Attempting genetic inference from directional asymmetry during convergent hindlimb reduction in squamates

Loss and reduction in paired appendages are common in vertebrate evolution. How often does such convergent evolution depend on similar developmental and genetic pathways? For example, many populations of the threespine stickleback and ninespine stickleback (Gasterosteidae) have independently evolved pelvic reduction, usually based on independent mutations that caused reduced Pitx1 expression. Reduced Pitx1 expression has also been implicated in pelvic reduction in manatees. Thus, hindlimb reduction stemming from reduced Pitx1 expression has arisen independently in groups that diverged tens to hundreds of millions of years ago, suggesting a potential for repeated use of Pitx1 across vertebrates. Notably, hindlimb reduction based on the reduction in Pitx1 expression produces left‐larger directional asymmetry in the vestiges. We used this phenotypic signature as a genetic proxy, testing for hindlimb directional asymmetry in six genera of squamate reptiles that independently evolved hindlimb reduction and for which genetic and developmental tools are not yet developed: Agamodon anguliceps, Bachia intermedia, Chalcides sepsoides, Indotyphlops braminus, Ophisaurus attenuatuas and O. ventralis, and Teius teyou. Significant asymmetry occurred in one taxon, Chalcides sepsoides, whose left‐side pelvis and femur vestiges were 18% and 64% larger than right‐side vestiges, respectively, suggesting modification in Pitx1 expression in that species. However, there was either right‐larger asymmetry or no directional asymmetry in the other five taxa, suggesting multiple developmental genetic pathways to hindlimb reduction in squamates and the vertebrates more generally.     

富营养化河水灌溉对稻田土壤氮磷养分贡献的影响——以太湖地区黄泥土为例

以太湖地区主要稻田土壤类型黄泥土为对象,利用当地富营养化河水对回填土柱和植稻原状土渗漏池进行模拟稻田灌溉试验,系统研究了灌溉水对稻田土壤氮磷营养的贡献.在回填土柱灌溉试验中,在试验初期,不同形态的氮素均有较高的淋失量,以后逐渐降低,表明初期淋失的氮素主要来自土壤,而不是灌溉河水.在整个水稻生长季,均观测到有可溶性有机氮淋失,表明富营养化河水灌溉条件下可溶性有机氮是稻田土壤主要的氮素淋失形态.在本试验中,磷素的淋失动态与氮素的淋失动态截然相反,淹水后很长一段时间内均没有土壤磷素淋失,但在淹水灌溉后期有大量的土壤磷素淋失损失,这可能是淹水后期土壤对磷的吸持已达到饱和状态,不能继续固持土壤中多余的磷所致.与回填土柱模拟灌溉淋洗试验相比,在当前供肥条件下,原状土渗漏池试验氮磷淋失量远低于回填土柱试验,而灌溉水对土壤氮磷养分的贡献远高于回填土柱.通过富营养化河水灌溉带入当季稻田的N量达到每公顷56.3 kg,其中有55.8 kg N可被土壤吸持和作物吸收,表明太湖地区稻田土壤对氮磷养分来说是一个环境友好的生态系统.在利用当地富营养化河水进行稻田土壤灌溉时可适量减少肥料施用量、优化氮磷肥料管理.     

Population dynamics of the Smith's red-backed vole in highlands of Shikoku

Population dynamics of theSmith 's red-backed vole predominantly common through uplands of Shikoku have been in some degree disclosed by the use of my own and Government Forest Station's samples collected since 1955 onward. It has proved that the upper-range population reaches its density peak possibly in late summer or early fall, but the lower-range one does probably in October–November as the seasonal trend in usual years. The upper one produced a peak three times at 3–4 year intervals, the first peak being an outbreak followed by a crash, during the last decade. It seems likely that all the populations through the range have, in the gross, fluctuated in phase after 1959 at least. The cyclic fluctuation may readily be explained by the theory of intrinsic mechanism, because no external factors are considered to have exerted a conclusive effect. Except what was concerned in the outbreak, the role of the social stress could be set at naught. The regulation of fecundiy by density was expressed more markedly in litter size and less in active reproductivity rate and incidence of pregnancy. The mean litter size at term as small as 2.00 is contrary to our expectation in view of the supposed prolific potential, nevertheless the observed frequency of litter poduction and intra-uterine survival rate has proved not to be so high as to make up for the small litter size. The problem in the postnatal mortality has remained to be solved.     

Sexual signal loss in field crickets maintained despite strong sexual selection favoring singing males

Evolutionary biologists commonly seek explanations for how selection drives the emergence of novel traits. Although trait loss is also predicted to occur frequently, few contemporary examples exist. In Hawaii, the Pacific field cricket (Teleogryllus oceanicus) is undergoing adaptive sexual signal loss due to natural selection imposed by eavesdropping parasitoids. Mutant male crickets (“flatwings”) cannot sing. We measured the intensity of sexual selection on wing phenotype in a wild population. First, we surveyed the relative abundance of flatwings and “normal‐wings” (nonmutants) on Oahu. Then, we bred wild‐mated females’ offspring to determine both female genotype with respect to the flatwing mutation and the proportion of flatwing males that sired their offspring. We found evidence of strong sexual selection favoring the production of song: females were predominantly homozygous normal‐wing, their offspring were sired disproportionately by singing males, and at the population level, flatwing males became less common following a single sexual selection event. We report a selection coefficient describing the total (pre‐ and postcopulatory) sexual selection favoring normal‐wing males in nature. Given the maintenance of the flatwing phenotype in Hawaii in recent years, this substantial sexual selection additionally suggests an approximate strength of opposing natural selection that favors silent males.     

Does mixed-species flocking influence how birds respond to a gradient of land-use intensity?

Conservation biology is increasingly concerned with preserving interactions among species such as mutualisms in landscapes facing anthropogenic change. We investigated how one kind of mutualism, mixed-species bird flocks, influences the way in which birds respond to different habitat types of varying land-use intensity. We use data from a well-replicated, large-scale study in Sri Lanka and the Western Ghats of India, in which flocks were observed inside forest reserves, in ‘buffer zones'' of degraded forest or timber plantations, and in areas of intensive agriculture. We find flocks affected the responses of birds in three ways: (i) species with high propensity to flock were more sensitive to land use; (ii) different flock types, dominated by different flock leaders, varied in their sensitivity to land use and because following species have distinct preferences for leaders, this can have a cascading effect on followers'' habitat selection; and (iii) those forest-interior species that remain outside of forests were found more inside flocks than would be expected by chance, as they may use flocks more in suboptimal habitat. We conclude that designing policies to protect flocks and their leading species may be an effective way to conserve multiple bird species in mixed forest and agricultural landscapes.     

Identifying new sex-linked genes through BAC sequencing in the dioecious plant Silene latifolia

Background

Silene latifolia represents one of the best-studied plant sex chromosome systems. A new approach using RNA-seq data has recently identified hundreds of new sex-linked genes in this species. However, this approach is expected to miss genes that are either not expressed or are expressed at low levels in the tissue(s) used for RNA-seq. Therefore other independent approaches are needed to discover such sex-linked genes.

Results

Here we used 10 well-characterized S. latifolia sex-linked genes and their homologs in Silene vulgaris, a species without sex chromosomes, to screen BAC libraries of both species. We isolated and sequenced 4 Mb of BAC clones of S. latifolia X and Y and S. vulgaris genomic regions, which yielded 59 new sex-linked genes (with S. vulgaris homologs for some of them). We assembled sequences that we believe represent the tip of the Xq arm. These sequences are clearly not pseudoautosomal, so we infer that the S. latifolia X has a single pseudoautosomal region (PAR) on the Xp arm. The estimated mean gene density in X BACs is 2.2 times lower than that in S. vulgaris BACs, agreeing with the genome size difference between these species. Gene density was estimated to be extremely low in the Y BAC clones. We compared our BAC-located genes with the sex-linked genes identified in previous RNA-seq studies, and found that about half of them (those with low expression in flower buds) were not identified as sex-linked in previous RNA-seq studies. We compiled a set of ~70 validated X/Y genes and X-hemizygous genes (without Y copies) from the literature, and used these genes to show that X-hemizygous genes have a higher probability of being undetected by the RNA-seq approach, compared with X/Y genes; we used this to estimate that about 30 % of our BAC-located genes must be X-hemizygous. The estimate is similar when we use BAC-located genes that have S. vulgaris homologs, which excludes genes that were gained by the X chromosome.

Conclusions

Our BAC sequencing identified 59 new sex-linked genes, and our analysis of these BAC-located genes, in combination with RNA-seq data suggests that gene losses from the S. latifolia Y chromosome could be as high as 30 %, higher than previous estimates of 10-20 %.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1698-7) contains supplementary material, which is available to authorized users.     

荒漠区地表凋落物分解对季节性降水增加的响应

为探讨季节性降水增加对荒漠生态系统凋落物分解的影响, 在古尔班通古特沙漠南缘, 选择粗柄独尾草(Eremurus inderiensis)叶、尖喙牻牛儿苗(Erodium oxyrrhynchum)叶、尖喙牻牛儿苗茎、沙漠绢蒿(Seriphidium santolinum)茎4种凋落物样品, 在2009-2011年研究了模拟季节降水增加(冬春增雪、夏季增水)和自然降水处理下凋落物的分解。持续2年的分解实验表明: (1)各组分凋落物的质量损失过程可以用负指数衰减方程较好地拟合(R²> 0.90); 经过637天的分解, 各组分凋落物质量残留率在自然降水、冬春增雪、夏季增水处理下均无显著性差异(p > 0.05)。粗柄独尾草叶、尖喙牻牛儿苗叶、尖喙牻牛儿苗茎、沙漠绢蒿茎在自然降水处理下的质量残留率分别为40.59%、35.50%、36.00%和63.96%; (2)各组分凋落物的质量残留率与N残留率显著正相关, 凋落物N的损失快于其质量损失, 且初始N含量与分解速率显著正相关(r = 0.60, p = 0.038), C/N解释了71%的地面凋落物分解速率。研究表明, 季节性的短暂降水增加对荒漠区地表凋落物分解没有显著影响, 凋落物初始化学组成是预测荒漠区地表凋落物分解的重要因素。     

水稻砷污染及其对砷的吸收和代谢机制

水稻是当今世界大部分地区(尤其是东南亚)的主要的粮食作物之一,同时也是砷(As)进入食物链的主要途径之一。日益严重的水稻田As污染,不但影响了稻米的产量和品质,而且通过食物链威胁着人体健康。如何减少水稻地上部(尤其是米粒)As的含量和降低其毒性,及提高水稻As耐性是亟需解决的世界食品安全问题。深入了解水稻对As的吸收、积累和代谢的生理及分子生物学机制是解决水稻As污染的关键途径。综述国内外研究,对今后深入研究提出建议。     

黄土高原生态分区及概况

黄土高原地域广阔,水土流失区域差异显著。为了有效治理水土流失,评估水土流失治理技术和模式及生态恢复建设工程的成效性,需要对黄土高原进行区域划分。依据自然条件、水土流失治理技术和模式的区域性特征及差异,基于国家基础地理信息系统数据的县级行政界,对其进行合并,进行生态分区的划分,并分别统计其气候、地形地貌、植被特征及水土流失现状,以期为黄土高原水土流失治理技术和模式的改良优化提供依据。主要结论如下:(1)黄土高原分为黄土高塬沟壑区,黄土丘陵沟壑区,沙地和农灌区,土石山区及河谷平原区。其中黄土高塬沟壑区和黄土丘陵沟壑区分别划分为两个副区。(2)黄土高原的气候、植被、水土流失具有明显的分区差异。降水和植被覆盖度自东南向西北递减,二者在空间分布上具有很好的一致性,降水量大的分区,植被覆盖度也高。在年际变化方面,丘陵沟壑区B2副区降水量呈增加趋势,其他分区呈减小趋势,变化均不显著。80年代以来,黄土高原和各生态分区的植被覆盖度均逐渐增加,黄土丘陵沟壑区的增加量最大。各分区的面平均气温均呈非显著增加趋势,90年代以来增温明显。(3)1970年以来,黄土高原侵蚀产沙强度减弱趋势显著,至2002—2015年,多年平均输沙模数在0.13—3924 t km~(-2) a~(-1)之间,侵蚀强度最大为中度侵蚀(2500—5000 t km~(-2) a~(-1)),但面积较小,主要分布于第二高塬沟壑区的泾河流域。