Phylogenetic Events Research Articles

The Importance of Time/Space in Diagnosing the Causality of Phylogenetic Events: Towards a ‘Chronobiogeographical’ Paradigm?

A shift from a traditional biogeographical paradigm in cladistic biogeography to a chronobiogeographical paradigm is proposed. The chronobiogeographical paradigm aims to utilize temporal data in conjunction with spatial data in the detection of discrete historical events, such as vicariance and vicariant speciation, in cladograms. The concepts of primary and secondary congruency are introduced in relation to the distinction between repeated area relationships (primary congruency) and common extrinsic causality (secondary congruency). Simple hypothetical examples demonstrate that area cladograms cannot be safely interpreted purely as representing the sequence of area fragmentation; rather, they reflect recency of biotic interaction. Temporal data are shown to have a direct and potentially profound influence on the results of traditional cladistic biogeographical analyses, indicating the necessity of developing a chronobiogeographical approach. The implementation of the paradigm is considered first from a theoretical viewpoint and then in the context of the type of empirical data usually available. An as yet undevised "time/space algorithm" is deemed necessary for the latter, and guidelines are presented for the development of such an algorithm. Finally, we argue that the most rigorous and philosophically justified approach to the detection of phylogenetic causal events can be found only when temporal and spatial data are considered simultaneously. Consequently, the chronobiogeographical paradigm is seen as a logical elaboration of, not a replacement for, the biogeographical paradigm.

The Importance of Time/Space in Diagnosing the Causality of Phylogenetic Events: Towards a "Chronobiogeographical" Paradigm?

The Importance of Time/Space in Diagnosing the Causality of Phylogenetic Events: Towards a "Chronobiogeographical" Paradigm?

The Importance of Time/Space in Diagnosing the Causality of Phylogenetic Events: Towards a "Chronobiogeographical" Paradigm?

The Importance of Time/Space in Diagnosing the Causality of Phylogenetic Events: Towards a "Chronobiogeographical" Paradigm?

The Importance of Time/Space in Diagnosing the Causality of Phylogenetic Events: Towards a "Chronobiogeographical" Paradigm?

The Importance of Time/Space in Diagnosing the Causality of Phylogenetic Events: Towards a "Chronobiogeographical" Paradigm?

Mitochondrial COI Sequences of Brachiopods: Genetic Code Shared with Protostomes and Limits of Utility for Phylogenetic Reconstruction

A 1230-bp region of the cytochrome c oxidase subunit I (COI) gene of mitochondrial DNA of each of 16 brachiopod species, representing all five living orders, was amplified by polymerase chain reaction and sequenced. Pairwise comparisons of sequence differences plotted against divergence times estimated from the brachiopod fossil record revealed that, although there are considerable variations in the expected substitution rate among different lineages, amino acid substitutions of the COI sequences may largely become saturated in 100 Ma, due mostly to multiple substitutions at the same site. Coinciding with this result, phylogenetic analysis indicated low bootstrap values for nodes corresponding to divergence events that occurred before 100 Ma, suggesting that COI sequences are suitable only for inference of phylogenetic events subsequent to the Mesozoic. Examination of brachiopod codons corresponding to invariant amino acids in the COI of various other animals suggest the nonuniversal codon relationships UGA = Trp, AUA = Met, AAA/G = Lys, and AGA/G = Ser. These are identical to those in mollusks, annelids, and arthropods, consistent with the conclusion that brachiopods are protostomes, as indicated by previous molecular analyses.

Evolution and phylogeny of the Diptera: a molecular phylogenetic analysis using 28S rDNA sequences.

Portions of the large ribosomal subunit RNA gene (28S rDNA) encompassing the D1 and the D7 region were obtained from 16 dipteran species and families to reconstruct early phylogenetic events in the order Diptera. For outgroup comparison, the corresponding sequences were used from representative taxa of the Siphonaptera, Mecoptera, and Lepidoptera. A subset of 488 unambiguously alignable sites was analyzed with respect to important sequence evolution parameters. We found (1) sequence variability is significantly higher in double-stranded sites than in single-stranded sites, (2) transitions are close to saturation in most pairwise sequence comparisons, (3) significant substitution rate heterogeneity exists across sites, and (4) significant substitution rate heterogeneity exists among lineages. Tree reconstruction was carried out with the neighbor joining, maximum parsimony, and maximum likelihood methods. Four major subgroups are consistently and robustly supported: the Brachycera, the Culicomorpha, the Tipulomorpha sensu stricto, and the hitherto controversial Bibionomorpha sensu lato, which includes the families Sciaridae, Mycetophilidae, Cecidomyiidae, Bibionidae, Scatopsidae, and Anisopodidae. The phylogenetic relationships within or among these subclades and the positions of the families Psychodidae and Trichoceridae were not robustly resolved. These results support the view that the mouthparts of extant dipteran larvae evolved from a derived ground state characterized by subdivided and obliquely moving mandibles. Furthermore, sequence divergence and the paleontological record consistently indicate that a period of rapid cladogenesis gave rise to the major dipteran subgroups.

Evolution and Phylogeny of the Diptera: A Molecular Phylogenetic Analysis Using 28S rDNA Sequences

Portions of the large ribosomal subunit RNA gene (28S rDNA) encompassing the Dl and the D7 region were obtained from 16 dipteran species and families to reconstruct early phylogenetic events in the order Diptera. For outgroup comparison, the corresponding sequences were used from representative taxa of the Siphonaptera, Mecoptera, and Lepidoptera. A subset of 488 unambiguously alignable sites was analyzed with respect to important sequence evolution parameters. We found (1) sequence variability is significantly higher in double-stranded sites than in single-stranded sites, (2) transitions are close to saturation in most pairwise sequence comparisons, (3) significant substitution rate heterogeneity exists across sites, and (4) significant substitution rate heterogeneity exists among lineages. Tree reconstruction was carried out with the neighbor joining, maximum parsimony, and maximum likelihood methods. Four major subgroups are consistently and robustly supported: the Brachycera, the Culicomorpha, the Tipulomorpha sensu stricto, and the hitherto controversial Bibionomorpha sensu lato, which includes the families Sciaridae, Mycetophilidae, Cecidomyiidae, Bibionidae, Scatopsidae, and Anisopodidae. The phylogenetic relationships within or among these subclades and the positions of the families Psychodidae and Trichoceridae were not robustly resolved. These results support the view that the mouthparts of extant dipteran larvae evolved from a derived ground state characterized by subdivided and obliquely moving mandibles. Furthermore, sequence divergence and the paleontological record consistently indicate that a period of rapid cladogenesis gave rise to the major dipteran subgroups.

Dating the evolutionary radiations of the true fungi

In this paper we construct a relative time scale for the origin and radiation of major lineages of the true fungi, using the 18S ribosomal RNA gene sequence data of 37 fungal species, and then calibrate the time scale using fossil evidence. Of the sequences, 28 were from the literature or data banks and the remaining 9 are new. To estimate the order of origin of fungal lineages we reconstructed the phylogeny of the fungi using aligned sequence data. To compensate for the differences in nucleotide substitution rates among various fungal lineages, we normalized the pairwise substitution data before estimating the relative timing of fungal divergences. We divided the fungi into nine groups. We then calculated the average percent substitution for each group, and also the average for all the groups, for the time period beginning when the fungi diverged from a common ancestor and ending at the present. We used the ratios of group-specific percent substitutions to the average percent substitution to normalize our pairwise substitution data matrix. To infer the relative timing of the origin of lineages we superimposed the normalized percentages of nucleotide substitutions onto the parsimony-based phylogeny. Calibrating the rate of sequence change involved relating the normalized percent substitution associated with phylogenetic events to fungal fossils, the ages of fungus hosts, and ages of symbionts. These calibration points were consistent with a substitution rate of 1% per lineage per 100 Ma. Based on phylogeny and calibrated percent substitution, the terrestrial fungi diverged from the chytrids approximately 550 Ma ago. After plants invaded the land approximately 400 Ma ago, ascomycetes split from basidiomycetes. Mushrooms, many ascomycetous yeasts, and common molds in the genera Penicillium and Aspergillus may have evolved after the origin of angiosperm plants and in the last 200 Ma. Key words: fungus evolution, molecular clock, ascomycete phylogeny, basidiomycete phylogeny, 18S rRNA.

DNA sequence variation at the period locus within and among species of the Drosophila melanogaster complex.

A 1.9-kilobase region of the period locus was sequenced in six individuals of Drosophila melanogaster and from six individuals of each of three sibling species: Drosophila simulans, Drosophila sechellia and Drosophila mauritiana. Extensive genealogical analysis of 174 polymorphic sites reveals a complex history. It appears that D. simulans, as a large population still segregating very old lineages, gave rise to the island species D. mauritiana and D. sechellia. Rather than considering these speciation events as having produced "sister" taxa, it seems more appropriate to consider D. simulans a parent species to D. sechellia and D. mauritiana. The order, in time, of these two phylogenetic events remains unclear. D. mauritiana supports a large number of polymorphisms, many of which are shared with D. simulans, and so appears to have begun and persisted as a large population. In contrast, D. sechellia has very little variation and seems to have experienced a severe population bottleneck. Alternatively, the low variation in D. sechellia could be due to recent directional selection and genetic hitchhiking at or near the per locus.

CONGRUENCE BETWEEN SUPERPOSITIONAL AND PHYLOGENETIC PATTERNS: COMPARING CLADISTIC PATTERNS WITH FOSSIL RECORDS

Abstract— As the only direct evidence of past organismic history, the fossil record has always figured importantly in the reconstruction of phylogeny. But the incomplete nature of the fossil record has also been cited as a basis for claiming that fossils play only a secondary role in developing phylogenetic hypotheses that encompass extant taxa. The reliability of fossil data in such applications is a function of the degree of fit between superpositional relationships and the sequence of phylogenetic events. Thirty‐eight vertebrate cases are examined for the fit between age data based on fossil first occurrences and phylogenetic results based on cladistic analysis. A general correspondence between superpositional and cladistic information is observed, although the degree of fit varies widely among cases. Horses, certain other ungulates, synapsids and basal archosaurs, which show very high correlations, are taxa characterized by an abundance of superpositional and cladistic data. Other groups, such as primates, show very poor correlations because certain major clades have either unreasonably short fossil durations or no fossil record at all. Correlations are also diminished when either fossil records or cladistic sequences are poorly resolved. In most cases, cladistic resolution was observed to exceed superpositional resolution. Correlations can be enhanced by more precise (e.g. radiometric) age dates, but these also place a high expectation on the fit between fossil first occurrence and cladistic results. Stratigraphic occurrence does not always provide a precise reflection of independently derived phylogenies, but the correspondence between age and cladistic information is remarkably high in a notable number of vertebrate examples.

Fossils, Topologies, Missing Data, and the Higher Level Phylogeny of Eutherian Mammals

?The claim that fossils strongly influence the outcome of phylogenetic analysis for extant taxa has been recently demonstrated in a study of higher amniote relationships (Gauthier, Kluge, and Rowe, 1988, Cladistics 4:105-209). Similar, albeit more limited, effects are also apparent in the case of higher (eutherian) mammal phylogeny. For example, the incorporation of selected fossil taxa shifts the balance of evidence concerning hyracoid relationships in favor of a close affinity between this order and sirenians and proboscideans (Tethytheria). The use of fossils introduces character conflict to a grouping of hyracoids and perissodactyls, indicating that some traits shared by extant hyracoids and extant perissodactyls were acquired independently. Al? though analysis of the combined (Recent and fossil) data set favors the hyracoid-tethythere dade over the hyracoid-perissodactyl dade in the most parsimonious tree, the former grouping is highly vulnerable to collapse when minor homoplasy is introduced. This instability is expected because the fossils function as transitional taxa, with the effect of reducing the number of characters for particular nodes. At the same time, such transitional taxa can more precisely represent the actual transformation events and accordingly provide important information on phylogenetic history. The overall effects of fossils in analysis of higher eutherian mammals is much more subtle than in the amniote case. A primary reason for this discrepancy appears to be the large proportion of characters for extant amniote taxa that show marked transformation relevant to early splitting events. This level of information loss though marked transformation is not as evident in the case of the mammalian orders. Both extant and fossil taxa can introduce major shifts to the original topology of a given tree. Nonetheless, the tendency for fossils to preserve characters lost in living taxa suggests a pivotal role for fossils in many current and pending studies. [Phylogeny; fossils; cladistics; eutherian mammals.] In recent years, the assertion that fossils only play a secondary role in phylogenetic reconstruction (Hennig, 1966; Patterson, 1981; Goodman, 1989) has been countered by cladistic studies that incorporate both fossil and extant taxa. A comprehensive study by Gauthier et al. (1988) was claimed as an example of the critical use of fossil taxa in establishing the interrelationships of higher amniotes. In lieu of the fossils, a close relationship between birds and mammals was suggested regardless of var? ious interpretations of the character evi? dence (Gardiner, 1982; Gauthier et al., 1988). When fossil taxa were added, any one of a number of fossil synapsids ("mam? mallike" reptiles) was sufficient to shift mammals outside a group that comprised turtles, lepidosaurs, crocodiles, and birds as successively closer relatives (Gauthier et al., 1988: their Fig. 3). This exercise effec? tively demonstrates that fossils can resolve phylogenetic events that may be out of reach of evidence derived purely from ex? tant forms. The amniote case, however, d es not erase the possibility that further a dition of extant taxa might critically overturn a phylogeny that incorporates fossils. Moreover, there is no guarantee that fossils will always have such a crucial bear? ing on phylogenetic questions involving extant taxa (Donoghue et al., 1989). Fossil data did not drastically alter the topology of the major seed plant groups indicated by extant taxa alone (Doyle and Donoghue, 1987). Addition of several higher fossil groups had little effect on the relationships identified for extant eutherian mammalian orders (Novacek, 1989). Fossils lacking a large proportion of relevant characters can contribute substantially to the instability and poor resolution of cladograms (Rowe, 1988; Greenwald, 1989; Novacek, 1989). What, then, are the circumstances under which fossils are likely to provide impor? tant insight on relationships among extant

Polyploidy in differentiation and evolution

Somatic and generative (germ-line) polyploidy are more widely spread phenomena among living organisms than generally thought. The occurrence of polyploidization and related events in normal and pathological differentiation, their recognized main functions, as well as the structural specificities of polyploid nuclei are reviewed, and the relationship between ontogenetic and phylogenetic events is discussed. The mechanisms leading to the polyploid state, as well as other processes resulting in a genomic condition different from the diploid one (such as DNA under-replication, gene amplification, and chromatin elimination), are briefly sketched. The various changes in chromosomal DNA described are, in conclusion, seen as evidence supporting the paradigm of a "fluid" or dynamic organization of the eukaryotic genome, as being part of a cybernetic feedback regulation system of gene expression. A model is proposed that unifies the aspects of DNA variation, chromatin structure, and diversification in ontogenesis and phylogenesis.

Evolutionary Patterns in Advanced Snakes

One prevalent view of phylogenetic events in advanced snakes holds that the fangs evolved along at least two pathways one (e.g. elapids) from ancestors with enlarged anterior and the other (e.g. viperids) from ancestors with enlarged posterior maxillary teeth. Selective forces driving these changes are presumed to arise from the increasing advantages of teeth and glands in venom injection. In this paper another plausible view of these events is proposed. First fangs of both elapids and viperids likely evolved from real maxillary teeth. In non-venomous snakes, differences in tooth morphology and function suggest that there may be some division of labor among anterior and posterior maxillary teeth. Anterior maxillary teeth, residing forward in the mouth likely serve the biological role of snaring and impaling prey during the strike. They are also conical frequently recurved and lack a secretion groove. On the other hand posterior teeth because of their geometric position on the maxilla and mechanical advantages, tend to serve as aids in preingestion manipulation and swallowing of prey. They are often blade shaped and occasionally bear a secretion groove along their sides. Although both front and rear maxillary teeth of nonvenomous snakes may be elongated this is likely to serve these different functional roles and hence they evolved under different selective pressures. When fangs evolved they did so several times independently but from rear maxillary teeth. In support one notes a) the similar position postorbital of venom and Duvernoy s glands b) similar embryonic development of fangs and rear maxillary teeth c) secretion groove when present, is found only on rear teeth and d) similar biological roles of some rear teeth and fangs. For ease in clearance of the prey during the strike the fangs are positioned forward in the mouth accomplished in viperid snakes by forward rotation of the maxilla and elapids by rostral anatomical migration to the front of the maxilla. Second, the adaptive advantage first favoring initial rear tooth enlargement likely centered not on their role in venom injection but rather on their role in preingestion manipulation and swallowing. However once enlarged, teeth would be preadapted for later modification into fangs under selection pressures arising from advantages of venom introduction. This has implications for the function and evolution of associated structures. Besides possibly subduring or even killing of prey the secretion of Duvernoy's gland may be involved in digestion or in neutralizing noxious or fouling products of the prey. The presence or absence of constriction need not be functionally tied to absence or presence of venom injection. The phylogenetic pathways outlined herein were likely traveled several times independently in advanced snakes.

An ancient divergence among the bacteria

The 16S ribosomal RNAs from two species of methanogenic bacteria, the mesophile Methanobacterium ruminantium and the thermophile Methanobacterium thermoautotrophicum, have been characterized in terms of the oligonucleotides produced by digestion with T1 ribonuclease. These two organisms are found to be sufficiently related that they can be considered members of the same genus or family. However, they bear only slight resemblance to "typical" Procaryotic genera; such as Escherichia, Bacillus and Anacystis. The divergence of the methanogenic bacteria from other bacteria may be the most ancient phylogenetic event yet detected--antedating considerably the divergence of the blue green algal line for example, from the main bacterial line.

Primate Phylogeny, Neutral Mutations, and "Molecular Clocks"

Read, D. W. (Department of Anthropology, University of California, Los Angeles, California 90024) 1975. Primate phylogeny, neutral mutations, and clocks. Syst. Zool. 24:209-221.-Dates for the primate phylogeny based on fossil evidence contradict those obtained from albumin as a Consequently the theoretical basis for a is reviewed to determine if the albumin has been calibrated in accordance with that theory. The neutral mutation model and data relating amino acid differences to time of divergence of species based on fossil evidence suggest a reasonably linear relationship when the number of differences is corrected for multiple mutations at the same locus. This disagrees with the assumption of a linear relationship between time and number of differences that has been used for calibrating the albumin clock. When corrected, the albumin clock yields dates that are contradicted by fossil evidence. It is then argued that the second assumption used for calibrating the clock, of an exponential relationship between ID values and amino acid differences, inadequately fits experimental data. Two plausible equations for relating ID values and amino acid differences that fit the data better are given. Depending 'on the equation used and the time assigned to the hominoid-cercopithecoid divergence, time estimates for the pongid-hominid split ranging from 5 X 106 to 12 X 10' years BP are obtained. As a date of 10 X 100 years BP for the pongid-hominid split is not contradicted by data on other proteins and is supported by evidence on regular change in cranial capacity with respect to time, the time period 10-15 X 10' years BP is a reasonable estimate for the hominid-pongid ivergence consistent with both the molecular and fossil evidence. [Primates; neutral mutations; molecular clocks.] The concept (Zuckerkandl and Pauling, 1965) is one of the more provocative ideas applicable to palaeontological data that has come out of molecular biology in the last few years. That it has enormous potential as a procedure for dating phylogenetic events is unquestioned. Equally unquestionable, though, is the fact that a clock' must be accurately calibrated if it is to fulfill its purpose. Dates for the primate phylogeny obtained from application of the concept to extant primates with albumin as the cloclk' (Sarich and Wilson, 1967a, 1967b; Sarich, 1968, 1971, 1972b; Wilson and Sarich, 1969) contradict those derived from fossil evidence. This discrepancy would, on the one hand, be a proper challenge to present interpretations of the fossil record if the 'clock dates are accurate, but on the other, simply be a meaningless issue if those dates are incorrect. Hence it needs to be determined whether the albumin has been accurately calibrated. Although dates for the primate phylogeny based on the fossil record contradict the albumin clock dates, and so seemingly are sufficient evidence for refuting the albumin clock dates (Leakey, 1970), the fossil evidence is not without controversy. Primate fossil data, especially the assignment of particular fossils to a specific taxon (such as the material belonging to the genus Ramapithecus to the family' Hominidae), are uncertain (cf. the recent reconstruction of Ranmpithecus wickeri by Walker and Andrews (1973) which challenges hominine status for Rampithecus) and so alone are insufficient evidence for refuting the albumin 'clock dates. The accuracy, or lack thereof, of the albumin <clock7 must be determined directly from the model and data used in its calibration. Criticisms (Buettner-Janusch, 1969;

PALEOBOTANY, PHYLOGENY, AND A NATURAL SYSTEM OF CLASSIFICATION

SummaryIn response to skeptics who feel that the contribution of paleobotany to phylogeny is minimal, I have presented a number of examples where the fossil plant record has played an important role in demonstrating origins and relationships of various plant groups. Work on Precambrian thallophytes is one area where knowledge of earliest plant forms is taking on a definite form. New finds on the origin and evolution of Devonian land plants are presenting a clearer picture of early vascular plant evolution. Existence of such plants as the Progymnospermopsida has made it possible to understand the steps leading to the origin of gymnosperms. We now have important new knowledge concerning the evolution of the seed habit, as well as subsequent seed plant evolution. These are but a few examples of the contribution of paleobotany to phylogeny. This increasing sophistication in understanding phylogenetic events is indispensible for a system of plant classification that reflects relationships. Such a system of classification, I maintain, is much more meaningful than any other.