Increased high‐latitude photosynthetic carbon gain offset by respiration carbon loss during an anomalous warm winter to spring transition

Arctic and boreal ecosystems play an important role in the global carbon (C) budget, and whether they act as a future net C sink or source depends on climate and environmental change. Here, we used complementary in situ measurements, model simulations, and satellite observations to investigate the net carbon dioxide (CO₂) seasonal cycle and its climatic and environmental controls across Alaska and northwestern Canada during the anomalously warm winter to spring conditions of 2015 and 2016 (relative to 2010–2014). In the warm spring, we found that photosynthesis was enhanced more than respiration, leading to greater CO₂ uptake. However, photosynthetic enhancement from spring warming was partially offset by greater ecosystem respiration during the preceding anomalously warm winter, resulting in nearly neutral effects on the annual net CO₂ balance. Eddy covariance CO₂ flux measurements showed that air temperature has a primary influence on net CO₂ exchange in winter and spring, while soil moisture has a primary control on net CO₂ exchange in the fall. The net CO₂ exchange was generally more moisture limited in the boreal region than in the Arctic tundra. Our analysis indicates complex seasonal interactions of underlying C cycle processes in response to changing climate and hydrology that may not manifest in changes in net annual CO₂ exchange. Therefore, a better understanding of the seasonal response of C cycle processes may provide important insights for predicting future carbon–climate feedbacks and their consequences on atmospheric CO₂ dynamics in the northern high latitudes.     

Linked‐read sequencing enables haplotype‐resolved resequencing at population scale

The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences – including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps – are still limited by the lack of high‐quality haplotype information. The newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype‐resolved genome resequencing at population scale, we investigated properties of linked‐read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25×, 20×, 15×, 10×, 7×, and 5×) with high‐coverage data (46–68×) of seven bird genomes mapped to a reference suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15× coverage, phased haplotypes span about 90% of the genome assembly, with 50% and 90% of phased sequences located in phase blocks longer than 1.25–4.6 Mb (N50) and 0.27–0.72 Mb (N90). Phasing accuracy reaches beyond 99% starting from 15× coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1 Mb [N50/N90] at 25× coverage), but only marginally improved phasing accuracy. Phase block contiguity improved with input DNA molecule length; thus, higher‐quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase‐sized genomes like birds, linked‐read sequencing at moderate depth opens an affordable avenue towards haplotype‐resolved genome resequencing at population scale.     

PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

Physcomitrella patens is a bryophyte model plant that is often used to study plant evolution and development. Its resources are of great importance for comparative genomics and evo‐devo approaches. However, expression data from Physcomitrella patens were so far generated using different gene annotation versions and three different platforms: CombiMatrix and NimbleGen expression microarrays and RNA sequencing. The currently available P. patens expression data are distributed across three tools with different visualization methods to access the data. Here, we introduce an interactive expression atlas, Physcomitrella Expression Atlas Tool (PEATmoss), that unifies publicly available expression data for P. patens and provides multiple visualization methods to query the data in a single web‐based tool. Moreover, PEATmoss includes 35 expression experiments not previously available in any other expression atlas. To facilitate gene expression queries across different gene annotation versions, and to access P. patens annotations and related resources, a lookup database and web tool linked to PEATmoss was implemented. PEATmoss can be accessed at https://peatmoss.online.uni-marburg.de     

Italian weedy rice—A case of de‐domestication?

Weedy rice is a representative of the extensive group of feral weeds that derive from crops, but has returned to the lifestyle of a wild species. These weeds develop either from a hybridization of crops with wild relatives (exoferality), or by mutation of crops to weedy forms (endoferality). Due to the close relation of weed and crop, the methods for weed‐targeted containment are limited to date. A deeper understanding of the development of such weeds might help to design more efficient and sustainable approaches for weed management. Weedy rice poses a serious threat to rice yields worldwide. It is widely accepted that weedy rice has originated independently in different regions all over the world. However, details of its evolution have remained elusive. In the current study, we investigated the history of weedy rice in northern Italy, the most important rice‐growing area in Europe. Our approach was to analyze genes related to weedy traits (SD1, sh4, Rc) in weedy rice accessions compared to cultivars, and to integrate these results with phenotypic and physiological data, as well as historical information about rice farming in Italy. We arrive at a working model for the timeline of evolution of weedy rice in Italy indicating that both exoferality and endoferality acted as forces driving the development of the diverse weedy rice populations found in the region today. Models of weed evolution can help to predict the direction which weed development might take and to develop new, sustainable methods to control feral weeds.     

Age‐related variation in the trophic characteristics of a marsupial carnivore,the Tasmanian devil Sarcophilus harrisii

Age‐related changes in diet have implications for competitive interactions and for predator–prey dynamics, affecting individuals and groups at different life stages. To quantify patterns of variation and ontogenetic change in the diets of Tasmanian devils Sarcophilus harrisii, a threatened marsupial carnivore, we analyzed variation in the stable isotope composition of whisker tissue samples taken from 91 individual devils from Wilmot, Tasmania from December 2014 to February 2017. Both δ¹³C and δ¹⁵N decreased with increasing age in weaned Tasmanian devils, indicating that as they age devils rely less on small mammals and birds, and more on large herbivores. Devils <12 months old had broader group isotopic niches, as estimated by Bayesian standard ellipses (SEA_B mode = 1.042) than devils from 12 to 23 months old (mode = 0.541) and devils ≥24 months old (mode = 0.532). Devils <24 months old had broader individual isotopic niches (SEA_B mode range 0.492–1.083) than devils ≥24 months old (mode range 0.092–0.240). A decrease in δ¹⁵N from the older whisker sections to the more recently grown sections in devils <24 months old likely reflects the period of weaning in this species, as this pattern was not observed in devils ≥24 months old. Our data reveal changes in the isotopic composition of devil whiskers with increasing age, accompanied by a reduction in isotopic variation both among population age classes and within individuals, reflecting the effect of weaning in early life, and a likely shift from an initially diverse diet of small mammals, birds, and invertebrates towards increasing consumption of larger herbivores in adulthood.     

Interaction of <i>Acaena elongata</i> L. with Arbuscular Mycorrhizal Fungi under Phosphorus Limitation Conditions in a Temperate Forest

The aim of this study was to analyze the performance of Acaena elongata colonized by arbuscular mycorrhizal fungi (AMF) to different phosphorus (P) concentrations, as a measure of AMF dependency. A. elongata, is a species from soils where P availability is limited, such as temperate forests. Our research questions were: 1) How do different P concentrations affect the AMF association in Acaena elongata, and 2) How does the AMF association influence A. elongata’s growth under different P concentrations? A. elongata’s growth, P content in plant tissue, AMF colonization and dependency were measured under four P concentrations: control (0 g P kg⁻¹ ), low (0.05 g P kg⁻¹ ), intermediate (0.2 g P kg⁻¹ ) and high (2 g P kg⁻¹ ) in different harvests. A complete randomized block design was applied. A. elongata’s growth was higher under -AMF in intermediate and high P concentrations, and the lowest growth corresponded to +AMF in the low and intermediate P concentration. We observed a negative effect on the root biomass under +AMF in intermediate P concentration, while the P concentration had a positive effect on the leaf area ratio. The AMF colonization in A. elongata decreased in the highest P concentration and it was favored under intermediate P concentration; while the low and the high concentrations generated a cost-benefit imbalance. Our results suggest that the performance of some plant species in soils with low P availability may not be favored by their association with AMF, but a synergy between AMF and intermediate P concentrations might drive A. elongata’s growth.     

Trophic ecology of an introduced top predator (Felis catus) on a small African oceanic islet (Santa Luzia,Cabo Verde Islands)

Studies on feral cat diet offer important ecological information and are the first step towards determining their impact upon endangered species. However, in comparing seasonal changes in diet with seasonal prey availability, the scarce amount of research into oceanic islands worldwide must be considered when deciding if a specific population is actually affected by cat predation. Cat diet was analysed on Santa Luzia (Cabo Verde Islands) since this invasive predator is considered one of the main threats to native endangered species that require conservation measures. These previous studies were carried out in different seasons, providing contrasting results, skinks being more preyed upon in the rainy season and mice in the driest periods. To check these different results, we focussed on how cat diet varied seasonally in response to changes in prey abundance. Saurians were the most important prey group, followed by mice, invertebrates and birds. No seasonal differences were, however, observed in the different prey groups consumed, saurians being the main prey in both seasons. All cases reflected their respective abundances. Results corroborate the generalist and opportunistic trophic ecology of feral cats, providing important information to assess their impact on prey populations and design future eradication programmes.