Rebecca T. Kimball

A phylogenomic study of birds reveals their evolutionary history.

Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined ∼32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.

Phylogenomic evidence for multiple losses of flight in ratite birds

Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.

Phylogeny and Systematics of Lemnaceae, the Duckweed Family

Abstract The minute, reduced plants of family Lemnaceae have presented a formidable challenge to systematic investigations. The simplified morphology of duckweeds has made it particularly difficult to reconcile their interspecific relationships. A comprehensive phylogenetic analysis of all currently recognized species of Lemnaceae has been carried out using more than 4,700 characters that include data from morphology and anatomy, flavonoids, allozymes, and DNA sequences from chloroplast genes (rbcL, matK) and introns (trnK, rpl16). All data are reasonably congruent (I(MF) < 6%) and contributed to strong nodal support in combined analyses. Our combined data yield a single, well-resolved, maximum parsimony tree with 30/36 nodes (83%) supported by bootstrap values that exceed 90%. Subfamily Wolffioideae is a monophyletic clade with 100% bootstrap support; however, subfamily Lemnoideae represents a paraphyletic grade comprising Landoltia, Lemna, and Spirodela. Combined data analysis confirms the monophyly of Landoltia, Lemna, Spirodela, Wolffia, and Wolffiella. Phylogenetic relationships are used to evaluate and refine the classification of duckweeds. Communicating Editor: Jeff H. Rettig

Evolution of Avian Plumage Dichromatism from a Proximate Perspective

Several studies have indicated that sexual plumage dichromatism is a result of four proximate mechanisms: estrogen, testosterone, luteinizing hormone, and nonhormonal factors. In estrogen‐dependent dichromatism, dull plumage coloration develops in the presence of estrogen, while bright coloration develops in its absence. In testosterone‐dependent and luteinizing hormone–dependent plumage dichromatism, bright plumage develops in the presence of these hormones, while dull plumage develops in their absence. Placing the proximate control of plumage dichromatism in a phylogenetic context suggests that estrogen‐dependent plumage dichromatism, found in the avian orders Struthioniformes, Galliformes, and Anseriformes, is likely to be ancestral in extant birds, while plumage dichromatism dependent on testosterone, luteinizing hormone, or nonhormonal factors is a more derived condition. An examination of the possible pathways leading to estrogen‐dependent plumage dichromatism suggests that the fewest evolutionary steps are to begin from a condition in which both sexes are more brightly colored, followed by selection for duller coloration in one sex. The fact that estrogen‐dependent dichromatism is ancestral in extant birds suggests that more brightly colored monochromatism may have been ancestral in modern lineages of birds.

Biogeography of discontinuously distributed hydrophytes : a molecular appraisal of intercontinental disjunctions

The extraordinarily wide distributional ranges of aquatic flowering plants have long stimulated phytogeographical discussion. Although aquatic plants occur rarely among the angiosperms, they represent a disproportionately large number of taxa with broad distributions including various intercontinental disjunctions that are manifest even at the species level. Throughout the nineteenth and early twentieth centuries, long‐range dispersal by waterfowl was the prevailing explanation for widespread aquatic plant distributions. This explanation gradually fell into disfavor as biologists raised doubts as to the ability of waterfowl to transport propagules across the extensive transoceanic distances between the continents on which an assortment of aquatic taxa now reside. During the twentieth century, the development of biogeographical displacement theory, i.e., “continental drift,” steadily began to supplant dispersal as the preferred explanation for discontinuous angiosperm distributions. Our study assesses the dispersal/displacement hypotheses from a temporal standpoint using molecular estimates of divergence time for a diverse sample of phylogenetically related aquatic taxa that exhibit discontinuous intercontinental distributions. With few exceptions, we found divergence times that are far too recent to implicate continental drift as a major determinant of discontinuous distributions in aquatic plants. We suggest that long‐distance dispersal by birds should continue to be regarded as a viable explanation for widely disjunct aquatic plant distributions, although such dispersal is likely to have involved a combination of overland as well as transoceanic migratory routes.

Co‐phylogeography and comparative population genetics of the threatened Galápagos hawk and three ectoparasite species: ecology shapes population histories within parasite communities

Comparative microevolutionary studies of multiple parasites occurring on a single host species can help shed light on the processes underlying parasite diversification. We compared the phylogeographical histories, population genetic structures and population divergence times of three co‐distributed and phylogenetically independent ectoparasitic insect species, including an amblyceran and an ischnoceran louse (Insecta: Phthiraptera), a hippoboscid fly (Insecta: Diptera) and their endemic avian host in the Galápagos Islands. The Galápagos hawk (Aves: Falconiformes: Buteo galapagoensis) is a recently arrived endemic lineage in the Galápagos Islands and its island populations are diverging evolutionarily. Each parasite species differed in relative dispersal ability and distribution within the host populations, which allowed us to make predictions about their degree of population genetic structure and whether they tracked host gene flow and colonization history among islands. To control for DNA region in comparisons across these phylogenetically distant taxa, we sequenced ~1 kb of homologous mitochondrial DNA from samples collected from all island populations of the host. Remarkably, the host was invariant across mitochondrial regions that were comparatively variable in each of the parasite species, to degrees consistent with differences in their natural histories. Differences in these natural history traits were predictably correlated with the evolutionary trajectories of each parasite species, including rates of interisland gene flow and tracking of hosts by parasites. Congruence between the population structures of the ischnoceran louse and the host suggests that the ischnoceran may yield insight into the cryptic evolutionary history of its endangered host, potentially aiding in its conservation management.

Dispersers shape fruit diversity in Ficus (Moraceae)

Seed dispersal by vertebrates is one of the most common and important plant–animal mutualisms, involving an enormous diversity of fruiting plants and frugivorous animals. Even though plant reproduction depends largely on seed dispersal, evolutionary ecologists have been unable to link co-occurring traits in fruits with differences in behavior, physiology, and morphology of fruit-eating vertebrates. Hence, the origin and maintenance of fruit diversity remains largely unexplained. Using a multivariate phylogenetic comparative test with unbiased estimates of odor and color in figs, we demonstrate that fruit traits evolve in concert and as predicted by differences in the behavior, physiology (perceptive ability) and morphology of their frugivorous seed dispersers. The correlated evolution of traits results in the convergence of general appearance of fruits in species that share disperser types. Observations at fruiting trees independently confirmed that differences in fig traits predict differences in dispersers. Taken together, these results demonstrate that differences among frugivores have shaped the evolution of fruit traits. More broadly, our results underscore the importance of mutualisms in both generating and maintaining biodiversity.

Error in Phylogenetic Estimation for Bushes in the Tree of Life

Many rapid radiations, or bushes, throughout the Tree of Life remain unresolved. Here, we investigated how the shape of a bush interacts with two key processes - coalescence and mutation - that can lead to errors in phylogenetic inference under specific conditions. For this study, we focused on the tradeoff between sampling more individuals per species and sampling more loci as well as the utility of a species tree method based upon gene tree reconciliation and the concatenation of multiple loci for resolving bushes. We examined different bush shapes, varying both the speciation rate during the radiation and the depth of the radiation, to encompass a broad range of situations. Using simulations based upon parameters derived from empirical studies, we investigated the performance of phylogenetic analyses under different conditions to identify approaches with the greatest potential to resolve difficult phylogenies. Sampling a single individual for more loci outperformed sampling multiple individuals for one locus in all cases except the most recent radiations. We found that error due to homoplastic mutations increased with depth, while error due to the coalescent process remained unchanged. These simulations also revealed that, for certain ancient bushes, analyses of concatenated data matrices surprisingly resulted in more accurate phylogenies than gene tree reconciliation. The poor performance of gene tree reconciliation in this study appeared to reflect the poor estimation of gene trees, not the superiority of concatenation per se. Our results suggest concatenation remains a useful approximate method for species tree estimation, even for rapid evolutionary radiations. However, improved estimation of gene trees combined with use of gene tree reconciliation has the greatest potential for resolving the remaining bushes of the Tree of Life.

Phylogenetic Utility of Avian Ovomucoid Intron G: A Comparison of Nuclear and Mitochondrial Phylogenies in Galliformes

Abstract A novel nuclear marker, the avian ovomucoid intron G (OVOG) was sequenced from 19 galliform taxa. Results of the phylogenetic analyses using OVOG were compared to those obtained using the mitochondrial cytochrome b (cytb) gene to determine the phylogenetic utility of OVOG. OVOG appeared to have strong phylogenetic signal for reconstructing relationships among genera and families, and the only difference between OVOG and cytb was in the placement of the New World quail (Odontophoridae). Genetic distances estimated using OVOG are approximately half of those estimated using cytb, although that relationship was not linear. OVOG exhibited patterns of nucleotide substitution very different from cytb, with OVOG having little base compositional bias, a relatively low transition–transversion ratio, and little among-site rate heterogeneity.

Mate choice by female red junglefowl: the issues of multiple ornaments and fluctuating asymmetry

The significance of multiple ornaments of male birds and other animals is currently not well understood. Male red junglefowl, Gallus gallus, possess a number of morphological traits that appear to be ornamental in nature. These traits include components of the colourful plumage and fleshy structures on the face and head, the single, medially-located comb, paired wattles and ear lappets. Some studies have implicated the comb in the mate choice decisions of female junglefowl, and some have also indicated that plumage of males is not important in this regard. To test for a possible role of other male morphological ornaments in female mate choice, and to evaluate the earlier counterintuitive findings concerning male plumage, we controlled comb size, and experimentally manipulated plumage, wattles and ear lappets of male red junglefowl. We also tested responses of female junglefowl to asymmetry of bilaterally paired male ornaments by manipulating the symmetry of the paired wattles, ear lappets and the ornate hackle feathers of the neck. None of these manipulations provided evidence that female red junglefowl are sensitive to asymmetry of paired ornaments of males. A series of tests involving a male with pronounced body asymmetry likewise produced negative results. In contrast to some other studies on birds, we obtained no evidence that female red junglefowl use symmetry of either ornamental or non-ornamental traits in mate choice decisions. Comb size, the only male trait shown to be used by females, both in the present study and in some earlier ones, did not correlate significantly with natural asymmetry in any of several measured traits. Copyright 1998 The Association for the Study of Animal Behaviour.