Evolutionary Biology

Food waste from households contributes the greatest proportion to total food waste in developed countries. Therefore, food waste reduction requires an understanding of the socio-economic (contextual and behavioural) factors that lead to its generation within the household. Addressing such a complex subject calls for sound methodological approaches that until now have been conditioned by the large number of factors involved in waste generation, by the lack of a recognised definition, and by limited available data. This work contributes to food waste generation literature by using one of the largest available datasets that includes data on the objective amount of avoidable household food waste, along with information on a series of socio-economic factors. In order to address one aspect of the complexity of the problem, machine learning algorithms (random forests and boruta) for variable selection integrated with linear modelling, model selection and averaging are implemented. Model se...

Sex determination is an important developmental event in the life cycle of all sexually reproducing plants. Recent studies of sex determination in many plant species, from ferns to maize, have been fruitful in identifying the diversity of genetic and epigenetic factors that are involved in determining the sex of the flower or individual. In those species amenable to genetic analysis, significant progress has been made toward identifying mutations that affect sex expression. By studying the interactions among these genes, pictures of how sex-determining signals are perceived to activate or repress male-or female-specific genes are emerging.

Antibiotic therapy has a dual impact: wanted, in which it immediately inhibits the growth of bacteria and the unwanted, which is responsible for the evolution of antibiotic resistance. The dissociation of therapeutic effectiveness from the possible risk of the antibiotic resistance may be attained by taking the advantage of specific relations between these drugs, and the methods in which mutations associated with resistance against a specific antibiotic may modify these relations or it may increase the sensitivity of the bacterium to the other antibiotics. Although the practical implementation of this notion needs considerable advancement and confirmation that depends upon the improvements in the field of genomics and diagnostics, these interventions propose new paradigms, which may confine or inverse the evolution of antibiotic resistance.

A new type of Lophosteus-finspine ist described. This fragment shows, that Lophosteus and Andreolepis may belong neither to the actinopterygians nor to the sarcopterygians. At present it is impossible to establish its relationships. K u r z f a s s u n g : Ein neuer Typ eines Lophosteus-Flossenstachels wird beschrieben. Dieser Rest zeigt, daf~ es sich bei Lophosteus und Andreolepis weder um Actinopterygier noch um Sarcopterygier handeln kann. Es ist beim derzeitigen Kenntnisstand jedoch noch nicht m6glich, die Beziehungen zu anderen niederen Vertebraten zu kl~iren. Im Jahre 1856 beschrieb PANDEI~ aus dem oberen Silur (Pridoli) des Ohesaare-Kliffs SW-Kiiste der Insel C)sel (= Saaremaa, Estland) Knochenbuchstfickchen von Fischen, die er teils dem Antiarch Pterichthys, teils einer von ihm hierfiir neu aufgestellen Gattung Lophosteus zuwies. Da damals noch nicht die Priiparation phosphatischer Fossilien in Kalken durch Essigs~iure bekannt war, stand ihm fiir seine Beschreibungen nur wenig Material zur Verfiigung. Auch der niichste Bearbeiter, ROHON (1893), konnte nur einige Knochenbruchstficke untersuchen. Immerhin war es RoHoN m6glich, von seinem Material Dfinnschliffe anzufertigen und die Histologie der Reste erstmals zu beschreiben. Aus den dabei gemachten Beobachtungen zog er folgende Schliisse: -alle Reste k6nnen unter dem Namen Lophosteus vereinigt werden; -die Reste geh6rten seiner Meinung nach nicht zu den Antiarchi, sondern zu den Holoptychida, das heitgt zu den Knochenfischen (Osteichthyes = Teleostomi). Der niichste Bearbeiter der Gattung Lophosteus war erst WALTER GROSS. Nachdem er 1968 fragliche Actinopterygierschuppen aus dem Obersilur von Gotland als Andreolepis hedei beschrieben hatte, konnte er 1969 und 1971 Schuppen, Zahnknochen, isolierte Einzelz~ihne und Bruchstiicke von Deckknochen mit Spuren des Sinnesliniensystems von Lophosteus superbus PANDER beschreiben. Ffir diese Untersuchungen stand Gl~oss eine sehr viel gr6t~ere Materialmenge (auch fiir eine grof~e Zahl von Diinnschliffen) als den beiden friiheren Bearbeitern zur Verffigung, da er Lophosteus-reiche Geschiebe in verdiinnter Essigs~iure aufl6ste. Die systematische Stellung konnte trotz der morphologischen Ahnlichkeit mit Actinopterygier-Schuppen nicht endgiiltig abgesichert werden. GRoss konnte * Anschrift des Autors: Dipl.-Geol. MARKUS OTTO,

Flower shape has evolved in most plants as a consequence of pollinator-mediated selection. Unfortunately, no study has explored the genetic variation of flower shape, despite that this information is crucial to understand its adaptive evolution. Our main goal here is to determine heritability of corolla shape in Erysimum mediohispanicum (Brassicaceae). Also, we explore heritability of other pollinator-selected traits in this plant species, such as plant size, flower display, and corolla size. In addition, we investigate genetic correlations between all these traits. We found significant heritability for one plant-size trait (stalk height), for number of flowers, for all corolla-size traits (corolla diameter, corolla tube length and corolla tube width), and for corolla shape. Consequently, this species retains a high ability to respond to the selection exerted by its pollinators. Genetic correlation was strong between all functionally related traits and between flower number and plant size, weak between corolla size and plant size and no correlation between corolla shape and any other trait. Thus, selection affecting some E. mediohispanicum traits would also indirectly affect other functionally related and unrelated traits. More importantly, the observed genetic correlation seems to be at least partially adaptive because positive correlational selection currently acts on the covariance between some of these traits (G ómez 2003; G ómez et al. 2006).

Copahue is an acidic geothermal volcanic region in the northwest corner of Neuquén Province, Argentina. In the area, there are various ponds, pools and hot springs with different temperatures, pH values and levels of anthropogenic influence. In this study, the prokaryotic biodiversity of five representative ponds was studied by using two complementary molecular ecology techniques: phylogenetic analysis of 16S rRNA bacterial and archaeal genes and FISH (or CARD-FISH) for quantitative estimation of biodiversity. The results, supported by multivariate statistical analysis, showed that the biodiversity in Copahue ponds seemed to be determined by temperature. High temperature ponds were dominated by archaea, mainly apparently novel representatives from the orders Sulfolobales and Thermoplasmatales that had no close cultivated relatives. By contrast, moderate temperature ponds were colonised by well-characterised sulphur-oxidising bacteria related to acidic environments, such as other geothermal sites or acid mine drainage, and archaea were absent. By combining the biodiversity results from this study and the reported physicochemical features of Copahue, a preliminary model of the possible biogeochemical interaction was outlined for moderate and high temperature ponds.

Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1 T as its type species, along with two other uncultivated metagenomeassembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-ofthe-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1 TS ), 'Igneacidithiobacillus siniensis' (S30A2 T ), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 TS ), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 TS ). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineagespecific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction.

Moelleriella pumatensis, a fungal pathogen infecting scale insect nymphs (Hemiptera), is described and illustrated as a new species from Pu Mat National Park in Vietnam. This species is unique in producing a golden yellow spore mass surrounding the stroma. In surveys throughout the year in Vietnam, only the anamorphic state has been found in the natural forest. Morphological characters and phylogenetic analysis of translation elongation factor 1-α (tef1) reveals this species as an anamorph of Moelleriella.

The present checklist of ants (Hymenoptera: Formicidae) of Ambon is the first comprehensive overview of ant species recorded on the island during the last 150 years. The species list is based on literature and museum collections' records combined with data from our field survey in 2010. In total, there are 74 ant species and subspecies representing 34 genera and six subfamilies known from Ambon. Five of the species found in undisturbed forest were exotic and indicate the overall habitat degradation on the island. The largest proportion of Ambon ant fauna are species with affinities to the Oriental region and species of Oriental-Austro-Melanesian origin. At least 20% of the species are regional endemics. In comparison to other islands in the region, the Ambon fauna seems more diverse and better sampled; however it is clear that a large part of it still remains to be described.

ObjectivesIn primates, allogrooming and other affiliative behaviors confer many benefits and may be influenced by many socioecological factors. Of these, the impact of anthropogenic factors remain relatively understudied. Here we ask whether interactions with humans decreased macaques' affiliative behaviors by imposing time‐constraints, or increased these behaviors on account of more free‐/available‐time due to macaques' consumption of high‐energy human foods.Materials and methodsIn Southern India, we collected data on human–macaque and macaque–macaque interactions using focal‐animal sampling on two groups of semi‐urban bonnet macaques for 11 months. For each macaque within each climatic season, we calculated frequencies of human–macaque interactions, rates of monitoring human activity and foraging on anthropogenic food, dominance ranks, grooming duration, number of unique grooming partners, and frequencies of other affiliative interactions.ResultsWe found strong evidence fo...

ObjectivesThe impact of anthropogenic environmental changes may impose strong pressures on the behavioral flexibility of free‐ranging animals. Here, we examine whether rates of interactions with humans had both a direct and indirect influence on the duration and distribution of social grooming in commensal rhesus macaques (Macaca mulatta).Materials and MethodsData were collected in two locations in the city of Shimla in northern India: an urban setting and a temple area. We divided these two locations in a series of similar‐sized physical blocks (N = 48) with varying rates of human–macaque interactions. We conducted focal observations on three free‐ranging rhesus macaque groups, one in the urban area and two in the temple area.ResultsOur analysis shows that macaques engaged in shorter grooming bouts and were more vigilant while grooming in focal sessions during which they interacted with people more frequently, suggesting that humans directly affected grooming effort and vigilance b...

The Malagasy giant pill-millipede genus Sphaeromimus de Saussure & Zehntner, 1902 is revised. Seven new species, S. titanus sp. n., S. vatovavy sp. n., S. lavasoa sp. n., S. andohahela sp. n., S. ivohibe sp. n., S. saintelucei sp. n., and S. andrahomana sp. n. were discovered, in one case with the help of sequence data, in the rainforests of southeastern Madagascar. The species are described using light- and scanning electron microscopy. A key to all 10 species of the genus is presented. All but one (S. andohahela) of the newly discovered species are microendemics each occurring in isolated forest fragments. The mitochondrial COI barcoding gene was amplified and sequenced for 18 Sphaeromimus specimens, and a dataset containing COI sequences of 28 specimens representing all Sphaeromimus species (except S. vatovavy) was analyzed. All species are genetically monophyletic. Interspecific uncorrected genetic distances were moderate (4-10%) to high (18-25%), whereas intraspecific variation...

Obligate intracellular symbionts of insects are metabolically and developmentally integrated with their hosts. Typically, reproduction fails in many insect nutritional endosymbioses when host insects are cured of their bacterial symbionts, and yet remarkably little is known about the processes that developmentally integrate host and symbiont. Here in the best studied insect obligate intracellular symbiosis, that of the pea aphid, Acyrthosiphon pisum, with the gammaproteobacterium Buchnera aphidicola, we tracked the expression and localization of amino acid transporter ApGLNT1 gene products during asexual embryogenesis. Recently being characterized as a glutamine transporter, ApGLNT1 has been proposed to be a key regulator of amino acid biosynthesis in A. pisum bacteriocytes. To determine when this important mediator of the symbiosis becomes expressed in aphid embryonic bacteriocytes, we applied whole-mount in situ hybridization and fluorescent immunostaining with a specific anti-ApG...

The Wnt pathways are evolutionarily well-conserved signal transduction pathways that are known to play important roles in all Metazoans investigated to date. Here, we examine the Wnt pathway genes and target genes present in the genome of the echinoderm Strongylocentrotus purpuratus. Analysis of the Wnt genes revealed that eleven of the thirteen reported Wnt subfamilies are represented in sea urchin, with the intriguing identification of a Wnt-A ortholog thought to be absent in deuterostomes. A phylogenetic study of the Frizzled proteins, the Wnt receptors, performed throughout the animal kingdom showed that not all Frizzled subfamilies were present in the metazoan common ancestor, e.g. Fz3/6 emerged later during evolution. Using sequence analysis, orthologs of the vast majority of the cellular machinery involved in transducing the three types of Wnt pathways were found in the sea urchin genome. Furthermore, of about one hundred target genes identified in other organisms, more than half have clear echinoderm orthologs. Thus, these analyses produce new inputs in the evolutionary history of the Wnt genes in an animal occupying a position that offers great insights into the basal properties of deuterostomes.

Prescribing individualized moderate exercise intensity is a useful method to reach positive effects on health status in obese adults. This study aimed to establish a practical reference equation to estimate the heart rate (HR) at individual ventilatory threshold (IVT) (HR IVT ). One hundred sixty-one obese subjects were clinically evaluated and characterized by anthropometric and body composition. Participants performed the six-minute walking test (6-MWT) and the cardiopulmonary exercise test to assess IVT. Multiple regression analysis for HR IVT , including 6-MWT, anthropometric, and body composition parameters, as independent variables, was performed for both gender separately. A cross-validation study was also performed to determine the accuracy of the prediction equation. Whereas HR IVT was not significantly different between males (121.5±18.3 bpm) and females (117.6±17.1 bpm), it differently correlated with physical and performance parameters. Therefore, two sex-specific equations were developed including 6-MWT HR and HR rest (R 2 = 0.69 and 0.65 and root mean square errors of 8.8 and 10.1 bpm for females and males, respectively). In conclusion, in female and male obese adults, the 6-MWT might be used to predict HR at IVT. These outcomes are useful to prescribe optimal physical activity intensity when gold standard methods (e.g. gas exchange analysis) are unavailable.

The use of the Individual Ventilatory Threshold (IVT), as parameter to prescribe exercise intensity in individuals with obesity, has become more frequent during the last years. This study aimed to evaluate the relationship between IVT and Maximal Fat Oxidation (MFO) in women with obesity. Fifty-two obese female adults (age = 43.6±10.9 years; BMI = 38.5±5.2 kg/m 2 ) were included in this study. According to the BMI classification, subjects were divided into three groups: Obese Class I (OBI, n = 16); Obese Class II (OBII, n = 20) and Obese Class III (OBIII, n = 16). All subjects performed an incremental graded exercise test to evaluate peak oxygen uptake (VO 2peak ), IVT and MFO. MFO was evaluated using a stoichiometric equation. Fat max zone was determined for each subject within 10% of fat oxidation rates at MFO. For each HR, %HR max , VO 2 and %VO 2peak variable, Pearson's correlation test was done between IVT and MFO exercise intensity. When statistical correlation was found we used a comparative statistical analysis to assess differences between IVT and MFO. Statistical significance was set at P � 0.05. For each HR, %HR max , VO 2 and %VO 2peak variable there was a positive significant correlation (P<0.01) between IVT and MFO. No significant differences were found for HR, % HR max , and VO 2 between IVT and MFO. %VO 2peak was significantly higher at IVT than at MFO (P = 0.03).

The review discusses, in a format of a timeline, the studies of different types of genetic variants, present in Homo sapiens, but absent in all other primate, mammalian, or vertebrate species, tested so far. The main characteristic of these variants is that they are found in regions of high evolutionary conservation. These sequence variations include single nucleotide substitutions (called human accelerated regions), deletions, and segmental duplications. The rationale for finding such variations in the human genome is that they could be responsible for traits, specific to our species, of which the human brain is the most remarkable. As became obvious, the vast majority of human-specific single nucleotide substitutions are found in noncoding, likely regulatory regions. A number of genes, associated with these human-specific alleles, often through novel enhancer activity, were in fact shown to be implicated in human-specific development of certain brain areas, including the prefrontal cortex. Human-specific deletions may remove regulatory sequences, such as enhancers. Segmental duplications, because of their large size, create new coding sequences, like new functional paralogs. Further functional study of these variants will shed light on evolution of our species, as well as on the etiology of neurodevelopmental disorders.

Prescribing individualized moderate exercise intensity is a useful method to reach positive effects on health status in obese adults. This study aimed to establish a practical reference equation to estimate the heart rate (HR) at individual ventilatory threshold (IVT) (HRIVT). One hundred sixty-one obese subjects were clinically evaluated and characterized by anthropometric and body composition. Participants performed the six-minute walking test (6-MWT) and the cardiopulmonary exercise test to assess IVT. Multiple regression analysis for HRIVT, including 6-MWT, anthropometric, and body composition parameters, as independent variables, was performed for both gender separately. A cross-validation study was also performed to determine the accuracy of the prediction equation. Whereas HRIVT was not significantly different between males (121.5±18.3 bpm) and females (117.6±17.1 bpm), it differently correlated with physical and performance parameters. Therefore, two sex-specific equations w...

The review discusses, in a format of a timeline, the studies of different types of genetic variants, present in Homo sapiens, but absent in all other primate, mammalian, or vertebrate species, tested so far. The main characteristic of these variants is that they are found in regions of high evolutionary conservation. These sequence variations include single nucleotide substitutions (called human accelerated regions), deletions, and segmental duplications. The rationale for finding such variations in the human genome is that they could be responsible for traits, specific to our species, of which the human brain is the most remarkable. As became obvious, the vast majority of human-specific single nucleotide substitutions are found in noncoding, likely regulatory regions. A number of genes, associated with these human-specific alleles, often through novel enhancer activity, were in fact shown to be implicated in human-specific development of certain brain areas, including the prefronta...

distribution of the surrounding downwelling light. Deep-sea fishes that have instead evolved to detect bioluminescent point sources have eyes constructed accordingly, typically having a high spatial resolution provided by a retinal area of tightly packed visual cells arranged in a deep pit-like fovea. Their eyes, though, are often quite small, with pupils only as large as necessary to detect points of light at ecologically meaningful distances, which in the nutritionally impoverished deep may only be a few body lengths. Further reading

The genetic relationships between the Pacific and the Atlantic populations of marine coastal biota in Southern South America have been analyzed in few studies, most of them relying on a single mitochondrial locus. We analyzed 10 polymorphic microsatellite loci, isolated from a dinucleotide-enriched Eleginops maclovinus genomic library, in a total of 240 individuals (48 from each of 5 sampled sites: 2 Atlantic, 2 Pacific and 1 in Beagle Channel). The results were contrasted against a previous work on the same species with mitochondrial DNA (mtDNA). Observed heterozygosity within localities ranged from 0.85 to 0.88 with the highest overall number of alleles observed at the northernmost locality on the Pacific side (Concepción), but no clear geographic pattern arose from the data. On the other hand, the number of private alleles was negatively correlated with latitude (Spearman's r s test, P = 0.017). Among-population variance was low but significant (1.35%; Po0.0001, analysis of molecular variance (AMOVA)) and low genetic differentiation between populations was observed (pairwise F ST values ranged from 0 to 0.021). A Mantel test revealed a significant correlation between geographic distances and F ST (r = 0.56, P = 0.047). This could be partially accounted by the Atlantic versus Pacific population differentiation detected in three different analyses (STRUCTURE, SAMOVA (Spatial Analysis of MOlecular VAriance) and a population phylogeny). The observed pattern is compatible with a history of separation into two glacial refugia that was better captured by the multilocus microsatellite data than by the mtDNA analysis.

Background: The impressive adaptive radiation of notothenioid fishes in Antarctic waters is generally thought to have been facilitated by an evolutionary key innovation, antifreeze glycoproteins, permitting the rapid evolution of more than 120 species subsequent to the Antarctic glaciation. By way of contrast, the second-most species-rich notothenioid genus, Patagonotothen, which is nested within the Antarctic clade of Notothenioidei, is almost exclusively found in the non-Antarctic waters of Patagonia. While the drivers of the diversification of Patagonotothen are currently unknown, they are unlikely to be related to antifreeze glycoproteins, given that water temperatures in Patagonia are well above freezing point. Here we performed a phylogenetic analysis based on genome-wide single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RADseq) in a total of twelve Patagonotothen species. Results: We present a well-supported, time-calibrated phylogenetic hypothesis including closely and distantly related outgroups, confirming the monophyly of the genus Patagonotothen with an origin approximately 3 million years ago and the paraphyly of both the sister genus Lepidonotothen and the family Notothenidae. Our phylogenomic and population genetic analyses highlight a previously unrecognized linage and provide evidence for shared genetic variation between some closely related species. We also provide a mitochondrial phylogeny showing mitonuclear discordance. Conclusions: Based on a combination of phylogenomic and population genomic approaches, we provide evidence for the existence of a new, potentially cryptic, Patagonotothen species, and demonstrate that genetic boundaries between some closely related species are diffuse, likely due to recent introgression and/or incomplete linage sorting. The detected mitonuclear discordance highlights the limitations of relying on a single locus for species barcoding. In addition, our time-calibrated phylogenetic hypothesis shows that the early burst of diversification roughly coincides with the onset of the intensification of Quaternary glacial cycles and that the rate of species accumulation may have been stepwise rather than constant. Our phylogenetic framework not only advances our understanding of the origin of a high-latitude marine radiation, but also provides the basis for the study of the ecology and life history of the genus Patagonotothen, as well as for their conservation and commercial management.

A novel bacterium, designated HME9613 T , was isolated from seawater of the Yellow Sea in the Republic of Korea. Cells of strain HME9613 T were Gram-stain-negative, aerobic, motile by gliding and rod-shaped. Strain HME9613 T grew optimally at 25 C, at pH 7 and in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HME9613 T formed a lineage within the genus Winogradskyella of the family Flavobacteriaceae, and showed highest sequence similarity to Winogardskyella exilis 022-2-26 T (95.9 %). The 16S rRNA gene sequence similarity between strain HME9613 T and other Winogradskyella species ranged from 93.7 to 95.9 %. The major fatty acids were iso-C 15 : 1 G, summed feature 3 (C 16 : 1 !7c and/or C 16 : 1 !6c) and iso-C 15 : 0 . The polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids and two unidentified lipids. The predominant respiratory quinone was menaquinone-6 (MK-6). The DNA G+C content of the strain HME9613 T was 38.4 mol%. On the basis of phenotypic, chemotaxonomic, phylogenetic and genotypic data, strain HME9613 T represents a novel species within the genus Winogradskyella, for which the name Winogradskyella maritima sp. nov. is proposed. The type strain is HME9613 T (=KCTC 42189 T =CECT 8979 T ).

A non-motile, orange-pigmented bacterium, designated strain HME7103T, was isolated from lagoon water in the Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME7103T formed a lineage within the genus Lacihabitans and family Cytophagaceae. Strain HME7103T was closely related to Lacihabitans soyangensis HME6675T (95.7 % 16S rRNA gene sequence similarity). The major fatty acids of strain HME7103T were summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c) and iso-C15 : 0. The major respiratory quinone was MK-7. The major polyamine was spermidine. The major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, one unidentified aminophospholipid and three unidentified polar lipids. The DNA G+C content of strain HME7103T was 40.6 mol%. On the basis of the evidence presented in this study, strain HME7103T represents a novel species within the genus Lacihabitans, for which the name Lacihabitans lacunae sp. nov. is proposed. T...

A novel Gram-stain-negative, aerobic and rod-shaped marine bacterium, designated strain HMF4135T, was isolated from a sand sample which was collected from the seashore of the South Sea, Republic of Korea. It required NaCl for growth and exhibited optimal growth at 30 °C, with 2 % (w/v) NaCl and at pH 7-8. Cellular fatty acids were dominated by C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω9c and C12 : 0 3-OH. The predominant isoprenoid quinone was ubiquinone-8 (Q-8). Polar lipids consisted of phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 41.9 mol%. Phylogeny based on 16S rRNA gene sequences showed that strain HMF4135T formed a distinct species-level lineage within the genus Thalassotalea of the class Gammaproteobacteria and was most closely related to Thalassotalea ponticola GJSW-36T (96.4 % similarity). Based on the distinctive phenotypic characteristics and phylogenetic analysis, it is concluded that strain HMF4135T represents a nov...

A novel, Gram-stain-negative, aerobic, non-motile and filamentous bacterial strain, designated HMF3829T, was isolated from wetland freshwater in Gyeong-an wetland, Republic of Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMF3829T formed a lineage within the genus Runella. Strain HMF3829T was closely related to Runella slithyformis DSM 19594T (95.2 % 16S rRNA gene sequence similarity), Runellalimosa DSM 17973T (94.9 %), Runellazeae NS12T (94.2 %) and Runella defluvii EMB13T (94.0 %). The major fatty acids of strain HMF3829T were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c), C16 : 1ω5c and iso-C17 : 0 3-OH. The predominant isoprenoid quinone was menaquinone 7 (MK-7). The polar lipids of strain HMF3829T consisted of phosphatidylethanolamine, three unidentified aminolipids, one unidentified phospholipid, three unidentified aminophospholipids and 12 unidentified lipids. The DNA G+C content of strain HMF3829T was 46.2 mol%. On t...

A novel bacterium, designated HMF3850 T , was isolated from freshwater collected from the Gyeong-an wetland, Republic of Korea. Cells were Gram-stain-negative, aerobic, straight rods, non-motile, and oxidase-and catalase-positive. Growth was observed at pH 6.0-8.0 and at 10-30 C on R2A agar. Comparative analysis of 16S rRNA gene sequences revealed that strain HMF3850 T is a member of the genus Emticicia, sharing highest sequence similarities with Emticicia aquatica HMF2925 T (96.7 % 16S rRNA gene sequence similarity), Emticicia sediminis JBR12 T (95.0 %), Emticicia ginsengisoli Gsoil 085 T (94.9 %) and Emticicia oligotrophica DSM 17448 T (94.7 %). The major fatty acids were iso-C 15 : 0 , summed feature 3 (C 16 : 1 !7c and/or C 16 : 1 !6c) and C 16 : 0 . The predominant respiratory quinone was MK-7. The major polar lipids were phosphatidylethanolamine, phosphatidylinositol, one unidentified aminophospholipid, two unidentified aminolipids and eight unidentified polar lipids. The DNA G+C content was 38.5 mol %. On the basis of the evidence presented in this study, strain HMF3850 T represents a novel species of the genus Emticicia, for which the name Emticicia paludis sp. nov. is proposed. The type strain is HMF3850 T (=KCTC 42851 T =CECT 9087 T ).

A Gram-stain-negative, curved rod-shaped and non-pigmented strain, HME8277 T , was isolated from surface seawater of the Yellow Sea in the Republic of Korea. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel strain was related most closely to Reinekea blandensis MED297 T (96.4 % 16S rRNA gene sequence similarity), Reinekea aestuarii IMCC4489 T (96.3 %) and Reinekea marinisedimentorum KMM 3655 T (95.8 %). The major fatty acids were summed feature 3 (comprising C 16 : 1 v7c and/or C 16 : 1 v6c; 43.0 %), C 16 : 0 (19.0 %) and summed feature 8 (comprising C 18 : 1 v7c and/or C 18 : 1 v6c; 15.0 %). The DNA G+C content was 46.1 mol%. The predominant respiratory quinone was Q-8. The major polar lipids of strain HME8277 T comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified phospholipids and four unidentified lipids. On the basis of polyphasic analyses, strain HME8277 T represents a novel species of the genus Reinekea, for which the name Reinekea marina sp. nov. is proposed. The type strain HME8277 T (5KACC 17315 T 5CECT 8288 T ). An emended description of the genus Reinekea is also provided. The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of strain HME8277 T is KC690143.

A Gram-staining-negative, motile by gliding, yellow-pigmented bacterial strain designated KNUS1T, was isolated from the Lake Paro in Korea. The phylogenetic tree based on 16S rRNA gene sequences showed that strain KNUS1T formed a distinct lineage within the genus Flavobacterium. Strain KNUS1T was closely related to Flavobacterium cheonhonense ARSA-15T (96.8 %), F. pectinovorum DSM 6368T (96.3 %) and F. dankookenses ARSA-19T (96.1 %). The major fatty acids of strain KNUS1T were iso-C15:0 and iso-C15:1 G. The major polyamine of strain KNUS1T strain was sym-homospermidine. The major polar lipids of strain KNUS1T were phosphatidylethanolamine, five unidentified aminolipids and three unidentified polar lipids. The major respiratory`quinone was menaquinone 6 (MK-6). The DNA G+C content of strain KNUS1T was 34.2 mol%. On the basis of the evidence presented in this study, strain KNUS1T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium paronense sp. no...

A Gram-stain-negative, non-motile and yellow-pigmented bacterium, designated HME8275T, was isolated from freshwater in Korea. The major fatty acids of strain HME8275T were summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c), C16 : 0 and iso-C15 : 0. The only respiratory quinone was MK-7. Polar lipid analysis showed phosphatidylethanolamine, two unidentified aminolipids, two unidentified aminophospholipids and three unidentified polar lipids. The DNA G+C content of strain HME8275T was 37.6 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HME8275T formed a lineage within the family Cytophagaceae and was related to Lacihabitans soyangensis HME6675T (92.6 % 16S rRNA gene sequence similarity), Leadbetterella byssophila 4M15T (89.0 %), Fluviimonas pallidilutea TQQ6T (89.7 %) and Emticicia oligotrophica GPTSA100-15T (89.8 %). On the basis of the evidence presented in this study, strain HME8275T represents a novel species of a new genus in the family Cyto...

A non-motile, red-pigmented bacterium, designated strain HMD1010T, was isolated from an artificial lake located within the campus of Hankuk University of Foreign Studies, Yongin, Korea. A phylogenetic tree based on 16S rRNA gene sequences showed that strain HMD1010T formed a lineage within the genus Hymenobacter and was closely related to the type strains of Hymenobacter rigui (96.7 % sequence similarity) and H. gelipurpurascens (95.6 %). The major fatty acids were C16 : 1ω5c (21.9 %), summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1ω7c; 17.2 %), iso-C15 : 0 (14.5 %) and summed feature 4 (anteiso-C17 : 1 B and/or iso-C17 : 1 I; 11.9 %). The DNA G+C content was 60.4 mol%. On the basis of the evidence presented in this study, strain HMD1010T represents a novel species of the genus Hymenobacter, for which the name Hymenobacter yonginensis sp. nov. was proposed. The type strain is HMD1010T ( = KCTC 22745T  = CECT 7546T).

Two non-motile, Gram-staining-negative, yellow-pigmented bacterial strains designated HMD1001T and HMD1033T were isolated from the water of a mesotrophic artificial lake in Korea. A phylogenetic tree based on 16S rRNA gene sequences indicated that both strains could be assigned to the genus Flavobacterium ; strain HMD1001T appeared most closely related to Flavobacterium fluvii H7T (96.8 % sequence similarity), F. succinicans DSM 4002T (96.6 %) and F. hydatis DSM 2063T (96.6 %) whereas strain HMD1033T appeared most closely related to Flavobacterium psychrolimnae LMG 2201T (96.2 %), F. segetis AT1048T (96.2 %) and F. weaverense AT1042T (96.2 %). The major fatty acids of strain HMD1001T were iso-C15 : 0 (21.5 %), summed feature 3 (comprising C16 : 1ω6c and/or C16 : 1ω7c; 18.0 %) and iso-C15 : 1 G (7.6 %), whereas those of HMD1033T were summed feature 3 (23.8 %), iso-C15 : 0 3-OH (16.9 %), iso-C15 : 0 (15.3 %) and anteiso-C15 : 0 (12.1 %). The genomic DNA G+C contents of strains HMD1001...

Apd1, a cytosolic yeast protein, and Aim32, its counterpart in the mitochondrial matrix, have a C-terminal thioredoxinlike ferredoxin domain and a widely divergent N-terminal domain. These proteins are found in bacteria, plants, fungi and unicellular pathogenic eukaryotes, but not in Metazoa. Our chemogenetic experiments demonstrate that the highly conserved cysteine and histidine residues within the C-X8-C-X24-75-H-X-G-G-H motif of the TLF domain of Apd1 and Aim32 proteins are essential for viability upon treatment of yeast cells with the redox potentiators gallobenzophenone or pyrogallol, respectively. UV-Vis, EPR and Mössbauer spectroscopy of purified wild type Apd1 and three His to Cys variants demonstrated that Cys207 and Cys216 are the ligands of the ferric ion and His255 and His259 are the ligands of the reducible iron ion of the [2Fe-2S]2+/1+ cluster. The [2Fe-2S] center of Apd1 (Em,7 = -164±5 mV, pKox1,2=7.9±0.1 and 9.7±0.1) differs from both dioxygenase (Em,7 ≈ -150 mV, pK...

African catfish (Clarias gariepinus) is one of the economically important species in Indonesian aquaculture that has experienced genetic deterioration. Thus, it should be genetically improved, mainly on the growth and disease resistance. The genetic improvement of those traits was initiated by forming the base population. The base population consisted of two populations, each resulting from a factorial mating design of a 2:2 ratio between 30 males and 30 females of Mutiara African catfish carrying major histocompatibility complex class I (MHC I) allele number 7. Forming the first base population resulted in 50 families, whereas the second resulted in 57 families. The potency of the base population in forming the next generation was then evaluated by estimating the genetic parameters, i.e., heritability, selection differential, selection intensity, and response to selection. Results of the estimation of genetic parameters for its body weight suggested that the heritability of both base populations was relatively high (0.33 and 0.44), with relatively low selection differential (28.07±11.39% and 23.78±7.42%) and selection intensity (1.13±0.22 and 1.13±0.19). The response to selection for body weight in the next generation was estimated at around 9.31-10.38%. Those results suggested that both base populations could be used in forming the next generation.

The Ising model is defined by an objective function using a quadratic formula of qubit variables. The problem of an Ising model aims to determine the qubit values of the variables that minimize the objective function, and many optimization problems can be reduced to this problem. In this paper, we focus on optimization problems related to permutations, where the goal is to find the optimal permutation out of the n! possible permutations of n elements. To represent these problems as Ising models, a commonly employed approach is to use a kernel that applies one-hot encoding to find any one of the n! permutations as the optimal solution. However, this kernel contains a large number of quadratic terms and high absolute coefficient values. The main contribution of this paper is the introduction of a novel permutation encoding technique called the dual-matrix domain wall, which significantly reduces the number of quadratic terms and the maximum absolute coefficient values in the kernel. S...

The evolutionary emergence of the first animals is thought to have been intimately associated to the formation of a primitive endomesodermal gut (i.egastrulation) from ancestral multi-cellular spheres, blastulae, more than 700 million years ago. However, the biochemical cues having been at the origin of endomesoderm formation remain a mystery.Here we find that hydrodynamic mechanical strains developed by sea wavelets on pre-bilaterianNematostella vectensisand pre-metazoanChoanoeca flexarepresentatives, which common ancestor dates back to more than 700 million years ago, can trigger gastrulation in a Myo-II dependent mechanotransductive process. Gastrulation in turn induces endomesoderm first biochemical specification through the mechanical activation of the βcat pathway in pre-bilaterianNematostella vectensis, like in Drosophila and zebrafish embryos, which common ancestor dates back to 600-700 million years ago.These observations converge to animal emergence that has been mechanotr...

A Middle Ordovician limestone succession, representing part of the Alai Formation (middle part of the Chiatsun Group) of the Himalayan Orogenic Belt, is well exposed at Jiacun section in Nyalam County to the west of the Mount Jolmo Lungma (Mount Everest), southern Xizang (Tibet), China. The succession, though reported previously, has yet to be investigated in detail,

As an obconical macrofossil with porous double-wall, Calathium was commonly present in reefs of Early to early Middle Ordovician age. The Calathium-bearing reefs thrived globally during the Early Ordovician, but this ecosystem collapsed in Middle Ordovician. A rare case of Calathium-microbial reefs was found from the middle part of the Yijianfang Formation (Darriwilian, late Middle Ordovician) of the Bachu area, located in the northwestern margin of the Tarim Basin, northwestern China. Surrounded by bioclastic grainstones, patch reefs here are well-developed and vary in size, with 1-4 m in thickness and 2-18 m in diameter. Three facies types are distinguished within the reef limestones: (1) Calathium-microbial framestone, (2) echinoderm-Calathium

Accurate diagnosis of tuberculosis, especially by using rapid molecular assays, can reduce transmission of drug resistant tuberculosis in communities. However, the frequency of resistance conferring mutations varies with geographic location of Mycobacterium tuberculosis, and this affects the efficiency of rapid molecular assays in detecting resistance. This has created need for characterizing drug resistant isolates from different settings to investigate frequencies of resistance conferring mutations. Here, we describe the prevalence and patterns of rifampicin-and isoniazid-resistance conferring mutations in isolates from Uganda, which could be useful in the management of MDR-TB patients in Uganda and other countries in sub-Saharan Africa. Ninety seven M. tuberculosis isolates were characterized, of which 38 were MDR, seven rifampicin-resistant, 12 isoniazid-mono-resistant, and 40 susceptible to rifampicin and isoniazid. Sequence analysis of the rpoB rifampicin-resistance determining region (rpoB/RRDR) revealed mutations in six codons: 588, 531, 526, 516, 513, and 511, of which Ser531Leu was the most frequent (40%, 18/45). Overall, the three mutations (Ser531Leu, His526Tyr, Asp516Tyr) frequently associated with rifampicin-resistance occurred in 76% of the rifampicin resistant isolates while 18% (8/45) of the rifampicin-resistant isolates lacked mutations in rpoB/RRDR. Furthermore, sequence analysis of katG and inhA gene promoter revealed mainly the Ser315Thr (76%, 38/50) and C(-15)T (8%, 4/50) mutations, respectively. These two mutations combined, which are frequently associated with isoniazid-resistance,

In this paper I describe the jaw adductor musculature in colubrid snakes that formerly belonged to the genus Elaphe Fitzinger. The group studied shows a high level of homoplasy, and particular lineages exhibit a mixture of advanced and primitive characters. The presence of the levator anguli oris in this group is questioned.

Different surveys in the Campechano–Petenense biogeographical province, including a part of Yucatan Peninsula, Belize, and North of Guatemala (Departments of Peten and Alta Verapaz), produced a list of 56 species of the Cladocera. Studied water bodies included small temporary pools, sinkholes (named cenotes), permanent lagoons, wetlands, and Peten Lake. We increase the number of known cladoceran species from Mexico by adding eight new records, and provide the first published species list for Belize, as well as for the Mayan Mountains and intermittent rivers from Guatemala. Interesting taxa found are Diaphanosoma bergamini Paggi & da Rocha, 1999; Macrothrix spinosa King, 1853; M. elegans Sars, 1901; Grimaldina brazzai Richard, 1892; Picripleuroxus quasidenticulatus Smirnov, 1996; Ephemeroporus tridentatus (Bergamin, 1939); Graptoleberis sp.; Alona cf. ossiani Sinev, 1998; Oxyurella ciliata Bergamin, 1939, and O. longicaudis (Birge, 1910). The majority of these species are Neotropical...

Previous studies have found that at most human loci, ancestral alleles are ''African,'' in the sense that they reach their highest frequency there. Conventional wisdom holds that this reflects a recent African origin of modern humans. This paper challenges that view by showing that the empirical pattern (of elevated allele frequencies within Africa) is not as pervasive as has been thought. We confirm this African bias in a set of mainly protein-coding loci, but find a smaller bias in Alu insertion polymorphisms, and an even smaller bias in noncoding loci. Thus, the strong bias that was originally observed must reflect some factor that varies among data sets-something other than population history. This factor may be the per-locus mutation rate: the African bias is most pronounced in loci where this rate is high. The distribution of ancestral alleles among populations has been studied using 2 methods. One of these involves comparing the fractions of loci that reach maximal frequency in each population. The other compares the average frequencies of ancestral alleles. The first of these methods reflects history in a manner that depends on the mutation rate. When that rate is high, ancestral alleles at most loci reach their highest frequency in the ancestral population. When that rate is low, the reverse is true. The other method-comparing averages-is unresponsive. Average ancestral allele frequencies are affected neither by mutation rate nor by the history of population size and migration. In the absence of selection and ascertainment bias, they should be the same everywhere. This is true of one data set, but not of 2 others. This also suggests the action of some factor, such as selection or ascertainment bias, that varies among data sets.

Adult control of Aedes albopictus via ultra-low volume is difficult because this species occurs primarily in peridomestic habitats where obstacles such as buildings and vegetation can disrupt spray plumes and droplet dispersion. We determined droplet penetration and characterization of a pyrethroid adulticide applied from the ground at mid (46.77 ml/ha) and maximum (93.53 ml/ha) label rates within cryptic habitats of urban and suburban environments. Droplets were collected from all habitats, with no significant differences detected between locations within the same application rate or collection method. No differences were detected in droplet densities (drops per mm 2 ) between rates within urban environments, but more droplets were collected in urban (149.93 ± 11.07 SE) than suburban sites (114.37 ± 11.32) at the maximum label rate (P = 0.003). The excellent penetration of aerosols into cryptic habitats of an urban site was likely due to the shorter spray paths afforded by our network of roads and alleys. Mid label rates displayed similar droplet density values as maximum label rates in urban areas, indicating that lower rates may be used effectively to reduce costs, lessen non-target effects, and increase environmental stewardship. Advances in formulations and technology are driving changes in adulticide applications, leading to use of the minimum effective dose for maximum efficacy, precision, and accountability.

To assess knowledge, pregnancy attitudes and contraceptive practices in relation to the Zika virus outbreak in Brazil. We interviewed 526 women 18 to 49 years old in primary health services in a Northeastern capital of Brazil, in 2016. They provided information about their knowledge of Zika transmission and health consequences, their receipt of counseling related to sexual and perinatal transmission of Zika, their pregnancy intentions and reassessment of contraceptive options in the context of the Zika virus outbreak. Awareness about Zika congenital syndrome was high, but knowledge about sexual transmission was low. Few women had changed pregnancy intentions or contraceptive practices in response to Zika. Pregnant women were more likely to access counseling about family planning, condom use and pregnancy postponement due to Zika virus than non-pregnant women, which may suggest that health system responses followed pregnancy occurrence. We observed missed opportunities for prevention...

Our 2007 book publication "Seashells of Southern Florida-Bivalves" reported on 379 nominal extant bivalve species in the Florida Keys. Bivalve research has remained an active field and this taxonomic update addresses 196 of these nominal species, many of which have undergone generic reallocations, synonymies, or reidentifications. A list of additional species newly recorded for the Keys is provided. Prior statements about synonyms and geographic ranges are revised in view of updated information. New nomenclatural actions and taxonomic decisions include: Modiolus americanus Leach, 1815 is a nomen protectum; its subjective senior synonym, Musculus papuanus Röding, 1798, is a nomen oblitum. Cytherea fulminata Menke, 1828 (currently Jasypitar fulminatus) is a nomen protectum; its subjective senior synonym, Venus holosericea Gmelin, 1791, is a nomen oblitum. Evidence is provided that Parahyotissa mcgintyi Harry, 1985 (currently in Hyotissa) qualified as a nomen protectum when Huber synonymized it in 2010 under the nomen oblitum Mytilus roseus Gmelin, 1791. Evidence is provided that Anomia simplex d'Orbigny, 1853 qualified as a nomen protectum when Huber synonymized it in 2010 under the nomen oblitum Anomia acontes J.E. Gray, 1850. Euvola marshallae Petuch and Myers, 2014 is a junior subjective synonym of Pecten (Amusium) marensis Weisbord, 1964. Brachidontes noronhensis Quintanilha, Fernandes, Guerra, Campos, and Weber, 2022, introduced as a "new name," is a nomen nudum. The declarations of nomina protecta/oblita in Huber's 2010 Compendium of Bivalves did not fulfill the requirements of the 1999 ICZN Code. Huber's works in 2010 and 2015 included misinterpretations of the 1999 ICZN Code, leading to numerous incorrect decisions on name priority. The 1968 Ph.D. dissertation of Stuardo is an unpublished work in the sense of the ICZN; subsequent use of the included Limidae manuscript names by Huber (2010, 2015) did not make them available.

The systematics of the molluscan class Bivalvia are explored using a 5-gene Sanger-based approach including the largest taxon sampling to date, encompassing 219 ingroup species spanning 93 (or 82%) of the 113 currently accepted bivalve families. This study was designed to populate the bivalve Tree of Life at the family level and to place many genera into a clear phylogenetic context, but also pointing to several major clades where taxonomic work is sorely needed. Despite not recovering monophyly of Bivalvia or Protobranchia-as in most previous Sanger-based approaches to bivalve phylogeny-our study provides increased resolution in many higher-level clades, and supports the monophyly of Autobranchia, Pteriomorphia, Heteroconchia, Palaeoheterodonta, Heterodonta, Archiheterodonta, Euheterodonta, Anomalodesmata, Imparidentia, and Neoheterodontei, in addition to many other lower clades. However, deep nodes within some of these clades, especially Pteriomorphia and Imparidentia, could not b...

Bivalves are an ancient and ubiquitous group of aquatic invertebrates with an estimated 10 000-20 000 living species. They are economically significant as a human food source, and ecologically important given their biomass and effects on communities. Their phylogenetic relationships have been studied for decades, and their unparalleled fossil record extends from the Cambrian to the Recent. Nevertheless, a robustly supported phylogeny of the deepest nodes, needed to fully exploit the bivalves as a model for testing macroevolutionary theories, is lacking. Here, we present the first phylogenomic approach for this important group of molluscs, including novel transcriptomic data for 31 bivalves obtained through an RNA-seq approach, and analyse these data with published genomes and transcriptomes of other bivalves plus outgroups. Our results provide a well-resolved, robust phylogenetic backbone for Bivalvia with all major lineages delineated, addressing long-standing questions about the m...