Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group

We present a revised molecular phylogeny of the Drosophila repleta group including 62 repleta group taxa and nine outgroup species based on four mitochondrial and six nuclear DNA sequence fragments. With ca. 100 species endemic to the New World, the repleta species group represents one of the major species radiations in the genus Drosophila. Most repleta group species are associated with cacti in arid or semiarid regions. Contrary to previous results, maximum likelihood and Bayesian phylogenies of the 10-gene dataset strongly support the monophyly of the repleta group. Several previously described subdivisions in the group were also recovered, despite poorly resolved relationships between these clades. Divergence time estimates suggested that the repleta group split from its sister group about 21millionyears ago (Mya), although diversification of the crown group began ca. 16Mya. Character mapping of patterns of host plant use showed that flat leaf Opuntia use is common throughout the phylogeny and that shifts in host use from Opuntia to the more chemically complex columnar cacti occurred several times independently during the history of this group. Although some species retained the use of Opuntia after acquiring the use of columnar cacti, there were multiple, phylogenetically independent instances of columnar cactus specialization with loss of Opuntia as a host. Concordant with our proposed timing of host use shifts, these dates are consistent with the suggested times when the Opuntioideae originated in South America. We discuss the generally accepted South American origin of the repleta group.     

How Difficult Is Inference of Mammalian Causal Gene Regulatory Networks?

Gene regulatory networks (GRNs) play a central role in systems biology, especially in the study of mammalian organ development. One key question remains largely unanswered: Is it possible to infer mammalian causal GRNs using observable gene co-expression patterns alone? We assembled two mouse GRN datasets (embryonic tooth and heart) and matching microarray gene expression profiles to systematically investigate the difficulties of mammalian causal GRN inference. The GRNs were assembled based on pieces of experimental genetic perturbation evidence from manually reading primary research articles. Each piece of perturbation evidence records the qualitative change of the expression of one gene following knock-down or over-expression of another gene. Our data have thorough annotation of tissue types and embryonic stages, as well as the type of regulation (activation, inhibition and no effect), which uniquely allows us to estimate both sensitivity and specificity of the inference of tissue specific causal GRN edges. Using these unprecedented datasets, we found that gene co-expression does not reliably distinguish true positive from false positive interactions, making inference of GRN in mammalian development very difficult. Nonetheless, if we have expression profiling data from genetic or molecular perturbation experiments, such as gene knock-out or signalling stimulation, it is possible to use the set of differentially expressed genes to recover causal regulatory relationships with good sensitivity and specificity. Our result supports the importance of using perturbation experimental data in causal network reconstruction. Furthermore, we showed that causal gene regulatory relationship can be highly cell type or developmental stage specific, suggesting the importance of employing expression profiles from homogeneous cell populations. This study provides essential datasets and empirical evidence to guide the development of new GRN inference methods for mammalian organ development.     

Saline paleolake of the Cañadón Asfalto Formation (Middle-Upper Jurassic), Cerro Cóndor, Chubut province (Patagonia), Argentina

The carbonate-evaporitic sequence of the Cañadón Asfalto Formation that crops out in Cañadón Carrizal (Chubut province, Argentina) is characterized by a lacustrine facies association. This sequence includes an extensive biohermal belt, flood facies with high lake-level and low lake-level stages, and desiccation–evaporation facies. The biohermal belt shows three growth-stages of microbial communities. This belt controlled sedimentation in nearby areas, favoring the formation of the pan lake of Cañadón Carrizal. High lake-level flood facies represent sedimentation during periods of great water input to the pan lake. Low lake-level flood facies are characterized by low-energy conditions and by the development of a shallow lake with marginal zones and palustrine subenvironments. Desiccation facies represent a dry mudflat that borders the saline lake. Evaporation facies are related to the shrinkage of the water body and to the migration of the shallower facies towards the center of the ephemeral lake.     

Tooth Size Variation in Assemblages of Tremacyllus (Hegetotheriidae,Notoungulata): Insights into Geographical Gradients,Systematics, and Sexual Dimorphism

Tooth size variation within fossil assemblages can be associated with intra- or interspecific variation, functional, developmental, and geographical factors, and/or sexual dimorphism. Understanding these sources of variation is necessary to develop diagnoses for fossil mammals, where teeth are usually the most frequent remains. Tremacyllus (Ameghino, 1891) (Hegetotheriidae, Notoungulata) is a genus of small-sized herbivorous mammals abundant in late Miocene to Pliocene outcrops of southern South America. Its simplified, euhypsodont dentition and size variability have hampered systematics studies and led, for instance, to an overestimation of the number of species. I analyzed tooth size variations within assemblages of Tremacyllus in a quantitative framework to test three hypotheses: (1) magnitudes of size variation are different among tooth loci and assemblages; (2) tooth size follows a geographical pattern within the analyzed sample (Bergmann’s rule), but is also associated with taxonomy; and (3) there is a correlation between size variation and sexual dimorphism reflected in distinguishable subgroups. Results indicate that patterns of variation might be associated with eruption time and/or functional position. Northwestern forms are larger than southwestern-Pampean ones, not conforming to Bergmann’s rule but revealing a strong influence of latitude. Size differences between assemblages agree with dental features that distinguish T. incipiens and T. impressus, allowing expanded species diagnoses. Two size subgroups might reflect sexual dimorphism in the absence of biostratigraphic or morphological differences between them. This interpretation indicates that northwestern specimens referred to T. diminutus should be referred to T. incipiens.