广义隐Markov模型在基因识别中的应用

广义隐Markov模型(GHMM)是基因识别的一种重要模型,但是其计算量比传统的隐Markov模型大得多,以至于不能直 接在基因识别中使用。根据原核生物基因的结构特点,提出了一种高效的简化算法,其计算量是序列长度的线性函数。在此 基础上,构建了针对原核生物基因的识别程序GeneMiner,对实际数据的测试表明,此算法是有效的。     

HOBOs, Tidbits and lizard models: the utility of electronic devices in field studies of ectotherm thermoregulation

1. A replicated experiment tested the null hypothesis that stand-alone electronic temperature recording devices produce sets of operative temperatures similar to those produced using lizard models.
2. Commercially available electronic temperature recording devices (HOBO XT™ with external probe and Tidbit™) produced sets of operative temperatures nearly identical to models designed to mimic the size, shape, scale architecture and colour of two species of common North American lizards.
3. Tidbits™ performed better than external probes.
4. These results suggest that electronic devices (especially Tidbits™) can be substituted for models in many applications and that size, morphology, scale architecture and colour contribute very little to temperature change in small-sized life-like models widely used in field-based studies on the thermal ecology of vertebrates.
5. Small differences between temperatures recorded by electronic devices and detailed lizard-shaped models fitted with thermal probes suggest that these models may nevertheless be necessary for certain kinds of studies.     

New species of Allopharynx (Digenea: Plagiorchiidae) and other helminths in Uranoscodon superciliosus (Squamata: Tropiduridae) from Amazonian Brazil

Allopharynx daileyi n. sp. (Digenea: Plagiorchiidae) from the small intestine of the tropidurid lizard Uranoscodon superciliosus from Amazonian Brazil is described and illustrated. Of the 11 currently recognized species of Allopharynx, we consider Allopharynx megorchis Simha, 1961 a synonym of Allopharynx mehrai (Gogate, 1935) Price 1938 and Allopharynx puertoricensis Acholonu, 1976 a synonym of Allopharynx riopedrensis Garcia-Diaz; thus, A. daileyi becomes the 10th species assigned to the genus. The trematode species Mesocoelium monas and 2 species of Nematoda, Africana chabaudi and Cosmocerca vrcibradici, were also present.     

Evolution and classification of cystine knot-containing hormones and related extracellular signaling molecules

The cystine knot three-dimensional structure is found in many extracellular molecules and is conserved among divergent species. The identification of proteins with a cystine knot structure is difficult by commonly used pairwise alignments because the sequence homology among these proteins is low. Taking advantage of complete genome sequences in diverse organisms, we used a complementary approach of pattern searches and pairwise alignments to screen the predicted protein sequences of five model species (human, fly, worm, slime mold, and yeast) and retrieved proteins with low sequence homology but containing a typical cystine knot signature. Sequence comparison between proteins known to have a cystine knot three-dimensional structure (transforming growth factor-beta, glycoprotein hormone, and platelet-derived growth factor subfamily members) identified new crucial amino acid residues (two hydrophilic amino acid residues flanking cysteine 5 of the cystine knot). In addition to the well known members of the cystine knot superfamily, novel subfamilies of proteins (mucins, norrie disease protein, von Willebrand factor, bone morphogenetic protein antagonists, and slit-like proteins) were identified as putative cystine knot-containing proteins. Phylogenetic analysis revealed the ancient evolution of these proteins and the relationship between hormones [e.g. transforming growth factor-beta (TGFbeta)] and extracellular matrix proteins (e.g. mucins). They are absent in the unicellular yeast genome but present in nematode, fly, and higher species, indicating that the cystine knot structure evolved in extracellular signaling molecules of multicellular organisms. All data retrieved by this study can be viewed at http://hormone.stanford.edu/.     

A molecular phylogenetic analysis of diversification in Amazonian Anolis lizards

We present a mitochondrial DNA (mtDNA) haplotype phylogeny for Amazonian Anolis lizards, including geographical sampling within four species distributed across the Amazon basin (A. fuscoauratus, A. nitens, A. ortonii and A. punctatus). Approximately 1500 bp of mtDNA encoding ND2, COI and four transfer RNAs (tRNAs) are reported for 39 specimens representing four to five populations of each widespread species, plus eight outgroups. These new sequences are aligned with eight previously published sequences, yielding 914 variable characters and 780 parsimony-informative characters. Phylogenetic analyses using maximum parsimony and maximum likelihood reject the hypothesis that Amazonian anoles form a monophyletic group excluding Central American and Caribbean anoles, and suggest multiple faunal exchanges among these regions. Haplotype divergence among geographical populations of A. nitens, whose variation was influential in formulating the Pleistocene refuge hypothesis of Amazonian speciation, is very large (13-22% sequence difference), suggesting that these populations separated well before the Pleistocene. Haplotype divergences among geographical populations of A. fuscoauratus (3-4%), A. punctatus (4-9%) and A. ortonii (6-8%) also indicate pre-Pleistocene differentiation within each species, but temporally incongruent patterns among species.     

New species of Rhabdias (Nematoda: Rhabdiasidae) and other helminths from Norops capito (Sauria: Polychrotidae) from Nicaragua

Rhabdias nicaraguensis n. sp. (Rhabditida: Rhabditidae) from the lungs of Norops capito (Sauria: Polychrotidae) is described and illustrated. Rhabdias nicaraguensis n. sp. represents the 54th species assigned to the genus and the 12th from the Neotropical realm. Of the 12 Neotropical Rhabdias species, nicaraguensis is most similar to tobagoensis and vellardi. These 3 species have equatorial placement of the vulva, inflated cuticle, and 6 small circumoral lips. Rhabdias nicaraguensis is easily separated from R. tobagoensis by the shape of the buccal cavity and from R. vellardi by body size and shape of the tail. Rhabdias nicaraguensis differs from both species by host preference, the amount of inflated cuticle covering the body, and the phasmids situated posterior to the midpoint of the tail.     

Environmental habituation and sexual composition affect juveniles' shoaling activity in a cichlid fish (Pelvicachromis taeniatus)

Group living is widespread in animals, and many fishes form shoals. Examining within-group interactions in fishes may contribute to the general understanding of dynamic social structures in animals. The sex ratio of a group has been shown to influence grouping decisions of fishes and can be expected to affect behaviour at group level. Behavioural experiments usually involve relatively short acclimatisation times, although the establishment of environmental habituation in fishes is understudied. This study tests whether the sex ratio and long-term habituation to experimental conditions influence general shoal performance (activity parameters, density) and responses of shoals to an acoustic-mechanical disturbance cue in juveniles of the cichlid fish Pelvicachromis taeniatus via individual tracking. The disturbance consisted of a defined hit against the experimental tank, which caused sudden noise and water movement. We found that a higher proportion of females increases shoal activity (swimming speed and distance covered), suggesting that female P. taeniatus are more active than males. Furthermore, shoal activity declined when shoals habituated to the experimental settings and with the time that the shoals were grouped together, which may reflect intensified group member familiarity. Moreover, behavioural changes after disturbance were weaker when individuals were kept with their group longer and more familiar to the experimental conditions. For prey species, lower activity might be beneficial under natural conditions due to lower conspicuousness of the group. We did not find any significant effects of the investigated factors on shoal density (mean interindividual distance) and speed synchronisation. The results indicate that sexual composition, familiarity between shoal members and habituation to the experimental environment affect shoal performance in a cichlid fish.     

N2-fixation by methanotrophs sustains carbon and nitrogen accumulation in pristine peatlands

Symbiotic relationships between N₂-fixing prokaryotes and their autotrophic hosts are essential in nitrogen (N)-limited ecosystems, yet the importance of this association in pristine boreal peatlands, which store 25 % of the world’s soil (C), has been overlooked. External inputs of N to bogs are predominantly atmospheric, and given that regions of boreal Canada anchor some of the lowest rates found globally (~1 kg N ha^?1 year^?1), biomass production is thought to be limited primarily by N. Despite historically low N deposition, we show that boreal bogs have accumulated approximately 12–25 times more N than can be explained by atmospheric inputs. Here we demonstrate high rates of biological N₂-fixation in prokaryotes associated with Sphagnum mosses that can fully account for the missing input of N needed to sustain high rates of C sequestration. Additionally, N amendment experiments in the field did not increase Sphagnum production, indicating that mosses are not limited by N. Lastly, by examining the composition and abundance of N₂-fixing prokaryotes by quantifying gene expression of 16S rRNA and nitrogenase-encoding nifH, we show that rates of N₂-fixation are driven by the substantial contribution from methanotrophs, and not from cyanobacteria. We conclude biological N₂-fixation drives high sequestration of C in pristine peatlands, and may play an important role in moderating fluxes of methane, one of the most important greenhouse gases produced in peatlands. Understanding the mechanistic controls on biological N₂-fixation is crucial for assessing the fate of peatland carbon stocks under scenarios of climate change and enhanced anthropogenic N deposition.     

The evolution of antennal courtship in diplazontine parasitoid wasps (Hymenoptera,Ichneumonidae, Diplazontinae)

Background

As predicted by theory, traits associated with reproduction often evolve at a comparatively high speed. This is especially the case for courtship behaviour which plays a central role in reproductive isolation. On the other hand, courtship behavioural traits often involve morphological and behavioural adaptations in both sexes; this suggests that their evolution might be under severe constraints, for instance irreversibility of character loss. Here, we use a recently proposed method to retrieve data on a peculiar courtship behavioural trait, i.e. antennal coiling, for 56 species of diplazontine parasitoid wasps. On the basis of a well-resolved phylogeny, we reconstruct the evolutionary history of antennal coiling and associated morphological modifications to study the mode of evolution of this complex character system.

Results

Our study reveals a large variation in shape, location and ultra-structure of male-specific modifications on the antennae. As for antennal coiling, we find either single-coiling, double-coiling or the absence of coiling; each state is present in multiple genera. Using a model comparison approach, we show that the possession of antennal modifications is highly correlated with antennal coiling behaviour. Ancestral state reconstruction shows that both antennal modifications and antennal coiling are highly congruent with the molecular phylogeny, implying low levels of homoplasy and a comparatively low speed of evolution. Antennal coiling is lost on two independent occasions, and never reacquired. A zero rate of regaining antennal coiling is supported by maximum parsimony, maximum likelihood and Bayesian approaches.

Conclusions

Our study provides the first comparative evidence for a tight correlation between male-specific antennal modifications and the use of the antennae during courtship. Antennal coiling in Diplazontinae evolved at a comparatively low rate, and was never reacquired in any of the studied taxa. This suggests that the loss of antennal coiling is irreversible on the timescale examined here, and therefore that evolutionary constraints have greatly influenced the evolution of antennal courtship in this group of parasitoid wasps. Further studies are needed to ascertain whether the loss of antennal coiling is irreversible on larger timescales, and whether evolutionary constraints have influenced courtship behavioural traits in a similar way in other groups.