Integrating anthropogenic factors into regional‐scale species distribution models—A novel application in the imperiled sagebrush biome

Species distribution models (SDMs) that rely on regional‐scale environmental variables will play a key role in forecasting species occurrence in the face of climate change. However, in the Anthropocene, a number of local‐scale anthropogenic variables, including wildfire history, land‐use change, invasive species, and ecological restoration practices can override regional‐scale variables to drive patterns of species distribution. Incorporating these human‐induced factors into SDMs remains a major research challenge, in part because spatial variability in these factors occurs at fine scales, rendering prediction over regional extents problematic. Here, we used big sagebrush (Artemisia tridentata Nutt.) as a model species to explore whether including human‐induced factors improves the fit of the SDM. We applied a Bayesian hurdle spatial approach using 21,753 data points of field‐sampled vegetation obtained from the LANDFIRE program to model sagebrush occurrence and cover by incorporating fire history metrics and restoration treatments from 1980 to 2015 throughout the Great Basin of North America. Models including fire attributes and restoration treatments performed better than those including only climate and topographic variables. Number of fires and fire occurrence had the strongest relative effects on big sagebrush occurrence and cover, respectively. The models predicted that the probability of big sagebrush occurrence decreases by 1.2% (95% CI: ?6.9%, 0.6%) when one fire occurs and cover decreases by 44.7% (95% CI: ?47.9%, ?41.3%) if at least one fire occurred over the 36 year period of record. Restoration practices increased the probability of big sagebrush occurrence but had minimal effect on cover. Our results demonstrate the potential value of including disturbance and land management along with climate in models to predict species distributions. As an increasing number of datasets representing land‐use history become available, we anticipate that our modeling framework will have broad relevance across a range of biomes and species.     

Optimizing return‐on‐effort for coral nursery and outplanting practices to aid restoration of the Great Barrier Reef

Coral nursery and outplanting practices have grown in popularity worldwide for targeted restoration of degraded “high value” reef sites, and recovery of threatened taxa. Success of these practices is commonly gauged from coral propagule growth and survival, which fundamentally determines the return‐on‐effort (RRE) critical to the cost‐effectiveness and viability of restoration programs. In many cases, RRE has been optimized from past successes and failures, which therefore presents a major challenge for locations such as the Great Barrier Reef (GBR) where no local history of restoration exists to guide best practice. In establishing the first multi‐taxa coral nursery on the GBR (Opal Reef, February 2018), we constructed a novel scoring criterion from concurrent measurements of growth and survivorship to guide our relative RRE, including nursery propagule numbers (stock density). We initially retrieved RRE scores from a database of global restoration efforts to date (n = 246; 52 studies) to evaluate whether and how success commonly varied among coral taxa. We then retrieved RRE scores for Opal Reef using initial growth and survivorship data for six key coral taxa, to demonstrate that RRE scores were high for all taxa predominantly via high survivorship over winter. Repeated RRE scoring in summer is therefore needed to capture the full dynamic range of success where seasonal factors regulating growth versus survivorship differ. We discuss how RRE scoring can be easily adopted across restoration practices globally to standardize and benchmark success, but also as a tool to aid decision‐making in optimizing future propagation (and outplanting) efforts.     

Seed germination and dormancy traits of forbs and shrubs important for restoration of North American dryland ecosystems

• In degraded dryland systems, native plant community re‐establishment following disturbance is almost exclusively carried out using seeds, but these efforts commonly fail. Much of this failure can be attributed to the limited understanding of seed dormancy and germination traits.
• We undertook a systematic classification of seed dormancy of 26 species of annual and perennial forbs and shrubs that represent key, dominant genera used in restoration of the Great Basin ecosystem in the western United States. We examined germination across a wide thermal profile to depict species‐specific characteristics and assessed the potential of gibberellic acid (GA₃) and karrikinolide (KAR₁) to expand the thermal germination envelope of fresh seeds.
• Of the tested species, 81% produce seeds that are dormant at maturity. The largest proportion (62%) exhibited physiological (PD), followed by physical (PY, 8%), combinational (PY + PD, 8%) and morphophysiological (MPD, 4%) dormancy classes. The effects of chemical stimulants were temperature‐ and species‐mediated. In general, mean germination across the thermal profile was improved by GA₃ and KAR₁ for 11 and five species, respectively. We detected a strong germination response to temperature in freshly collected seeds of 20 species. Temperatures below 10 °C limited the germination of all except Agoseris heterophylla, suggesting that in their dormant state, the majority of these species are thermally restricted.
• Our findings demonstrate the utility of dormancy classification as a foundation for understanding the critical regenerative traits in these ecologically important species and highlight its importance in restoration planning.

     

大小兴安岭可培养细菌的资源多样性

细菌作为微生物中的重要组成部分, 在有机质的形成与分解、维持生态系统平衡、促进动植物发育等多方面都有着重要作用。2014-2017年, 我们采用常见培养基分离纯培养法及16S rRNA基因序列分析方法对大小兴安岭地区土壤可培养细菌的群落结构和多样性进行了调查研究。结果表明: 从大小兴安岭地区的17个自然保护区内不同生境的土壤中分离获得3,180个菌株, 隶属于24属120种。其中, 芽孢杆菌属(Bacillus)的种数和株数最多, 分别为38种和2,419株, 是大小兴安岭地区可培养细菌的绝对优势类群(占总株数的76.1%); 其次是短杆菌属(Brevibacterium)(13.0%)。大兴安岭地区的物种数、Simpson多样性指数和Shannon-Wiener指数高于小兴安岭地区。优势类群芽孢杆菌属的枯草芽孢杆菌(B. subtilis)、苏云金芽孢杆菌(B. thuringiensis)、巨大芽孢杆菌(B. megaterium)等有重要的生产及科学研究价值。     

Invasion genetics from eDNA and thousands of larvae: A targeted metabarcoding assay that distinguishes species and population variation of zebra and quagga mussels

Identifying species and population genetic compositions of biological invasions at early life stages and/or from environmental (e)DNA using targeted high‐throughput sequencing (HTS) metabarcode assays offers powerful and cost‐effective means for early detection, analysis of spread patterns, and evaluating population changes. The present study develops, tests, and applies this method with a targeted sequence assay designed to simultaneously identify and distinguish between the closely related invasive Eurasian zebra and quagga mussels (Dreissena polymorpha and D. rostriformis) and their relatives and discern their respective population genetic patterns. Invasions of these dreissenid mussel species have markedly changed freshwater ecosystems throughout North America and Europe, exerting severe ecological and economic damage. Their planktonic early life stages (eggs and larvae) are morphologically indistinguishable, yet each species exerts differential ecological effects, with the quagga often outcompeting the zebra mussel as adults. Our targeted assay analyzes genetic variation from a diagnostic sequence region of the mitochondrial (mt)DNA cytochrome oxidase I (COI) gene, to assess temporal and spatial inter‐ and intra‐specific genetic variability. The assay facilitates analysis of environmental (e)DNA from water, early life stages from thousands of individuals, and simultaneous analysis of 50–100 tagged field‐collected samples. Experiments evaluated its accuracy and performance using: (a) mock laboratory communities containing known DNA quantities per taxon, (b) aquaria with mixed‐species/haplotype compositions of adults, and (c) field‐collected water and plankton versus traditional sampling of adult communities. Results delineated species compositions, relative abundances, and population‐level diversity differences among ecosystems, habitats, time series, and life stages from two allopatric concurrent invasions in the Great Lakes (Lake Erie) and the Hudson River, which had separate founding histories. Findings demonstrate application of this targeted assay and our approach to accurately and simultaneously discern species‐ and population‐level differences across spatial and temporal scales, facilitating early detection and ecological understanding of biological invasions.     

Integration of ground survey and remote sensing derived data: Producing robust indicators of habitat extent and condition

The availability of suitable habitat is a key predictor of the changing status of biodiversity. Quantifying habitat availability over large spatial scales is, however, challenging. Although remote sensing techniques have high spatial coverage, there is uncertainty associated with these estimates due to errors in classification. Alternatively, the extent of habitats can be estimated from ground‐based field survey. Financial and logistical constraints mean that on‐the‐ground surveys have much lower coverage, but they can produce much higher quality estimates of habitat extent in the areas that are surveyed. Here, we demonstrate a new combined model which uses both types of data to produce unified national estimates of the extent of four key habitats across Great Britain based on Countryside Survey and Land Cover Map. This approach considers that the true proportion of habitat per km² (Z_i) is unobserved, but both ground survey and remote sensing can be used to estimate Z_i. The model allows the relationship between remote sensing data and Z_i to be spatially biased while ground survey is assumed to be unbiased. Taking a statistical model‐based approach to integrating field survey and remote sensing data allows for information on bias and precision to be captured and propagated such that estimates produced and parameters estimated are robust and interpretable. A simulation study shows that the combined model should perform best when error in the ground survey data is low. We use repeat surveys to parameterize the variance of ground survey data and demonstrate that error in this data source is small. The model produced revised national estimates of broadleaved woodland, arable land, bog, and fen, marsh and swamp extent across Britain in 2007.     

Isolation and characterization of microsatellite loci in Penstemon rostriflorus (Plantaginaceae) and cross‐species amplification

Eight novel microsatellite primer pairs are presented for Penstemon rostriflorus, representing the first microsatellite markers available for this genus. Loci were characterized for 20 individuals from two populations in the Great Basin, USA. All loci are polymorphic within P. rostriflorus (seven to 13 alleles per locus; observed heterozygosity between 0.40 and 0.95), and therefore useful for population genetic studies within the species. Cross‐species transferability was tested on 40 additional species of Penstemon, and results indicate that these primers pairs will likely be useful for population genetic studies on many Penstemon species.     

Huffmanela selachii n. sp. (Nematoda: Trichosomoididae: Huffmanelinae): A new species infecting the skin of the great hammerhead shark (Sphyrna mokarran) and the blacktip reef shark (Carcharhinus melanopterus) in the Arabian Gulf,off-shore Saudi Arabia

From January 2017 - December 2019, 75 out of 850 (8.8 %) great hammerhead sharks from the Arabian Gulf had skin lesions of black irregular discolorations on the ventral surface of the head. The lesions consisted of pencil-like lineations often advancing forward by about 2 mm in back-and-forth looped scribbles often forming a relatively linear bands of about 5–7 cm wide. Similar lesions were also found in the blacktip reef shark from the same area within the same period, and consisted of straight to irregular black lines, extended indiscriminately across the skin of the sharks. Microscopic examination of the skin revealed the presence of dark-brown eggs exhibiting the spindle or ellipsoidal eggs characteristic of Huffmanela sp. The morphometrics of eggs from both hosts were similar (62.9–89.9 μm long and 29.3–56.1 μm wide). The eggshells were smooth with polar plugs protruding or not, with an abruptly truncated crown-like or shoulder-like collar surrounding the plug. The eggs were only found in the epidermal layer of the skin. Based on the unique morphometrics of the eggs, we report a new species, named: Huffmanela selachii n. sp.. This appears to be the first report of Huffmanela from either the great hammerhead shark or the blacktip reef shark, and the third reported Huffmanela in sharks from the Arabian Gulf. It is also one of few species reported from connecting waters of the greater Indian Ocean. This new finding contributes to our understanding of the diversity and ubiquity of Huffmanela sp. in marine creatures.     

商代前期中原地区多品种农作物种植制度的初探：以河南新郑望京楼遗址为例

农业经济的发展是华夏文明形成的最重要的前提条件之一,郑洛地区作为夏商王朝建都和统治的核心区域,其农业经济发展状况一直是学术界研究的重点问题。相关研究表明,多品种农作物种植制度在龙山时期中原地区的出现,在华夏文明的形成过程中可能起到了至关重要的作用。为了探索这一种植制度在商代前期中原地区的具体实践情况,本文选取河南新郑望京楼遗址夏商时期（二里头文化和二里岗文化时期）29例先民肢骨和23例先民肋骨进行C、N稳定同位素分析。结果表明,先民骨胶原的δ¹³C值变化范围为-18.1‰~7.0‰,平均值为-9.5‰±2.1‰（n=52）,δ¹⁵N值变化范围为7.3‰~10.5‰,平均值为8.9‰±0.7‰（n=52）,先民仍以C₄类食物（粟黍）为主,但是也包含少量C₃类（水稻、小麦或大豆）食物,证明中原地区自龙山时代出现的多品种农作物种植制度,在商代得以延续,但是粟作农业的主导地位,始终未发生明显变化,这可能与中原地区长期以来的旱作农业经济模式习惯有关。     

Prevalence and species richness of trematode parasites only partially recovers after the 2011 Tohoku,Japan, earthquake tsunami

Trematode parasites have complex life cycles and use a variety of host species across different trophic levels. Thus, they can be used as indicators of disturbance and recovery of coastal ecosystems. Estuaries on the Pacific coast of northeastern Japan were heavily affected by the 2011 Tohoku earthquake tsunami. To evaluate the effect of the tsunami on the trematode community, we examined trematodes in the mud snail, Batillaria attramentaria, at five study sites (three sites severely exposed to the tsunami and two sites sheltered from the tsunami) in Sendai Bay for 2 years prior to and 8 years after the tsunami. While the trematode prevalence decreased at all study sites, the species richness decreased only at the sites exposed to the tsunami. Although parasitism increased over the study period post-tsunami, the community had not fully recovered 8 years after the event. Trematode community structure has changed every year since the tsunami and has not stabilised. This could be explained by the alteration of first and second intermediate host communities. Our study suggests that it will take more time for the recovery of the trematode community and the associated coastal ecosystem in the Tohoku region.