Molecular systematics of the New World monkeys

We report here the results of a comparative immunological study of the evolution of primate albumins and transferrins with special reference to the systematics of the New World monkeys. The resulting albumin and transferrin phylogenies are shown to be highly concordant with one another and with data from other laboratories on globin and fibrinopeptide sequences, DNA hybridization, and further immunological studies. We also provide evidence for a probable interdependence of albumin and transferrin rates of evolution which produces a very tight clustering of the total number of amino acid substitutions for the two molecules along lineages of equal time depth, thus providing an even better rationale for the use of these data in the formulation of molecular evolutionary clocks. We again emphasize that the analysis of immunological data is not dependent on non-molecular information or assumptions concerning rates of evolution, and that the analysis provides its own indications of interpretative problems.Specifically we find that the clade Primates must now include Tupaia and Cynocephalus (the “flying lemur”), as well as Tarsius, Anthropoidea, Lemuriformes, and Lorisiformes, and that the New World monkeys share a long period of common ancestry with the Catarrhini subsequent to the divergence of other primate lineages. The catarrhine-platyrrhine divergence is placed at around 35 million years ago, thus strengthening the case for an African derivation of the New World monkeys. The extant New World monkey lineages are then seen as sharing a long period of common ancestry subsequent to that divergence, with their radiation beginning in the early Miocene. From this radiation we see seven equally distinct lineages: (1) Aotus, (2) Callicebus, (3) Cebus, (4) Saimiri, (5) Ateles-Lagothrix-Alouatta, (6) Pithecia-Cacajao, and (7) Callimico-Callithrix-Cebuella-Saguinus-Leontideus. Within those, Ateles with Lagothrix, and Callimico with Callithrix-Cebuella form further subgroups.     

Molecular systematics

Journal of Molecular Evolution -     

An analysis of clutch-size in New World passerine birds

Variation in clutch-size among New World passerine birds was analysed with respect to four variables: body-mass, geographic latitude, the frequency of nest predation, and the structure of the nest. Data were analysed separately by averaging traits at three taxonomic levels: species, genus, and subfamily. Allometric scaling with body-mass did not account for significant variation in clutch-size regardless of the taxonomic level of analysis. Latitudinal effects on clutch-size were highly significant at all taxonomic levels. For species building small-pensile nests and open-cup nests, nest predation had a significant partial effect on clutch-size, with latitude held constant. When nest predation and latitude were held constant, clutch-size was significantly different among species building small-pensile nests, open-cup nests, and domed nests. These results suggest that New World passerine clutch-size is related to at least three variables: latitudinal effects, nest predation, and nest structure.     

Metabolic capacity and the evolution of biogeographic patterns in oscine and suboscine passerine birds

Biogeographic analyses of passerine birds demonstrate that suboscines are numerically dominant in South America, whereas oscines are dominant elsewhere. This suggests that oscines generally outcompete suboscines and that suboscine dominance likely persists in South America because of its long isolation from other continents, where oscines have diversified. One hypothesis for oscine competitive superiority is that oscines possess higher metabolic capacities than suboscines, and this favors oscines in most habitats. We tested this hypothesis by comparing summit metabolic rates (M(sum), maximum thermoregulatory metabolic rate) between oscines and suboscines using conventional and phylogenetically informed statistical approaches. We predicted that if the metabolic-capacity hypothesis is valid, then oscines should have higher M(sum) than suboscines. Both conventional and phylogenetically informed ANCOVA on regressions of log M(sum) against log mass showed that oscines had higher M(sum) than suboscines: least squares mean M(sum) was 74% greater for oscines. Moreover, conventional and phylogenetically informed multiple regressions identified log mass, winter-range temperature, and clade (oscines vs. suboscines) as significant effectors of log M(sum). Thus, oscines have generally higher M(sum) than suboscines, which is consistent with the metabolic-capacity hypothesis and suggests that metabolic capacity is one factor influencing the evolution of broad biogeographical patterns in passerines.     

Molecular systematics of the Canidae

Despite numerous systematic studies, the relationships among many species within the dog family, Canidae, remain unresolved. Two problems of broad evolutionary significance are the origins of the taxonomically rich canidae fauna of South America and the development in three species of the trenchant heel, a unique meat-cutting blade on the lower first molar. The first problem is of interest because the fossil record provides little evidence for the origins of divergent South American species such as the maned wolf and the bush dog. The second issue is problematic because the trenchant heel, although complex in form, may have evolved independently to assist in the processing of meat. We attempted to resolve these two issues and five other specific taxonomic controversies by phylogenetic analysis of 2,001 base pairs of mitochondrial DNA (mtDNA) sequence data from 23 canidae species. The mtDNA tree topology, coupled with data from the fossil record, and estimates of rates of DNA sequence divergence suggest at least three and possibly four North American invasions of South America. This result implies that an important chapter in the evolution of modern canids remains to be discovered in the fossil record and that the South American canidae endemism is as much the result of extinction outside of South America as it is due to speciation within South America. The origin of the trenchant heel is not well resolved by our data, although the maximum parsimony tree is weakly consistent with a single origin followed by multiple losses of the character in several extant species. A combined analysis of the mtDNA data and published morphological data provides unexpected support for a monophyletic South American canidae clade. However, the homogeneity partition tests indicate significant heterogeneity between the two data sets.     

Molecular systematics of Lachancea yeasts

This work presents the results of molecular-genetic investigation of a new yeast genus, Lachancea Kurtzman (2003). Analysis of rRNA sequences and molecular karyotyping have shown genetic homogeneity of the genus Lachancea. Yeasts of this genus have an identical haploid number of chromosomes equal to eight, whereas limiting chromosome sizes significantly differ in various species. The largest range of chromosome bands was registered in L. cidri strains (400-2800 kb), while the smallest was found in L. waltii (1400-2800 kb). The intra- and interspecies polymorphism of Lachancea chromosomes is discussed.     

Sexually selected traits predict patterns of species richness in a diverse clade of suboscine birds

Whether sexual selection acts as an "engine of speciation" is controversial. Some studies suggest that it promotes the evolution of reproductive isolation, while others find no relationship between sexual selection and species richness. However, the explanatory power of previous models may have been constrained because they employed coarse-scale, between-family comparisons and used mating systems and morphological cues as surrogates for sexual selection. In birds, an obvious missing predictor is song, a sexually selected trait that functions in mate choice and reproductive isolation. We investigated the extent to which plumage dichromatism and song structure predicted species richness in a diverse family of Neotropical suboscine birds, the antbirds (Thamnophilidae). These analyses revealed a positive relationship between the intensity of sexual selection and diversity: genera with higher levels of dichromatism and lower-pitched, more complex songs contained greater numbers of species. This relationship held when controlling for phylogeny and was strengthened by the inclusion of subspecies, suggesting that sexual selection has played a role in the diversification of antbirds. This is the first study to reveal correlations between song structure and species diversity, emphasizing the importance of acoustic signals, and within-family analyses, in comparative studies of sexual selection.     

Molecular systematics of citrus-associated Alternaria species

The causal agents of Alternaria brown spot of tangerines and tangerine hybrids, Alternaria leaf spot of rough lemon and Alternaria black rot of citrus historically have been referred to as Alternaria citri or A. alternata. Ten species of Alternaria recently were described among a set of isolates from leaf lesions on rough lemon (Citrus jambhiri) and tangelo (C. paradisi × C. reticulata), and none of these isolates was considered representative of A. alternata or A. citri. To test the hypothesis that these newly described morphological species are congruent with phylogenetic species, selected Alternaria brown spot and leaf spot isolates, citrus black rot isolates (post-harvest pathogens), isolates associated with healthy citrus tissue and reference species of Alternaria from noncitrus hosts were scored for sequence variation at five genomic regions and used to estimate phylogenies. These data included 432 bp from the 5' end of the mitochondrial ribosomal large subunit (mtLSU), 365 bp from the 5' end of the beta-tubulin gene, 464 bp of an endopolygalacturonase gene (endoPG) and 559 and 571 bp, respectively, of two anonymous genomic regions (OPA1-3 and OPA2-1). The mtLSU and beta-tubulin phylogenies clearly differentiated A. limicola, a large-spored species causing leaf spot of Mexican lime, from the small-spored isolates associated with citrus but were insufficiently variable to resolve evolutionary relationships among the small-spored isolates from citrus and other hosts. Sequence analysis of translation elongation factor alpha, calmodulin, actin, chitin synthase and 1, 3, 8-trihydroxynaphthalene reductase genes similarly failed to uncover significant variation among the small-spored isolates. Phylogenies estimated independently from endoPG, OPA1-3 and OPA2-1 data were congruent, and analysis of the combined data from these regions revealed nine clades, eight of which contained small-spored, citrus-associated isolates. Lineages inferred from analysis of the combined dataset were in general agreement with described morphospecies, however, three clades contained more than one morphological species and one morphospecies (A. citrimacularis) was polyphyletic. Citrus black rot isolates also were found to be members of more than a single lineage. The number of morphospecies associated with citrus exceeded that which could be supported under a phylogenetic species concept, and isolates in only five of nine phylogenetic lineages consistently were correlated with a specific host, disease or ecological niche on citrus. We advocate collapsing all small-spored, citrus-associated isolates of Alternaria into a single phylogenetic species, A. alternata.     

Molecular systematics of the genus Neotoma

DNA sequences from the mitochondrial DNA cytochrome-b gene were used to infer the systematic relationships of 13 species of wood rats (genus Neotoma). Parsimony, likelihood, and neighbor-joining analyses produced similar topologies in most cases and produced six systematic conclusions. First, results of previous studies were supported in the recognition of N. floridana magister as distinct species (N. magister). Second, evidence was provided for the recognition of cryptic species within N. albigula (N. albigula and N. leucodon) and N. mexicana (N. mexicana, N. isthmica, and N. picta). Third, the subgenus Neotoma is composed of four species groups (floridana, lepida, mexicana, and micropus). Fourth, support was provided for placement of N. stephensi within the lepida species group. Fifth, support was provided for the recognition of Hodomys as a separate genus, sister to Xenomys. Sixth, support for the elevation of the subgenus Teonoma to generic status is discussed.     

Minimal effects of latitude on present-day speciation rates in New World birds

The tropics contain far greater numbers of species than temperate regions, suggesting that rates of species formation might differ systematically between tropical and non-tropical areas. We tested this hypothesis by reconstructing the history of speciation in New World (NW) land birds using BAMM, a Bayesian framework for modelling complex evolutionary dynamics on phylogenetic trees. We estimated marginal distributions of present-day speciation rates for each of 2571 species of birds. The present-day rate of speciation varies approximately 30-fold across NW birds, but there is no difference in the rate distributions for tropical and temperate taxa. Using macroevolutionary cohort analysis, we demonstrate that clades with high tropical membership do not produce species more rapidly than temperate clades. For nearly any value of present-day speciation rate, there are far more species in the tropics than the temperate zone. Any effects of latitude on speciation rate are marginal in comparison to the dramatic variation in rates among clades.     

Molecular systematics of sponges (Porifera)

The first application of molecular systematics to sponges was in the 1980s, using allozyme divergence to dis-criminate between conspecific and congeneric sponge populations. Since this time, a fairly large database has been accumulated and, although the first findings seemed to indicate that sponge species were genetically more divergent than those of other marine invertebrates, a recent review of the available dataset indicates that levels of interspecific gene identities in most sponges fall within the normal range found between species of other invertebrates. Nevertheless, some sponge genera have species that are extremely divergent from each other, suggesting a possible polyphyly of these genera. In the 1990s, molecular studies comparing sequences of ribosomal RNA have been used to reappraise the phylogenetic relationships among sponge genera, families, orders and classes. Both the 18S small subunit and the 28S large subunit rRNA genes have been sequenced (41 complete or partial and 75 partial sequences, respectively). Sequences of 18S rRNA show good support for Porifera being true Metazoa, but they are not informative for resolving relationships among genera, families or orders. 28S rRNA domains D1 and D2 appear to be more informative for the terminal nodes and provide resolution for internal topologies in sufficiently closely related species, but the deep nodes between orders or classes cannot be resolved using this molecule. Recently, a more conserved gene, Hsp70, has been used to try to resolve the relationships in the deep nodes. Metazoan monophyly is very well supported. Nevertheless, the divergence between the three classes of Porifera, as well as the divergence between Porifera, Cnidaria and Ctenophora, is not resolved. Research is in progress using other genes such as those of the homeodomain, the tyrosine kinase domain, and those coding for the aggregation factor. For the moment the dataset for these genes is too restricted to resolve the phylogenetic relationships of these phyla. However, whichever the genes, the phylogenies obtained suggest that Porifera could be paraphyletic and that the phylogenetic relationships of most of the families and orders of the Demospongiae have to be reassessed. The Calcarea and Hexactinellida are still to be studied at the molecular level.     

Molecular systematics of the Old World Astragalus (Fabaceae) as inferred from nrDNA ITS sequence data

This study represents a nuclear rDNA ITS-based phylogenetic analyses of a greater sampling of the Old WorldAstragalus compared to our previous work (212 vs. 134 taxa). Phylogenetic relationships among 212 species (213 accessions) of the Old WorldAstragalus, including newly segregated monotypic genusPodlechiella, the two aneuploid New WorldAstragalus, and five related genera, were inferred from analyses of nuclear rDNA ITS sequences using maximum parsimony. A total of 658 nucleotide sites and four binary characters for indels were analyzed. The results of phylogenetic analyses suggest sect.Phyllolobium, comprising mostly the Chinese species, is placed outside of the so-calledAstragalus s. str. and is a well-supported monophyletic group. The monotypic annual segregate genusThlaspidium (≡Astragalus sect.Thlaspidium, A. thlaspi), is clearly nested withinAstragalus s. str. Among the many sections analyzed here, only sects.Cenanthrum, Caraganella, Eremophysa, Incani, Laxiflori, andLotidium are strongly supported as monophyletic. Our analysis, in agreement with previous studies, shows that the North American euploidAstragalus species are scattered throughout the Old World groups of the genus.     

Molecular systematics of polychaetes (Annelida)

Hydrobiologia - Some progress has been made in the field of molecular systematics of polychaetes over the past couple of years. In particular, phylogenetic analyses of sequence data from the 18S...