Non-molecular Data Research Articles

A Study on Plant Structure

This paper propose image processing algorithms to recognize The Plant structure in Plant Kingdom. Anatomy is one of the oldest disciplines of plant science, and there is a huge amount of accumulated knowledge. At the same time, anatomy is highly important as a linking medium between several key branches of modern plant science. Detailed anatomical studies, these days using X-ray microtomography, allow much more detailed understanding of plant fossils and thus facilitate the accumulation of greatly extended non-molecular data sets. The use of anatomy is one of most efficient ways of increasing the number of characters in data sets employed to link fossil and extant plants. This link is essential for achieving the ambitious goal of acquiring a holistic knowledge of plant evolution combining the direct, but fragmentary evidence from the fossil record and the indirect, though highly informative data of molecular phylogenetics and phylogenomics. Anatomy is one of key tools of evo-devo research. Indeed, analyses of gene expression patterns are performed using anatomical techniques. More importantly, developmental biology of plants explores functioning of plant meristems and aspects of cell and tissue differentiation, the topics that have a long history of research in the framework of plant anatomy. Anatomy provides detailed information of the developmental processes in extant and extinct plants. Obviously, the detailed knowledge assembled through centuries of anatomical research has great perspectives of use in evolutionary developmental biology. Many theories developed in plant anatomy can be tested using molecular tools (e.g. Povilus et al., 2020), but it is important to pose the questions. Anatomy has many implications for plant physiology and ecology and provides an excellent tool for investigating historical aspects of these disciplines, including those related to climate change.

Evolutionary Sparse Learning for Phylogenomics

We introduce a supervised machine learning approach with sparsity constraints for phylogenomics, referred to as evolutionary sparse learning (ESL). ESL builds models with genomic loci—such as genes, proteins, genomic segments, and positions—as parameters. Using the Least Absolute Shrinkage and Selection Operator, ESL selects only the most important genomic loci to explain a given phylogenetic hypothesis or presence/absence of a trait. ESL models do not directly involve conventional parameters such as rates of substitutions between nucleotides, rate variation among positions, and phylogeny branch lengths. Instead, ESL directly employs the concordance of variation across sequences in an alignment with the evolutionary hypothesis of interest. ESL provides a natural way to combine different molecular and nonmolecular data types and incorporate biological and functional annotations of genomic loci in model building. We propose positional, gene, function, and hypothesis sparsity scores, illustrate their use through an example, and suggest several applications of ESL. The ESL framework has the potential to drive the development of a new class of computational methods that will complement traditional approaches in evolutionary genomics, particularly for identifying influential loci and sequences given a phylogeny and building models to test hypotheses. ESL’s fast computational times and small memory footprint will also help democratize big data analytics and improve scientific rigor in phylogenomics.

Uncovering patterns of the evolution of genomic sequence entropy and complexity.

The lack of consensus concerning the biological meaning of entropy and complexity of genomes and the different ways to assess these data hamper conclusions concerning what are the causes of genomic entropy variation among species. This study aims to evaluate the entropy and complexity of genomic sequences of several species without using homologies to assess relationships among these variables and non-molecular data (e.g., the number of individuals) to seek a trigger of interspecific genomic entropy variation. The results indicate a relationship among genomic entropy, genome size, genomic complexity, and the number of individuals: species with a small number of individuals harbors large genome, and hence, low entropy but a higher complexity. We defined that the complexity of a genome relies on the entropy of each DNA segment within genome. Then, the entropy andcomplexity of a genome reflects its organization solely. Exons of vertebrates harbor smaller entropies than non-exon regions (likely by the repeats that accumulated from duplications), whereas other taxonomic groups do not present this pattern. Our findings suggest that small initial population might have defined current genomic entropy and complexity:actual genomes are lesscomplex than ancestral ones. Besides, our data disagree with the relationship between phenotype and genomic entropies previously established. Finally, by establishing the relationship between genomic entropy/complexity with the number of individuals and genome size, under an evolutive perspective, ideas concerning the genomic variability may emerge.

Integral Phylogenomic Approach over Ilex L. Species from Southern South America.

The use of molecular markers with inadequate variation levels has resulted in poorly resolved phylogenetic relationships within Ilex. Focusing on southern South American and Asian species, we aimed at contributing informative plastid markers. Also, we intended to gain insights into the nature of morphological and physiological characters used to identify species. We obtained the chloroplast genomes of I. paraguariensis and I. dumosa, and combined these with all the congeneric plastomes currently available to accomplish interspecific comparisons and multilocus analyses. We selected seven introns and nine IGSs as variable non-coding markers that were used in phylogenomic analyses. Eight extra IGSs were proposed as candidate markers. Southern South American species formed one lineage, except for I. paraguariensis, I. dumosa and I. argentina, which occupied intermediate positions among sampled taxa; Euroasiatic species formed two lineages. Some concordant relationships were retrieved from nuclear sequence data. We also conducted integral analyses, involving a supernetwork of molecular data, and a simultaneous analysis of quantitative and qualitative morphological and phytochemical characters, together with molecular data. The total evidence tree was used to study the evolution of non-molecular data, evidencing fifteen non-ambiguous synapomorphic character states and consolidating the relationships among southern South American species. More South American representatives should be incorporated to elucidate their origin.

Diversity Down Below

Ecology![Figure][1] CREDIT: OKEA/THINKSTOCK Despite a surge of research efforts in recent years, the challenges faced by soil biologists remain daunting. Knowledge of even the basic elements of the biodiversity that is so visible above ground—in particular, species diversity and distribution—remains far more rudimentary where life below the soil surface is concerned. Soil fungi are a case in point. A key component of the soil ecosystem, its global species diversity, has tended to be estimated by various proxies. From a study of the fungi of boreal forest soils in Alaska, Taylor et al. suggest that previous estimates of fungal diversity, which hitherto hovered between 0.5 and 1.5 million, might need to be revised upward. Fungal DNA sequence data from their samples yielded just over 1000 discrete fungal taxa—many more than had been estimated from nonmolecular data. Within the soil, the fungal species communities were found to be highly structured and correlated with abiotic variables such as pH and soil horizon, and with the species composition of the understory plant community. The revealed fungus:plant ratio of 17:1, if reflected globally, would extrapolate to at least 6 million fungal species, suggesting in turn that 98% of fungi have yet to be described—a figure that remains to be corroborated by similarly detailed sampling across a range of other soil ecosystems. Ecol. Monogr. 84 , 3 (2014). [1]: pending:yes

2matrix: A utility for indel coding and phylogenetic matrix concatenation(1.).

• Premise of the study: Phylogenetic analysis of DNA and amino acid sequences requires the creation of files formatted specifically for each analysis package. Programs currently available cannot simultaneously code inferred insertion/deletion (indel) events in sequence alignments and concatenate data sets.• Methods and Results: A novel Perl script, 2matrix, was created to concatenate matrices of non-molecular characters and/or aligned sequences and to code indels. 2matrix outputs a variety of formats compatible with popular phylogenetic programs.• Conclusions: 2matrix efficiently codes indels and concatenates matrices of sequences and non-molecular data. It is available for free download under a GPL (General Public License) open source license (https://github.com/nrsalinas/2matrix/archive/master.zip).

Chirleja buckii, a new genus and species of lichenized-fungi from Tierra del Fuego, southern South America

Chirleja, a new genus of lichenized-fungi, is described to accommodate C. buckii, a new species from southern South America with an unusual morphology and mode of reproduction. Through an approach that utilizes both molecular and non-molecular data, the species is shown to represent a previously unknown lineage within the family Icmadophilaceae characterized by the production of sporodochia and a sterile dimorphic thallus that resembles the unrelated genus Leprocaulon.

Molecular phylogeny of the Entomophthoromycota

The Entomophthoromycota is a ubiquitous group of fungi best known as pathogens of a wide variety of economically important insect pests, and other soil invertebrates. This group of fungi also includes a small number of parasites of reptiles, vertebrates (including humans), macromycetes, fern gametophytes, and desmid algae, as well as some saprobic species. Here we report on recent studies to resolve the phylogenetic relationships within the Entomophthoromycota and to reliably place this group among other basal fungal lineages. Bayesian Interference (BI) and Maximum Likelihood (ML) analyses of three genes (nuclear 18S and 28S rDNA, mitochondrial 16S, and the protein-coding RPB2) as well as non-molecular data consistently and unambiguously identify 31 taxa of Entomophthoromycota as a monophyletic group distinct from other Zygomycota and flagellated fungi. Using the constraints of our multi-gene dataset we constructed the most comprehensive rDNA phylogeny yet available for Entomophthoromycota. The taxa studied here belong to five distinct, well-supported lineages. The Basidiobolus clade is the earliest diverging lineage, comprised of saprobe species of Basidiobolus and the undescribed snake parasite Schizangiella serpentis nom. prov. The Conidiobolus lineage is represented by a paraphyletic grade of trophically diverse species that include saprobes, insect pathogens, and facultative human pathogens. Three well supported and exclusively entomopathogenic lineages in the Entomophthoraceae center around the genera Batkoa, Entomophthora and Zoophthora, although several genera within this crown clade are resolved as non-monophyletic. Ancestral state reconstruction suggests that the ancestor of all Entomophthoromycota was morphologically similar to species of Conidiobolus. Analyses using strict, relaxed, and local molecular clock models documented highly variable DNA substitution rates among lineages of Entomophthoromycota. Despite the complications caused by different rates of molecular evolution among lineages, our dating analysis indicates that the Entomophthoromycota originated 405±90million years ago. We suggest that entomopathogenic lineages in Entomophthoraceae probably evolved from saprobic or facultatively pathogenic ancestors during or shortly after the evolutionary radiation of the arthropods.

Behavioural vs. molecular sources of conflict between nuclear and mitochondrial DNA: the role of male‐biased dispersal in a Holarctic sea duck

Genetic studies of waterfowl (Anatidae) have observed the full spectrum of mitochondrial (mt) DNA population divergence, from apparent panmixia to deep, reciprocally monophyletic lineages. Yet, these studies often found weak or no nuclear (nu) DNA structure, which was often attributed to male-biased gene flow, a common behaviour within this family. An alternative explanation for this 'conflict' is that the smaller effective population size and faster sorting rate of mtDNA relative to nuDNA lead to different signals of population structure. We tested these alternatives by sequencing 12 nuDNA introns for a Holarctic pair of waterfowl subspecies, the European goosander (Mergus merganser merganser) and the North American common merganser (M. m.americanus), which exhibit strong population structure in mtDNA. We inferred effective population sizes, gene flow and divergence times from published mtDNA sequences and simulated expected differentiation for nuDNA based on those histories. Between Europe and North America, nuDNA Ф(ST) was 3.4-fold lower than mtDNA Ф(ST) , a result consistent with differences in sorting rates. However, despite geographically structured and monophyletic mtDNA lineages within continents, nuDNA Ф(ST) values were generally zero and significantly lower than predicted. This between- and within-continent contrast held when comparing mtDNA and nuDNA among published studies of ducks. Thus, male-mediated gene flow is a better explanation than slower sorting rates for limited nuDNA differentiation within continents, which is also supported by nonmolecular data. This study illustrates the value of quantitatively testing discrepancies between mtDNA and nuDNA to reject the null hypothesis that conflict simply reflects different sorting rates.

A phylogeny and evolutionary natural history of mesoamerican toads (Anura: Bufonidae: Incilius) based on morphology, life history, and molecular data

We combine mitochondrial and nuclear DNA sequence data with non-molecular (morphological and natural history) data to conduct phylogenetic analyses and generate an evolutionary hypothesis for the relationships among nearly every species of Mesoamerican bufonid in the genus Incilius. We collected a total of 5,898 aligned base-pairs (bp) of sequence data from mitochondrial (mtDNA: 12S–16S, cyt b, ND2–CO1, including tRNAsTRP–TYR and the origin of light strand replication; total 4,317 bp) and nuclear (CXCR4 and RAG1; total 1,581 bp) loci from 52 individual toads representing 37 species. For the non-molecular data, we collected 44 characters from 29 species. We also include Crepidophryne, a genus that has not previously been included in molecular analyses. We present results of parsimony and Bayesian analyses for these data separately and combined. Relationships based on the non-molecular data were poorly supported and did not resolve a monophyletic Incilius (Rhinella marina was nested within). Our molecular data provide significant support to most of the relationships. Our combined analyses demonstrate that inclusion of a considerably smaller dataset (44 vs. 5,898 characters) of non-molecular characters can provide significant support where the molecular relationships were lacking support. Our combined results indicate that Crepidophryne is nested within Incilius; therefore, we place the former in the synonymy of the latter taxon. Our study provides the most comprehensive evolutionary framework for Mesoamerican bufonids (Incilius), which we use as a starting point to invoke discussion on the evolution of their unique natural history traits.

Angiosperm phylogeny inferred from sequences of four mitochondrial genes

Abstract An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atp1, matR, nad5, and rps3, from 380 species that represent 376 genera and 296 families of seed plants. It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB, matK, and rbcL, and nuclear 18S rDNA. The basalmost lineage consists of Amborella and Nymphaeales (including Hydatellaceae). Austrobaileyales follow this clade and are sister to the mesangiosperms, which include Chloranthaceae, Ceratophyllum, magnoliids, monocots, and eudicots. With the exception of Chloranthaceae being sister to Ceratophyllum, relationships among these five lineages are not well supported. In eudicots, Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales, Gunnerales, Saxifragales, Vitales, Berberidopsidales, and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids. Within rosids, the COM (Celastrales–Oxalidales–Malpighiales) clade is sister to malvids (or rosid II), instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms. Santalales and Caryophyllales are members of an expanded asterid clade. This study shows that the mitochondrial genes are informative markers for resolving relationships among genera, families, or higher rank taxa across angiosperms. The low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes, as found in this study, make them particularly useful for reconstructing ancient phylogenetic relationships. A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes, nuclear genes, and non-molecular data to reconstruct the underlying organismal phylogeny.

Quantifying model errors using similarity to training data

When making a prediction with a statistical model, it is not sufficient to know that the model is good, in the sense that it is able to make accurate predictions on test data. Another relevant question is: How good is the model for a specific sample whose properties we wish to predict? Stated another way: Is the sample within or outside the model's domain of applicability or what is the degree to which a test compound is within the model's domain of applicability. Numerous studies have been done on determining appropriate measures to address this question [1-4]. Here we focus on a derivative question: Can we determine an applicability domain measure suitable for deriving quantitative error bars -- that is, error bars which accurately reflect the expected error when making predictions for specified values of the domain measure? Such a measure could then be used to provide an indication of the confidence in a given prediction (i.e. the likely error in a prediction based on to what degree the test compound is part of the model's domain of applicability).Ideally, we wish such a measure to be simple to calculate and to understand, to apply to models of all types -- including classification and regression models for both molecular and non-molecular data - and to be free of adjustable parameters. Consistent with recent work by others [5,6], the measures we have seen that best meet these criteria are distances to individual samples in the training data. We describe our attempts to construct a recipe for deriving quantitative error bars from these distances.

Phylogeny reconstruction of Callitris Vent. (Cupressaceae) and its allies leads to inclusion of Actinostrobus within Callitris

Relationships between Callitris, Actinostrobus and Neocallitropsis, members of the southern hemisphere ‘callitroid clade’ (Callitroideae sensu Gadek et al. 2000) of Cupressaceae, are estimated using a database of 42 morphological and anatomical characters. Callitris is paraphyletic, with Actinostrobus being closer to a large well supported clade of 15 Australian species of Callitris than are C. baileyi, C. macleayana and the New Caledonian taxa. The New Caledonian unispecific endemic, Neocallitropsis, is sister to the clade comprising all Callitris and Actinostrobus species. There are marked differences between this estimate of the phylogeny and two recent estimates based on nuclear encoded DNA sequence data and non-molecular data, respectively, but some simlarities to the molecular estimate are highlighted and lead us here to formally include Actinostrobus within Callitris. Further molecular data are needed to test these results and explore the cause of the conflict between these estimates of the phylogeny within the group, and the status of Neocallitropsis.

The Lanius excubitor (Aves, Passeriformes) conundrum—Taxonomic dilemma when molecular and non-molecular data tell different stories

The phylogeny of 18 taxa in the Lanius excubitor complex, and the related species L. sphenocercus, L. ludovicianus and L. somalicus, was estimated based on the mitochondrial cytochrome b gene and the non-coding D-loop (in total ∼1.3 kb). According to the mitochondrial gene tree, Lanius excubitor s.l. is non-monophyletic, with some of its subspecies being more closely related to L. sphenocercus, L. ludovicianus, and L. somalicus. Also the division of the L. excubitor complex into a northern ( L. excubitor) and a southern ( L. meridionalis) species, as has been proposed based on morphological and ecological similarity and geographical distributions, is not compatible with the mitochondrial tree. Overall, genetic divergences among the ingroup taxa are small, indicating a recent radiation. A tree based on the nuclear ornithine decarboxylase (ODC) introns 6–7 is unresolved with respect to the ingroup, but provides strong support for a clade containing the Lanius excubitor complex, L. sphenocercus, L. ludovicianus and L. somalicus. We discuss the incongruence between the current taxonomy and the mitochondrial gene tree, and conclude that based on the latter the Lanius excubitor complex may be treated as at least six species, L. borealis, L. elegans, L. excubitor, L. lahtora, L. meridionalis, and L. uncinatus, but that other taxonomic treatments are also possible. However, uncertainty regarding to which extent the mitochondrial gene tree reflects the species phylogeny prevents us from recommending taxonomic change without further investigation. This study highlights the possible danger of relying on a single molecular marker, such as mitochondrial DNA, in taxonomic revisions and phylogenetic inference.

Phylogenetic Analyses of Postcranial Skeletal Morphology in Didelphid Marsupials

In this study I provide a phylogenetic hypothesis for didelphid Marsupials including a suite of 114 postcranial characters. The postcranial evidence was cladistically analyzed separately and concatenated with a nonmolecular data set previously published (71 cranio-dental-external characters). A combined analysis was done including published IRBP (interphotoreceptor retinoid binding protein, 1158 bp), DMP-1 (dentin matrix protein 1, 1176 bp), and RAG-1 (recombinase-activating gene, 2790 bp) sequences to the nonmolecular data set. In order to compare and evaluate the influence of the inclusion of postcranial morphology to previous hypotheses, the taxon sampling of didelphine ingroup was almost similar to the one used in recent series of papers on didelphid phylogeny. The postcranial information includes 48 characters from the axial skeleton, 37 from the anterior limb, and 29 from the posterior limb. I present anatomical descriptions for each postcranial character, adding details of different conditions observed among didelphine ingroup, as well as some functional implications. Different hypotheses that are discussed as polymorphic characters are alternatively treated as composite entries (CO) and transformation series (TS) in morphological and combined analyses. Different codings of polymorphic postcranial characters produce topologies that in general are not contradictory. The principal difference is the loss of resolution of trees in TS analysis, compared to CO analysis in postcranial evidence, whereas the support values were in general low in both codings. The topology obtained from postcranial evidence supported some already recovered relationships, such as the monophyly of the large opossums (Didelphis, Philander, Chironectes, Lutreolina, and Metachirus), and several polytypic groups such as Didelphis, Monodelphis, Marmosops, Thylamys, Micoureus, and Philander. Additionally, the intermediate position of Hyladelphys between calorumyines and didelphines is kept in CO analysis. The inclusion of the postcranial data set to previous nonmolecular evidence causes little incongruence, although some modifications in the topology and support values were detected. The effect of different codings of polymorphic characters was similar respect to the postcranial-only data set. In this case, the topology obtained with CO analysis was also notably better resolved than TS analysis. Similarly to the postcranial-only analysis, the topologies obtained in the total morphological evidence applying the two kinds of codings are highly congruent, but the TS treatment seemed not to contribute to retention of more phylogenetic information, since the CO analysis was better resolved. The relationships obtained adding the postcranial evidence to published combined data set (i.e., morphology, IRBP, DMP-1, and RAG-1 sequences) were mostly better resolved and supported in the CO coding than the morphological analyses, although the TS coding causes loss of resolution in the strict consensus. In this sense, some strong differences on deep branch topology can be detected depending on the treatment applied to polymorphic entries and partitioned analyses (e.g., phylogenetic condition of the mouse opossums, nodes C and B). Including the postcranial evidence in the total data set, I also recovered the intermediate position of Hyladelphys, but never the distantly related clades recently recovered by the inclusion of RAG-1 sequences (clades B I in Gruber, K.F., R.S. Voss, and S.A. Jansa. 2007. Base-compositional heterogeneity in the RAG1 locus among didelphid marsupials: implications for phylogenetic inference and the evolution of GC content. Systematic Biology 56: 1–14). However, the position of Metachirus nudicaudatus and Tlacuatzin canescens is highly affected. Excluding the last gene, the partitioned combined analysis considering postcranial evidence was highly congruent with previous IRBP, morphology, and combined topologies, especially in the TS analysis, w

Phylogenetic relationships of Ruteae (Rutaceae): New evidence from the chloroplast genome and comparisons with non-molecular data

Phylogenetic analyses of three cpDNA markers ( matK, rpl16, and trnL– trnF) were performed to evaluate previous treatments of Ruteae based on morphology and phytochemistry that contradicted each other, especially regarding the taxonomic status of Haplophyllum and Dictamnus. Trees derived from morphological, phytochemical, and molecular datasets of Ruteae were then compared to look for possible patterns of agreement among them. Furthermore, non-molecular characters were mapped on the molecular phylogeny to identify uniquely derived states and patterns of homoplasy in the morphological and phytochemical datasets. The phylogenetic analyses determined that Haplophyllum and Ruta form reciprocally exclusive monophyletic groups and that Dictamnus is not closely related to the other genera of Ruteae. The different types of datasets were partly incongruent with each other. The discordant phylogenetic patterns between the phytochemical and molecular trees might be best explained in terms of convergence in secondary chemical compounds. Finally, only a few non-molecular synapomorphies provided support for the clades of the molecular tree, while most of the morphological characters traditionally used for taxonomic purposes were found to be homoplasious. Within the context of the phylogenetic relationships supported by molecular data, Ruta, the type genus for the family, can only be diagnosed by using a combination of plesiomorphic, homoplasious, and autapomorphic morphological character states.

Laying the Foundation for a Genomic Rosetta Stone: Creating Information Hubs through the Use of Consensus Identifiers

Given the growing wealth of downstream information, the integration of molecular and non-molecular data on a given organism has become a major challenge. For micro-organisms, this information now includes a growing collection of sequenced genes and complete genomes, and for communities of organisms it includes metagenomes. Integration of the data is facilitated by the existence of authoritative, community-recognized, consensus identifiers that may form the heart of so-called information knuckles. The Genomic Standards Consortium (GSC) is building a mapping of identifiers across a group of federated databases with the aim to improve navigation across these resources and to enable the integration of their information in the near future. In particular, this is possible because of the existence of INSDC Genome Project Identifiers (GPIDs) and accession numbers, and the ability of the community to define new consensus identifiers such as the culture identifiers used in the StrainInfo.net bioportal. Here we outline (1) the general design of the Genomic Rosetta Stone project, (2) introduce example linkages between key databases (that cover information about genomes, 16S rRNA gene sequences, and microbial biological resource centers), and (3) make an open call for participation in this project providing a vision for its future use.

Sequences of low-copy nuclear gene support the monophyly of Ostrya and paraphyly of Carpinus (Betulaceae)

Coryloideae consists of four genera: Corylus, Ostryopsis, Carpinus, and Ostrya. While both molecular and non-molecular data support the close relationship of Carpinus and Ostrya, the monophyly of the two genera has remained controversial. In this study, sequences of the nuclear nitrate reductase (Nia) were used to test the naturalness of the two genera. Ostrya species form a robust clade, supporting the monophyly of the genus. The clade, however, is located between Carpinus cordata and the remaining species of Carpinus, indicating that Carpinus is paraphyletic, and Ostrya has evolved from within Carpinus. Within Carpinus, section Distegocarpus is polyphyletic, whereas section Carpinus is a clade where subsections Polyneurae and Carpinus are more closely related to each other than either is to subsection Monbeigianae.

Evolution of taxodiaceous Cupressaceae (Coniferopsida)

The evolution of taxodiaceous Cupressaceae has been discussed controversially, because phylogenetic analyses using non-molecular data show major differences to molecular analyses. To solve this problem, we used non-molecular data with a high probability of homology. With these type of data, we could show for the first time in taxodiaceous Cupressaceae that phylogenetic trees of molecular and non-molecular data share the same topology. Investigation of female cone development also contributes to better understanding of morphology and anatomy in taxodiaceous Cupressaceae. Additional developmental, fossil and cone configuration data support the topology constructed by using the molecular and non-molecular data.

Speciation in Duckweeds (Lemnaceae): Phylogenetic and Ecological Inferences

Species of duckweeds (Letnnaceae) that were resolved as sister taxa in a phylogeny based on combined molecular and non-molecular data were compared for morphological, physiological, and ecological attributes to infer factors important in the initial divergence leading to speciation. The ability to survive extreme conditions such as desiccation and cold temperatures is the most common difference identified between species. Two morphological characters facilitating survival in extreme environments are production of special resting buds called turions and increased seed production. The prevalent geographic pattern for species pairs consists of one restricted species occurring on the periphery of a more widespread taxon; this pattern indicates that divergence of peripheral isolates is a common geographical mode of speciation in duckweeds. Other species differ in optimal environmental conditions for growth, and these species are largely sympatric. In only one instance does it appear that divergence and speciation occurred following long-distance dispersal. Sympatric species pairs have the lowest molecular divergence; widespread primarily allopatric, and distantly allopatric species have the highest molecular divergence. Despite infrequent sexual reproduction, some degree of detectable variation (molecular, physiological, etc.) occurs within populations and among populations of the same species. Molecular evidence indicates that variation within duckweeds extends from the population and intraspecific levels to very different levels of divergence among recognized species. Contrary to the appearance of morphological and ecological uniformity implied by their reduced morphology and restricted occurrence in fresh water habitats, duckweeds are not a group in evolutionary stasis. Rather, these smallest of all flowering plants are dynamic evolutionarily, and comprise a model system for studying plant evolution and speciation.