Genetic and historic evidence for climate-driven population fragmentation in a top cetacean predator: the harbour porpoises in European water

Recent climate change has triggered profound reorganization in northeast Atlantic ecosystems, with substantial impact on the distribution of marine assemblages from plankton to fishes. However, assessing the repercussions on apex marine predators remains a challenging issue, especially for pelagic species. In this study, we use Bayesian coalescent modelling of microsatellite variation to track the population demographic history of one of the smallest temperate cetaceans, the harbour porpoise (Phocoena phocoena) in European waters. Combining genetic inferences with palaeo-oceanographic and historical records provides strong evidence that populations of harbour porpoises have responded markedly to the recent climate-driven reorganization in the eastern North Atlantic food web. This response includes the isolation of porpoises in Iberian waters from those further north only approximately 300 years ago with a predominant northward migration, contemporaneous with the warming trend underway since the ‘Little Ice Age’ period and with the ongoing retreat of cold-water fishes from the Bay of Biscay. The extinction or exodus of harbour porpoises from the Mediterranean Sea (leaving an isolated relict population in the Black Sea) has lacked a coherent explanation. The present results suggest that the fragmentation of harbour distribution range in the Mediterranean Sea was triggered during the warm ‘Mid-Holocene Optimum’ period (approx. 5000 years ago), by the end of the post-glacial nutrient-rich ‘Sapropel’ conditions that prevailed before that time.     

Elimination of subterranean termite (Isoptera: Rhinotermitidae) colonies using a refined cellulose bait matrix containing noviflumuron when monitored and replenished quarterly

Using a quarterly (3-mo) monitoring and bait-replenishment interval, 122 subterranean termite colonies throughout the United States were baited with a refined cellulose bait matrix containing 0.5% noviflumuron. All colonies were eliminated in less than 1 yr after initiation of baiting as determined by long-term monitoring and genetic markers. Sixty-three percent of the colonies were eliminated during the first quarter after the initiation of baiting and 77% of colonies were eliminated after consuming two bait tubes or less. This suggests that a single baiting cycle and bait installed in response to a single active monitoring device were sufficient to eliminate the majority of colonies. Although termites temporarily abandoned stations after depleting bait, workers resumed feeding when baits were replenished. Colonies that consumed large amounts of bait before elimination foraged into multiple stations, thus allowing adequate amounts of bait to sustain feeding. The time to eliminate termite colonies with bait replenished quarterly was similar to that previously reported for laminated cellulose bait replenished monthly. Our data support the conclusion that extending the bait replenishment interval from monthly to quarterly for bait tubes with refined cellulose containing 0.5% noviflumuron did not adversely impact colony elimination.     

Phenotypic and genetic divergence among harbour porpoise populations associated with habitat regions in the North Sea and adjacent seas

Determining the mechanisms that generate population structure is essential to the understanding of speciation and the evolution of biodiversity. Here, we investigate a geographical range that transects two habitat gradients, the North Sea to North Atlantic transition, and the temperate to subpolar regions. We studied the harbour porpoise (Phocoena phocoena), a small odontocete inhabiting both subpolar and temperate waters. To assess differentiation among putative populations, we measured morphological variation at cranial traits (N = 462 individuals) and variation at eight microsatellite loci for 338 of the same individuals from Norwegian, British and Danish waters. Significant morphological differentiation reflected the size of the buccal cavity. Porpoises forage in relatively shallow waters preying mainly on benthic species in British and Danish waters, and on mesopelagic and pelagic fish off the coast of Norway. We suggest that the observed differentiation may be explained by resource specialization and either adaptation or developmental responses to different local habitats.     

Detection and confirmation of serum lipid biomarkers for preeclampsia using direct infusion mass spectrometry

Despite substantial research, the early diagnosis of preeclampsia remains elusive. Lipids are now recognized to be involved in regulation and pathophysiology of some disease. Shotgun lipidomic studies were undertaken to determine whether serum lipid biomarkers exist that predict preeclampsia later in the same in pregnancy. A discovery study was performed using sera collected at 12–14 weeks pregnancy from 27 controls with uncomplicated pregnancies and 29 cases that later developed preeclampsia. Lipids were extracted and analyzed by direct infusion into a TOF mass spectrometer. MS signals, demonstrating apparent differences were selected, their abundances determined, and statistical differences tested. Statistically significant lipid markers were reevaluated in a second confirmatory study having 43 controls and 37 preeclampsia cases. Multi-marker combinations were developed using those lipid biomarkers confirmed in the second study. The initial study detected 45 potential preeclampsia markers. Of these, 23 markers continued to be statistically significant in the second confirmatory set. Most of these markers, representing several lipid classes, were chemically characterized, typically providing lipid class and potential molecular components using MS². Several multi-marker panels with areas under the curve >0.85 and high predictive values were developed. Developed panels of serum lipidomic biomarkers appear to be able to identify most women at risk for preeclampsia in a given pregnancy at 12–14 weeks gestation.     

DIABLA: a new screening method for the discovery of protein targets

Dynamic isoelectric/anisotropy binding ligand assay (DIABLA) is a new method to identify proteins in a complex sample that bind to a molecule of interest. This is accomplished by first using capillary isoelectric focusing (cIEF) to separate the proteins in a capillary based on their isoelectric point. This separation is performed while the compound being tested is present in the separation buffer. When the proteins are focused, the entire capillary is scanned to identify regions of nonzero anisotropy, which are locations where the test compound is interacting with a focused protein band. DIABLA was demonstrated by observing the binding of fluorescein-tagged progesterone to an MCF-7 breast cancer cell lysate. The proteins were tagged with rhodamine to permit their observation and then focused in the presence of the tagged progesterone. Anisotropy measurements show that progesterone binds to six different proteins bands in the sample.     

Climate change drives speciation in the southern rock agama (Agama atra) in the Cape Floristic Region, South Africa

Aim Vicariance has played a major role in the evolution of the southern rock agama, Agama atra (Reptilia: Agamidae), and it is hypothesized that habitat shifts will affect small‐scale patterns of gene flow. The Cape Floristic Region (CFR) is known for high levels of diversity and endemism; thus we set out to investigate whether genetic structuring of CFR populations of A. atra corresponds to regional environmental shifts. Location Cape Fold Mountains and the Cape Floristic Region of South Africa. Methods The phylogeographical structure of 116 individuals of A. atra was determined by making use of 988 characters derived from two mitochondrial DNA fragments (control region and the NADH dehydrogenase subunit 2 coding region, ND2). Most animals originated from the CFR, but to gain a better understanding of the processes and patterns of dispersal within the species, 17 additional specimens from outside the CFR were also included and analysed in a phylogenetic context. Results Parsimony and Bayesian analyses revealed four distinct CFR clades (Cape clades) associated with geography. Phylogenetic analyses suggest that populations of A. atra in the CFR region are not entirely isolated from other populations, because some individuals from outside the CFR were nested within the four main Cape clades. The combined mitochondrial DNA data set revealed 59 distinct haplotypes in the CFR. Analysis of molecular variance (amova ) confirmed the high degree of genetic structure among the Cape clades, with more than 75% of the genetic variation found among the geographical areas. A spatial amova suggested that a ‘central clade’ originally defined as one of the four Cape clades may contain several additional populations. The main cladogenesis of A. atra within the CFR is estimated to have taken place c. 0.64–2.36 Ma. Main conclusions Agama atra shows at least four distinct genetic provinces within the CFR region, which highlights the conservation importance of this biologically diverse area. The dates of separation among the clades coincide well with the documented Pleistocene climate fluctuations, which might have contributed towards the isolation among lineages; the congruent genetic structure of A. atra with other CFR taxa further supports vicariance as a main isolating factor.     

Morphology,ornaments and performance in two chameleon ecomorphs: is the casque bigger than the bite?

The evolution of ecomorphs within a species may represent either unique evolutionary events or multiple convergent events in similar environments. Functional studies of differing morphological traits of ecomorphs have been important to elucidate their role in adaptive radiations. The Cape dwarf chameleon, Bradypodion pumilum, has two ecomorphs: a large, brightly colored, ornate form found in closed habitats, and a small, dull form with reduced ornamentation found in open vegetation. The typical form is known to use casque size to communicate fighting ability, but it is unknown whether this is an honest signal and whether casque size is related to bite force. We show through a population genetic analysis that these ecomorphs are not separate genetic lineages but the result of multiple transitions between closed and open habitats. From measurements of ornamental and non-ornamental morphological characters and bite force in 105 chameleons, we find that bite force is significantly related to head size and is best predicted by head width. Bite force was reasonably predicted by casque height in ecomorphs from closed habitats, but not in those from open habitats. For size-adjusted data, open habitat males had wider heads, biting harder than closed habitat males. Our data suggest honesty in signaling for closed habitat ecomorphs, but for open habitat ecomorphs communication is different, a finding commensurate with the common framework for species radiations.     

Comparison of linkage disequilibrium and haplotype diversity on macro- and microchromosomes in chicken

Background

Toll like receptors (TLR) play the central role in the recognition of pathogen associated molecular patterns (PAMPs). Mutations in the TLR1, TLR2 and TLR4 genes may change the ability to recognize PAMPs and cause altered responsiveness to the bacterial pathogens.

Results

The study presents association between TLR gene mutations and increased susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP) infection. Novel mutations in TLR genes (TLR1- Ser150Gly and Val220Met; TLR2 – Phe670Leu) were statistically correlated with the hindrance in recognition of MAP legends. This correlation was confirmed subsequently by measuring the expression levels of cytokines (IL-4, IL-8, IL-10, IL-12 and IFN-γ) in the mutant and wild type moDCs (mocyte derived dendritic cells) after challenge with MAP cell lysate or LPS. Further in silico analysis of the TLR1 and TLR4 ectodomains (ECD) revealed the polymorphic nature of the central ECD and irregularities in the central LRR (leucine rich repeat) motifs.

Conclusion

The most critical positions that may alter the pathogen recognition ability of TLR were: the 9^th amino acid position in LRR motif (TLR1–LRR10) and 4^th residue downstream to LRR domain (exta-LRR region of TLR4). The study describes novel mutations in the TLRs and presents their association with the MAP infection.