Search PubMed⌕ Search

Biomedical subjects

J A Kirsch

Publications and source records attributed to J A Kirsch.

At least 19 recordsLinked to original sources
PubMed2001

Convergence and divergence in the evolution of aquatic birds.

Aquatic birds exceed other terrestrial vertebrates in the diversity of their adaptations to aquatic niches. For many species this has created difficulty in understanding their evolutionary origin and, in particular, for the flamingos, hamerkop, shoebill and pelecaniforms. Here, new evidence from nuclear and mitochondrial DNA sequences and DNA-DNA hybridization data indicates extensive morphological convergence and divergence in aquatic birds. Among the unexpected findings is a grouping of flamingos and grebes, species which otherwise show no resemblance. These results suggest that the traditional characters used to unite certain aquatic groups, such as totipalmate feet, foot-propelled diving and long legs, evolved more than once and that organismal change in aquatic birds has proceeded at a faster pace than previously recognized.

Animals↗
PubMed1999

Total evidence, consensus, and bat phylogeny: A distance-based approach.

Resolution of the total evidence (i.e., character congruence) versus consensus (i.e., taxonomic congruence) debate has been impeded by (1) a failure to employ validation methods consistently across both tree-building and consensus analyses, (2) the incomparability of methods for constructing as opposed to those for combining trees, and (3) indifference to aspects of trees other than their topologies. We demonstrate a uniform, distance-based approach which allows for comparability among the results of character- and taxonomic-congruence studies, whether or not an identical suite of taxa has been included in all contributing data sets. Our results indicate that total-evidence and consensus trees differ little in topology if branch lengths are taken into account when combining two or more trees. In addition, when character-state data are converted to distances, our method permits their combination with information produced by techniques which generate distances directly. Moreover, treating all data sets or trees as distance matrices avoids the problem that different numbers of characters in contributing studies may confound the conclusions of a total-evidence or consensus analysis. Our protocol is illustrated with an example involving bats, in which the three component studies based on serology, DNA hybridization, and anatomy imply distinct phylogenies. However, the total-evidence and consensus trees support a fourth, somewhat different, topology resolved at all but one node and which conforms closely to the currently accepted higher category classification of Chiroptera.

Animals↗
PubMed1998

The platypus is not a rodent: DNA hybridization, amniote phylogeny and the palimpsest theory.

We present DNA-hybridization data on 21 amniotes and two anurans showing that discrimination is obtained among most of these at the class and lower levels. Trees generated from these data largely agree with conventional views, for example in not associating birds and mammals. However, the sister relationships found here of the monotremes to marsupials, and of turtles to the alligator, are surprising results which are nonetheless consistent with the results of some other studies. The Marsupionta hypothesis of Gregory is reviewed, as are opinions about the placement of chelonians. Anatomical and reproductive data considered by Gregory do not unequivocally preclude a marsupial-monotreme special relationship, and there is other recent evidence for placing turtles within the Diapsida. We conclude that the evidential meaning of the molecular data is as shown in the trees, but that the topologies may be influenced by a base-compositional bias producing a seemingly slow evolutionary rate in monotremes, or by algorithmic artefacts (in the case of turtles as well).

Animals↗
PubMed1998

Base-compositional biases and the bat problem. III. The questions of microchiropteran monophyly.

Using single-copy DNA hybridization, we carried out a whole genome study of 16 bats (from ten families) and five outgroups (two primates and one each dermopteran, scandentian, and marsupial). Three of the bat species represented as many families of Rhinolophoidea, and these always associated with the two representatives of Pteropodidae. All other microchiropterans, however, formed a monophyletic unit displaying interrelationships largely in accord with current opinion. Thus noctilionoids comprised one clade, while vespertilionids, emballonurids, and molossids comprised three others, successively more closely related in that sequence. The unexpected position of rhinolophoids may be due either to the high AT bias they share with pteropodids, or it may be phylogenetically authentic. Reanalysis of the data with varying combinations of the five outgroups does not indicate a rooting problem, and the inclusion of many bat lineages divided at varying levels similarly discounts long branch attraction as an explanation for the pteropodid-rhinolophoid association. If rhinolophoids are indeed specially related to pteropodids, many synapomorphies of Microchiroptera are called into question, not least the unitary evolution of echolocation (although this feature may simply have been lost in pteropodids). Further, a rhinolophoid-pteropodid relationship--if true--has serious implications for the classification of bats. Finally, among the outgroups, an apparent sister-group relation of Dermoptera and Primates suggests that flying lemurs do not represent the ancestors of some or all bats; yet, insofar as gliding of the type implemented in dermopterans is an appropriate model for the evolution of powered mammalian flying, the position of Cynocephalus in our tree indirectly strengthens the argument that true flight could have evolved more than once among bats.

Animals↗
PubMed1998

Base-compositional biases and the bat problem. II. DNA-hybridization trees based on AT- and GC-enriched tracers.

We conducted a series of parallel DNA-hybridization experiments on a small group of bats (species of Pteropus, Rhinolophus, Noctilio and Pteronotus) and outgroups (Lemur, Cynocephalus, Didelphis), using whole-genome labels and tracers made from extracts enriched with AT and two levels of GC content. FITCH (additive phylogenetic trees) topologies were constructed from the four sets of comparisons, indexed as both delta Tmode and delta NPHs (normalized percentage of hybridization). Based on our previous work showing that the shared AT bias of pteropodids and some microchiropterans may affect the rank-ordering of taxa based on either AT- or GC-rich labels, our expectation was that the resulting trees would show differing topologies when generated from tracers made with the variously enriched DNA extracts. Whereas there was some variation among the trees, most of them grouped the bats together, and almost all paired the representative megachiropteran and rhinolophoid microchiropteran as sister-taxa in contrast to the other microchiropterans. As the pteropodid-rhinolophoid relationship is an unexpected and unlikely one, we attribute this association to an AT bias that was not obviated even by our most GC-rich labels, and suggest that such a bias may compromise the truth of some molecular trees. Accordingly, we believe the broader issue of bat monophyly remains unresolved by DNA-hybridization and probably also by gene-sequencing studies.

Animals↗
PubMed1997

DNA hybridization evidence for the principal lineages of hummingbirds (Aves:Trochilidae).

The spectacular evolutionary radiation of hummingbirds (Trochilidae) has served as a model system for many biological studies. To begin to provide a historical context for these investigations, we generated a complete matrix of DNA hybridization distances among 26 hummingbirds and an outgroup swift (Chaetura pelagica) to determine the principal hummingbird lineages. FITCH topologies estimated from symmetrized delta TmH-C values and subjected to various validation methods (bootstrapping, weighted jackknifing, branch length significance) indicated a fundamental split between hermit (Eutoxeres aquila, Threnetes ruckeri; Phaethornithinae) and nonhermit (Trochilinae) hummingbirds, and provided strong support for six principal nonhermit clades with the following branching order: (1) a predominantly lowland group comprising caribs (Eulampis holosericeus) and relatives (Androdon aequatorialis and Heliothryx barroti) with violet-ears (Colibri coruscans) and relatives (Doryfera ludovicae); (2) an Andean-associated clade of highly polytypic taxa (Eriocnemis, Heliodoxa, and Coeligena); (3) a second endemic Andean clade (Oreotrochilus chimborazo, Aglaiocercus coelestis, and Lesbia victoriae) paired with thorntails (Popelairia conversii); (4) emeralds and relatives (Chlorostilbon mellisugus, Amazilia tzacatl, Thalurania colombica, Orthorhyncus cristatus and Campylopterus villaviscensio); (5) mountain-gems (Lampornis clemenciae and Eugenes fulgens); and (6) tiny bee-like forms (Archilochus colubris, Myrtis fanny, Acestrura mulsant, and Philodice mitchellii). Corresponding analyses on a matrix of unsymmetrized delta values gave similar support for these relationships except that the branching order of the two Andean clades (2, 3 above) was unresolved. In general, subsidiary relationships were consistent and well supported by both matrices, sometimes revealing surprising associations between forms that differ dramatically in plumage and bill morphology. Our results also reveal some basic aspects of hummingbird ecologic and morphologic evolution. For example, most of the diverse endemic Andean assemblage apparently comprises two genetically divergent clades, whereas the majority of North American hummingbirds belong a single third clade. Genetic distances separating some morphologically distinct genera (Oreotrochilus, Aglaiocercus, Lesbia; Myrtis, Acestrura, Philodice) were no greater than among congeneric (Coeligena) species, indicating that, in hummingbirds, morphological divergence does not necessarily reflect level of genetic divergence.

Americas↗
PubMed1994

DNA-DNA hybridization-based phylogeny for "higher" nonpasserines: reevaluating a key portion of the avian family tree.

A matrix of delta T mode values for 10 birds, including 9 nonpasserines and a suboscine passerine flycatcher, was generated by DNA-DNA hybridization. Within the most derived lineages, all bootstrapped and jackknifed FITCH trees lend strong support to sister-groupings of the two swift families, of hummingbirds to swifts, and of these to a clade containing both owls and night-hawks. The outgroup duck roots the tree between the woodpecker (Piciformes) and the remaining taxa, indicating that Piciformes are among the earliest branches within nonpasserines. However, the succeeding branches to kingfisher, mousebird, and suboscine passerine flycatcher are based on short internodes that are poorly supported by bootstrapping and that give inconsistent results in jackknifing. Although these 3 orders may have arisen through rapid or near-simultaneous divergence, placement of the "advanced" Passeriformes deep within a more "primitive" radiation indicates that nonpasserines are paraphyletic, echoing the same distinction for reptiles with respect to their advanced descendants. Despite significant rate variation among different taxa, these results largely concur with those obtained with the same technique by Sibley and Ahlquist, who used the delta T50H measure and UPGMA analysis. This agreement lends credence to some of their more controversial claims.

Animals↗
PubMed1994

Jackknifing of weighted trees: validation of phylogenies reconstructed from distance matrices.

The jackknife strict consensus has been used to detect topological incompatibilities in phylogenetic trees derived from distance data. We here extend this approach to account for branch lengths, as well as topological relationships, when comparing jackknife pseudoreplicates. The average consensus procedure is used to derive a tree reflecting the agreement among the jackknife phylogenies. Combining the average tree with a minimum and a maximum consensus provides information about jackknife tree variability; the range consensus between the minimum and the maximum represents the topological agreement among them. We also demonstrate the effect of the number of pseudoreplicates on the resulting consensus trees by considering single and multiple deletions. The jackknife extensions that we propose are applied to both hypothetical and DNA-DNA hybridization distance data. Consideration of branch lengths reveals greater stability of the jackknife phylogeny than would be demonstrated by a strict consensus based on topology alone.

Animals↗
PubMed1994

Phylogeny through brain traits: more characters for the analysis of mammalian evolution.

We have assembled data on nine brain traits, in addition to the fifteen we have previously described, which provide new evidence for assessing mammalian relationships. States of these characters are tabulated as they occur in each of 152 mammalian species, providing data in numerically ordered form, useful for multiple analyses of phylogenetic relationships in programs which take into account variations in several different characters simultaneously. Derived states of each of the nine traits are characteristic of certain restricted groups of mammals; (1) mirroring of the complete SI body representation in isocortex (anthropoid primates); (2) loss of the accessory olfactory bulbs (sirenians, cetaceans, most bats, catarrhine primates); (3) Rindenkerne, clumps of cell bodies in layer 6 of cerebral cortex (sirenians); (4) posteriorly-pointing digits in the SI body representation (bats, both mega- and micro-); (5) equivalent tectopetal connections to the anterior colliculus of one side from both retinas, rather than predominantly from the contralateral retina (primates and megabats); (6) loss of lamination in dorsal cochlear nuclei (anthropoid primates, bats, seals, sirenians, cetaceans); (7) separation of claustrum from cerebral cortex (diprotodont marsupials, carnivores, artiodactyls, perissodactyls, hyracoids, cetaceans and primates), (8) presence of a complete secondary (SII) somatic sensory region of cerebral cortex (therians-all extant mammals other than monotremes), and (9) presence of a distinct external cuneate nucleus among the nuclei of the dorsal columns (all mammalian groups except monotremes and sirenians). Two examples of phylogenetic trees derived from these data are presented. These sample trees maintain the segregation of the monotremes and the marsupials, and the basic dichotomy of placentals seen in our earlier trees based entirely on brain data. They also show: an orderly sequence of bifurcations (rather than the commonly seen multifurcation near the base of the radiation) in the reconstruction of placental relationships; extremes of derivation for the Cetacea, the Chiroptera, and the Sirenia (in concordance with trees based on other data); a ferungulate association of Carnivora, Perissodactyla, Artiodactyla, Hyracoidea and Sirenia; and an assemblage of related Dermoptera, Primates, Scandentia, and Chiroptera which in this model also includes Insectivora and Macroscelidea. Analyses based on brain characters can reinforce conclusions based on other data, while at the same time introducing new ideas about relationships. Neural traits provide a source of data independent of those commonly used in phylogenetic analysis, and are extremely valuable for testing old hypotheses and for introducing new ones.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed1991

DNA hybridization evidence for the Australasian affinity of the American marsupial Dromiciops australis.

DNA hybridization was used to compare representatives of the major groups of marsupials and a eutherian outgroup. Because of the large genetic distances separating marsupial families, trees were calculated from normalized percentages of hybridization; thermal-melting statistics, however, gave identical topologies for the well-supported clades. The most notable results were the association of the only extant microbiotheriid, Dromiciops australis, an American marsupial, with the Australasian Diprotodontia, and of both together with the Dasyuridae. Estimates of the rate of divergence among marsupial genomes suggest that the Dromiciops-Diprotodontia split occurred approximately 50 million years ago, well after the establishment of the major clades of marsupials but before deep oceanic barriers prohibited dispersal among Australia, Antarctica, and South America. Because Dromiciops is nested within an Australasian group, it seems likely that dispersal from Australia accounts for its present distribution.

Animals↗
PubMed1990

DNA hybridization, cladistics, and the phylogeny of phalangerid marsupials.

Single-copy DNA/DNA hybridization experiments and numerical cladistic analyses of anatomical characters were used to investigate relationships among nine phalangerid (Marsupialia) species from four different genera. Both rate-dependent and rate-independent analyses of molecular data indicate that species of Trichosurus from one clade and that Strigocuscus, Phalanger, and Spilocuscus form a second. Within the latter group, Spilocuscus is excluded from a Strigocuscus-Phalanger clade, which, in turn, is not fully resolved on a jackknife strict consensus tree. Minimum-length Dollo, Wagner, and Camin-Sokal parisomy trees based on 35 anatomical characters, in contrast, suggest placement of Strigocuscus with Trichosurus rather than with Spilocuscus and Phalanger. However, there are two derived characters that support the alternative arrange of Strigocuscus with Spilocuscus and Phalanger and one character that further unites Strigocuscus and Phalanger. Thus, DNA hybridization results are not inconsistent with the distribution of derived character states among anatomical characters, only with minimum-length trees based on character data.

Animals↗
PubMed1990

DNA/DNA hybridization studies of the carnivorous marsupials. I: The intergeneric relationships of bandicoots (Marsupialia: Perameloidea).

A complete suite of comparisons among six bandicoot species and one outgroup marsupial was generated using the hydroxyapatite chromatography method of DNA/DNA hybridization; heterologous comparisons were also made with three other bandicoot taxa. Matrices of delta Tm's, delta modes, and delta T50Hs were generated and corrected for nonreciprocity, homoplasy, and, in the case of delta Tm's, normalized percent hybridization; these matrices were analyzed using the FITCH algorithm in Felsenstein's PHYLIP (version 3.1). Uncorrected and nonreciprocity-corrected matrices were also jackknifed and analyzed with FITCH to test for consistency. Finally, sample scores for delta Tm, delta mode, and delta T50H matrices were bootstrapped and then subjected to phylogenetic analysis. These manipulations were carried out, in part, to address criticisms of the statistics used to summarize DNA/DNA hybridization (especially T50H) and the method itself. However, with the exception of an unresolved trichotomy among the two Echymipera species and Peroryctes longicauda, all trees showed the same branchpoints. Except in the case of the tree generated from reciprocal-corrected delta Tm data, nodes were stable under jackknifing; and, again excepting the above-mentioned trichotomy, all nodes were supported by 95% or more of the bootstrapped trees. These results suggest that, despite arguments to the contrary, all three summary statistics can be valid for DNA/DNA hybridization data. Of taxonomic interest is the placement of Echymipera spp. and Peroryctes longicauda together and separate from the more distant Peroryctes raffrayanus; the genus Peroryctes is thus at least paraphyletic. The trees further grouped Echymipera-plus-Peroryctes as the sister group of Isoodon-plus-Perameles. Limited hybridizations with Macrotis lagotis suggest that its current position as representative of an entirely distinct family of perameloids is correct.

Animals↗
PubMed1989

Rates of single-copy DNA evolution in phalangeriform marsupials.

DNA/DNA hybridization was used to investigate the relationships of taxa representing the phalangeriform marsupial families Acrobatidae, Burramyidae, Macropodidae, Petauridae, Phalangeridae, and Pseudocheiridae and (as an outgroup) the bandicoot family Peramelidae. In the course of this, a marked rate slowdown was noted in the burramyid lineage represented by Cercartetus caudatus; ANOVA (with Tukey's test) and F-ratio tests of both corrected and uncorrected data matrices confirmed this rate disparity. As burramyids are small, short-generation-time phalangeriforms, these data present a striking counterexample to the common view that rates of change in DNA sequences are inversely correlated with generation time.

Analysis of Variance↗
PubMed1988

Conflict over the molecular clock.

Figure 3 (p. 1310) in the report "A 115-kD polypeptide immunologically related to erythrocyte band 3 is present in Golgi membranes" by S. Kellokumpu et al. (2 Dec., p. 1308) was incorrectly printed. The correct figure is reproduced below.

Animals↗
PubMed1984

Brain traits through phylogeny: evolution of neural characters.

We have previously derived a hypothetical tree of the lines of mammalian descent, based upon a comprehensive numerical taxonomic cross-analysis of primitive and derived states of 15 brain traits in 38 representative species. In this communication we use this tree to describe the probable sequence of changes that have taken place in phylogenetic history. 2 characters proved to be multiply convergent, occurring in parallel in several disparate lines of descent. The remaining 9 characters each appeared in ancestors of one or another of the lineages and characterize related progeny.

Animals↗
PubMed1983

Phylogeny through brain traits: trees generated by neural characters.

Phylogenetic trees were computed by the Wagner algorithm from data on up to 15 brain characters scored on 154 specimens of 134 mammalian species. Because the data were not complete on all specimens, only one tree, of 18 taxa, was generated on all 15 features; a tree of 99 species was computed from 10 characters, and trees of 38 species from 10 and 12. The 38-taxon trees were considered best because they preserved most completely the integrity of mammalian orders. All trees consistently separated the subclasses of mammals and suggested that rodents, insectivores, and the tree shrew were most derived on the basis of brain characters. The trees' shapes are sensitive to small alterations in character scorings, largely because of the relatively few characters available and small differences in the number of states among them.

Animals↗