Hybridization between closely related songbirds is related to human habitat disturbance

Human habitat disturbances can promote hybridization between closely related, but typically reproductively isolated, species. We explored whether human habitat disturbances are related to hybridization between two closely related songbirds, black-capped and mountain chickadees, using both genomic and citizen science data sets. First, we genotyped 409 individuals from across both species' ranges using reduced-representation genome sequencing and compared measures of genetic admixture to a composite measure of human landscape disturbance. Then, using eBird observations, we compared human landscape disturbance values for sites where phenotypically diagnosed hybrids were observed to locations where either parental species was observed to determine whether hybrid chickadees are reported in more disturbed areas. We found that hybridization between black-capped and mountain chickadees positively correlates with human habitat disturbances. From genomic data, we found that (1) hybrid index (HI) significantly increased with habitat disturbance, (2) more hybrids were sampled in disturbed habitats, (3) mean HIs were higher in disturbed habitats versus wild habitats, and (4) hybrids were detected in habitats with significantly higher disturbance values than parentals. Using eBird data, we found that both hybrid and black-capped chickadees were significantly more disturbance-associated than mountain chickadees. Surprisingly, we found that nearly every black-capped chickadee we sampled contained some proportion of hybrid ancestry, while we detected very few mountain chickadee backcrosses. Our results highlight that hybridization between black-capped and mountain chickadees is widespread, but initial hybridization is rare (few F1s were detected). We conclude that human habitat disturbances can erode pre-zygotic reproductive barriers between chickadees and that post-zygotic isolation is incomplete. Understanding what becomes of recently hybridizing species following large-scale habitat disturbances is a new, but pressing, consideration for successfully preserving genetic biodiversity in a rapidly changing world.     

Contemporary changes in phenotypic variation,and the potential consequences for eco-evolutionary dynamics

Most studies assessing rates of phenotypic change focus on population mean trait values, whereas a largely overlooked additional component is changes in population trait variation. Theoretically, eco-evolutionary dynamics mediated by such changes in trait variation could be as important as those mediated by changes in trait means. To date, however, no study has comprehensively summarised how phenotypic variation is changing in contemporary populations. Here, we explore four questions using a large database: How do changes in trait variances compare to changes in trait means? Do different human disturbances have different effects on trait variance? Do different trait types have different effects on changes in trait variance? Do studies that established a genetic basis for trait change show different patterns from those that did not? We find that changes in variation are typically small; yet we also see some very large changes associated with particular disturbances or trait types. We close by interpreting and discussing the implications of our findings in the context of eco-evolutionary studies.     

Vegetation history and human activity during the last 6000 years on the central Catalan coast (northeastern Iberian Peninsula)

In this paper, we present the results of four pollen diagrams obtained from the northeastern coast of the Iberian Peninsula. These data, together with a set of 11 radiocarbon dates, allow us to make some suggestions about human activity in this area mainly during the last 6000 years. We have established four main stages of this activity. Phase I (7000–3000 B.P.) shows some sporadic human clearance without qualitative and/or quantitative changes inside the natural woodland, except for slight oscillations in AP values. These clearances are synchronous with Neolithic and Bronze Age settlements. Phase II (3000–1500/1300 B.P.) demonstrates a different human action on the landscape along the Catalan coast. Sampling sites located in rich agricultural plains and close to urban centres show continuous woodland clearance during the Iberian period and especially during Roman times. In contrast, at boring sites far from these towns, the irregular and sporadic woodland disturbances continue, although these become more common. Phase III (1500/1300–850 B.P.) shows further woodland clearance fires along the coast. Pollen, archaeological and historical evidence allow us to relate this to the introduction of grazing in the coastal area, connected with seasonal transhumance between the littoral and mountain regions. Phase IV (850–300/150 B.P.) is characterised by the final clearance of woodland and the development of olive farming. During this phase the agrarian Mediterranean landscape was definitively formed.     

Emissions of nitrous oxide from three tropical forests in Southern China in response to simulated nitrogen deposition

Emissions of nitrous oxide (N₂O) from the soil following simulated nitrogen (N) deposition in a disturbed (pine), a rehabilitated (pine and broadleaf mixed) and a mature (monsoon evergreen broadleaf) tropical forest in southern China were studied. The following hypotheses were tested: (1) addition of N will increase soil N₂O emission in tropical forests; and (2) any observed increase will be more pronounced in the mature forest than in the disturbed or rehabilitated forest due to the relatively high initial soil N concentration in the mature forest. The experiment was designed with four N treatment levels (three replicates; 0, 50, 100, 150 kg N ha⁻¹ year⁻¹ for C (Control), LN (Low-N), MN (Medium-N), and HN (High-N) treatment, respectively) in the mature forest, but only three levels in the disturbed and rehabilitated forests (C, LN and MN). Between October 2005 to September 2006, soil N₂O flux was measured using static chamber and gas chromatography methodology. Nitrogen had been applied previously to the plots since July 2003 and continued during soil N₂O flux measurement period. The annual mean rates of soil N₂O emission in the C plots were 24.1 ± 1.5, 26.2 ± 1.4, and 29.3 ± 1.6 μg N₂O–N m⁻² h⁻¹ in the disturbed, rehabilitated and mature forest, respectively. There was a significant increase in soil N₂O emission following N additions in the mature forest (38%, 41%, and 58% when compared to the C plots for the LN, MN, and HN plots, respectively). In the disturbed forest a significant increase (35%) was observed in the MN plots, but not in the LN plots. The rehabilitated forest showed no significant response to N additions. Increases in soil N₂O emission occurred primarily in the cool-dry season (November, December and January). Our results suggest that the response of soil N₂O emission to N deposition in tropical forests in southern China may vary depending on the soil N status and land-use history of the forest.     

Rapid expansion of lichen woodlands within the closed-crown boreal forest zone over the last 50 years caused by stand disturbances in eastern Canada

Aim Our two main goals are first to evaluate the resilience of the boreal forest according to latitude across the closed‐crown forest zone using the post‐disturbance distribution and cover of lichen woodlands and closed‐crown forests as a metric, and second to identify the disturbance factors responsible for the regeneration and degradation of the closed‐crown forest according to latitude since the 1950s. Location The study area extends between 70°00′ and 72°00′ W and throughout the closed‐crown forest zone, from its southern limit near 47°30′ N to its northern limit at the contact with the lichen woodland zone at around 52°40′ N. Methods Recent (1972–2002) and old (1954–1956) aerial photos were used to map the distribution of lichen woodlands across the closed‐crown forest zone. Forest disturbances such as fire, spruce budworm (Choristoneura fumiferana (Clemens)) outbreak, and logging were recorded on each set of aerial photos. Each lichen woodland and stand disturbance was validated by air‐borne surveys and digitized using GIS software. Results Over the last 50 years, the area occupied by lichen woodlands has increased according to latitude; that is, 9% of the area that was occupied by closed‐crown forests has shifted to lichen woodlands. Although logging activities have been concentrated in the same areas during the last 50 years, the area covered by logging has increased significantly. Outbreaks by the spruce budworm occurred predominantly in the southern (47°30′ N to 48°30′ N) and central (48°53′ N to 50°42′ N) parts of the study area, where balsam fir stands are extensive. In the northern part of the study area (51°–52°40′ N), extensive fires affected the distribution and cover of closed‐crown forests and lichen woodlands. Main conclusions Over the last 50 years, the area occupied by closed‐crown forests has decreased dramatically, and the ecological conditions that allow closed‐crown forests to establish and develop are currently less prevalent. Fire is by far the main disturbance, reducing the ability of natural closed‐crown forests to self‐regenerate whatever the latitude. Given the current biogeographical shift from dense to open forests, the northern part of the closed‐crown forest zone is in a process of dramatic change towards the dominance of northern woodlands.     

A fish-based multimetric index for Brazilian savanna streams

Multimetric indices (MMI) have been widely used to assess ecosystem conditions because they are low-cost, employ a rapid field method, and can incorporate various biological metrics at different levels of biological organization. Our objective was to create a fish-based multimetric index applicable to all streams of the Brazilian savanna biome (Cerrado), the second largest biome in Brazil and deemed a global biodiversity hotspot. We evaluated 156 sites in two river basins (Paraná and São Francisco) and selected metrics capable of distinguishing stream-sites across a gradient of anthropogenic disturbances. We employed two different MMI approaches to determine if an MMI based on natural variation-adjusted metrics performed better than one based on unadjusted metrics. In addition, we assessed the performance of the two final MMIs and their sensitivity to anthropogenic pressures at local (LDI), catchment (CDI) and both scales integrated (IDI). Finally, we employed the power of a probability sample survey design to infer headwater stream conditions across a hydrologic region of approximately 47,000 km². Our final MMI for Brazilian savanna streams included six metrics: % common species; % characiform individuals; % loricariid individuals; % trichomycterid individuals; % invertivore species, and % Poecilia reticulata individuals. MMI₁ (unadjusted metrics) performed better than MMI₂ (natural variation-adjusted metrics) in discriminating least- and most-disturbed sites, but MMI₂ distinguished intermediate from most-disturbed sites better than MMI₁. Both indices were negatively correlated with the CDI scores; however, only MMI₂ was negatively correlated with the IDI scores. We inferred that 709 km (9.35%) of streams in the studied hydrologic region were in good condition, 8115 km (82.73%) were intermediate, and 641 km (7.91%) were in poor condition. We conclude that the MMIs proposed in this study have great potential for widespread application because they integrate data from two of the most important Brazilian river basins included in a biome that represents more than 20% of the country. Furthermore, the metrics retained in the indexes are easy to access with a rapid low-cost field method. However, their feasibility in areas influenced by mining, as well as in different biomes, should be tested.     

Activation of protein phosphatase-2A1 by HIV-1 Vpr cell death causing peptide in intact CD(4+) T cells and in vitro

HIV-1, the etiologic agent of human AIDS, causes cell death in host and non-host cells via HIV-1 Vpr, one of its auxiliary gene product. HIV-1 Vpr can also cause cell cycle arrest in several cell types. The cellular processes that link HIV-1 Vpr to the cell death machinery are not well characterized. Here, we show that the C terminal portion of HIV-1 Vpr which encompasses amino acid residues 71-96 (HIV-1 Vpr(71-96)), also termed HIV-1 Vpr cell death causing peptide, is an activator of protein phosphatase-2A(1) when applied extracellularly to CD(4+) T cells. HIV-1 Vpr(71-96) is a direct activator of protein phosphatase-2A(1) that has been purified from CD(4+) T cells. Full length HIV-1 Vpr by itself does not cause the activation of protein phosphatase-2A(1) in vitro. HIV-1 Vpr(71-96) also causes the activation of protein phosphatase-2A(0) and protein phosphatase-2A(1) from brain, liver, and adipose tissues. These results indicate that HIV-1 can cause cell death of infected cells and non-infected host and non-host cells via HIV-1 Vpr derived C terminal peptide(s) which act(s) by cell penetration and targeting of a key controller of the cell death machinery, namely, protein phosphatase-2A(1). The activation of other members of the protein phosphatase-2A subfamily of enzymes which are involved in the control of several metabolic pathways in brain, liver, and adipose tissues by HIV-1 Vpr derived C terminal peptide(s) may underlie various metabolic disturbances that are associated with HIV-1 infection.     

Diversity assessment of benthic macroinvertebrate communities in Banco National Park (Banco Stream,Côte d'Ivoire)

In the present study, a first inventory of benthic macroinvertebrates in the Banco Stream, Côte d'Ivoire, and the correlations between environmental variables and taxonomic richness were analysed. Seven stations were sampled monthly over a 1‐year period, using a hand net (10 × 10 cm, 250 μm mesh, 50 cm length). One hundred and thirty‐two macroinvertebrate taxa were recorded. These taxa were distributed among 74 families and 15 orders belonging to Insecta (118 taxa; 89% of total richness), Oligochaeta (seven taxa), Crustacea (five taxa) and Mollusca (two taxa). Kruskal–Wallis test revealed significant difference (at least P < 0.05) in macroinvertebrate richness between upstream stations (S1 and S2) and stations S4, S5 and S6. Chironominae and Tanypodinae (Insecta) were the two very frequent taxa in all the stations. Lumbriculidae (Oligochaeta), Desmocaris trispinosa (Crustacea) and Eurymetra sp. (Insecta) were frequently found in the samples. Hierarchical cluster analysis revealed three groups of sampling stations according to taxonomic similarity. Taxonomic richness was significantly and negatively correlated with conductivity, while it was significantly and positively correlated with substrate types (woody debris and gravel). Due to the fact that Banco stream is the locality type of an endemic shrimp species (Macrobrachium thysi), this basin is of high conservation priority.     

A protocol to transfer a fed-batch platform process into semi-perfusion mode: The benefit of automated small-scale bioreactors compared to shake flasks as scale-down model

Continuous processes such as perfusion processes can offer advantages compared to fed-batch or batch processes in bio-processing: improved product quality (e.g. for labile products), increased product yield, and cost savings. In this work, a semi-perfusion process was established in shake flasks and transferred to an automated small-scale bioreactor by daily media exchange via centrifugation based on an existing fed-batch process platform. At first the development of a suitable medium and feed composition, the glucose concentration required by the cells and the cell-specific perfusion rate were investigated in shake flasks as the conventional scale-down system. This lead to an optimized process with a threefold higher titer of 10 g/L monoclonal antibody compared to the standard fed-batch. To proof the suitability and benefit as a small-scale model, the established semi-perfusion process was transferred to an automated small-scale bioreactor with improved pH and dissolved oxygen control. The average specific productivity improved from 24.16 pg/(c*d) in the fed-batch process and 36.04 pg/c*d in the semi-perfusion shake flask to 38.88 pg/(c*d) in the semi-perfusion process performed in the controlled small-scale bioreactor, thus illustrating the benefits resulting from the applied semi-perfusion approach, especially in combination with controlled DO and pH settings. © 2019 The Authors. Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 35: e2757, 2019.