The evolutionary history of the DMRT3 ‘Gait keeper’ haplotype

A previous study revealed a strong association between the DMRT3:Ser301STOP mutation in horses and alternate gaits as well as performance in harness racing. Several follow‐up studies have confirmed a high frequency of the mutation in gaited horse breeds and an effect on gait quality. The aim of this study was to determine when and where the mutation arose, to identify additional potential causal mutations and to determine the coalescence time for contemporary haplotypes carrying the stop mutation. We utilized sequences from 89 horses representing 26 breeds to identify 102 SNPs encompassing the DMRT3 gene that are in strong linkage disequilibrium with the stop mutation. These 102 SNPs were genotyped in an additional 382 horses representing 72 breeds, and we identified 14 unique haplotypes. The results provided conclusive evidence that DMRT3:Ser301STOP is causal, as no other sequence polymorphisms showed an equally strong association to locomotion traits. The low sequence diversity among mutant chromosomes demonstrated that they must have diverged from a common ancestral sequence within the last 10 000 years. Thus, the mutation occurred either just before domestication or more likely some time after domestication and then spread across the world as a result of selection on locomotion traits.     

To pace or not to pace: a pilot study of four‐ and five‐gaited Icelandic horses homozygous for the DMRT3 ‘Gait Keeper’ mutation

The Icelandic horse is a breed known mainly for its ability to perform the ambling four‐beat gait ‘tölt’ and the lateral two‐beat gait pace. The natural ability of the breed to perform these alternative gaits is highly desired by breeders. Therefore, the discovery that a nonsense mutation (C>A) in the DMRT3 gene was the main genetic factor for horses' ability to perform gaits in addition to walk, trot and canter was of great interest. Although several studies have demonstrated that homozygosity for the DMRT3 mutation is important for the ability to pace, only about 70% of the homozygous mutant (AA) Icelandic horses are reported to pace. The aim of the study was to genetically compare four‐ and five‐gaited (i.e. horses with and without the ability to pace) AA Icelandic horses by performing a genome‐wide association (GWA) analysis. All horses (n = 55) were genotyped on the 670K Axiom Equine Genotyping Array, and a GWA analysis was performed using the genabel package in r . No SNP demonstrated genome‐wide significance, implying that the ability to pace goes beyond the presence of a single gene variant. Despite its limitations, the current study provides additional information regarding the genetic complexity of pacing ability in horses. However, to fully understand the genetic differences between four‐ and five‐gaited AA horses, additional studies with larger sample materials and consistent phenotyping are needed.     

Where are the frame-shifted gene ‘duplications’?

Evolution by gene duplication has been well documented, mostly by the discovery of two or more similar amino-acid sequences in proteins translated from one haploid genome. The sequences differ by interpolation and deletion of amino-acids as well as substitution. This is evidence for triplet (codon) addition or subtraction; do deletions/interpolations of one or two nucleotides (frame-shifting mutations) occur? If they are not seen (as in haemoglobins) either this is because they are not generated (the genetic code constrains DNA events); they are generated but edited (gene conversion?); gametes containing them are selected against; or they are actively and rapidly selected against evolutionarily. If they are seen (as in immunoglobulins, possibly) they may generate somatic diversity (as in antibodies) and there may be a limbo of more-or-less changed structural sequences, returning to translation (and selection) only by another frame-shifting event. This suggestion combines neutral mutation theory with pan-selectionism.     

‘Dancing the image’: materiality and spirituality in Andean religious ‘images’

In the Christian tradition, representing the divine has often been considered both an impossible and yet necessary endeavour rooted in the human need in certain moments of weakness to visualize God. In this article, based on research findings from fieldwork carried out with urban indigenous groups in La Paz, Bolivia, I suggest that the articulation of local and Catholic representational traditions and practices has produced an understanding of the religious image not so much as an object of detached contemplation or a reference to a religious symbol but rather as an energized element which physically shapes the relationship and exchange between the material and the spiritual world. I suggest that through a study of Andean religious images we may be able to produce an alternative ontological perspective on the relationship between the spiritual, material, and living worlds.

Résumé

Dans la tradition chrétienne, la représentation du divin est souvent considérée comme une gageure impossible et pourtant nécessaire, motivée par la nécessité humaine de visualiser Dieu dans les moments de faiblesse. À partir des matériaux de terrain obtenus auprès de groupes autochtones urbains à La Paz, en Bolivie, l'auteur suggère ici que l'articulation des traditions et pratiques de représentation locales et catholiques a conduit à concevoir l'image religieuse moins comme un objet de contemplation détachée ou une référence à un symbole religieux que comme un élément chargé d'énergie, qui donne physiquement forme à la relation et aux échanges entre le monde matériel et le monde spirituel. L'article suggère qu'à travers l'étude des images religieuses andines, on pourrait élaborer un autre point de vue ontologique sur la relation entre les mondes spirituel, matériel et vivant.     

Unravelling the Philosophies Underlying ‘Animal Personality’ Studies: A Brief Re‐Appraisal of the Field

The last decade has seen lots of studies on ‘animal personality’ (i.e. the study of consistent between‐individual behavioural differences). As timely and promising as this field is, its development has come with a diversity of research questions. As an unfortunate consequence, it now suffers from substantial confusion about what ‘animal personality’ is, and how relevant related research frameworks are. Here, we stress the current inconsistencies and sources of confusion pertaining to the field, and their consequences on terminology used and miscommunication between researchers. In an attempt to unravel and clarify the concepts underlying the field, we identify two distinct, but complementary, theory‐driven conceptual frameworks: the intra‐individual variability (IIV) approach and the life‐history (LH) approach, which we believe encompass the vast majority of existing ‘personality studies’. Finally, we argue in favour of theory‐driven studies of consistent behavioural differences and state that the integrative statistical properties of random regression models should not override the merit of alternative conceptual frameworks. We then provide brief guidelines and warnings for a parsimonious and sound use of terminology.     

Chrysanthemum expressing a linalool synthase gene ‘smells good’, but ‘tastes bad’ to western flower thrips

Herbivore‐induced plant volatiles are often involved in direct and indirect plant defence against herbivores. Linalool is a common floral scent and found to be released from leaves by many plants after herbivore attack. In this study, a linalool/nerolidol synthase, FaNES1, was overexpressed in the plastids of chrysanthemum plants (Chrysanthemum morifolium). The volatiles of FaNES1 chrysanthemum leaves were strongly dominated by linalool, but they also emitted small amount of the C11‐homoterpene, (3E)‐4,8‐dimethyl‐1,3,7‐nonatriene, a derivative of nerolidol. Four nonvolatile linalool glycosides in methanolic extracts were found to be significantly increased in the leaves of FaNES1 plants compared to wild‐type plants. They were putatively identified by LC‐MS‐MS as two linalool–malonyl–hexoses, a linalool–pentose–hexose and a glycoside of hydroxy–linalool. A leaf‐disc dual‐choice assay with western flower thrips (WFT, Frankliniella occidentalis) showed, initially during the first 15 min of WFT release, that FaNES1 plants were significantly preferred. This gradually reversed into significant preference for the control, however, at 20–28 h after WFT release. The initial preference was shown to be based on the linalool odour of FaNES1 plants by olfactory dual‐choice assays using paper discs emitting pure linalool at similar rates as leaf discs. The reversal of preference into deterrence could be explained by the initial nonvolatile composition of the FaNES1 plants, as methanolic extracts were less preferred by WFT. Considering the common occurrence of linalool and its glycosides in plant tissues, it suggests that plants may balance attractive fragrance with ‘poor taste’ using the same precursor compound.     

The phylogenetic distribution and morphological variation of the ‘pouch’ in female snakes

Siegel D.S., Miralles A, Trauth S.E. and Aldridge R.D. 2011. The phylogenetic distribution and morphological variation of the ‘pouch’ in female snakes. —Acta Zoologica (Stockholm) 93 : 400–408. The urodaeum of female snakes is a chamber that receives the oviducts, urinary ducts, and intestine. Previous studies have indicated that a derived region of unknown function persists between the urodaeum and oviducts in some snakes of the Colubroides. This structure was recently termed the ‘pouch’; however, it is also commonly referred to as the vaginal pouch. A broad sampling of female snakes revealed that the pouch evolved once on the branch leading to Colubroides. The presence of the pouch in Colubroides is not unambiguous, as this feature was lost in some members of the Atractaspididae and Lamprophiidae. Variation was also observed in pouch morphology between taxa of the Colubroides. Variation included the following: (1) whether the pouch was bifurcated and if so, were the arms of the pouch separated caudally, (2) whether separated pouch arms were split by a caudal bifurcation of the urodaeum or through medial septa of the pouch arms, and (3) the absence or presence of oviducal papillae invading the cranial/lateral extremity of the pouch. The variation in pouch morphology observed does not appear to be correlated with the evolutionary history of Colubroides and polymorphism within families is common.     

Cleaner Wrasses Keep Track of the ‘When’ and ‘What’ in a Foraging Task1

In recent years evidence has accumulated that at least some animals can remember the ‘what’, ‘where’ and ‘when’ of personal experiences. Currently, evidence for such ability is taxonomically restricted to birds and mammals. Here, we demonstrate for the first time that cleaner wrasses Labroides dimidiatus are able to remember when they interacted with what after a single event. In nature, cleaners remove ectoparasites from other reef fishes, so‐called clients. Clients are depleted, non‐stationary food patches at the end of an interaction and replenished only after a delay. In our experiments, we presented twelve cleaners every 2.5 min, a choice between two of a total of four plates with different colours and patterns. One plate was always accessible but contained a non‐preferred food item while the other three contained a preferred food item, but allowed a next feeding event only after 5, 10 or 15 min. Thus, to maximise food intake, cleaners had to remember for each choice when they had last interacted with which plate. When confronted with two plates offering preferred food, cleaners showed an overall significant preference for the plate that allowed access during the trial. For six cleaners, the preference was significant. Also, on trials involving the always accessible plate, cleaners discriminated between trials in which they had to eat the non‐preferred food and trials on which they could eat the preferred food. In conclusion, cleaners are able to track the ‘when’ and ‘what’ (or possibly ‘who’) within a biologically meaningful time period.     

Detection and Identification of ‘Candidatus Phytoplasma prunorum’, ‘Candidatus Phytoplasma mali’ and ‘Candidatus Phytoplasma pyri’ in Stone Fruit Trees in Poland

A survey was made to determine the incidence of phytoplasmas in 39 sweet and sour cherry, peach, nectarine, apricot and plum commercial and experimental orchards in seven growing regions of Poland. Nested polymerase chain reaction (PCR) using the phytoplasma‐universal primer pairs P1/P7 followed by R16F2n/R16R2 showed the presence of phytoplasmas in 29 of 435 tested stone fruit trees. The random fragment length polymorphism (RFLP) patterns obtained after digestion of the nested PCR products separately with RsaI, AluI and SspI endonucleases indicated that selected Prunus spp. trees were infected by phytoplasmas belonging to three different subgroups of the apple proliferation group (16SrX‐A, ‐B, ‐C). Nucleotide sequence analysis of 16S rDNA fragment amplified with primers R16F2n/R16R2 confirmed the PCR/Restriction Fragment Length Polymorphism (RFLP) results and revealed that phytoplasma infecting sweet cherry cv. Regina (Reg), sour cherry cv. Sokowka (Sok), apricots cv. Early Orange (EO) and AI/5, Japanese plum cv. Ozark Premier (OzPr) and peach cv. Redhaven (RedH) was closely related to isolate European stone fruit yellows‐G1 of the ‘Candidatus Phytoplasma prunorum’ (16SrX‐B). Sequence and phylogenetic analyses resulted in the highest similarity of the 16S rDNA fragment of phytoplasma from nectarine cv. Super Queen (SQ) with the parallel sequence of the strain AP15 of the ‘Candidatus Phytoplasma mali’ (16SrX‐A). The phytoplasma infecting sweet cherry cv. Kordia (Kord) was most similar to the PD1 strain of the ‘Candidatus Phytoplasma pyri’ (16SrX‐C). This is the first report of the occurrence of ‘Ca. P. prunorum’, ‘Ca. P. mali’ and ‘Ca. P. pyri’ in naturally infected stone fruit trees in Poland.     

Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a ‘sweet’ crop with ‘bitter’ genomes

Sugarcane (Saccharum spp.) is a highly energy‐efficient crop primarily for sugar and bio‐ethanol production. Sugarcane genetics and cultivar improvement have been extremely challenging largely due to its complex genomes with high polyploidy levels. In this study, we deeply sequenced the coding regions of 307 sugarcane germplasm accessions. Nearly five million sequence variations were catalogued. The average of 98× sequence depth enabled different allele dosages of sequence variation to be differentiated in this polyploid collection. With selected high‐quality genome‐wide SNPs, we performed population genomic studies and environmental association analysis. Results illustrated that the ancient sugarcane hybrids, S. barberi and S. sinense, and modern sugarcane hybrids are significantly different in terms of genomic compositions, hybridization processes and their potential ancestry contributors. Linkage disequilibrium (LD) analysis showed a large extent of LD in sugarcane, with 962.4 Kbp, 2739.2 Kbp and 3573.6 Kbp for S. spontaneum, S. officinarum and modern S. hybrids respectively. Candidate selective sweep regions and genes were identified during domestication and historical selection processes of sugarcane in addition to genes associated with environmental variables at the original locations of the collection. This research provided an extensive amount of genomic resources for sugarcane community and the in‐depth population genomic analyses shed light on the breeding and evolution history of sugarcane, a highly polyploid species.     

Ecophysiological function of leaf ‘windows’ in Lithops species – ‘Living Stones’ that grow underground

Leaf temperatures were lower when light entry at the leaf tip window was prevented through covering the window with reflective tape, relative to leaf temperatures of plants with leaf tip windows covered with transparent tape. This was true when leaf temperatures were measured with an infrared thermometer, but not with a fine‐wire thermocouple. Leaf tip windows of Lithops growing in high‐rainfall regions of southern Africa were larger than the windows of plants (numerous individuals of 17 species) growing in areas with less rainfall and, thus, more annual insolation. The results of this study indicate that leaf tip windows of desert plants with an underground growth habit can allow entry of supra‐optimal levels of radiant energy, thus most likely inhibiting photosynthetic activity. Consequently, the size of the leaf tip windows correlates inversely with habitat solar irradiance, minimising the probability of photoinhibition, while maximising the absorption of irradiance in cloudy, high‐rainfall regions.     

Oncogenic transformation of 3T3 cells is associated with conversion from an ‘adult’ to an ‘embryonic’ esterase isoenzyme pattern

Soluble esterases from virus-transformed sublines of 3T3 Swiss mouse fibroblasts exhibit an isoenzyme pattern in polyacrylamide gel electrophoresis similar to the pattern exhibited by primary mouse embryo cells but distinct from that exhibited by 3T3 cells. The soluble esterase isoenzyme pattern exhibited by 3T3 cells is similar to that exhibited by primary and secondary fibroblastoid cells derived from adult Swiss mouse kidney, suggesting that, despite its embryonic origin, 3T3 is an ‘adult’ cell line selected and maintained in that state by the requirement that it exhibits a low saturation density and a characteristic morphology in culture. The pattern of soluble esterase isoenzymes is similar in growing and non-growing 3T3 cells, although the specific activity is higher in preparations from non-growing cells. Sparse 3T3 cells contain at least three detergent-soluble esterase isoenzymes present at much lower levels in denser cultures.The esterase and amidase enzyme activities measured in solution with the fluorogenic substrates fluorescein diacetate and rhodamine diacetate, respectively, are substantially higher in three subcellular fractions from virus-transformed 3T3 mouse fibroblasts than in the corresponding fractions from 3T3 mouse fibroblasts or from primary mouse embryo cells. The largest increases in activity associated with viral transformation were observed in membrane-associated esterases.     

The AAT1 locus is critical for the biosynthesis of esters contributing to ‘ripe apple’ flavour in ‘Royal Gala’ and ‘Granny Smith’ apples

The ‘fruity’ attributes of ripe apples (Malus × domestica) arise from our perception of a combination of volatile ester compounds. Phenotypic variability in ester production was investigated using a segregating population from a ‘Royal Gala’ (RG; high ester production) × ‘Granny Smith’ (GS; low ester production) cross, as well as in transgenic RG plants in which expression of the alcohol acyl transferase 1 (AAT1) gene was reduced. In the RG × GS population, 46 quantitative trait loci (QTLs) for the production of esters and alcohols were identified on 15 linkage groups (LGs). The major QTL for 35 individual compounds was positioned on LG2 and co‐located with AAT1. Multiple AAT1 gene variants were identified in RG and GS, but only two (AAT1‐RGa and AAT1‐GSa) were functional. AAT1‐RGa and AAT1‐GSa were both highly expressed in the cortex and skin of ripe fruit, but AAT1 protein was observed mainly in the skin. Transgenic RG specifically reduced in AAT1 expression showed reduced levels of most key esters in ripe fruit. Differences in the ripe fruit aroma could be perceived by sensory analysis. The transgenic lines also showed altered ratios of biosynthetic precursor alcohols and aldehydes, and expression of a number of ester biosynthetic genes increased, presumably in response to the increased substrate pool. These results indicate that the AAT1 locus is critical for the biosynthesis of esters contributing to a ‘ripe apple’ flavour.