Middle Triassic conodont apparatus architecture revealed by synchrotron X-ray microtomography

The composition of conodont apparatuses is crucial for understanding the feeding mechanisms of these early vertebrates. However, the multielement apparatus reconstructions of most species remain equivocal because they have been inferred from loose element collections, guided by knowledge from rare articulated ‘bedding plane assemblages’ and fused clusters, often from distantly related taxa. Even these natural assemblages can be difficult to interpret because the component elements can be closely juxtaposed or embedded in matrix, making it hard to discern the morphology of each element and their relative positions within the architecture of the feeding apparatus. Here we report five exceptionally preserved conodont clusters from the Middle Triassic Luoping Biota, Yunnan Province, Southwest China. These materials were scanned using synchrotron radiation X-ray tomographic microscopy (SRXTM), revealing the morphology and positional homology of the component elements in the fused clusters. We confirm that the apparatus of Nicoraella was composed of eight types of elements, comprising a total of 15 elements. SRXTM reveals the positional homologies of the component elements, viz. a single alate element is located in the S₀ position, flanked successively abaxially by pairs of breviform digyrate S₁ and S₂ elements, bipennate S₃ and S₄ elements, and a pair of inwardly curved breviform digyrate M elements. Carminate elements occupy the P₁ and P₂ positions. The apparatus of Nicoraella is among the most completely characterised of all conodonts and serves as a template for the reconstruction of gondollellids.     

Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents

This study is the first large‐scale genetic population study of a widespread climax species of seagrass, Thalassia hemprichii, in the Western Indian Ocean (WIO). The aim was to understand genetic population structure and connectivity of T. hemprichii in relation to hydrodynamic features. We genotyped 205 individual seagrass shoots from 11 sites across the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite markers. Seagrass shoots were sampled in Kenya, Tanzania (mainland and Zanzibar), Mozambique, and Madagascar: 4–26°S and 33–48°E. We assessed clonality and visualized genetic diversity and genetic population differentiation. We used Bayesian clustering approaches (TESS) to trace spatial ancestry of populations and used directional migration rates (DivMigrate) to identify sources of gene flow. We identified four genetically differentiated groups: (a) samples from the Zanzibar channel; (b) Mozambique; (c) Madagascar; and (d) the east coast of Zanzibar and Kenya. Significant pairwise population genetic differentiation was found among many sites. Isolation by distance was detected for the estimated magnitude of divergence (D_EST), but the three predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) also determine genetic connectivity and genetic structure. Directional migration rates indicate that Madagascar acts as an important source population. Overall, clonality was moderate to high with large differences among sampling sites, indicating relatively low, but spatially variable sexual reproduction rates. The strongest genetic break was identified for three sites in the Zanzibar channel. Although isolation by distance is present, this study suggests that the three regionally predominant ocean current systems (i.e., East African Coastal Current, North East Madagascar Current, and the South Equatorial Current) rather than distance determine genetic connectivity and structure of T. hemprichii in the WIO. If the goal is to maintain genetic connectivity of T. hemprichii within the WIO, conservation planning and implementation of marine protection should be considered at the regional scale—across national borders.     

Deciphering the global phylogeography of a coastal shrub (Scaevola taccada) reveals the influence of multiple forces on contemporary population structure

The phylogeography of coastal plant species is heavily influenced by past sealevel fluctuations, dispersal barriers, and life-history traits, such as long-distance dispersal ability of the propagules. Unlike the widely studied mangroves, phylogeographic patterns have remained mostly obscure for other coastal plant species. In this study, we sampled 42 populations of Scaevola taccada (Gaertn.) Roxb., a coastal shrub of the family Goodeniaceae, from 17 countries across its distribution range. We used five chloroplast DNA (cpDNA) and 14 nuclear microsatellite (simple sequence repeat [SSR]) markers to assess the influence of abiotic factors and population genetic processes on the phylogeographic pattern of the species. Geographical distribution of cpDNA haplotypes suggests that the species originated in Australia, followed by historical dispersal and expansion of its geographic range. Multiple abiotic factors, including the sealevel changes during the Pleistocene, the presence of landmasses like the Malay Peninsula, and contemporary oceanic circulation patterns, restricted gene flow between geographically distinct populations, thereby creating low haplotype diversity and a strong population structure. Population genetic processes acted on these isolated populations, leading to high nuclear genetic diversity and population differentiation, as revealed from analyzing the polymorphic SSR loci. Although genetic divergence was mostly concordant between cpDNA and SSR data, asymmetrical gene flow and ancestral polymorphism could explain the discordance in the detailed genetic structure. Overall, our findings indicate that abiotic factors and population genetic processes interactively influenced the evolutionary history and current phylogeographic pattern of S. taccada across its distribution range.     

The chromosome-scale assembly of the Canary Islands endemic spider Dysdera silvatica (Arachnida,Araneae) sheds light on the origin and genome structure of chemoreceptor gene families in chelicerates

Here, we present the chromosome-level genome assembly of Dysdera silvatica Schmidt, 1981, a nocturnal ground-dwelling spider endemic from the Canary Islands. The genus Dysdera has undergone a remarkable diversification in this archipelago mostly associated with shifts in the level of trophic specialization, becoming an excellent model to study the genomic drivers of adaptive radiations. The new assembly (1.37 Gb; scaffold N50 of 174.2 Mb), was performed using the chromosome conformation capture scaffolding technique, represents a continuity improvement of more than 4500 times with respect to the previous version. The seven largest scaffolds or pseudochromosomes, which cover 87% of the total assembly size, probably correspond with the seven chromosomes of the karyotype of this species, including a characteristic large X chromosome. To illustrate the value of this new resource we performed a comprehensive analysis of the two major arthropod chemoreceptor gene families (i.e., gustatory and ionotropic receptors). We identified 545 chemoreceptor sequences distributed across all pseudochromosomes, with a notable underrepresentation in the X chromosome. At least 54% of them localize in 83 genomic clusters with a significantly lower evolutionary distances between them than the average of the family, suggesting a recent origin of many of them. This chromosome-level assembly is the first high-quality genome representative of the Synspermiata clade, and just the third among spiders, representing a new valuable resource to gain insights into the structure and organization of chelicerate genomes, including the role that structural variants, repetitive elements and large gene families played in the extraordinary biology of spiders.     

Urbanization and Mismatch with Protected Areas Place the Conservation of a Threatened Species at Risk

In this work, we report the predicted distribution of the threatened fluminense swallowtail butterfly, Parides ascanius (Cramer 1775), and correlate it to the presence of urban and protected areas within its range. The distribution was modeled using a genetic algorithm. The predicted distribution of the fluminense swallowtail shows high agreement within Rio de Janeiro state, in a near-continuous strip of 2,038,253 ha along the coastal lowlands, 17.8 percent of which is within urban areas. Only 8.7 percent (178,187 ha) of the remaining (nonurban) predicted model overlapped at least partially with protected areas (19 in all). Almost half of these protected areas also overlapped with urban areas, resulting in an additional loss of 58,751 ha. In seven of 19 protected areas, the distribution of P. ascanius was predicted by less than 50 percent of the models; five of the remaining protected areas are less restrictive reserves. Despite the wide distribution predicted by the models, only two of the observed occurrence points matched the predicted distribution within protected areas. Modeling threatened species distribution is a useful tool for highlighting gaps in networks of protected areas and should aid in planning to fill these gaps. However, in several developing countries with high biodiversity, there is insufficient basic biological information for many threatened species. In these cases, prospecting field studies are urgently needed.     

Positioning of the mouse Hox gene clusters in the nuclei of developing embryos and differentiating embryoid bodies

Expression of Hox genes located on different chromosomes is precisely regulated and synchronized during development. In order to test the hypothesis that the Hox loci might cluster in nuclear space in order to share regulatory components, we performed 3D FISH on cryosections of developing mouse embryos and differentiating embryoid bodies. We did not observe any instances of co-localization of 4 different Hox alleles. Instances of 2 different alleles touching each other were found in 20-47% of nuclei depending on the tissue. The frequency of such “kissing” events was not significantly different in cells expressing a high proportion of the Hox clusters when compared to cells expressing none or only a few Hox genes. We found that the HoxB and HoxC clusters, which are located in gene-rich regions, were involved more frequently in gene kissing in embryonic nuclei. In the case of HoxB, this observation correlated with the positioning of the corresponding chromosome towards the interior of the nucleus. Our results indicate that co-regulation of the different Hox clusters is not associated with co-localization of the loci at a single regulatory compartment and that the chromosomal context may influence the extent to which they contact each other in the nucleus.     

Eco-efficiency of urban material metabolism: a case study in Shenzhen, China

The keys of studying urban sustainable development are material metabolism flux and efficiency. Metabolism flux of urban materials can only reflect the metabolism velocity, while its eco-efficiency can determine the metabolism capacity to support socio-economic development. The general model and the measure model of the eco-efficiency were set up, based on the source recycle (decreasing the consumption of crude resources) and the terminal recycle (decreasing the discharge of pollutants) of production and life. These models were employed to study material metabolism flux and efficiency in Shenzhen, China. Results showed that water, energy and waste metabolism fluxes have increased since 1998 with constant socio-economic development, and their eco-efficiencies have also increased rapidly. When GDP rose by 2.7 times, the metabolism fluxes of urban water and electricity rose by 1.5 and 3.0 times, respectively. When the added value of industry rose by 3.7 times, the metabolism fluxes of industrial water, electricity, energy and waste rose by 1.9, 3.5, 2.7 and 2.0 times, respectively. When population rose by 1.5 times, the metabolism fluxes of residential water and electricity rose by 1.8 and 1.7 times, respectively. During the period, the resource efficiency, environmental efficiency and eco-efficiency rose by 1.8, 3.7 and 2.3 times, respectively. Whereas the efficiency of material metabolism has been improved in Shenzhen, the scarcity of material resources has become more and more serious. Therefore, it is necessary to further improve the efficiency of material metabolism. The keys of improving the eco-efficiency of urban material metabolism are the increasing of resource and environmental efficiencies, and the establishing of the recycling chain of re-utilization of waste resources.     

Low-salinity transitions drive abrupt microbial response to sea-level change

The salinisation of many coastal ecosystems is underway and is expected to continue into the future because of sea-level rise and storm intensification brought about by the changing climate. However, the response of soil microbes to increasing salinity conditions within coastal environments is poorly understood, despite their importance for nutrient cascading, carbon sequestration and wider ecosystem functioning. Here, we demonstrate deterioration in the productivity of a top-tier microbial group (testate amoebae) with increasing coastal salinity, which we show to be consistent across phylogenetic groups, salinity gradients, environment types and latitude. Our results show that microbial changes occur in the very early stages of marine inundation, presaging more radical changes in soil and ecosystem function and providing an early warning of coastal salinisation that could be used to improve coastal planning and adaptation.     

Spit it out: Monkeys disperse the unorthodox and toxic seeds of Clivia miniata (Amaryllidaceae)

Seeds of many Amaryllidaceae are unorthodox (recalcitrant) and toxic, and cannot survive ingestion, yet are packaged in brightly colored fruits suggestive of zoochory. Seed dispersal and germination of the understory amaryllid, Clivia miniata, were investigated in KwaZulu‐Natal, South Africa. Motion‐activated cameras revealed that samango monkeys (Cercopithecus mitis labiatus) are the primary disperser of C. miniata seeds. They eat the mesocarp and, to a lesser extent, the exocarp, and spit the large (13 mm diameter) seeds whole and cleaned onto the forest floor. Most seeds were dispersed farther than 1 m from the parent. Experimental removal of the fruit pulp had a small positive effect on the rate of seed germination, but did not affect subsequent seedling growth rates. The main advantages of monkey dispersal of Clivia seeds appear to be short‐distance dispersal away from the dense foliage of clumped parent plants and occasional long‐distance dispersal through cheek‐pouching behavior.     

基于COⅠ基因对温州沿海岛屿疣荔枝螺遗传多样性研究

温州沿海岛屿众多,水文环境复杂,疣荔枝螺（Reishia clavigera）是岩相潮间带常见种,对其群体间遗传多样性的分析,有助于合理保护和开发利用种质资源。本实验对温州沿海14个典型岛屿的158个疣荔枝螺个体,进行细胞色素氧化酶亚基Ⅰ（COⅠ）基因片段序列测定,得到158 条长度为672 bp的序列,A、T、C、G 四种碱基含量分别为23.0%、38.4%、17.4%和21.2%。共检测到保守位点562个,变异位点108 个,其中包括简约信息位点57 个,单突变位点51 个。所有个体的核苷酸多样性指数Pi为0.008 0 ± 0.029 7,单倍型多样性为指数Hd为0.978 ± 0.006,平均核苷酸差异度为5.328。群体间遗传距离在0.005 7 ~ 0.011 1之间,群体内遗传距离在0.005 7 ~ 0.010 8之间,不同疣荔枝螺群体之间的遗传距离处于同一水平。霓屿岛和大竹峙岛群体内遗传距离最小,洞头岛群体内遗传距离最大。共检测到102 个单倍型,大部分单倍型聚合为一支,没有形成明显的区系结构,各个岛屿的疣荔枝螺存在基因交流。