DNA/DNA hybridization studies of carnivorous marsupials. III. Relationships among species ofDidelphis (Didelphidae)

We report three sets of DNA hybridization experiments conducted to determine relationships among species ofDidelphis (D. albiventris, D. marsupialis, D. virginiana). The 1989 and 1991 sets had fewer replicates per cell than the 1990 series (3.4 and 5.4 vs 9), but in 1991 we distinguished two populations ofD. marsupialis and utilized several individuals for each heterologous comparison. BothPhilander opossum andLutreolina crassicaudata were used as outgroups in 1989, but onlyLutreolina was included in subsequent sets. For each set, we calculated all four standard indices of thermal stability (T _mode,T _m,T ₅₀ H, and NPH) and constructed trees by least-squares (FITCH) and neighbor-joining methods, both before and after correction for asymmetric reciprocal cell values. Subsets of the 1989 data lacking eitherPhilander orLutreolina were analyzed similarly. To explore measurement imprecision, the corrected and uncorrected matrices for each of the four indices were bootstrapped 100 times for the 1989 set and subsets and 1000 times for the 1990 and 1991 sets. Again, for the 1990 and 1991 data, an additional 100 bootstrapped distances were fitted to user trees representing the three possible pairings ofDidelphis spp. to determine the significance of the FITCH branch lengths. The successive experimental sets generated increasingly consistent evidence for pairingD. marsupialis withD. albiventris. The 1989 experiments involved just 85 comparisons, and only T _mode's pairedD. marsupialis withD. albiventris (at bootstrap percentages of 70% or above), but did so whetherPhilander orLutreolina or both were included as the outgroup(s). FITCH and neighbor-joining trees had identical topologies for T _mode's but sometimes differed for the other measures. In contrast, all but one of the corresponding FITCH and neighborjoining trees matched for the 1990 and 1991 data, and three of the four distance measures (T _mode, T _m, and T ₅₀ H) unitedD. marsupialis withD. albiventris at bootstrap percentages averaging 81%; NPH gave a different result for 1990, associatingD. marsupialis withD. virginiana. Further, all but 2 of the 16 matrices for 1990 and 1991 gave mean bootstrapped branch lengths for a consensus pairing that were positive and at least one standard deviation from zero, despite the very short internodes recovered. These results illustrate that the potential of DNA hybridization for resolving very close relationships depends on both the index and the experimental design employed. We conclude that of the three species,D. albiventris andD. marsupialis shared a more recent common ancestor and estimate thatDidelphis spp. have diverged at about 0.39% in nucleotide sequence per myr.Deceased.     

Concerted Shifts in Absorption Maxima of Yellow and Red Plumage Carotenoids Support Specialized Tuning of Chromatic Signals to Different Visual Systems in Near-Passerine Birds

Recent evidence that absorption maxima (λR_min) expressed by colorful plumage pigments align to diagnostic cone sensitivities of affiliated visual systems suggests that birds employ specialized signals in relation to their color vision. However, these studies compared different pigments and clades for the violet (porphyrins in non-passerines) and ultraviolet (carotenoids in passerines) sensitive system, which confounds chemistry and phylogeny with tuning patterns. To test whether signal alignments to violet (VS) and ultraviolet (UVS) systems transcend confounding factors, parallel analyses were conducted for a diversity of near-passerines, a group in which plumage carotenoids occur in taxa with either visual system. Conventional and phylogenetically informed analyses confirmed earlier findings: short wavelength absorbing (yellow carotenoid) pigments aligned λR_min with the violet-sensitive (V) cone of VS species but with the short wavelength-sensitive (S) cone of UVS species, whereas long wavelength-absorbing (red carotenoid) pigments aligned only with the S cone of VS species. More extensive variation among VS yellow carotenoids produced λR_min alignments to cone sensitivities that differed at shorter (peaks) versus longer (overlaps) wavelengths. Ancestral trait reconstructions indicated that signals evolved to match pre-existing VS systems, but did not resolve scenarios for UVS systems. Regardless of historical details, alignments expressed a higher-level pattern in which λR_min values were blue-shifted for yellow and red carotenoids in VS compared to UVS species, a pattern opposite that expressed by receptor sensitivities between systems. Thus, generalized functional designs attributed to avian color vision allow for specialized visual communication through the development of chromatic signals suited to each perceptual system.     

Retinoic acid receptor alpha2 is a growth suppressor epigenetically silenced in MCF-7 human breast cancer cells.

Retinoic acid (RA) receptor (RAR) beta2 has been shown to be underexpressed in human breast cancer cells, including MCF-7 cells, and recent reports have suggested that hypermethylation of the RAR beta2 promoter and 5'-UTR is the underlying cause. Here we show that RAR alpha2 is also underexpressed in MCF-7 breast cancer cells, at both the message and the protein level, relative to normal or nontumorigenic breast epithelial cells. Bisulfite sequencing of the CpG island in the RAR alpha2 promoter revealed highly penetrant and uniform cytosine methylation in MCF-7 cells. Pretreatment with the DNA methyltransferase inhibitor, azacytidine, followed by treatment with RA and a histone deacetylase inhibitor, trichostatin A, resulted in partial promoter demethylation and RAR alpha2 induction, which strongly suggested that promoter hypermethylation is responsible for RAR alpha2 underexpression. We compared the outcome of ectopic expression in MCF-7 cells of matched levels of RAR alpha2 and RAR beta2. On the basis of a clonogenic assay, RAR alpha2 displayed ligand-dependent growth-suppressive activity similar to that of RARb eta2; thus, 10 and 20 nM RA inhibited clonogenic growth by 52 and 80%, respectively, in RAR alpha2-transfected cells compared with 75 and 77%, respectively, in RAR beta2-transfected cells. We conclude that the silencing of the RAR alpha2 promoter by hypermethylation may play a contributory role in the dysregulation of RA signaling in mammary tumorigenesis.     

Physical Alignments Between Plumage Carotenoid Spectra and Cone Sensitivities in Ultraviolet-Sensitive (UVS) Birds (Passerida: Passeriformes)

Among birds, single cone sensitivities responsible for color vision appear surprisingly conserved even though chromatic signals vary greatly. Thus it is widely held that avian visual signal and receptor characteristics are rarely aligned. Analysis of a diverse passerine clade (Passerida) with characteristically ultraviolet-sensitive (UVS) vision revealed that plumage carotenoid reflectance spectra matched cone maximal sensitivities at several levels: (1) plumage carotenoid reflectance minima and maxima in aggregate aligned with the four UVS single cones; (2) the corresponding reflectance features of yellow (hydroxy- and ε-keto) and red (3- and 4-β-keto) carotenoid classes aligned with different combinations of cones; (3) pairs of reflectance features (e.g. one minimum and one maximum) of each carotenoid class aligned with pairs of (opponent) cones that evoke chromatic perception; (4) passerid plumage carotenoids aligned more closely to their own (UVS) visual system than to the distinctive homologous cone classes of the violet-sensitive system found in other birds. The ubiquitous occurrence of plumage carotenoids ipso facto demonstrates that alignments of avian visual signals and receptors are widespread, and provides novel evidence that carotenoids are important to avian communication. Moreover, alignment of different physical spectra to different cone combinations in a fixed receptor array provides a straightforward mechanism that accommodates signal diversity within the context of a relatively conserved visual system. The distinct patterns of variation and alignment observed for yellow versus red carotenoids further suggest that these pigment classes convey different physical aspects of content, which may foster carotenoid-based plumage diversity through signal design trade-offs.     

Origin of hummingbird faunas

Ecological studies of hummingbird communities have emphasized the importance of local conditions and contemporary interactions in the development of these varied faunas. A time-calibrated, DNA hybridization-based phylogeny of the principal hummingbird lineages was used to examine historical aspects of hummingbird faunas in the species-rich tropical lowlands and Andes, and the relatively depauperate West Indies and temperate regions of Central and North America. Parsimony reconstructions of ancestral distributions indicate that these faunas are polyphyletic in origin, comprising several to many independent lineages. Based on the timing of geologic and cladogenic events, hummingbird faunas appear to have arisen more often by colonization than by large-scale vicariance, with multiple dispersals across water gaps, elevational gradients, and latitude. The extent to which particular lineages colonized different regions depended, however, on lineage ecology as well as on the habitat and age of the fauna. In general, the oldest extant trochilofauna, which today occupies the tropical lowlands, was the principal source of colonizing taxa. However, all regions except possibly the West Indies contributed taxa now found elsewhere, including in the tropical lowlands. The Andean fauna comprises several lineages with lowland origin (hermits, Mangoes, Brilliants, Coquettes, Emeralds) as well as at least one that arose in temperate regions outside South America (Bees). At least two lineages that colonized the West Indies gave rise to endemic genera (Mangoes to Eulampis, and Emeralds to Orthorhyncus). Even groups that diversified in the highlands (Brilliants and Bees) gave rise to taxa that subsequently reinvaded the tropical lowlands. As the result of these varied histories, hummingbird communities cannot be arranged easily with respect to organizational complexity and coevolution with nectar sources. Although the physically insular faunas in the Andes and West Indies differ markedly in diversity, both were more strongly affected by colonization than the other faunas. A high potential for coevolution between hummingbirds and plants probably facilitated the successful establishment and radiation of the several Andean-associated lineages. However, coexistence between the two most diverse Andean clades may have been favoured initially through different habitat preferences by their extra-Andean ancestors. In the tropical lowlands, by comparison, the basic separation between the forest-dwelling hermits and canopy and edge-dwelling nonhermits appears to have evolved in situ. The low species and morphologic diversity of hummingbirds breeding north of Mexico reflects the predominance there of a single relatively recent lineage. The regional coexistence of numerous unrelated lineages implies that patterns of ancestry, colonization, and extinction contribute to the make-up of contemporary species-rich hummingbird faunas and serves to qualify the view that hummingbird communities are coadapted assemblages that resist change.     

Tempo and mode of hummingbird evolution

Lack of adequate historical data has hindered understanding of the evolutionary tempo and mode of many ecologically well-characterized avian radiations. DNA hybridization distances among 28 hummingbirds (Trochilidae) were used to establish a timescale for this family's radiation into more than 330 species. Under a variety of analytical assumptions, genetic distances calibrated with a fossil divergence date corrected for incompleteness in the geologic record indicated that all extant hummingbird lineages began to diverge in the Early Miocene, approximately 40 Myr (million years) after the Paleocene date estimated for the divergence of hummingbirds and swifts. The long period prior to the radiation of living forms provides ample time for divergent evolution to produce the large morphological gap that has tended to obscure the sister-relationship of hummingbirds and swifts. The Miocene radiation of extant hummingbird lineages itself began with the divergence of the hermit and nonhermit subfamilies approximately 17 Ma (million years ago), followed by the rapid divergence of two Andean and one principally Central and North American clade at approximately 12 Ma. Younger subsidiary lineages, including ones found mainly in the Andes or in North America, date to the later Miocene-earlier Pliocene, approximately 6 Ma. The DNA hybridization-based chronology thus indicates a protracted, rather than stricdy rapid, radiation. Evidence from a broader spectrum of organisms supports the general pattern that higher taxonomic structure within many extant continental families evolved in the Miocene, suggesting that a common environmental pacemaker initiated radiation in unrelated groups. Compared to those in the Pleistocene, radiations tracing to the Miocene may have depended less on rapid climate cycling than on creation of new habitats by major geologic and climatic upheavals. For extant hummingbirds, a principal cause for their Miocene diversification probably was the ability of the ecologically generalized subfamily of nonhermits to radiate in montane areas created by the Andean and other orogenies. Similar interactions between new habitats and their exploitation by ecological generalists may explain, at least in part, the contemporaneous radiation of Passeriformes, the most diverse avian order.     

Joint effects of feeding and breeding behaviour on trophic dimorphism in hummingbirds

A survey of 166 hummingbird species reveals novel associations of bill-length sexual dimorphism (BLSD) with plumage and breeding behaviours. Across all species, female bills become proportionately longer than male bills (higher female-to-male BLSD ratio) as sexual dichromatism increases. However, male bills are proportionately longer (lower female-to-male BLSD ratio) in both lekkers (traditional group display) and clustered breeders (female harems or colonial nests) compared with dispersed breeders. The overall positive association of plumage with BLSD suggests that social status determines priority of access to nectar-providing flowers. Furthermore, the distinctive BLSD associated with breeding aggregations may arise from behaviours that impose constraints on the usual male priority at flowers: female dominance over males around nest colonies and male residence on lek-mating territories. These various factors appear to alter plumage and bill characters of both sexes to produce the range of dimorphisms within the various dispersed and aggregated breeding system categories. Feedback loops caused by ecological consequences of breeding behaviour may alter the evolutionary dynamics of breeding systems, bird-plant interactions, and competing pollinators, as well as help explain the lek paradox.     

Patagial complex evolution in hummingbirds and swifts (Apodiformes): a molecular phylogenetic perspective

Studies of the role of flight in vertebrate evolution often have focused on the propatagial muscle complex because this structure forms the wing's leading edge. However, historical narratives about the evolution of flight anatomy are compromised because traditional higher-level taxonomies typically are based in part on the propatagium itself. To avoid this circularity, I used a consensus molecular phylogeny to examine propatagial evolution in the highly aerial sister groups, hummingbirds and swifts (Apodiformes). Mapping of anatomy on molecular-based phylogeny indicates that structural variation in M .  tensor propatagialis pars brevis (TPB) is congruent with the major subclades of both hummingbirds and swifts. However, the humeral tendon and broad attachment of the fleshy belly of TPB with M .  extensor metacarpi radialis (EMR) most likely underwent parallel change in hummingbirds and swifts, while the distal tendon present only in hummingbirds changed from a thin sheet to a strong tendon. The combination of divergent (within hummingbirds or swifts) and parallel (between hummingbirds and swifts) evolutionary patterns implies that the taxonomic value of the propatagial complex in apodiformes depends on anatomical component and level of divergence. The congruence of anatomy with molecular phylogeny provides independent criteria for designating relatively ancestral versus derived clades of apodiformes. Based on these polarities, living hummingbirds and swifts express additional parallel trends from arboreal to more aerial foraging styles, and from depauperate to species-rich clades. Within apodiformes, the link of flight anatomy with taxonomic and ecologic diversity suggests that elaboration of locomotor modes was important for apodiform diversification, echoing a similar pattern for birds relative to their reptilian ancestors.  © 2002 The Linnean Society of London, Biological Journal of the Linnean Society , 2002, 77 , 211–219.     

Experimental analysis of variance for DNA hybridization: II. Precision

Using DNAs from the Virginia opossum (Didelphis virginiana), we estimated the variance components for two classes of replicate hybrids: different drivers matched to the same tracer and different homoduplexes made from tracers matched to identical drivers. A nested analysis of variance (ANOVA) was used to partition total variance among four levels: Individuals, extracts, preparations, and different aliquots from the same preparation. The variance contributed by these levels depended on the kind of hybrid replicate (driver or tracer) and on the index of thermal stability (T_mode, T_m, T₅₀H, or Normalized Percentage Hybridization). For replicate drivers, significant variance contributions were made by (1) individuals to T_m, (2) extracts to T_mode and NPH but not T_m, and (3) different preparations to NPH. The composite T₅₀H measure calculated from both T_m and NPH revealed effects from both constituent indices. For replicate tracers, preparation error was the single most consistent effect across all indices, followed by extract effects for those indices that incorporated a measure of percent hybridization (T₅₀H NPH). Total variance of the four indices was qualitatively similar for both drivers and tracers: T_mode ranked lowest, followed in order by T_m, T₅₀H, and NPH, with the variance of NPH being as much as 100 times greater than for T_mode. These results provide guidelines for the design of experiments to generate DNA hybridization-based phylogenies and to assess their robustness with bootstrapping. Replicate drivers for a distance matrix based on T_m should use different individuals, whereas one based on T_mode could minimally use different extracts from the same individual. Thus, T_mode may be the index of choice for DNA hybridization experiments when material, time, and money are limited.Correspondence to: R. Bleiweiss     

Experimental analysis of variance for DNA hybridization: I. Accuracy

We used tissues of the Virginia opossum (Didelphis virginiana) to examine the experimental accuracy of DNA hybridization statistics of thermal stability (T_mode, T_m, T₅₀H, and NPH) with respect to systematic biases in counting radioactivity in elution fractions, and column position and loading order of hybrids in the thermal elution device. We failed to detect any change in the mean melting temperatures among five replicate ¹²⁵I-labeled hybrids counted over 72 h. Furthermore, column position in the automated thermal elution device (TED) did not bias the statistics of aliquots loaded over a few minutes from a single large mother hybrid. On the other hand, the normalized percentage hybridization (NPH) increased as much as 3–5% for aliquots loaded during 1 h from a similar mother hybrid. A parallel but less consistent increase was noted for T₅₀H, which incorporates a measure of NPH. This NPH effect disappeared when hybrids were prepared individually and diluted and loaded in turn—the usual procedure in our laboratory. Replicate distances measured as NPH appear to be sensitive to departures from the normal-distribution assumption of least-squares regression. We recommend that replicate cell values of NPH be transformed to improve their fit to a normal distribution prior to analysis by least-squares phylogenetic algorithms such as those available in Felsenstein's PHYLIP package. Thus, potential sources of inaccuracy in DNA hybridization data can be avoided with simple precautions.