB400 degrades chlorinated biphenyls and has been a model system for potential use in the bioremediation of polychlorinated biphenyls, while some strains of B. cepacia are plant and human pathogens. The fatty acid methyl ester profile, sole carbon source utilization, and biochemical tests confirmed that strain LB400 was a member of the genus Burkholderia. The 16S rRNA gene sequence showed that this strain was not as closely related to B. cepacia as previously suspected or to other known pathogens of this genus, but is closely related to B. phenazinium, B. caribensis, B, graminis, and three unnamed Burkholderia spp. not known to be pathogenic.

ki ctes over whether molecular sequence data should be partitioned for phylogenetic analysis often confound two types of heterogeneity among partitions. We distinguish historical heterogeneity (i.e., different partitions have different evolutionary relationships) from dynamic heterogeneity (i.e., different partitions show different patterns of sequence evolution) and explore the impact of the latter on phylogenetic accuracy and precision with a two-gene, mitochondrial data set for cranes. The well-established phylogeny of cranes allows us to contrast tree-based estimates of relevant parameter values with estimates based on pairwise comparisons and to ascertain the effects of incorporating different amounts of process information into phylogenetic estimates. We show that codon positions in the cytochrome b and NADH dehydrogenase subunit 6 genes are dynamically heterogenous under both Poisson and invariable-sites + gamma-rates versions of the F84 model and that heterogeneity includes variation in base composition and transition bias as well as substitution rate. Estimates of transition-bias and relative-rate parameters from pairwise sequence comparisons were comparable to those obtained as tree-based maximum likelihood estimates. Neither rate-category nor mixed-model partitioning strategies resulted in a loss of phylogenetic precision relative to unpartitioned analyses. We suggest that weighted-average distances provide a computationally feasible alternative to direct maximum likelihood estimates of phylogeny for mixed-model analyses of large, dynamically heterogenous data sets.