The genetic architecture underlying the evolution of a rare piscivorous life history form in brown trout after secondary contact and strong introgression

Identifying the genetic basis underlying phenotypic divergence and reproductive isolation is a longstanding problem in evolutionary biology. Genetic signals of adaptation and reproductive isolation are often confounded by a wide range of factors, such as variation in demographic history or genomic features. Brown trout ( ) in the Loch Maree catchment, Scotland, exhibit reproductively isolated divergent life history morphs, including a rare piscivorous (ferox) life history form displaying larger body size, greater longevity and delayed maturation compared to sympatric benthivorous brown trout. Using a dataset of 16,066 SNPs, we analyzed the evolutionary history and genetic architecture underlying this divergence. We found that ferox trout and benthivorous brown trout most likely evolved after recent secondary contact of two distinct glacial lineages, and identified 33 genomic outlier windows across the genome, of which several have most likely formed through selection. We further identified twelve candidate genes and biological pathways related to growth, development and immune response potentially underpinning the observed phenotypic differences. The identification of clear genomic signals divergent between life history phenotypes and potentially linked to reproductive isolation, through size assortative mating, as well as the identification of the underlying demographic history, highlights the power of genomic studies of young species pairs for understanding the factors shaping genetic differentiation

Patterned probes for high precision 4D-STEM bragg measurements.

Nanoscale strain mapping by four-dimensional scanning transmission electron microscopy (4D-STEM) relies on determining the precise locations of Bragg-scattered electrons in a sequence of diffraction patterns, a task which is complicated by dynamical scattering, inelastic scattering, and shot noise. These features hinder accurate automated computational detection and position measurement of the diffracted disks, limiting the precision of measurements of local deformation. Here, we investigate the use of patterned probes to improve the precision of strain mapping. We imprint a "bullseye" pattern onto the probe, by using a binary mask in the probe-forming aperture, to improve the robustness of the peak finding algorithm to intensity modulations inside the diffracted disks. We show that this imprinting leads to substantially improved strain-mapping precision at the expense of a slight decrease in spatial resolution. In experiments on an unstrained silicon reference sample, we observe an improvement in strain measurement precision from 2.7% of the reciprocal lattice vectors with standard probes to 0.3% using bullseye probes for a thin sample, and an improvement from 4.7% to 0.8% for a thick sample. We also use multislice simulations to explore how sample thickness and electron dose limit the attainable accuracy and precision for 4D-STEM strain measurements

Mendelian microsatellite loci for the Caribbean coral Acropora palmata

The genus Acropora constitutes the most species-rich clade of hermatypic corals, and its members are important reef builders throughout their broad tropical range. In the Caribbean, acroporid populations have declined over the last 2 decades due to disease, hurricanes, predation, and bleaching episodes, and some are now subjects of conservation efforts. Genetic estimates of population connectivity and clonal structure should be part of these efforts, but such studies have been hampered by low levels of mitochondrial DNA variation in corals, and an apparent dearth of variable single-copy nuclear markers. Developing microsatellite markers in Acropora has proven especially difficult. We used Southern blotting to reveal that, indeed, some microsatellite motifs (AAC, AAG) are rare in the genome of the Caribbean species Acropora palmata. However, repeats with the motif AAT are both abundant and variable. We developed 8 polymorphic microsatellite markers for A. palmata, and performed crosses to confirm co-dominant inheritance patterns. Five of the 8 markers tested show simple Mendelian inheritance (mean observed heterozygosity = 0.84, mean number of alleles per locus = 8.6). Along with outcrossed sexual larvae, individual egg donors also produced some triploid and selfed larvae that developed normally and survived for 80 h, when the experiment was terminated. The markers reveal variation among 3 Florida populations of A. palmata and among clones within 1 of these populations. Seven of the markers amplify DNA from A. cervicornis and 8 from the hybrid A. prolifera. These markers should prove to be valuable tools for developing conservation strategies for Caribbean acroporid species. © Inter-Research 2005

Mezcala – a new segregate genus of mimosoid legume (Leguminosae, Caesalpinioideae, mimosoid clade) narrowly endemic to the Balsas Depression in Mexico

Recent results have demonstrated that the genus Desmanthus is non-monophyletic because the genus Kanaloa is nested within it, with a single species, Desmanthus balsensis placed as sister to the clade comprising Kanaloa plus the remaining species of Desmanthus. Here we transfer D. balsensis to a new segregate genus Mezcala, discuss the morphological features supporting this new genus, present a key to distinguish Mezcala from closely related genera in the Leucaena subclade, and provide a distribution map of M. balsensis

Disintegration of the genus Prosopis L. (Leguminosae, Caesalpinioideae, mimosoid clade)

Robust evidence from phylogenomic analyses of 997 nuclear genes has recently shown, beyond doubt, that the genus Prosopis is polyphyletic with three separate lineages, each with affinities to other genera of mimosoids: (i) Prosopis africana is an isolated lineage placed in the grade of Plathymenia, Newtonia and Fillaeopsis that subtends the core mimosoid clade; (ii) the remaining Old World species of Prosopis form a clade that is sister to the Indo-Nepalese monospecific genus Indopiptadenia and (iii) New World Prosopis has the Namibian / Namaqualand monospecific endemic genus Xerocladia nested within it. This means that it is now clear that maintaining the unity of the genus Prosopis sensu Burkart (1976) is no longer tenable. These three distinct lineages of Prosopis species correspond directly to Burkart’s (1976) sectional classification of the genus, to previously recognised genera and to the differences in types of armature that underpin Burkart’s sections. Here, we address this non-monophyly by resurrecting three segregate genera – Anonychium, Neltuma and Strombocarpa and provide 57 new name combinations where necessary, while maintaining the morphologically distinctive and geographically isolated genera Xerocladia and Indopiptadenia. The genus Prosopis itself is reduced to just three species and an emended description is presented. The impacts of these name changes for a genus of such high ecological and human use importance are discussed. These impacts are mitigated by clear differences in armature which facilitate identification and by potential benefits from the deeper biological understanding brought about by recognition of these divergent lineages at generic rank. We provide an identification key to genera and present a map showing the distributions of the segregate genera, as well as drawings and photos illustrating variation in armature and fruits

Multiple Continental Radiations and Correlates of Diversification in Lupinus (Leguminosae): Testing for Key Innovation with Incomplete Taxon Sampling

Replicate radiations provide powerful comparative systems to address questions about the interplay between opportunity and innovation in driving episodes of diversification and the factors limiting their subsequent progression. However, such systems have been rarely documented at intercontinental scales. Here, we evaluate the hypothesis of multiple radiations in the genus Lupinus (Leguminosae), which exhibits some of the highest known rates of net diversification in plants. Given that incomplete taxon sampling, background extinction, and lineage-specific variation in diversification rates can confound macroevolutionary inferences regarding the timing and mechanisms of cladogenesis, we used Bayesian relaxed clock phylogenetic analyses as well as MEDUSA and BiSSE birth-death likelihood models of diversification, to evaluate the evolutionary patterns of lineage accumulation in Lupinus. We identified 3 significant shifts to increased rates of net diversification (r) relative to background levels in the genus (r = 0.18-0.48 lineages/myr). The primary shift occurred approximately 4.6 Ma (r = 0.48-1.76) in the montane regions of western North America, followed by a secondary shift approximately 2.7 Ma (r = 0.89-3.33) associated with range expansion and diversification of allopatrically distributed sister clades in the Mexican highlands and Andes. We also recovered evidence for a third independent shift approximately 6.5 Ma at the base of a lower elevation eastern South American grassland and campo rupestre clade (r = 0.36-1.33). Bayesian ancestral state reconstructions and BiSSE likelihood analyses of correlated diversification indicated that increased rates of speciation are strongly associated with the derived evolution of perennial life history and invasion of montane ecosystems. Although we currently lack hard evidence for "replicate adaptive radiations” in the sense of convergent morphological and ecological trajectories among species in different clades, these results are consistent with the hypothesis that iteroparity functioned as an adaptive key innovation, providing a mechanism for range expansion and rapid divergence in upper elevation regions across much of the New Worl

Cost-effectiveness of paediatric central venous catheters in the UK:A secondary publication from the CATCH clinical trial

Background: Antibiotic-impregnated central venous catheters (CVCs) reduce the risk of bloodstream infections (BSIs) in patients treated in pediatric intensive care units (PICUs). However, it is unclear if they are cost-effective from the perspective of the National Health Service (NHS) in the UK.Methods: Economic evaluation alongside the CATCH trial (ISRCTN34884569) to estimate the incremental cost effectiveness ratio (ICER) of antibiotic-impregnated (rifampicin and minocycline), heparin-bonded and standard polyurethane CVCs. The 6-month costs of CVCs and hospital admissions and visits were determined from administrative hospital data and case report forms.Results: BSIs were detected in 3.59% (18/502) of patients randomized to standard, 1.44% (7/486) to antibiotic and 3.42% (17/497) to heparin CVCs. Lengths of hospital stay did not differ between intervention groups. Total mean costs (95% confidence interval) were: £45,663 (£41,647–£50,009) for antibiotic, £42,065 (£38,322–£46,110) for heparin, and £44,503 (£40,619–£48,666) for standard CVCs. As heparin CVCs were not clinically effective at reducing BSI rate compared to standard CVCs, they were considered not to be cost-effective. The ICER for antibiotic vs. standard CVCs, of £54,057 per BSI avoided, was sensitive to the analytical time horizon.Conclusions: Substituting standard CVCs for antibiotic CVCs in PICUs will result in reduced occurrence of BSI but there is uncertainty as to whether this would be a cost-effective strategy for the NHS

Pleistocene diversification of unifoliolate-leaved Lupinus (Leguminosae: Papilionoideae) in Florida

The importance and prevalence of recent ice-age and post-glacial speciation and species diversification during the Pleistocene across many organismal groups and physiographic settings are well established. However, the extent to which Pleistocene diversification can be attributed to climatic oscillations and their effects on distribution ranges and population structure remains debatable. In this study, we use morphologic, geographic and genetic (RADseq) data to document Pleistocene speciation and intra-specific diversification of the unifoliolate-leaved clade of Florida Lupinus, a small group of species largely restricted to inland and coastal sand ridges across the Florida peninsula and panhandle. Phylogenetic and demographic analyses alongside morphological and geographic evidence suggest that recent speciation and intra-specific divergence within this clade were driven by a combination of non-adaptive allopatric divergence caused by edaphic niche conservatism and opportunities presented by the emergence of new post-glacial sand ridge habitats. These results highlight the central importance of even modest geographic isolation and short periods of allopatric divergence following range expansion in the emergence of new taxa and add to the growing evidence that Pleistocene climatic oscillations may contribute to rapid diversification in a myriad of physiographic settings. Furthermore, our results shed new light on long-standing taxonomic debate surrounding the number of species in the Florida unifoliate Lupinus clade providing support for recognition of five species and a set of intra-specific variants. The important conservation implications for the narrowly restricted, highly endangered species Lupinus aridorum, which we show to be genetically distinct from its sister species Lupinus westianus, are discussed