Geographically contrasting biodiversity reductions in a widespread New Zealand seabird

Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the impacts of human arrival on this taxon. Our analyses show that the southeast South Island (Otago) lineage was formerly widespread across coastal South Island, but experienced dramatic population extinctions, range retraction and lineage loss soon after human arrival. By comparison, the southernmost (Foveaux Strait) lineage has experienced a relatively stable demographic and biogeographic history since human arrival, retaining much of its mitochondrial diversity. Archaeological data suggest that these contrasting demographic histories (retraction vs. stability) reflect differential human impacts in mainland South Island vs. Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human‐driven faunal declines.     

Geographically widespread mitochondrial lineages of the African saw-wings inconsistent with species boundaries

The African saw-wings (genus Psalidoprocne) are a group of swallows endemic to sub-Saharan Africa. Although currently described as five species with several subspecies, the taxonomy of the saw-wings is unclear. We sequenced two mitochondrial genes (ND2 and cytb; 1 717 sites) from 20 individuals in order to investigate phylogenetic relationships across the range of Psalidoprocne. We obtained similar results from maximum likelihood (RAxML) and Bayesian (BEAST) phylogenetic analyses, which reveal multiple well-supported mitochondrial clades in the genus. The geographic overlap of distinct lineages suggests reproductive isolation, although these clades do not correspond entirely to current species designations.     

Faunal standards for the restoration of terrestrial ecosystems: a framework and its application to a high-profile case study

Assessments of ecosystem restoration have traditionally focused on soil and vegetation, often with little consideration of fauna. It is critical to include fauna in such assessments, not just because of their intrinsic biodiversity value but also because of the many ecological roles that animals play in restoration processes. However, a widely accepted framework for specifying faunal standards for restoration is lacking. Here we present such a framework, incorporating: (1) the identification of appropriate reference conditions; (2) the taxa to be targeted for assessment; (3) the attributes of these taxa to be measured; (4) acceptable similarity with reference conditions; and (5) robust sampling methodologies for reliable assessment. We illustrate this framework using the restoration program at Ranger Uranium Mine in the Australian seasonal tropics, which aims to establish an environment similar to the surrounding World Heritage-listed Kakadu National Park, corresponding to “full recovery” according to Society for Ecosystem Restoration's standards. Our case study has especially high restoration standards, but our framework has wide applicability to the specification of faunal standards for ecosystem restoration.     

Parameter identification for a stochastic SEIRS epidemic model: case study influenza

Journal of Mathematical Biology - A recent parameter identification technique, the local lagged adapted generalized method of moments, is used to identify the time-dependent disease transmission...     

上升性理论在经济系统中的应用——以甘肃省为例

如何定量地判断增长与发展之间的关系,是生态学、经济学及可持续发展相关学科讨论的一个重要问题。Ulanowicz从生态系统的角度出发,提出用上升性这个宏观指标对增长与发展进行定量描述。以甘肃省为例讨论了上升性理论在经济系统中的应用。研究结果表明,在1987～1995年甘肃省系统总吞吐量(实物型)年均增加6.30%,上升性(A)增加近2倍,但是平均相互信息却从0.460比特降到0.336比特,这表明在这8a间甘肃省处于不可持续的发展状况。在1995～2002年,甘肃省系统总吞吐量(实物型)仍不断增加,但年均增加率从1987～1995年的6.30%降到2.13%,上升性(A)增加了2倍多,平均相互信息从0.336比特增加到0.499比特,这表明在这7a间甘肃省朝着可持续的方向发展。根据Ulanowicz对系统进化阶段的划分,甘肃省在1987～2002年处于增长阶段即处于进化的初级阶段。对研究结果的分析表明,要实现甘肃省的可持续发展,需提高资源的利用效率,实现资源的循环利用,并加强资源在部门之间的流通性及分配的公平性。     

The use of neural networks to aid in microorganism identification: a case study ofHaemophilus species identification

The adipamidase of a mutant strainBrevibacterium sp. R312 involved in the degradation of adiponitrile to adipic acid was purified. Its N-terminal amino acid sequence was shown to be identical toBrevibacterium sp. R312 enantio-selective amidase andRhodococcus sp. N-774 amidase.     

Molecular resolution of marine turtle stock composition in fishery bycatch: a case study in the Mediterranean

Based on an extensive sampling regime from both nesting populations and bycatch, frequency analyses of mitochondrial (mt) DNA control region haplotypes in the Mediterranean were used to assess the genetic structure and stock composition of the loggerhead sea turtle, Caretta caretta, in different marine fisheries. The analyses show the following. (i) In drifting longline fisheries working in Mediterranean pelagic habitats 53–55% of turtles caught originated from the Mediterranean stock; (ii) In bottom-trawl fisheries all turtle bycatch is derived from this regional stock; (iii) This regional stock contribution to fishery bycatch suggests that the population size of the Mediterranean loggerhead nesting population is significantly larger than previously thought. This is consistent with a recent holistic estimate based on the discovery of a large rookery in Libya. (iv) Present impact of fishery-related mortality on the Mediterranean nesting population is probably incompatible with its long-term conservation. Sea turtle conservation regulations are urgently needed for the Mediterranean fisheries. (v) The significant divergence of mtDNA haplotype frequencies of the Turkish loggerhead colonies define this nesting population as a particularly important management unit. Large immature and adult stages from this management unit seem to be harvested predominantly by Egyptian fisheries. (vi) Combined with other data, our findings suggest that all the nesting populations in the Mediterranean should be considered as management units sharing immature pelagic habitats throughout the Mediterranean (and possibly the eastern Atlantic), with distinct and more localized benthic feeding habitats in the eastern basin used by large immatures and adults. (vii) Between the strict oceanic pelagic and the benthic stages, immature turtles appear to live through an intermediate neritic stage, in which they switch between pelagic and benthic foods.     

Genetic identification of source and likely vector of a widespread marine invader

The identification of native sources and vectors of introduced species informs their ecological and evolutionary history and may guide policies that seek to prevent future introductions. Population genetics provides a powerful set of tools to identify origins and vectors. However, these tools can mislead when the native range is poorly sampled or few molecular markers are used. Here, we traced the introduction of the Asian seaweed Gracilaria vermiculophylla (Rhodophyta) into estuaries in coastal western North America, the eastern United States, Europe, and northwestern Africa by genotyping more than 2,500 thalli from 37 native and 53 non‐native sites at mitochondrial cox1 and 10 nuclear microsatellite loci. Overall, greater than 90% of introduced thalli had a genetic signature similar to thalli sampled from the coastline of northeastern Japan, strongly indicating this region served as the principal source of the invasion. Notably, northeastern Japan exported the vast majority of the oyster Crassostrea gigas during the 20th century. The preponderance of evidence suggests G. vermiculophylla may have been inadvertently introduced with C. gigas shipments and that northeastern Japan is a common source region for estuarine invaders. Each invaded coastline reflected a complex mix of direct introductions from Japan and secondary introductions from other invaded coastlines. The spread of G. vermiculophylla along each coastline was likely facilitated by aquaculture, fishing, and boating activities. Our ability to document a source region was enabled by a robust sampling of locations and loci that previous studies lacked and strong phylogeographic structure along native coastlines.     

An analysis of genetic stock identification on a small geographical scale using microsatellite markers,and its application in the management of a mixed‐stock fishery for Atlantic salmon Salmo salar in Ireland

A genetic stock identification (GSI) study was undertaken in a fishery for Atlantic salmon Salmo salar to determine the effects of restrictive fishery management measures on the stock composition of the fishery, and if accurate and precise stock composition estimates could be achieved on the small geographical scale where this fishery operates, using a suite of only seven microsatellite loci. The stock composition of the Foyle fishery was shown to comprise almost exclusively of Foyle origin fish in the 3 years after restrictive measures were introduced in 2007, compared to 85% the year before. This showed that the restrictive measures resulted in the Foyle fishery being transformed from a mixed‐stock fishery to an almost exclusively single‐stock fishery, and showed how GSI studies can guide and evaluate management decisions to successfully manage these fisheries. Highly accurate and precise stock composition estimates were achieved in this study, using both cBAYES and ONCOR genetic software packages. This suggests accurate and precise stock composition is possible even on small geographical scales.     

生态系统生产总值核算制度及管理应用——以深圳为例

“两山”理念提升了我国各级各地政府对生态价值的认识和重视,自然资本核算在全球学界研究及应用已进入新的阶段。如何开展常态化的核算与应用,如何将科研分析转化为管理制度,成为该领域新的研究命题。深圳积极响应中央政府要求,开展生态系统服务价值核算,服务生态治理,在全国（乃至全球）率先制定了第一个政府生态系统生产总值（GEP）核算制度体系。介绍了深圳GEP核算制度体系的建设过程,描述了深圳GEP核算的主要特点,以及"十三五"期间（2016-2020年）深圳GEP试算的结果,讨论了深圳GEP在城市治理方面的应用路径。     

JUMPptm: Integrated software for sensitive identification of post-translational modifications and its application in Alzheimer's disease study

Background : Mass spectrometry (MS)-based proteomic analysis of posttranslational modifications (PTMs) usually requires the pre-enrichment of modified proteins or peptides. However, recent ultra-deep whole proteome profiling generates millions of spectra in a single experiment, leaving many unassigned spectra, some of which may be derived from PTM peptides. Methods : Here we present JUMPptm, an integrative computational pipeline, to extract PTMs from unenriched whole proteome. JUMPptm combines the advantages of JUMP, MSFragger and Comet search engines, and includes de novo tags, customized database search and peptide filtering, which iteratively analyzes each PTM by a multi-stage strategy to improve sensitivity and specificity. Results : We applied JUMPptm to the deep brain proteome of Alzheimer's disease (AD), and identified 34,954 unique peptides with phosphorylation, methylation, acetylation, ubiquitination, and others. The phosphorylated peptides were validated by enriched phosphoproteome from the same sample. TMT-based quantification revealed 482 PTM peptides dysregulated at different stages during AD progression. For example, the acetylation of numerous mitochondrial proteins is significantly decreased in AD. A total of 60 PTM sites are found in the pan-PTM map of the Tau protein. Conclusion : The JUMPptm program is an effective tool for pan-PTM analysis and the resulting AD pan-PTM profile serves as a valuable resource for AD research.     

Computational identification of three-way junctions in folded RNAs: a case study in Arabidopsis

Three-way junctions in folded RNAs have been investigated both experimentally and computationally. The interest in their analysis stems from the fact that they have significantly been found to possess a functional role. In recent work, three-way junctions have been categorized into families depending on the relative lengths of the segments linking the three helices. Here, based on ideas originating from computational geometry, an algorithm is proposed for detecting three-way junctions in data sets of genes that are related to a metabolic pathway of interest. In its current implementation, the algorithm relies on a moving window that performs energy minimization folding predictions, and is demonstrated on a set of genes that are involved in purine metabolism in plants. The pattern matching algorithm can be extended to other organisms and other metabolic cycles of interest in which three-way junctions have been or will be discovered to play an important role. In the test case presented here with, the computational prediction of a three-way junction in Arabidopsis that was speculated to have an interesting functional role is verified experimentally.     

Design of character‐based DNA barcode motif for species identification: A computational approach and its validation in fishes

The DNA barcodes are generally interpreted using distance‐based and character‐based methods. The former uses clustering of comparable groups, based on the relative genetic distance, while the latter is based on the presence or absence of discrete nucleotide substitutions. The distance‐based approach has a limitation in defining a universal species boundary across the taxa as the rate of mtDNA evolution is not constant throughout the taxa. However, character‐based approach more accurately defines this using a unique set of nucleotide characters. The character‐based analysis of full‐length barcode has some inherent limitations, like sequencing of the full‐length barcode, use of a sparse‐data matrix and lack of a uniform diagnostic position for each group. A short continuous stretch of a fragment can be used to resolve the limitations. Here, we observe that a 154‐bp fragment, from the transversion‐rich domain of 1367 COI barcode sequences can successfully delimit species in the three most diverse orders of freshwater fishes. This fragment is used to design species‐specific barcode motifs for 109 species by the character‐based method, which successfully identifies the correct species using a pattern‐matching program. The motifs also correctly identify geographically isolated population of the Cypriniformes species. Further, this region is validated as a species‐specific mini‐barcode for freshwater fishes by successful PCR amplification and sequencing of the motif (154 bp) using the designed primers. We anticipate that use of such motifs will enhance the diagnostic power of DNA barcode, and the mini‐barcode approach will greatly benefit the field‐based system of rapid species identification.     

Stable isotope analyses in otoliths of silver carp: a pilot study in identification of natal sources and stock differences

Silver carp, Hypophthalmichthys molitrix, is one of the four major fishes in China for fishing and aquaculture. The Yangtze River and associated waterbodies are important home to silver carp. In this study, we collected 135 otoliths of juvenile silver carp from the two rivers and the Poyang Lake, and analyzed for stable oxygen and carbon isotope ratios (δ¹⁸O and δ¹³C). The isotopic data and correlation of δ¹⁸O versus δ¹³C showed a clear separation and significant differences (p?<?0.001 for both δ¹³C and δ¹⁸O) between otoliths from the Ganjiang River and the Yangtze River at δ¹⁸O values around ?10‰. The Poyang Lake samples were overlapped with those of the Ganjiang River, but distinctly different from the Yangtze River samples. These isotopic signatures agree well with the previous genetic investigation results that there are marked distinctions between one population in the Ganjiang River and the other in the Yangtze River, and the Poyang Lake population belongs to the Ganjiang River rather than to the Yangtze River. Thus we concluded that stable isotope analyses of otoliths can be effectively used to study natal sources and stock differences of silver carp.     

The gnd gene of Buchnera as a new,effective DNA barcode for aphid identification

DNA barcoding uses a standard DNA sequence to facilitate species identification. Although the COI gene has been adopted as the standard, COI alone is imperfect due to several shortcomings. The primary endosymbiont of aphids, Buchnera, has higher evolutionary rates and interspecies divergence than its co‐diverging aphid hosts, making it a potential tool for resolving the ambiguities in aphid taxonomy. We compared the effectiveness of employing two different DNA regions, gnd and COI, for the discrimination of over 100 species of aphids. The mean interspecific divergence of the gnd region was significantly higher than the mean intraspecific variation; there were nearly nonoverlapping distributions between the intra‐ and interspecific samples. In contrast, COI showed a lower interspecific divergence, which led to difficulties in identifying closely related species. Our results show that gnd can identify species in the Aphididae, which suggests that the gnd region of Buchnera is a potentially effective barcode for aphid species identification. We also recommend the 2‐locus combination of gnd + COI as the aphid barcode. This will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of aphids.     

Parameter identification of a dynamic model of CHO cell cultures: an experimental case study

In this paper, we address the problem of parameter identification in dynamic models of animal cultures, and we propose a step-by-step procedure, which gradually considers more detailed models. This procedure allows subsets of parameters to be estimated at each step, which can be used in the initialization of the next identification step. Finally, the full parameter set can be re-estimated starting from the results of the last step. The efficiency of the procedure is illustrated with a simulation case study and with the identification of a dynamic model from experimental data collected in CHO cell culture.     

Microsatellites and single nucleotide polymorphisms in avian hybrid identification: a comparative case study

The correct identification of hybrids is essential in avian hybridisation studies, but selection of the appropriate set of genetic markers for this purpose is at times complicated. Microsatellites and single nucleotide polymorphisms (SNPs) are currently the most commonly used markers in this field. We compare the efficiency of these two marker types, and their combination, in the identification of the threatened avian species, the greater spotted eagle and the lesser spotted eagle, as well as hybrids between the two species. We developed novel SNP markers from genome-wide distributed 122 candidate introns using only sympatric samples, and tested these markers successfully in 60 sympatric and allopatric spotted eagles using Bayesian model-based approaches. Comparatively, only one out of twelve previously described avian nuclear intron markers showed significant species-specific allele frequency difference, thus stressing the importance of selecting the proper markers. Twenty microsatellites outperformed selected nine SNPs in species identification, but were poorer in hybrid detection, whereas the resolution power of ten microsatellites remained too low for correct assignment. A combination of SNPs and microsatellites resulted in the most efficient and accurate identification of all individuals. Our study shows that the use of various sets of markers could lead to strikingly different assignment results, hybridisation studies may have been affected by too low a resolution power of used markers, and that an appropriate set of markers is essential for successful hybrid identification.