Phylogeography and species distribution modelling of Cryptocephalusbarii (Coleoptera: Chrysomelidae): is this alpine endemic species close to extinction?

Combining distribution modelling and phylogeography to understand present, past and future of an endangered spider

BACKGROUND

Understanding how endangered species respond to climatic changes is fundamental for their conservation. Due to its restricted geographic range, its sensitivity to the ongoing global warming and its continuing decline, the Southwestern-Alpine endemic wolf spider Vesubia jugorum is currently classified as Endangered in the IUCN Red List. Here, we combined species distribution modelling (SDM) and phylogeographic inference to describe the present, the past and the future of this species in light of the mtDNA genetic structure of extant populations.

RESULTS

Phylogenetic and network analyses show a high level of genetic differentiation and a strong genetic structure of the populations, likely explicable by a long history of isolation and survival in separate refugia. The SDM projection into past climatic conditions supports these results by showing a smaller distribution range compared to present, mostly restricted to the Maritime and Ligurian Alps, which possibly served as main refugium. Future forecast shows a significant shift in the bioclimatic range towards higher altitudes and latitudes, with a drastic decrease of habitat suitability in the central and south-eastern parts of the range, with consequent general loss of haplotype diversity.

CONCLUSION

SDM and phylogeographic inference support the hypothesis that the current distribution and the genetic structure of the extant populations mirror the survival in situ of Vesubia jugorum across repeated glacial and interglacial phases, in line with the 'long-term stability hypothesis'. Future predictions show a significant shift in the bioclimatic range that V. jugorum will be likely unable to track, with profound impact on its long-term survival and its genetic diversity. Our considerations have implication for conservation genetics, highlighting the pivotal role of the transboundary protected areas of the SW-Alps in promoting conservation efforts for this species.

Population differentiation and dynamics of five pioneer species of Gaultheria from the secondary forests in subtropical China

BACKGROUND

The influence of native secondary succession associated with anthropogenic disturbance on the biodiversity of the forests in subtropical China remains uncertain. In particular, the evolutionary response of small understory shrubs, particularly pioneer species inhabiting continuously disturbed habitats, to topographic heterogeneity and climate change is poorly understood. This study aimed to address this knowledge gap by focusing on the Gaultheria crenulata group, a clade of small pioneer shrubs in subtropical China.

RESULTS

We examined the genetic structure and demographic history of all five species of the G. crenulata group with two maternally inherited chloroplast DNA (cpDNA) fragments and two biparentally inherited low-copy nuclear genes (LCG) over 89 natural populations. We found that the genetic differentiation of this group was influenced by the geomorphological boundary between different regions of China in association with Quaternary climatic events. Despite low overall genetic diversity, we observed an isolation-by-distance (IBD) pattern at a regional scale, rather than isolation-by-environment (IBE), which was attributed to ongoing human disturbance in the region.

CONCLUSION

Our findings suggest that the genetic structure of the G. crenulata group reflects the interplay of geological topography, historical climates, and anthropogenic disturbance during the Pliocene-Pleistocene-Holocene periods in subtropical China. The observed IBD pattern, particularly prominent in western China, highlights the role of limited dispersal and gene flow, possibly influenced by physical barriers or decreased connectivity over geographic distance. Furthermore, the east-to-west trend of gene flow, potentially facilitated by the East Asian monsoon system, underscores the complex interplay of biotic and abiotic factors shaping the genetic dynamics of pioneer species in subtropical China's secondary forests. These findings can be used to assess the impact of environmental changes on the adaptation and persistence of biodiversity in subtropical forest ecosystems.

Assessing future shifts in habitat suitability and connectivity to old-growth forests to support the conservation of the endangered giant noctule

Background

Suitable climate and availability of habitats for roosting, foraging, and dispersing are critical for the long-term persistence of bat species. The giant noctule (Nyctalus lasiopterus) represents one of the lesser-known European bats, especially regarding the environmental factors which shape its distribution.

Methodology

We integrated climate-based ecological niche models with information about topography and rivers' network to model weighted suitability for N. lasiopterus in the western Palearctic. The weighted suitability map was then used to estimate connectivity among the distinct occurrence localities of N. lasiopterus, as well as from these latter towards European old-growth forests, under current conditions and different combinations of future timeframes (2030, 2050, 2070) and shared socioeconomic pathways (SSPs 3.70 and 5.85).

Results

Current weighted suitability is highest in Andalusia, northern Iberia, southwestern France, peninsular Italy, coastal Balkans and Anatolia, with dispersed suitable patches elsewhere. A north-eastward shift of weighted suitability emerges in the considered future scenarios, especially under SSP 5.85. The major current ecological corridors for N. lasiopterus are predicted within a 'belt' connecting northern Spain and southwestern France, as well as in the Italian Alps. However, following changes in weighted suitability, connectivity would increase in central-eastern Europe in the future. The bioclimatic niche of the western N. lasiopterus populations does not overlap with those of the central and eastern ones, and it only overlaps with climatic conditions characterizing old-growth forests in western Europe.

Conclusions

The outcomes of our analyses would help in designing specific conservation measures for the distinct groups of giant noctule populations, favoring the possibility of range expansion and movement towards forested habitats.

Unsupervised machine learning and geometric morphometrics as tools for the identification of inter and intraspecific variations in the Anopheles Maculipennis complex

Geometric morphometric analysis was combined with two different unsupervised machine learning algorithms, UMAP and HDBSCAN, to visualize morphological differences in wing shape among and within four Anopheles sibling species (An. atroparvus, An. melanoon, An. maculipennis s.s. and An. daciae sp. inq.) of the Maculipennis complex in Northern Italy. Specifically, we evaluated: 1) wing shape variation among and within species; 2) the consistencies between groups of An. maculipennis s.s. and An. daciae sp. inq. identified based on COI sequences and wing shape variability; and 3) the spatial and temporal distribution of different morphotypes. UMAP detected at least 13 main patterns of variation in wing shape among the four analyzed species and mapped intraspecific morphological variations. The relationship between the most abundant COI haplotypes of An. daciae sp. inq. and shape ordination/variation was not significant. However, morphological variation within haplotypes was reported. HDBSCAN also recognized different clusters of morphotypes within An. daciae sp. inq. (12) and An. maculipennis s.s. (4). All morphotypes shared a similar pattern of variation in the subcostal vein, in the anal vein and in the radio-medial cross-vein of the wing. On the contrary, the marginal part of the wings remained unchanged in all clusters of both species. Any spatial-temporal significant difference was observed in the frequency of the identified morphotypes.  Our study demonstrated that machine learning algorithms are a useful tool combined with geometric morphometrics and suggest to deepen the analysis of inter and intra specific shape variability to evaluate evolutionary constrains related to wing functionality.

Climate change favours connectivity between virus-bearing pest and rice cultivations in sub-Saharan Africa, depressing local economies

Aims

Rice is a staple food for many countries, being fundamental for a large part of the worlds’ population. In sub-Saharan Africa, its importance is currently high and is likely to become even more relevant, considering that the number of people and the per-capita consumption are both predicted to increase. The flea beetles belonging to the Chaetocnema pulla species group (pulla group), a harmful rice pest, are an important vector of the Rice Yellow Mottle Virus, a disease which leads even to 80–100% yield losses in rice production. We present a continental-scale study aiming at: (1) locating current and future suitable territories for both pulla group and rice; (2) identifying areas where rice cultivations may occur without suffering the presence of pulla group using an Ecological Niche Modelling (ENM) approach; (3) estimating current and future connectivity among pulla group populations and areas predicted to host rice cultivations, based on the most recent land-use estimates for future agricultural trends; (4) proposing a new connectivity index called “Pest Aggression Index” (PAI) to measure the agricultural susceptibility to the potential future invasions of pests and disease; (5) quantifying losses in terms of production when rice cultivations co‐occur with the pulla group and identifying the SSA countries which, in the future inferred scenarios, will potentially suffer the greatest losses.

Location

Sub-Saharan Africa.

Methods

Since the ongoing climate and land-use changes affect species’ distributions, we first assess the impact of these changes through a spatially-jackknifed Maxent-based Ecological Niche Modelling in GIS environment, for both the pulla group and rice, in two climatic/socioeconomic future scenarios (SSP_2.45 and 3.70). We then assess the connectivity potential of the pulla group populations towards rice cultivations, for both current and future predictions, through a circuit theory-based approach (Circuitscape implemented in Julia language). We finally measure the rice production and GPD loss per country through the spatial index named “Pest Aggression Index”, based on the inferred connectivity magnitude.

Results

The most considerable losses in rice production are observed for Liberia, Sierra Leone and Madagascar in all future scenarios (2030, 2050, 2070). The future economic cost, calculated as USD lost from rice losses/country’s GDP results are high for Central African Republic (−0.6% in SSP_2.45 and −3.0% in SSP_3.70) and Guinea–Bissau (−0.4% in SSP_2.45 and −0.68% in SSP_3.70), with relevant losses also obtained for other countries.

Main conclusions

Since our results are spatially explicit and focused on each country, we encourage careful land-use planning. Our findings could support best practices to avoid the future settlement of new cultivations in territories where rice would be attacked by pulla group and the virus, bringing economic and biodiversity losses.

Factors affecting the efficiency of molecular species delimitation in a species-rich insect family

In the context of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating species discovery through DNA taxonomy and inventory through DNA metabarcoding. In this study, the effect of some intrinsic factors on the efficiency of various single-marker species delimitation methods (fixed and variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP) was tested on more than 90 empirical data sets, derived from a set of 7,237 COI sequences attributed to 542 leaf beetles species (Coleoptera: Chrysomelidae). The considered factors were: (i) the number of haplotypes per species (as a proxy for genetic diversity), (ii) the geographic distance among conspecific collection localities (as a proxy of sampling width), (iii) the difficulty related to morphological identification of species, and (iv) the taxonomic rank. Distance-based methods, with on average more than 70% of match with morphological identification, outperformed those relying on phylogenetic trees, with less than 59%. A high number of haplotypes per species was found to have a negative effect on delimitation efficiency, whereas large geographic distances within species had a positive effect. All methods delimitations (except for GMYC) were significantly affected by the presence of species that are difficult to be identified, decreasing their efficiency. Finally, the only method influenced by the taxonomic rank of the data set was GMYC, showing lower efficiency in data sets at the genus than at higher levels. The observed biases we highlighted affecting efficiency could be accounted for when developing input data sets for species delimitation analyses to obtain a more reliable representation of biological diversity.

Spatial distribution of stygobitic crustacean harpacticoids at the boundaries of groundwater habitat types in Europe

The distribution patterns of stygobitic crustacean harpacticoids at the boundaries of three different groundwater habitat types in Europe were analysed through a GIS proximity analysis and fitted to exponential models. The results showed that the highest frequency of occurrences was recorded in aquifers in consolidated rocks, followed by the aquifers in unconsolidated sediments and, finally, by the practically non-aquiferous rocks. The majority of the stygobitic harpacticoid species were not able to disperse across the boundaries between two adjacent habitats, with 66% of the species occurring in a single habitat type. The species were not evenly distributed, and 35–69% of them occurred from 2 to 6 km to the boundaries, depending on the adjacent habitat types. The distribution patterns were shaped by features extrinsic to the species, such as the hydrogeological properties of the aquifers, and by species’ intrinsic characteristics such as the preference for a given habitat type and dispersal abilities. Most boundaries between adjacent habitat types resulted to be “breaches”, that is transmissive borders for stygobitic harpacticoids, while others were “impermeable walls”, that is absorptive borders. Our results suggest that conservation measures of groundwater harpacticoids should consider how species are distributed within the different groundwater habitat types and at their boundaries to ensure the preservation of species metapopulations within habitat patches and beyond them.

Phylogenetics and population structure of the steppe species Hycleus polymorphus (Coleoptera: Meloidae: Mylabrini) reveal multiple refugia in Mediterranean mountain ranges

Many continental species distributed in the Eurasian steppe occur as relict populations in the mountains of Western Europe. Their biogeographical responses to Quaternary climate changes have been poorly studied; however, they could have responded as cold-adapted species. We investigated the biogeographic history of a steppe beetle, Hycleus polymorphus, using mitochondrial and nuclear DNA sequences (COI, CAD, ITS2), and species distribution modelling (SDM) under present and past bioclimatic envelopes. We first performed a phylogenetic assessment to define species boundaries within the H. polymorphus species group. Specimens previously treated as Hycleus humerosus on morphological grounds are assigned to H. polymorphus, and those identified as Hycleus zebraeus assigned to Hycleus atratus. ITS2 data analyses revealed a strong phylogeographical structure of H. polymorphus populations, with four haplogroups corresponding to the (i) Italian Alps, (ii) French Alps and Pyrenees, (iii) South Balkan and Pontic mountains, and (iv) North Dinaric Alps. Based on these analyses and the SDM, we propose that during a glacial period, following the spread of steppic habitat, H. polymorphus underwent a range expansion from Asia to South-West Europe. Within the Mediterranean area, during the last interglacial the climatic suitability for the species was limited to mountains that acted as refugia and prompted allopatric divergence into four main lineages.

Preliminary Analysis of the Diet of Triturus carnifex and Pollution in Mountain Karst Ponds in Central Apennines

Mountain karst ponds are sensitive environments, hosting complex trophic networks where amphibians play a major role, often as top predators. The diet of the Italian crested newt (Triturus carnifex) is still poorly known for populations occupying mountain karst ponds. These are traditionally used as livestock’s watering points, leading to water pollution due to excreta and wading behavior. The aim of this paper is to understand the relationship between T. carnifex diet composition, assessed through the stomach flushing technique, and physical and chemical characteristics in mountain ponds, focusing on parameters altered by livestock pressure, such as ammonium concentration and dissolved oxygen. The high diversity of prey items found within the newts’ gut contents confirms the generalist diet even in mountain ponds. The number of prey taxa, their relative abundance and Shannon–Wiener diversity index show variations among the sampled sites, related to livestock organic pollution. Moreover, we report the very first European records of microplastic items in amphibians’ stomach content, which also represent the first evidence for Caudata worldwide. Our findings suggest that livestock pressure directly influences T. carnifex diet and highlight that the emerging issue of plastics is a threat even in remote high-altitude environments.

Investigating the Current and Future Co-Occurrence of Ambrosia artemisiifolia and Ophraella communa in Europe through Ecological Modelling and Remote Sensing Data Analysis

The common ragweed Ambrosia artemisiifolia has spread throughout Europe since the 1800s, infesting croplands and causing severe allergic reactions. Recently, the ragweed leaf beetle Ophraella communa was found in Italy and Switzerland; considering that it feeds primarily on A. artemisiifolia in its invaded ranges, some projects started biological control of this invasive plant through the adventive beetle. In this context of a ‘double’ invasion, we assessed the influence of climate change on the spread of these alien species through ecological niche modelling. Considering that A. artemisiifolia mainly lives in agricultural and urbanized areas, we refined the models using satellite remote-sensing data; we also assessed the co-occurrence of the two species in these patches. A. artemisiifolia is predicted to expand more than O. communa in the future, with the medium and high classes of suitability of the former increasing more than the latter, resulting in lower efficacy for O. communa to potentially control A. artemisiifolia in agricultural and urbanized patches. Although a future assessment was performed through the 2018 land-cover data, the predictions we propose are intended to be a starting point for future assessments, considering that the possibility of a shrinkage of target patches is unlikely to occur.