Discrete Morphological Traits Research Articles

Systematic Revision of Thomasomys cinereus (Rodentia: Cricetidae: Sigmodontinae) from Northern Peru and Southern Ecuador, With Descriptions of Three New Species

Thomasomys cinereus is the type species of Thomasomys, type genus of the sigmodontine tribe Thomasomyini. As currently recognized, Thomasomys includes 48 species, all of which are endemic to humid montane or premontane forests in the tropical Andes. Although it has been suggested that T. cinereus is a species complex, this hypothesis has yet to be critically evaluated. Herein we provide a revision of the species based on a qualitative assessment of external, craniodental, and soft morphological traits; morphometric analyses; a phylogenetic analysis based on cytochrome b gene sequences; species delimitation methods; and first-hand examination of type material. Our analyses of genetic data recovered four distinct clades within T. cinereus, one corresponding to T. cinereus sensu stricto (restricted to the montane forests delimited by the Río Marañón, Río Huancabamba, and Río Tablachaca in Cajamarca department, Peru) and three new species: Thomasomys lojapiuranus, sp. nov., from the montane forests of Piura department, Peru, and Loja province, Ecuador; T. shallqukucha, sp. nov., restricted to the Kañaris montane forests in the Peruvian department of Lambayeque; and T. pagaibambensis, sp. nov., restricted to the montane forests of Pagaibamba in Cajamarca department, Peru. These species can be distinguished by several discrete morphological traits of the skull, dentition, mandible, stomach, palatal rugae, and glans penis. Genetic distances among these taxa range from 5.06%–7.65% at the cytochrome b locus, and delimitation analyses based on cytochrome b sequence data support their recognition as distinct species. Our results suggest the existence of previously unsuspected dispersal barriers in the Andes of northern Peru, and they confirm that the Río Marañón is a formidable barrier that limits the distribution of species of Thomasomys as well as other sigmodontine rodents.

One step closer but still far from solving the puzzle – The phylogeny of marine associated mites (Acari, Oribatida, Ameronothroidea) inferred from morphological and molecular genetic data

Abstract Marine associated oribatid mites belong mainly to the Ameronothroidea which represent a very small percentage of all Oribatida. Over the last decades the systematics and evolutionary history of this group has been discussed controversially and still there is no consensus concerning several issues. The extreme marine environment may have resulted in parallel morphologies complicating the classification and estimation of phylogeny based on discrete morphological traits. In the present study, we performed a molecular genetic study using a mitochondrial and two nuclear markers to infer the phylogeny of this group. Additionally, we reconstructed the phylogeny of Ameronothroidea based on morphological data using different algorithms. Both methods resulted in largely congruent topologies and highlight the following important points: the Ameronothroidea represent a paraphyletic assemblage; the Podacaridae are a distinct family and should be excluded from Ameronothridae; the Fortuyniidae, Selenoribatidae and Tegeocranellidae constitute a monophyletic lineage; and certain genera of Selenoribatidae need a revision. These results demonstrate that the classification of Ameronothroidea and certain positions within this group need to be thoroughly reconsidered and revised. The present study also shows that phylogenetic estimates based on coded morphological data can be a very helpful tool for verifying and supporting molecular phylogenies.

Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila.

The loss of discrete morphological traits, the most common evolutionary transition, is typically driven by changes in developmental gene expression. Mutations accumulating in regulatory elements of these genes can disrupt DNA binding sites for transcription factors patterning their spatial expression, or delete entire enhancers. Regulatory elements, however, may be silenced through changes in chromatin accessibility or the emergence of repressive elements. Here, we show that increased chromatin accessibility at the gene yellow, combined with the gain of a repressor site, underlies the loss of a wing spot pigmentation pattern in a Drosophila species. The gain of accessibility of this repressive element is regulated by E93, a transcription factor governing the progress of metamorphosis. This convoluted evolutionary scenario contrasts with the parsimonious mutational paths generally envisioned and often documented for morphological losses. It illustrates how evolutionary changes in chromatin accessibility may directly contribute to morphological diversification.

Unearthing Modes of Climatic Adaptation in Underground Storage Organs Across Liliales.

Testing adaptive hypotheses about how continuous traits evolve in association with developmentally structured discrete traits, while accounting for the confounding influence of other, hidden, evolutionary forces, remains a challenge in evolutionary biology. For example, geophytes are herbaceous plants-with underground buds-that use underground storage organs (USOs) to survive extended periods of unfavorable conditions. Such plants have evolved multiple times independently across all major vascular plant lineages. Even within closely related lineages, however, geophytes show impressive variation in the morphological modifications and structures (i.e.,"types" of USOs) that allow them to survive underground. Despite the developmental and structural complexity of USOs, the prevailing hypothesis is that they represent convergent evolutionary "solutions" to a common ecological problem, though some recent research has drawn this conclusion into question. We extend existing phylogenetic comparative methods to test for links between the hierarchical discrete morphological traits associated with USOs and adaptation to environmental variables, using a phylogeny of 621 species in Liliales. We found that plants with different USO types do not differ in climatic niche more than expected by chance, with the exception of root morphology, where modified roots are associated with lower temperature seasonality. These findings suggest that root tubers may reflect adaptations to different climatic conditions than those represented by other types of USOs. Thus, the tissue type and developmental origin of the USO structure may influence the way it mediates ecological relationships, which draws into question the appropriateness of ascribing broad ecological patterns uniformly across geophytic taxa. This work provides a new framework for testing adaptive hypotheses and for linking ecological patterns across morphologically varying taxa while accounting for developmental (non-independent) relationships in morphological data. [Climatic niche evolution; geophytes; imperfect correspondence; macroevolution.].

Geographic Variation in Cranial Morphology of the Southern Mountain Cavy, Microcavia australis (Rodentia, Caviidae): Taxonomic Implications, with the Description of a New Species.

Pablo Teta, Ricardo A. Ojeda, Sergio O. Lucero, and Guillermo D'Elía (2017) We analyzed the geographic variation in cranial morphology of the Southern Mountain Cavy, Microcavia australis, throughout of its distributional range. Our analysis allows us to recognize three geographically allopatric morphotypes. These morphotypes differ in the general size and shape of the skull and discrete morphological traits of the zygomatic arch, palate and mesopterygoid fossa. Based on these results, we restrict the name australis to populations distributed in southern Argentina and west-central Andes and the name maenas to the morphotype of northwestern and central Argentina. The third morphotype occurs in the Dry Chaco ecoregion and is described here as a new species.

A molecular phylogeny of the Sematophyllaceae s.l. (Hypnales) based on plastid, mitochondrial and nuclear markers, and its taxonomic implications

AbstractThe Sematophyllaceae s.l. (Sematophyllaceae+Pylaisiadelphaceae) is a family of pleurocarpous mosses that is widely distributed throughout the globe, with centers of diversity in tropical forests. The circumscriptions of the family and its genera have been unstable, due to reductions in morphological complexity and alternative weightings of discrete morphological traits. Based on a sample spanning much of the generic diversity of the family, we inferred the phylogenetic relationships within the Sematophyllaceae s.l. from the variation in eight molecular markers from all three genomes (nuclear, mitochondrial, chloroplast). The Sematophyllaceae s.l. was resolved as monophyletic, as was the Sematophyllaceae s.str.; whereas the Pylaisiadelphaceae was found to be paraphyletic, although its monophyly could not be rejected. The morphological definition of the Pylaisiadelphaceae remains dubious, in the absence of unambiguous synapomorphies. The relationships of the clades of Pylaisiadelphaceae and Sematophyllaceae are discussed with respect to the circumscription of morphogenera, with a focus on the Sematophyllaceae crown clade (Aptychopsis, Chionostomum, Colobodontium, Donnellia, Macrohymenium, Paranapiacabaea, Pterogoniopsis, Rhaphidorrhynchium, Schroeterella, Sematophyllum, Warburgiella). Most genera of Sematophyllaceae were resolved as polyphyletic (e.g., Acroporium, Donnellia, Schroeterella, Sematophyllum, Trichosteleum) indicative of severe homoplasy in their putative diagnostic traits. We propose 4 new genera (Brittonodoxa, Microcalpe, Pocsia, Vitalia) and 19 new combinations (Aptychopsis cylindrothecia, A. estrellae, A. tequendamensis, Brittonodoxa allinckxiorum, B. cataractae, B. lithophila, B. squarrosa, B. steyermarkii, B. subpinnata, Microcalpe subsimplex, Pocsia matutina, Pterogoniopsis paulista, Schroeterella exigua, Trichosteleum amnigenum, T. lonchophyllum, Vitalia caespitosa, V. cuspidifera, V. esmeraldica, V. galipensis)

Bayesian phylogenetic estimation of fossil ages.

Recent advances have allowed for both morphological fossil evidence and molecular sequences to be integrated into a single combined inference of divergence dates under the rule of Bayesian probability. In particular, the fossilized birth–death tree prior and the Lewis-Mk model of discrete morphological evolution allow for the estimation of both divergence times and phylogenetic relationships between fossil and extant taxa. We exploit this statistical framework to investigate the internal consistency of these models by producing phylogenetic estimates of the age of each fossil in turn, within two rich and well-characterized datasets of fossil and extant species (penguins and canids). We find that the estimation accuracy of fossil ages is generally high with credible intervals seldom excluding the true age and median relative error in the two datasets of 5.7% and 13.2%, respectively. The median relative standard error (RSD) was 9.2% and 7.2%, respectively, suggesting good precision, although with some outliers. In fact, in the two datasets we analyse, the phylogenetic estimate of fossil age is on average less than 2 Myr from the mid-point age of the geological strata from which it was excavated. The high level of internal consistency found in our analyses suggests that the Bayesian statistical model employed is an adequate fit for both the geological and morphological data, and provides evidence from real data that the framework used can accurately model the evolution of discrete morphological traits coded from fossil and extant taxa. We anticipate that this approach will have diverse applications beyond divergence time dating, including dating fossils that are temporally unconstrained, testing of the ‘morphological clock', and for uncovering potential model misspecification and/or data errors when controversial phylogenetic hypotheses are obtained based on combined divergence dating analyses.This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

Phylogeny and taxonomic revision of Thelonectria discophora (Ascomycota, Hypocreales, Nectriaceae) species complex

Specimens regarded as Thelonectria discophora (Thelonectria, Nectriaceae, Hypocreales) constitute a conspicuous group of saprobic fungi on decaying plant material, characterized by red perithecia each with a broad mammiform (nipple-like) apex. The asexual state is characterized by a cylindrocarpon-like morphology, with 3–5 septate macroconidia, unicellular microconidia and chlamydospores that are rarely produced in culture. In the past, T. discophora was regarded as one species with a wide geographic distribution. However, a recent study rejected the monophyly and cosmopolitan distribution of this species, and showed the existence of at least 16 cryptic species distributed in three main groups. By combining the results of phylogenetic analyses of six nuclear loci and morphological studies, we revised the taxonomy of the T. discophora species complex, resulting in the description of 12 new species and four new combinations based on historic names. Even though molecular phylogenetic analyses strongly support the segregation of these species, and are in agreement with previous studies, individual diagnostic morphological characters for each species could not be identified. However, discrete morphological traits corresponding to each of the three main groups of species were discovered. Lineages could be differentiated based on the average values of morphological traits as well as the presence/absence of characteristic asexual propagules and colony growth at 30C. Descriptions, illustrations are provided for the recognized species.

Variation for Canopy Morphology in Little Bluestem

ABSTRACTLittle bluestem, Schizachyrium scoparium (Michx.) Nash, is a native grass that has been shown to have high levels of genetic variation for traits such as biomass yield, disease resistance, plant height, leafiness, maturity, and seed yield. If high levels of genetic variation exist for these traits, it is likely that it would exist for other traits as well. Thus, the objectives were to describe the variation in traits that contribute to canopy morphology within and among little bluestem parental lines, an F1 plant population, and selected F1 populations. Plants were classified as not upright (NU), upright compact (UC), or upright open (UO) on the basis of their shape. As expected, all parental lines expressed considerable variation for frequencies of discrete morphological traits and for continuous morphological traits. The F1 plant population was characterized by 12.2% NU plants, 22.4% UC plants, and 65.4% UO plants. The selected populations were fixed for several discrete variables, including growth form, lack of lodging, and little or no leaf rust. To fully exploit the genetic variability of little bluestem, it would be necessary to obtain ecotypes from throughout its natural range and breed and select for new genetic variation that could be captured through recurrent selection. Little bluestem is an ideal species for breeding new cultivars and/or germplasm lines for pasture and rangeland renovation, roadside revegetation, wildlife habitat, and recreation areas.

Partial penetrance facilitates developmental evolution in bacteria.

Development normally occurs similarly in all individuals within an isogenic population, but mutations often affect the fate of individual organisms differently1-4. This phenomenon, known as partial penetrance, has been observed in diverse developmental systems. However, it remains unclear how the underlying genetic network specifies the set of possible alternative fates and how the relative frequencies of these fates evolve5-8. Here, we identify a stochastic cell fate determination process that operates in Bacillus subtilis sporulation mutants and show how it allows genetic control of the penetrance of multiple fates. Mutations in an inter-compartmental signaling process generate a set of discrete alternative fates not observed in wild-type cells, including rare formation of two viable “twin” spores, rather than one within a single cell. By genetically modulating chromosome replication and septation, we could systematically tune the penetrance of each mutant fate. Furthermore, signaling and replication perturbations synergize to dramatically increase the penetrance of twin sporulation. These results suggest a potential pathway for developmental evolution between monosporulation and twin sporulation through states of intermediate twin penetrance. Furthermore, time-lapse microscopy of twin sporulation in wild-type Clostridium oceanicum showed a strong resemblance to twin sporulation in these B. subtilis mutants9,10. Together the results suggest that noise can facilitate developmental evolution by enabling the initial expression of discrete morphological traits at low penetrance, and allowing their stabilization by gradual adjustment of genetic parameters.

A Bayesian approach for evaluating the impact of historical events on rates of diversification

Evolutionary biologists often wish to explore the impact of a particular historical event (e.g., the origin of a novel morphological trait, an episode of biogeographic dispersal, or the onset of an ecological association) on rates of diversification (speciation minus extinction). We describe a Bayesian approach for evaluating the correlation between such events and differential rates of diversification that relies on cross-validation predictive densities. This approach exploits estimates of the marginal posterior probability for the rate of diversification (in the unaffected part of the tree) and the marginal probability for the timing of the event to generate a predictive distribution of species diversity that would be expected had the event not occurred. The realized species diversity can then be compared to this predictive diversity distribution to assess whether rates of diversification associated with the event are significantly higher or lower than expected. Although simple, this Bayesian approach provides a robust inference framework that accommodates various sources of uncertainty, including error associated with estimates of divergence times, diversification-rate parameters, and event history. Furthermore, the proposed approach is relatively flexible, allowing exploration of various types of events (including changes in discrete morphological traits, episodes of biogeographic movement, etc.) under both hypothesis-testing and data-exploration inference scenarios. Importantly, the cross-validation predictive densities approach facilitates evaluation of both replicated and unique historical events. We demonstrate this approach with empirical examples concerning the impact of morphological and biogeographic events on rates of diversification in Adoxaceae and Lupinus, respectively.

Analysis of function in the absence of extant functional homologues: a case study using mesotheriid notoungulates (Mammalia)

We use two approaches to test hypotheses regarding function in a group of extinct mammals (Family Mesotheriidae, Order Notoungulata) that lack any close extant relatives: a principle-derived paradigm method and empirically derived analog method. Metric and discrete morphological traits of mesotheriid postcranial elements are found to be consistent with the morphology predicted by a modified version of Hildebrand's paradigm for scratch diggers. Ratios of in-force to out-force lever arms based on skeletal elements indicate that the mesotheriids examined had limbs modified for high out-forces (i.e., they were “low geared”), consistent with the digging hypothesis. Other mesotheriid characters, such as cleft ungual phalanges, a curved olecranon, and a highly modified pelvis (with extra vertebrae incorporated into the sacrum and fusion between the ischium and the axial skeleton) are regarded as being functionally significant for digging and also occur in a variety of extant diggers. Analog methods indicate that mesotheriids share numerous traits common to a variety of extant diggers. Principal component analyses of postcranial elements indicate that mesotheriids consistently share morphometric space with larger extant fossorial mammals: aardvark, anteaters, wombats, and badger. Likewise, discriminant function analyses categorized mesotheriids as fossorial, though imperfectly analogous to the extant diggers analyzed. Thus, both theory-driven and empirically derived methods of estimating function in these extinct taxa support a digging hypothesis for the mesotheriids examined. Adaptations for digging in both the forelimb and sacropelvic functional complexes of mesotheriids provide independent support for the fossorial hypothesis.

Lingual incisor traits in modern hominoids and an assessment of their utility for fossil hominoid taxonomy

The morphology of the anterior dentition has received scant attention for purposes of taxonomic discrimination. Recently, however, lingual incisor morphology was used in differentiating several Miocene ape species and genera. This paper assesses the utility of this morphology for taxonomic discrimination by examining the nature and patterns of variation in lingual incisor morphology in extensive samples of modern chimpanzees, gorillas, orangutans, and gibbons. This paper documents discrete morphological traits on the lingual side of incisors. Trait frequencies are used in univariate and multivariate analyses to examine the apportionment of variation in species, subspecies, and populations. A correlation between lingual incisor traits, tooth dimensions, and sex attempts to determine if such factors affect the manifestation of traits. Finally, the findings are applied to understanding patterns of variation in the Miocene hominids. The study demonstrates that: 1) lingual incisor morphology differs substantially between the hylobatids and great apes; 2) variation in incisor traits is high within species, and most of it is found within local populations; and 3) incisor traits do not correlate significantly with incisor dimensions or sex. Species and to some extent subspecies of extant hominoids can be differentiated statistically using lingual incisor traits, but the frequency of traits such as continuous or discontinuous cingulum, or the presence or absence of pillars, differentiates them. Given this pattern of variation, I argue that it is necessary to assume and document similar patterns of variation in Miocene apes before incisor morphology is used for differentiating taxa.

A linkage map of hexaploid oat based on grass anchor DNA clones and its relationship to other oat maps

A cultivated oat linkage map was developed using a recombinant inbred population of 136 F6:7 lines from the cross 'Ogle' x 'TAM O-301'. A total of 441 marker loci, including 355 restriction fragment length polymorphism (RFLP) markers, 40 amplified fragment length polymorphisms (AFLPs), 22 random amplified polymorphic DNAs (RAPDs), 7 sequence-tagged sites (STSs), 1 simple sequence repeat (SSR), 12 isozyme loci, and 4 discrete morphological traits, was mapped. Fifteen loci remained unlinked, and 426 loci produced 34 linkage groups (with 2-43 loci each) spanning 2049 cM of the oat genome (from 4.2 to 174.0 cM per group). Comparisons with other Avena maps revealed 35 genome regions syntenic between hexaploid maps and 16-34 regions conserved between diploid and hexaploid maps. Those portions of hexaploid oat maps that could be compared were completely conserved. Considerable conservation of diploid genome regions on the hexaploid map also was observed (89-95%); however, at the whole-chromosome level, colinearity was much lower. Comparisons among linkage groups, both within and among Avena mapping populations, revealed several putative homoeologous linkage group sets as well as some linkage groups composed of segments from different homoeologous groups. The relationships between many Avena linkage groups remain uncertain, however, due to incomplete coverage by comparative markers and to complications introduced by genomic duplications and rearrangements.