Phylogenomics of Piranhas and Pacus (Serrasalmidae) Uncovers How Dietary Convergence and Parallelism Obfuscate Traditional Morphological Taxonomy.

The Amazon and neighboring South American river basins harbor the world's most diverse assemblages of freshwater fishes. One of the most prominent South American fish families is the Serrasalmidae (pacus and piranhas), found in nearly every continental basin. Serrasalmids are keystone ecological taxa, being some of the top riverine predators as well as the primary seed dispersers in the flooded forest. Despite their widespread occurrence and notable ecologies, serrasalmid evolutionary history and systematics are controversial. For example, the sister taxon to serrasalmids is contentious, the relationships of major clades within the family are inconsistent across different methodologies, and half of the extant serrasalmid genera are suggested to be non-monophyletic. We analyzed exon capture to reexamine the evolutionary relationships among 63 (of 99) species across all 16 serrasalmid genera and their nearest outgroups, including multiple individuals per species to account for cryptic lineages. To reconstruct the timeline of serrasalmid diversification, we time-calibrated this phylogeny using two different fossil-calibration schemes to account for uncertainty in taxonomy with respect to fossil teeth. Finally, we analyzed diet evolution across the family and comment on associated changes in dentition, highlighting the ecomorphological diversity within serrasalmids. We document widespread non-monophyly of genera within Myleinae, as well as between Serrasalmus and Pristobrycon, and propose that reliance on traits like teeth to distinguish among genera is confounded by ecological homoplasy, especially among herbivorous and omnivorous taxa. We clarify the relationships among all serrasalmid genera, propose new subfamily affiliations, and support hemiodontids as the sister taxon to Serrasalmidae. [Characiformes; exon capture; ichthyochory; molecular time-calibration; piscivory.].

Microanatomical diversification of the zona pellucida in aplochelioid killifishes.

This study investigates zona pellucida (ZP) ultrastructure in fertilized eggs of annual killifishes (suborder Aplocheiloidei), a group of highly specialized fishes that are able to survive desiccation for several weeks to months before they hatch. Little is known about ZP or chorionic ultrastructure sustaining these life-history modes, so scanning electron microscopy (SEM) was used to describe this trait in a large number of aplocheiloids with a focus on the family Rivulidae and the genus Hypsolebias. New images of ZP ultrastructure for 52 aplocheiloid species are provided, more than doubling the number characterized thus far. The evolution of chorionic structure within this group is studied using these new data. Characters were coded into a morphological matrix and optimized onto a consensus phylogeny to assess phylogenetic signal and reconstruct ancestral character states. Although ZP characters seem highly homoplastic and exhibit a large amount of structural convergence among lineages, aplocheiloid killifishes have evolved a number of unique structures associated with the chorion. Some annual species seem to have lost long filaments because eggs are deposited in the soil instead of being adhered to aquatic plants.

Composition and interrelationships of a large Neotropical freshwater fish group, the subfamily Cheirodontinae (Characiformes: Characidae): a case study based on mitochondrial and nuclear DNA sequences.

Characidae is the most species-rich family of freshwater fishes in the order Characiformes, with more than 1000 valid species that correspond to approximately 55% of the order. Few hypotheses about the composition and internal relationships within this family are available and most fail to reach an agreement. Among Characidae, Cheirodontinae is an emblematic group that includes 18 genera (1 fossil) and approximately 60 described species distributed throughout the Neotropical region. The taxonomic and systematic history of Cheirodontinae is complex, and only two hypotheses about the internal relationships in this subfamily have been reported to date. In the present study, we test the composition and relationships of fishes assigned to Cheirodontinae based on a broad taxonomic sample that also includes some characid incertae sedis taxa that were previously considered to be part of Cheirodontinae. We present phylogenetic analyses of a large molecular dataset of mitochondrial and nuclear DNA sequences. Our results reject the monophyly of Cheirodontinae as previously conceived, as well as the tribes Cheirodontini and Compsurini, and the genera Cheirodon, Compsura, Leptagoniates, Macropsobrycon, Odontostilbe, and Serrapinnus. On the basis of these results we propose: (1) the exclusion of Amazonspinther and Spintherobolus from the subfamily Cheirodontinae since they are the sister-group of all remaining Characidae; (2) the removal of Macropsobrycon xinguensis of the genus Macropsobrycon; (3) the removal of Leptagoniates pi of the genus Leptagoniates; (4) the inclusion of Leptagoniates pi in the subfamily Cheirodontinae; (5) the removal of Cheirodon stenodon of the genus Cheirodon and its inclusion in the subfamily Cheirodontinae under a new genus name; (6) the need to revise the polyphyletic genera Compsura, Odontostilbe, and Serrapinnus; and (7) the division of Cheirodontinae in three newly defined monophyletic tribes: Cheirodontini, Compsurini, and Pseudocheirodontini. Our results suggest that our knowledge about the largest Neotropical fish family, Characidae, still is incipient.

Molecular systematics of the neotropical shovelnose catfish genus Pseudoplatystoma Bleeker 1862 based on nuclear and mtDNA markers.

Pseudoplatystoma is a commercially important genus of Neotropical migratory catfishes widely distributed in all major river basins of South America. Historically, only three species were recognized, but a recent revision proposed eight putative morphospecies for the genus. A molecular study based on mitochondria DNA (mtDNA) provided support for recognition of only some of the species and raised questions about species boundaries in this group. We present a more encompassing analysis based on mtDNA (cytochrome b, 818bp) and nuclear DNA-based phylogenies (Rag1 intron 1, 664bp and S7 intron 1, 635bp) for a more extensive sampling (279 individuals from 42 localities) of all putative species in all major river basins. Patterns generated by individual gene genealogies and a multispecies coalescent analysis provided evidence to suggest recognition of only four distinct species in this genus: Pseudoplatystoma magdaleniatum, Pseudoplatystoma corruscans, Pseudoplatystoma tigrimun (sensu lato) and Pseudoplatystoma fasciatum (sensu lato). The species phylogeny places P. magdaleniatum as the sister group to all the other species in the genus, but the relationships among P. fasciatum s.l, P. tigrimum s.l., and P. corruscans could not be resolved with confidence.

Isolation and characterization of eight polymorphic microsatellite markers for the migratory characiform fish, Salminus brasiliensis.

Eight polymorphic microsatellite loci were isolated and characterized for the migratory freshwater fish Salminus brasiliensis (Characiformes) and tested on 67 individuals from nine geographically distant locations along the Paraná Basin. The number of alleles per locus ranged from four to 14, with observed heterozygosity estimates ranging from 0·15 to 0·79.

The Casiquiare river acts as a corridor between the Amazonas and Orinoco river basins: biogeographic analysis of the genus Cichla.

The Casiquiare River is a unique biogeographic corridor between the Orinoco and Amazonas basins. We investigated the importance of this connection for Neotropical fishes using peacock cichlids (Cichla spp.) as a model system. We tested whether the Casiquiare provides a conduit for gene flow between contemporary populations, and investigated the origin of biogeographic distributions that span the Casiquiare. Using sequences from the mitochondrial control region of three focal species (C. temensis, C. monoculus, and C. orinocensis) whose distributions include the Amazonas, Orinoco, and Casiquiare, we constructed maximum likelihood phylograms of haplotypes and analyzed the populations under an isolation-with-migration coalescent model. Our analyses suggest that populations of all three species have experienced some degree of gene flow via the Casiquiare. We also generated a mitochondrial genealogy of all Cichla species using >2000 bp and performed a dispersal-vicariance analysis (DIVA) to reconstruct the historical biogeography of the genus. This analysis, when combined with the intraspecific results, supports two instances of dispersal from the Amazonas to the Orinoco. Thus, our results support the idea that the Casiquiare connection is important across temporal scales, facilitating both gene flow and the dispersal and range expansion of species.

Low variation but strong population structure in mitochondrial control region of the plains topminnow, Fundulus sciadicus.

The plains topminnow Fundulus sciadicus is a freshwater killifish endemic to the Great Plains of North America. Rising concerns for future viability of this species have prompted recent changes in its conservation status. In this study, the results of a range-wide population genetic survey based on the sequence of entire mitochondrial control region (CR) are presented. A total of 181 fish were collected from 11 sites in Nebraska and 10 sites in Missouri spanning the distribution range of the species. Seven polymorphic sites were found in the 966 base pairs of the CR, and only nine unique haplotypes were detected among all fish. Phylogenetic analysis and statistical parsimony networks identified two distinct clades. The first included fish in the Osage, Gasconade and Spring River drainages in Missouri, while the second included individuals from Nebraska and the Lamine River in Missouri, although the Lamine River is much closer to the other Missouri sites than to the Nebraska sites. Pair-wise F(ST) and average population distances indicated that populations from most drainages are genetically distinct, as 93% of the total molecular variance was attributed to among-drainage effects. Four sites within the main distributions of this species and a highly disjunct site from the south-western portion of the range are suggested as potential targets for conservation.

Autoimmune hemolytic anemia following allogeneic hematopoietic stem cell transplantation in adult patients.

Autoimmune hemolytic anemia (AIHA) after allogeneic hematopoietic stem cell transplantation (HSCT) is still not well characterized. The aim of this study was to analyze the incidence and risk factors for the development of AIHA, as well as its prognosis and response to treatment in a series of patients undergoing allogeneic HSCT at a single institution. Between 1996 and 2004, 272 adult patients with a variety of malignant hematopoietic disorders underwent allogeneic HSCT. Direct antiglobulin testing was performed in routine pretransfusion compatibility testing or after clinical suspicion of AIHA. Twelve patients developed AIHA after HSCT at a median time of 147 days (range, 41-170). The 3-year cumulative incidence of AIHA was 4.44%. Eight cold antibodies and four warm antibodies were detected. Multivariate analysis shows that HSCT from unrelated donors (P=0.02) and the development of chronic extensive graft-versus-host disease (GVHD) (P=0.0004) were the only independent factors associated with AIHA. Two patients are still alive. AIHA was never the primary cause of death but added morbidity in patients with other concomitant complications. Patients undergoing HSCT from unrelated donors and those who develop chronic extensive GVHD are especially predisposed for this complication.

Patterns of infection and infection-related mortality in patients with steroid-refractory acute graft versus host disease.

This study aimed to characterize the incidence, etiology and outcome of infectious episodes in patients with steroid refractory acute GvHD (SR-GvHD). The cohort included 127 adults treated with inolimomab (77%) or etanercept (23%) owing to acute 2-4 SR-GvHD, with a response rate of 43% on day +30 and a 4-year survival of 15%. The 1-year cumulative incidences of bacterial, CMV and invasive fungal infection were 74%, 65% and 14%, respectively. A high rate (37%) of enterococcal infections was observed. Twenty patients (15.7%) developed BK virus-hemorrhagic cystitis and five percent had an EBV reactivation with only one case of PTLD. One-third of long-term survivors developed pneumonia by a community respiratory virus and/or encapsulated bacteria, mostly associated with chronic GvHD. Infections were an important cause of non-relapse mortality, with a 4-year incidence of 46%. In multivariate analysis, use of rituximab in the 6 months before SCT (hazard ratio; HR 4.2; 95% confidence interval; CI 1.1-16.3), severe infection before SR-GvHD onset (HR 5.8; 95% CI 1.3-26.3) and a baseline C-reactive protein >15 UI/mL (HR 2.9; 95% CI 1.1-8.5) were associated with infection-related mortality. High rates of opportunistic infections with remarkable mortality warrant further efforts to optimize long-term outcomes after SR-GvHD.

Tacrolimus plus sirolimus with or without ATG as GVHD prophylaxis in HLA-mismatched unrelated donor allogeneic stem cell transplantation.

HLA-matched related or unrelated donors are not universally available. Consequently, patients can be offered hematopoietic stem cell transplantation (HSCT) from alternative donors, including mismatched unrelated donors (MMURD), known to cause a higher incidence of acute GVHD (aGVHD) and chronic GVHD. In vivo T-cell-depletion strategies, such as antithymocyte globulin (ATG) therapy, significantly decrease the risk of GVHD. We performed a multicenter, retrospective study comparing tacrolimus (TAC) and sirolimus (SIR) with or without ATG in 104 patients (TAC-SIR=45, TAC-SIR-ATG=59) who underwent MMURD HSCT. Use of ATG was associated with a lower incidence, albeit not statistically significant, of grades 2-4 aGVHD (46% vs 64%, P=0.09), no difference in grades 3-4 aGVHD (10% vs 15%, P=0.43), a trend for a lower incidence of moderate/severe chronic GVHD (16% vs 37%, P=0.09) and more frequent Epstein-Barr virus reactivation (54% vs 18%, P=0.0002). There were no statistically significant differences in 3-year overall survival (OS) (TAC-SIR-ATG=40% (95% confidence interval (CI)=24-56%) vs TAC-SIR=54% (95% CI=37-70%), P=0.43) or 3-year cumulative incidence of relapse/progression (TAC-SIR-ATG=40% (95% CI=28-58%) vs TAC-SIR=22% (95% CI=13-39%), P=0.92). An intermediate Center for International Blood & Marrow Transplant Research disease risk resulted in a significantly lower non-relapse mortality and better OS at 3 years. Our study suggests that addition of ATG to TAC-SIR in MMURD HSCT does not affect OS when compared with TAC-SIR alone.

Impact of Epstein Barr virus-related complications after high-risk allo-SCT in the era of pre-emptive rituximab.

We monitored 133 high-risk allo-SCT recipients for 6 months after transplant for EBV reactivation by quantitative real-time PCR. Rituximab was given as pre-emptive therapy for viremia >1000 copies/mL. The 1-year cumulative incidence of EBV reactivation was 29.4% (95% confidence interval (CI): 18-40) in patients monitored due to initial high-risk characteristics (n=93) and 31.8% (95% CI: 19.7-44) in those followed because of the development of refractory GVHD (n=40). Overall response rate to Rituximab was 83%. Nine patients (9.6%) developed post-transplant lymphoproliferative disorder (PTLD) at a median of +62 days after SCT. Eight of them showed a concomitant CMV reactivation. Second SCT was the only risk factor associated with EBV infection and PTLD in multivariate analysis (hazard ratio (HR) 2.6 (95% CI: 1.1-6.4; P=0.04) and HR 6.4 (95%CI: 1.3-32; P=0.02)). The development of EBV reactivation was not associated with non-relapse mortality or OS (P=0.97 and P=0.84, respectively).

The phylogenetic position of the zebrafish (Danio rerio), a model system in developmental biology: an invitation to the comparative method.

The zebrafish, Danio (Brachydanio) rerio, has become one of the most widely studied model systems in developmental biology. We present a DNA-based phylogeny of zebrafish and other species of the genus Danio, and the genera Rasbora, Puntius and Cyprinus. Homologous regions of the large (16S) mitochondrial ribosomal RNA gene were amplified by the polymerase chain reaction and directly sequenced. The phylogeny revealed: (i) the zebrafish, Danio (Brachydanio) rerio, is identical in its 16S sequence to its aquarium breeding morph, the leopard danio; (ii) the pearl danio (Danio albolineatus) is more closely related to the zebrafish than the giant danio (Danio aequipinnatus); and (iii) species of the genus Rasbora (hetermorpha, trilineata, elegans, pauciperforata, dorsiocellata) are more closely related to the danios than members of the genus Puntius (tetrazona, conchonius) and Cyprinus, the carp. All of these species are readily available in the aquarium trade, easily kept and bred in captivity, and amenable to developmental work. It is hoped that this molecular phylogeny will invite developmental biologists to use the comparative method to ask questions about function (e.g. cellular and genetic aspects) and evolution of zebrafish developmental biology in a phylogenetic context.

Cryptic speciation and patterns of phenotypic variation of a highly variable acanthocephalan parasite.

An investigation of a parasite species that is broadly host- and habitat-specific and exhibits alternative transmission strategies was undertaken to examine intraspecific variability and if it can be attributed to cryptic speciation or environmentally induced plasticity. Specimens of an acanthocephalan parasite, Leptorhynchoides thecatus, collected throughout North America were analysed phylogenetically using sequences of the cytochrome oxidase I gene and the internal transcribed spacer region. Variation in host use, habitat use, and transmission were examined in a phylogenetic context to determine if they were more likely phylogenetically based or due to environmental influences. Results indicated that most of the variation detected can be explained by the presence of cryptic species. The majority of these species have narrow host and microhabitat specificities although one species, which also may comprise a complex of species, exhibits broad host and habitat specificity. Alternate transmission pathways only occurred in two of the cryptic species and correlate with host use patterns. Taxa that mature in piscivorous piscine hosts use a paratenic fish host to bridge the trophic gap between their amphipod intermediate host and piscivorous definitive host. One potential example of environmentally induced variation was identified in three populations of these parasites, which differ on their abilities to infect different host species.

Germ-line chimerism and paternal care in marmosets (Callithrix kuhlii).

The formation of viable genetic chimeras in mammals through the transfer of cells between siblings in utero is rare. Using microsatellite DNA markers, we show here that chimerism in marmoset (Callithrix kuhlii) twins is not limited to blood-derived hematopoietic tissues as was previously described. All somatic tissue types sampled were found to be chimeric. Notably, chimerism was demonstrated to be present in germ-line tissues, an event never before documented as naturally occurring in a primate. In fact, we found that chimeric marmosets often transmit sibling alleles acquired in utero to their own offspring. Thus, an individual that contributes gametes to an offspring is not necessarily the genetic parent of that offspring. The presence of somatic and germ-line chimerism may have influenced the evolution of the extensive paternal and alloparental care system of this taxon. Although the exact mechanisms of sociobiological change associated with chimerism have not been fully explored, we show here that chimerism alters relatedness between twins and may alter the perceived relatedness between family members, thus influencing the allocation of parental care. Consistent with this prediction, we found a significant correlation between paternal care effort and the presence of epithelial chimerism, with males carrying chimeric infants more often than nonchimeric infants. Therefore, we propose that the presence of placental chorionic fusion and the exchange of cell lines between embryos may represent a unique adaptation affecting the evolution of cooperative care in this group of primates.

Molecular evolution of ependymin and the phylogenetic resolution of early divergences among euteleost fishes.

The rate and pattern of DNA evolution of ependymin, a single-copy gene coding for a highly expressed glycoprotein in the brain matrix of teleost fishes, is characterized and its phylogenetic utility for fish systematics is assessed. DNA sequences were determined from catfish, electric fish, and characiforms and compared with published ependymin sequences from cyprinids, salmon, pike, and herring. Among these groups, ependymin amino acid sequences were highly divergent (up to 60% sequence difference), but had surprisingly similar hydropathy profiles and invariant glycosylation sites, suggesting that functional properties of the proteins are conserved. Comparison of base composition at third codon positions and introns revealed AT-rich introns and GC-rich third codon positions, suggesting that the biased codon usage observed might not be due to mutational bias. Phylogenetic information content of third codon positions was surprisingly high and sufficient to recover the most basal nodes of the tree, in spite of the observation that pairwise distances (at third codon positions) were well above the presumed saturation level. This finding can be explained by the high proportion of phylogenetically informative nonsynonymous changes at third codon positions among these highly divergent proteins. Ependymin DNA sequences have established the first molecular evidence for the monophyly of a group containing salmonids and esociforms. In addition, ependymin suggests a sister group relationship of electric fish (Gymnotiformes) and Characiformes, constituting a significant departure from currently accepted classifications. However, relationships among characiform lineages were not completely resolved by ependymin sequences in spite of seemingly appropriate levels of variation among taxa and considerably low levels of homoplasy in the data (consistency index = 0.7). If the diversification of Characiformes took place in an "explosive" manner, over a relatively short period of time this pattern should also be observed using other phylogenetic markers. Poor conservation of ependymin's primary structure hinders the design of efficient primers for PCR that could be used in wide-ranging fish systematic studies. However, alternative methods like PCR amplification from cDNA used here should provide promising comparative sequence data for the resolution of phylogenetic relationships among other basal lineages of teleost fishes.

The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences.

Phylogenetic relationships among fishes from ostariophysan orders, characiform families, and serrasalmin genera (e.g., "piranhas") were examined using partial mitochondrial ribosomal DNA sequences of the 12S and 16S genes. Phylogenetic information content of these sequences was assessed at three levels of taxonomic inclusiveness by analyzing the patterns of nucleotide substitution using secondary structure models. Conserved and variable regions were identified, mapped onto the structural models, and compared at increasing levels of taxonomic divergence. In general, loop regions (unpaired) exhibited a higher level of variation than did stem regions (paired). A high proportion of compensatory substitutions was observed in stem regions in three data sets, suggesting strong selection to maintain the secondary structure. Saturation due to multiple substitutions was indicated by decreasing transition/transversion ratios and strong structural constraints on variation in comparisons among orders of Ostariophysi but was not obvious among families of Characiformes and was not detected among serrasalmin genera. Reliable phylogenetic signal successfully reconstructed relationships among serrasalmin genera. However, aside from a few well-supported clades, relationships could not be reconstructed with confidence among characiform families and ostariophysan orders. The reciprocal monophyly of African and Neotropical characiform lineages was rejected (based on maximum likelihood ratio tests), and some support for previous hypotheses based on morphology was provided by the molecular data. The radiation of characiform fishes is discussed in a historical biogeographic context.

Population structure and biogeography of migratory freshwater fishes (Prochilodus: Characiformes) in major South American rivers.

Mitochondrial DNA (mtDNA) sequences were used to infer the phylogenetic relationships of Prochilodus species in the Paraná, Amazonas, Orinoco, and Magdalena basins. Sequences of ATPase subunits 6 and 8 (total 840 bp) were obtained for 21 Prochilodus specimens from the four river systems. Using Semaprochilodus as an outgroup, phylogenetic analyses showed that: (i) each river basin contains a monophyletic group of mtDNA lineages; and (ii) the branching order places Magdalena in a basal position with subsequent branching of Orinoco, Amazon and Paraná. The mitochondrial control region was sequenced for 26 P. lineatus (from the Paraná basin) and six other Prochilodus specimens from the Magdalena, Orinoco and Amazon. All 26 control region haplotypes were unique with sequence divergence ranging from 0.3 to 3.6%. The control region phylogeny is well resolved but phylogenetic structure is not associated with geography. For example, mtDNA haplotypes from the upper Paraná (Mogui Guassú) and the upper Bermejo, separated by at least 2600 km, have close genealogical ties. Phylogeographic analyses, including nested clade analysis, suggest high levels of gene flow within this basin.

Detection and isolation of nuclear haplotypes by PCR-SSCP.

SSCP (single-strand conformational polymorphism) is used widely in the field of human biomedicine, but its potential as a population genetics tool for the recovery of nuclear gene genealogies remains to be realized. We describe and illustrate a use for SSCP in the physical isolation of nuclear haplotypes that circumvents several difficulties associated with more conventional cloning procedures. The DNA sequence can be determined directly from the isolated haplotypes and used for phylogenetic inference. SSCP provides a convenient first step toward generating nuclear genealogies for population studies.

Phylogenetic assessment of length variation at a microsatellite locus.

Sixty-six haplotypes at a locus containing a simple dinucleotide (CA)n microsatellite repeat were isolated by PCR-single-strand conformational polymorphism from populations of the horseshoe crab Limulus polyphemus. These haplotypes were sequenced to assess nucleotide variation directly. Thirty-four distinct sequences (alleles) were identified in a region 570 bp long that included the microsatellite motif. In the repeat region itself, CA-number varied in integer values from 5 to 11 across alleles, except that a (CA)8 class was not observed. Differences among alleles were due also to polymorphisms at 22 sites in regions immediately flanking the microsatellite repeats. Nucleotide substitutions in these regions were used to estimate phylogenetic relationships among alleles, and the gene phylogeny was used to trace the evolution of length variation and CA repeat numbers. A low correlation between size variation and genealogical relationships among alleles suggests that absolute fragment size (as normally scored in microsatellite assays) is an unreliable indicator of historical affinities among alleles. This finding on the molecular fine structure of microsatellite variation suggests the need for caution in the use of repeat counts at microsatellite loci as secure indicators of allelic relationships.