Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

Recently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated or that may cross species barriers through introgressive hybridization. Here we use a reduced‐representation genomic approach to explore divergence among six species of southern capuchino seedeaters, a group of recently radiated sympatric passerine birds in the genus Sporophila. For the first time in these taxa, we discovered a small proportion of markers that appeared differentiated among species. However, when assessing the significance of these signatures of divergence, we found that similar patterns can also be recovered from random grouping of individuals representing different species. A detailed demographic inference indicates that genetic differences among Sporophila species could be the consequence of neutral processes, which include a very large ancestral effective population size that accentuates the effects of incomplete lineage sorting. As these neutral phenomena can generate genomic scan patterns that mimic those of markers involved in speciation and phenotypic differentiation, they highlight the need for caution when ascertaining and interpreting differentiated markers between species, especially when large numbers of markers are surveyed. Our study provides new insights into the demography of the southern capuchino radiation and proposes controls to distinguish signal from noise in similar genomic scans.     

Model‐based approach to test hard polytomies in the Eulaemus clade of the most diverse South American lizard genus Liolaemus (Liolaemini,Squamata)

Lack of resolution in a phylogenetic tree is usually represented as a polytomy, and often adding more data (loci and taxa) resolves the species tree. These are the ‘soft’ polytomies, but in other cases additional data fail to resolve relationships; these are the ‘hard’ polytomies. This latter case is often interpreted as a simultaneous radiation of lineages in the history of a clade. Although hard polytomies are difficult to address, model‐based approaches provide new tools to test these hypotheses. Here, we used a clade of 144 species of the South American lizard clade Eulaemus to estimate phylogenies using a traditional concatenated matrix and three species tree methods: *BEAST, BEST, and minimizing deep coalescences (MDC). The different species tree methods recovered largely discordant results, but all resolved the same polytomy (e.g. very short internodes amongst lineages and low nodal support in Bayesian methods). We simulated data sets under eight explicit evolutionary models (including hard polytomies), tested these against empirical data (a total of 14 loci), and found support for two polytomies as the most plausible hypothesis for diversification of this clade. We discuss the performance of these methods and their limitations under the challenging scenario of hard polytomies. © 2015 The Linnean Society of London     

Dynamics of an ant-ant obligate mutualism: colony growth, density dependence and frequency dependence

In insect societies, worker vs. queen development (reproductive caste) is typically governed by environmental factors, but many Pogonomyrmex seed-harvester ants exhibit strict genetic caste determination, resulting in an obligate mutualism between two reproductively isolated lineages. Same-lineage matings produce fertile queens while alternate-lineage matings produce sterile workers. Because new virgin queens mate randomly with multiple males of each lineage type, and both worker and queen phenotypes are required for colony growth and future reproduction, fitness is influenced by the relative frequency of each lineage involved in the mutualistic breeding system. While models based solely on frequency-dependent selection predict the convergence of lineage frequencies towards equal (0.5/0.5), we surveyed the lineage ratios of 49 systems across the range of the mutualism and found that the global lineage frequency differed significantly from equal. Multiple regression analysis of our system survey data revealed that the density and relative frequency of one lineage decreases at lower elevations, while the frequency of the alternate lineage increases with total colony density. While the production of the first worker cohort is largely frequency dependent, relying on the random acquisition of worker-biased sperm stores, subsequent colony growth is independent of lineage frequency. We provide a simulation model showing that a net ecological advantage held by one lineage can lead to the maintenance of stable but asymmetric lineage frequencies. Collectively, these findings suggest that a combination of frequency-dependent and frequency-independent mechanisms can generate many different localized and independently evolving system equilibria.     

Efficient inducible Cre-mediated recombination in Tcf21 cell lineages in the heart and kidney

Tcf21 is a Class II bHLH family member with essential roles in the formation of the lungs, kidneys, gonads, spleen, and heart. Here, we report the utility of a mouse line with targeted insertion of a tamoxifen-inducible Cre recombinase, MerCreMer at the Tcf21 locus. This mouse line will permit the inducible expression of Cre recombinase in Tcf21-expressing cells. Using ROSA26 reporter mice, we show that Cre recombinase is specifically and robustly activated in multiple Tcf21-expressing tissues during embryonic and postnatal development. The expression profile in the kidney is particularly dynamic with the ability to cause recombination in mesangial cells at one time of induction and podocytes at another time. These features make the Tcf21-driven inducible Cre line (Tcf21(iCre) ) a valuable genetic tool for spatiotemporal gene function analysis and lineage tracing of cells in the heart, kidney, cranial muscle, and gonads.     

Clonal domains in postlarval Platynereis dumerilii (Annelida: Polychaeta)

Following an enzymatic procedure for softening the egg envelope, blastomeres in the embryo of the polychaete Platynereis dumerilii were injected with TRITC-dextran. Injection was successful in the following blastomeres: AB, CD, A, B, C, D, 1a-1d, 1A-1D, 4d, and 4d(1). The distribution of fluorescent label was recorded by confocal laser scanning microscopy of young, three-segmented worms after 3 or 4 days of development, in some cases also in 1-day-old trochophore larvae. Results were documented by single optical sections, by stacking a limited number or a complete set of optical sections, and by computer-generated surface views of both the labeled tissue domains and the body contours from complete image stacks of whole worms. With respect to their descent from the embryonic cell pattern, five major compartments can be distinguished which together compose the body of the young worm: 1) The epispheric, epidermal, and neural region of the head, composed of four domains arranged as quasi-radial sectors derived from micromeres 1a, 1b (left and right ventral), and 1c and 1d (right and left dorsal). 2) A posttrochal epidermal region of the head originating from micromeres 2a(1)-2c(1) and constituting the ventral and lateral posttrochal epidermis of the head. 3) A stomodeal-ectomesodermal region of the head, including the stomodeum (micromeres 2a(2) and 2c(2)), its mesodermal envelope, and head mesoderm (micromeres 3a-3d). 4) A solid cone composed of the four terminal macromeres 4A-4D, forming the core of the trunk as the endoderm anlage. 5) An epidermal and mesodermal coating of the trunk originating from the dorsal micromeres 2d and 4d. The region of the so-called (first, anterior) peristomial cirri at the posterior flanks of the head is also composed of 2d- and 4d-derived trunk tissue, thus corroborating the postulated descent of this region and its appendages from a cephalized anteriormost trunk segment and its parapodia. The cell-lineage domains of the first and third micromere tiers are arranged left or right of the sagittal plane, while two micromeres of the second quartet are in a lateral and, initially, two in a median position (2b ventral and 2d dorsal). The offspring of micromere 2d expand from a dorsal position toward the ventral midline and those of cell 4d from a posterior-dorsal site toward the anterior, initially forming two lateral bands. In the epispheric part of the head, part of the neurectodermal tissue derived from micromeres 1a and 1b interweaves in a medio-sagittal bar, and part of the first micromere offspring of all four quadrants (1a-1d) combine in forming a central brain neuropil. Each of the latter sends neurites through both of the circumesophageal connectives. Paired muscle tracts extend through the head toward the base of the antennae and are probably derived from micromeres 3a and 3b. A mesodermal envelope of the stomodeum is probably built by the 3c and 3d micromeres. The formation of symmetry and the nature of the body axes in the embryo and adult of Platynereis dumerilii are discussed. J. Morphol.     

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.     

Multiple roles for Nodal in the epiblast of the mouse embryo in the establishment of anterior-posterior patterning

The TGFbeta family member Nodal has been shown to be involved in a variety of processes in development, including early axis formation. Here, we use a conditional gene inactivation strategy to show a specific requirement for Nodal in the epiblast. Complete inactivation of the Nodal locus in the epiblast using the Sox2-Cre deleter strain results in a failure to establish global anterior-posterior patterning, a phenotype that resembles the Nodal null phenotype. By contrast, mosaic inactivation of Nodal in the epiblast using the Mox2-Cre (MORE) deleter strain affects formation of the anterior mesendoderm and subsequent anterior neurectoderm patterning. Furthermore, ES cell chimera experiments indicate that Nodal-deficient ES cells preferentially populate the anterior compartment of the epiblast, suggesting that cell mixing in the epiblast is not random and that Nodal signaling mediates a novel anterior-posterior cell-sorting process within the epiblast before gastrulation.     

Lineage-specific cell disruption in living mice by Cre-mediated expression of diphtheria toxin A chain

We have established a transgenic mouse line in which floxed neomycin resistant cassette was inserted between the CAG promoter and EGFP. When these transgenic mice were mated with Cre-expressing transgenic animals, the offspring obtained were fluorescent green. We then established a transgenic mouse line in which EGFP in the above construct was replaced by diphtheria toxin A chain (DT). When the latter transgenic mice were mated with mice expressing Cre restricted to germ cells, we obtained healthy but sterile offspring due to a disruption of germ line cells by DT expression. We predict that this strategy will be useful for the construction of new animal models for human diseases, featuring a variety of missing cell lineages produced by disruption with DT.