Distribution Of Character States Research Articles

Leveraging National Germplasm Collections to Determine Significantly Associated Categorical Traits in Crops: Upland and Pima Cotton as a Case Study.

Observable qualitative traits are relatively stable across environments and are commonly used to evaluate crop genetic diversity. Recently, molecular markers have largely superseded describing phenotypes in diversity surveys. However, qualitative descriptors are useful in cataloging germplasm collections and for describing new germplasm in patents, publications, and/or the Plant Variety Protection (PVP) system. This research focused on the comparative analysis of standardized cotton traits as represented within the National Cotton Germplasm Collection (NCGC). The cotton traits are named by ‘descriptors’ that have non-numerical sub-categories (descriptor states) reflecting the details of how each trait manifests or is absent in the plant. We statistically assessed selected accessions from three major groups of Gossypium as defined by the NCGC curator: (1) “Stoneville accessions (SA),” containing mainly Upland cotton (Gossypium hirsutum) cultivars; (2) “Texas accessions (TEX),” containing mainly G. hirsutum landraces; and (3) Gossypium barbadense (Gb), containing cultivars or landraces of Pima cotton (Gossypium barbadense). For 33 cotton descriptors we: (a) revealed distributions of character states for each descriptor within each group; (b) analyzed bivariate associations between paired descriptors; and (c) clustered accessions based on their descriptors. The fewest significant associations between descriptors occurred in the SA dataset, likely reflecting extensive breeding for cultivar development. In contrast, the TEX and Gb datasets showed a higher number of significant associations between descriptors, likely correlating with less impact from breeding efforts. Three significant bivariate associations were identified for all three groups, bract nectaries:boll nectaries, leaf hair:stem hair, and lint color:seed fuzz color. Unsupervised clustering analysis recapitulated the species labels for about 97% of the accessions. Unexpected clustering results indicated accessions that may benefit from potential further investigation. In the future, the significant associations between standardized descriptors can be used by curators to determine whether new exotic/unusual accessions most closely resemble Upland or Pima cotton. In addition, the study shows how existing descriptors for large germplasm datasets can be useful to inform downstream goals in breeding and research, such as identifying rare individuals with specific trait combinations and targeting breakdown of remaining trait associations through breeding, thus demonstrating the utility of the analytical methods employed in categorizing germplasm diversity within the collection.

Skeletal Anatomy of Acaenasuchus Geoffreyi Long and Murry, 1995 (Archosauria: Pseudosuchia) and its Implications for the Origin of the Aetosaurian Carapace

ABSTRACT Acaenasuchus geoffreyi is a diminutive armored archosaur from the Upper Triassic Chinle Formation of northern Arizona, U.S.A., with uncertain evolutionary relationships and skeletal maturity. Known only from osteoderms, the taxon has been considered a valid taxon of aetosaur, juvenile specimens synonymous with the aetosaur Desmatosuchus spurensis, or a non-aetosaurian pseudosuchian archosaur. Here, we describe new fossils of Acaenasuchus geoffreyi that represent cranial, vertebral, and appendicular elements as well as previously unknown variations in the dorsal carapace and ventral shield. The skull bones are ornamented with the same anastomosing complex of ridges and grooves found on the paramedian and lateral osteoderms, and the appendicular skeleton resembles that of Revueltosaurus callenderi, Euscolosuchus olseni, aetosaurs, and other armored archosaurs such as erpetosuchids. Histology of osteoderms from the hypodigm of Acaenasuchus geoffreyi shows multiple growth lines, laminar tissue, and low vascularity, evidence that the individuals were close to skeletal maturity and not young juveniles. A revised phylogenetic analysis of early archosaurs recovers Acaenasuchus geoffreyi and Euscolosuchus olseni as sister taxa and members of a new clade that is the sister taxon of Aetosauria. This new phylogeny depicts a broader distribution of osteoderm character states previously thought to only occur in aetosaurs, demonstrating the danger of using only armor character states in aetosaur taxonomy and phylogeny. Acaenasuchus geoffreyi is also a good example of how new fossils can stabilize ‘wild card’ taxa in phylogenetic analyses and contributes to our understanding of the evolution of the aetosaur carapace.

A Bayesian extension of phylogenetic generalized least squares: Incorporating uncertainty in the comparative study of trait relationships and evolutionary rates.

Phylogenetic comparative methods use tree topology, branch lengths, and models of phenotypic change to take into account nonindependence in statistical analysis. However, these methods normally assume that trees and models are known without error. Approaches relying on evolutionary regimes also assume specific distributions of character states across a tree, which often result from ancestral state reconstructions that are subject to uncertainty. Several methods have been proposed to deal with some of these sources of uncertainty, but approaches accounting for all of them are less common. Here, we show how Bayesian statistics facilitates this task while relaxing the homogeneous rate assumption of the well-known phylogenetic generalized least squares (PGLS) framework. This Bayesian formulation allows uncertainty about phylogeny, evolutionary regimes, or other statistical parameters to be taken into account for studies as simple as testing for coevolution in two traits or as complex as testing whether bursts of phenotypic change are associated with evolutionary shifts in intertrait correlations. A mixture of validation approaches indicates that the approach has good inferential properties and predictive performance. We provide suggestions for implementation and show its usefulness by exploring the coevolution of ankle posture and forefoot proportions in Carnivora.

Two new species of fossil Paratydeidae (Acari: Trombidiformes) from the late Eocene amber highlight ultraslow morphological evolution in a soil-inhabiting arthropod lineage

We describe two species of soil mite of the family Paratydeidae from the late Eocene Rovno amber: Scolotydaeus vlaskini sp. nov. and Tanytydeus pogrebnyaki sp. nov. This is the first formal description of fossils from the family Paratydeidae. These exceptionally well-preserved fossils have very similar morphologies compared to extant species, suggesting that Paratydeidae is a lineage that has experienced extremely slow rates of phenotypic evolution. To infer rates of morphological evolution in this group, we used a combination of tip dating (from the fossils) and internal node dating (based on molecular outgroup time-calibrated analysis) in a Bayesian phylogenetic framework. This analysis inferred Paratydeidae as an ancient lineage, originating 242 Ma (stem group) and diversifying 150 Ma (crown group), having ultraslow average rates of morphological evolution, i.e. 4.53e-04 changes per site per million years, which is equivalent to one change in any of the characters per 46.0 million years, per each branch of the tree. Based on our divergence time estimates, we suggest that the present global distribution of the group could be explained by their early evolution on the Pangaean supercontinent. Analysis of character state distributions in the fossil specimens suggests later extinction of ancestral taxa in the Palaearctic.http://zoobank.org/urn:lsid:zoobank.org:pub:265A36D2-B6AE-4150-B5B6-59054D33CEA0

Sternal elements of early dinosaurs fill a critical gap in the evolution of the sternum in Avemetatarsalia (Reptilia: Archosauria)

ABSTRACTThe sternum is a functionally important but poorly understood component of the pectoral girdle in both living and extinct dinosaurs. When ossified, the dinosaur sternum consists of paired plates situated just posterior to the clavicles and scapulocoracoid. In Avialae, the sternal plates are fused at the midline to form a single element, aiding in powered flight. Our understanding of the early evolutionary history of the theropod sternum is complicated by a lack of fossil material, especially outside Maniraptoriformes, both because of taphonomic biases and incomplete ossification. Here, we report the oldest-known dinosaur sternal plates from the Late Triassic taxon Tawa hallae recovered from the Hayden Quarry at Ghost Ranch, New Mexico, as well as an isolated sternal plate from just south of Petrified Forest National Park, Arizona. These specimens expand the fossil record and allow for reconstruction of early theropod sternal musculature. They bear morphological features that are surprisingly similar to sternal traits in avialans, including a sternocoracoidal process, costal processes, and possible homologs to the ‘coracoid facet’ and pila coracoidea. The presence of these features in T. hallae pushes their appearance back to the Late Triassic, well before the development of the modern avian sternum. The variable distribution of sternal character states across avemetatarsalians was previously recognized in later Cretaceous avialans and can now be shown to also characterize the early evolution of the theropod sternum.

Morphological and molecular characters to describe a marbled newt hybrid zone in the Iberian peninsula

I document the contiguous distribution of the marbled newt species Triturus marmoratus and T. pygmaeus over the western part of the Iberian peninsula with a suite of morphological and molecular genetic data from altogether 141 populations. Morphological characters that identify the species are body size and the colour pattern character ‘Links’. Links is the number of transversal connections following the green surface at the lateral sides of the newts’ body. Large adults with few Links are T. marmoratus and small adults with many Links are T. pygmaeus. However, no morphological identification criterion is entirely adequate. Eight molecular genetic markers show markedly bimodal character state distributions that give rise to sharp species range descriptions, with T. marmoratus in the north of the Iberian peninsula and T. pygmaeus in the south and along most of the Atlantic coast of Portugal. I encountered ten genetically admixed populations that are all located at the T. marmoratus - T. pygmaeus species range interface, suggesting widespread but limited interspecific hybridization. A latitudinal transect across Portugal confirmed the narrow and steep transition from one to the other species for morphological and molecular characters alike. In central Portugal the position of the hybrid zone coincides with the river Tejo. However, the cline for mitochondrial DNA is relatively wide and shallow and its centre is positioned south of the river. In view of published data that reconstruct the northward advance of T. pygmaeus along the Portuguese coast at the expense of T. marmoratus, I propose that T. marmoratus had a wider range in central Portugal too, where it was eventually superseded by T. pygmaeus. I hypothesize that ‘marmoratus’ mtDNA haplotypes found south of the Tejo constitute a ‘genetic footprint’ left behind in T. pygmaeus by the receding species T. marmoratus.

Combinatorial Scoring of Phylogenetic Trees and Networks Based on Homoplasy-Free Characters.

Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for tree/network construction, it becomes important to measure how well the constructed networks capture the given character relationship across the species. We propose a novel method for measuring the specificity of a given phylogenetic network in terms of the total number of distributions of homoplasy-free character states at the leaves that the network may impose. While for binary phylogenetic trees, this number has an exact formula and depends only on the number of leaves and character states but not on the tree topology, the situation is much more complicated for nonbinary trees or networks. Nevertheless, we develop an algorithm for combinatorial enumeration of such distributions, which is applicable for arbitrary trees and networks under some reasonable assumptions. We further extend our algorithm to a special class of characters that follow Dollo's law of irreversibility.

The peristomial plates of ophiuroids (Echinodermata: Ophiuroidea) highlight an incongruence between morphology and proposed phylogenies.

The peristomial plates are skeletal components of the interbrachial frame (or mouth frame), which is located below the true mouth of ophiuroids. Whilst the peristomial plates were extensively described and used as diagnostic characters by some early workers, for the past 100 years they have been largely neglected as a taxonomic resource. In this investigation the peristomial plates of 48 species representing 21 families were examined directly, and information on a further 61 species, including representatives of another eight families, was obtained from the published literature. Observations were made with regard to fragmentation state, relative size and orientation of the peristomial plates. Although fragmentation state showed little consistency at any taxonomic level, relative size and orientation segregated a group of families comprising species with relatively small, inclined peristomial plates, viz. Ophiotrichidae, Ophiopholidae, Ophiactidae, Amphiuridae and Ophiocomidae, together with a single hemieuryalid species–Ophioplocus januarii. The distribution of peristomial plate traits was strongly correlated with that of several other character states pertaining to the interbrachial frame. This supported the proposition that two major types of interbrachial frame are present in ophiuroids (designated ‘A’ and ‘B’). Current phylogenies inferred from both morphological and molecular data imply that type B is derived and has evolved independently at least twice in the orders Amphilepidida and Ophiacanthida. This represents a remarkable example of evolutionary convergence. An analysis of the distribution of all interbrachial frame character states suggested that within the Amphilepidida paedomorphosis was probably responsible for the complete reversion of the interbrachial frame to the ancestral type A condition in two families (Ophiothamnidae and Amphilepididae) of suborder Gnathophiurina and possibly responsible for varying degrees of trait reversal in the four families of suborder Ophionereidina. Such paedomorphic events may have been associated with a secondary return to the deep-sea from shallow-sea environments.

On defining a unique phylogenetic tree with homoplastic characters

This paper discusses the problem of whether creating a matrix with all the character state combinations that have a fixed number of steps (or extra steps) on a given tree T, produces the same tree T when analyzed with maximum parsimony or maximum likelihood. Exhaustive enumeration of cases up to 20 taxa for binary characters, and up to 12 taxa for 4-state characters, shows that the same tree is recovered (as unique most likely or most parsimonious tree) as long as the number of extra steps is within 1/4 of the number of taxa. This dependence, 1/4 of the number of taxa, is discussed with a general argumentation, in terms of the spread of the character changes on the tree used to select character state distributions. The present finding allows creating matrices which have as much homoplasy as possible for the most parsimonious or likely tree to be predictable, and examination of these matrices with hill-climbing search algorithms provides additional evidence on the (lack of a) necessary relationship between homoplasy and the ability of search methods to find optimal trees.

Multivariate analysis of morphological diversity among closely related Daucus species and subspecies in Tunisia

The genus Daucus includes about 20–25 species worldwide. Northern Africa represents a major center of diversity of Daucus, with Tunisia thought to contain 11 species and seven subspecies. The greatest taxonomic problems, however, and the greatest economic importance relative to immediate use in breeding, is in a group of species and subspecies in the Daucus carota L. clade, all containing 2n = 18 chromosomes. We assessed morphological diversity from a Daucus L. germplasm collection of nine individuals each from 45 accessions (405 individuals in total), at the National Gene Bank of Tunisia, of the following wild and one cultivated members of this clade: D. carota subsp. capillifolius (Gilli) Arbizu, D. carota subsp. carota, D. carota subsp. gummifer (Syme) Hook. f., D. carota subsp. sativus (Hoffm.) Arcangeli (cultivated), D. sahariensis Murb., and putative hybrids of D. carota subsp. carota and subsp. capillifolius. A prior study showed the effectiveness of fruit characters to identify several species and subspecies in the collection, but distinction between some closely related D. carota subspecies was difficult. In order to resolve the taxonomic classification, we tested 32 quantitative and qualitative morphological characters from leaves, stems and flowers on a field collection of 45 accessions corresponding to the different species/subspecies. The Shannon–Weaver diversity (H’) index was used to study the phenotypic diversity. The estimated H’ ranged from monomorphic for umbel type, position of involucral bracts on primary umbel, anther color, and symmetry of peripheral flowers to highly polymorphic for other traits. The highest (0.98) and the lowest (0.26) H’ values were recorded for flowering pattern within plants and foliage coverage. Multivariate analyses of principal components and dendrograms of all data and canonical discriminate analysis of the quantitative data supported the subdivision of the Daucus collection into five groups with various degrees of distinctness: (1) D. sahariensis, (2) D. carota subsp. capillifolius, (3) D. carota subsp. carota, very similar to (4) D. carota subsp. gummifer, and (5) D. carota subsp. sativus intergrading with putative hybrids between D. carota subsp. capillifolius and D. carota subsp. carota. Individual character state distribution plots provide useful characters and insights into taxonomic problems in the D. carota clade that we here discuss in reference to ongoing molecular studies in Daucus.

The phylogenetic system of primates—character evolution in the light of a consolidated tree

Molecular analyses of the last decades helped solving the major open questions on the external and internal phylogenetic relationships of primates. The present review uses these data for the inference of character evolution along the branches of the primate tree. Altogether, more than 200 evolutionary changes in hard and soft tissue anatomy/morphology, behavior, physiology, and protein constitution are presented in the context of their functional relevance and adaptive value. The compilation focuses on primates as a whole and on the higher-ranked primate subtaxa with living representatives: Strepsirhini: Lorisiformes, Galagidae, Lorisidae, Lemuriformes; Haplorhini: Tarsioidea, Anthropoidea, Platyrrhini, Atelidae + Cebidae, Atelidae, Cebidae, Aotinae, Callithrichinae, Cebinae, Pitheciidae, Pithecinae, Catarrhini, Cercopithecoidea, Cercopithecinae, Colobinae, Colobini, and Hominoidea. Within Hominoidea character evolution is traced down to more peripheral branches: Hylobatidae, Hominidae, Pongo, Homininae, Gorilla, Pan + Homo, Pan, and modern humans. Character states in extinct representatives of Plesiadapiformes, Omomyoidea, Propliopithecidae, Hominini, etc. are always taken into account; they are presented in detail whenever character-state distribution in living species is ambiguous or misleading. The taxonomic sample and the characters included combine to a phylogenetic system that illustrates primate evolution and diversity. The data presented additionally provide a detailed picture of the evolutionary steps and trends involved in hominization. Reflections on the frequently underestimated role of polymorphisms in phylogenetic analyses complete the survey.

Biases of tree-independent-character-subsampling methods

Observed Variability (OV) and Tree Independent Generation of Evolutionary Rates (TIGER) are quick and easy-to-apply tree-independent methods that have been proposed to provide unbiased estimates of each character’s rate of evolution and serve as the basis for excluding rapidly evolving characters. Both methods have been applied to multiple phylogenomic datasets, and in many cases the authors considered their trees inferred from the OV- and TIGER-delimited sub-matrices to be better estimates of the phylogeny than their trees based on all characters. In this study we use four sets of simulations and an empirical phylogenomic example to demonstrate that both methods share a systematic bias against characters with more symmetric distributions of character states, against characters with greater observed character-state space, and against large clades in the context of character conflict. As a result these methods can favor convergences and reversals over synapomorphy, exacerbate long-branch attraction, and produce mutually exclusive phylogenetic inferences that are dependent upon differential taxon sampling. We assert that neither OV nor TIGER should be relied upon to increase the ratio of phylogenetic to non-phylogenetic signal in a data matrix. We also assert that skepticism is warranted for empirical phylogenetic results that are based on OV- and/or TIGER-based character deletion wherein a small clade is supported after deletion of characters, yet is contradicted by a larger clade when the entire data matrix was analyzed.

Morphological evidence on blattarian phylogeny: “phylogenetic histories and stories” (Insecta, Dictyoptera)

The hypotheses of Grandcolas and Klass on blattarian phylogeny are compared through a scrutiny of all stages of phylogenetic analysis: taxon sampling; morphological studies; establishment of topographic homologies; treatment and presentation of characters, states, and state distribution over taxa; cladistic analysis and support of clades. Grandcolas' hypothesis is difficult to test due to inadequate documentation in several stages. In the testable subsets, many mishomologizations between male genital (phallomere) components and many misscorings for phallomere and non-phallomere characters are demonstrated. Through the use of high-rank taxa as terminal taxa in the matrix, much support for alternative clades is neglected. With the exception of some that are uncontroversial, the clades established by Grandcolas lose their support when the necessary character revisions are performed; of the 52 clade autapomorphies indicated in the cladogram, 7 remain here untested, 7 are accepted, and 38 are refuted. The scenarios of dictyopteran evolution built by Grandcolas on his phylogenetic results cannot he upheld. Klass' hypothesis appears more strongly supported, being based on more detailed morphological observations and homology discussions and considering evidence from all character state distributions. It is thus another demonstration that extensive and detailed morphological investigations and structural comparisons between taxa are essential for morphology-based phylogenetic work, in particular if complex and diverse organs (such as the dictyopteran phallomeres) are used. Some further general issues of phylogeny reconstruction are also referred to, and the importance of the topographic homology level, which precedes the primary (s.s.) and secondary levels, is emphasized.

New approaches to examining and interpreting patterns of dental morphological variability in Miocene cricetids

Morphometrical studies were carried out on the dental material of Democricetodon from the Calatayud-Montalbán Basin. Principal component analyses were incorporated into the analyses to reduce the number of metrical and morphological variables. Morphological variability was studied as the morphological distribution of character states, based on multivariate statistics, and plotted against time. The results of these analyses indicate that increased dental size is significantly correlated to the dental morphological value in the two Democricetodon lineages studied. We found that the rates of change in variables are not linear and that periods of higher rates can be correlated with global climatic changes. In addition, morphological variability is significantly correlated with relative abundances of the studied taxa. High morphological variability, as a proxy of niche breadth, may result from increased intraspecific interferences or from the relaxation of interspecific interactions caused by a decrease in primary productivity.

Coalescence vs. concatenation: Sophisticated analyses vs. first principles applied to rooting the angiosperms

It has recently been concluded that phylogenomic data from 310 nuclear genes support the clade of (Amborellales, Nymphaeales) as sister to the remaining angiosperms and that shortcut coalescent phylogenetic methods outperformed concatenation for these data. We falsify both of those conclusions here by demonstrating that discrepant results between the coalescent and concatenation analyses are primarily caused by the coalescent methods applied (MP-EST and STAR) not being robust to the highly divergent and often mis-rooted gene trees that were used. This result reinforces the expectation that low amounts of phylogenetic signal and methodological artifacts in gene-tree reconstruction can be more problematic for shortcut coalescent methods than is the assumption of a single hierarchy for all genes by concatenation methods when these approaches are applied to ancient divergences in empirical studies. We also demonstrate that a third coalescent method, ASTRAL, is more robust to mis-rooted gene trees than MP-EST or STAR, and that both Observed Variability (OV) and Tree Independent Generation of Evolutionary Rates (TIGER), which are two character subsampling procedures, are biased in favor of characters with highly asymmetrical distributions of character states when applied to this dataset. We conclude that enthusiastic application of novel tools is not a substitute for rigorous application of first principles, and that trending methods (e.g., shortcut coalescent methods applied to ancient divergences, tree-independent character subsampling), may be novel sources of previously under-appreciated, systematic errors.

Putative floral brood-site mimicry, loss of autonomous selfing, and reduced vegetative growth are significantly correlated with increased diversification in Asarum (Aristolochiaceae)

The drivers of angiosperm diversity have long been sought and the flower–arthropod association has often been invoked as the most powerful driver of the angiosperm radiation. We now know that features that influence arthropod interactions cannot only affect the diversification of lineages, but also expedite or constrain their rate of extinction, which can equally influence the observed asymmetric richness of extant angiosperm lineages. The genus Asarum (Aristolochiaceae; ∼100 species) is widely distributed in north temperate forests, with substantial vegetative and floral divergence between its three major clades, Euasarum, Geotaenium, and Heterotropa. We used Binary-State Speciation and Extinction Model (BiSSE) Net Diversification tests of character state distributions on a Maximum Likelihood phylogram and a Coalescent Bayesian species tree, inferred from seven chloroplast markers and nuclear rDNA, to test for signal of asymmetric diversification, character state transition, and extinction rates of floral and vegetative characters. We found that reduction in vegetative growth, loss of autonomous self-pollination, and the presence of putative fungal-mimicking floral structures are significantly correlated with increased diversification in Asarum. No significant difference in model likelihood was identified between symmetric and asymmetric rates of character state transitions or extinction. We conclude that the flowers of the Heterotropa clade may have converged on some aspects of basidiomycete sporocarp morphology and that brood-site mimicry, coupled with a reduction in vegetative growth and the loss of autonomous self-pollination, may have driven diversification within Asarum.

Lost and found: The third molars of Callimico goeldii and the evolution of the callitrichine postcanine dentition

This study tests the hypothesis that the third molars of Callimico goeldii represent a reversal in evolutionary tooth loss within the Callitrichinae. Loss of third molars is part of a suite of unusual characters that has been used to unite marmosets and tamarins in a clade to the exclusion of Callimico. However, molecular phylogenetic studies provide consistent support for the hypothesis that marmosets are more closely related to Callimico than to tamarins, raising the possibility that some or all of the features shared by marmosets and tamarins are homoplastic. Here, I use the binary-state speciation and extinction (BiSSE) model and a sample of 249 extant primate species to demonstrate that, given the shape of the primate phylogenetic tree and the distribution of character states in extant taxa, models in which M3 loss is constrained to be irreversible are much less likely than models in which reversals are allowed to occur. This result provides support for the idea that the last common ancestor of Callimico and marmosets was characterized by the two-molared phenotype. The M3s of Callimico therefore appear to be secondarily derived rather than plesiomorphic. This conclusion may also apply to the other apparently plesiomorphic traits found in Callimico. Hypotheses regarding the re-evolution of M3 in the callitrichine clade and the origin and maintenance of the two-molared phenotype are discussed.

Morphometrics of Daucus (Apiaceae): a counterpart to a phylogenomic study.

Molecular phylogenetics of genome-scale data sets (phylogenomics) often produces phylogenetic trees with unprecedented resolution. A companion phylogenomics analysis of Daucus using 94 conserved nuclear orthologs supported many of the traditional species but showed unexpected results that require morphological analyses to help interpret them in a practical taxonomic context. We evaluated character state distributions, stepwise discriminant analyses, canonical variate analyses, and hierarchical cluster analyses from 40 morphological characters from 81 accessions of 14 taxa of Daucus and eight species in related genera in an experimental plot. Most characters showed tremendous variation with character state overlap across many taxa. Multivariate analyses separated the outgroup taxa easily from the Daucus ingroup. Concordant with molecular analyses, most species form phenetic groups, except the same taxa that are problematical in the molecular results: (1) the subspecies of D. carota, (2) D. sahariensis and D. syrticus, and (3) D. broteri and D. guttatus. Phenetic analyses, in combination with molecular data, support many Daucus species, but mostly by overlapping ranges of size and meristic variation. The subspecies of D. carota are poorly separated morphologically, are paraphyletic, and all could be recognized at the subspecies rank under D. carota. Daucus sahariensis and D. syrticus are so similar morphologically that they could be placed in synonymy. Combined molecular and morphological data support three species in accessions previously identified as D. broteri and D. guttatus. Molecular and morphological results support the new combination Daucus carota subsp. capillifolius.

Behavioral and ecological factors account for variation in the mass-independent energy expenditures of endotherms.

A persistent controversy has concerned the identification of the factors that influence the quantitative variation in the physiological characters of species, an example of which is the basal rate of metabolism of endotherms. The most important factor accounting for its variation is body mass as long as the range in mass is appreciable. But mass never accounts for all of the variation and none if species have the same mass. Most of the residual variation around the mass curve is associated with behavioral characters, ecological factors, and phylogeny, i.e., history. These agents influence energy expenditure by different means and at different stages in the life history of species. Phylogeny describes the historic origin, evolution, and distribution of character states in contemporary species. However, the level of energy expenditure is quantitatively determined by the collective of realized states in combination with conditions in the environment. Therefore, two stages determine energy expenditure: (1) the evolution of character states and (2) their impact in conjunction with conditions on the environment. Behavioral characters and ecological factors, when coupled with log10 mass, usually account for >94 % of the variation in the log10 basal rates of birds and mammals, a capacity not found in phylogenetic analyses. The difficulty of determining a direct impact of phylogeny on physiological characters results from its correlation with behavioral characters. When appropriate, the passerine/non-passerine dichotomy in birds and the sub/infraclass dichotomy in mammals combine with behavioral characters, ecological factors, and log10 mass to increase r (2) to account for 96-99 % of the variation in log10 basal rate. This occurs because dichotomies incorporate factors other than those already in the analyses. The clearest demonstration of the direct impact of character states is the equality of energy expenditure in species convergent with species from other clades without any evidence of the clade to which the species belong. A multifactorial approach depends on the inclusion of life history characteristics of species, but this analysis applies only to continuous, quantitative relationships, which are often modified by discontinuous agents. Distinctive character states distinguish species and therefore must be included in any attempt to account for differences in their level of energy expenditure. No analysis that ignores life history characteristics can account for the quantitative variation in energy expenditure beyond that associated with body mass.

Floral Evolution in the Detarieae (Leguminosae): Phylogenetic Evidence for Labile Floral Development in an Early-Diverging Legume Lineage

Premise of research. We examine floral evolution and phylogenetic relationships in the monophyletic Detarieae and related lineages of Caesalpinioideae. Tribe Detarieae (82 genera) includes nearly half of the genera in subfamily Caesalpinioideae and represents some of the most diverse legumes with respect to floral morphology.Methodology. A total of 67 floral ontogenetic and morphological characters were combined with DNA sequences from the plastid trnL-F and matK regions of 34 Detarieae species and representatives of Cassieae, Cercideae, Caesalpinieae, Papilionoideae, and Mimosoideae, for which we have near-complete ontogenetic series. The morphological and ontogenetic characters were optimized onto the resulting most parsimonious phylogenetic trees and Bayesian topology to study character evolution.Pivotal results. Our study supports previously proposed relationships within the tribe Detarieae and among caesalpinioid lineages and indicates that certain features (bracteole and hypanthium characters, sepal initiation, anther position in bud, overlap in timing of initiation of organ whorls) are phylogenetically informative for particular clades whereas others (reductions in petal and stamen number, sepal and petal initiation patterns) have evolved multiple times in parallel in the Detarieae and other Caesalpinioideae. These analyses suggest that modifications that occur early in ontogeny can be good phylogenetic characters for distinguishing both major taxonomic groups and more closely related taxa and that morphological differences that differentiate species within genera can be caused by changes that occur at all stages of ontogeny. Phylogenetic distribution of character states and ontogenetic evidence suggest that in the Caesalpinioideae, loss or suppression of organs within a whorl, both of which are very common, usually does not affect development in subsequent whorls.Conclusions. Our analyses reveal several switches from zygomorphy to actinomorphy (and vice versa), but in Caesalpinioideae (contrary to Papilionoideae), zygomorphy is likely not clearly associated with higher diversification rates. This study suggests that floral initiation patterns are much more variable in Caesalpinioideae than in the other two subfamilies. Although particular patterns may be canalized in certain lineages of the subfamily (Cercideae, Caesalpinieae), in other clades (Detarieae, Dialiinae) floral development is more labile, explaining the high diversity in floral morphology encountered overall in the paraphyletic Caesalpinioideae.