Duarte et al.
Abstract.-- The model of development and evolution of complex morphological structures conceived by Atchley and Hall (1991), which establishes that changes at the macroscopic, morphogenetic level can be statistically detected as variation in skeletal units at distinct scales, was applied in combination with the formalism of geometric morphometrics to study variation in mandible shape among populations of the rodent species Thrichomys apereoides. The thin-plate spline technique produced geometric descriptors of shape derived from anatomical landmarks in the mandible which were used with graphical and inferential approaches to partition the contribution of global and localized components to the observed differentiation in mandible shape. A major pattern of morphologic differentiation in T. apereoides is attributable to localized components of shape at smaller geometric scales associated with specific morphogenetic units of the mandible. On the other hand, a clinal trend of variation is associated primarily with localized components of shape at larger geometric scales. Morphogenetic mechanisms assumed to be operating to produce the observed differentiation in the specific units the mandible include mesenchymal condensation differentiation, muscle hypertrophy, and tooth growth. Perspectives for the application of models of morphological evolution and geometric morphometrics to morphologically based systematic biology are considered. [Morphological evolution; complex morphological structures; geometric morphometrics; thin-plate splines; Thrichomys apereoides.]
Gatesy and Arctander
Abstract. --The saola, Pseudoryx nghetinhensis, was unknown to science until its formal description in 1993. This endangered species is a member of the ruminant artiodactyl family Bovidae (cattle, sheep, goats, and antelopes). However, given its puzzling combination of morphological traits, the specific affinities of Pseudoryx within Bovidae are controversial. A preliminary genetic investigation suggested that Pseudoryx should be placed in the subfamily Bovinae (cattle, buffaloes, spiral-horned antelopes, and nilgai), but a recent cladistic analysis of skeletal and dental characters allied Pseudoryx with caprine bovids (sheep, goats, musk oxen, goat antelopes, and Pantholops). The morphological and molecular hypotheses differ in assigning the saola to either of the two most divergent clades of Bovidae. In this report, phylogenetic analyses of DNA sequences from five genes are used to test these alternatives. Protein coding regions, introns, and ribosomal DNAs from the nuclear and mitochondrial genomes discount the hypothesis that Pseudoryx is a close relative of Caprinae. Instead, combined analyses of the DNA data and published morphological evidence place Pseudoryx with Bovini (cattle and buffaloes), a subclade of Bovinae. In separate analysis, the matrix of morphological characters links Pseudoryx with caprine bovids, but in the context of the molecular data, the gross anatomical evidence strongly supports a grouping of Pseudoryx with Bovinae. Surprisingly, the morphological partition provides the most character support in the combined analysis. This striking result is obscured by separate analyses of the individual data sets and the taxonomic congruence approach. [saola, Pseudoryx, Bovidae, Vu Quang, hidden support]
Giribet et al.
Abstract.--Triploblastic relationships were examined in the light of molecular and morphological evidence. Representatives for all triploblastic "phyla" (except Loricifera) were represented by both sources of phylogenetic data. The 18S ribosomal (rDNA) sequence data for 145 terminal taxa and 276 morphological characters coded for 36 supraspecific taxa were combined in a total evidence regime to determine the most consistent picture of triploblastic relationships for these data. Only triploblastic taxa are used to avoid rooting with distant outgroups, as seems to be the case due to the extreme distance that separates diploblastic from triploblastic taxa based on 18S rDNA data. Multiple phylogenetic analyses are performed with variable analysis parameters yielding largely inconsistent results for certain groups such as Chaetognatha, Acoela and Nemertodermatida. A normalized incongruence length metric is used to assay the relative merit of the multiple analyses. The combined analysis with lowest character incongruence yields the following scheme of relationships of four main clades: (1) Deuterostomia [((Echinodermata + Enteropneusta) (Cephalochordata (Urochordata + Vertebrata)))]; (2) Ecdysozoa [(((Priapulida + Kinorhyncha)(Nematoda + Nematomorpha))((Onychophora + Tardigrada)Arthropoda))]; (3) Trochozoa [((Phoronida + Brachiopoda)(Entoprocta(Nemertea(Sipuncula(Mollusca(Pogonophora(Echiura + Annelida)))))))]; and (4) Platyzoa [((Gnathostomulida(Cycliophora + Syndermata))(Gastrotricha + Plathelminthes))]. Chaetognatha, Nemertodermatida, and Bryozoa cannot be assigned to any one of these four groups. For the first time a data analysis recognizes a clade of acoelomates, the Platyzoa (sensu Cavalier-Smith, 1998). Other relationships that corroborate some morphological analyses are the existence of a clade that groups Gnathostomulida + Syndermata (=Gnathifera) that is expanded to include the enigmatic phylum Cycliophora, as sister group to Syndermata. [18S rRNA; morphology; phylogeny; Metazoa; Triploblastica; Platyzoa; Ecdysozoa]
Hormiga et al
Abstract.-- Extreme sexual body size dimorphism (SSD), in which males are only a small fraction of the size of the females, occurs only in a few, mostly marine, taxonomic groups. Spiders are the only terrestrial group in which small males are relatively common, particularly among orb-weavers (especially in the families Tetragnathidae and Araneidae) and crab spiders (Thomisidae). We use a taxonomic sample of 80 genera to study the phylogenetic patterns (origins and reversals) of SSD in orb-weaving spiders (Orbiculariae). We collected and compiled male and female size data (adult body length) for 536 species. Size data were treated as a continuous character and ancestral sizes, for males and females separately, were reconstructed using Wagner parsimony on a cladogram for the 80 genera used in this study. Of the 80 genera in the analysis, 24 were female-biased dimorphic (twice or more the body length of the male); the remaining 56 genera were monomorphic. Under parsimony only four independent origins of dimorphism are required: in the theridiid genus Tidarren, in the distal nephilines, in the "argiopoid clade," and in the araneid genus Kaira. Dimorphism has reversed to monomorphism at least seven times, all of them within the large "argiopoid clade." The four independent origins of dimorphism represent two separate instances of an increase in female size coupled with a decrease of male size (involving only two genera), and two separate instances of an increase in female size with male size either remaining the same or increasing, but not as much as females (involving 30 genera). In orb-weaving spiders far more taxa are sexually dimorphic as a result of female size increase (22 genera) than as a result of male size decrease (two genera). SSD in orb-weaving spiders encompasses several independent evolutionary histories that together suggest a variety of evolutionary pathways. This multiplicity strongly refutes all efforts to date to find a general explanation for either the origin or maintenance (or both) of SSD, because the different pathways very likely will require distinctly different, possibly unique, explanations. Each pattern must be understood historically before its origin and maintenance can be explained in ecological and evolutionary terms. The most frequently cited example of male dwarfism in spiders, the golden orb spider genus Nephila (Tetragnathidae), is in fact a case of female giantism, not male dwarfism. [Araneae; continuous characters; Orbiculariae; parsimony; sexual size dimorphism; spiders.]
Maddison and McMahon
Abstract. --- Populations of the jumping spider Habronattus pugillis Griswold isolated on nearby mountain ranges in southern Arizona are differentiated in many features of the males (color, shape and orientation of setae on face, shape of carapace, markings of palpi and legs, motions during courtship behavior). These features are (mostly) consistent within a range and different between ranges. The concentration of differences to male courtship behavior and body parts exposed to the female during courtship and correlations between form and courtship behavior suggest sexual selection was involved in the differentiation. A phylogenetic analysis of the populations yields a tree that for the most part groups geographic neighbors, but the history of H. pugillis populations may not be adequately described by a tree. Geographic proximity of apparent convergences suggests that populations from at least some of the mountain ranges acquired characteristics through introgression. Lowering of the woodland habitat during the last glacial period probably brought some populations into contact, but it is not clear if the interrange woodlands would have provided corridors for extensive mixing. [Phylogeny; differentiation; homoplasy; hybridization; sexual selection; geographic variation; speciation; spiders; Salticidae.]
Miyamoto et al.
Abstract.--The complete protein-coding sequences of the c-myc proto-oncogene were determined for five species of four new orders of eutherian (placental) mammals. These newly obtained sequences were aligned to each other and to other available orthologues for the phylogenetic estimation of eutherian interordinal relationships. Several measures of sequence difference and base composition were first calculated to assess the major evolutionary properties of the three codon positions and two protein-coding exons of the gene. On the basis of these calculations, different parsimony, distance, and maximum likelihood approaches were adopted, with the most sophisticated involving the separate, then combined, likelihood analyses of the third codon positions of exon 2 vs. all other sites. These phylogenetic approaches provide clear support for the grouping of Chiroptera (bats) with Artiodactyla (ruminants, camels, and pigs) and Carnivora (cats, dogs, and their allies), an interordinal arrangement that receives strong corroboration from other lines of evidence including complete mitochondrial DNA sequences. In contrast, these analyses fail to provide strong to reasonable support for any other interordinal group. This study concludes with specific recommendations about sampling and other strategies for maximizing the phylogenetic contributions of the c-myc gene to the continued resolution of the eutherian ordinal tree. [Eutherian mammals; Chiroptera; phylogeny; c-myc gene; DNA sequences; maximum likelihood.]
Paterson et al.
Abstract. - We investigated the coevolutionary history of seabirds (orders Procellariiformes and Sphenisciformes) and their lice (order Phthiraptera). Independent trees were produced for the seabirds (tree derived from 12S ribosomal RNA (rRNA), isozyme, and behavioral data) and their lice (trees derived from 12S rRNA data). Brooks parsimony analysis (BPA) supported a general history of cospeciation (consistency index = 0.84, retention index = 0.81). We inferred that the homoplasy in the BPA was caused by one intrahost speciation, one potential host switching and eight or nine sorting events. Using reconciliation analysis we quantified the cost of fitting the louse tree onto the seabird tree. The reconciled TreeMap tree postulated one host switching, nine cospeciation, three or four intrahost speciation and 11 to 14 sorting events. The number of cospeciation events was significantly more than would be expected due to chance. The sequence data were used to test for rate heterogeneity for both seabirds and lice. The seabird tree showed no significant rate heterogeneity over all of its branches whereas part of the louse tree did show rate heterogeneity. An examination of the codivergent nodes revealed that seabirds and lice have cospeciated synchronously, and that lice have evolved at about 5.5 times the rate of seabirds. Sequence data supported some of the postulated intrahost speciation events (Halipeurus pre-dated the evolution of their present hosts). Sequence data also supported some of the postulated host-switching events. These results demonstrate the value of sequence data and reconciliation analyses in unraveling complex histories between hosts and their parasites. [BPA; cospeciation; host-switching; lice; Procellariiformes; reconciliation analysis; relative rate test; seabirds; sorting events; Sphenisciformes.]
Renner et al
Abstract. -Previous studies of the small Southern Hemisphere family Atherospermataceae have drawn contradictory conclusions regarding the number of transantarctic disjunctions and role of transoceanic dispersal in its evolution. Clarification of intergeneric relationships is critical to resolving (1) whether the two Chilean species, Laurelia sempervirens and Laureliopsis philippiana, are related to different Australpacific species, implying two transantarctic disjunctions as suggested by morphology; (2) where the group is likely to have originated; and (3) whether observed disjunctions reflect the breakup of Gondwana. We analyzed chloroplast DNA sequences from six regions (the rbcL gene, the rpl16 intron, and the trnL-trnF, trnT-trnL, psbA-trnH, and atpB-rbcL spacer regions; together 4,338 bp) for all genera and most species of Atherospermataceae, using parsimony and maximum likelihood (ML). The family's sister group, the Chilean endemic Gomortega nitida (Gomortegaceae), was used to root the tree. Parsimony and ML yielded identical single best trees that contain three well supported clades (>80% bootstrap): Daphnandra and Doryphora from south-eastern Australia; Atherosperma and Nemuaron from Australia-Tasmania and New Caledonia, respectively; and Laurelia novae-zelandiae and Laureliopsis philippiana from New Zealand and Chile, respectively. The second Chilean species, Laurelia sempervirens, is sister to this last clade. A likelihood ratio test rejects the molecular clock for the full rbcL data set, but the clock assumption holds for the ingroup. The atherosperm fossil record goes back to the Upper Cretaceous and includes pollen, wood, and leaf fossils from Europe, Africa, South America, Antarctica, New Zealand, and Tasmania. Calibration of rbcL substitution rates with the fossils suggest an initial diversification of the family at 100-140 million years ago (MYA), likely in West Gondwana, early entry into Antarctica, and long distance dispersal to New Zealand and New Caledonia at 50-30 MYA by the ancestors of L. novae-zelandiae and Nemuaron. [Biogeography, Gondwana, likelihood ratio test, maximum likelihood, molecular clock, phylogeny, rbcL substitution rates]
Sang and Zhong
Abstract. - Hybridization is an important evolutionary mechanism in plants and has been increasingly documented in animals. Difficulty in reconstruction of reticulate evolution, however, has been a long-standing problem in phylogenetics. Consequently, hybrid speciation may play a major role in causing topological incongruence between gene trees. The incongruence, in turn, offers an opportunity to detect hybrid speciation. Here we characterized certain distinctions between hybridization and other biological processes, including lineage sorting, paralogy, and lateral gene transfer, that are responsible for topological incongruence between gene trees. Given two incongruent gene trees with three taxa, A, B, and C, B is a sister group of A on gene tree 1 but a sister group of C on gene tree 2. With a theoretical model based on the molecular clock, we demonstrate that time of divergence of each gene between taxa A and C is nearly equal in the case of hybridization (B is a hybrid) or lateral gene transfer, but differs significantly in the case of lineage sorting or paralogy. A bootstrap test was developed to test these alternative hypotheses. The model and test were extended to account for incongruent gene trees with numerous taxa. Computer simulation studies supported the validity of the theoretical model and bootstrap test when each gene evolves at a constant rate. The computer simulation also suggested that the model remains valid as long as the rate heterogeneity occurs proportionally in the same taxa for both genes. Although the model could not test hypotheses of hybridization versus lateral gene transfer as the cause of incongruence, these two processes may be distinguished by comparison of phylogenies of multiple unlinked genes [hybridization, phylogeny, gene tree, species tree, topological incongruence].
Abstract. - Three-taxon statement analysis (3TA) and standard cladistic analysis (SCA) were evaluated relative to propositions of taxic homology. There are definite distinctions between complement relation homologues and paired homologues. The complement relation is discussed, relative to rooting, parsimony and taxic propositions of homology. The complement relation, as implemented in SCA, only makes sense because SCA is a simple evolutionary model of character-state transformation. 3TA is a method for implementing complement relation data from a taxic perspective. The standard approach to cladistic analysis distinguishes taxa by rooting a tree, which means that that approach is incompatible with taxic propositions of homology because a taxic homology is a hypothesis of relationship between taxa that possess a homologue relative to taxa that lack a homologue. It is not necessary to treat paired homologues from a transformational perspective to distinguish informative from uninformative data. 3TA yields results significantly different from those of SCA. SCA, which seeks to minimize tree length, may not maximize the relation of homology (congruence) relative to a tree. [Taxic homology, cladistics, three-taxon statement analysis]
Wagner and Sidor
Abstract. - Paleontologists frequently contrast clade rank (i.e., nodal or patristic distance from the base of a cladogram) with age rank (i.e., relative first known appearances of the analyzed taxa) to measure the degree of congruence between the estimated phylogeny and the fossil record. Although some potential biases of these methods have been examined (e.g., the effect of tree imbalance), other properties of age rank / clade rank (ARCR) comparisons have not been studied in detail. A basic premise of ARCR metrics is that outgroup taxa diverged earlier than ingroups and thus should first appear in older strata. For example, given phylogeny (A,(B,C)), then taxon A should be sampled before either taxon B or taxon C. We examine this premise in the context of (1) phylogenetic theory, (2) taxonomic practice, (3) sampling intensity (R), and (4) factors other than sampling intensity (including cladogram accuracy). Simulations combining clade evolution and sampling over time indicate a poor relationship between ARCR metrics and R when all taxa are apomorphy-based monophyletic groups. However, a good relationship exists when taxa are either stem-based monophyletic groups or if workers include taxa without a priori decisions about monophyly or paraphyly. These results are not surprising because cladograms predict the order in which lineages diverged (which applies to stem-based monophyletic taxa) and the order in which morphologic grades appeared (which applies to paraphyletic taxa relative to derived monophyletic groups). Other factors that elevate ARCR metrics when average R is the same include high temporal variation in R, budding instead of bifurcating speciation patterns, low extinction rates, cladogram inaccuracy and (to a much lesser extent) large clade size. These results suggest several plausible explanations for patterned differences in ARCR metrics among clades, thereby compromising their validity as measures of the quality of the fossil record. [fossils, parsimony, simulations, stratigraphic consistency.]
Abstract. -Nucleotide sequences of the mitochondrial protein coding cytochrome (cytb) b (650 bp) and small-subunit 12S ribosomal RNA (~350 bp) genes were used in analyses of phylogenetic relationships among extant phrynosomatid sand lizards, including an examination of competing hypotheses regarding the evolution of "earlessness." Sequences were obtained from all currently recognized species of sand lizards as well as representatives of the first and second outgroups and analyzed using both parsimony and likelihood methods. The cyt b data offer strong support for relationships corresponding with relatively recent divergences and moderate to low levels of support for relationships reflecting more ancient divergences within the clade. These data support monophyly of the "earless" taxa, the placement of Uma as the sister taxon to the other sand lizards, and monophyly of all four taxa traditionally ranked as genera. All well-supported relationships in the 12S phylogeny are completely congruent with well-supported relationships in the cyt b phylogeny; however, the 12S data alone provide very little support for deeper divergences. Phylogenetic relationships within species are concordant with geography and suggest patterns of phylogeographic differentiation, including the conclusion that at least one currently recognized species (Holbrookia maculata) is composed of more than one species. By independently optimizing likelihood model parameters for various subsets of the data, we found that nucleotide substitution processes vary widely between genes, and among the structural and functional regions or classes of sites within each gene. Therefore, we compared competing phylogenetic hypotheses using parameter estimates specific to those subsets, analyzing the subsets separately and in various combinations. The hypothesis supported by the cyt b data was favored over rival hypotheses in all but one of the five comparisons made using the entire data set, including the set of partitions that best explained the data, although we were unable to confidently reject (P < 0.05) alternative hypotheses. Our results highlight the importance of optimizing models and parameter estimates for different genes or parts thereof--a strategy that takes advantages of the strengths of both combining and partitioning data. [Phrynosomatidae; Sand lizards; Phylogeny; Mitochondrial DNA; Cytochrome b; 12S RNA; Combining data; Maximum Likelihood]