Phylogeography of Mus (Nannomys) minutoides (Rodentia,Muridae) in West Central African savannahs: singular vicariance in neighbouring populations

We studied the phylogeography of the strict savannah pygmy mice Mus (Nannomys) minutoides in West Central Africa. A total of 846 base pairs of the cytochrome b sequence were obtained for 66 individuals collected in Gabon, Cameroon, Republic of Congo and Central African Republic. These sequences were compared to those of M. minutoides from other African countries and to eight other species of the genus Mus. We performed maximum likelihood, Bayesian and nested clade analyses, as well as neutrality tests and time estimates. We show that M. minutoides is a well‐differentiated monophyletic species that separated from other pygmy mice 1.17 Myr ago. A distinct West Central African M. minutoides clade diverged early from the other African populations of the species, with a more recent common ancestor dating 0.14 Myr. West Central African populations are globally homogeneous, despite the present fragmentation of savannahs by the rain forest. However, our analyses show an unexpected vicariance between geographically close savannahs, embedded in the rain forest in Central Gabon. One of these populations is genetically more similar to very distant peripheral populations than to three closely neighbouring populations situated on both sides of the Ogooué River. A non‐river geographical barrier probably persisted in this area, durably isolating these local populations. This hypothesis about the history of the savannah landscape should be testable through the biogeographical analysis of other strict savannah small mammal species.     

Increase in Alphaproteobacteria in association with a polychaete,Capitella sp. I,in the organically enriched sediment

We conducted bioremediation experiments on the organically enriched sediment on the sea floor just below a fish farm, introducing artificially mass-cultured colonies of deposit-feeding polychaete, Capitella sp. I. To clarify the association between the Capitella and bacteria on the efficient decomposition of the organic matter in the sediment in the experiments, we tried to identify the bacteria that increased in the microbial community in the sediment with dense patches of the Capitella. The relationship between TOC and quinone content of the sediment as an indicator of the bacterial abundance was not clear, while a significant positive correlation was found between Capitella biomass and quinone content of the sediment. In particular, ubiquinone-10, which is present in members of the class Alphaproteobacteria, increased in the sediment with dense patches of the Capitella. We performed denaturing gradient gel electrophoresis (DGGE) analyses to identify the alphaproteobacterial species in the sediment with dense patches of the worm, using two DGGE fragments obtained from the sediment samples and one fragment from the worm body. The sequences of these DGGE fragments were closely related to the specific members of the Roseobacter clade. In the associated system with the Capitella and the bacteria in the organically enriched sediment, the decomposition of the organic matter may proceed rapidly. It is very likely that the Capitella works as a promoter of bacteria in the organically enriched sediment, and feeds the increased bacteria as one of the main foods, while the bacteria decompose the organic matter in the sediment with the assistance of the Capitella.     

Macroevolutionary trends in the Dinosauria: Cope's rule

Cope's rule is the tendency for body size to increase over time along a lineage. A set of 65 phylogenetically independent comparisons, between earlier and later genera, show that Cope's rule applied in dinosaurs: later genera were on average about 25% longer than the related earlier genera to which they were compared. The tendency for size to increase was not restricted to a particular clade within the group, nor to a particular time within its history. Small lineages were more likely to increase in size, and large lineages more likely to decrease: this pattern may indicate an intermediate optimum body size, but can also be explained as an artefact of data error. The rate of size increase estimated from the phylogenetic comparisons is significantly higher than the rate seen across the fauna as a whole. This difference could indicate that within-lineage selection for larger size was opposed by clade selection favouring smaller size, but data limitations mean that alternative explanations (which we discuss) cannot be excluded. We discuss ways of unlocking the full potential usefulness of phylogenies for studying the dynamics of evolutionary trends.     

Dispersal, habitat differences, and comparative phylogeography of Southeast Asian seahorses (Syngnathidae: Hippocampus)

Four distinct phylogeographical patterns across Southeast Asia were observed for four species of seahorse (genus Hippocampus) with differing ecologies. For all species, genetic differentiation (based on cytochrome b sequence comparisons) was significantly associated with sample site (Phi(ST) = 0.190-0.810, P < 0.0001) and with geographical distance (Mantel's r = 0.37-0.59, P < 0.019). Geographic locations of genetic breaks were inconsistent across species in 7/10 comparisons, although some similarities across species were also observed. The two shallow-water species (Hippocampus barbouri and Hippocampus kuda) have colonized the Sunda Shelf to a lesser degree than the two deeper-water species (Hippocampus spinosissimus and Hippocampus trimaculatus). In all species the presence of geographically restricted haplotypes in the Philippines could indicate past population fragmentation and/or long-distance colonization. A nested clade analysis (NCA) revealed that long-distance colonization and/or fragmentation were likely the dominant forces that structure populations of the two shallow-water species, whereas range expansion and restricted dispersal with isolation by distance were proportionally more important in the history of the two deeper-water species. H. trimaculatus has the most widespread haplotypes [average clade distance (D(c)) of nonsingleton haplotypes = 1169 km], indicating potentially high dispersal capabilities, whereas H. barbouri has the least widespread haplotypes (average D(c) = 67 km) indicating potentially lower dispersal capabilities. Pleistocene separation of marine basins and postglacial flooding of the Sunda Shelf are extrinsic factors likely to have contributed to the phylogeographical structure observed, whereas differences among the species appear to reflect their individual ecologies.     

Pan-European phylogeography of the aquatic snail Theodoxus fluviatilis (Gastropoda: Neritidae)

Investigating the geographical distribution of genetic lineages within species is critical to our understanding of how species evolve. As many species inhabit large and complex ranges, it is important that phylogeographical research take into account the entire range of widespread species to clarify how myriad extrinsic variables have affected their evolutionary history. Using phylogenetic, nested clade, and mismatch distribution analyses on a portion of the mitochondrial COI gene, I demonstrate that the wide-ranging freshwater snail Theodoxus fluviatilis possesses in parallel many of the phylogeographical patterns seen in less widespread freshwater species of Europe. Fragmentary forces play a major part in structuring the range of this species, with 12 of 14 geographically structured nested clades displaying a distribution consistent with fragmentation or restricted dispersal. Certain regions of southern Europe harbour the majority of genetic diversity (total haplotype diversity, H = 0.87), particularly Italy (H = 0.87) and areas surrounding the Black Sea (H = 0.81). Post-Pleistocene range expansion is pronounced, with the majority of northern European populations (95% of sample sites) having arisen from northern Italian individuals that initially colonized northern Germany. Additionally, two highly divergent haplotype lineages present in northern Germany imply that there were at least two postglacial recolonization routes. Estuaries may also provide a means of dispersal given that no genetic differentiation was found between estuarine populations and neighbouring freshwater populations. Taken together, these data reveal a species with a complex genetic history resulting from the fragmentary effects of European geology as well as continuous and discrete range expansion related to their aquatic biology.     

Evolutionary history of the northern leopard frog: reconstruction of phylogeny, phylogeography, and historical changes in population demography from mitochondrial DNA

This study uses a combined methodological approach including phylogenetic, phylogeographic, and demographic analyses to understand the evolutionary history of the northern leopard frog, Rana pipiens. We tested hypotheses concerning how (or if) known geological events and key features of the species biology influenced the contemporary geographic and genetic distribution of R. pipiens. We assayed mitochondrial DNA variation from 389 individuals within 35 populations located throughout the species range. Our a priori expectations for patterns and processes influencing the current genetic structure of R. pipiens were supported by the data. However, our analyses revealed specific aspects of R. pipiens evolutionary history that were unexpected. The phylogenetic analysis indicated that R. pipiens is split into populations containing discrete eastern or western haplotypes, with the Mississippi River and Great Lakes region dividing the geographic ranges. Nested clade analysis indicated that the biological process most often invoked to explain the pattern of haplotype position is restricted gene flow with isolation by distance. Demographic analyses showed evidence of both historical bottlenecks and population expansions. Surprisingly, the genetic evidence indicated that the western haplotypes had significantly reduced levels of genetic diversity relative to the eastern haplotypes and that major range expansions occurred in both regions well before the most recent glacial retreat. This study provides a detailed history of how a widespread terrestrial vertebrate responded to episodic Pleistocene glacial events in North America. Moreover, this study illustrates how complementary methods of data analysis can be used to disentangle recent and ancient effects on the genetic structure of a species.     

Historic cycles of fragmentation and expansion in Parnassius smintheus (papilionidae) inferred using mitochondrial DNA

Climate oscillations of the Quaternary drove the repeated expansion and contraction of ecosystems. Alpine organisms were probably isolated in sky island refugia during warm interglacials, such as now, and expanded their range by migrating down-slope during glacial periods. We used population genetic and phylogenetic approaches to infer how paleoclimatic events influenced the distribution of genetic variation in the predominantly alpine butterfly Parnassius smintheus. We sequenced a 789 bp region of cytochrome oxidase I for 385 individuals from 20 locations throughout the Rocky Mountains, ranging from southern Colorado to northern Montana. Analyses revealed at lease two centers of diversity in the northern and southern Rocky Mountains and strong population structure. Nested clade analysis suggested that the species experienced repeated cycles of population expansion and fragmentation. The estimated ages of these events, assuming a molecular clock, corresponded with paleoclimatic data on habitat expansion and contraction over the past 400,000 years. We propose that alpine butterflies persisted in an archipelago of isolated sky islands during interglacials and that populations expanded and became more connected during cold glacial periods. An archipelago model implies that the effects of genetic drift and selection varied among populations, depending on their latitude, area, and local environment. Alpine organisms are sensitive indicators of climate change and their history can be used to predict how high-elevation ecosystems might respond to further climate warming.     

Identification of TNF-alpha-responsive NF-kappaB p65-binding element in the distal promoter of the mouse serine protease inhibitor SerpinE2

Serine protease inhibitor SerpinE2 is known as a cytokine-inducible gene. Here, we investigated whether tumor necrosis factor alpha-(TNF-alpha)-induced expression of SerpinE2 is mediated by the nuclear factor-kappaB (NF-kappaB) p65 subunit. Both steady state and TNF-alpha-induced expression of SerpinE2 mRNA were abrogated in p65-/- murine embryonic fibroblasts (MEFs). Reconstitution with wild-type p65 rescued SerpinE2 mRNA expression in an IkappaB kinase beta-dependent manner. Electrophoresis mobility shift assay and ChIP assay demonstrated that p65 bound to the kappaB-like DNA sequence located at approximately -9 kbp in the SerpinE2 promoter. In addition, TNF-alpha stimulated luciferase gene expression driven by the kappaB-like element in the reconstituted MEFs, but not in p65-/- MEFs. These results indicated that activation of NF-kappaB p65 plays an important role in TNF-alpha-induced expression of SerpinE2.     

Comparative floral structure and systematics in Ochnaceae s.l. (Ochnaceae,Quiinaceae and Medusagynaceae; Malpighiales)

Ochnaceae s.l. (Ochnaceae, Quiinaceae and Medusagynaceae), one of the well‐supported subclades of the large order Malpighiales retrieved so far in molecular phylogenetic studies, were comparatively studied with regard to floral structure using microtome section series and scanning electron microscopy (SEM). Floral morphology, anatomy and histology also strongly reflect this close relationship. Potential synapomorphies of the subclade include: flowers nectarless, sepals of different sizes within a flower, petals not retarded in development and forming the protective organs of advanced floral buds, petal aestivation contort, petals with three vascular traces, petals reflexed over the sepals and directed toward the pedicel, polystemony, anthers almost or completely basifixed, gynoecium often with more than five carpels, short gynophore present, styles separate for at least their uppermost part and radiating outwards, suction‐cup‐shaped stigmas, vasculature forming a dorsal band of bundles in the upper stylar region, gynoecium epidermis with large, radially elongate cells, ovules either weakly crassinucellar or incompletely tenuinucellar with an endothelium, abundance of tanniferous tissues and sclerenchyma in floral organs. The most strongly supported subclade of two of the three families in molecular analyses, Quiinaceae and Medusagynaceae, is also particularly well supported by floral structural features, including the presence of functionally and morphologically unisexual flowers, a massive thecal septum that persists after anther dehiscence, styles radiating outward from the ovary, two lateral ovules per carpel, positioned one above the other, conspicuous longitudinal ribs on the ovary wall at anthesis, and a ‘false endothelium’ on the nucellus at anthesis. Additionally, the group fits well in Malpighiales and further emphasizes the relationship of Malpighiales with Celastrales and Oxalidales, and thus the unity of the COM clade. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 170 , 299–392.     

Chloroplast DNA variation and phylogeographic patterns in the Chinese endemic marsh herb Sagittaria potamogetifolia

We examined chloroplast DNA (cpDNA) atpB–rbcL intergenic spacer sequences variation within Sagittaria potamogetifolia, an endangered and endemic marsh herb in China. Sequence data were obtained from 54 individuals in six extant populations of the species. Sequences appeared to evolve neutral (Tajima's criterion D = −1.59826, 0.1 > P > 0.05 and Fu and Li's tests D* = −1.44484, P > 0.1; F* = −1.83446, P > 0.1). Eleven haplotypes were identified in S. potamogetifolia. A relatively high level of haplotype diversity (h = 0.0.699) and low level of nucleotide diversity (pi = 0.0035 ± 0.0020) were detected in S. potamogetifolia. Pairwise comparisons of F_st and Nm deduced from cpDNA variation suggested no significant genetic differentiation between populations of S. potamogetifolia excepted for the WY-1 population. Low genetic differentiation among populations and also among regions was consistently indicated by both hierarchical analyses of molecular variance (AMOVA) and the structure of a neighbor-joining tree. Lack of population differentiation between populations or between regions in cpDNA sequences may be due to effects of lower substitution rates or lineage sorting. In the minimum spanning network, all tip haplotypes except for the haplotype J were unique to a particular population, while the interior nodes except for the haplotype E were widespread (haplotype A). From nested clade analysis (NCA), the evolutionary events such as restricted gene flow with isolation by distance and allopatric fragmentation were inferred to responsible for the current distribution of S. potamogetifolia populations, as well as their genetic diversity.