Bayesian Optimality Criteria Research Articles

Phylogenetic relationships among spiny pocket mice (Heteromys) inferred from mitochondrial and nuclear sequence data

In recent years molecular data have been used increasingly to estimate phylogenies and aid in species delimitation. We generated and analyzed sequence data for spiny pocket mice (Heteromys) for the mitochondrial gene cytochrome b (1,140 base pairs [bp]) and 2 nuclear gene segments, MYH6 (252 bp) and EN2 (189 bp). We used maximum-parsimony, maximum-likelihood, and Bayesian optimality criteria to estimate relationships among species and provide a framework for using a species-delimitation method to investigate the possibility of multiple species within the widespread H. desmarestianus group. We recovered several well-supported clades within this complex, including H. goldmani, H. oresterus, and H. nubicolens. Incorporating karyotype, allozyme, and morphological data from earlier studies, we found sufficient supporting evidence to justify maintaining H. goldmani, H. oresterus, and H. nubicolens as species and identifying 4 additional clades as candidate species. We present a revised taxonomic arrangement within the genus. The subgenus Xylomys should be retained and be composed of H. nelsoni. The subgenus Heteromys should be divided into 3 species groups: the H. anomalus group (H. anomalus and H. australis) together with H. catopterius, H. oasicus, and H. teleus (insertae sedis); the H. gaumeri group (H. gaumeri); and H. desmarestianus group (H. desmarestianus, H. goldmani, H. oresterus, H. nubicolens, and the 4 candidate species). DOI: 10.1644/09-MAMM-A-287.1.

Evolution and systematic value of fruit and seed characters in Adoxaceae (Dipsacales)

AbstractThis study presents a description of the morphology and anatomy of the fruits and seeds of Adoxa, Sambucus, and Viburnum. A phylogenetic study included Adoxa moschatellina, Sinadoxa corydalifolia, Sambucus, Tetradoxa omeiensis, and Viburnum. All major clades of Caprifoliaceae, the sister family of Adoxaceae, were sampled and used as outgroup. Maximum parsimony and Bayesian inference optimality criteria were used to analyze three datasets, molecular data (ITS, trnK, matK), morphological data (21 fruit and seed characters), and a combined dataset. We used parsimony optimization to study character evolution. Results of the phylogenetic analyses were congruent with previously published results. Viburnum is the basalmost lineage in the family and sister to subfamily Adoxoideae. In Adoxoideae, Sambucus is sister to the Adoxina clade (i.e., Adoxa, Sinadoxa, and Tetradoxa). Our results also confirmed the sister relationship between Sinadoxa corydalifolia and Adoxa plus Tetradoxa. For the first time, clear autapomorphies are described for Sambucus, such as a long, slender, cylindrical embryo, sclereids with a u–shaped sclerification pattern, a rugose endocarp surface, and numerous, small calcium oxalate crystals in the endocarp sclereids. Character evolution in Sambucus, however, is complex and a broader sampling is required to draw firm conclusions. The evolution toward Viburnum is marked by a number of shifts such as the development of small, amorphous crystals in endosperm cells and a well–developed, parenchymatous seed coat. Based on our results and previous studies we hypothesize a paedomorphic event took place at the origin of Adoxina. Evidence supporting this hypothesis is the presence of green fruits, weakly sclerified endocarp sclereids, small seeds, and semi–inferior ovaries in Adoxina. Finally, our results indicate that the first Adoxaceae were characterized by tricarpellate ovaries with an endocarp composed of an outer layer of sclereids and an inner layer of fibers. A thorough study of the fruits and seeds of Sinadoxa and Tetradoxa is vital to fully understand fruit and seed evolution in Adoxaceae.

Polyphyly of Xylosandrus Reitter inferred from nuclear and mitochondrial genes (Coleoptera: Curculionidae: Scolytinae)

The Xyleborina ambrosia beetle genus Xylosandrus contains 54 species, several of which are of economic importance. The monophyly of the genus was tested using a data set comprised of multiple gene loci: 28S rDNA; the mitochondrial gene cytochrome oxidase I (COI); and the nuclear genes arginine kinase (ArgK), rudimentary (CAD), and Elongation Factor 1alpha (EF-1alpha). The nuclear protein-coding genes CAD and ArgK were used for the first time in phylogenetics of Scolytinae. Analyses were performed using Parsimony and Bayesian optimality criteria. Our analyses included 43 specimens representing 15 Xylosandrus species and 20 species from Amasa, Anisandrus, Cnestus, Euwallacea and Xyleborus, and two species from the outgroup genus Coccotrypes. All analyses recovered a polyphyletic Xylosandrus. Several species of Xylosandrus were consistently placed in clades with the genera Anisandrus and Cnestus with high support values (100% bootstrap support). Among these, was the economically important invasive species X. mutilatus, which was consistently recovered as part of the "Cnestus" clade. In our analyses, both CAD and ArgK demonstrated phylogenetic utility across varying nodal depths. Despite the selection of genes with signals at complementary phylogenetic depths, the data set used herein did not resolve the phylogeny of Xylosandrus and related genera. Since the taxon sample available for molecular work represents only a fraction of Xylosandrus species, a complete revision that combines molecular and morphological data in a total evidence approach is recommended for the genus.

Evolution of fruit and seed characters in the Diervilla and Lonicera clades (Caprifoliaceae, Dipsacales).

The Diervilla and Lonicera clades are members of the family Caprifoliaceae (Dipsacales sensu Donoghue et al., 2001, Harvard Papers in Botany 6: 459-479). So far, the intergeneric relationships of the Lonicera clade and the systematic position of Heptacodium remain equivocal. By studying fruit and seed morphology and anatomy, an attempt is made to clarify these issues. In addition, this study deals with the evolution of fruit and seed characters of the Diervilla and Lonicera clades with reference to allied taxa. Light and scanning electron microscopy were used for the morphological and anatomical investigations. Phylogenetic analyses were carried out by applying the parsimony and Bayesian inference optimality criteria. Character evolution was studied by means of parsimony optimization and stochastic character mapping. Diervilla and Weigela (Diervilla clade) are characterized by several unique traits in Dipsacales, including capsules with numerous seeds, seed coats without sclerified outer tangential exotestal cell walls, and dehiscent fruits. Seeds with completely sclerified exotestal cells and fleshy fruits characterize the Lonicera clade. Leycesteria and Lonicera have berries, ovaries without sterile carpels and several seeds per locule, whereas Symphoricarpos and Triosteum have drupes, ovaries with one or two sterile carpels and a single seed per locule. Heptacodium shares several characteristics with members of the Linnina clade, e.g. achenes, single-seeded fruits and a compressed, parenchymatous seed coat. The results confirm the monophyly of the Diervilla and Lonicera clades and allow us to hypothesize a close relationship between Leycesteria and Lonicera and between Symphoricarpos and Triosteum. Fruit and seed morphology and anatomy point to a sister relationship of Heptacodium with the Linnina clade, rather than with the Lonicera clade.

Genetic differentiation of theChlorospingus ophthalmicuscomplex in Mexico and Central America

Genetic variation in the common bush‐tanagerChlorospingus ophthalmicuscomplex in Mesoamerica was studied. An 800‐bp mitochondrial DNA fragment, including a portion of COII, full tRNA‐Lys, ATP8, and partial ATP6, was sequenced and analyzed for 96 individuals of the species and related taxa, resulting in a detailed framework of genetic differentiation in the northern half of the distribution of the complex. Phylogenetic analyses based on maximum parsimony, maximum likelihood, and Bayesian optimality criteria found deep divergence between South American and Mesoamerican isolates, and seven differentiated populations corresponding to clear geographic breaks across the highlands of Mesoamerica. These distinct populations coincide with geographic structure found in previous analyses of morphological and molecular data forChlorospingusophthalmicus, as well as in previous phylogeographic studies of other taxa in the region. Species status for these populations is discussed under the evolutionary and biological species concepts.

On the number of support points of maximin and Bayesian optimal designs

We consider maximin and Bayesian D-optimal designs for nonlinear regression models. The maximin criterion requires the specification of a region for the nonlinear parameters in the model, while the Bayesian optimality criterion assumes that a prior for these parameters is available. On interval parameter spaces, it was observed empirically by many authors that an increase of uncertainty in the prior information (i.e., a larger range for the parameter space in the maximin criterion or a larger variance of the prior in the Bayesian criterion) yields a larger number of support points of the corresponding optimal designs. In this paper, we present analytic tools which are used to prove this phenomenon in concrete situations. The proposed methodology can be used to explain many empirically observed results in the literature. Moreover, it explains why maximin D-optimal designs are usually supported at more points than Bayesian D-optimal designs.

Molecular Phylogenetic Relationships Among Crested-tailed Mice (Genus Habromys)

We examined genealogical relationships among six of seven species of crested-tailed mice (Habromys chinanteco, H. delicatulus, H. ixtlani, H. lepturus, H. lophurus, and H. simulatus) using DNA sequence data from the cytochrome-b gene. Gene trees based on maximum likelihood, Bayesian inference and maximum parsimony were largely congruent in that H. lepturus and H. ixtlani were closely related and formed the sister group to H. lophurus. All analyses also arranged H. chinanteco and H. simulatus as sister taxa. These results are concordant with the phenetic groupings of Carleton et al. (2002) based on morphology. Our unweighted maximum parsimony trees did not resolve placement of H. delicatulus relative to other taxa. However, analyses using weighted maximum parsimony, maximum likelihood and Bayesian inference optimality criteria recovered a sister group relationship between H. delicatulus and the clade comprised of ((H. lepturus H. ixtlani)(H. lophurus)). This relationship differs from the overall phenetic similarity of H. delicatulus with H. simulatus and H. chinanteco, influenced by the small size of these three taxa, but is consistent with some derived features of the phallus (Carleton et al., 2002). Based on our sequence data, a specimen from Michoacan, Mexico, recently assigned to Peromyscus sagax likely was inadvertently misidentified (Tiemann-Boege et al., 2000) and actually represents a new locality record for H. delicatulus. Finally, we comment on the conservation status of species of Habromys.

PHYLOGENETICS OF SPINY POCKET MICE (GENUS LIOMYS): ANALYSIS OF CYTOCHROMEbBASED ON MULTIPLE HEURISTIC APPROACHES

We examined phylogenetic relationships among species of Liomys, including L. adspersus (Panamanian spiny pocket mouse), L. irroratus (Mexican spiny pocket mouse), L. pictus (painted spiny pocket mouse), L. salvini (Salvin’s spiny pocket mouse), and L. spectabilis (Jaliscan spiny pocket mouse), several species of Heteromys, as well as representatives of other genera of heteromyids and 2 geomyids by using 1,140 base pairs of the mitochondrial cytochrome-b gene. Gene sequences analyzed under maximum-parsimony (MP), maximumlikelihood (ML), and Bayesian inference optimality criteria converged on essentially identical gene tree topologies. Liomys is paraphyletic relative to Heteromys and this relationship is well supported, with L. adspersus and L. salvini arranged as basal taxa relative to Heteromys. Our gene trees also recovered L. pictus as paraphyletic relative to L. spectabilis and these 2 taxa formed the sister group to L. irroratus. Constraint trees that held the genera Heteromys and Liomys as monophyletic (MP and ML criteria) were significantly longer or less likely (P , 0.009 and 0.046, respectively) than our optimal trees, whereas trees that arranged L. pictus as monophyletic relative to L. spectabilis were not significantly longer (P , 0.101) under the MP criterion, but were significantly less likely under the ML criterion (P , 0.020).

Molecular phylogeny of the palm genus Chamaedorea, based on the low-copy nuclear genes PRK and RPB2

Sequence data from the low-copy nuclear genes encoding phosphoribulokinase (PRK) and the second largest subunit of RNA polymerase II (RPB2) are used to generate the first phylogenetic analysis of Chamaedorea (Arecaceae: Arecoideae: Chamaedoreeae), the largest neotropical genus of palms. The prevailing current taxonomy of Chamaedorea recognizes approximately 100 species in eight subgenera, all delimited using floral characters, which provide a useful starting point to explore species-level systematics. Sequence data from 63 species, including representatives of all eight subgenera, were analyzed using maximum parsimony and Bayesian inference optimality criteria. Genus Chamaedorea is resolved as monophyletic with strong support in all separate and combined analyses. The less species-rich subgenera are convincingly monophyletic and can be diagnosed using morphological synapomorphies. In contrast, the two largest subgenera, Chamaedorea and Chamaedoropsis, which are supposedly distinguishable from each other by the degree of connation in the staminate petals, are both resolved as highly polyphyletic. Several well supported monophyletic groups resolved by these gene regions have never before been proposed within Chamaedorea and are challenging to delimit using morphological criteria. Although PRK proved more informative than RPB2, both regions have strong utility for interpreting species-level relationships among the palms, which are notoriously recalcitrant subjects for molecular phylogenetic studies. In addition, a paralog of the target copy of PRK identified during the analysis represents a potentially valuable source of phylogenetic information for future studies.

MULTIPLE-OBJECTIVE DESIGNS IN A DOSE-RESPONSE EXPERIMENT

This article is an extension of the work of Huang and Wong [1], who found dual-objective designs for models with a continuous outcome. We consider quantal dose-response experiments with a binary outcome and develop multiple-objective designs for two or more Bayesian optimality criteria. Using the logit model as an illustrative example, we construct numerically optimal designs for estimating model parameters and percentiles, with possibly unequal interest in each of the objectives. We also show that the popular equal dosage assignment rule can be a rather inefficient design for estimating model parameters under a Bayesian setup.

Bayes D-optimal and E-optimal block designs

Bayes designs are considered for a two-way analysis of variance model with a normal prior for treatments and blocks, one of the treatments acting as a control. The existence of an optimal allocation is proved for each Bayesian optimality criterion, i.e. each criterion defined on the posterior covariance matrix for the treatments. Under a special assumption on the treatment prior, the structure of the optimal design is specified; for the case of only one test treatment such a design is universally optimal. Bayes D- and E-optimal designs are found as special cases and results are compared with classical ones. Two examples are included.